From 62204641e9bcbe4590fe857e9e5f9e57f16ab139 Mon Sep 17 00:00:00 2001 From: matthewcornell Date: Wed, 5 Feb 2025 20:46:15 -0500 Subject: [PATCH 1/2] issue #28: clean up renv usage to fix incompatibility between stored CRAN repositories and renv version. update README.md files. regenerate renv.lock files --- Dockerfile | 5 +- README.md | 38 +- covid_ar6_pooled/README.md | 16 +- covid_ar6_pooled/renv.lock | 4409 ++++++++++++++++++++++++++++------- covid_gbqr/README.md | 16 +- covid_gbqr/renv.lock | 4409 ++++++++++++++++++++++++++++------- flu_ar2/README.md | 8 +- flu_ar2/renv.lock | 3996 ++++++++++++++++++++++++++------ flu_flusion/README.md | 10 +- flu_flusion/renv.lock | 4411 +++++++++++++++++++++++++++++------- 10 files changed, 14152 insertions(+), 3166 deletions(-) diff --git a/Dockerfile b/Dockerfile index f22f823..5f7c69c 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM rocker/r-ver:4.3.2 +FROM rocker/r-ver:4.4.1 # install general OS utilities RUN apt-get update && apt-get install -y --no-install-recommends \ @@ -76,7 +76,8 @@ RUN pip3 install -r requirements.txt # install required R packages using renv COPY "${MODEL_DIR}/renv.lock" ./ ENV RENV_PATHS_LIBRARY="renv/library" -RUN Rscript -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))" +RUN /rocker_scripts/setup_R.sh https://p3m.dev/cran/__linux__/jammy/2025-02-05 +RUN Rscript -e "install.packages('renv')" RUN Rscript -e "renv::restore()" # clone https://github.com/reichlab/container-utils. ADD is a hack ala https://stackoverflow.com/questions/35134713/disable-cache-for-specific-run-commands diff --git a/README.md b/README.md index 0e8b249..87f9ea8 100644 --- a/README.md +++ b/README.md @@ -77,18 +77,34 @@ Generating this file is somewhat Python tooling-specific. For example, [pipenv]( A `renv.lock` file is generated via the following steps. As noted above, the "install required R libraries via CRAN" step will vary depending on the individual model's needs. Below we show the commands for the `flu_ar2` model, but you will need to change them for yours. -- start a fresh temporary [rocker/r-ver:4.3.2](https://hub.docker.com/layers/rocker/r-ver/4.3.2/images/sha256-8b25859fbf21a7075bbc2285ebfe06bb8a14dd83e4576df11ff46f14a8620636?context=explore) container via `docker run --rm -it --name temp_container rocker/r-ver:4.3.2 /bin/bash` -- install the required OS libraries and applications (see "install general OS utilities" and "install OS binaries required by R packages" in the [Dockerfile](Dockerfile)) -- install renv via `Rscript -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))"` -- create a project directory via `mkdir /proj ; cd /proj` -- initialize renv via `Rscript -e "renv::init(bare = TRUE)"` -- install required R libraries. NB: these will vary depending on the model (see each model's `README.md` for the actual list). For example: +1. start a fresh temporary [rocker/r-ver:4.4.1](https://hub.docker.com/layers/rocker/r-ver/4.4.1/images/sha256-f3ef082e63ca36547fcf0c05a0d74255ddda6ca7bd88f1dae5a44ce117fc3804) container via: + ```bash + docker run --rm -it --name temp_container rocker/r-ver:4.4.1 /bin/bash + ``` +2. install the required OS libraries and applications (see "install general OS utilities" and "install OS binaries required by R packages" in the [Dockerfile](Dockerfile)) +3. specify repo via: + ```bash + /rocker_scripts/setup_R.sh https://p3m.dev/cran/__linux__/jammy/2025-02-05 + ``` +4. install renv via: + ```bash + Rscript -e "install.packages('renv')" + ``` +5. create a project directory and initialize renv via: + ```bash + mkdir /proj ; cd /proj + Rscript -e "renv::init(bare = TRUE)" + ``` +6. install required R libraries. NB: these will vary depending on the model (see each model's `README.md` for the actual list). For example: ```bash Rscript -e "renv::install(c('lubridate', 'readr', 'remotes'))" - Rscript -e "renv::install('arrow', repos = c('https://apache.r-universe.dev', 'https://cran.r-project.org'))" + Rscript -e "renv::install('arrow')" Rscript -e "renv::install('reichlab/zoltr')" - Rscript -e "renv::install('hubverse-org/hubData')" - Rscript -e "renv::install('hubverse-org/hubVis')" + Rscript -e "renv::install('hubverse-org/hubData@*release')" + Rscript -e "renv::install('hubverse-org/hubVis@*release')" + ``` +7. create `renv.lock` from within the R interpreter (this fails in bash) via: + ```R + renv::settings$snapshot.type('all') ; renv::snapshot() ``` -- create `renv.lock` from within the R interpreter (this fails in bash) via `renv::settings$snapshot.type('all') ; renv::snapshot()` -- copy the new `/proj/renv.lock` file out from the container +8. copy the new `/proj/renv.lock` file out from the container diff --git a/covid_ar6_pooled/README.md b/covid_ar6_pooled/README.md index 4d2b589..f80f335 100644 --- a/covid_ar6_pooled/README.md +++ b/covid_ar6_pooled/README.md @@ -14,15 +14,15 @@ This should result in a model output file and pdfs with plots under `covid_ar6_p # requirements.txt renv and details -`requirements.txt` and `renv.lock` were generated according to [README.md](..%2FREADME.md). For `renv.lock`, we installed these specific libraries: +`requirements.txt` and `renv.lock` were generated according to [README.md](../README.md). For `renv.lock`, we installed these specific libraries: ```bash Rscript -e "renv::install(c('lubridate', 'readr', 'dplyr'))" -Rscript -e "renv::install('arrow', repos = c('https://apache.r-universe.dev', 'https://cran.r-project.org'))" -Rscript -e "renv::install('git::https://github.com/reichlab/zoltr')" -Rscript -e "renv::install('git::https://github.com/hubverse-org/hubData')" -Rscript -e "renv::install('git::https://github.com/hubverse-org/hubVis')" -Rscript -e "renv::install('git::https://github.com/hubverse-org/hubEnsembles')" -Rscript -e "renv::install('git::https://github.com/reichlab/covidData')" -Rscript -e "renv::install('git::https://github.com/reichlab/idforecastutils')" +Rscript -e "renv::install('arrow')" +Rscript -e "renv::install('reichlab/zoltr')" +Rscript -e "renv::install('hubverse-org/hubData@*release')" +Rscript -e "renv::install('hubverse-org/hubVis@*release')" +Rscript -e "renv::install('hubverse-org/hubEnsembles@*release')" +Rscript -e "renv::install('reichlab/covidData')" +Rscript -e "renv::install('reichlab/idforecastutils')" ``` diff --git a/covid_ar6_pooled/renv.lock b/covid_ar6_pooled/renv.lock index 3d7f0c1..f8092b1 100644 --- a/covid_ar6_pooled/renv.lock +++ b/covid_ar6_pooled/renv.lock @@ -1,447 +1,1130 @@ { "R": { - "Version": "4.3.2", + "Version": "4.4.1", "Repositories": [ { "Name": "CRAN", - "URL": "https://p3m.dev/cran/2024-02-28" + "URL": "https://p3m.dev/cran/2025-02-05" } ] }, "Packages": { "KernSmooth": { "Package": "KernSmooth", - "Version": "2.23-22", + "Version": "2.23-24", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-05-16", + "Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)", + "Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"Matt.Wand@uts.edu.au\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"ripley@stats.ox.ac.uk\", comment = \"R port and updates\"))", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Depends": [ + "R (>= 2.5.0)", "stats" ], - "Hash": "2fecebc3047322fa5930f74fae5de70f" + "Suggests": [ + "MASS", + "carData" + ], + "Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".", + "License": "Unlimited", + "ByteCompile": "yes", + "NeedsCompilation": "yes", + "Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MASS": { "Package": "MASS", - "Version": "7.3-60", + "Version": "7.3-60.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-01-12", + "Revision": "$Rev: 3641 $", + "Depends": [ + "R (>= 4.4.0)", "grDevices", "graphics", - "methods", "stats", "utils" ], - "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"ripley@stats.ox.ac.uk\"), person(\"Bill\", \"Venables\", role = \"ctb\"), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MMWRweek": { "Package": "MMWRweek", "Version": "0.1.3", "Source": "Repository", + "Type": "Package", + "Title": "Convert Dates to MMWR Day, Week, and Year", + "Date": "2020-04-22", + "Author": "Jarad Niemi ", + "Maintainer": "Jarad Niemi ", + "Suggests": [ + "testthat" + ], + "Description": "The first day of any MMWR week is Sunday. MMWR week numbering is sequential beginning with 1 and incrementing with each week to a maximum of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at least four days in the calendar year. This package provides functionality to convert Dates to MMWR day, week, and year and the reverse.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "URL": "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf", + "RoxygenNote": "7.0.1", + "NeedsCompilation": "no", "Repository": "CRAN", - "Hash": "4329e57e2536e12afe479e8571416dbc" + "Encoding": "UTF-8" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-1.1", + "Version": "1.7-0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2024-03-16", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", + "License": "GPL (>= 2) | file LICENCE", + "URL": "https://Matrix.R-forge.R-project.org", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's matrix implementation\"))", + "Depends": [ + "R (>= 4.4.0)", + "methods" + ], + "Imports": [ "grDevices", "graphics", "grid", "lattice", - "methods", "stats", "utils" ], - "Hash": "1a00d4828f33a9d690806e98bd17150c" + "Suggests": [ + "MASS", + "datasets", + "sfsmisc", + "tools" + ], + "Enhances": [ + "SparseM", + "graph" + ], + "LazyData": "no", + "LazyDataNote": "not possible, since we use data/*.R and our S4 classes", + "BuildResaveData": "no", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] (), Mikael Jagan [aut] (), Timothy A. Davis [ctb] (, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (base R's matrix implementation)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" }, "R6": { "Package": "R6", "Version": "2.5.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Encapsulated Classes with Reference Semantics", + "Authors@R": "person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@stdout.org\")", + "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.", + "Depends": [ + "R (>= 3.0)" ], - "Hash": "470851b6d5d0ac559e9d01bb352b4021" + "Suggests": [ + "testthat", + "pryr" + ], + "License": "MIT + file LICENSE", + "URL": "https://r6.r-lib.org, https://github.com/r-lib/R6/", + "BugReports": "https://github.com/r-lib/R6/issues", + "RoxygenNote": "7.1.1", + "NeedsCompilation": "no", + "Author": "Winston Chang [aut, cre]", + "Maintainer": "Winston Chang ", + "Repository": "CRAN", + "Encoding": "UTF-8" }, "RColorBrewer": { "Package": "RColorBrewer", "Version": "1.1-3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Date": "2022-04-03", + "Title": "ColorBrewer Palettes", + "Authors@R": "c(person(given = \"Erich\", family = \"Neuwirth\", role = c(\"aut\", \"cre\"), email = \"erich.neuwirth@univie.ac.at\"))", + "Author": "Erich Neuwirth [aut, cre]", + "Maintainer": "Erich Neuwirth ", + "Depends": [ + "R (>= 2.0.0)" ], - "Hash": "45f0398006e83a5b10b72a90663d8d8c" + "Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.", + "License": "Apache License 2.0", + "NeedsCompilation": "no", + "Repository": "CRAN", + "Encoding": "UTF-8" }, "RSocrata": { "Package": "RSocrata", "Version": "1.7.15-1", "Source": "GitHub", + "Type": "Package", + "Title": "Download or Upload 'Socrata' Data Sets", + "Description": "Provides easier interaction with 'Socrata' open data portals . Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SODA) web query, or a 'Socrata' \"human-friendly\" URL, returns an R data frame. Converts dates to 'POSIX' format and manages throttling by 'Socrata'. Users can upload data to 'Socrata' portals directly from R.", + "Date": "2023-08-13", + "Author": "Hugh Devlin, Ph. D., Tom Schenk, Jr., Gene Leynes, Nick Lucius, John Malc, Mark Silverberg, and Peter Schmeideskamp", + "Maintainer": "\"Gene Leynes\" ", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "httr (>= 1.0.0)", + "jsonlite (>= 0.9.16)", + "mime (>= 0.3)", + "plyr (>= 1.8.4)" + ], + "Suggests": [ + "testthat (>= 0.10.0)", + "roxygen2 (>= 4.1.0)", + "readr (>= 0.2.2)" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/Chicago/RSocrata", + "BugReports": "https://github.com/Chicago/RSocrata/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "Chicago", "RemoteRepo": "RSocrata", "RemoteRef": "master", - "RemoteSha": "7c35f916590f6d030ae133b25bb223cab495891c", - "Requirements": [ - "R", - "httr", - "jsonlite", - "mime", - "plyr" - ], - "Hash": "3d997827d605fe0045876019c9671c18" + "RemoteSha": "7c35f916590f6d030ae133b25bb223cab495891c" }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.12", + "Version": "1.0.14", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Seamless R and C++ Integration", + "Date": "2025-01-11", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", + "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. 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It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. 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This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ "grDevices", "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "crosstalk": { "Package": "crosstalk", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "htmltools", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" ], - "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "data.table": { "Package": "data.table", - "Version": "1.15.0", + "Version": "1.16.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "methods" ], - "Hash": "cfbbb4aed6e78cd45f17123a9ec9981a" + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), 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person(\"Nitish\", \"Jha\", role=\"ctb\"), person(\"Joshua\", \"Wu\", role=\"ctb\"), person(\"Iago\", \"Giné-Vázquez\", role=\"ctb\"), person(\"Anirban\", \"Chetia\", role=\"ctb\"), person(\"Doris\", \"Amoakohene\", role=\"ctb\"), person(\"Ivan\", \"Krylov\", role=\"ctb\") )", + "NeedsCompilation": "yes", + "Author": "Tyson Barrett [aut, cre] (), Matt Dowle [aut], Arun Srinivasan [aut], Jan Gorecki [aut], Michael Chirico [aut] (), Toby Hocking [aut] (), Benjamin Schwendinger [aut] (), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Ivan Krylov [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "CRAN" }, "digest": { "Package": "digest", - "Version": "0.6.34", + "Version": "0.6.37", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", + "Date": "2024-08-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "utils" ], - "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a" + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" }, "distfromq": { "Package": "distfromq", "Version": "1.0.4", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "reichlab", - "RemoteRepo": "distfromq", - "RemoteRef": "main", - "RemoteSha": "aa675113f396777a49632b9a7e6076d83c3c91ff", - "Requirements": [ + "Title": "Reconstruct a Distribution from a Collection of Quantiles", + "Authors@R": "c( person(\"Evan\", \"Ray\", , \"elray@umass.edu\", role = c(\"aut\", \"cre\")), person(\"Aaron\", \"Gerding\", , \"agerding@umass.edu\", role = \"aut\"), person(\"Li\", \"Shandross\", , \"lshandross@umass.edu\", role = \"ctb\"), person(\"Nick\", \"Reich\", , \"nick@umass.edu\", role = \"ctb\") )", + "Description": "Given a set of predictive quantiles from a distribution, estimate the distribution and create `d`, `p`, `q`, and `r` functions to evaluate its density function, distribution function, and quantile function, and generate random samples. On the interior of the provided quantiles, an interpolation method such as a monotonic cubic spline is used; the tails are approximated by a location-scale family.", + "License": "GPL (>= 3)", + "URL": "http://reichlab.io/distfromq/", + "Imports": [ "checkmate", "purrr", "splines", @@ -449,354 +1132,937 @@ "utils", "zeallot" ], - "Hash": "5f8e6b6eec1d45a31107f5433ea8934e" + "Suggests": [ + "dplyr", + "ggplot2", + "knitr", + "rmarkdown", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.1", + "Author": "Evan Ray [aut, cre], Aaron Gerding [aut], Li Shandross [ctb], Nick Reich [ctb]", + "Maintainer": "Evan Ray ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "reichlab", + "RemoteRepo": "distfromq", + "RemoteRef": "main", + "RemoteSha": "aa675113f396777a49632b9a7e6076d83c3c91ff" }, "dplyr": { "Package": "dplyr", "Version": "1.1.4", "Source": "Repository", - 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Reich [ctb] (), Evan L. 