version 3.1.1

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: pairwiseComparisons
 Title: Multiple Pairwise Comparison Tests
-Version: 3.1.0
+Version: 3.1.1
 Authors@R: 
     person(given = "Indrajeet",
            family = "Patil",
@@ -21,16 +21,19 @@ URL: https://indrajeetpatil.github.io/pairwiseComparisons/,
         https://github.com/IndrajeetPatil/pairwiseComparisons
 BugReports: https://github.com/IndrajeetPatil/pairwiseComparisons/issues
 Depends: R (>= 3.6.0)
-Imports: BayesFactor, dplyr, insight (>= 0.10.0), ipmisc (>= 4.1.0),
-        PMCMRplus, parameters, purrr, rlang, stats, WRS2
+Imports: BayesFactor, dplyr, ipmisc, parameters (>= 0.10.0), PMCMRplus
+        (>= 1.7.1), purrr, rlang, stats, WRS2
 Suggests: knitr, rmarkdown, spelling, testthat
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 RoxygenNote: 7.1.1
+Config/testthat/edition: 3
+Config/testthat/parallel: true
+Config/testthat/start-first: watcher, parallel*
 NeedsCompilation: no
-Packaged: 2020-10-28 16:01:35 UTC; inp099
+Packaged: 2020-12-03 10:42:57 UTC; inp099
 Author: Indrajeet Patil [cre, aut, cph]
     (<https://orcid.org/0000-0003-1995-6531>, @patilindrajeets)
 Repository: CRAN
-Date/Publication: 2020-10-28 21:40:07 UTC
+Date/Publication: 2020-12-03 13:10:02 UTC

MD5

@@ -1,33 +1,33 @@
-a80b43db255edb9696db72367adc4197 *DESCRIPTION
+b7523a4d56f260682f657b326dee562b *DESCRIPTION
 882a34304fbad2094a2e16309dd9884b *LICENSE
-83dc6a06496388898152343fe7e65b7b *NAMESPACE
-0a64b2368bc4a0104f3b43288c051ec6 *NEWS.md
+d01c3925d5ddad42ca8384af4d952934 *NAMESPACE
+a1163686402776cadcf129db23c6ee3a *NEWS.md
 ed4748c9ff53303f377e6e98edb322c0 *R/data.R
-d2fe0760e69c44e71090edbaae7fd5d8 *R/global_vars.R
-9e94141f213503d677ccd7549dfa3765 *R/helpers.R
-5682b69a42635a23afa66b5114377f40 *R/pairwise_comparisons.R
-8c059bae5d217b3973d025e43b3a9d22 *R/reexports.R
-5bd1bf4c99bd015312e845bd7aa6e638 *README.md
+9a29bbadc219c24b95b03dc3cd1b2ba3 *R/global_vars.R
+8883101818c9d68263cf1fd0440e96ae *R/helpers.R
+c02951dc3c29414e99811cfab171c4fc *R/pairwise_comparisons.R
+9d3bb59d8086f258a0417f92645dfe83 *R/reexports.R
+760fd6aa91fa90748ba33d1fca0211a2 *README.md
 60e0e78acc2c42531f52352f480329c2 *data/bugs_long.rdata
 c5ee4fa2f5ea32bdf87e02ea71a415f8 *data/iris_long.rdata
 91069babfae39db7b08f35ede31084f2 *data/movies_long.rdata
 54a342a94ac6e4232913e999a95d4e94 *data/movies_wide.rdata
 2664a73ea8c7701c767239b0613dc913 *inst/CITATION
-ea19f918d9a9b69dc86fa200b709e856 *inst/WORDLIST
+47a20c5943dc882c5aa35c0c37e0b130 *inst/WORDLIST
 802fc4c2df4afaaf8de39a8b423f5a7b *man/bugs_long.Rd
-cdd673e67a6eb0665f2810f11ecc3e97 *man/figures/README-ggsignif-1.png
+734551817a14e501488fefcdfe5cc798 *man/figures/README-ggsignif-1.png
 fee4de0c3a90e593231760a3236aa44a *man/figures/README-ggsignif2-1.png
 8aa93283e08db18090dc39423bd9b612 *man/figures/logo.png
 253003637707cb3641bb791336692759 *man/iris_long.Rd
 6e4d56978f52276057b7b86e9eac5033 *man/movies_long.Rd
 0ebeb6520377257ca07f34ee5d266bbc *man/movies_wide.Rd
 976ce17abcc524c608d6ea80b9d272e1 *man/p_adjust_text.Rd
 7f7a1340e8dc84311cdd4405cae5b169 *man/pairwise_caption.Rd
-1dca7c5f544d8a1726886d3a1d7fcab8 *man/pairwise_comparisons.Rd
-138bdb68b99668f0280256e155f42437 *man/reexports.Rd
+6ce41c2c41a482dfd6bb4e4ec0a51085 *man/pairwise_comparisons.Rd
+25a47783641bee60b059593ce32cbe44 *man/reexports.Rd
 4393414902910ca83ac7faf83be60afb *tests/README.md
 dbd9bab057163c01c320d0b9d3bb9620 *tests/spelling.R
 ac503b90bd70b6f265dc58b04d55fec1 *tests/testthat.R
 b4600bff9ebb72c2aa12385dfa17f746 *tests/testthat/test-pairwise_caption_helpers.R
-73e847f52e6098e5313893ce4b2a909e *tests/testthat/test-pairwise_comparisons_between.R
-2ee60f3d1481f35ec3d604057b725b1f *tests/testthat/test-pairwise_comparisons_within.R
+2a0a3c290119e35a4341bc4949151002 *tests/testthat/test-pairwise_comparisons_between.R
+684ced6cea3b38be17fc3f81b62f0599 *tests/testthat/test-pairwise_comparisons_within.R

