Merge pull request #10 from DeclareDesign/internet-on-cran-issue

internet on cran issue

.github/.gitignore

@@ -0,0 +1 @@
+*.html

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

@@ -0,0 +1,52 @@
+# 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:
+  push:
+    branches: [main, master]
+  pull_request:
+
+name: R-CMD-check.yaml
+
+permissions: read-all
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+
+    name: ${{ matrix.config.os }} (${{ matrix.config.r }})
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - {os: macos-latest,   r: 'release'}
+          - {os: windows-latest, r: 'release'}
+          - {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 }}
+      R_KEEP_PKG_SOURCE: yes
+      RGL_USE_NULL: true
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::rcmdcheck
+          needs: check
+
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
-Version: 1.0.12
-Date: 2024-10-07 18:00:19 UTC
-SHA: 1802077891d79bc7df8b64a7d51448970b34ea27
+Version: 1.0.14
+Date: 2025-01-09 03:31:52 UTC
+SHA: a9b8be8e63c000ea11d43be156e4b17770fa9c21

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: rdss
 Title: Companion Datasets and Functions for Research Design in the Social Sciences
-Version: 1.0.12
+Version: 1.0.14
 Authors@R: 
     c(person("Graeme", "Blair", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9164-2102")),
              person("Alexander", "Coppock", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0002-5733-2386")),
              person("Macartan", "Humphreys", email = "[email protected]", role = c("aut"), comment = c(ORCID = "0000-0001-7029-2326")))
 Description: Helper functions to accompany the Blair, Coppock, and Humphreys (2022) "Research Design in the Social Sciences: Declaration, Diagnosis, and Redesign" <https://book.declaredesign.org>. 'rdss' includes datasets, helper functions, and plotting components to enable use and replication of the book. 
-Imports: dplyr, rlang (>= 1.0.0), generics, ggplot2, tibble, tidyr, dataverse, readr, marginaleffects, broom, purrr, estimatr, randomizr
+Imports: dplyr, rlang (>= 1.0.0), generics, ggplot2, tibble, tidyr, dataverse, readr, broom, purrr, estimatr, randomizr
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
@@ -17,6 +17,7 @@ Suggests:
     rdrobust, 
     DIDmultiplegt, 
     broom.mixed, 
+    marginaleffects,
     grf, 
     CausalQueries, 
     metafor, 

NAMESPACE

@@ -53,7 +53,6 @@ importFrom(ggplot2,element_text)
 importFrom(ggplot2,margin)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_minimal)
-importFrom(marginaleffects,predictions)
 importFrom(purrr,as_vector)
 importFrom(purrr,map)
 importFrom(purrr,map_chr)

NEWS.md

@@ -1,3 +1,8 @@
+# rdss 1.0.14
+
+* fixes issue with intermittent test failure
+* deprecates tidy_stan in favor of new broom.mixed::tidy function
+
 # rdss 1.0.12
 
 * address bugs with future package

R/get_replication_file.R

@@ -157,7 +157,7 @@
 #'
 #' @examples
 #'
-#' \donttest{
+#' \dontrun{
 #' # Requires internet access
 #' if(curl::has_internet()) {
 #'   diagnosis_2.1 <- get_rdss_file("diagnosis_2.1")

R/helpers-multilevel-regression-poststratification.R

@@ -13,13 +13,18 @@
 #'
 #' @export
 #'
-#' @importFrom marginaleffects predictions
 #' @importFrom dplyr group_by summarize
 #' @importFrom stats weighted.mean
 #' @importFrom rlang `!!` enquo
 #'
 post_stratification_helper <- function(model_fit, data, group, weights) {
-  predictions(
+
+  if(!requireNamespace("marginaleffects")){
+    message("The post_stratification_helper function requires the 'marginaleffects' package.")
+    return(invisible())
+  }
+
+  marginaleffects::predictions(
     model_fit,
     newdata = data,
     type = "response",

R/helpers-stanreg.R

@@ -2,35 +2,29 @@
 
 #' Tidy results from a stanreg regression and exponentiate the estimated coefficient
 #'
-#' Note no standard errors or other summary statistics are provided
+#' This function is deprecated. Please use the 'tidy' function from the 'broom.mixed' package.
 #'
 #' See https://book.declaredesign.org/choosing-an-answer-strategy.html#bayesian-formalizations
 #'
 #' @param x A stanreg fit from stan_glm
 #' @param conf.int Logical indicating whether or not to include a confidence interval in the tidied output. Defaults to FALSE.
 #' @param conf.level The confidence level to use for the confidence interval if conf.int = TRUE. Must be strictly greater than 0 and less than 1. Defaults to 0.95, which corresponds to a 95 percent confidence interval.
-#' @param exponentiate Logical indicating whether or not to exponentiate the the coefficient estimates. Defaults to FALSE. Note that standard errors are not included when \code{exponentiate = TRUE}.
+#' @param exponentiate Logical indicating whether or not to exponentiate the the coefficient estimates. Defaults to FALSE.
 #' @param ... Other arguments to broom.mixed::tidy
 #'
 #' @return data.frame of results
 #'
 #' @export
 tidy_stan <- function(x, conf.int = FALSE, conf.level = 0.95, exponentiate = FALSE, ...) {
+
+  message("This function is deprecated. Please use the 'tidy' function from the 'broom.mixed' package.")
+
   if(!requireNamespace("broom.mixed")){
-    message("The tidy_exponentiate function requires the 'broom.mixed' package.")
+    message("The tidy_stan function requires the 'broom.mixed' package.")
     return(invisible())
   }
 
-  ret <- broom.mixed::tidy(x, conf.int = conf.int, conf.level = conf.level, ...)
-
-  if (exponentiate) {
-    ret$estimate <- exp(ret$estimate)
-    if("conf.low" %in% colnames(ret)){
-      ret$conf.low <- exp(ret$conf.low)
-      ret$conf.high <- exp(ret$conf.high)
-    }
-    ret$std.error <- NULL
-  }
+  ret <- broom.mixed::tidy(x, conf.int = conf.int, conf.level = conf.level, exponentiate = exponentiate, ...)
 
   ret
 }

cran-comments.md

@@ -1,13 +1,13 @@
 ## Submission
 
-rdss 1.0.10 was archived off CRAN, principally because the `prediction` package was archived. This version switches to the `marginaleffects` package.
+rdss 1.0.12 was archived off CRAN, due to an issue which was intermittent in the Additional_issues on CRAN. This has been fixed. 
 
 ## Test environments
 
 * local OS X install (release)
 * ubuntu on github actions (devel, release, oldrel)
-* windows on github actions (devel, release, oldrel)
-* OS X on Github actions (devel, release, oldrel)
+* windows on github actions (release)
+* OS X on Github actions (release)
 * win-builder (devel, release, oldrel)
 
 ## R CMD check results

rdss.Rproj

@@ -1,8 +1,9 @@
 Version: 1.0
+ProjectId: 7cca6168-e54d-486c-99b7-b0664e7caddd
 
 RestoreWorkspace: No
 SaveWorkspace: No
-AlwaysSaveHistory: Default
+AlwaysSaveHistory: No
 
 EnableCodeIndexing: Yes
 UseSpacesForTab: Yes