cran 0.4.0 submission

IndrajeetPatil · Apr 11, 2020 · 576ae2d · 576ae2d · lintr-bot · Apr 16, 2020
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diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2020-01-29.
-Once it is accepted, delete this file and tag the release (commit de42720a84).
+This package was submitted to CRAN on 2020-04-11.
+Once it is accepted, delete this file and tag the release (commit 1089a38490).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: statsExpressions
 Title: Expressions with Statistical Details
-Version: 0.4.0.9000
+Version: 0.4.0
 Authors@R: 
     person(given = "Indrajeet",
            family = "Patil",
@@ -21,23 +21,22 @@ URL: https://indrajeetpatil.github.io/statsExpressions,
 BugReports: 
     https://github.com/IndrajeetPatil/statsExpressions/issues
 Depends: 
-    R (>= 3.5.0)
+    R (>= 3.6.0)
 Imports:
     boot,
-    broomExtra (>= 2.6.0),
-    correlation (>= 0.1.1),
+    broomExtra (>= 3.0.0),
+    correlation (>= 0.2.0),
     dplyr,
-    effectsize (>= 0.2.9.9),
+    effectsize (>= 0.3.0),
     ez,
-    ipmisc (>= 1.3.0),
+    ipmisc (>= 2.0.0),
     metafor,
     metaplus,
     purrr,
     rcompanion,
     rlang,
     stats,
-    tibble,
-    tidyBF (>= 0.1.0.9000),
+    tidyBF (>= 0.2.0),
     tidyr,
     WRS2
 Suggests:
@@ -48,12 +47,6 @@ Suggests:
     testthat
 VignetteBuilder: 
     knitr
-Remotes:
-    easystats/correlation,
-    easystats/effectsize,
-    IndrajeetPatil/broomExtra,
-    IndrajeetPatil/ipmisc,
-    IndrajeetPatil/tidyBF
 Encoding: UTF-8
 Language: en-US
 LazyData: true

diff --git a/NAMESPACE b/NAMESPACE
@@ -57,7 +57,6 @@ importFrom(dplyr,recode)
 importFrom(dplyr,rename)
 importFrom(dplyr,rename_all)
 importFrom(dplyr,select)
-importFrom(dplyr,tibble)
 importFrom(effectsize,cohens_d)
 importFrom(effectsize,eta_squared)
 importFrom(effectsize,hedges_g)
@@ -110,8 +109,6 @@ importFrom(stats,na.omit)
 importFrom(stats,oneway.test)
 importFrom(stats,t.test)
 importFrom(stats,wilcox.test)
-importFrom(tibble,as_tibble)
-importFrom(tibble,tribble)
 importFrom(tidyBF,bf_contingency_tab)
 importFrom(tidyBF,bf_corr_test)
 importFrom(tidyBF,bf_meta)

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# statsExpressions 0.4.0.9000
+# statsExpressions 0.4.0
 
 BREAKING CHANGES
 
@@ -9,6 +9,8 @@ BREAKING CHANGES
 
 MAJOR CHANGES
 
+  - Minimum R version bumped to `R 3.6.0`.
+
   - Retires the internal `effsize_t_parametric` helper function in favor of
     relying functions from `effectsize`, which is now added as a dependency.
     Similarly, `statsExpressions` now relies on `effectsize` to compute effect

diff --git a/R/helpers_contingency_tabs_expressions.R b/R/helpers_contingency_tabs_expressions.R
@@ -40,7 +40,6 @@
 #'
 #' @importFrom dplyr select mutate rename filter
 #' @importFrom rlang !! enquo as_name ensym exec
-#' @importFrom tibble tribble
 #' @importFrom tidyr uncount drop_na
 #' @importFrom stats mcnemar.test chisq.test
 #' @importFrom rcompanion cramerV cohenG cramerVFit
@@ -109,7 +108,7 @@ expr_contingency_tab <- function(data,
   data %<>%
     dplyr::select(.data = ., {{ x }}, {{ y }}, {{ counts }}) %>%
     tidyr::drop_na(data = .) %>%
-    tibble::as_tibble(x = .)
+    as_tibble(x = .)
 
