Merge bd1f9ad into 0e7f772

.github/workflows/check-full.yaml

@@ -1,9 +1,11 @@
 on:
   push:
     branches:
+      - main
       - master
   pull_request:
     branches:
+      - main
       - master
 
 name: R-CMD-check
@@ -30,53 +32,68 @@ jobs:
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
-      CRAN: ${{ matrix.config.cran }}
+      RSPM: ${{ matrix.config.rspm }}
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
       - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-r@master
         with:
           r-version: ${{ matrix.config.r }}
+          http-user-agent: ${{ matrix.config.http-user-agent }}
 
       - uses: r-lib/actions/setup-pandoc@master
 
       - name: Query dependencies
         run: |
           install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), "depends.Rds", version = 2)
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
         shell: Rscript {0}
 
       - name: Cache R packages
         if: runner.os != 'Windows'
-        uses: actions/cache@v1
+        uses: actions/cache@v2
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-${{ hashFiles('depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-
+          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-
 
       - name: Install system dependencies
         if: runner.os == 'Linux'
-        env:
-          RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
         run: |
-          Rscript -e "remotes::install_github('r-hub/sysreqs')"
-          sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
-          sudo -s eval "$sysreqs"
-
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "16.04"))')
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("rcmdcheck")
         shell: Rscript {0}
 
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
       - name: Check
-        run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
 
+      - name: Show testthat output
+        if: always()
+        run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@main
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/check-release.yaml

@@ -1,4 +1,12 @@
-on: [push, pull_request]
+on:
+  push:
+    branches:
+      - main
+      - master
+  pull_request:
+    branches:
+      - main
+      - master
 
 name: R-CMD-check
 

API

@@ -6,7 +6,8 @@ bf_contingency_tab(data, x, y = NULL, counts = NULL, ratio = NULL, sampling.plan
 bf_corr_test(data, x, y, bf.prior = 0.707, top.text = NULL, output = "dataframe", k = 2L, ...)
 bf_expr(bf.object, k = 2L, conf.level = 0.95, conf.method = "hdi", centrality = "median", top.text = NULL, anova.design = FALSE, ...)
 bf_extractor(bf.object, ...)
-bf_meta(data, d = prior("norm", c(mean = 0, sd = 0.3)), tau = prior("invgamma", c(shape = 1, scale = 0.15)), k = 2L, output = "dataframe", top.text = NULL, ...)
+bf_meta(data, d = prior("norm", c(mean = 0, sd = 0.3)), tau = prior("invgamma", c(shape = 1, scale = 0.15)), k = 2L, conf.level = 0.95, output = "dataframe", top.text = NULL, ...)
+bf_meta_random(data, d = prior("norm", c(mean = 0, sd = 0.3)), tau = prior("invgamma", c(shape = 1, scale = 0.15)), k = 2L, conf.level = 0.95, output = "dataframe", top.text = NULL, ...)
 bf_oneway_anova(data, x, y, subject.id = NULL, bf.prior = 0.707, top.text = NULL, output = "dataframe", paired = FALSE, k = 2L, ...)
 bf_ttest(data, x, y = NULL, subject.id = NULL, test.value = 0, paired = FALSE, bf.prior = 0.707, top.text = NULL, output = "dataframe", k = 2L, ...)
 meta_data_check(data)

DESCRIPTION

@@ -22,7 +22,11 @@ URL: https://indrajeetpatil.github.io/tidyBF/,
 BugReports: https://github.com/IndrajeetPatil/tidyBF/issues
 Remotes:  
     easystats/insight,
-    IndrajeetPatil/ipmisc
+    easystats/bayestestR,
+    easystats/parameters,
+    easystats/performance,
+    IndrajeetPatil/ipmisc,
+    richarddmorey/BayesFactor/pkg/BayesFactor
 Encoding: UTF-8
 Language: en-US
 LazyData: true
@@ -32,12 +36,15 @@ RoxygenNote: 7.1.1
 Depends: 
     R (>= 3.6.0)
 Imports: 
-    BayesFactor,
+    BayesFactor (>= 0.9.12-4.3),
+    bayestestR (>= 0.7.5),
     dplyr,
-    insight (>= 0.9.6.1),
+    insight (>= 0.10.1),
     ipmisc (>= 4.1.0),
+    lme4,
     metaBMA,
-    parameters,
+    parameters (>= 0.8.6.1),
+    performance (>= 0.5.0),
     rlang,
     tidyr
 Suggests: 

