deprecate tidy_stan

.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")'

NEWS.md

@@ -1,3 +1,7 @@
+# rdss 1.0.14
+
+* deprecates tidy_stan in favor of new broom.mixed::tidy function
+
 # rdss 1.0.12
 
 * address bugs with future package

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
 }