Merge 4f4327c into c990501

IndrajeetPatil · Sep 4, 2020 · 415ee12 · 415ee12
2 parents c990501 + 4f4327c
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diff --git a/.travis.yml b/.travis.yml
@@ -37,7 +37,6 @@ r_packages:
   - LaplacesDemon
   - logspline
   - testthat
-  - devtools
   - remotes
   - knitr
   - rmarkdown

diff --git a/API b/API
@@ -9,10 +9,10 @@ pairwise_p(data, x, y, type = "parametric", paired = FALSE, var.equal = FALSE, t
 
 ## Reexported objects
 
-::%$%
+magrittr::%$%
 zeallot::%<-%
-::%<>%
-::%>%
+magrittr::%<>%
+magrittr::%>%
 rlang::%|%
 rlang::%||%
 rlang:::=

diff --git a/CRAN-RELEASE b/CRAN-RELEASE
@@ -1,2 +1,2 @@
-This package was submitted to CRAN on 2020-06-23.
-Once it is accepted, delete this file and tag the release (commit b0b6801fdc).
+This package was submitted to CRAN on 2020-09-04.
+Once it is accepted, delete this file and tag the release (commit 8ab15c7).
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: pairwiseComparisons
 Title: Multiple Pairwise Comparison Tests
-Version: 1.1.2.9000
+Version: 2.0.0
 Authors@R: 
     person(given = "Indrajeet",
            family = "Patil",

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,12 @@
-# pairwiseComparisons 1.1.2.9000
+# pairwiseComparisons 2.0.0
+
+  - 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.
+
 
 # pairwiseComparisons 1.1.2
 

diff --git a/R/data.R b/R/data.R
@@ -2,13 +2,9 @@
 #' @name movies_wide
 #' @details Modified dataset from `ggplot2movies` package.
 #'
-#' The internet movie database, \url{http://imdb.com/}, is a website devoted
-#' to collecting movie data supplied by studios and fans.  It claims to be the
-#' biggest movie database on the web and is run by amazon.  More information
-#' about imdb.com can be found online,
-#' \url{http://imdb.com/help/show_leaf?about}, including information about
-#' the data collection process,
-#' \url{http://imdb.com/help/show_leaf?infosource}.
+#' The internet movie database, \url{https://imdb.com/}, is a website devoted
+#' to collecting movie data supplied by studios and fans. It claims to be the
+#' biggest movie database on the web and is run by amazon.
 #'
 #' Movies were selected for inclusion if they had a known length and had been
 #' rated by at least one imdb user.  Small categories such as documentaries
@@ -41,13 +37,9 @@
 #' @name movies_long
 #' @details Modified dataset from `ggplot2movies` package.
 #'
-#' The internet movie database, \url{http://imdb.com/}, is a website devoted
+#' The internet movie database, \url{https://imdb.com/}, is a website devoted
 #' to collecting movie data supplied by studios and fans.  It claims to be the
-#' biggest movie database on the web and is run by amazon.  More about
-#' information imdb.com can be found online,
-#' \url{http://imdb.com/help/show_leaf?about}, including information about
-#' the data collection process,
-#' \url{http://imdb.com/help/show_leaf?infosource}.
+#' biggest movie database on the web and is run by amazon.
 #'
 #' Movies were are identical to those selected for inclusion in movies_wide but this
 #' dataset has been constructed such that every movie appears in one and only one

diff --git a/R/games_howell.R b/R/games_howell.R
@@ -78,39 +78,32 @@ games_howell <- function(data, x, y) {
       )
 
     # sigma standard error
-    se <-
-      sqrt(x = 0.5 * (std[combs[1, x]] / n[combs[1, x]] + std[combs[2, x]] / n[combs[2, x]]))
+    se <- sqrt(x = 0.5 * (std[combs[1, x]] / n[combs[1, x]] + std[combs[2, x]] / n[combs[2, x]]))
 
