CRAN submission RC 0.13.1 (#593)

* CRAN submission RC 0.13.1 * lintr * revdep-results * bump datawizard as well * skip on lin/mac, increase tolerance * update wordlist * bump see * add tolerance for emmGrid tests * check for internet access cf. easystats/easystats#362 * Remove unnecessary re-export easystats/easystats#292 * format_error * fix lintr * renamed * rename back, dev version now * skip on cran * run tests in parallel * shorten example to avoid yet another note * Update bayesfactor_restricted.Rd --------- Co-authored-by: Indrajeet Patil <[email protected]> Co-authored-by: Dominique Makowski <[email protected]>
easystats · Apr 7, 2023 · 035da1e · 035da1e
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diff --git a/.lintr b/.lintr
@@ -12,7 +12,7 @@ linters: linters_with_defaults(
     object_usage_linter = NULL,
     todo_comment_linter = NULL,
     undesirable_function_linter(c("mapply" = NA, "sapply" = NA, "setwd" = NA)),
-    undesirable_operator_linter = NULL,
     unnecessary_concatenation_linter(allow_single_expression = FALSE),
+    undesirable_operator_linter = NULL,
     defaults = linters_with_tags(tags = NULL)
   )
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: bayestestR
 Title: Understand and Describe Bayesian Models and Posterior Distributions
-Version: 0.13.0.10
+Version: 0.13.1
 Authors@R:
     c(person(given = "Dominique",
              family = "Makowski",
@@ -67,7 +67,7 @@ Depends:
     R (>= 3.6)
 Imports:
     insight (>= 0.19.1),
-    datawizard (>= 0.6.5),
+    datawizard (>= 0.7.0),
     graphics,
     methods,
     stats,
@@ -80,6 +80,7 @@ Suggests:
     blavaan,
     bridgesampling,
     brms,
+    curl,
     effectsize,
     emmeans,
     gamm4,
@@ -105,7 +106,7 @@ Suggests:
     rmarkdown,
     rstan,
     rstanarm,
-    see (>= 0.7.4),
+    see (>= 0.7.5),
     testthat,
     tweedie
 License: GPL-3
@@ -118,6 +119,8 @@ Language: en-US
 RoxygenNote: 7.2.3.9000
 Roxygen: list(markdown = TRUE)
 Config/testthat/edition: 3
+Config/testthat/parallel: true
+Config/rcmdcheck/ignore-inconsequential-notes: true
 Config/Needs/website:
     rstudio/bslib,
     r-lib/pkgdown,

diff --git a/NAMESPACE b/NAMESPACE
@@ -622,7 +622,6 @@ export(pd_to_p)
 export(point_estimate)
 export(print_html)
 export(print_md)
-export(reshape_ci)
 export(reshape_draws)
 export(reshape_iterations)
 export(rnorm_perfect)
@@ -640,6 +639,5 @@ export(simulate_ttest)
 export(spi)
 export(unupdate)
 export(weighted_posteriors)
-importFrom(datawizard,reshape_ci)
 importFrom(insight,print_html)
 importFrom(insight,print_md)
diff --git a/R/bayesfactor_restricted.R b/R/bayesfactor_restricted.R
@@ -33,15 +33,15 @@
 #' set.seed(444)
 #' library(bayestestR)
 #' prior <- data.frame(
-#'   A = rnorm(1000),
-#'   B = rnorm(1000),
-#'   C = rnorm(1000)
+#'   A = rnorm(500),
+#'   B = rnorm(500),
+#'   C = rnorm(500)
 #' )
 #'
 #' posterior <- data.frame(
-#'   A = rnorm(1000, .4, 0.7),
-#'   B = rnorm(1000, -.2, 0.4),
-#'   C = rnorm(1000, 0, 0.5)
+#'   A = rnorm(500, .4, 0.7),
+#'   B = rnorm(500, -.2, 0.4),
+#'   C = rnorm(500, 0, 0.5)
 #' )
 #'
 #' hyps <- c(

diff --git a/R/mediation.R b/R/mediation.R
@@ -345,7 +345,7 @@ print.bayestestR_mediation <- function(x, digits = 3, ...) {
   cat(insight::export_table(x, digits = digits))
   cat("\n")
 
