Merge branch 'release/0.14.0'

.Rbuildignore

@@ -8,3 +8,5 @@
 ^\.vscode$
 ^.lintr$
 ^CHANGELOG\.md$
+^cran-comments\.md$
+^CRAN-SUBMISSION$

.github/workflows/R-CMD-check.yaml

@@ -23,12 +23,12 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest, r: "release"}
-          - {os: windows-latest, r: "release"}
-          - {os: windows-latest, r: "3.6"}
-          # - {os: ubuntu-latest, r: "devel", http-user-agent: "release"}
-          - {os: ubuntu-latest, r: "release"}
-          - {os: ubuntu-latest, r: "oldrel-1"}
+          - { os: macOS-latest, r: "release" }
+          - { os: windows-latest, r: "release" }
+          - { os: windows-latest, r: "3.6" }
+          - { os: ubuntu-latest, r: "devel", http-user-agent: "release" }
+          - { os: ubuntu-latest, r: "release" }
+          - { os: ubuntu-latest, r: "oldrel-1" }
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
@@ -38,10 +38,6 @@ jobs:
       # https://github.com/actions/checkout
       - uses: actions/checkout@v3
 
-      - name: System dependencies
-        if: ${{ matrix.config.os == 'macOS-latest' }}
-        run: brew install gdal
-
       # https://github.com/r-lib/actions/tree/v2/setup-pandoc
       - uses: r-lib/actions/setup-pandoc@v2
 

.gitignore

@@ -3,3 +3,4 @@
 .RData
 .DS_Store
 README.html
+CRAN-SUBMISSION

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: coursekata
-Title: Packages and Functions for CourseKata Courses
-Version: 0.13.0
-Date: 2023-10-05
+Title: Packages and Functions for 'CourseKata' Courses
+Version: 0.14.0
+Date: 2023-10-11
 Authors@R: c(
     person("Adam", "Blake", , "[email protected]", role = c("cre", "aut"),
            comment = c(ORCID = "0000-0001-7881-8652")),
@@ -11,32 +11,28 @@ Authors@R: c(
            comment = c(ORCID = "0000-0001-6107-7827"))
   )
 Description: Easily install and load all packages and functions used in
-    CourseKata courses. Aid teaching with helper functions and augment
+    'CourseKata' courses. Aid teaching with helper functions and augment
     generic functions to provide cohesion between the network of packages.
-    Learn more about CourseKata at <https://www.coursekata.org>.
+    Learn more about 'CourseKata' at <https://coursekata.org>.
 License: AGPL (>= 3)
-URL: https://www.github.com/UCLTALL/coursekata-r
-BugReports: https://www.github.com/UCLTALL/coursekata-r/issues
+URL: https://github.com/coursekata/coursekata-r
+BugReports: https://github.com/coursekata/coursekata-r/issues
 Depends:
     R (>= 3.6)
 Imports:
     cli (>= 3.2.0),
-    crayon (>= 1.5.0),
     dslabs (>= 0.7.4),
     ggformula (>= 0.10.1),
     ggplot2 (>= 3.3.5),
     glue (>= 1.6.2),
-    lifecycle (>= 1.0.1),
     Lock5withR (>= 1.2.2),
     lsr (>= 0.5.2),
-    magrittr (>= 2.0.2),
     Metrics,
     mosaic (>= 1.8.3),
     pak,
     palmerpenguins,
     purrr (>= 0.3.4),
     rlang (>= 1.0.2),
-    rstudioapi (>= 0.13),
     supernova (>= 2.5.1),
     vctrs (>= 0.4.1),
     viridisLite,
@@ -48,7 +44,6 @@ Suggests:
     mockr (>= 0.1),
     readr (>= 2.1.2),
     readxl (>= 1.4.0),
-    rgdal,
     usethis (>= 2.1.6),
     simstudy (>= 0.5.0),
     testthat (>= 3.1.2),

NAMESPACE

@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%>%")
 export(PRE)
 export(b)
 export(b0)
@@ -19,7 +18,6 @@ export(fVal)
 export(fit_stats)
 export(fitstats)
 export(gf_model)
-export(gf_model_old)
 export(lower)
 export(middle)
 export(p)
@@ -34,9 +32,7 @@ importFrom(Lock5withR,locket)
 importFrom(Metrics,sse)
 importFrom(dslabs,take_poll)
 importFrom(glue,glue)
-importFrom(lifecycle,deprecated)
 importFrom(lsr,cohensD)
-importFrom(magrittr,"%>%")
 importFrom(mosaic,qdist)
 importFrom(palmerpenguins,path_to_file)
 importFrom(stats,lm)

NEWS.md

@@ -1,5 +1,17 @@
 # `coursekata` change log
 
+## coursekata 0.14.0
+
+- Remove deprecated `gf_model_old()` function
+
+## coursekata 0.13.1
+
+- Fix issue where startup message was not being displayed
+- Make dependent startup package messages visible by default
+- Add `coursekata.quiet` option to suppress startup messages
+- Document `coursekata.quickstart` and `coursekata.quiet` options in README
+- Trim unused packages in preparation for CRAN submission
+
 ## coursekata 0.13.0
 
