Merge pull request #28 from ACCLAB/v0.2.0

v0.2.0

.Rbuildignore

@@ -1,3 +1,5 @@
+^Meta$
+^doc$
 ^CRAN-RELEASE$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.gitignore

@@ -1,3 +1,5 @@
+Meta
+doc
 .Rproj.user
 .Rhistory
 .RData
@@ -6,3 +8,5 @@
 .DS_Store
 *.DS_Store
 inst/doc
+# revdevcheck temp folder
+revdep

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dabestr
 Type: Package
 Title: Data Analysis using Bootstrap-Coupled Estimation
-Version: 0.1.0
+Version: 0.2.0
 Authors@R: c(
     person("Joses W.", "Ho", 
           email = "[email protected]", role = c("cre", "aut")),
@@ -32,7 +32,6 @@ Imports:
     cowplot,
     dplyr,
     ggplot2 (>= 3.0),
-    grid,
     forcats,
     ggforce,
     ggbeeswarm,

NEWS.md

@@ -1,3 +1,7 @@
+# dabestr v0.2.0
+
+* This release fixes a bug that plotted the categories alphabetically in Gardner-Altman plots. (# 24).
+
 # dabestr v0.1.0
 
 * First release of dabestr.

R/main.R

@@ -151,13 +151,6 @@
 #'                               )
 #'
 #'
-#' # Constructing the confidence intervals on 10000 bootstrap resamples.
-#' unpaired_mean_diff_n10000 <- dabest(
-#'                                iris, Species, Petal.Width,
-#'                                idx = c("setosa", "versicolor", "virginica"),
-#'                                paired = FALSE,
-#'                                reps = 10000
-#'                                )
 #'
 #' # Using pipes to munge your data and then passing to `dabest`.
 #' # First, we generate some synthetic data.
@@ -179,11 +172,11 @@
 #'
 #'
 #' @section References:
-#' \href{https://www.jstor.org/stable/2246110}{Bootstrap Confidence Intervals.}
+#' \href{https://projecteuclid.org/euclid.ss/1032280214}{Bootstrap Confidence Intervals.}
 #' DiCiccio, Thomas J., and Bradley Efron.
 #' Statistical Science: vol. 11, no. 3, 1996. pp. 189–228.
 #'
-#'   \href{https://www.crcpress.com/An-Introduction-to-the-Bootstrap/Efron-Tibshirani/p/book/9780412042317}{An Introduction to the Bootstrap.} Efron, Bradley, and R. J. Tibshirani. 1994. CRC Press.
+#' \href{https://www.crcpress.com/An-Introduction-to-the-Bootstrap/Efron-Tibshirani/p/book/9780412042317/}{An Introduction to the Bootstrap.} Efron, Bradley, and R. J. Tibshirani. 1994. CRC Press.
 #'
 #'
 #' @importFrom magrittr %>%
@@ -376,6 +369,13 @@ dabest <- function(
 
   colnames(summaries) <- c(x_quoname, func_quoname)
 
+  # Order the summaries by the idx.
+  summaries[[x_quoname]] <-
+    summaries[[x_quoname]] %>%
+    factor(all_groups, ordered = TRUE)
+
+  summaries <- summaries %>% dplyr::arrange(!!x_enquo)
+
 
 
   #### Assemble only the data used to create the plot. ####

R/plot.R

@@ -115,14 +115,11 @@
 #' # Create a Gardner-Altman estimation plot.
 #' plot(unpaired_mean_diff)
 #'
-#' # Create a Cumming estimation plot instead.
-#' plot(unpaired_mean_diff, float.contrast = FALSE)
 #'
 #'
 #' # Comparing versicolor and virginica petal width to setosa petal width.
 #' shared_control_data <- dabest(iris, Species, Petal.Width,
-#'                               idx = c("setosa", "versicolor", "virginica"),
-#'                               paired = FALSE
+#'                               idx = c("setosa", "versicolor", "virginica")
 #'                               )
 #'
 #' # Create a Cumming estimation plot.
@@ -233,12 +230,12 @@ plot.dabest <- function(x, ...,
     }
 
     for.plot <- dplyr::bind_rows(for.plot)
-
-    for.plot[[x_quoname]] <-
-      for.plot[[x_quoname]] %>%
-      factor(all.groups, ordered = TRUE)
   }
 
+  for.plot[[x_quoname]] <-
+    for.plot[[x_quoname]] %>%
+    factor(all.groups, ordered = TRUE)
+
 
   #### Compute the Ns. ####
   Ns <-

cran-comments.md

@@ -1,31 +1,18 @@
-## Resubmission
-This is a resubmission. In this version I have:
 
-* Cleaned the LICENSE file. Note that the package is licensed under 
-the BSD 3-Clause Clear License, which is a variant of the BSD 3-Clause 
-License that explicitly does not grant any patent rights
-<https://choosealicense.com/licenses/bsd-3-clause-clear/>. 
-It does not seem to be listed in the license templates on CRAN
-<https://cran.r-project.org/web/licenses/>.
-
-* Fixed the DOI markup.
-
-* Removed the redundant "in R" from the title.
-
-* Added reference about the plots and methods in the Description field 
-of DESCRIPTION.
+## v0.2.0
+This is a update to the package, fixing a bug in the previous release.
 
 
 ## Test environments
-* local OS X install, R 3.5.0
-* local debian install, R 3.5.1
+* local OS X install, R 3.5.2
+* local debian install, R 3.5.2
 * ubuntu 14.04.5 (on travis-ci, devel and release)
 * win-builder (devel and release)
 
 
 ## R CMD check results
 There were no ERRORs, WARNINGs, or NOTEs.
-
+  
 
 ## Downstream dependencies
 There are currently no downstream dependencies for this package.