-  prop_mediated[] <- lapply(prop_mediated, function(i) insight::format_value(i, as_percent = TRUE))
+  prop_mediated[] <- lapply(prop_mediated, insight::format_value, as_percent = TRUE)
   insight::print_color(
     sprintf(
       "Proportion mediated: %s [%s, %s]\n",

diff --git a/R/p_to_bf.R b/R/p_to_bf.R
@@ -60,11 +60,11 @@ p_to_bf.numeric <- function(x, log = FALSE, n_obs = NULL, ...) {
   p <- x
   # Validate n_obs
   if (is.null(n_obs)) {
-    stop("Argument `n_obs` must be specified.", call. = FALSE)
+    insight::format_error("Argument `n_obs` must be specified.")
   } else if (length(n_obs) == 1L) {
     n_obs <- rep(n_obs, times = length(p))
   } else if (length(n_obs) != length(p)) {
-    stop("`n_obs` must be of length 1 or same length as `p`.", call. = FALSE)
+    insight::format_error("`n_obs` must be of length 1 or same length as `p`.")
   }
 
   # Convert
@@ -112,7 +112,7 @@ p_to_bf.default <- function(x, log = FALSE, ...) {
       n_obs <- list(...)$n_obs
     }
   } else {
-    stop("Argument `x` must be a model object, or a numeric vector of p-values.", call. = FALSE)
+    insight::format_error("Argument `x` must be a model object, or a numeric vector of p-values.")
   }
 
   out <- p_to_bf(p, n_obs = n_obs, log = log)

diff --git a/R/reexports.R b/R/reexports.R
diff --git a/README.Rmd b/README.Rmd
@@ -145,7 +145,8 @@ describe_posterior(
   centrality = "all"
 )
 ```
-```{r message=FALSE, warning=FALSE,echo=FALSE}
+
+```{r message=FALSE, warning=FALSE, echo=FALSE, eval=curl::has_internet()}
 model <- insight::download_model("brms_zi_3")
 describe_posterior(
   model,
@@ -158,10 +159,7 @@ describe_posterior(
 ```
 
 
-*bayestestR* also includes [**many other features**](https://easystats.github.io/bayestestR/reference/index.html) useful for your Bayesian analsyes. Here are some more examples:
-
-
-
+*bayestestR* also includes [**many other features**](https://easystats.github.io/bayestestR/reference/index.html) useful for your Bayesian analyses. Here are some more examples:
 