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Used to interact with 'hubverse' schema, Hub configuration files and model outputs and designed to be primarily used internally by other 'hubverse' packages. See Reich et al. (2022) for an overview of Collaborative Hubs.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/hubverse-org/hubUtils, https://hubverse-org.github.io/hubUtils/", + "BugReports": "https://github.com/hubverse-org/hubUtils/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ "checkmate", "cli", "curl", @@ -861,44 +2182,88 @@ "tibble", "utils" ], - "Hash": "68342b09c9fb78b5ed3b33d656d1a266" + "Suggests": [ + "arrow (>= 17.0.0)", + "dplyr", + "knitr", + "rmarkdown", + "testthat (>= 3.2.0)" + ], + "Config/Needs/website": "hubverse-org/hubStyle", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.2", + "Author": "Anna Krystalli [aut, cre] (), Li Shandross [ctb], Nicholas G. Reich [ctb] (), Evan L. 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Kamvar [ctb] (), Consortium of Infectious Disease Modeling Hubs [cph]", + "Maintainer": "Anna Krystalli ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "Infectious-Disease-Modeling-Hubs", + "RemoteRepo": "hubUtils", + "RemoteRef": "main", + "RemoteSha": "2cc6dac48328ed38cdf20d1c0f29813a67b87ec6" }, "hubVis": { "Package": "hubVis", "Version": "0.1.1.9000", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "Infectious-Disease-Modeling-Hubs", - "RemoteRepo": "hubVis", - "RemoteRef": "main", - "RemoteSha": "d6f23598026d8485176e059144251c74e77f62f1", - "Requirements": [ - "RColorBrewer", + "Title": "Plotting methods for hub models output", + "Authors@R": "c( person(\"Lucie\", \"Contamin\", , \"contamin@pitt.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5797-1279\")), person(\"Harry\", \"Hochheiser\", role = \"ctb\"), person(\"Zhian\", \"Kamvar\", role = \"ctb\"), person(\"Anna\", \"Krystalli\", role = \"ctb\"), person(\"Nicholas G.\", \"Reich\", role = \"ctb\"), person(family = \"Consortium of Infectious Disease Modeling Hubs\", role = c(\"cph\")))", + "Description": "Plotting methods for hub models output.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Imports": [ "cli", "dplyr", "ggplot2", "grDevices", - "hubUtils", + "hubUtils (>= 0.0.1)", "methods", "plotly", "purrr", + "RColorBrewer", "scales", "stats" ], - "Hash": "52886fe27334199e93f47bbe99c59976" + "Suggests": [ + "hubData", + "hubExamples (>= 0.0.0.9001)", + "rmarkdown", + "testthat (>= 3.0.0)", + "vdiffr" + ], + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.2", + "URL": "https://github.com/hubverse-org/hubVis, https://hubverse-org.github.io/hubVis/", + "BugReports": "https://github.com/hubverse-org/hubVis/issues", + "Config/testthat/edition": "3", + "Config/Needs/website": "hubverse-org/hubStyle", + "Author": "Lucie Contamin [aut, cre] (), Harry Hochheiser [ctb], Zhian Kamvar [ctb], Anna Krystalli [ctb], Nicholas G. Reich [ctb], Consortium of Infectious Disease Modeling Hubs [cph]", + "Maintainer": "Lucie Contamin ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "Infectious-Disease-Modeling-Hubs", + "RemoteRepo": "hubVis", + "RemoteRef": "main", + "RemoteSha": "d6f23598026d8485176e059144251c74e77f62f1", + "Remotes": "hubverse-org/hubUtils, hubverse-org/hubData, hubverse-org/hubExamples" }, "idforecastutils": { "Package": "idforecastutils", "Version": "0.0.0.9000", - "Source": "git", - "RemoteType": "git", - "RemoteUrl": "https://github.com/reichlab/idforecastutils", - "RemoteRef": "", - "Requirements": [ + "Source": "GitHub", + "Title": "Utility functions for general infectious disease forecasting use", + "Authors@R": "c( person(\"Li\", \"Shandross\", , \"lshandross@umass.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0008-1348-1954\")), person(\"Evan\", \"Ray\", , \"elray@umass.edu\", role = c(\"aut\")) )", + "Description": "A set of utility functions for various infectious disease forecasting models, exercises, and rounds.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.2", + "Imports": [ "cli", "covidData", - "distfromq", + "distfromq (>= 1.0.2)", "dplyr", "forcats", "ggplot2", @@ -911,836 +2276,2294 @@ "rlang", "scales" ], - "Hash": "17230ef8407182bc792e50916b3eab71" + "Suggests": [ + "ggforce", + "hubExamples", + "readr", + "testthat (>= 3.0.0)", + "tidyr" + ], + "Config/testthat/edition": "3", + "Author": "Li Shandross [aut, cre] (), Evan Ray [aut]", + "Maintainer": "Li Shandross ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "reichlab", + "RemoteRepo": "idforecastutils", + "RemoteRef": "main", + "RemoteSha": "0caa1626d98276aaf148641b12394ba6f6b5fa27", + "Remotes": "Infectious-Disease-Modeling-Hubs/hubEnsembles, Infectious-Disease-Modeling-Hubs/hubExamples, Infectious-Disease-Modeling-Hubs/hubUtils, Infectious-Disease-Modeling-Hubs/hubVis, reichlab/distfromq, reichlab/covidData" }, "ini": { "Package": "ini", "Version": "0.3.1", "Source": "Repository", + "Type": "Package", + "Title": "Read and Write '.ini' Files", + "Date": "2018-05-19", + "Author": "David Valentim Dias", + "Maintainer": "David Valentim Dias ", + "Description": "Parse simple '.ini' configuration files to an structured list. 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This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, \"Ceci n'est pas un pipe.\"", + "License": "MIT + file LICENSE", + "URL": "https://magrittr.tidyverse.org, https://github.com/tidyverse/magrittr", + "BugReports": "https://github.com/tidyverse/magrittr/issues", + "Depends": [ + "R (>= 3.4.0)" + ], + "Suggests": [ + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat" ], - "Hash": "7ce2733a9826b3aeb1775d56fd305472" + "VignetteBuilder": "knitr", + "ByteCompile": "Yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.1.2", + "NeedsCompilation": "yes", + "Author": "Stefan Milton Bache [aut, cph] (Original author and creator of magrittr), Hadley Wickham [aut], Lionel Henry [cre], RStudio [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" }, "matrixStats": { "Package": "matrixStats", - "Version": "1.2.0", + "Version": "1.5.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Depends": [ + "R (>= 3.4.0)" + ], + "Suggests": [ + "utils", + "base64enc", + "ggplot2", + "knitr", + "markdown", + "microbenchmark", + "R.devices", + "R.rsp" ], - "Hash": "33a3ca9e732b57244d14f5d732ffc9eb" + "VignetteBuilder": "R.rsp", + "Title": "Functions that Apply to Rows and Columns of Matrices (and to Vectors)", + "Authors@R": "c( person(\"Henrik\", \"Bengtsson\", role=c(\"aut\", \"cre\", \"cph\"), email=\"henrikb@braju.com\"), person(\"Constantin\", \"Ahlmann-Eltze\", role = \"ctb\"), person(\"Hector\", \"Corrada Bravo\", role=\"ctb\"), person(\"Robert\", \"Gentleman\", role=\"ctb\"), person(\"Jan\", \"Gleixner\", role=\"ctb\"), person(\"Peter\", \"Hickey\", role=\"ctb\"), person(\"Ola\", \"Hossjer\", role=\"ctb\"), person(\"Harris\", \"Jaffee\", role=\"ctb\"), person(\"Dongcan\", \"Jiang\", role=\"ctb\"), person(\"Peter\", \"Langfelder\", role=\"ctb\"), person(\"Brian\", \"Montgomery\", role=\"ctb\"), person(\"Angelina\", \"Panagopoulou\", role=\"ctb\"), person(\"Hugh\", \"Parsonage\", role=\"ctb\"), person(\"Jakob Peder\", \"Pettersen\", role=\"ctb\"))", + "Author": "Henrik Bengtsson [aut, cre, cph], Constantin Ahlmann-Eltze [ctb], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Jan Gleixner [ctb], Peter Hickey [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb], Brian Montgomery [ctb], Angelina Panagopoulou [ctb], Hugh Parsonage [ctb], Jakob Peder Pettersen [ctb]", + "Maintainer": "Henrik Bengtsson ", + "Description": "High-performing functions operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. 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It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.", + "License": "MIT + file LICENSE", + "URL": "https://tidyselect.r-lib.org, https://github.com/r-lib/tidyselect", + "BugReports": "https://github.com/r-lib/tidyselect/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli (>= 3.3.0)", + "glue (>= 1.3.0)", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.0.4)", + "vctrs (>= 0.5.2)", "withr" ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" + "Suggests": [ + "covr", + "crayon", + "dplyr", + "knitr", + "magrittr", + "rmarkdown", + "stringr", + "testthat (>= 3.1.1)", + "tibble (>= 2.1.3)" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "true", + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.0.9000", + "NeedsCompilation": "yes", + "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" }, "timechange": { "Package": "timechange", "Version": "0.3.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" + "Title": "Efficient Manipulation of Date-Times", + "Authors@R": "c(person(\"Vitalie\", \"Spinu\", email = \"spinuvit@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Google Inc.\", role = c(\"ctb\", \"cph\")))", + "Description": "Efficient routines for manipulation of date-time objects while accounting for time-zones and daylight saving times. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" ], - "Hash": "5ac22900ae0f386e54f1c307eca7d843" + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "tzdb": { "Package": "tzdb", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" ], - "Hash": "f561504ec2897f4d46f0c7657e488ae1" + "LinkingTo": [ + "cpp11 (>= 0.4.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "utf8": { "Package": "utf8", "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8", + "BugReports": "https://github.com/patperry/r-utf8/issues", + "Depends": [ + "R (>= 2.10)" ], - "Hash": "62b65c52671e6665f803ff02954446e9" + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. [cph, dtc] (Unicode Character Database)", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" }, "vctrs": { "Package": "vctrs", "Version": "0.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", + "Title": "Vector Helpers", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"data.table team\", role = \"cph\", comment = \"Radix sort based on data.table's forder() and their contribution to R's order()\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.", + "License": "MIT + file LICENSE", + "URL": "https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs", + "BugReports": "https://github.com/r-lib/vctrs/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", "glue", - "lifecycle", - "rlang" + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "bit64", + "covr", + "crayon", + "dplyr (>= 0.8.5)", + "generics", + "knitr", + "pillar (>= 1.4.4)", + "pkgdown (>= 2.0.1)", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble (>= 3.1.3)", + "waldo (>= 0.2.0)", + "withr", + "xml2", + "zeallot" ], - "Hash": "c03fa420630029418f7e6da3667aac4a" + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-GB", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Lionel Henry [aut], Davis Vaughan [aut, cre], data.table team [cph] (Radix sort based on data.table's forder() and their contribution to R's order()), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "viridisLite": { "Package": "viridisLite", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" ], - "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" }, "vroom": { "Package": "vroom", "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.", + "License": "MIT + file LICENSE", + "URL": "https://vroom.r-lib.org, https://github.com/tidyverse/vroom", + "BugReports": "https://github.com/tidyverse/vroom/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ "bit64", - "cli", - "cpp11", + "cli (>= 3.2.0)", "crayon", "glue", "hms", - "lifecycle", + "lifecycle (>= 1.0.3)", "methods", - "progress", - "rlang", + "rlang (>= 0.4.2)", "stats", - "tibble", + "tibble (>= 2.0.0)", "tidyselect", - "tzdb", - "vctrs", + "tzdb (>= 0.1.1)", + "vctrs (>= 0.2.0)", "withr" ], - "Hash": "390f9315bc0025be03012054103d227c" + "Suggests": [ + "archive", + "bench (>= 1.1.0)", + "covr", + "curl", + "dplyr", + "forcats", + "fs", + "ggplot2", + "knitr", + "patchwork", + "prettyunits", + "purrr", + "rmarkdown", + "rstudioapi", + "scales", + "spelling", + "testthat (>= 2.1.0)", + "tidyr", + "utils", + "waldo", + "xml2" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.0)", + "progress (>= 1.2.1)", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "nycflights13, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Copyright": "file COPYRIGHTS", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3.9000", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" }, "withr": { "Package": "withr", - "Version": "3.0.0", + "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics" + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" ], - "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" }, "xfun": { "Package": "xfun", - "Version": "0.42", + "Version": "0.50", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ "grDevices", "stats", "tools" ], - "Hash": "fd1349170df31f7a10bd98b0189e85af" + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown (>= 0.4)", + "commonmark", + "knitr (>= 1.47)", + "remotes", + "pak", + "rhub", + "renv", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs", + "rmarkdown" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "xml2": { "Package": "xml2", "Version": "1.3.6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Parse XML", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Foundation\", role = \"ctb\", comment = \"Copy of R-project homepage cached as example\") )", + "Description": "Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org/, https://github.com/r-lib/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ "cli", "methods", - "rlang" + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.0.0)" ], - "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Jim Hester [aut], Jeroen Ooms [aut], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "yaml": { "Package": "yaml", - "Version": "2.3.8", + "Version": "2.3.10", "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" + "Encoding": "UTF-8" }, "zeallot": { "Package": "zeallot", "Version": "0.1.