Merge pull request #98 from egouldo/tidy_styler

tidy styler

.github/CONTRIBUTING.md

@@ -0,0 +1,47 @@
+# Contributing to ManyEcoEvo
+
+This outlines how to propose a change to ManyEcoEvo.
+For a detailed discussion on contributing to this and other tidyverse packages, please see the [development contributing guide](https://rstd.io/tidy-contrib) and our [code review principles](https://code-review.tidyverse.org/).
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file. 
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file. 
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed. 
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal 
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("egouldo/ManyEcoEvo", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`. 
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing. 
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   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/rd-formatting.html), for documentation.  
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests. 
+   Contributions with test cases included are easier to accept.  
+
+## Code of Conduct
+
+Please note that the ManyEcoEvo 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.

.github/ISSUE_TEMPLATE/issue_template.md

@@ -0,0 +1,16 @@
+---
+name: Bug report or feature request
+about: Describe a bug you've seen or make a case for a new feature
+---
+
+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](http://reprex.tidyverse.org/) before, start by reading <https://www.tidyverse.org/help/#reprex>.
+
+For more advice on how to write a great issue, see <https://code-review.tidyverse.org/issues/>.
+
+Brief description of the problem
+
+```r
+# insert reprex here
+```

.github/SUPPORT.md

@@ -0,0 +1,35 @@
+# Getting help with ManyEcoEvo
+
+Thanks for using ManyEcoEvo!
+Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
+
+## Make a reprex
+
+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 incredible 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.
+
+## Where to ask?
+
+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](https://github.com/egouldo/ManyEcoEvo/issues/new).  
+
+*   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/egouldo/ManyEcoEvo/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.
+
+## What happens next?
+
+To be as efficient as possible, development of tidyverse packages tends to be very bursty, so you shouldn't worry if you don't get an immediate response.
+Typically we don't look at a repo until a sufficient quantity of issues accumulates, then there’s a burst of intense activity as we focus our efforts. 
+That makes development more efficient because it avoids expensive context switching between problems, at the cost of taking longer to get back to you. 
+This process makes a good reprex particularly important because it might be multiple months between your initial report and when we start working on it. 
+If we can’t reproduce the bug, we can’t fix it!

.github/workflows/pr-commands.yaml

@@ -0,0 +1,85 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  issue_comment:
+    types: [created]
+
+name: pr-commands.yaml
+
+permissions: read-all
+
+jobs:
+  document:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/document') }}
+    name: document
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::roxygen2
+          needs: pr-document
+
+      - name: Document
+        run: roxygen2::roxygenise()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add man/\* NAMESPACE
+          git commit -m 'Document'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+  style:
+    if: ${{ github.event.issue.pull_request && (github.event.comment.author_association == 'MEMBER' || github.event.comment.author_association == 'OWNER') && startsWith(github.event.comment.body, '/style') }}
+    name: style
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/pr-fetch@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}
+
+      - uses: r-lib/actions/setup-r@v2
+
+      - name: Install dependencies
+        run: install.packages("styler")
+        shell: Rscript {0}
+
+      - name: Style
+        run: styler::style_pkg()
+        shell: Rscript {0}
+
+      - name: commit
+        run: |
+          git config --local user.name "$GITHUB_ACTOR"
+          git config --local user.email "[email protected]"
+          git add \*.R
+          git commit -m 'Style'
+
+      - uses: r-lib/actions/pr-push@v2
+        with:
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

.lintr

@@ -0,0 +1,10 @@
+linters: linters_with_defaults(
+  commented_code_linter = NULL,
+  object_usage_linter = NULL,
+  seq_linter = NULL, #fine for forloops, not great in mutate calls
+  line_length_linter(120)
+  ) # see vignette("lintr")
+encoding: "UTF-8"
+exclusions: list(
+  "data-raw/analyst_data"
+  )

