Merge pull request #5 from Zadchow/testing

Testing Developments Pushed to Master

.Rbuildignore

@@ -7,6 +7,7 @@
 ^codecov\.yml$
 ^_config\.yml$
 ^docs$
+^examples$
 ^_pkgdown\.yml$
 ^README\.Rmd$
 ^README-.*\.png$
@@ -19,3 +20,9 @@
 ^\.RData$
 ^\.Rhistory$
 ^\.circleci$
+^revdep$
+^Makefile$
+^\.covrignore$
+^LICENSE\.md$
+^usethis\.R$
+

.covrignore

@@ -0,0 +1,2 @@
+R/deprec-*.R
+R/compat-*.R

.github/CONTRIBUTING.md

@@ -0,0 +1,48 @@
+# Contributing to concurve
+
+This outlines how to propose a change to concurve. For more detailed
+info about contributing to this, and other tidyverse packages, please see the
+[**development contributing guide**](https://rstd.io/tidy-contrib).
+
+### Fixing typos
+
+Small typos or grammatical errors in documentation may be edited directly using
+the GitHub web interface, so long as the changes are made in the _source_ file.
+
+*  YES: you edit a roxygen comment in a `.R` file below `R/`.
+*  NO: you edit an `.Rd` file below `man/`.
+
+### Prerequisites
+
+Before you make a substantial pull request, you should always file an issue and
+make sure someone from the team agrees that it’s a problem. If you’ve found a
+bug, create an associated issue and illustrate the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex).
+
+### Pull request process
+
+*  We recommend that you create a Git branch for each pull request (PR).  
+*  Look at the Travis and AppVeyor build status before and after making changes.
+The `README` should contain badges for any continuous integration services used
+by the package.  
+*  New code should follow the tidyverse [style guide](https://style.tidyverse.org).
+You can use the [styler](https://CRAN.R-project.org/package=styler) package to
+apply these styles, but please don't restyle code that has nothing to do with 
+your PR.  
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with
+[Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/markdown.html), 
+for documentation.  
+*  We use [testthat](https://cran.r-project.org/package=testthat). Contributions
+with test cases included are easier to accept.  
+*  For user-facing changes, add a bullet to the top of `NEWS.md` below the
+current development version header describing the changes made followed by your
+GitHub username, and links to relevant issue(s)/PR(s).
+
+### Code of Conduct
+
+Please note that the concurve project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.
+
+### See tidyverse [development contributing guide](https://rstd.io/tidy-contrib)
+for further details.

.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,11 @@
+Please briefly describe your problem and what output you expect. If you have a question, please don't use this form. Instead, ask on <https://stackoverflow.com/> or <https://community.rstudio.com/>.
+
+Please include a minimal reproducible example (AKA a reprex). If you've never heard of a [reprex](https://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+
+---
+
+Brief description of the problem
+
+```r
+# insert reprex here
+```

.github/SUPPORT.md

@@ -0,0 +1,35 @@
+# Getting help with concurve
+
+Thanks for using concurve. Before filing an issue, there are a few places
+to explore and pieces to put together to make the process as smooth as possible.
+
+Start by making a minimal **repr**oducible **ex**ample using the 
+[reprex](https://reprex.tidyverse.org/) package. If you haven't heard of or used 
+reprex before, you're in for a treat! Seriously, reprex will make all of your 
+R-question-asking endeavors easier (which is a pretty insane ROI for the five to 
+ten minutes it'll take you to learn what it's all about). For additional reprex
+pointers, check out the [Get help!](https://www.tidyverse.org/help/) section of
+the tidyverse site.
+
+Armed with your reprex, the next step is to figure out [where to ask](https://www.tidyverse.org/help/#where-to-ask). 
+
+  * If it's a question: start with [community.rstudio.com](https://community.rstudio.com/), 
+    and/or StackOverflow. There are more people there to answer questions.  
+  * If it's a bug: you're in the right place, file an issue.  
+  * If you're not sure: let the community help you figure it out! If your 
+    problem _is_ a bug or a feature request, you can easily return here and 
+    report it. 
+
+Before opening a new issue, be sure to [search issues and pull requests](https://github.com/tidyverse/concurve/issues) to make sure the 
+bug hasn't been reported and/or already fixed in the development version. By 
+default, the search will be pre-populated with `is:issue is:open`. You can 
+[edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/) 
+(e.g. `is:pr`, `is:closed`) as needed. For example, you'd simply
+remove `is:open` to search _all_ issues in the repo, open or closed.
+
+
+If you _are_ in the right place, and need to file an issue, please review the 
+["File issues"](https://www.tidyverse.org/contribute/#issues) paragraph from 
+the tidyverse contributing guidelines.
+
+Thanks for your help!