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ee9b643aa8331c45d8d82eb3a137c9bc" + "Type": "Package", + "Title": "Multiple, Unpacking, and Destructuring Assignment", + "Authors@R": "c( person(given = \"Nathan\", family = \"Teetor\", email = \"nathanteetor@gmail.com\", role = c(\"aut\", \"cre\")), person(given = \"Paul\", family = \"Teetor\", role = \"ctb\"))", + "Description": "Provides a %<-% operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.", + "URL": "https://github.com/nteetor/zeallot", + "BugReports": "https://github.com/nteetor/zeallot/issues", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "6.0.1", + "VignetteBuilder": "knitr", + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "purrr", + "magrittr" + ], + "NeedsCompilation": "no", + "Author": "Nathan Teetor [aut, cre], Paul Teetor [ctb]", + "Maintainer": "Nathan Teetor ", + "Repository": "CRAN" }, "zoltr": { "Package": "zoltr", "Version": "1.0.1", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "reichlab", - "RemoteRepo": "zoltr", - "RemoteRef": "master", - "RemoteSha": "3344e2a95969042977ae2f89fef672244348569f", - "Requirements": [ - "MMWRweek", - "base64url", + "Title": "Interface to the 'Zoltar' Forecast Repository API", + "Authors@R": "c( person(\"Matthew\", \"Cornell\", role = c(\"aut\", \"cre\"), email = \"cornell@umass.edu\"), person(\"Nicholas\", \"Reich\", role = c(\"aut\", \"cph\"), email = \"nick@schoolph.umass.edu\"))", + "Description": "'Zoltar' is a website that provides a repository of model forecast results in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time series forecasts for prediction challenges of interest to the modeling community. This package provides functions for working with the 'Zoltar' API, including connecting and authenticating, getting meta information (projects, models, and forecasts, and truth), and uploading, downloading, and deleting forecast and truth data.", + "URL": "https://github.com/reichlab/zoltr , http://reichlab.io/zoltr/", + "BugReports": "https://github.com/reichlab/zoltr/issues", + "License": "GPL-3", + "Encoding": "UTF-8", + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "webmockr", + "mockery" + ], + "Imports": [ "data.table", - "dplyr", "httr", "jsonlite", - "lubridate", - "magrittr", "readr", + "base64url", + "dplyr", + "MMWRweek", + "utils", "rlang", - "utils" + "magrittr", + "lubridate" ], - "Hash": "aa318d451907140ef0883d51435b87c5" + "RoxygenNote": "7.3.1", + "VignetteBuilder": "knitr", + "Roxygen": "list(markdown = TRUE)", + "Author": "Matthew Cornell [aut, cre], Nicholas Reich [aut, cph]", + "Maintainer": "Matthew Cornell ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "reichlab", + "RemoteRepo": "zoltr", + "RemoteRef": "master", + "RemoteSha": "3344e2a95969042977ae2f89fef672244348569f" } } } diff --git a/covid_gbqr/README.md b/covid_gbqr/README.md index 7f00801..7599cbb 100644 --- a/covid_gbqr/README.md +++ b/covid_gbqr/README.md @@ -14,15 +14,15 @@ This should result in a model output file and pdfs with plots under `covid_gbqr/ # requirements.txt renv and details -`requirements.txt` and `renv.lock` were generated according to [README.md](..%2FREADME.md). For `renv.lock`, we installed these specific libraries: +`requirements.txt` and `renv.lock` were generated according to [README.md](../README.md). For `renv.lock`, we installed these specific libraries: ```bash Rscript -e "renv::install(c('lubridate', 'readr', 'dplyr'))" -Rscript -e "renv::install('arrow', repos = c('https://apache.r-universe.dev', 'https://cran.r-project.org'))" -Rscript -e "renv::install('git::https://github.com/reichlab/zoltr')" -Rscript -e "renv::install('git::https://github.com/hubverse-org/hubData')" -Rscript -e "renv::install('git::https://github.com/hubverse-org/hubVis')" -Rscript -e "renv::install('git::https://github.com/hubverse-org/hubEnsembles')" -Rscript -e "renv::install('git::https://github.com/reichlab/covidData')" -Rscript -e "renv::install('git::https://github.com/reichlab/idforecastutils')" +Rscript -e "renv::install('arrow')" +Rscript -e "renv::install('reichlab/zoltr')" +Rscript -e "renv::install('hubverse-org/hubData@*release')" +Rscript -e "renv::install('hubverse-org/hubVis@*release')" +Rscript -e "renv::install('hubverse-org/hubEnsembles@*release')" +Rscript -e "renv::install('reichlab/covidData')" +Rscript -e "renv::install('reichlab/idforecastutils')" ``` diff --git a/covid_gbqr/renv.lock b/covid_gbqr/renv.lock index 3d7f0c1..b076966 100644 --- a/covid_gbqr/renv.lock +++ b/covid_gbqr/renv.lock @@ -1,447 +1,1130 @@ { "R": { - "Version": "4.3.2", + "Version": "4.4.1", "Repositories": [ { "Name": "CRAN", - "URL": "https://p3m.dev/cran/2024-02-28" + "URL": "https://p3m.dev/cran/2025-02-05" } ] }, "Packages": { "KernSmooth": { "Package": "KernSmooth", - "Version": "2.23-22", + "Version": "2.23-24", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-05-16", + "Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)", + "Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"Matt.Wand@uts.edu.au\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"ripley@stats.ox.ac.uk\", comment = \"R port and updates\"))", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Depends": [ + "R (>= 2.5.0)", "stats" ], - "Hash": "2fecebc3047322fa5930f74fae5de70f" + "Suggests": [ + "MASS", + "carData" + ], + "Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".", + "License": "Unlimited", + "ByteCompile": "yes", + "NeedsCompilation": "yes", + "Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MASS": { "Package": "MASS", - "Version": "7.3-60", + "Version": "7.3-60.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-01-12", + "Revision": "$Rev: 3641 $", + "Depends": [ + "R (>= 4.4.0)", "grDevices", "graphics", - "methods", "stats", "utils" ], - "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"ripley@stats.ox.ac.uk\"), person(\"Bill\", \"Venables\", role = \"ctb\"), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MMWRweek": { "Package": "MMWRweek", "Version": "0.1.3", "Source": "Repository", + "Type": "Package", + "Title": "Convert Dates to MMWR Day, Week, and Year", + "Date": "2020-04-22", + "Author": "Jarad Niemi ", + "Maintainer": "Jarad Niemi ", + "Suggests": [ + "testthat" + ], + "Description": "The first day of any MMWR week is Sunday. MMWR week numbering is sequential beginning with 1 and incrementing with each week to a maximum of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at least four days in the calendar year. This package provides functionality to convert Dates to MMWR day, week, and year and the reverse.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "URL": "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf", + "RoxygenNote": "7.0.1", + "NeedsCompilation": "no", "Repository": "CRAN", - "Hash": "4329e57e2536e12afe479e8571416dbc" + "Encoding": "UTF-8" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-1.1", + "Version": "1.7-0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2024-03-16", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", + "License": "GPL (>= 2) | file LICENCE", + "URL": "https://Matrix.R-forge.R-project.org", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's matrix implementation\"))", + "Depends": [ + "R (>= 4.4.0)", + "methods" + ], + "Imports": [ "grDevices", "graphics", "grid", "lattice", - "methods", "stats", "utils" ], - "Hash": "1a00d4828f33a9d690806e98bd17150c" + "Suggests": [ + "MASS", + "datasets", + "sfsmisc", + "tools" + ], + "Enhances": [ + "SparseM", + "graph" + ], + "LazyData": "no", + "LazyDataNote": "not possible, since we use data/*.R and our S4 classes", + "BuildResaveData": "no", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] (), Mikael Jagan [aut] (), Timothy A. Davis [ctb] (, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (base R's matrix implementation)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" }, "R6": { "Package": "R6", "Version": "2.5.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Encapsulated Classes with Reference Semantics", + "Authors@R": "person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@stdout.org\")", + "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. 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Qualitative, sequential, and diverging color palettes based on HCL colors are provided along with corresponding ggplot2 color scales. Color palette choice is aided by an interactive app (with either a Tcl/Tk or a shiny graphical user interface) and shiny apps with an HCL color picker and a color vision deficiency emulator. Plotting functions for displaying and assessing palettes include color swatches, visualizations of the HCL space, and trajectories in HCL and/or RGB spectrum. Color manipulation functions include: desaturation, lightening/darkening, mixing, and simulation of color vision deficiencies (deutanomaly, protanomaly, tritanomaly). Details can be found on the project web page at and in the accompanying scientific paper: Zeileis et al. 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McWhite [aut] (), Achim Zeileis [aut, cre] ()", + "Maintainer": "Achim Zeileis ", + "Repository": "CRAN" }, "covidData": { "Package": "covidData", "Version": "1.0.1", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "reichlab", - "RemoteRepo": "covidData", - "RemoteRef": "master", - "RemoteSha": "a45c3f65b249af3299445856b0180eb4c87639a1", - "Requirements": [ - "MMWRweek", - "RSocrata", + "Title": "Versioned Data for COVID-19", + "Authors@R": "person(given = \"Evan\", family = \"Ray\", role = c(\"aut\", \"cre\"), email = \"elray@umass.edu\")", + "Description": "Versioned Data for COVID-19", + "License": "MIT", + "Imports": [ "dplyr", "here", "httr", "lubridate", "magrittr", + "MMWRweek", "purrr", "readr", + "RSocrata", "rvest", "tibble", "tidyr", "xml2" ], - "Hash": "4c7e6104073978deb4b0124f52c49985" + "Suggests": [ + "covidcast" + ], + "Encoding": "UTF-8", + "LazyData": "true", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.1.2", + "Author": "Evan Ray [aut, cre]", + "Maintainer": "Evan Ray ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "reichlab", + "RemoteRepo": "covidData", + "RemoteRef": "master", + "RemoteSha": "a45c3f65b249af3299445856b0180eb4c87639a1", + "Remotes": "Chicago/RSocrata" }, "cpp11": { "Package": "cpp11", - "Version": "0.4.7", + "Version": "0.5.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "A C++11 Interface for R's C Interface", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", email = \"davis@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0003-4777-038X\")), person(\"Jim\",\"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Romain\", \"François\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Benjamin\", \"Kietzman\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" ], - "Hash": "5a295d7d963cc5035284dcdbaf334f4e" + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "crayon": { "Package": "crayon", - "Version": "1.5.2", + "Version": "1.5.3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ "grDevices", "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "crosstalk": { "Package": "crosstalk", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "htmltools", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.", + "License": "MIT + file LICENSE", + "Imports": [ + "htmltools (>= 0.3.6)", "jsonlite", - "lazyeval" + "lazyeval", + "R6" + ], + "Suggests": [ + "shiny", + "ggplot2", + "testthat (>= 2.1.0)", + "sass", + "bslib" ], - "Hash": "ab12c7b080a57475248a30f4db6298c0" + "URL": "https://rstudio.github.io/crosstalk/, https://github.com/rstudio/crosstalk", + "BugReports": "https://github.com/rstudio/crosstalk/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", + "NeedsCompilation": "no", + "Author": "Joe Cheng [aut], Carson Sievert [aut, cre] (), Posit Software, PBC [cph, fnd], jQuery Foundation [cph] (jQuery library and jQuery UI library), jQuery contributors [ctb, cph] (jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt), Mark Otto [ctb] (Bootstrap library), Jacob Thornton [ctb] (Bootstrap library), Bootstrap contributors [ctb] (Bootstrap library), Twitter, Inc [cph] (Bootstrap library), Brian Reavis [ctb, cph] (selectize.js library), Kristopher Michael Kowal [ctb, cph] (es5-shim library), es5-shim contributors [ctb, cph] (es5-shim library), Denis Ineshin [ctb, cph] (ion.rangeSlider library), Sami Samhuri [ctb, cph] (Javascript strftime library)", + "Maintainer": "Carson Sievert ", + "Repository": "CRAN" }, "curl": { "Package": "curl", - "Version": "5.2.0", + "Version": "6.2.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Type": "Package", + "Title": "A Modern and Flexible Web Client for R", + "Authors@R": "c( person(\"Jeroen\", \"Ooms\", role = c(\"aut\", \"cre\"), email = \"jeroenooms@gmail.com\", comment = c(ORCID = \"0000-0002-4035-0289\")), person(\"Hadley\", \"Wickham\", role = \"ctb\"), person(\"Posit Software, PBC\", role = \"cph\"))", + "Description": "Bindings to 'libcurl' for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" ], - "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "data.table": { "Package": "data.table", - "Version": "1.15.0", + "Version": "1.16.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "methods" ], - "Hash": "cfbbb4aed6e78cd45f17123a9ec9981a" + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), person(\"Pasha\",\"Stetsenko\", role=\"ctb\"), person(\"Tom\",\"Short\", role=\"ctb\"), person(\"Steve\",\"Lianoglou\", role=\"ctb\"), person(\"Eduard\",\"Antonyan\", role=\"ctb\"), person(\"Markus\",\"Bonsch\", role=\"ctb\"), person(\"Hugh\",\"Parsonage\", role=\"ctb\"), person(\"Scott\",\"Ritchie\", role=\"ctb\"), person(\"Kun\",\"Ren\", role=\"ctb\"), person(\"Xianying\",\"Tan\", role=\"ctb\"), person(\"Rick\",\"Saporta\", role=\"ctb\"), person(\"Otto\",\"Seiskari\", role=\"ctb\"), person(\"Xianghui\",\"Dong\", role=\"ctb\"), person(\"Michel\",\"Lang\", role=\"ctb\"), person(\"Watal\",\"Iwasaki\", role=\"ctb\"), person(\"Seth\",\"Wenchel\", role=\"ctb\"), person(\"Karl\",\"Broman\", role=\"ctb\"), person(\"Tobias\",\"Schmidt\", role=\"ctb\"), person(\"David\",\"Arenburg\", role=\"ctb\"), person(\"Ethan\",\"Smith\", role=\"ctb\"), person(\"Francois\",\"Cocquemas\", role=\"ctb\"), person(\"Matthieu\",\"Gomez\", role=\"ctb\"), person(\"Philippe\",\"Chataignon\", role=\"ctb\"), person(\"Nello\",\"Blaser\", role=\"ctb\"), person(\"Dmitry\",\"Selivanov\", role=\"ctb\"), person(\"Andrey\",\"Riabushenko\", role=\"ctb\"), person(\"Cheng\",\"Lee\", role=\"ctb\"), person(\"Declan\",\"Groves\", role=\"ctb\"), person(\"Daniel\",\"Possenriede\", role=\"ctb\"), person(\"Felipe\",\"Parages\", role=\"ctb\"), person(\"Denes\",\"Toth\", role=\"ctb\"), person(\"Mus\",\"Yaramaz-David\", role=\"ctb\"), person(\"Ayappan\",\"Perumal\", role=\"ctb\"), person(\"James\",\"Sams\", role=\"ctb\"), person(\"Martin\",\"Morgan\", role=\"ctb\"), person(\"Michael\",\"Quinn\", role=\"ctb\"), person(\"@javrucebo\",\"\", role=\"ctb\"), person(\"@marc-outins\",\"\", role=\"ctb\"), person(\"Roy\",\"Storey\", role=\"ctb\"), person(\"Manish\",\"Saraswat\", role=\"ctb\"), person(\"Morgan\",\"Jacob\", role=\"ctb\"), person(\"Michael\",\"Schubmehl\", role=\"ctb\"), person(\"Davis\",\"Vaughan\", role=\"ctb\"), person(\"Leonardo\",\"Silvestri\", role=\"ctb\"), person(\"Jim\",\"Hester\", role=\"ctb\"), 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person(\"Nitish\", \"Jha\", role=\"ctb\"), person(\"Joshua\", \"Wu\", role=\"ctb\"), person(\"Iago\", \"Giné-Vázquez\", role=\"ctb\"), person(\"Anirban\", \"Chetia\", role=\"ctb\"), person(\"Doris\", \"Amoakohene\", role=\"ctb\"), person(\"Ivan\", \"Krylov\", role=\"ctb\") )", + "NeedsCompilation": "yes", + "Author": "Tyson Barrett [aut, cre] (), Matt Dowle [aut], Arun Srinivasan [aut], Jan Gorecki [aut], Michael Chirico [aut] (), Toby Hocking [aut] (), Benjamin Schwendinger [aut] (), Pasha Stetsenko [ctb], Tom Short [ctb], Steve Lianoglou [ctb], Eduard Antonyan [ctb], Markus Bonsch [ctb], Hugh Parsonage [ctb], Scott Ritchie [ctb], Kun Ren [ctb], Xianying Tan [ctb], Rick Saporta [ctb], Otto Seiskari [ctb], Xianghui Dong [ctb], Michel Lang [ctb], Watal Iwasaki [ctb], Seth Wenchel [ctb], Karl Broman [ctb], Tobias Schmidt [ctb], David Arenburg [ctb], Ethan Smith [ctb], Francois Cocquemas [ctb], Matthieu Gomez [ctb], Philippe Chataignon [ctb], Nello Blaser [ctb], Dmitry Selivanov [ctb], Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Ivan Krylov [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "CRAN" }, "digest": { "Package": "digest", - "Version": "0.6.34", + "Version": "0.6.37", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", + "Date": "2024-08-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "utils" ], - "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a" + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" }, "distfromq": { "Package": "distfromq", "Version": "1.0.4", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "reichlab", - "RemoteRepo": "distfromq", - "RemoteRef": "main", - "RemoteSha": "aa675113f396777a49632b9a7e6076d83c3c91ff", - "Requirements": [ + "Title": "Reconstruct a Distribution from a Collection of Quantiles", + "Authors@R": "c( person(\"Evan\", \"Ray\", , \"elray@umass.edu\", role = c(\"aut\", \"cre\")), person(\"Aaron\", \"Gerding\", , \"agerding@umass.edu\", role = \"aut\"), person(\"Li\", \"Shandross\", , \"lshandross@umass.edu\", role = \"ctb\"), person(\"Nick\", \"Reich\", , \"nick@umass.edu\", role = \"ctb\") )", + "Description": "Given a set of predictive quantiles from a distribution, estimate the distribution and create `d`, `p`, `q`, and `r` functions to evaluate its density function, distribution function, and quantile function, and generate random samples. 