NAMESPACE

@@ -1,12 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
-export("%$%")
 export("%<-%")
 export("%<>%")
 export("%>%")
-export("%|%")
-export("%||%")
-export(":=")
 export(as_tibble)
 export(p_adjust_text)
 export(pairwise_caption)
@@ -16,6 +12,7 @@ importFrom(BayesFactor,ttestBF)
 importFrom(PMCMRplus,durbinAllPairsTest)
 importFrom(PMCMRplus,gamesHowellTest)
 importFrom(PMCMRplus,kwAllPairsDunnTest)
+importFrom(PMCMRplus,toTidy)
 importFrom(WRS2,lincon)
 importFrom(WRS2,rmmcp)
 importFrom(dplyr,across)
@@ -30,25 +27,20 @@ importFrom(dplyr,rowwise)
 importFrom(dplyr,select)
 importFrom(dplyr,starts_with)
 importFrom(dplyr,ungroup)
-importFrom(insight,standardize_names)
-importFrom(ipmisc,"%$%")
 importFrom(ipmisc,"%<-%")
 importFrom(ipmisc,"%<>%")
 importFrom(ipmisc,"%>%")
 importFrom(ipmisc,as_tibble)
 importFrom(ipmisc,long_to_wide_converter)
-importFrom(ipmisc,signif_column)
 importFrom(ipmisc,specify_decimal_p)
 importFrom(ipmisc,stats_type_switch)
 importFrom(ipmisc,tibble)
 importFrom(parameters,model_parameters)
+importFrom(parameters,standardize_names)
 importFrom(purrr,map2)
 importFrom(purrr,map_dfr)
 importFrom(rlang,"!!!")
 importFrom(rlang,"!!")
-importFrom(rlang,"%|%")
-importFrom(rlang,"%||%")
-importFrom(rlang,":=")
 importFrom(rlang,as_string)
 importFrom(rlang,enquo)
 importFrom(rlang,ensym)

NEWS.md

@@ -1,8 +1,15 @@
+# pairwiseComparisons 3.1.1
+
+  - Minor internal refactoring.
+
+  - Removes the unnecessary (and confusing) `significance` column from all
+    outputs.
+
 # pairwiseComparisons 3.1.0
 
   - To be consistent with the rest of the `ggstatsverse`, the Bayes Factor
     results are now always shown in favor of null over alternative (`BF01`).
-    
+
   - `pairwise_comparisons` function gets `subject.id` argument relevant for
     repeated measures design.
 
@@ -13,7 +20,7 @@
 
   - `pairwise_caption` function has changed its output to reflect changes made
     to the *p*-value labels.
-    
+
   - Major internal refactoring to get rid of the following dependencies:
     `broomExtra`, `dunn.test`, `forcats`, and `tidyr`. This comes at the cost of
     omission of few of the details that were previously included in the output
@@ -27,7 +34,7 @@
 
   - Fixes a bug which affected results for within-subjects design when the
     dataframe wasn't sorted by `x` (#19).
-  
+
   - This fix also now makes the results more consistent, such that irrespective
     of which type of statistics is chosen the `group1` and `group2` columns are
     in identical order.
@@ -47,13 +54,13 @@
 
   - Removes dependence on `jmv` and instead relies on `dunn.test` and
     `PMCMRplus`. This significantly reduces number of dependencies.
-  
+
   - The non-parametric Dwass test has been changed to Dunn test.
 