NAMESPACE

@@ -13,6 +13,7 @@ export(bf_corr_test)
 export(bf_expr)
 export(bf_extractor)
 export(bf_meta)
+export(bf_meta_random)
 export(bf_oneway_anova)
 export(bf_ttest)
 export(meta_data_check)
@@ -21,15 +22,16 @@ export(tibble)
 importFrom(BayesFactor,anovaBF)
 importFrom(BayesFactor,contingencyTableBF)
 importFrom(BayesFactor,correlationBF)
-importFrom(BayesFactor,extractBF)
 importFrom(BayesFactor,logMeanExpLogs)
 importFrom(BayesFactor,ttestBF)
+importFrom(bayestestR,describe_prior)
+importFrom(dplyr,bind_cols)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
-importFrom(dplyr,recode)
 importFrom(dplyr,rename)
-importFrom(dplyr,rename_all)
+importFrom(dplyr,rename_with)
 importFrom(dplyr,select)
+importFrom(dplyr,starts_with)
 importFrom(dplyr,tibble)
 importFrom(insight,standardize_names)
 importFrom(ipmisc,"%$%")
@@ -42,9 +44,12 @@ importFrom(ipmisc,long_to_wide_converter)
 importFrom(ipmisc,red)
 importFrom(ipmisc,specify_decimal_p)
 importFrom(ipmisc,tibble)
+importFrom(lme4,findbars)
+importFrom(lme4,nobars)
 importFrom(metaBMA,meta_random)
 importFrom(metaBMA,prior)
 importFrom(parameters,model_parameters)
+importFrom(performance,r2_bayes)
 importFrom(rlang,"%|%")
 importFrom(rlang,"%||%")
 importFrom(rlang,":=")

NEWS.md

@@ -25,10 +25,16 @@ BREAKING CHANGES
 
   - The *t*-test and ANOVA tests get `subject.id` argument relevant for repeated
     measures design.
+
+  - Renames `bf_meta` to `bf_meta_random`. The previous alias is retained for
+    now but will be retired in future releases. 
 
 MAJOR CHANGES
 
   - Replaces the heavier `broomExtra` dependency with `parameters`.
+
+  - `bf_oneway_anova` now returns model-averaged R-squared posterior as a
+    measure of effect size.
 
 # tidyBF 0.3.0
 

R/bf_contingency_tab.R

@@ -205,10 +205,10 @@ bf_contingency_tab <- function(data,
   # the final expression
   if (is.null(top.text)) bf01_expr <- bf01_expr$expr
 
-  # return the text results or the dataframe with results
+  # return the expression or the dataframe
   switch(
     EXPR = output,
-    "dataframe" = dplyr::select(df, -dplyr::matches("error|time|code")),
+    "dataframe" = df,
     bf01_expr
   )
 }

R/bf_meta.R → R/bf_meta_random.R

@@ -1,5 +1,5 @@
 #' @title Bayes factor for random-effects meta-analysis
-#' @name bf_meta
+#' @name bf_meta_random
 #'
 #' @importFrom metaBMA meta_random prior
 #'
@@ -10,7 +10,7 @@
 #' @inheritParams bf_expr
 #' @inheritParams bf_ttest
 #' @inheritParams metaBMA::meta_random
-#' @inheritDotParams metaBMA::meta_random -y -SE
+#' @inheritDotParams metaBMA::meta_random -y -SE -ci
 #'
 #' @examples
 #'
@@ -44,7 +44,7 @@
 #'   ))
 #'
 #' # to get dataframe
-#' bf_meta(
+#' bf_meta_random(
 #'   data = df,
 #'   k = 3,
 #'   iter = 1500,
@@ -57,13 +57,14 @@
 #' @export
 