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Reich [ctb] (), Evan L. 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Reich [ctb] (), Consortium of Infectious Disease Modeling Hubs [cph]", + "Maintainer": "Li Shandross ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "hubverse-org", + "RemoteRepo": "hubEnsembles", + "RemoteRef": "v0.1.9", + "RemoteSha": "9ba5eab32295632bb88e486f6dad796abadea74f", + "Remotes": "hubverse-org/hubExamples, hubverse-org/hubUtils, hubverse-org/hubVis, reichlab/distfromq" }, "hubUtils": { "Package": "hubUtils", - "Version": "0.3.0.9000", + "Version": "0.4.0.9000", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "Infectious-Disease-Modeling-Hubs", - "RemoteRepo": "hubUtils", - "RemoteRef": "main", - "RemoteSha": "aa3e9208bb2f50f89d26aad08c83db77134b4d19", - "Requirements": [ - "R", + "Title": "Core 'hubverse' Utilities", + "Authors@R": "c( person(\"Anna\", \"Krystalli\", , \"annakrystalli@googlemail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-2378-4915\")), person(\"Li\", \"Shandross\", , \"lshandross@umass.edu\", role = \"ctb\"), person(\"Nicholas G.\", \"Reich\", , \"nick@umass.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3503-9899\")), person(\"Evan L.\", \"Ray\", , \"elray@umass.edu\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", , \"zkamvar@gmail.com\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0003-1458-7108\")), person(\"Consortium of Infectious Disease Modeling Hubs\", role = \"cph\") )", + "Description": "Core set of low-level utilities common across the 'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files and model outputs and designed to be primarily used internally by other 'hubverse' packages. See Reich et al. (2022) for an overview of Collaborative Hubs.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/hubverse-org/hubUtils, https://hubverse-org.github.io/hubUtils/", + "BugReports": "https://github.com/hubverse-org/hubUtils/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ "checkmate", "cli", "curl", @@ -861,44 +2182,88 @@ "tibble", "utils" ], - "Hash": "68342b09c9fb78b5ed3b33d656d1a266" + "Suggests": [ + "arrow (>= 17.0.0)", + "dplyr", + "knitr", + "rmarkdown", + "testthat (>= 3.2.0)" + ], + "Config/Needs/website": "hubverse-org/hubStyle", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.2", + "Author": "Anna Krystalli [aut, cre] (), Li Shandross [ctb], Nicholas G. Reich [ctb] (), Evan L. 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Kamvar [ctb] (), Consortium of Infectious Disease Modeling Hubs [cph]", + "Maintainer": "Anna Krystalli ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "hubverse-org", + "RemoteRepo": "hubUtils", + "RemoteRef": "main", + "RemoteSha": "2cc6dac48328ed38cdf20d1c0f29813a67b87ec6" }, "hubVis": { "Package": "hubVis", - "Version": "0.1.1.9000", + "Version": "0.1.1", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "Infectious-Disease-Modeling-Hubs", - "RemoteRepo": "hubVis", - "RemoteRef": "main", - "RemoteSha": "d6f23598026d8485176e059144251c74e77f62f1", - "Requirements": [ - "RColorBrewer", + "Title": "Plotting methods for hub models output", + "Authors@R": "c( person(\"Lucie\", \"Contamin\", , \"contamin@pitt.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0001-5797-1279\")), person(\"Harry\", \"Hochheiser\", role = \"ctb\"), person(\"Zhian\", \"Kamvar\", role = \"ctb\"), person(\"Anna\", \"Krystalli\", role = \"ctb\"), person(\"Nicholas G.\", \"Reich\", role = \"ctb\"), person(family = \"Consortium of Infectious Disease Modeling Hubs\", role = c(\"cph\")))", + "Description": "Plotting methods for hub models output.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Imports": [ "cli", "dplyr", "ggplot2", "grDevices", - "hubUtils", + "hubUtils (>= 0.0.1)", "methods", "plotly", "purrr", + "RColorBrewer", "scales", "stats" ], - "Hash": "52886fe27334199e93f47bbe99c59976" + "Suggests": [ + "hubData", + "hubExamples (>= 0.0.0.9001)", + "rmarkdown", + "testthat (>= 3.0.0)", + "vdiffr" + ], + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.2", + "URL": "https://github.com/hubverse-org/hubVis, https://hubverse-org.github.io/hubVis/", + "BugReports": "https://github.com/hubverse-org/hubVis/issues", + "Config/testthat/edition": "3", + "Config/Needs/website": "hubverse-org/hubStyle", + "Author": "Lucie Contamin [aut, cre] (), Harry Hochheiser [ctb], Zhian Kamvar [ctb], Anna Krystalli [ctb], Nicholas G. Reich [ctb], Consortium of Infectious Disease Modeling Hubs [cph]", + "Maintainer": "Lucie Contamin ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "hubverse-org", + "RemoteRepo": "hubVis", + "RemoteRef": "v0.1.1", + "RemoteSha": "9f15bbf56e733f8599ed56ac64cfa7c44fd98205", + "Remotes": "hubverse-org/hubUtils, hubverse-org/hubData, hubverse-org/hubExamples" }, "idforecastutils": { "Package": "idforecastutils", "Version": "0.0.0.9000", - "Source": "git", - "RemoteType": "git", - "RemoteUrl": "https://github.com/reichlab/idforecastutils", - "RemoteRef": "", - "Requirements": [ + "Source": "GitHub", + "Title": "Utility functions for general infectious disease forecasting use", + "Authors@R": "c( person(\"Li\", \"Shandross\", , \"lshandross@umass.edu\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0009-0008-1348-1954\")), person(\"Evan\", \"Ray\", , \"elray@umass.edu\", role = c(\"aut\")) )", + "Description": "A set of utility functions for various infectious disease forecasting models, exercises, and rounds.", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.2", + "Imports": [ "cli", "covidData", - "distfromq", + "distfromq (>= 1.0.2)", "dplyr", "forcats", "ggplot2", @@ -911,836 +2276,2294 @@ "rlang", "scales" ], - "Hash": "17230ef8407182bc792e50916b3eab71" + "Suggests": [ + "ggforce", + "hubExamples", + "readr", + "testthat (>= 3.0.0)", + "tidyr" + ], + "Config/testthat/edition": "3", + "Author": "Li Shandross [aut, cre] (), Evan Ray [aut]", + "Maintainer": "Li Shandross ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "reichlab", + "RemoteRepo": "idforecastutils", + "RemoteRef": "main", + "RemoteSha": "0caa1626d98276aaf148641b12394ba6f6b5fa27", + "Remotes": "Infectious-Disease-Modeling-Hubs/hubEnsembles, Infectious-Disease-Modeling-Hubs/hubExamples, Infectious-Disease-Modeling-Hubs/hubUtils, Infectious-Disease-Modeling-Hubs/hubVis, reichlab/distfromq, reichlab/covidData" }, "ini": { "Package": "ini", "Version": "0.3.1", "Source": "Repository", + "Type": "Package", + "Title": "Read and Write '.ini' Files", + "Date": "2018-05-19", + "Author": "David Valentim Dias", + "Maintainer": "David Valentim Dias ", + "Description": "Parse simple '.ini' configuration files to an structured list. 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Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized. 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It also includes tools for working with missing values (both implicit and explicit).", + "License": "MIT + file LICENSE", + "URL": "https://tidyr.tidyverse.org, https://github.com/tidyverse/tidyr", + "BugReports": "https://github.com/tidyverse/tidyr/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ + "cli (>= 3.4.1)", + "dplyr (>= 1.0.10)", "glue", - "lifecycle", + "lifecycle (>= 1.0.3)", "magrittr", - "purrr", - "rlang", - "stringr", - "tibble", - "tidyselect", + "purrr (>= 1.0.1)", + "rlang (>= 1.1.1)", + "stringr (>= 1.5.0)", + "tibble (>= 2.1.1)", + "tidyselect (>= 1.2.0)", "utils", - "vctrs" + "vctrs (>= 0.5.2)" + ], + "Suggests": [ + "covr", + "data.table", + "knitr", + "readr", + "repurrrsive (>= 1.1.0)", + "rmarkdown", + "testthat (>= 3.0.0)" ], - "Hash": "915fb7ce036c22a6a33b5a8adb712eb1" + "LinkingTo": [ + "cpp11 (>= 0.4.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "RoxygenNote": "7.3.0", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Davis Vaughan [aut], Maximilian Girlich [aut], Kevin Ushey [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "tidyselect": { "Package": "tidyselect", - "Version": "1.2.0", + "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", - "glue", - "lifecycle", - "rlang", - "vctrs", + "Title": "Select from a Set of Strings", + "Authors@R": "c( person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.", + "License": "MIT + file LICENSE", + "URL": "https://tidyselect.r-lib.org, https://github.com/r-lib/tidyselect", + "BugReports": "https://github.com/r-lib/tidyselect/issues", + "Depends": [ + "R (>= 3.4)" + ], + "Imports": [ + "cli (>= 3.3.0)", + "glue (>= 1.3.0)", + "lifecycle (>= 1.0.3)", + "rlang (>= 1.0.4)", + "vctrs (>= 0.5.2)", "withr" ], - "Hash": "79540e5fcd9e0435af547d885f184fd5" + "Suggests": [ + "covr", + "crayon", + "dplyr", + "knitr", + "magrittr", + "rmarkdown", + "stringr", + "testthat (>= 3.1.1)", + "tibble (>= 2.1.3)" + ], + "VignetteBuilder": "knitr", + "ByteCompile": "true", + "Config/testthat/edition": "3", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.0.9000", + "NeedsCompilation": "yes", + "Author": "Lionel Henry [aut, cre], Hadley Wickham [aut], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" }, "timechange": { "Package": "timechange", "Version": "0.3.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" + "Title": "Efficient Manipulation of Date-Times", + "Authors@R": "c(person(\"Vitalie\", \"Spinu\", email = \"spinuvit@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Google Inc.\", role = c(\"ctb\", \"cph\")))", + "Description": "Efficient routines for manipulation of date-time objects while accounting for time-zones and daylight saving times. The package includes utilities for updating of date-time components (year, month, day etc.), modification of time-zones, rounding of date-times, period addition and subtraction etc. Parts of the 'CCTZ' source code, released under the Apache 2.0 License, are included in this package. See for more details.", + "Depends": [ + "R (>= 3.3)" ], - "Hash": "c5f3c201b931cd6474d17d8700ccb1c8" + "License": "GPL (>= 3)", + "Encoding": "UTF-8", + "LinkingTo": [ + "cpp11 (>= 0.2.7)" + ], + "Suggests": [ + "testthat (>= 0.7.1.99)", + "knitr" + ], + "SystemRequirements": "A system with zoneinfo data (e.g. /usr/share/zoneinfo) as well as a recent-enough C++11 compiler (such as g++-4.8 or later). On Windows the zoneinfo included with R is used.", + "BugReports": "https://github.com/vspinu/timechange/issues", + "URL": "https://github.com/vspinu/timechange/", + "RoxygenNote": "7.2.1", + "NeedsCompilation": "yes", + "Author": "Vitalie Spinu [aut, cre], Google Inc. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" ], - "Hash": "5ac22900ae0f386e54f1c307eca7d843" + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "tzdb": { "Package": "tzdb", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" ], - "Hash": "f561504ec2897f4d46f0c7657e488ae1" + "LinkingTo": [ + "cpp11 (>= 0.4.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "utf8": { "Package": "utf8", "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8", + "BugReports": "https://github.com/patperry/r-utf8/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" ], - "Hash": "62b65c52671e6665f803ff02954446e9" + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. [cph, dtc] (Unicode Character Database)", + "Maintainer": "Kirill Müller ", + "Repository": "CRAN" }, "vctrs": { "Package": "vctrs", "Version": "0.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cli", + "Title": "Vector Helpers", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = \"aut\"), person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"data.table team\", role = \"cph\", comment = \"Radix sort based on data.table's forder() and their contribution to R's order()\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Defines new notions of prototype and size that are used to provide tools for consistent and well-founded type-coercion and size-recycling, and are in turn connected to ideas of type- and size-stability useful for analysing function interfaces.", + "License": "MIT + file LICENSE", + "URL": "https://vctrs.r-lib.org/, https://github.com/r-lib/vctrs", + "BugReports": "https://github.com/r-lib/vctrs/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Imports": [ + "cli (>= 3.4.0)", "glue", - "lifecycle", - "rlang" + "lifecycle (>= 1.0.3)", + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "bit64", + "covr", + "crayon", + "dplyr (>= 0.8.5)", + "generics", + "knitr", + "pillar (>= 1.4.4)", + "pkgdown (>= 2.0.1)", + "rmarkdown", + "testthat (>= 3.0.0)", + "tibble (>= 3.1.3)", + "waldo (>= 0.2.0)", + "withr", + "xml2", + "zeallot" ], - "Hash": "c03fa420630029418f7e6da3667aac4a" + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "Language": "en-GB", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut], Lionel Henry [aut], Davis Vaughan [aut, cre], data.table team [cph] (Radix sort based on data.table's forder() and their contribution to R's order()), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "viridisLite": { "Package": "viridisLite", "Version": "0.4.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Type": "Package", + "Title": "Colorblind-Friendly Color Maps (Lite Version)", + "Date": "2023-05-02", + "Authors@R": "c( person(\"Simon\", \"Garnier\", email = \"garnier@njit.edu\", role = c(\"aut\", \"cre\")), person(\"Noam\", \"Ross\", email = \"noam.ross@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Bob\", \"Rudis\", email = \"bob@rud.is\", role = c(\"ctb\", \"cph\")), person(\"Marco\", \"Sciaini\", email = \"sciaini.marco@gmail.com\", role = c(\"ctb\", \"cph\")), person(\"Antônio Pedro\", \"Camargo\", role = c(\"ctb\", \"cph\")), person(\"Cédric\", \"Scherer\", email = \"scherer@izw-berlin.de\", role = c(\"ctb\", \"cph\")) )", + "Maintainer": "Simon Garnier ", + "Description": "Color maps designed to improve graph readability for readers with common forms of color blindness and/or color vision deficiency. The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" ], - "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" }, "vroom": { "Package": "vroom", "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.", + "License": "MIT + file LICENSE", + "URL": "https://vroom.r-lib.org, https://github.com/tidyverse/vroom", + "BugReports": "https://github.com/tidyverse/vroom/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ "bit64", - "cli", - "cpp11", + "cli (>= 3.2.0)", "crayon", "glue", "hms", - "lifecycle", + "lifecycle (>= 1.0.3)", "methods", - "progress", - "rlang", + "rlang (>= 0.4.2)", "stats", - "tibble", + "tibble (>= 2.0.0)", "tidyselect", - "tzdb", - "vctrs", + "tzdb (>= 0.1.1)", + "vctrs (>= 0.2.0)", "withr" ], - "Hash": "390f9315bc0025be03012054103d227c" + "Suggests": [ + "archive", + "bench (>= 1.1.0)", + "covr", + "curl", + "dplyr", + "forcats", + "fs", + "ggplot2", + "knitr", + "patchwork", + "prettyunits", + "purrr", + "rmarkdown", + "rstudioapi", + "scales", + "spelling", + "testthat (>= 2.1.0)", + "tidyr", + "utils", + "waldo", + "xml2" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.0)", + "progress (>= 1.2.1)", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "nycflights13, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Copyright": "file COPYRIGHTS", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3.9000", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" }, "withr": { "Package": "withr", - "Version": "3.0.0", + "Version": "3.0.