.gitignore

@@ -2,3 +2,4 @@
 .Rhistory
 .RData
 .Ruserdata
+inst/doc

.travis.yml

@@ -1,12 +1,15 @@
 # R for travis: see documentation at https://docs.travis-ci.com/user/languages/r
 
 language: R
-sudo: false
 cache: packages
 
-r_packages:
-  - covr
-
-after_success:
-  - Rscript -e 'library(covr); codecov()'
-  - Rscript -e 'covr::coveralls()'
+matrix:
+  include:
+  - r: devel
+  - r: release
+    after_success:
+    - Rscript -e 'covr::codecov()'
+  - r: oldrel
+  - r: 3.4
+  - r: 3.3
+  - r: 3.2

DESCRIPTION

@@ -1,35 +1,77 @@
-Package: concurve
 Type: Package
-Date: 2019-09-18
-Title: Computes and Plots Consonance (Confidence) Intervals, P-Values, and S-Values to Form Consonance and Surprisal Functions
-Version: 2.1.0
-Authors@R: c(
-    person("Zad R.", "Chow", , "[email protected]", role = c("aut", "cre"),
-      comment = c(ORCID = "0000-0003-1545-8199")
-    ),
-    person("Andrew D.", "Vigotsky", role = "aut",
-      comment = c(ORCID = "0000-0003-3166-0688")
-    )
-    )
+Package: concurve
+Title: Computes and Plots Compatibility (Confidence) Intervals,
+    P-Values, S-Values, & Likelihood Intervals to Form Consonance,
+    Surprisal, & Likelihood Functions
+Version: 2.3.0
+Date: 2019-12-04
+Authors@R: 
+    c(person(given = "Zad R.",
+             family = "Chow",
+             role = c("aut", "cre"),
+             email = "[email protected]",
+             comment = c(ORCID = "0000-0003-1545-8199")),
+      person(given = "Andrew D.",
+             family = "Vigotsky",
+             role = "aut",
+             comment = c(ORCID = "0000-0003-3166-0688")))
 Maintainer: Zad R. Chow <[email protected]>
-Description: Allows one to compute consonance (confidence) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance and surprisal functions allowing one to see what effect sizes are compatible with the test model at various consonance levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052), Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>, Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>, Chow ZR, Greenland S. (2019) <arXiv:1909.08579>, and Greenland S, Chow ZR. (2019) <arXiv:1909.08583>.
-Imports: parallel,
-         ggplot2,
-         metafor,
-         dplyr,
-         tibble,
-         survival, 
-         survminer,
-         scales
+Description: Allows one to compute consonance (confidence)
+    intervals for various statistical tests along with their corresponding
+    P-values, S-values, and likelihoods. The intervals can be plotted to
+    create consonance, surprisal, and likelihood functions allowing one to
+    see what effect sizes are compatible with the test model at various
+    consonance levels rather than being limited to one interval estimate
+    such as 95%. These methods are discussed by Poole C. (1987)
+    <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002)
+    <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007)
+    <arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2008,
+    ISBN:9781451190052), Amrhein V, Trafimow D, Greenland S. (2019)
+    <doi:10.1080/00031305.2018.1543137>, Greenland S. (2019)
+    <doi:10.1080/00031305.2018.1529625>, Chow ZR, Greenland S. (2019)
+    <arXiv:1909.08579>, and Greenland S, Chow ZR. (2019)
+    <arXiv:1909.08583>.
+License: GPL-3 | file LICENSE
+URL: https://data.lesslikely.com/concurve/,
+    https://github.com/zadchow/concurve, https://lesslikely.com/
+BugReports: https://github.com/zadchow/concurve/issues
+Imports: 
+    bcaboot,
+    boot,
+    compiler,
+    dplyr,
+    flextable,
+    ggplot2,
+    knitr,
+    metafor,
+    officer,
+    parallel,
+    pbmcapply,
+    ProfileLikelihood,
+    rlang (>= 0.1.2),
+    scales,
+    survival,
+    survminer,
+    tibble,
+    tidyr,
+    MASS,
+    methods
 Suggests:
+    covr,
+    roxygen2,
+    spelling,
     testthat,
-    knitr,
-    covr
-License: GPL-3 | file LICENSE
-URL: https://data.lesslikely.com/concurve/, https://github.com/Zadchow/concurve, https://lesslikely.com/
-BugReports: https://github.com/Zadchow/concurve/issues
-VignetteBuilder: knitr
+    rmarkdown,
+    Lock5Data
+VignetteBuilder: 
+    knitr
+ByteCompile: true
 Encoding: UTF-8
+Language: en-US
 LazyData: true
-RoxygenNote: 6.1.1
-X-schema.org-keywords: confidence, compatibility, consonance, surprisal, interval, function, curve
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.0.2
+X-schema.org-keywords: confidence, compatibility, consonance,
+    surprisal, interval, function, curve
+Depends: 
+    R (>= 3.2)