     # upper confidence limit for mean difference
-    conf.high <- lapply(X = 1:NCOL(combs), FUN = function(x) {
-      mean.diff + stats::qtukey(
-        p = 0.95,
-        nmeans = groups,
-        df = df
-      ) * se
-    })[[1]]
+    conf.high <-
+      lapply(
+        X = 1:NCOL(combs),
+        FUN = function(x) mean.diff + stats::qtukey(p = 0.95, nmeans = groups, df = df) * se
+      )
 
     # lower confidence limit for mean difference
-    conf.low <- lapply(X = 1:NCOL(combs), FUN = function(x) {
-      mean.diff - stats::qtukey(
-        p = 0.95,
-        nmeans = groups,
-        df = df
-      ) * se
-    })[[1]]
+    conf.low <-
+      lapply(
+        X = 1:NCOL(combs),
+        FUN = function(x) mean.diff - stats::qtukey(p = 0.95, nmeans = groups, df = df) * se
+      )
 
     # Group Combinations
     group1 <- as.character(combs[1, x])
     group2 <- as.character(combs[2, x])
 
     # Collect all statistics into list
-    stats <- list(group1, group2, mean.diff, se, t, df, p, conf.high, conf.low)
+    stats <- list(group1, group2, mean.diff, se, t, df, p, conf.high[[1]], conf.low[[1]])
   })
 
   # unlist statistics collected earlier
-  stats.unlisted <- lapply(statistics, function(x) {
-    unlist(x)
-  })
+  stats.unlisted <- lapply(statistics, function(x) unlist(x))
 
   # create dataframe from flattened list
   results <-
@@ -121,8 +114,7 @@ games_howell <- function(data, x, y) {
     ))
 
   # select columns that should be numeric and change with as.numeric
-  results[, 3:ncol(results)] <-
-    round(as.numeric(as.matrix(results[, 3:ncol(results)])), digits = 3)
+  results[, 3:ncol(results)] <- round(as.numeric(as.matrix(results[, 3:ncol(results)])), digits = 3)
 
   # Rename data frame columns
   colnames(results) <-

diff --git a/R/pairwise_comparisons.R b/R/pairwise_comparisons.R
@@ -3,8 +3,8 @@
 #' @description Calculate parametric, non-parametric, and robust pairwise
 #'   comparisons between group levels with corrections for multiple testing.
 #'
-#' @param data A dataframe (or a tibble) from which variables specified are to
-#'   be taken. A matrix or tables will **not** be accepted.
+#' @param data A dataframe from which variables specified are to be taken. A
+#'   matrix or tables will **not** be accepted.
 #' @param x The grouping variable from the dataframe `data`.
 #' @param y The response (a.k.a. outcome or dependent) variable from the
 #'   dataframe `data`.
@@ -187,16 +187,20 @@ pairwise_comparisons <- function(data,
 
   # ---------------------------- data cleanup -------------------------------
 
-  # creating a dataframe
+  # creating a dataframe (it's important for the data to be sorted by `x`)
   df_internal <-
     long_to_wide_converter(
-      data = data,
+      data = dplyr::arrange(data, {{ x }}),
       x = {{ x }},
       y = {{ y }},
       paired = paired,
       spread = FALSE
     )
 
+  # for some tests, it's better to have these as vectors
+  x_vec <- df_internal %>% dplyr::pull({{ x }})
+  y_vec <- df_internal %>% dplyr::pull({{ y }})
+
   # ---------------------------- parametric ---------------------------------
 
   if (type %in% c("parametric", "bayes")) {
@@ -253,16 +257,15 @@ pairwise_comparisons <- function(data,
 