   # x and y need to be factors; drop the unused levels of the factors
 

diff --git a/R/helpers_effsize_ci.R b/R/helpers_effsize_ci.R
@@ -23,7 +23,6 @@
 #'   `95%` lower and upper confidence intervals (`0.95`).
 #' @param ... Currently ignored.
 #'
-#' @importFrom tibble as_tibble
 #' @importFrom dplyr select contains
 #' @importFrom boot boot
 #' @importFrom rlang !! enquo

diff --git a/R/helpers_meta_analysis_expressions.R b/R/helpers_meta_analysis_expressions.R
@@ -20,7 +20,7 @@
 #' @inheritDotParams metafor::rma -yi -sei -tau2 -level
 #'
 #' @importFrom metafor rma
-#' @importFrom dplyr rename_all recode mutate tibble
+#' @importFrom dplyr rename_all recode mutate
 #' @importFrom tidyBF meta_data_check
 #'
 #' @examples
@@ -92,7 +92,7 @@ expr_meta_parametric <- function(data,
   # create a dataframe with coefficients
   df_tidy <-
     coef(summary(meta_res)) %>%
-    tibble::as_tibble(.) %>%
+    as_tibble(.) %>%
     dplyr::rename_all(
       .tbl = .,
       .funs = dplyr::recode,
@@ -124,7 +124,7 @@ expr_meta_parametric <- function(data,
   df_glance <-
     with(
       data = meta_res,
-      expr = dplyr::tibble(
+      expr = tibble(
         tau2 = tau2,
         se.tau2 = se.tau2,
         k = k,
@@ -248,8 +248,8 @@ expr_meta_robust <- function(data,
   df_tidy <-
     meta_res %>% {
       dplyr::inner_join(
-        x = tibble::as_tibble(as.data.frame(.$results), rownames = "term"),
-        y = tibble::as_tibble(as.data.frame(.$profile@summary@coef), rownames = "term"),
+        x = as_tibble(as.data.frame(.$results), rownames = "term"),
+        y = as_tibble(as.data.frame(.$profile@summary@coef), rownames = "term"),
         by = "term"
       ) %>%
         dplyr::rename_all(.tbl = ., .funs = tolower) %>%

diff --git a/R/helpers_miscellaneous.R b/R/helpers_miscellaneous.R
@@ -273,7 +273,7 @@ rcompanion_cleaner <- function(object) {
   if (inherits(object, "list")) object <- object[[1]]
 
   # rename columns uniformly
-  tibble::as_tibble(object) %>%
+  as_tibble(object) %>%
     dplyr::rename_all(
       .tbl = .,
       .funs = dplyr::recode,

diff --git a/R/helpers_t_test_expressions.R b/R/helpers_t_test_expressions.R
@@ -85,7 +85,7 @@ expr_t_parametric <- function(data,
   data %<>%
     dplyr::select(.data = ., {{ x }}, {{ y }}) %>%
     dplyr::mutate(.data = ., {{ x }} := droplevels(as.factor({{ x }}))) %>%
-    as_tibble(x = .)
+    as_tibble(.)
 
   # properly removing NAs if it's a paired design
   if (isTRUE(paired)) {
@@ -363,7 +363,6 @@ expr_t_nonparametric <- function(data,
 #' @importFrom dplyr select
 #' @importFrom rlang !! enquo
 #' @importFrom WRS2 yuen yuen.effect.ci
-#' @importFrom tibble tribble
 #'
 #' @examples
 #' \donttest{
@@ -422,7 +421,7 @@ expr_t_robust <- function(data,
   data %<>%
     dplyr::select(.data = ., {{ x }}, {{ y }}) %>%
     dplyr::mutate(.data = ., {{ x }} := droplevels(as.factor({{ x }}))) %>%
-    as_tibble(x = .)
+    as_tibble(.)
 