 # function body
-bf_meta <- function(data,
-                    d = prior("norm", c(mean = 0, sd = 0.3)),
-                    tau = prior("invgamma", c(shape = 1, scale = 0.15)),
-                    k = 2L,
-                    output = "dataframe",
-                    top.text = NULL,
-                    ...) {
+bf_meta_random <- function(data,
+                           d = prior("norm", c(mean = 0, sd = 0.3)),
+                           tau = prior("invgamma", c(shape = 1, scale = 0.15)),
+                           k = 2L,
+                           conf.level = 0.95,
+                           output = "dataframe",
+                           top.text = NULL,
+                           ...) {
 
   # check the data contains needed column
   meta_data_check(data)
@@ -77,6 +78,7 @@ bf_meta <- function(data,
       SE = data$std.error,
       d = d,
       tau = tau,
+      ci = conf.level,
       ...
     )
 
@@ -99,21 +101,27 @@ bf_meta <- function(data,
           ", ",
           widehat(italic(delta))["mean"]^"posterior",
           " = ",
-          d.pmean,
-          ", CI"["95%"],
+          estimate,
+          ", CI"[conf.level]^"HDI",
           " [",
-          d.pmean.LB,
+          estimate.LB,
           ", ",
-          d.pmean.UB,
-          "]"
+          estimate.UB,
+          "]",
+          ", ",
+          italic("r")["Cauchy"]^"JZS",
+          " = ",
+          bf.prior
         )
       ),
       env = list(
         top.text = top.text,
         bf = specify_decimal_p(x = -log(df$bf10[[1]]), k = k),
-        d.pmean = specify_decimal_p(x = df$mean[[1]], k = k),
-        d.pmean.LB = specify_decimal_p(x = df$hpd95_lower[[1]], k = k),
-        d.pmean.UB = specify_decimal_p(x = df$hpd95_upper[[1]], k = k)
+        conf.level = paste0(conf.level * 100, "%"),
+        estimate = specify_decimal_p(x = df$mean[[1]], k = k),
+        estimate.LB = specify_decimal_p(x = df$hpd95_lower[[1]], k = k),
+        estimate.UB = specify_decimal_p(x = df$hpd95_upper[[1]], k = k),
+        bf.prior = specify_decimal_p(x = mod$jzs$rscale_discrete[[1]], k = k)
       )
     )
 
@@ -127,3 +135,11 @@ bf_meta <- function(data,
     bf01_expr
   )
 }
+
+# aliases -----------------------------------------------------------------
+
+#' @rdname bf_meta_random
+#' @aliases bf_meta_random
+#' @export
+
+bf_meta <- bf_meta_random

R/bf_oneway_anova.R

@@ -5,6 +5,7 @@
 #' @importFrom dplyr mutate
 #' @importFrom rlang new_formula enexpr expr
 #' @importFrom ipmisc long_to_wide_converter
+#' @importFrom lme4 nobars findbars
 #'
 #' @param data A dataframe (or a tibble) from which variables specified are to
 #'   be taken. A matrix or tables will **not** be accepted.

R/global_vars.R

@@ -1,7 +1,17 @@
 # defining global variables and functions to appease R CMD Check
 
 utils::globalVariables(
-  names = c(".", "bf10", "rowid"),
+  names = c(
+    ".",
+    "bf10",
+    "rowid",
+    "bf.prior",
+    "component",
+    "estimate",
+    "estimate.LB",
+    "estimate.UB",
+    "term"
+  ),
   package = "tidyBF",
   add = FALSE
 )