       # tidy dataframe with results from pairwise tests
       df_tidy <-
-        broomExtra::tidy(
-          stats::pairwise.t.test(
-            x = df_internal %>% dplyr::pull({{ y }}),
-            g = df_internal %>% dplyr::pull({{ x }}),
-            p.adjust.method = "none",
-            paired = paired,
-            alternative = "two.sided",
-            na.action = na.omit
-          )
+        stats::pairwise.t.test(
+          x = y_vec,
+          g = x_vec,
+          p.adjust.method = "none",
+          paired = paired,
+          alternative = "two.sided",
+          na.action = na.omit
         ) %>%
+        broomExtra::tidy(.) %>%
         p_adjust_column_adder(df = ., p.adjust.method = p.adjust.method)
 
       # combining mean difference and results from pairwise t-test
@@ -310,23 +313,20 @@ pairwise_comparisons <- function(data,
         )
       ) %>%
       dplyr::rowwise() %>%
-      dplyr::mutate(label = paste(
-        "list(~log[e](BF[10])",
-        "==",
-        specify_decimal_p(x = log_e_bf10, k = k),
-        ")",
-        sep = ""
+      dplyr::mutate(label = paste0(
+        "list(~log[e](BF[10])", "==", specify_decimal_p(x = log_e_bf10, k = k), ")"
       )) %>%
       dplyr::ungroup() %>%
       dplyr::mutate(.data = ., test.details = "Student's t-test")
 
     # early return (no further cleanup required)
-    return(dplyr::bind_cols(dplyr::select(df, group1, group2), df_tidy) %>%
+    return(
       dplyr::mutate_if(
-        .tbl = .,
+        .tbl = dplyr::bind_cols(dplyr::select(df, group1, group2), df_tidy),
         .predicate = is.factor,
         .funs = ~ as.character(.)
-      ))
+      )
+    )
   }
 
   # ---------------------------- nonparametric ----------------------------
@@ -337,8 +337,8 @@ pairwise_comparisons <- function(data,
       invisible(utils::capture.output(df <-
         as.data.frame(
           dunn.test::dunn.test(
-            x = df_internal %>% dplyr::pull({{ y }}),
-            g = df_internal %>% dplyr::pull({{ x }}),
+            x = y_vec,
+            g = x_vec,
             table = FALSE,
             kw = FALSE,
             label = FALSE,
@@ -375,29 +375,23 @@ pairwise_comparisons <- function(data,
 
     # converting the entered long format data to wide format
     if (isTRUE(paired)) {
-      x_vec <- df_internal %>% dplyr::pull({{ x }})
-      y_vec <- df_internal %>% dplyr::pull({{ y }})
-
       # creating model object
       mod <-
         PMCMRplus::durbinAllPairsTest(
           y = na.omit(matrix(
             data = y_vec,
             ncol = length(unique(x_vec)),
-            dimnames = list(
-              seq(1, length(y_vec) / length(unique(x_vec))),
-              unique(x_vec)
-            )
+            dimnames = list(seq(1, length(y_vec) / length(unique(x_vec))), unique(x_vec))
           )),
           p.adjust.method = "none"
         )
 
       # combining into one dataframe
       df <-
         dplyr::bind_cols(
-          matrix_to_tidy(m = mod$statistic, col_names = c("group1", "group2", "W")),
+          matrix_to_tidy(m = mod$statistic, col_names = c("group2", "group1", "W")),
           dplyr::select(
-            matrix_to_tidy(m = mod$p.value, col_names = c("group1", "group2", "p.value")),
+            matrix_to_tidy(m = mod$p.value, col_names = c("group2", "group1", "p.value")),
             -dplyr::contains("group")
           )
         )
@@ -485,8 +479,8 @@ pairwise_comparisons <- function(data,
     dplyr::mutate(label = specify_decimal_p(x = p.value, k = k, p.value = TRUE)) %>%
     dplyr::mutate(
       label = dplyr::case_when(
-        label == "< 0.001" ~ paste("list(~italic(p)[", adjust_text, "]<=", "0.001", ")", sep = " "),
-        TRUE ~ paste("list(~italic(p)[", adjust_text, "]==", label, ")", sep = " ")
+        label == "< 0.001" ~ paste0("list(~italic(p)[", adjust_text, "]<=", "0.001", ")"),
+        TRUE ~ paste0("list(~italic(p)[", adjust_text, "]==", label, ")")
       )
     ) %>%
     dplyr::mutate(