   # ---------------------------- between-subjects design --------------------
 
@@ -446,9 +445,10 @@ expr_t_robust <- function(data,
 
     # effect size dataframe
     effsize_df <-
-      tibble::tribble(
-        ~estimate, ~conf.low, ~conf.high,
-        effsize_obj$effsize[[1]], effsize_obj$CI[[1]], effsize_obj$CI[[2]]
+      tibble(
+        estimate = effsize_obj$effsize[[1]],
+        conf.low = effsize_obj$CI[[1]],
+        conf.high = effsize_obj$CI[[2]]
       )
 
     # Yuen's test for trimmed means
@@ -461,9 +461,10 @@ expr_t_robust <- function(data,
 
     # tidying it up
     stats_df <-
-      tibble::tribble(
-        ~statistic, ~parameter, ~p.value,
-        stats_obj$test[[1]], stats_obj$df[[1]], stats_obj$p.value[[1]]
+      tibble(
+        statistic = stats_obj$test[[1]],
+        parameter = stats_obj$df[[1]],
+        p.value = stats_obj$p.value[[1]]
       )
 
     # subtitle parameters

diff --git a/README.Rmd b/README.Rmd
@@ -25,7 +25,7 @@ Package | Status | Usage | GitHub | References
 ----------------- | ----------------- | ----------------- | ----------------- | -----------------
 [![CRAN_Release_Badge](http://www.r-pkg.org/badges/version-ago/statsExpressions)](https://CRAN.R-project.org/package=statsExpressions) | [![Build Status](https://travis-ci.org/IndrajeetPatil/statsExpressions.svg?branch=master)](https://travis-ci.org/IndrajeetPatil/statsExpressions) | [![Daily downloads badge](https://cranlogs.r-pkg.org/badges/last-day/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions) | [![GitHub version](https://img.shields.io/badge/GitHub-0.4.0.9000-orange.svg?style=flat-square)](https://github.com/IndrajeetPatil/statsExpressions/) | [![Website](https://img.shields.io/badge/website-statsExpressions-orange.svg?colorB=E91E63)](https://indrajeetpatil.github.io/statsExpressions/)
 [![CRAN Checks](https://cranchecks.info/badges/summary/statsExpressions)](https://cran.r-project.org/web/checks/check_results_statsExpressions.html) | [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/IndrajeetPatil/statsExpressions?branch=master&svg=true)](https://ci.appveyor.com/project/IndrajeetPatil/statsExpressions) | [![Weekly downloads badge](https://cranlogs.r-pkg.org/badges/last-week/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions) | [![Forks](https://img.shields.io/badge/forks-`r itdepends:::get_github_info("statsExpressions")$forks[[1]]`-blue.svg)](https://github.com/IndrajeetPatil/statsExpressions/) | [![Features](https://img.shields.io/badge/features-statsExpressions-orange.svg?colorB=2196F3)](https://indrajeetpatil.github.io/statsExpressions/reference/index.html)