Makefile

@@ -0,0 +1,26 @@
+# h/t to @jimhester and @yihui for this parse block:
+# https://github.com/yihui/knitr/blob/dc5ead7bcfc0ebd2789fe99c527c7d91afb3de4a/Makefile#L1-L4
+# Note the portability change as suggested in the manual:
+# https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Writing-portable-packages
+PKGNAME = `sed -n "s/Package: *\([^ ]*\)/\1/p" DESCRIPTION`
+PKGVERS = `sed -n "s/Version: *\([^ ]*\)/\1/p" DESCRIPTION`
+
+
+all: check
+
+build:
+	R CMD build .
+
+check: build
+	R CMD check --no-manual $(PKGNAME)_$(PKGVERS).tar.gz
+
+install_deps:
+	Rscript \
+	-e 'if (!requireNamespace("remotes") install.packages("remotes")' \
+	-e 'remotes::install_deps(dependencies = TRUE)'
+
+install: install_deps build
+	R CMD INSTALL $(PKGNAME)_$(PKGVERS).tar.gz
+
+clean:
+	@rm -rf $(PKGNAME)_$(PKGVERS).tar.gz $(PKGNAME).Rcheck

NAMESPACE

@@ -1,14 +1,24 @@
 exportPattern("^[[:alpha:]]+")
 import(parallel)
+import(pbmcapply)
+import(bcaboot)
+import(boot)
 import(ggplot2)
+import(ProfileLikelihood)
 import(dplyr)
+import(tidyr)
+import(flextable)
+import(officer)
+import(knitr)
 import(tibble)
 import(survival)
 import(survminer)
 import(metafor)
 import(scales)
 importFrom("stats", "coef", "confint", "confint.default", "confint.lm",
                 "lm", "quantile", "t.test", "cor.test", "qnorm")
+  importFrom("methods", "is")
+  importFrom("stats", "approxfun", "integrate")
 importFrom("graphics", "axis", "par", "polygon", "text")
 importFrom("stats", "logLik", "model.frame", "model.matrix",
              "model.response", "na.fail")

NEWS.md

@@ -1,3 +1,20 @@
+# concurve 2.3.0
+
+## Major changes 
+* `ggconcurve()` is now `ggcurve()`.
+* `ggcurve()` plots confidence (consonance) distributions, densities, likelihood, and deviance functions. 
+* `plot_curve()` is now deprecated. Please use `ggcurve()` instead. 
+* `curve_compare()` compares two functions and calculates the area between the curve. 
+* `plot_compare() `allows two separate functions to be plotted and compared simultaneously.
+* `curve_table()` produces publication-ready tables of relevant statistics.
+* `curve_boot()` uses bootstrapping to approximate the consonance functions via the [`boot`](https://cran.r-project.org/package=boot) and [`bcaboot`](https://cran.r-project.org/package=bcaboot) packages. 
+* `curve_lik()` produces likelihood functions by transforming the objects from the [`ProfileLikelihood`](https://cran.r-project.org/package=ProfileLikelihood) package.
+
+## Minor changes 
+
+* All functions now provide progress on how long it will take to complete the task.
+* Interval widths are now provided as measures of precision. 
+
 # concurve 2.1.0
 
 ## Major changes 

R/concurve-package.R

@@ -0,0 +1,8 @@
+#' @keywords internal
+"_PACKAGE"
+
+# The following block is used by usethis to automatically manage
+# roxygen namespace tags. Modify with care!
+## usethis namespace: start
+## usethis namespace: end
+NULL