 # pairwiseComparisons 0.3.1
 
   - Adapts to breaking changes in upcoming release of `broom 0.7.0`.
-  
+
   - Thanks to Sarah, the package has a hexsticker. :)
 
 # pairwiseComparisons 0.3.0
@@ -81,6 +88,7 @@
     function now instead adds two columns (`test.details` and
     `p.value.adjustment`) to all outputs specifying which test was carried out
     and which adjustment method is being used for *p*-value correction.
+
   - Gets rid of `groupedstats` and `crayon` from dependencies.
 
 # pairwiseComparisons 0.1.2
@@ -93,10 +101,11 @@
   - The `p.value.label` in the output dataframe has been renamed to `label` to
     consider the possibility that Bayes Factor tests might also be supported in
     future.
-    
+
   - The label now specified whether the *p*-value was adjusted or not for
     multiple comparisons.
 
 # pairwiseComparisons 0.1.0
 
   - First release of the package.
+

R/global_vars.R

@@ -11,7 +11,6 @@ utils::globalVariables(
     "group1",
     "group2",
     "log_e_bf10",
-    "p.crit",
     "p.value",
     "psihat"
   ),

R/helpers.R

@@ -1,41 +1,20 @@
 #' @name PMCMR_to_tibble
-#' @note Adapted from `dfrtopics::gather_matrix()`.
 #'
-#' @importFrom stats na.omit
-#' @importFrom dplyr bind_cols contains select
+#' @importFrom dplyr contains select rename
+#' @importFrom PMCMRplus toTidy
 #'
 #' @keywords internal
 #' @noRd
 
 # function body
 PMCMR_to_tibble <- function(mod, ...) {
-  # combining statistic and p-value columns
-  dplyr::bind_cols(
-    matrix_to_tidy(mod$statistic, "statistic"),
-    dplyr::select(matrix_to_tidy(mod$p.value, "p.value"), -dplyr::contains("group"))
-  )
-}
-
-#' @keywords internal
-#' @noRd
-
-matrix_to_tidy <- function(m, col_name = "value", ...) {
-  result <-
-    data.frame(
-      group2 = rep(rownames(m), each = ncol(m)),
-      group1 = rep(colnames(m), times = nrow(m)),
-      value = as.numeric(base::t(m)),
-      stringsAsFactors = FALSE
-    )
-
-  names(result)[3] <- col_name
-  as_tibble(stats::na.omit(result))
+  dplyr::select(PMCMRplus::toTidy(mod), -dplyr::contains("method")) %>%
+    dplyr::rename(group2 = group1, group1 = group2)
 }
 
 #' @importFrom BayesFactor ttestBF
 #' @importFrom dplyr mutate
-#' @importFrom parameters model_parameters
-#' @importFrom insight standardize_names
+#' @importFrom parameters model_parameters standardize_names
 #' @importFrom rlang exec new_formula !!!
 #'
 #' @noRd
@@ -47,9 +26,6 @@ bf_internal_ttest <- function(data,
                               paired = FALSE,
                               bf.prior = 0.707,
                               ...) {
-  # make sure both quoted and unquoted arguments are allowed
-  c(x, y) %<-% c(rlang::ensym(x), rlang::ensym(y))
-
   # have a proper cleanup with NA removal
   data %<>%
     ipmisc::long_to_wide_converter(
@@ -62,24 +38,23 @@ bf_internal_ttest <- function(data,
 
   # relevant arguments
   if (isTRUE(paired)) bf.args <- list(x = data[[2]], y = data[[3]])
-  if (isFALSE(paired)) bf.args <- list(formula = rlang::new_formula({{ y }}, {{ x }}))
+  if (isFALSE(paired)) bf.args <- list(formula = rlang::new_formula(y, x))
 
   # creating a BayesFactor object
   bf_object <-
     rlang::exec(
       .fn = BayesFactor::ttestBF,
       rscale = bf.prior,
       paired = paired,
-      progress = FALSE,
       data = as.data.frame(data),
       !!!bf.args
     )
 
   # extracting Bayes Factors and other details
-  parameters::model_parameters(bf_object, ...) %>%
-    insight::standardize_names(data = ., style = "broom") %>%
-    dplyr::rename(.data = ., "bf10" = "bayes.factor") %>%
-    dplyr::mutate(.data = ., log_e_bf10 = log(bf10))
+  parameters::model_parameters(bf_object, verbose = FALSE, ...) %>%
+    parameters::standardize_names(data = ., style = "broom") %>%
+    dplyr::rename("bf10" = "bayes.factor") %>%
+    dplyr::mutate(log_e_bf10 = log(bf10))
 }