-[![minimal R version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg)](https://cran.r-project.org/) | [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/) | [![Monthly downloads badge](https://cranlogs.r-pkg.org/badges/last-month/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions) | [![Github Issues](https://img.shields.io/badge/issues-`r itdepends:::get_github_info("statsExpressions")$open_issues[[1]]`-red.svg)](https://github.com/IndrajeetPatil/statsExpressions/issues) | [![vignettes](https://img.shields.io/badge/vignettes-0.3.1-orange.svg?colorB=FF5722)](https://CRAN.R-project.org/package=statsExpressions/vignettes/)
+[![minimal R version](https://img.shields.io/badge/R%3E%3D-3.6.0-6666ff.svg)](https://cran.r-project.org/) | [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/) | [![Monthly downloads badge](https://cranlogs.r-pkg.org/badges/last-month/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions) | [![Github Issues](https://img.shields.io/badge/issues-`r itdepends:::get_github_info("statsExpressions")$open_issues[[1]]`-red.svg)](https://github.com/IndrajeetPatil/statsExpressions/issues) | [![vignettes](https://img.shields.io/badge/vignettes-0.4.0-orange.svg?colorB=FF5722)](https://CRAN.R-project.org/package=statsExpressions/vignettes/)
 [![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/IndrajeetPatil/statsExpressions.svg)](https://github.com/IndrajeetPatil/statsExpressions) | [![Coverage Status](https://coveralls.io/repos/github/IndrajeetPatil/statsExpressions/badge.svg?branch=master)](https://coveralls.io/github/IndrajeetPatil/statsExpressions?branch=master) | [![Total downloads badge](https://cranlogs.r-pkg.org/badges/grand-total/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions) | [![Github Stars](https://img.shields.io/github/stars/IndrajeetPatil/statsExpressions.svg?style=social&label=Github)](https://github.com/IndrajeetPatil/statsExpressions) | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2074621.svg)](https://doi.org/10.5281/zenodo.3386122)
 [![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html) | [![Codecov test coverage](https://codecov.io/gh/IndrajeetPatil/statsExpressions/branch/master/graph/badge.svg)](https://codecov.io/gh/IndrajeetPatil/statsExpressions?branch=master) | [![Covrpage Summary](https://img.shields.io/badge/covrpage-Last_Build_2020_03_22-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/blob/master/tests/README.md) | [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master) | [![GitHub last commit](https://img.shields.io/github/last-commit/IndrajeetPatil/statsExpressions.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master)
 [![status](https://tinyverse.netlify.com/badge/statsExpressions)](https://CRAN.R-project.org/package=statsExpressions) |  [![R build status](https://github.com/IndrajeetPatil/statsExpressions/workflows/R-CMD-check/badge.svg)](https://github.com/IndrajeetPatil/statsExpressions) | [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/statsExpressions/community) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) | [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/IndrajeetPatil/statsExpressions/issues)