 ## Point-estimates
 

diff --git a/README.md b/README.md
@@ -159,9 +159,9 @@ describe_posterior(
 )
 ## Summary of Posterior Distribution
 ## 
-## Parameter |    Median |        95% CI |     pd |   ps
-## -----------------------------------------------------
-## Posterior | -8.68e-03 | [-1.96, 1.92] | 50.35% | 0.46
+## Parameter | Median |        95% CI |     pd |   ps
+## --------------------------------------------------
+## Posterior |   0.01 | [-1.97, 1.99] | 50.58% | 0.47
 ```
 
 `describe_posterior()` works for many objects, including more complex
@@ -239,7 +239,7 @@ describe_posterior(
 
 *bayestestR* also includes [**many other
 features**](https://easystats.github.io/bayestestR/reference/index.html)
-useful for your Bayesian analsyes. Here are some more examples:
+useful for your Bayesian analyses. Here are some more examples:
 
 ## Point-estimates
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,20 +1,13 @@
-## Test environments
-
-* local Windows install, R 4.1.2
-
-* ubuntu 18.04 (on gitub-actions-ci), R 4.1.2
-
-* win-builder (devel and release)
-
-## R CMD check results
-
-0 errors | 0 warnings | 0 note
-
-
 ## revdepcheck results
 
-We checked 18 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 22 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
- * We failed to check 0 packages
+ * We failed to check 1 packages
+
+Issues with CRAN packages are summarised below.
+
+### Failed to check
 
+* snSMART (NA)
+  Reason: JAGS was not installed.
diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -58,6 +58,7 @@ Littman
 Liu
 Lodewyckx
 Ly
+Makowski
 MCMCglmm
 MCSE
 MPE

diff --git a/man/bayesfactor_restricted.Rd b/man/bayesfactor_restricted.Rd
diff --git a/man/reexports.Rd b/man/reexports.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,26 +1,32 @@
 # Platform
 
-|field    |value                                      |
-|:--------|:------------------------------------------|
-|version  |R version 4.1.1 (2021-08-10)               |
-|os       |Windows 10 x64 (build 19043)               |
-|system   |x86_64, mingw32                            |
-|ui       |RStudio                                    |
-|language |(EN)                                       |
-|collate  |English_United Kingdom.1252                |
-|ctype    |English_United Kingdom.1252                |
-|tz       |Europe/Berlin                              |
-|date     |2021-10-29                                 |
-|rstudio  |1.4.1717 Juliet Rose (desktop)             |
-|pandoc   |2.15 @ C:/PROGRA~1/Pandoc/ (via rmarkdown) |
+|field    |value                                    |
+|:--------|:----------------------------------------|
+|version  |R version 4.2.3 (2023-03-15 ucrt)        |
+|os       |Windows 10 x64 (build 19045)             |
+|system   |x86_64, mingw32                          |
+|ui       |RStudio                                  |
+|language |(EN)                                     |
+|collate  |German_Germany.utf8                      |
+|ctype    |German_Germany.utf8                      |
+|tz       |Europe/Berlin                            |
+|date     |2023-03-21                               |
+|rstudio  |2022.12.0+353 Elsbeth Geranium (desktop) |
+|pandoc   |NA                                       |
 
 # Dependencies
 
-|package    |old    |new    |<U+0394>  |
+|package    |old    |new    |Δ  |
 |:----------|:------|:------|:--|
-|bayestestR |0.11.0 |0.11.5 |*  |
-|datawizard |0.2.1  |0.2.1  |   |
-|insight    |0.14.5 |0.14.5 |   |
+|bayestestR |0.13.0 |0.13.1 |*  |
+|datawizard |0.6.5  |0.6.5  |   |
+|insight    |0.19.1 |0.19.1 |   |
 
 # Revdeps
 
+## Failed to check (1)
+
+|package |version |error |warning |note |
+|:-------|:-------|:-----|:-------|:----|
+|snSMART |0.2.2   |1     |        |     |
+
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,7 +1,12 @@
 ## revdepcheck results
 
-We checked 18 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 22 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
- * We failed to check 0 packages
+ * We failed to check 1 packages
 
+Issues with CRAN packages are summarised below.
+
+### Failed to check
+
+* snSMART (NA)
diff --git a/revdep/data.sqlite b/revdep/data.sqlite
diff --git a/revdep/failures.md b/revdep/failures.md
@@ -1 +1,70 @@
-*Wow, no problems at all. :)*
+# snSMART
+
+<details>
+
+* Version: 0.2.2
+* GitHub: https://github.com/sidiwang/snSMART
+* Source code: https://github.com/cran/snSMART
+* Date/Publication: 2022-11-16 15:00:11 UTC
+* Number of recursive dependencies: 55
+
+Run `revdep_details(, "snSMART")` for more info
+
+</details>
+
+## In both
+
+*   checking whether package 'snSMART' can be installed ... ERROR
+    ```
+    Installation failed.
+    See 'D:/mail/Documents/Coding/R/easystats/bayestestR/revdep/checks/snSMART/new/snSMART.Rcheck/00install.out' for details.
+    ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package 'snSMART' ...
+** package 'snSMART' successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+*** moving datasets to lazyload DB
+** byte-compile and prepare package for lazy loading
+Error: .onLoad failed in loadNamespace() for 'rjags', details:
+  call: fun(libname, pkgname)
+  error: Failed to locate any version of JAGS version 4
+
+The rjags package is just an interface to the JAGS library
+Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
+http://www.sourceforge.net/projects/mcmc-jags/files
+Execution halted
+ERROR: lazy loading failed for package 'snSMART'
+* removing 'D:/mail/Documents/Coding/R/easystats/bayestestR/revdep/checks/snSMART/new/snSMART.Rcheck/snSMART'
+
+
+```
+### CRAN
+
+```
+* installing *source* package 'snSMART' ...
+** package 'snSMART' successfully unpacked and MD5 sums checked
+** using staged installation
+** R
+** data
+*** moving datasets to lazyload DB
+** byte-compile and prepare package for lazy loading
+Error: .onLoad failed in loadNamespace() for 'rjags', details:
+  call: fun(libname, pkgname)
+  error: Failed to locate any version of JAGS version 4
+
+The rjags package is just an interface to the JAGS library
+Make sure you have installed JAGS-4.x.y.exe (for any x >=0, y>=0) from
+http://www.sourceforge.net/projects/mcmc-jags/files
+Execution halted
+ERROR: lazy loading failed for package 'snSMART'
+* removing 'D:/mail/Documents/Coding/R/easystats/bayestestR/revdep/checks/snSMART/old/snSMART.Rcheck/snSMART'
+
+
+```