diff --git a/README.Rmd b/README.Rmd
@@ -6,7 +6,7 @@ output: github_document
 
 ```{r, echo = FALSE}
 # show me all columns
-options(tibble.width = Inf)
+options(tibble.width = Inf, pillar.bold = TRUE)
 
 knitr::opts_chunk$set(
   collapse = TRUE,
@@ -23,12 +23,12 @@ knitr::opts_chunk$set(
 
 Package | Status | Usage | GitHub | References
 ----------------- | ----------------- | ----------------- | ----------------- | -----------------
-[![CRAN_Release_Badge](http://www.r-pkg.org/badges/version-ago/pairwiseComparisons)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![Travis Build Status](https://travis-ci.org/IndrajeetPatil/pairwiseComparisons.svg?branch=master)](https://travis-ci.org/IndrajeetPatil/pairwiseComparisons) | [![Daily downloads badge](https://cranlogs.r-pkg.org/badges/last-day/pairwiseComparisons?color=blue)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![GitHub version](https://img.shields.io/badge/GitHub-1.1.1-orange.svg?style=flat-square)](https://github.com/IndrajeetPatil/pairwiseComparisons/) | [![Website](https://img.shields.io/badge/website-pairwiseComparisons-orange.svg?colorB=E91E63)](https://indrajeetpatil.github.io/pairwiseComparisons/)
+[![CRAN_Release_Badge](http://www.r-pkg.org/badges/version-ago/pairwiseComparisons)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![Travis Build Status](https://travis-ci.org/IndrajeetPatil/pairwiseComparisons.svg?branch=master)](https://travis-ci.org/IndrajeetPatil/pairwiseComparisons) | [![Daily downloads badge](https://cranlogs.r-pkg.org/badges/last-day/pairwiseComparisons?color=blue)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![GitHub version](https://img.shields.io/badge/GitHub-2.0.0-orange.svg?style=flat-square)](https://github.com/IndrajeetPatil/pairwiseComparisons/) | [![Website](https://img.shields.io/badge/website-pairwiseComparisons-orange.svg?colorB=E91E63)](https://indrajeetpatil.github.io/pairwiseComparisons/)
 [![CRAN Checks](https://cranchecks.info/badges/summary/pairwiseComparisons)](https://cran.r-project.org/web/checks/check_results_pairwiseComparisons.html) | [![AppVeyor Build Status](https://ci.appveyor.com/api/projects/status/github/IndrajeetPatil/pairwiseComparisons?branch=master&svg=true)](https://ci.appveyor.com/project/IndrajeetPatil/pairwiseComparisons) | [![Weekly downloads badge](https://cranlogs.r-pkg.org/badges/last-week/pairwiseComparisons?color=blue)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![Forks](https://img.shields.io/badge/forks-`r itdepends:::get_github_info("pairwiseComparisons")$forks[[1]]`-blue.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons/) | [![Rdoc](https://www.rdocumentation.org/badges/version/pairwiseComparisons)](https://www.rdocumentation.org/packages/pairwiseComparisons)
-[![minimal R version](https://img.shields.io/badge/R%3E%3D-3.6.0-6666ff.svg)](https://cran.r-project.org/) | [![lifecycle](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://www.tidyverse.org/lifecycle/) | [![Monthly downloads badge](https://cranlogs.r-pkg.org/badges/last-month/pairwiseComparisons?color=blue)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![Github Issues](https://img.shields.io/badge/issues-`r itdepends:::get_github_info("pairwiseComparisons")$open_issues[[1]]`-red.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons/issues) | [![vignettes](https://img.shields.io/badge/vignettes-1.0.0-orange.svg?colorB=FF5722)](https://github.com/IndrajeetPatil/pairwiseComparisons/blob/master/README.md)