 - Add `coursekata.quickstart` option, which can reduce load times significantly.
@@ -18,7 +30,7 @@
 
 ## coursekata 0.10.0
 
-- Add [`Metrics` package](https://cran.r-project.org/web/packages/Metrics/index.html)
+- Add [`Metrics` package](https://CRAN.R-project.org/package=Metrics)
 - Remove `zargle`
 
 ## coursekata 0.9.4

R/coursekata-package.R

@@ -4,7 +4,6 @@
 ## usethis namespace: start
 #' @import rlang
 #' @importFrom glue glue
-#' @importFrom lifecycle deprecated
 ## usethis namespace: end
 NULL
 

R/coursekata_attach.R

@@ -1,35 +1,37 @@
 #' Attach the CourseKata course packages
+#'
+#' @param quietly Whether to suppress messages.
+#'
 #' @return A named logical vector indicating which packages were attached.
+#'
 #' @export
 #' @examples
 #' coursekata_attach()
-coursekata_attach <- function() {
+coursekata_attach <- function(quietly = FALSE) {
   to_attach <- coursekata_detached()
-  invisible(suppressPackageStartupMessages(pkg_require(to_attach)))
+  invisible(pkg_require(to_attach, quietly = quietly))
 }
 
 
 #' Information about CourseKata packages.
+#'
 #' @param pkgs A character vector of packages being loaded.
+#'
 #' @return A coursekata_attachments object, also of class data.frame with a row for each course
 #'   package and a column for each of the `package` name, `version`, and whether it is currently
 #'   `attached`.
-#' @keywords internal
+#'
+#' @noRd
 coursekata_attach_message <- function(pkgs) {
   if (length(pkgs) == 0) return(NULL)
 
-  is_dark_theme <- rstudioapi::isAvailable() &&
-    rstudioapi::hasFun("getThemeInfo") &&
-    rstudioapi::getThemeInfo()$dark
-  theme <- themes[[if (is_dark_theme) "dark" else "light"]]
-
   info <- coursekata_packages()
   version <- ifelse(is.na(info$version), "", info$version)
-  pkgs <- theme$pkg(paste(
-    ifelse(info$attached, theme$good(cli::symbol$tick), theme$bad("x")),
-    theme$text(format(info$package)),
+  pkgs <- paste(
+    ifelse(info$attached, cli::col_green(cli::symbol$tick), cli::col_red("x")),
+    cli::col_green(format(info$package)),
     cli::ansi_align(version, max(cli::ansi_nchar(version)))
-  ))
+  )
 
   paste(
     cli::rule(
@@ -40,19 +42,3 @@ coursekata_attach_message <- function(pkgs) {
     sep = "\n"
   )
 }
-
-
-themes <- list(
-  light = list(
-    text = cli::col_black,
-    pkg = cli::col_blue,
-    good = cli::col_green,
-    bad = cli::col_red
-  ),
-  dark = list(
-    text = cli::col_white,
-    pkg = cli::col_br_blue,
-    good = cli::col_br_green,
-    bad = cli::col_br_red
-  )
-)

R/coursekata_install.R

@@ -1,5 +1,7 @@
 #' Install or update all CourseKata packages.
+#'
 #' @param ... Arguments passed on to [`pak::pkg_install`].
+#'
 #' @return The state of all the packages after any updates have been performed.
 #'
 #' @export

R/coursekata_packages.R

@@ -12,8 +12,8 @@ coursekata_pkgs <- rev(c(
 #'
 #' @return A data frame with three variables: the name of the package `package`, the `version`, and
 #'   whether it is currently `attached`.
-#' @export
 #'
+#' @export
 #' @examples
 #' coursekata_packages()
 coursekata_packages <- function(check_remote_version = FALSE) {
@@ -37,16 +37,20 @@ coursekata_packages <- function(check_remote_version = FALSE) {
 
 
 #' List all currently attached CourseKata course packages
+#'
 #' @return A character vector of the course packages that have been attached.
-#' @keywords internal
+#'
+#' @noRd
 coursekata_attached <- function() {
   coursekata_pkgs[pkg_is_attached(coursekata_pkgs)]
 }
 
 
 #' List all currently NOT attached CourseKata course packages
+#'
 #' @return A character vector of the course packages that are not attached.
-#' @keywords internal
+#'
+#' @noRd
 coursekata_detached <- function() {
   coursekata_pkgs[!pkg_is_attached(coursekata_pkgs)]
 }

R/coursekata_repos.R

@@ -3,12 +3,11 @@
 #' Ensures a default CRAN is set if one is not already set, and adds the repository for
 #' fivethirtyeightdata.
 #'
-#' @param repos Optionally set a repository character vector to augment. If one of the values is not
-#'   named CRAN, the RStudio CRAN server will be added.
+#' @param repos Optionally set a repository character vector to augment.
 #'
 #' @return A set of repositories that can be used to install or update the CourseKata packages.
-#' @export
 #'
+#' @export
 #' @examples
 #' coursekata_repos()
 coursekata_repos <- function(repos = getOption("repos")) {