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics" + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" + ], + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" ], - "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" }, "xfun": { "Package": "xfun", - "Version": "0.42", + "Version": "0.50", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ "grDevices", "stats", "tools" ], - "Hash": "fd1349170df31f7a10bd98b0189e85af" + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown (>= 0.4)", + "commonmark", + "knitr (>= 1.47)", + "remotes", + "pak", + "rhub", + "renv", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs", + "rmarkdown" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "xml2": { "Package": "xml2", "Version": "1.3.6", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Parse XML", + "Authors@R": "c( person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = c(\"aut\", \"cre\")), person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Jeroen\", \"Ooms\", role = \"aut\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(\"R Foundation\", role = \"ctb\", comment = \"Copy of R-project homepage cached as example\") )", + "Description": "Work with XML files using a simple, consistent interface. Built on top of the 'libxml2' C library.", + "License": "MIT + file LICENSE", + "URL": "https://xml2.r-lib.org/, https://github.com/r-lib/xml2", + "BugReports": "https://github.com/r-lib/xml2/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ "cli", "methods", - "rlang" + "rlang (>= 1.1.0)" + ], + "Suggests": [ + "covr", + "curl", + "httr", + "knitr", + "magrittr", + "mockery", + "rmarkdown", + "testthat (>= 3.0.0)" ], - "Hash": "1d0336142f4cd25d8d23cd3ba7a8fb61" + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "SystemRequirements": "libxml2: libxml2-dev (deb), libxml2-devel (rpm)", + "Collate": "'S4.R' 'as_list.R' 'xml_parse.R' 'as_xml_document.R' 'classes.R' 'format.R' 'import-standalone-obj-type.R' 'import-standalone-purrr.R' 'import-standalone-types-check.R' 'init.R' 'nodeset_apply.R' 'paths.R' 'utils.R' 'xml2-package.R' 'xml_attr.R' 'xml_children.R' 'xml_document.R' 'xml_find.R' 'xml_missing.R' 'xml_modify.R' 'xml_name.R' 'xml_namespaces.R' 'xml_node.R' 'xml_nodeset.R' 'xml_path.R' 'xml_schema.R' 'xml_serialize.R' 'xml_structure.R' 'xml_text.R' 'xml_type.R' 'xml_url.R' 'xml_write.R' 'zzz.R'", + "Config/testthat/edition": "3", + "NeedsCompilation": "yes", + "Author": "Hadley Wickham [aut, cre], Jim Hester [aut], Jeroen Ooms [aut], Posit Software, PBC [cph, fnd], R Foundation [ctb] (Copy of R-project homepage cached as example)", + "Maintainer": "Hadley Wickham ", + "Repository": "CRAN" }, "yaml": { "Package": "yaml", - "Version": "2.3.8", + "Version": "2.3.10", "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" + "Encoding": "UTF-8" }, "zeallot": { "Package": "zeallot", "Version": "0.1.0", "Source": "Repository", - "Repository": "CRAN", - "Hash": "ee9b643aa8331c45d8d82eb3a137c9bc" + "Type": "Package", + "Title": "Multiple, Unpacking, and Destructuring Assignment", + "Authors@R": "c( person(given = \"Nathan\", family = \"Teetor\", email = \"nathanteetor@gmail.com\", role = c(\"aut\", \"cre\")), person(given = \"Paul\", family = \"Teetor\", role = \"ctb\"))", + "Description": "Provides a %<-% operator to perform multiple, unpacking, and destructuring assignment in R. The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.", + "URL": "https://github.com/nteetor/zeallot", + "BugReports": "https://github.com/nteetor/zeallot/issues", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "6.0.1", + "VignetteBuilder": "knitr", + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "purrr", + "magrittr" + ], + "NeedsCompilation": "no", + "Author": "Nathan Teetor [aut, cre], Paul Teetor [ctb]", + "Maintainer": "Nathan Teetor ", + "Repository": "CRAN" }, "zoltr": { "Package": "zoltr", "Version": "1.0.1", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "reichlab", - "RemoteRepo": "zoltr", - "RemoteRef": "master", - "RemoteSha": "3344e2a95969042977ae2f89fef672244348569f", - "Requirements": [ - "MMWRweek", - "base64url", + "Title": "Interface to the 'Zoltar' Forecast Repository API", + "Authors@R": "c( person(\"Matthew\", \"Cornell\", role = c(\"aut\", \"cre\"), email = \"cornell@umass.edu\"), person(\"Nicholas\", \"Reich\", role = c(\"aut\", \"cph\"), email = \"nick@schoolph.umass.edu\"))", + "Description": "'Zoltar' is a website that provides a repository of model forecast results in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time series forecasts for prediction challenges of interest to the modeling community. This package provides functions for working with the 'Zoltar' API, including connecting and authenticating, getting meta information (projects, models, and forecasts, and truth), and uploading, downloading, and deleting forecast and truth data.", + "URL": "https://github.com/reichlab/zoltr , http://reichlab.io/zoltr/", + "BugReports": "https://github.com/reichlab/zoltr/issues", + "License": "GPL-3", + "Encoding": "UTF-8", + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "webmockr", + "mockery" + ], + "Imports": [ "data.table", - "dplyr", "httr", "jsonlite", - "lubridate", - "magrittr", "readr", + "base64url", + "dplyr", + "MMWRweek", + "utils", "rlang", - "utils" + "magrittr", + "lubridate" ], - "Hash": "aa318d451907140ef0883d51435b87c5" + "RoxygenNote": "7.3.1", + "VignetteBuilder": "knitr", + "Roxygen": "list(markdown = TRUE)", + "Author": "Matthew Cornell [aut, cre], Nicholas Reich [aut, cph]", + "Maintainer": "Matthew Cornell ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "reichlab", + "RemoteRepo": "zoltr", + "RemoteRef": "master", + "RemoteSha": "3344e2a95969042977ae2f89fef672244348569f" } } } diff --git a/flu_ar2/README.md b/flu_ar2/README.md index 97cd286..a062706 100644 --- a/flu_ar2/README.md +++ b/flu_ar2/README.md @@ -16,12 +16,12 @@ This should result in a model output file and a pdf with a plot under `flu_ar2/o # requirements.txt renv and details -`requirements.txt` and `renv.lock` were generated according to [README.md](..%2FREADME.md). For `renv.lock`, we installed these specific libraries: +`requirements.txt` and `renv.lock` were generated according to [README.md](../README.md). For `renv.lock`, we installed these specific libraries: ```bash Rscript -e "renv::install(c('lubridate', 'readr', 'remotes'))" -Rscript -e "renv::install('arrow', repos = c('https://apache.r-universe.dev', 'https://cran.r-project.org'))" +Rscript -e "renv::install('arrow')" Rscript -e "renv::install('reichlab/zoltr')" -Rscript -e "renv::install('hubverse-org/hubData')" -Rscript -e "renv::install('hubverse-org/hubVis')" +Rscript -e "renv::install('hubverse-org/hubData@*release')" +Rscript -e "renv::install('hubverse-org/hubVis@*release')" ``` diff --git a/flu_ar2/renv.lock b/flu_ar2/renv.lock index 840ce95..2117203 100644 --- a/flu_ar2/renv.lock +++ b/flu_ar2/renv.lock @@ -1,695 +1,1842 @@ { "R": { - "Version": "4.3.2", + "Version": "4.4.1", "Repositories": [ { "Name": "CRAN", - "URL": "https://p3m.dev/cran/2024-02-28" + "URL": "https://p3m.dev/cran/2025-02-05" } ] }, "Packages": { "KernSmooth": { "Package": "KernSmooth", - "Version": "2.23-22", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Version": "2.23-24", + "Source": "Repository", + "Priority": "recommended", + "Date": "2024-05-16", + "Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)", + "Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"Matt.Wand@uts.edu.au\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"ripley@stats.ox.ac.uk\", comment = \"R port and updates\"))", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Depends": [ + "R (>= 2.5.0)", "stats" ], - "Hash": "2fecebc3047322fa5930f74fae5de70f" + "Suggests": [ + "MASS", + "carData" + ], + "Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".", + "License": "Unlimited", + "ByteCompile": "yes", + "NeedsCompilation": "yes", + "Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MASS": { "Package": "MASS", - "Version": "7.3-60", + "Version": "7.3-60.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-01-12", + "Revision": "$Rev: 3641 $", + "Depends": [ + "R (>= 4.4.0)", "grDevices", "graphics", - "methods", "stats", "utils" ], - "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"ripley@stats.ox.ac.uk\"), person(\"Bill\", \"Venables\", role = \"ctb\"), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MMWRweek": { "Package": "MMWRweek", "Version": "0.1.3", "Source": "Repository", + "Type": "Package", + "Title": "Convert Dates to MMWR Day, Week, and Year", + "Date": "2020-04-22", + "Author": "Jarad Niemi ", + "Maintainer": "Jarad Niemi ", + "Suggests": [ + "testthat" + ], + "Description": "The first day of any MMWR week is Sunday. MMWR week numbering is sequential beginning with 1 and incrementing with each week to a maximum of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at least four days in the calendar year. This package provides functionality to convert Dates to MMWR day, week, and year and the reverse.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "URL": "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf", + "RoxygenNote": "7.0.1", + "NeedsCompilation": "no", "Repository": "CRAN", - "Hash": "4329e57e2536e12afe479e8571416dbc" + "Encoding": "UTF-8" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-1.1", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Version": "1.7-0", + "Source": "Repository", + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2024-03-16", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", + "License": "GPL (>= 2) | file LICENCE", + "URL": "https://Matrix.R-forge.R-project.org", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's matrix implementation\"))", + "Depends": [ + "R (>= 4.4.0)", + "methods" + ], + "Imports": [ "grDevices", "graphics", "grid", "lattice", - "methods", "stats", "utils" ], - "Hash": "1a00d4828f33a9d690806e98bd17150c" + "Suggests": [ + "MASS", + "datasets", + "sfsmisc", + "tools" + ], + "Enhances": [ + "SparseM", + "graph" + ], + "LazyData": "no", + "LazyDataNote": "not possible, since we use data/*.R and our S4 classes", + "BuildResaveData": "no", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] (), Mikael Jagan [aut] (), Timothy A. Davis [ctb] (, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (base R's matrix implementation)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" }, "R6": { "Package": "R6", "Version": "2.5.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Encapsulated Classes with Reference Semantics", + "Authors@R": "person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@stdout.org\")", + "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. 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(2020, Journal of Statistical Software, ).", + "Depends": [ + "R (>= 3.0.0)", + "methods" + ], + "Imports": [ "graphics", - "methods", + "grDevices", "stats" ], - "Hash": "f20c47fd52fae58b4e377c37bb8c335b" + "Suggests": [ + "datasets", + "utils", + "KernSmooth", + "MASS", + "kernlab", + "mvtnorm", + "vcd", + "tcltk", + "shiny", + "shinyjs", + "ggplot2", + "dplyr", + "scales", + "grid", + "png", + "jpeg", + "knitr", + "rmarkdown", + "RColorBrewer", + "rcartocolor", + "scico", + "viridis", + "wesanderson" + ], + "VignetteBuilder": "knitr", + "License": "BSD_3_clause + file LICENSE", + "URL": "https://colorspace.R-Forge.R-project.org/, https://hclwizard.org/", + "BugReports": "https://colorspace.R-Forge.R-project.org/contact.html", + "LazyData": "yes", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "NeedsCompilation": "yes", + "Author": "Ross Ihaka [aut], Paul Murrell [aut] (), Kurt Hornik [aut] (), Jason C. Fisher [aut] (), Reto Stauffer [aut] (), Claus O. Wilke [aut] (), Claire D. 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Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.", + "License": "MIT + file LICENSE", + "URL": "https://cpp11.r-lib.org, https://github.com/r-lib/cpp11", + "BugReports": "https://github.com/r-lib/cpp11/issues", + "Depends": [ + "R (>= 4.0.0)" + ], + "Suggests": [ + "bench", + "brio", + "callr", + "cli", + "covr", + "decor", + "desc", + "ggplot2", + "glue", + "knitr", + "lobstr", + "mockery", + "progress", + "rmarkdown", + "scales", + "Rcpp", + "testthat (>= 3.2.0)", + "tibble", + "utils", + "vctrs", + "withr" ], - "Hash": "5a295d7d963cc5035284dcdbaf334f4e" + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/Needs/cpp11/cpp_register": "brio, cli, decor, desc, glue, tibble, vctrs", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Davis Vaughan [aut, cre] (), Jim Hester [aut] (), Romain François [aut] (), Benjamin Kietzman [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "crayon": { "Package": "crayon", - "Version": "1.5.2", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Version": "1.5.3", + "Source": "Repository", + "Title": "Colored Terminal Output", + "Authors@R": "c( person(\"Gábor\", \"Csárdi\", , \"csardi.gabor@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Brodie\", \"Gaslam\", , \"brodie.gaslam@yahoo.com\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ "grDevices", "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "crosstalk": { "Package": "crosstalk", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "htmltools", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" + ], + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" ], - "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "data.table": { "Package": "data.table", - "Version": "1.15.0", + "Version": "1.16.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "methods" ], - "Hash": "cfbbb4aed6e78cd45f17123a9ec9981a" + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), 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Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Ivan Krylov [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "CRAN" }, "digest": { "Package": "digest", - "Version": "0.6.34", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Version": "0.6.37", + "Source": "Repository", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", 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\"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", + "Date": "2024-08-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "utils" ], - "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a" + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" }, "dplyr": { "Package": "dplyr", "Version": "1.1.4", "Source": "Repository", - 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This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. 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It is updated periodically to reflect changes made by political bodies to time zone boundaries, UTC offsets, and daylight saving time rules. Additionally, this package provides a C++ interface for working with the 'date' library. 'date' provides comprehensive support for working with dates and date-times, which this package exposes to make it easier for other R packages to utilize. Headers are provided for calendar specific calculations, along with a limited interface for time zone manipulations.", + "License": "MIT + file LICENSE", + "URL": "https://tzdb.r-lib.org, https://github.com/r-lib/tzdb", + "BugReports": "https://github.com/r-lib/tzdb/issues", + "Depends": [ + "R (>= 3.5.0)" + ], + "Suggests": [ + "covr", + "testthat (>= 3.0.0)" + ], + "LinkingTo": [ + "cpp11 (>= 0.4.2)" + ], + "Biarch": "yes", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Davis Vaughan [aut, cre], Howard Hinnant [cph] (Author of the included date library), Posit Software, PBC [cph, fnd]", + "Maintainer": "Davis Vaughan ", + "Repository": "CRAN" }, "utf8": { "Package": "utf8", "Version": "1.2.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Unicode Text Processing", + "Authors@R": "c(person(given = c(\"Patrick\", \"O.\"), family = \"Perry\", role = c(\"aut\", \"cph\")), person(given = \"Kirill\", family = \"M\\u00fcller\", role = \"cre\", email = \"kirill@cynkra.com\"), person(given = \"Unicode, Inc.\", role = c(\"cph\", \"dtc\"), comment = \"Unicode Character Database\"))", + "Description": "Process and print 'UTF-8' encoded international text (Unicode). Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8", + "BugReports": "https://github.com/patperry/r-utf8/issues", + "Depends": [ + "R (>= 2.10)" ], - "Hash": "62b65c52671e6665f803ff02954446e9" + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. 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The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" + ], + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" }, "vroom": { "Package": "vroom", "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. The writer formats the data in parallel and writes to disk asynchronously from formatting.", + "License": "MIT + file LICENSE", + "URL": "https://vroom.r-lib.org, https://github.com/tidyverse/vroom", + "BugReports": "https://github.com/tidyverse/vroom/issues", + "Depends": [ + "R (>= 3.6)" + ], + "Imports": [ "bit64", - "cli", - "cpp11", + "cli (>= 3.2.0)", "crayon", "glue", "hms", - "lifecycle", + "lifecycle (>= 1.0.3)", "methods", - "progress", - "rlang", + "rlang (>= 0.4.2)", "stats", - "tibble", + "tibble (>= 2.0.0)", "tidyselect", - "tzdb", - "vctrs", + "tzdb (>= 0.1.1)", + "vctrs (>= 0.2.0)", "withr" ], - "Hash": "390f9315bc0025be03012054103d227c" + "Suggests": [ + "archive", + "bench (>= 1.1.0)", + "covr", + "curl", + "dplyr", + "forcats", + "fs", + "ggplot2", + "knitr", + "patchwork", + "prettyunits", + "purrr", + "rmarkdown", + "rstudioapi", + "scales", + "spelling", + "testthat (>= 2.1.0)", + "tidyr", + "utils", + "waldo", + "xml2" + ], + "LinkingTo": [ + "cpp11 (>= 0.2.0)", + "progress (>= 1.2.1)", + "tzdb (>= 0.1.1)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "nycflights13, tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Config/testthat/parallel": "false", + "Copyright": "file COPYRIGHTS", + "Encoding": "UTF-8", + "Language": "en-US", + "RoxygenNote": "7.2.3.9000", + "NeedsCompilation": "yes", + "Author": "Jim Hester [aut] (), Hadley Wickham [aut] (), Jennifer Bryan [aut, cre] (), Shelby Bearrows [ctb], https://github.com/mandreyel/ [cph] (mio library), Jukka Jylänki [cph] (grisu3 implementation), Mikkel Jørgensen [cph] (grisu3 implementation), Posit Software, PBC [cph, fnd]", + "Maintainer": "Jennifer Bryan ", + "Repository": "CRAN" }, "withr": { "Package": "withr", - "Version": "3.0.0", - "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "grDevices", - "graphics" + "Version": "3.0.2", + "Source": "Repository", + "Title": "Run Code 'With' Temporarily Modified Global State", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\"), person(\"Lionel\", \"Henry\", , \"lionel@posit.co\", role = c(\"aut\", \"cre\")), person(\"Kirill\", \"Müller\", , \"krlmlr+r@mailbox.org\", role = \"aut\"), person(\"Kevin\", \"Ushey\", , \"kevinushey@gmail.com\", role = \"aut\"), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\"), person(\"Winston\", \"Chang\", role = \"aut\"), person(\"Jennifer\", \"Bryan\", role = \"ctb\"), person(\"Richard\", \"Cotton\", role = \"ctb\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.", + "License": "MIT + file LICENSE", + "URL": "https://withr.r-lib.org, https://github.com/r-lib/withr#readme", + "BugReports": "https://github.com/r-lib/withr/issues", + "Depends": [ + "R (>= 3.6.0)" + ], + "Imports": [ + "graphics", + "grDevices" ], - "Hash": "d31b6c62c10dcf11ec530ca6b0dd5d35" + "Suggests": [ + "callr", + "DBI", + "knitr", + "methods", + "rlang", + "rmarkdown (>= 2.12)", + "RSQLite", + "testthat (>= 3.0.0)" + ], + "VignetteBuilder": "knitr", + "Config/Needs/website": "tidyverse/tidytemplate", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "Collate": "'aaa.R' 'collate.R' 'connection.R' 'db.R' 'defer-exit.R' 'standalone-defer.R' 'defer.R' 'devices.R' 'local_.R' 'with_.R' 'dir.R' 'env.R' 'file.R' 'language.R' 'libpaths.R' 'locale.R' 'makevars.R' 'namespace.R' 'options.R' 'par.R' 'path.R' 'rng.R' 'seed.R' 'wrap.R' 'sink.R' 'tempfile.R' 'timezone.R' 'torture.R' 'utils.R' 'with.R'", + "NeedsCompilation": "no", + "Author": "Jim Hester [aut], Lionel Henry [aut, cre], Kirill Müller [aut], Kevin Ushey [aut], Hadley Wickham [aut], Winston Chang [aut], Jennifer Bryan [ctb], Richard Cotton [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Lionel Henry ", + "Repository": "CRAN" }, "xfun": { "Package": "xfun", - "Version": "0.42", + "Version": "0.50", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Type": "Package", + "Title": "Supporting Functions for Packages Maintained by 'Yihui Xie'", + "Authors@R": "c( person(\"Yihui\", \"Xie\", role = c(\"aut\", \"cre\", \"cph\"), email = \"xie@yihui.name\", comment = c(ORCID = \"0000-0003-0645-5666\")), person(\"Wush\", \"Wu\", role = \"ctb\"), person(\"Daijiang\", \"Li\", role = \"ctb\"), person(\"Xianying\", \"Tan\", role = \"ctb\"), person(\"Salim\", \"Brüggemann\", role = \"ctb\", email = \"salim-b@pm.me\", comment = c(ORCID = \"0000-0002-5329-5987\")), person(\"Christophe\", \"Dervieux\", role = \"ctb\"), person() )", + "Description": "Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.", + "Depends": [ + "R (>= 3.2.0)" + ], + "Imports": [ "grDevices", "stats", "tools" ], - "Hash": "fd1349170df31f7a10bd98b0189e85af" + "Suggests": [ + "testit", + "parallel", + "codetools", + "methods", + "rstudioapi", + "tinytex (>= 0.30)", + "mime", + "litedown (>= 0.4)", + "commonmark", + "knitr (>= 1.47)", + "remotes", + "pak", + "rhub", + "renv", + "curl", + "xml2", + "jsonlite", + "magick", + "yaml", + "qs", + "rmarkdown" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/yihui/xfun", + "BugReports": "https://github.com/yihui/xfun/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "VignetteBuilder": "litedown", + "NeedsCompilation": "yes", + "Author": "Yihui Xie [aut, cre, cph] (), Wush Wu [ctb], Daijiang Li [ctb], Xianying Tan [ctb], Salim Brüggemann [ctb] (), Christophe Dervieux [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "yaml": { "Package": "yaml", - "Version": "2.3.8", + "Version": "2.3.10", "Source": "Repository", + "Type": "Package", + "Title": "Methods to Convert R Data to YAML and Back", + "Date": "2024-07-22", + "Suggests": [ + "RUnit" + ], + "Author": "Shawn P Garbett [aut], Jeremy Stephens [aut, cre], Kirill Simonov [aut], Yihui Xie [ctb], Zhuoer Dong [ctb], Hadley Wickham [ctb], Jeffrey Horner [ctb], reikoch [ctb], Will Beasley [ctb], Brendan O'Connor [ctb], Gregory R. Warnes [ctb], Michael Quinn [ctb], Zhian N. Kamvar [ctb], Charlie Gao [ctb]", + "Maintainer": "Shawn Garbett ", + "License": "BSD_3_clause + file LICENSE", + "Description": "Implements the 'libyaml' 'YAML' 1.1 parser and emitter () for R.", + "URL": "https://github.com/vubiostat/r-yaml/", + "BugReports": "https://github.com/vubiostat/r-yaml/issues", + "NeedsCompilation": "yes", "Repository": "CRAN", - "Hash": "29240487a071f535f5e5d5a323b7afbd" + "Encoding": "UTF-8" }, "zoltr": { "Package": "zoltr", "Version": "1.0.1", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "reichlab", - "RemoteRepo": "zoltr", - "RemoteRef": "master", - "RemoteSha": "3344e2a95969042977ae2f89fef672244348569f", - "Requirements": [ - "MMWRweek", - "base64url", + "Title": "Interface to the 'Zoltar' Forecast Repository API", + "Authors@R": "c( person(\"Matthew\", \"Cornell\", role = c(\"aut\", \"cre\"), email = \"cornell@umass.edu\"), person(\"Nicholas\", \"Reich\", role = c(\"aut\", \"cph\"), email = \"nick@schoolph.umass.edu\"))", + "Description": "'Zoltar' is a website that provides a repository of model forecast results in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time series forecasts for prediction challenges of interest to the modeling community. This package provides functions for working with the 'Zoltar' API, including connecting and authenticating, getting meta information (projects, models, and forecasts, and truth), and uploading, downloading, and deleting forecast and truth data.", + "URL": "https://github.com/reichlab/zoltr , http://reichlab.io/zoltr/", + "BugReports": "https://github.com/reichlab/zoltr/issues", + "License": "GPL-3", + "Encoding": "UTF-8", + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "webmockr", + "mockery" + ], + "Imports": [ "data.table", - "dplyr", "httr", "jsonlite", - "lubridate", - "magrittr", "readr", + "base64url", + "dplyr", + "MMWRweek", + "utils", "rlang", - "utils" + "magrittr", + "lubridate" ], - "Hash": "aa318d451907140ef0883d51435b87c5" + "RoxygenNote": "7.3.1", + "VignetteBuilder": "knitr", + "Roxygen": "list(markdown = TRUE)", + "Author": "Matthew Cornell [aut, cre], Nicholas Reich [aut, cph]", + "Maintainer": "Matthew Cornell ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "reichlab", + "RemoteRepo": "zoltr", + "RemoteRef": "master", + "RemoteSha": "3344e2a95969042977ae2f89fef672244348569f" } } } diff --git a/flu_flusion/README.md b/flu_flusion/README.md index baf3fae..a62eeb6 100644 --- a/flu_flusion/README.md +++ b/flu_flusion/README.md @@ -16,15 +16,15 @@ This should result in a model output file and a pdf with a plot under `flu_flusi # requirements.txt renv and details -`requirements.txt` and `renv.lock` were generated according to [README.md](..%2FREADME.md). For `renv.lock`, we installed these specific libraries: +`requirements.txt` and `renv.lock` were generated according to [README.md](../README.md). For `renv.lock`, we installed these specific libraries: ```bash Rscript -e "renv::install(c('dplyr'))" -Rscript -e "renv::install('arrow', repos = c('https://apache.r-universe.dev', 'https://cran.r-project.org'))" +Rscript -e "renv::install('arrow')" Rscript -e "renv::install('reichlab/zoltr')" -Rscript -e "renv::install('hubverse-org/hubData')" -Rscript -e "renv::install('hubverse-org/hubVis')" -Rscript -e "renv::install('hubverse-org/hubEnsembles')" +Rscript -e "renv::install('hubverse-org/hubData@*release')" +Rscript -e "renv::install('hubverse-org/hubVis@*release')" +Rscript -e "renv::install('hubverse-org/hubEnsembles@*release')" Rscript -e "renv::install('reichlab/covidData')" Rscript -e "renv::install('reichlab/idforecastutils')" ``` diff --git a/flu_flusion/renv.lock b/flu_flusion/renv.lock index f20cc2c..b076966 100644 --- a/flu_flusion/renv.lock +++ b/flu_flusion/renv.lock @@ -1,450 +1,1130 @@ { "R": { - "Version": "4.3.2", + "Version": "4.4.1", "Repositories": [ { - "Name": "CRAN - p3m.dev", - "URL": "https://p3m.dev/cran/2024-02-28" - }, - { - "Name": "CRAN - r-project.org", - "URL": "https://cloud.r-project.org" + "Name": "CRAN", + "URL": "https://p3m.dev/cran/2025-02-05" } ] }, "Packages": { "KernSmooth": { "Package": "KernSmooth", - "Version": "2.23-22", + "Version": "2.23-24", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-05-16", + "Title": "Functions for Kernel Smoothing Supporting Wand & Jones (1995)", + "Authors@R": "c(person(\"Matt\", \"Wand\", role = \"aut\", email = \"Matt.Wand@uts.edu.au\"), person(\"Cleve\", \"Moler\", role = \"ctb\", comment = \"LINPACK routines in src/d*\"), person(\"Brian\", \"Ripley\", role = c(\"trl\", \"cre\", \"ctb\"), email = \"ripley@stats.ox.ac.uk\", comment = \"R port and updates\"))", + "Note": "Maintainers are not available to give advice on using a package they did not author.", + "Depends": [ + "R (>= 2.5.0)", "stats" ], - "Hash": "2fecebc3047322fa5930f74fae5de70f" + "Suggests": [ + "MASS", + "carData" + ], + "Description": "Functions for kernel smoothing (and density estimation) corresponding to the book: Wand, M.P. and Jones, M.C. (1995) \"Kernel Smoothing\".", + "License": "Unlimited", + "ByteCompile": "yes", + "NeedsCompilation": "yes", + "Author": "Matt Wand [aut], Cleve Moler [ctb] (LINPACK routines in src/d*), Brian Ripley [trl, cre, ctb] (R port and updates)", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MASS": { "Package": "MASS", - "Version": "7.3-60", + "Version": "7.3-60.2", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Priority": "recommended", + "Date": "2024-01-12", + "Revision": "$Rev: 3641 $", + "Depends": [ + "R (>= 4.4.0)", "grDevices", "graphics", - "methods", "stats", "utils" ], - "Hash": "a56a6365b3fa73293ea8d084be0d9bb0" + "Imports": [ + "methods" + ], + "Suggests": [ + "lattice", + "nlme", + "nnet", + "survival" + ], + "Authors@R": "c(person(\"Brian\", \"Ripley\", role = c(\"aut\", \"cre\", \"cph\"), email = \"ripley@stats.ox.ac.uk\"), person(\"Bill\", \"Venables\", role = \"ctb\"), person(c(\"Douglas\", \"M.\"), \"Bates\", role = \"ctb\"), person(\"Kurt\", \"Hornik\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"Albrecht\", \"Gebhardt\", role = \"trl\", comment = \"partial port ca 1998\"), person(\"David\", \"Firth\", role = \"ctb\"))", + "Description": "Functions and datasets to support Venables and Ripley, \"Modern Applied Statistics with S\" (4th edition, 2002).", + "Title": "Support Functions and Datasets for Venables and Ripley's MASS", + "LazyData": "yes", + "ByteCompile": "yes", + "License": "GPL-2 | GPL-3", + "URL": "http://www.stats.ox.ac.uk/pub/MASS4/", + "Contact": "", + "NeedsCompilation": "yes", + "Author": "Brian Ripley [aut, cre, cph], Bill Venables [ctb], Douglas M. Bates [ctb], Kurt Hornik [trl] (partial port ca 1998), Albrecht Gebhardt [trl] (partial port ca 1998), David Firth [ctb]", + "Maintainer": "Brian Ripley ", + "Repository": "CRAN" }, "MMWRweek": { "Package": "MMWRweek", "Version": "0.1.3", "Source": "Repository", + "Type": "Package", + "Title": "Convert Dates to MMWR Day, Week, and Year", + "Date": "2020-04-22", + "Author": "Jarad Niemi ", + "Maintainer": "Jarad Niemi ", + "Suggests": [ + "testthat" + ], + "Description": "The first day of any MMWR week is Sunday. MMWR week numbering is sequential beginning with 1 and incrementing with each week to a maximum of 52 or 53. MMWR week #1 of an MMWR year is the first week of the year that has at least four days in the calendar year. This package provides functionality to convert Dates to MMWR day, week, and year and the reverse.", + "License": "GPL (>= 2) | file LICENSE", + "LazyLoad": "yes", + "URL": "http://wwwn.cdc.gov/nndss/document/MMWR_Week_overview.pdf", + "RoxygenNote": "7.0.1", + "NeedsCompilation": "no", "Repository": "CRAN", - "Hash": "4329e57e2536e12afe479e8571416dbc" + "Encoding": "UTF-8" }, "Matrix": { "Package": "Matrix", - "Version": "1.6-1.1", + "Version": "1.7-0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "VersionNote": "do also bump src/version.h, inst/include/Matrix/version.h", + "Date": "2024-03-16", + "Priority": "recommended", + "Title": "Sparse and Dense Matrix Classes and Methods", + "Description": "A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.", + "License": "GPL (>= 2) | file LICENCE", + "URL": "https://Matrix.R-forge.R-project.org", + "BugReports": "https://R-forge.R-project.org/tracker/?atid=294&group_id=61", + "Contact": "Matrix-authors@R-project.org", + "Authors@R": "c(person(\"Douglas\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"Martin\", \"Maechler\", role = c(\"aut\", \"cre\"), email = \"mmaechler+Matrix@gmail.com\", comment = c(ORCID = \"0000-0002-8685-9910\")), person(\"Mikael\", \"Jagan\", role = \"aut\", comment = c(ORCID = \"0000-0002-3542-2938\")), person(\"Timothy A.