+[![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/pairwiseComparisons?color=blue)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![Github Issues](https://img.shields.io/badge/issues-`r itdepends:::get_github_info("pairwiseComparisons")$open_issues[[1]]`-red.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons/issues) | [![vignettes](https://img.shields.io/badge/vignettes-2.0.0-orange.svg?colorB=FF5722)](https://github.com/IndrajeetPatil/pairwiseComparisons/blob/master/README.md)
 [![GitHub code size in bytes](https://img.shields.io/github/languages/code-size/IndrajeetPatil/pairwiseComparisons.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons) | [![Coverage Status](https://coveralls.io/repos/github/IndrajeetPatil/pairwiseComparisons/badge.svg?branch=master)](https://coveralls.io/github/IndrajeetPatil/pairwiseComparisons?branch=master) | [![Total downloads badge](https://cranlogs.r-pkg.org/badges/grand-total/pairwiseComparisons?color=blue)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![Github Stars](https://img.shields.io/github/stars/IndrajeetPatil/pairwiseComparisons.svg?style=social&label=Github)](https://github.com/IndrajeetPatil/pairwiseComparisons) | [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2074621.svg)](https://doi.org/10.5281/zenodo.2074621)
 [![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/pairwiseComparisons/branch/master/graph/badge.svg)](https://codecov.io/gh/IndrajeetPatil/pairwiseComparisons?branch=master) | [![Covrpage Summary](https://img.shields.io/badge/covrpage-Last_Build_2020_05_29-brightgreen.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons/blob/master/tests/README.md) | [![Last-changedate](https://img.shields.io/badge/last%20change-`r gsub('-', '--', Sys.Date())`-yellowgreen.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons/commits/master) | [![GitHub last commit](https://img.shields.io/github/last-commit/IndrajeetPatil/pairwiseComparisons.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons/commits/master)
-[![status](https://tinyverse.netlify.com/badge/pairwiseComparisons)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![R build status](https://github.com/IndrajeetPatil/pairwiseComparisons/workflows/R-CMD-check/badge.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons) | [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/pairwiseComparisons/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/pairwiseComparisons/issues)
+[![status](https://tinyverse.netlify.com/badge/pairwiseComparisons)](https://CRAN.R-project.org/package=pairwiseComparisons) | [![R build status](https://github.com/IndrajeetPatil/pairwiseComparisons/workflows/R-CMD-check/badge.svg)](https://github.com/IndrajeetPatil/pairwiseComparisons) | [![Gitter chat](https://badges.gitter.im/gitterHQ/gitter.png)](https://gitter.im/pairwiseComparisons/community) | [![Project Status](http://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active) | [![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg?style=flat)](https://github.com/IndrajeetPatil/pairwiseComparisons/issues)
 
 # Introduction <img src="man/figures/logo.png" align="right" width="240" />
 
@@ -233,7 +233,8 @@ library(ggsignif)
 mtcars$cyl <- as.factor(mtcars$cyl)
 
 # creating a basic plot
-p <- ggplot(mtcars, aes(cyl, wt)) + geom_boxplot()
+p <- ggplot(mtcars, aes(cyl, wt)) +
+  geom_boxplot()
 
 # using `pairwiseComparisons` package to create a dataframe with results
 (df <-
@@ -308,8 +309,7 @@ of commitment):
 
   - Review code
 
-  - Add new functionality (in the form of new plotting functions or helpers for
-    preparing subtitles)
+  - Add new functionality
 
 Please note that this project is released with a 
 [Contributor Code of Conduct](https://github.com/IndrajeetPatil/pairwiseComparisons/blob/master/.github/CODE_OF_CONDUCT.md). By participating in this project you agree to abide by its terms.