R/data.R

@@ -21,7 +21,7 @@
 #' @references
 #' De Cock, Dean, (2011). Ames, Iowa: Alternative to the Boston Housing Data as an end of semester
 #' regression project, *Journal of Statistics Education, 19*(3).
-#' <https://dx.doi.org/10.1080/10691898.2011.11889627>
+#' \doi{10.1080/10691898.2011.11889627}
 #'
 #' @format A data frame with 2930 observations on the following 80 variables:
 #' \describe{
@@ -117,7 +117,7 @@
 #' @references
 #' Kline, J. A., Fisher, M. A., Pettit, K. L., Linville, C. T., & Beck, A. M. (2019). Controlled
 #' clinical trial of canine therapy versus usual care to reduce patient anxiety in the emergency
-#' department. *PloS One, 14*(1), e0209232. <https://doi.org/10.1371/journal.pone.0209232>
+#' department. *PloS One, 14*(1), e0209232. \doi{10.1371/journal.pone.0209232}
 #'
 #' @format A data frame with 84 observations on the following 53 variables:
 #' \describe{

R/distribution_parts.R

@@ -16,7 +16,6 @@
 #'
 #' @rdname distribution_parts
 #' @export
-#'
 #' @examples
 #'
 #' upper(1:10, .1)
@@ -66,6 +65,15 @@ upper <- function(x, prop = .025, greedy = TRUE) {
   values[order(values$original_pos), "in_zone", drop = TRUE]
 }
 
+#' Calculate the number of values in the tail of a distribution
+#'
+#' @param x The distribution of values to check.
+#' @param prop The proportion of values to find.
+#' @param greedy Whether the function should be greedy, as per the description above.
+#'
+#' @return The number of values in the tail of the distribution.
+#'
+#' @noRd
 tail_size <- function(x, prop, greedy) {
   na_rm <- stats::na.omit(x)
   tail_unbiased <- length(na_rm) * prop

R/estimate_extraction.R

@@ -104,19 +104,25 @@ p <- function(object, data = NULL, all = FALSE, predictor = character(), type =
 }
 
 #' Convert a potentially complex predictor to a character vector of terms.
+#'
 #' @param predictor The predictor(s) to return estimates for.
+#'
 #' @return A character vector of terms.
-#' @keywords internal
+#'
+#' @noRd
 convert_predictor <- function(predictor) {
   purrr::map_if(c(predictor), is_formula, ~ deparse(f_rhs(.x))) %>%
     purrr::flatten_chr()
 }
 
 #' Convert a formula and data to an [`lm`] object.
+#'
 #' @param object A [`lm`] object, or [`formula`].
 #' @param data If `object` is a formula, the data to fit the formula to as a [`data.frame`].
+#'
 #' @return An [`lm`] object.
-#' @keywords internal
+#'
+#' @noRd
 convert_lm <- function(object, data) {
   if ("lm" %in% class(object) == FALSE) {
     data_call <- rlang::enquo(data)
@@ -131,19 +137,27 @@ convert_lm <- function(object, data) {
 }
 
 #' Assert that the arguments to the estimate extraction functions are valid.
+#'
 #' @param all Whether to return all the estimates (e.g. all *F*-values).
 #' @param predictor The predictor(s) to return estimates for.
 #' @param type The type (1, 2, 3) of sums of squares to use.
-#' @keywords internal
+#'
+#' @return Nothing, but throws an error if the arguments are invalid.
+#'
+#' @noRd
 check_extract_args <- function(all, predictor, type = 3) {
   vctrs::vec_assert(all, logical(), 1)
   vctrs::vec_assert(predictor, character())
   vctrs::vec_assert(type, numeric(), 1)
 }
 
 #' Determine if the fitted model is the empty/null model.
+#'
 #' @param fit A fitted linear model to pass to supernova.
-#' @keywords internal
+#'
+#' @return Nothing, but throws an error if the model is empty.
+#'
+#' @noRd
 check_empty_model <- function(fit) {
   models <- supernova::generate_models(fit)
   if (length(models) == 0) {
@@ -152,11 +166,15 @@ check_empty_model <- function(fit) {
 }
 
 #' Extract a statistic from a supernova table and name the values
+#'
 #' @param fit A fitted linear model to pass to supernova.
 #' @param type The type (1, 2, 3) of sums of squares to use.
 #' @param stat The statistic from the supernova (as named in the `supernova(...)$tbl`).
 #' @param predictor Optionally specify which terms to return (instead of all of them).
-#' @keywords internal
+#'
+#' @return A named list (one for each term, where term is the name) of the values of the statistic.
+#'
+#' @noRd
 extract_stat <- function(fit, type, stat, predictor = character(0)) {
   sup_out <- supernova(fit, type)
   vals <- sup_out$tbl[[stat]]