DESCRIPTION

@@ -1,76 +1,71 @@
 Package: ManyEcoEvo
 Title: Meta-analyse data from 'Many-Analysts' style studies
 Version: 2.3.0
-Authors@R: c(person(given = "Elliot",
-                    family = "Gould", 
-                    email =  "[email protected]", 
-                    role = c("aut", "cre"), 
-                    comment = c(ORCID = "https://orcid.org/0000-0002-6585-538X")),
-             person(given = "Hannah S.", 
-                    family = "Fraser", 
-                    role = "aut",
-                    comment = c(ORCID = "https://orcid.org/0000-0003-2443-4463")),
-             person(given = "Shinichi",
-                    family = "Nakagawa",
-                    role = "aut",
-                    comment = c(ORCID = "https://orcid.org/0000-0002-7765-5182")),
-             person(given = "Timothy H.",
-                    family = "Parker",
-                    role = "aut",
-                    comment = c(ORCID = "https://orcid.org/0000-0003-2995-5284"))
-           )
-Description: The ManyEcoEvo package provides a set of functions for
-    aiding data cleaning, preparation and conducting analysis for
-    multi-analyst style studies. It also contains datasets from the
-    ManyEcoEvo project for reproducing the ManyEcoEvo analysis.
+Authors@R: c(
+    person("Elliot", "Gould", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "https://orcid.org/0000-0002-6585-538X")),
+    person("Hannah S.", "Fraser", role = "aut",
+           comment = c(ORCID = "https://orcid.org/0000-0003-2443-4463")),
+    person("Shinichi", "Nakagawa", role = "aut",
+           comment = c(ORCID = "https://orcid.org/0000-0002-7765-5182")),
+    person("Timothy H.", "Parker", role = "aut",
+           comment = c(ORCID = "https://orcid.org/0000-0003-2995-5284"))
+  )
+Description: The ManyEcoEvo package provides a set of functions for aiding
+    data cleaning, preparation and conducting analysis for multi-analyst
+    style studies. It also contains datasets from the ManyEcoEvo project
+    for reproducing the ManyEcoEvo analysis.
 License: GPL (>= 3)
+URL: https://github.com/egouldo/ManyEcoEvo,
+    https://egouldo.github.io/ManyEcoEvo/
+BugReports: https://github.com/egouldo/ManyEcoEvo/issues
 Depends: 
     R (>= 2.10)
 Imports:
     betapart,
-    dplyr,
-    tidyselect,
-    pointblank,
-    tibble,
     cli,
     data.table,
+    dplyr,
     forcats,
     fs,
     glue,
     here,
+    lifecycle,
     lme4,
+    magrittr,
     metafor,
     naniar,
-    magrittr,
-    tidyr,
-    rlang,
+    pointblank,
     purrr,
-    tidyselect
+    rlang,
+    tibble,
+    tidyr,
+    tidyselect,
+    tidyselect,
+    withr
 Suggests:
-    targets,
-    qs,
     broom.mixed,
-    metaviz,
     ggeffects,
+    knitr,
+    metaviz,
     parameters,
-    performance,
     parsnip,
-    workflows,
-    timetk,
-    recipes,
-    sae,
+    performance,
     pracma,
     progress,
-    knitr,
-    rmarkdown
+    qs,
+    recipes,
+    rmarkdown,
+    sae,
+    targets,
+    timetk,
+    workflows
+VignetteBuilder: 
+    knitr
 Remotes:
-  daniel1noble/orchaRd,
-  NightingaleHealth/ggforestplot
+    daniel1noble/orchaRd,
+    NightingaleHealth/ggforestplot
 Encoding: UTF-8
 LazyData: false
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-URL: https://github.com/egouldo/ManyEcoEvo,
-     https://egouldo.github.io/ManyEcoEvo/
-BugReports: https://github.com/egouldo/ManyEcoEvo/issues
-VignetteBuilder: knitr

NAMESPACE

@@ -114,6 +114,7 @@ import(metafor)
 import(recipes)
 import(rlang)
 import(see)
+import(tidyr)
 importFrom(EnvStats,stat_n_text)
 importFrom(broom,tidy)
 importFrom(broom.mixed,tidy)
@@ -141,6 +142,7 @@ importFrom(dplyr,summarise)
 importFrom(forcats,fct_relevel)
 importFrom(ggplot2,ggplot)
 importFrom(glue,glue)
+importFrom(lifecycle,deprecated)
 importFrom(lme4,lmer)
 importFrom(magrittr,"%>%")
 importFrom(metaviz,viz_funnel)
@@ -177,7 +179,5 @@ importFrom(tibble,tibble)
 importFrom(tidyr,hoist)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
-importFrom(tidyr,separate)
-importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
 importFrom(timetk,step_box_cox)

R/ManyEcoEvo-package.R

@@ -0,0 +1,9 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+#' @import rlang
+#' @importFrom glue glue
+#' @importFrom lifecycle deprecated
+## usethis namespace: end
+NULL

R/Z_VZ_preds.R

@@ -8,26 +8,28 @@
 #' @return A tibble with columns \code{Z} and \code{VZ}
 #' @family Analysis-level functions
 #' @export
-Z_VZ_preds <- function(yi, yi_se, mu_p, sd_p ){
-  #TODO should we pass in whole DF as arg instead of yi + yi_se??
+Z_VZ_preds <- function(yi, yi_se, mu_p, sd_p) {
+  # TODO should we pass in whole DF as arg instead of yi + yi_se??
   # We want to be able to keep the values linked to their corresponding
   # scenario_value!
-  na_args <- purrr::discard(c(yi, yi_se, mu_p, sd_p), is.na) %>% 
+  na_args <- purrr::discard(c(yi, yi_se, mu_p, sd_p), is.na) %>%
     length()
-  
-  if(na_args < 3){
+
+  if (na_args < 3) {
     cli::cli_alert_danger("Required values for computing Z/VZ predictions missing:")
     cli::cli_alert_warning("Returning {.val NA} for quadrupple:")
-    cli::cli_ol(c("yi {.val {yi}},",
-                  "yi_se {.val {yi_se}},", 
-                  "mu_p {.val {mu_p}}",
-                  "sd_p {.val {sd_p}}"))
-    return(NA) #TODO single NA value OR, tibble with NA's?
+    cli::cli_ol(c(
+      "yi {.val {yi}},",
+      "yi_se {.val {yi_se}},",
+      "mu_p {.val {mu_p}}",
+      "sd_p {.val {sd_p}}"
+    ))
+    return(NA)
   }
-  
-  
+
+
   Z <- (yi - mu_p) / sd_p
   VZ <- yi_se / sd_p
-  
-  return(tibble(Z, VZ)) 
-}
+
+  return(tibble(Z, VZ))
+}