Merge pull request #58 from poissonconsulting/sensitivity

Add sensitivity functions to produce vector of new pars that vary sd without changing mean

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

@@ -1,9 +1,5 @@
 # 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
-#
-# NOTE: This workflow is overkill for most R packages and
-# check-standard.yaml is likely a better choice.
-# usethis::use_github_action("check-standard") will install it.
 on:
   push:
     branches: [main, master]
@@ -12,9 +8,10 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
-    if: "!contains(github.event.head_commit.message, 'skip ci')"
     runs-on: ${{ matrix.config.os }}
 
     name: ${{ matrix.config.os }} (${{ matrix.config.r }})
@@ -24,23 +21,17 @@ jobs:
       matrix:
         config:
           - {os: macos-latest,   r: 'release'}
-
           - {os: windows-latest, r: 'release'}
-          # use 4.1 to check with rtools40's older compiler
-          - {os: windows-latest, r: '4.1'}
-
-          - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: 'oldrel-2'}
-          - {os: ubuntu-latest,   r: 'oldrel-3'}
+          - {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
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -58,14 +49,4 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
-
-      - name: action-slack
-        if: failure()
-        env:
-          SLACK_WEBHOOK_URL: ${{ secrets.SLACK_WEBHOOK_URL }}
-        uses: 8398a7/action-slack@v3.0.0
-        with:
-          status: ${{ job.status }}
-          author_name: "github action: ${{github.workflow}}"
-          fields: repo, ref, commit, author, message
-
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'

DESCRIPTION

@@ -2,10 +2,10 @@ Package: extras
 Title: Helper Functions for Bayesian Analyses
 Version: 0.6.1.9000
 Authors@R: c(
-    person("Joe", "Thorley", , "joe@poissonconsulting.ca", role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0002-7683-4592")),
-    person("Nicole", "Hill", , "nicole@poissonconsulting.ca", role = "aut",
+    person("Nicole", "Hill", , "nicole@poissonconsulting.ca", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-7623-2153")),
+    person("Joe", "Thorley", , "joe@poissonconsulting.ca", role = "aut",
+           comment = c(ORCID = "0000-0002-7683-4592")),
     person("Kirill", "Müller", role = "ctb",
            comment = c(ORCID = "0000-0002-1416-3412")),
     person("Nadine", "Hussein", role = "ctb",
@@ -22,7 +22,7 @@ URL: https://poissonconsulting.github.io/extras/,
     https://github.com/poissonconsulting/extras
 BugReports: https://github.com/poissonconsulting/extras/issues
 Depends: 
-    R (>= 3.6)
+    R (>= 4.3.0)
 Imports:
     chk,
     lifecycle,
@@ -41,10 +41,11 @@ Suggests:
     testthat (>= 3.0.0),
     tibble,
     tidyr,
-    viridis
+    viridis,
+    withr
 Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr

NAMESPACE

@@ -124,6 +124,17 @@ export(res_pois_zi)
 export(res_skewnorm)
 export(res_student)
 export(rskewnorm)
+export(sens_beta)
+export(sens_exp)
+export(sens_gamma)
+export(sens_gamma_pois)
+export(sens_gamma_pois_zi)
+export(sens_lnorm)
+export(sens_neg_binom)
+export(sens_norm)
+export(sens_pois)
+export(sens_skewnorm)
+export(sens_student)
 export(sextreme)
 export(skewness)
 export(step)

R/dev.R

@@ -20,7 +20,7 @@ dev_beta_binom <- function(x, size = 1, prob = 0.5, theta = 0, res = FALSE) {
   opt_p <- rep(NA, length(x))
   bol <- !is.na(x) & !is.na(size) & !is.na(theta)
   for (i in seq_along(x)) {
-    if (bol[i] & !is.na(bol[i])) {
+    if (bol[i] && !is.na(bol[i])) {
     opt_p[i] <- stats::optimize(opt_beta_binom, interval = c(0, 1), x = x[i],
                                 size = size[i], theta = theta[i], tol = 1e-8)$minimum
     }

R/params.R

@@ -29,5 +29,8 @@
 #' @param lower.tail A flag specifying whether to return the lower or upper tail of the distribution.
 #' @param q A vector of quantiles.
 #' @param p A vector of probabilities.
+#' @param sd_mult A non-negative multiplier on the standard deviation of the distribution.
+#' @param alpha The first shape parameter of the Beta distribution.
+#' @param beta The second shape parameter of the Beta distribution.
 #' @name params
 NULL