diff --git a/README.md b/README.md
@@ -7,9 +7,9 @@
 | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
 | [![CRAN\_Release\_Badge](http://www.r-pkg.org/badges/version-ago/statsExpressions)](https://CRAN.R-project.org/package=statsExpressions)                                  | [![Build Status](https://travis-ci.org/IndrajeetPatil/statsExpressions.svg?branch=master)](https://travis-ci.org/IndrajeetPatil/statsExpressions)                                                      | [![Daily downloads badge](https://cranlogs.r-pkg.org/badges/last-day/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions)                            | [![GitHub version](https://img.shields.io/badge/GitHub-0.4.0.9000-orange.svg?style=flat-square)](https://github.com/IndrajeetPatil/statsExpressions/)                    | [![Website](https://img.shields.io/badge/website-statsExpressions-orange.svg?colorB=E91E63)](https://indrajeetpatil.github.io/statsExpressions/)                          |
 | [![CRAN Checks](https://cranchecks.info/badges/summary/statsExpressions)](https://cran.r-project.org/web/checks/check_results_statsExpressions.html)                      | [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/IndrajeetPatil/statsExpressions?branch=master&svg=true)](https://ci.appveyor.com/project/IndrajeetPatil/statsExpressions) | [![Weekly downloads badge](https://cranlogs.r-pkg.org/badges/last-week/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions)                          | [![Forks](https://img.shields.io/badge/forks-5-blue.svg)](https://github.com/IndrajeetPatil/statsExpressions/)                                                           | [![Features](https://img.shields.io/badge/features-statsExpressions-orange.svg?colorB=2196F3)](https://indrajeetpatil.github.io/statsExpressions/reference/index.html)    |
-| [![minimal R version](https://img.shields.io/badge/R%3E%3D-3.5.0-6666ff.svg)](https://cran.r-project.org/)                                                                | [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/)                                                                                         | [![Monthly downloads badge](https://cranlogs.r-pkg.org/badges/last-month/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions)                        | [![Github Issues](https://img.shields.io/badge/issues-6-red.svg)](https://github.com/IndrajeetPatil/statsExpressions/issues)                                             | [![vignettes](https://img.shields.io/badge/vignettes-0.3.1-orange.svg?colorB=FF5722)](https://CRAN.R-project.org/package=statsExpressions/vignettes/)                     |
+| [![minimal R version](https://img.shields.io/badge/R%3E%3D-3.6.0-6666ff.svg)](https://cran.r-project.org/)                                                                | [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/)                                                                                         | [![Monthly downloads badge](https://cranlogs.r-pkg.org/badges/last-month/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions)                        | [![Github Issues](https://img.shields.io/badge/issues-6-red.svg)](https://github.com/IndrajeetPatil/statsExpressions/issues)                                             | [![vignettes](https://img.shields.io/badge/vignettes-0.4.0-orange.svg?colorB=FF5722)](https://CRAN.R-project.org/package=statsExpressions/vignettes/)                     |
 | [![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/IndrajeetPatil/statsExpressions.svg)](https://github.com/IndrajeetPatil/statsExpressions) | [![Coverage Status](https://coveralls.io/repos/github/IndrajeetPatil/statsExpressions/badge.svg?branch=master)](https://coveralls.io/github/IndrajeetPatil/statsExpressions?branch=master)             | [![Total downloads badge](https://cranlogs.r-pkg.org/badges/grand-total/statsExpressions?color=blue)](https://CRAN.R-project.org/package=statsExpressions)                         | [![Github Stars](https://img.shields.io/github/stars/IndrajeetPatil/statsExpressions.svg?style=social&label=Github)](https://github.com/IndrajeetPatil/statsExpressions) | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2074621.svg)](https://doi.org/10.5281/zenodo.3386122)                                                                 |
-| [![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)                                                          | [![Codecov test coverage](https://codecov.io/gh/IndrajeetPatil/statsExpressions/branch/master/graph/badge.svg)](https://codecov.io/gh/IndrajeetPatil/statsExpressions?branch=master)                   | [![Covrpage Summary](https://img.shields.io/badge/covrpage-Last_Build_2020_03_22-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/blob/master/tests/README.md) | [![Last-changedate](https://img.shields.io/badge/last%20change-2020--04--08-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master)         | [![GitHub last commit](https://img.shields.io/github/last-commit/IndrajeetPatil/statsExpressions.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master) |
+| [![Licence](https://img.shields.io/badge/licence-GPL--3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0.en.html)                                                          | [![Codecov test coverage](https://codecov.io/gh/IndrajeetPatil/statsExpressions/branch/master/graph/badge.svg)](https://codecov.io/gh/IndrajeetPatil/statsExpressions?branch=master)                   | [![Covrpage Summary](https://img.shields.io/badge/covrpage-Last_Build_2020_03_22-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/blob/master/tests/README.md) | [![Last-changedate](https://img.shields.io/badge/last%20change-2020--04--11-yellowgreen.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master)         | [![GitHub last commit](https://img.shields.io/github/last-commit/IndrajeetPatil/statsExpressions.svg)](https://github.com/IndrajeetPatil/statsExpressions/commits/master) |
 | [![status](https://tinyverse.netlify.com/badge/statsExpressions)](https://CRAN.R-project.org/package=statsExpressions)                                                    | [![R build status](https://github.com/IndrajeetPatil/statsExpressions/workflows/R-CMD-check/badge.svg)](https://github.com/IndrajeetPatil/statsExpressions)                                            | [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/statsExpressions/community)                                                                       | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active)                                                               | [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/IndrajeetPatil/statsExpressions/issues)      |
 
 # Introduction