\", \"Davis\", role = \"ctb\", comment = c(ORCID = \"0000-0001-7614-6899\", \"SuiteSparse libraries\", \"collaborators listed in dir(system.file(\\\"doc\\\", \\\"SuiteSparse\\\", package=\\\"Matrix\\\"), pattern=\\\"License\\\", full.names=TRUE, recursive=TRUE)\")), person(\"George\", \"Karypis\", role = \"ctb\", comment = c(ORCID = \"0000-0003-2753-1437\", \"METIS library\", \"Copyright: Regents of the University of Minnesota\")), person(\"Jason\", \"Riedy\", role = \"ctb\", comment = c(ORCID = \"0000-0002-4345-4200\", \"GNU Octave's condest() and onenormest()\", \"Copyright: Regents of the University of California\")), person(\"Jens\", \"Oehlschlägel\", role = \"ctb\", comment = \"initial nearPD()\"), person(\"R Core Team\", role = \"ctb\", comment = \"base R's matrix implementation\"))", + "Depends": [ + "R (>= 4.4.0)", + "methods" + ], + "Imports": [ "grDevices", "graphics", "grid", "lattice", - "methods", "stats", "utils" ], - "Hash": "1a00d4828f33a9d690806e98bd17150c" + "Suggests": [ + "MASS", + "datasets", + "sfsmisc", + "tools" + ], + "Enhances": [ + "SparseM", + "graph" + ], + "LazyData": "no", + "LazyDataNote": "not possible, since we use data/*.R and our S4 classes", + "BuildResaveData": "no", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Douglas Bates [aut] (), Martin Maechler [aut, cre] (), Mikael Jagan [aut] (), Timothy A. Davis [ctb] (, SuiteSparse libraries, collaborators listed in dir(system.file(\"doc\", \"SuiteSparse\", package=\"Matrix\"), pattern=\"License\", full.names=TRUE, recursive=TRUE)), George Karypis [ctb] (, METIS library, Copyright: Regents of the University of Minnesota), Jason Riedy [ctb] (, GNU Octave's condest() and onenormest(), Copyright: Regents of the University of California), Jens Oehlschlägel [ctb] (initial nearPD()), R Core Team [ctb] (base R's matrix implementation)", + "Maintainer": "Martin Maechler ", + "Repository": "CRAN" }, "R6": { "Package": "R6", "Version": "2.5.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Title": "Encapsulated Classes with Reference Semantics", + "Authors@R": "person(\"Winston\", \"Chang\", role = c(\"aut\", \"cre\"), email = \"winston@stdout.org\")", + "Description": "Creates classes with reference semantics, similar to R's built-in reference classes. Compared to reference classes, R6 classes are simpler and lighter-weight, and they are not built on S4 classes so they do not require the methods package. These classes allow public and private members, and they support inheritance, even when the classes are defined in different packages.", + "Depends": [ + "R (>= 3.0)" + ], + "Suggests": [ + "testthat", + "pryr" ], - "Hash": "470851b6d5d0ac559e9d01bb352b4021" + "License": "MIT + file LICENSE", + "URL": "https://r6.r-lib.org, https://github.com/r-lib/R6/", + "BugReports": "https://github.com/r-lib/R6/issues", + "RoxygenNote": "7.1.1", + "NeedsCompilation": "no", + "Author": "Winston Chang [aut, cre]", + "Maintainer": "Winston Chang ", + "Repository": "CRAN", + "Encoding": "UTF-8" }, "RColorBrewer": { "Package": "RColorBrewer", "Version": "1.1-3", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R" + "Date": "2022-04-03", + "Title": "ColorBrewer Palettes", + "Authors@R": "c(person(given = \"Erich\", family = \"Neuwirth\", role = c(\"aut\", \"cre\"), email = \"erich.neuwirth@univie.ac.at\"))", + "Author": "Erich Neuwirth [aut, cre]", + "Maintainer": "Erich Neuwirth ", + "Depends": [ + "R (>= 2.0.0)" ], - "Hash": "45f0398006e83a5b10b72a90663d8d8c" + "Description": "Provides color schemes for maps (and other graphics) designed by Cynthia Brewer as described at http://colorbrewer2.org.", + "License": "Apache License 2.0", + "NeedsCompilation": "no", + "Repository": "CRAN", + "Encoding": "UTF-8" }, "RSocrata": { "Package": "RSocrata", "Version": "1.7.15-1", "Source": "GitHub", + "Type": "Package", + "Title": "Download or Upload 'Socrata' Data Sets", + "Description": "Provides easier interaction with 'Socrata' open data portals . Users can provide a 'Socrata' data set resource URL, or a 'Socrata' Open Data API (SODA) web query, or a 'Socrata' \"human-friendly\" URL, returns an R data frame. Converts dates to 'POSIX' format and manages throttling by 'Socrata'. Users can upload data to 'Socrata' portals directly from R.", + "Date": "2023-08-13", + "Author": "Hugh Devlin, Ph. D., Tom Schenk, Jr., Gene Leynes, Nick Lucius, John Malc, Mark Silverberg, and Peter Schmeideskamp", + "Maintainer": "\"Gene Leynes\" ", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ + "httr (>= 1.0.0)", + "jsonlite (>= 0.9.16)", + "mime (>= 0.3)", + "plyr (>= 1.8.4)" + ], + "Suggests": [ + "testthat (>= 0.10.0)", + "roxygen2 (>= 4.1.0)", + "readr (>= 0.2.2)" + ], + "License": "MIT + file LICENSE", + "URL": "https://github.com/Chicago/RSocrata", + "BugReports": "https://github.com/Chicago/RSocrata/issues", + "RoxygenNote": "7.2.3", + "Encoding": "UTF-8", "RemoteType": "github", "RemoteHost": "api.github.com", "RemoteUsername": "Chicago", "RemoteRepo": "RSocrata", "RemoteRef": "master", - "RemoteSha": "7c35f916590f6d030ae133b25bb223cab495891c", - "Requirements": [ - "R", - "httr", - "jsonlite", - "mime", - "plyr" - ], - "Hash": "3d997827d605fe0045876019c9671c18" + "RemoteSha": "7c35f916590f6d030ae133b25bb223cab495891c" }, "Rcpp": { "Package": "Rcpp", - "Version": "1.0.12", + "Version": "1.0.14", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ + "Title": "Seamless R and C++ Integration", + "Date": "2025-01-11", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Romain\", \"Francois\", role = \"aut\", comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"JJ\", \"Allaire\", role = \"aut\", comment = c(ORCID = \"0000-0003-0174-9868\")), person(\"Kevin\", \"Ushey\", role = \"aut\", comment = c(ORCID = \"0000-0003-2880-7407\")), person(\"Qiang\", \"Kou\", role = \"aut\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Nathan\", \"Russell\", role = \"aut\"), person(\"Iñaki\", \"Ucar\", role = \"aut\", comment = c(ORCID = \"0000-0001-6403-5550\")), person(\"Doug\", \"Bates\", role = \"aut\", comment = c(ORCID = \"0000-0001-8316-9503\")), person(\"John\", \"Chambers\", role = \"aut\"))", + "Description": "The 'Rcpp' package provides R functions as well as C++ classes which offer a seamless integration of R and C++. Many R data types and objects can be mapped back and forth to C++ equivalents which facilitates both writing of new code as well as easier integration of third-party libraries. Documentation about 'Rcpp' is provided by several vignettes included in this package, via the 'Rcpp Gallery' site at , the paper by Eddelbuettel and Francois (2011, ), the book by Eddelbuettel (2013, ) and the paper by Eddelbuettel and Balamuta (2018, ); see 'citation(\"Rcpp\")' for details.", + "Imports": [ "methods", "utils" ], - "Hash": "5ea2700d21e038ace58269ecdbeb9ec0" + "Suggests": [ + "tinytest", + "inline", + "rbenchmark", + "pkgKitten (>= 0.1.2)" + ], + "URL": "https://www.rcpp.org, https://dirk.eddelbuettel.com/code/rcpp.html, https://github.com/RcppCore/Rcpp", + "License": "GPL (>= 2)", + "BugReports": "https://github.com/RcppCore/Rcpp/issues", + "MailingList": "rcpp-devel@lists.r-forge.r-project.org", + "RoxygenNote": "6.1.1", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Romain Francois [aut] (), JJ Allaire [aut] (), Kevin Ushey [aut] (), Qiang Kou [aut] (), Nathan Russell [aut], Iñaki Ucar [aut] (), Doug Bates [aut] (), John Chambers [aut]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" }, "arrow": { "Package": "arrow", - "Version": "18.1.0", - "Source": "Repository", - "Repository": "https://apache.r-universe.dev", - "RemoteUrl": "https://github.com/apache/arrow", - "RemoteRef": "apache-arrow-18.1.0", - "RemoteSha": "6a0414bd9a91e890ec6a45369bf61f405180628c", - "Requirements": [ - "R", - "R6", + "Version": "18.1.0.1", + "Source": "Repository", + "Title": "Integration to 'Apache' 'Arrow'", + "Authors@R": "c( person(\"Neal\", \"Richardson\", email = \"neal.p.richardson@gmail.com\", role = c(\"aut\")), person(\"Ian\", \"Cook\", email = \"ianmcook@gmail.com\", role = c(\"aut\")), person(\"Nic\", \"Crane\", email = \"thisisnic@gmail.com\", role = c(\"aut\")), person(\"Dewey\", \"Dunnington\", role = c(\"aut\"), email = \"dewey@fishandwhistle.net\", comment = c(ORCID = \"0000-0002-9415-4582\")), person(\"Romain\", \"Fran\\u00e7ois\", role = c(\"aut\"), comment = c(ORCID = \"0000-0002-2444-4226\")), person(\"Jonathan\", \"Keane\", email = \"jkeane@gmail.com\", role = c(\"aut\", \"cre\")), person(\"Drago\\u0219\", \"Moldovan-Gr\\u00fcnfeld\", email = \"dragos.mold@gmail.com\", role = c(\"aut\")), person(\"Jeroen\", \"Ooms\", email = \"jeroen@berkeley.edu\", role = c(\"aut\")), person(\"Jacob\", \"Wujciak-Jens\", email = \"jacob@wujciak.de\", role = c(\"aut\")), person(\"Javier\", \"Luraschi\", email = \"javier@rstudio.com\", role = c(\"ctb\")), person(\"Karl\", \"Dunkle Werner\", email = \"karldw@users.noreply.github.com\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0003-0523-7309\")), person(\"Jeffrey\", \"Wong\", email = \"jeffreyw@netflix.com\", role = c(\"ctb\")), person(\"Apache Arrow\", email = \"dev@arrow.apache.org\", role = c(\"aut\", \"cph\")) )", + "Description": "'Apache' 'Arrow' is a cross-language development platform for in-memory data. 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This package was inspired by the 'chalk' 'JavaScript' project.", + "License": "MIT + file LICENSE", + "URL": "https://r-lib.github.io/crayon/, https://github.com/r-lib/crayon", + "BugReports": "https://github.com/r-lib/crayon/issues", + "Imports": [ "grDevices", "methods", "utils" ], - "Hash": "e8a1e41acf02548751f45c718d55aa6a" + "Suggests": [ + "mockery", + "rstudioapi", + "testthat", + "withr" + ], + "Config/Needs/website": "tidyverse/tidytemplate", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.1", + "Collate": "'aaa-rstudio-detect.R' 'aaaa-rematch2.R' 'aab-num-ansi-colors.R' 'aac-num-ansi-colors.R' 'ansi-256.R' 'ansi-palette.R' 'combine.R' 'string.R' 'utils.R' 'crayon-package.R' 'disposable.R' 'enc-utils.R' 'has_ansi.R' 'has_color.R' 'link.R' 'styles.R' 'machinery.R' 'parts.R' 'print.R' 'style-var.R' 'show.R' 'string_operations.R'", + "NeedsCompilation": "no", + "Author": "Gábor Csárdi [aut, cre], Brodie Gaslam [ctb], Posit Software, PBC [cph, fnd]", + "Maintainer": "Gábor Csárdi ", + "Repository": "CRAN" }, "crosstalk": { "Package": "crosstalk", "Version": "1.2.1", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R6", - "htmltools", + "Type": "Package", + "Title": "Inter-Widget Interactivity for HTML Widgets", + "Authors@R": "c( person(\"Joe\", \"Cheng\", role = \"aut\", email = \"joe@posit.co\"), person(\"Carson\", \"Sievert\", role = c(\"aut\", \"cre\"), email = \"carson@posit.co\", comment = c(ORCID = \"0000-0002-4958-2844\")), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")), person(family = \"jQuery Foundation\", role = \"cph\", comment = \"jQuery library and jQuery UI library\"), person(family = \"jQuery contributors\", role = c(\"ctb\", \"cph\"), comment = \"jQuery library; authors listed in inst/www/shared/jquery-AUTHORS.txt\"), person(\"Mark\", \"Otto\", role = \"ctb\", comment = \"Bootstrap library\"), person(\"Jacob\", \"Thornton\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Bootstrap contributors\", role = \"ctb\", comment = \"Bootstrap library\"), person(family = \"Twitter, Inc\", role = \"cph\", comment = \"Bootstrap library\"), person(\"Brian\", \"Reavis\", role = c(\"ctb\", \"cph\"), comment = \"selectize.js library\"), person(\"Kristopher Michael\", \"Kowal\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(family = \"es5-shim contributors\", role = c(\"ctb\", \"cph\"), comment = \"es5-shim library\"), person(\"Denis\", \"Ineshin\", role = c(\"ctb\", \"cph\"), comment = \"ion.rangeSlider library\"), person(\"Sami\", \"Samhuri\", role = c(\"ctb\", \"cph\"), comment = \"Javascript strftime library\") )", + "Description": "Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). 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Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.", + "License": "MIT + file LICENSE", + "SystemRequirements": "libcurl (>= 7.62): libcurl-devel (rpm) or libcurl4-openssl-dev (deb)", + "URL": "https://jeroen.r-universe.dev/curl", + "BugReports": "https://github.com/jeroen/curl/issues", + "Suggests": [ + "spelling", + "testthat (>= 1.0.0)", + "knitr", + "jsonlite", + "later", + "rmarkdown", + "httpuv (>= 1.4.4)", + "webutils" ], - "Hash": "ce88d13c0b10fe88a37d9c59dba2d7f9" + "VignetteBuilder": "knitr", + "Depends": [ + "R (>= 3.0.0)" + ], + "RoxygenNote": "7.3.2.9000", + "Encoding": "UTF-8", + "Language": "en-US", + "NeedsCompilation": "yes", + "Author": "Jeroen Ooms [aut, cre] (), Hadley Wickham [ctb], Posit Software, PBC [cph]", + "Maintainer": "Jeroen Ooms ", + "Repository": "CRAN" }, "data.table": { "Package": "data.table", - "Version": "1.15.0", + "Version": "1.16.4", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Extension of `data.frame`", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "methods" ], - "Hash": "cfbbb4aed6e78cd45f17123a9ec9981a" + "Suggests": [ + "bit64 (>= 4.0.0)", + "bit (>= 4.0.4)", + "R.utils", + "xts", + "zoo (>= 1.8-1)", + "yaml", + "knitr", + "markdown" + ], + "Description": "Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.", + "License": "MPL-2.0 | file LICENSE", + "URL": "https://r-datatable.com, https://Rdatatable.gitlab.io/data.table, https://github.com/Rdatatable/data.table", + "BugReports": "https://github.com/Rdatatable/data.table/issues", + "VignetteBuilder": "knitr", + "Encoding": "UTF-8", + "ByteCompile": "TRUE", + "Authors@R": "c( person(\"Tyson\",\"Barrett\", role=c(\"aut\",\"cre\"), email=\"t.barrett88@gmail.com\", comment = c(ORCID=\"0000-0002-2137-1391\")), person(\"Matt\",\"Dowle\", role=\"aut\", email=\"mattjdowle@gmail.com\"), person(\"Arun\",\"Srinivasan\", role=\"aut\", email=\"asrini@pm.me\"), person(\"Jan\",\"Gorecki\", role=\"aut\"), person(\"Michael\",\"Chirico\", role=\"aut\", comment = c(ORCID=\"0000-0003-0787-087X\")), person(\"Toby\",\"Hocking\", role=\"aut\", comment = c(ORCID=\"0000-0002-3146-0865\")), person(\"Benjamin\",\"Schwendinger\",role=\"aut\", comment = c(ORCID=\"0000-0003-3315-8114\")), 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Andrey Riabushenko [ctb], Cheng Lee [ctb], Declan Groves [ctb], Daniel Possenriede [ctb], Felipe Parages [ctb], Denes Toth [ctb], Mus Yaramaz-David [ctb], Ayappan Perumal [ctb], James Sams [ctb], Martin Morgan [ctb], Michael Quinn [ctb], @javrucebo [ctb], @marc-outins [ctb], Roy Storey [ctb], Manish Saraswat [ctb], Morgan Jacob [ctb], Michael Schubmehl [ctb], Davis Vaughan [ctb], Leonardo Silvestri [ctb], Jim Hester [ctb], Anthony Damico [ctb], Sebastian Freundt [ctb], David Simons [ctb], Elliott Sales de Andrade [ctb], Cole Miller [ctb], Jens Peder Meldgaard [ctb], Vaclav Tlapak [ctb], Kevin Ushey [ctb], Dirk Eddelbuettel [ctb], Tony Fischetti [ctb], Ofek Shilon [ctb], Vadim Khotilovich [ctb], Hadley Wickham [ctb], Bennet Becker [ctb], Kyle Haynes [ctb], Boniface Christian Kamgang [ctb], Olivier Delmarcell [ctb], Josh O'Brien [ctb], Dereck de Mezquita [ctb], Michael Czekanski [ctb], Dmitry Shemetov [ctb], Nitish Jha [ctb], Joshua Wu [ctb], Iago Giné-Vázquez [ctb], Anirban Chetia [ctb], Doris Amoakohene [ctb], Ivan Krylov [ctb]", + "Maintainer": "Tyson Barrett ", + "Repository": "CRAN" }, "digest": { "Package": "digest", - "Version": "0.6.34", + "Version": "0.6.37", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Authors@R": "c(person(\"Dirk\", \"Eddelbuettel\", role = c(\"aut\", \"cre\"), email = \"edd@debian.org\", comment = c(ORCID = \"0000-0001-6419-907X\")), person(\"Antoine\", \"Lucas\", role=\"ctb\"), person(\"Jarek\", \"Tuszynski\", role=\"ctb\"), person(\"Henrik\", \"Bengtsson\", role=\"ctb\", comment = c(ORCID = \"0000-0002-7579-5165\")), person(\"Simon\", \"Urbanek\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2297-1732\")), person(\"Mario\", \"Frasca\", role=\"ctb\"), person(\"Bryan\", \"Lewis\", role=\"ctb\"), person(\"Murray\", \"Stokely\", role=\"ctb\"), person(\"Hannes\", \"Muehleisen\", role=\"ctb\"), person(\"Duncan\", \"Murdoch\", role=\"ctb\"), person(\"Jim\", \"Hester\", role=\"ctb\"), person(\"Wush\", \"Wu\", role=\"ctb\", comment = c(ORCID = \"0000-0001-5180-0567\")), person(\"Qiang\", \"Kou\", role=\"ctb\", comment = c(ORCID = \"0000-0001-6786-5453\")), person(\"Thierry\", \"Onkelinx\", role=\"ctb\", comment = c(ORCID = \"0000-0001-8804-4216\")), person(\"Michel\", \"Lang\", role=\"ctb\", comment = c(ORCID = \"0000-0001-9754-0393\")), person(\"Viliam\", \"Simko\", role=\"ctb\"), person(\"Kurt\", \"Hornik\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4198-9911\")), person(\"Radford\", \"Neal\", role=\"ctb\", comment = c(ORCID = \"0000-0002-2473-3407\")), person(\"Kendon\", \"Bell\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9093-8312\")), person(\"Matthew\", \"de Queljoe\", role=\"ctb\"), person(\"Dmitry\", \"Selivanov\", role=\"ctb\"), person(\"Ion\", \"Suruceanu\", role=\"ctb\"), person(\"Bill\", \"Denney\", role=\"ctb\"), person(\"Dirk\", \"Schumacher\", role=\"ctb\"), person(\"András\", \"Svraka\", role=\"ctb\"), person(\"Sergey\", \"Fedorov\", role=\"ctb\"), person(\"Will\", \"Landau\", role=\"ctb\", comment = c(ORCID = \"0000-0003-1878-3253\")), person(\"Floris\", \"Vanderhaeghe\", role=\"ctb\", comment = c(ORCID = \"0000-0002-6378-6229\")), person(\"Kevin\", \"Tappe\", role=\"ctb\"), person(\"Harris\", \"McGehee\", role=\"ctb\"), person(\"Tim\", \"Mastny\", role=\"ctb\"), person(\"Aaron\", \"Peikert\", role=\"ctb\", comment = c(ORCID = \"0000-0001-7813-818X\")), person(\"Mark\", \"van der Loo\", role=\"ctb\", comment = c(ORCID = \"0000-0002-9807-4686\")), person(\"Chris\", \"Muir\", role=\"ctb\", comment = c(ORCID = \"0000-0003-2555-3878\")), person(\"Moritz\", \"Beller\", role=\"ctb\", comment = c(ORCID = \"0000-0003-4852-0526\")), person(\"Sebastian\", \"Campbell\", role=\"ctb\"), person(\"Winston\", \"Chang\", role=\"ctb\", comment = c(ORCID = \"0000-0002-1576-2126\")), person(\"Dean\", \"Attali\", role=\"ctb\", comment = c(ORCID = \"0000-0002-5645-3493\")), person(\"Michael\", \"Chirico\", role=\"ctb\", comment = c(ORCID = \"0000-0003-0787-087X\")), person(\"Kevin\", \"Ushey\", role=\"ctb\"))", + "Date": "2024-08-19", + "Title": "Create Compact Hash Digests of R Objects", + "Description": "Implementation of a function 'digest()' for the creation of hash digests of arbitrary R objects (using the 'md5', 'sha-1', 'sha-256', 'crc32', 'xxhash', 'murmurhash', 'spookyhash', 'blake3', 'crc32c', 'xxh3_64', and 'xxh3_128' algorithms) permitting easy comparison of R language objects, as well as functions such as'hmac()' to create hash-based message authentication code. Please note that this package is not meant to be deployed for cryptographic purposes for which more comprehensive (and widely tested) libraries such as 'OpenSSL' should be used.", + "URL": "https://github.com/eddelbuettel/digest, https://dirk.eddelbuettel.com/code/digest.html", + "BugReports": "https://github.com/eddelbuettel/digest/issues", + "Depends": [ + "R (>= 3.3.0)" + ], + "Imports": [ "utils" ], - "Hash": "7ede2ee9ea8d3edbf1ca84c1e333ad1a" + "License": "GPL (>= 2)", + "Suggests": [ + "tinytest", + "simplermarkdown" + ], + "VignetteBuilder": "simplermarkdown", + "Encoding": "UTF-8", + "NeedsCompilation": "yes", + "Author": "Dirk Eddelbuettel [aut, cre] (), Antoine Lucas [ctb], Jarek Tuszynski [ctb], Henrik Bengtsson [ctb] (), Simon Urbanek [ctb] (), Mario Frasca [ctb], Bryan Lewis [ctb], Murray Stokely [ctb], Hannes Muehleisen [ctb], Duncan Murdoch [ctb], Jim Hester [ctb], Wush Wu [ctb] (), Qiang Kou [ctb] (), Thierry Onkelinx [ctb] (), Michel Lang [ctb] (), Viliam Simko [ctb], Kurt Hornik [ctb] (), Radford Neal [ctb] (), Kendon Bell [ctb] (), Matthew de Queljoe [ctb], Dmitry Selivanov [ctb], Ion Suruceanu [ctb], Bill Denney [ctb], Dirk Schumacher [ctb], András Svraka [ctb], Sergey Fedorov [ctb], Will Landau [ctb] (), Floris Vanderhaeghe [ctb] (), Kevin Tappe [ctb], Harris McGehee [ctb], Tim Mastny [ctb], Aaron Peikert [ctb] (), Mark van der Loo [ctb] (), Chris Muir [ctb] (), Moritz Beller [ctb] (), Sebastian Campbell [ctb], Winston Chang [ctb] (), Dean Attali [ctb] (), Michael Chirico [ctb] (), Kevin Ushey [ctb]", + "Maintainer": "Dirk Eddelbuettel ", + "Repository": "CRAN" }, "distfromq": { "Package": "distfromq", "Version": "1.0.4", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "reichlab", - "RemoteRepo": "distfromq", - "RemoteRef": "main", - "RemoteSha": "aa675113f396777a49632b9a7e6076d83c3c91ff", - "Requirements": [ + "Title": "Reconstruct a Distribution from a Collection of Quantiles", + "Authors@R": "c( person(\"Evan\", \"Ray\", , \"elray@umass.edu\", role = c(\"aut\", \"cre\")), person(\"Aaron\", \"Gerding\", , \"agerding@umass.edu\", role = \"aut\"), person(\"Li\", \"Shandross\", , \"lshandross@umass.edu\", role = \"ctb\"), person(\"Nick\", \"Reich\", , \"nick@umass.edu\", role = \"ctb\") )", + "Description": "Given a set of predictive quantiles from a distribution, estimate the distribution and create `d`, `p`, `q`, and `r` functions to evaluate its density function, distribution function, and quantile function, and generate random samples. 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Kamvar [ctb] (), Nicholas G. Reich [ctb] (), Consortium of Infectious Disease Modeling Hubs [cph]", + "Maintainer": "Li Shandross ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "hubverse-org", + "RemoteRepo": "hubEnsembles", + "RemoteRef": "v0.1.9", + "RemoteSha": "9ba5eab32295632bb88e486f6dad796abadea74f", + "Remotes": "hubverse-org/hubExamples, hubverse-org/hubUtils, hubverse-org/hubVis, reichlab/distfromq" }, "hubUtils": { "Package": "hubUtils", - "Version": "0.3.0.9000", + "Version": "0.4.0.9000", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "Infectious-Disease-Modeling-Hubs", - "RemoteRepo": "hubUtils", - "RemoteRef": "main", - "RemoteSha": "fd6c3a4013f1b6306d2abdc38c7f519736f169b6", - "Requirements": [ - "R", + "Title": "Core 'hubverse' Utilities", + "Authors@R": "c( person(\"Anna\", \"Krystalli\", , \"annakrystalli@googlemail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-2378-4915\")), person(\"Li\", \"Shandross\", , \"lshandross@umass.edu\", role = \"ctb\"), person(\"Nicholas G.\", \"Reich\", , \"nick@umass.edu\", role = \"ctb\", comment = c(ORCID = \"0000-0003-3503-9899\")), person(\"Evan L.\", \"Ray\", , \"elray@umass.edu\", role = \"ctb\"), person(\"Zhian N.\", \"Kamvar\", , \"zkamvar@gmail.com\", role = c(\"ctb\"), comment = c(ORCID = \"0000-0003-1458-7108\")), person(\"Consortium of Infectious Disease Modeling Hubs\", role = \"cph\") )", + "Description": "Core set of low-level utilities common across the 'hubverse'. Used to interact with 'hubverse' schema, Hub configuration files and model outputs and designed to be primarily used internally by other 'hubverse' packages. See Reich et al. (2022) for an overview of Collaborative Hubs.", + "License": "MIT + file LICENSE", + "URL": "https://github.com/hubverse-org/hubUtils, https://hubverse-org.github.io/hubUtils/", + "BugReports": "https://github.com/hubverse-org/hubUtils/issues", + "Depends": [ + "R (>= 2.10)" + ], + "Imports": [ "checkmate", "cli", "curl", @@ -864,47 +2182,88 @@ "tibble", "utils" ], - "Hash": "7854d1ca87caa182d2e71e0674aade58" + "Suggests": [ + "arrow (>= 17.0.0)", + "dplyr", + "knitr", + "rmarkdown", + "testthat (>= 3.2.0)" + ], + "Config/Needs/website": "hubverse-org/hubStyle", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "LazyData": "true", + "Roxygen": "list(markdown = TRUE)", + "RoxygenNote": "7.3.2", + "Author": "Anna Krystalli [aut, cre] (), Li Shandross [ctb], Nicholas G. Reich [ctb] (), Evan L. 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They work in terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the 'macOS' 'R.app'. 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This package also contains helper functions to compile 'LaTeX' documents, and install missing 'LaTeX' packages automatically.", + "Imports": [ + "xfun (>= 0.48)" + ], + "Suggests": [ + "testit", + "rstudioapi" ], - "Hash": "5ac22900ae0f386e54f1c307eca7d843" + "License": "MIT + file LICENSE", + "URL": "https://github.com/rstudio/tinytex", + "BugReports": "https://github.com/rstudio/tinytex/issues", + "Encoding": "UTF-8", + "RoxygenNote": "7.3.2", + "NeedsCompilation": "no", + "Author": "Yihui Xie [aut, cre, cph] (), Posit Software, PBC [cph, fnd], Christophe Dervieux [ctb] (), Devon Ryan [ctb] (), Ethan Heinzen [ctb], Fernando Cagua [ctb]", + "Maintainer": "Yihui Xie ", + "Repository": "CRAN" }, "tzdb": { "Package": "tzdb", "Version": "0.4.0", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", - "cpp11" + "Title": "Time Zone Database Information", + "Authors@R": "c( person(\"Davis\", \"Vaughan\", , \"davis@posit.co\", role = c(\"aut\", \"cre\")), person(\"Howard\", \"Hinnant\", role = \"cph\", comment = \"Author of the included date library\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "Provides an up-to-date copy of the Internet Assigned Numbers Authority (IANA) Time Zone Database. 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Input, validate, normalize, encode, format, and display.", + "License": "Apache License (== 2.0) | file LICENSE", + "URL": "https://ptrckprry.com/r-utf8/, https://github.com/patperry/r-utf8", + "BugReports": "https://github.com/patperry/r-utf8/issues", + "Depends": [ + "R (>= 2.10)" ], - "Hash": "62b65c52671e6665f803ff02954446e9" + "Suggests": [ + "cli", + "covr", + "knitr", + "rlang", + "rmarkdown", + "testthat (>= 3.0.0)", + "withr" + ], + "VignetteBuilder": "knitr, rmarkdown", + "Config/testthat/edition": "3", + "Encoding": "UTF-8", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "yes", + "Author": "Patrick O. Perry [aut, cph], Kirill Müller [cre], Unicode, Inc. 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The color maps are also perceptually-uniform, both in regular form and also when converted to black-and-white for printing. This is the 'lite' version of the 'viridis' package that also contains 'ggplot2' bindings for discrete and continuous color and fill scales and can be found at .", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "Depends": [ + "R (>= 2.10)" + ], + "Suggests": [ + "hexbin (>= 1.27.0)", + "ggplot2 (>= 1.0.1)", + "testthat", + "covr" ], - "Hash": "c826c7c4241b6fc89ff55aaea3fa7491" + "URL": "https://sjmgarnier.github.io/viridisLite/, https://github.com/sjmgarnier/viridisLite/", + "BugReports": "https://github.com/sjmgarnier/viridisLite/issues/", + "RoxygenNote": "7.2.3", + "NeedsCompilation": "no", + "Author": "Simon Garnier [aut, cre], Noam Ross [ctb, cph], Bob Rudis [ctb, cph], Marco Sciaini [ctb, cph], Antônio Pedro Camargo [ctb, cph], Cédric Scherer [ctb, cph]", + "Repository": "CRAN" }, "vroom": { "Package": "vroom", "Version": "1.6.5", "Source": "Repository", - "Repository": "CRAN", - "Requirements": [ - "R", + "Title": "Read and Write Rectangular Text Data Quickly", + "Authors@R": "c( person(\"Jim\", \"Hester\", role = \"aut\", comment = c(ORCID = \"0000-0002-2739-7082\")), person(\"Hadley\", \"Wickham\", , \"hadley@posit.co\", role = \"aut\", comment = c(ORCID = \"0000-0003-4757-117X\")), person(\"Jennifer\", \"Bryan\", , \"jenny@posit.co\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6983-2759\")), person(\"Shelby\", \"Bearrows\", role = \"ctb\"), person(\"https://github.com/mandreyel/\", role = \"cph\", comment = \"mio library\"), person(\"Jukka\", \"Jylänki\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Mikkel\", \"Jørgensen\", role = \"cph\", comment = \"grisu3 implementation\"), person(\"Posit Software, PBC\", role = c(\"cph\", \"fnd\")) )", + "Description": "The goal of 'vroom' is to read and write data (like 'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial indexing step, then reads the values lazily , so only the data you actually use needs to be read. 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The operator unpacks the right-hand side of an assignment into multiple values and assigns these values to variables on the left-hand side of the assignment.", + "URL": "https://github.com/nteetor/zeallot", + "BugReports": "https://github.com/nteetor/zeallot/issues", + "License": "MIT + file LICENSE", + "Encoding": "UTF-8", + "RoxygenNote": "6.0.1", + "VignetteBuilder": "knitr", + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "purrr", + "magrittr" + ], + "NeedsCompilation": "no", + "Author": "Nathan Teetor [aut, cre], Paul Teetor [ctb]", + "Maintainer": "Nathan Teetor ", + "Repository": "CRAN" }, "zoltr": { "Package": "zoltr", "Version": "1.0.1", "Source": "GitHub", - "RemoteType": "github", - "RemoteHost": "api.github.com", - "RemoteUsername": "reichlab", - "RemoteRepo": "zoltr", - "RemoteRef": "master", - "RemoteSha": "3344e2a95969042977ae2f89fef672244348569f", - "Requirements": [ - "MMWRweek", - "base64url", + "Title": "Interface to the 'Zoltar' Forecast Repository API", + "Authors@R": "c( person(\"Matthew\", \"Cornell\", role = c(\"aut\", \"cre\"), email = \"cornell@umass.edu\"), person(\"Nicholas\", \"Reich\", role = c(\"aut\", \"cph\"), email = \"nick@schoolph.umass.edu\"))", + "Description": "'Zoltar' is a website that provides a repository of model forecast results in a standardized format and a central location. It supports storing, retrieving, comparing, and analyzing time series forecasts for prediction challenges of interest to the modeling community. This package provides functions for working with the 'Zoltar' API, including connecting and authenticating, getting meta information (projects, models, and forecasts, and truth), and uploading, downloading, and deleting forecast and truth data.", + "URL": "https://github.com/reichlab/zoltr , http://reichlab.io/zoltr/", + "BugReports": "https://github.com/reichlab/zoltr/issues", + "License": "GPL-3", + "Encoding": "UTF-8", + "Suggests": [ + "testthat", + "knitr", + "rmarkdown", + "webmockr", + "mockery" + ], + "Imports": [ "data.table", - "dplyr", "httr", "jsonlite", - "lubridate", - "magrittr", "readr", + "base64url", + "dplyr", + "MMWRweek", + "utils", "rlang", - "utils" + "magrittr", + "lubridate" ], - "Hash": "aa318d451907140ef0883d51435b87c5" + "RoxygenNote": "7.3.1", + "VignetteBuilder": "knitr", + "Roxygen": "list(markdown = TRUE)", + "Author": "Matthew Cornell [aut, cre], Nicholas Reich [aut, cph]", + "Maintainer": "Matthew Cornell ", + "RemoteType": "github", + "RemoteHost": "api.github.com", + "RemoteUsername": "reichlab", + "RemoteRepo": "zoltr", + "RemoteRef": "master", + "RemoteSha": "3344e2a95969042977ae2f89fef672244348569f" } } } From 76e362ead845b18820b4077d6db2eb34b6833007 Mon Sep 17 00:00:00 2001 From: matthewcornell Date: Thu, 6 Feb 2025 12:34:48 -0500 Subject: [PATCH 2/2] incorporate PR comment suggestions --- Dockerfile | 5 ++++- README.md | 2 +- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/Dockerfile b/Dockerfile index 5f7c69c..c03226b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -73,9 +73,12 @@ COPY "${MODEL_DIR}/requirements.txt" ./ RUN pip3 install --upgrade pip RUN pip3 install -r requirements.txt -# install required R packages using renv +# install required R packages using renv - see https://rstudio.github.io/renv/articles/docker.html COPY "${MODEL_DIR}/renv.lock" ./ ENV RENV_PATHS_LIBRARY="renv/library" + +# Guidance for setting default CRAN mirror: https://rocker-project.org/images/versioned/r-ver.html#switch-the-default-cran-mirror +# Posit Public Package Manager setup: https://p3m.dev/client/#/repos/cran/setup RUN /rocker_scripts/setup_R.sh https://p3m.dev/cran/__linux__/jammy/2025-02-05 RUN Rscript -e "install.packages('renv')" RUN Rscript -e "renv::restore()" diff --git a/README.md b/README.md index 87f9ea8..3a0819f 100644 --- a/README.md +++ b/README.md @@ -82,7 +82,7 @@ A `renv.lock` file is generated via the following steps. As noted above, the "in docker run --rm -it --name temp_container rocker/r-ver:4.4.1 /bin/bash ``` 2. install the required OS libraries and applications (see "install general OS utilities" and "install OS binaries required by R packages" in the [Dockerfile](Dockerfile)) -3. specify repo via: +3. specify the [p3m repository snapshot to a particular date](https://p3m.dev/client/#/repos/cran/setup?distribution=ubuntu-22.04&r_environment=other&snapshot=2025-02-05) (this allows binary packages to be installed for faster builds) (see the [rocker-project guidance for switching the default CRAN mirror](https://rocker-project.org/images/versioned/r-ver.html#switch-the-default-cran-mirror)): ```bash /rocker_scripts/setup_R.sh https://p3m.dev/cran/__linux__/jammy/2025-02-05 ```