Merge pull request #144 from sunroofgod/dev

v2023.9.12

.Rbuildignore

@@ -10,3 +10,5 @@
 ^CONTRIBUTING.MD$
 ^figures$
 ^dabestr.Rmd$
+^cran-comments\.md$
+^revdep$

.github/workflows/R-CMD-check.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [dev]
+    branches: [dev, master]
   pull_request:
-    branches: [dev]
+    branches: [dev, master]
 
 name: R-CMD-check
 

.github/workflows/pkgdown.yaml

@@ -2,9 +2,9 @@
 # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [dev]
+    branches: [master]
   pull_request:
-    branches: [dev]
+    branches: [master]
   release:
     types: [published]
   workflow_dispatch:

.gitignore

@@ -1,7 +1,7 @@
 # Byte-compiled / optimized / DLL files
 
-# Knitted html file
-dabestr.html
+# Testing Files
+dabestr.Rmd
 
 # Mac
 **/.DS_Store
@@ -14,3 +14,4 @@ dabestr.html
 .RProfile
 docs
 inst/doc
+figures

DESCRIPTION

@@ -1,14 +1,16 @@
 Package: dabestr
 Type: Package
 Title: Data Analysis using Bootstrap-Coupled Estimation
-Version: 0.9.9.9
+Version: 2023.9.12
 Authors@R: c(
-  person("Kah Seng", "Lian", email = "[email protected]", role = c("cre", "aut")),
-  person("Zhuoyu", "Wang", email = "[email protected],edu", role = c("aut")),
-  person("Jun Yang", "Liao", email = "[email protected]", role = c("aut")),
-  person("Joses W.", "Ho", email = "[email protected]", role = c("aut")),
+  person("Yishan", "Mai", email = "[email protected]", role = c("aut", "cre")),
+  person("Kah Seng", "Lian", email = "[email protected]", role = c("aut")),
+  person("Zhuoyu", "Wang", email = "[email protected],edu", role = "aut"),
+  person("Jun Yang", "Liao", email = "[email protected]", role = "aut"),
+  person("Joses W.", "Ho", email = "[email protected]", role = "aut"),
   person("ACCLAB", role = c("cph", "fnd")),
-  person("Tayfun", "Tumkaya", role = c("ctb")))
+  person("Tayfun", "Tumkaya", role = "aut"),
+  person("Felicia", role = "aut"))
 Description: Data Analysis using Bootstrap-Coupled ESTimation.
   Estimation statistics is a simple framework that avoids the pitfalls of
   significance testing. It uses familiar statistical concepts: means,
@@ -22,7 +24,7 @@ Description: Data Analysis using Bootstrap-Coupled ESTimation.
   separate but aligned axes.
   Estimation plots are introduced in Ho et al., Nature Methods 2019, 1548-7105.
   <doi:10.1038/s41592-019-0470-3>.
-  The free-to-view PDF is located at <https://rdcu.be/bHhJ4>.
+  The free-to-view PDF is located at <https://www.nature.com/articles/s41592-019-0470-3.epdf?author_access_token=Euy6APITxsYA3huBKOFBvNRgN0jAjWel9jnR3ZoTv0Pr6zJiJ3AA5aH4989gOJS_dajtNr1Wt17D0fh-t4GFcvqwMYN03qb8C33na_UrCUcGrt-Z0J9aPL6TPSbOxIC-pbHWKUDo2XsUOr3hQmlRew%3D%3D>.
 License: Apache License (>= 2)
 Encoding: UTF-8
 URL: https://github.com/ACCLAB/dabestr,
@@ -42,22 +44,20 @@ Imports:
   grid,
   scales,
   ggsci,
-  colorspace,
   cli,
   boot,
   stats,
   stringr,
-  coin,
-  mvtnorm,
-  multcomp,
-  brunnermunzel
+  brunnermunzel,
+  methods
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 Suggests: 
     testthat (>= 3.0.0),
     vdiffr,
     knitr,
-    rmarkdown
+    rmarkdown,
+    kableExtra
 Config/testthat/edition: 3
 LazyData: true
-VignetteBuilder: knitr
+VignetteBuilder: knitr, kableExtra

NEWS.md

@@ -1,5 +1,25 @@
-# dabestr v0.9.9.9
-* This is the current pre-official, teaser release version of dabestr.
+# dabestr v2023.9.12
+This release is a complete rebuild of dabestr. 
+
+Previous functions from v0.3.0 and before are now depreciated.
+
+#### Main API
+This version of dabestr features a new Main API. The following functions have been sequentially organised for their intended procedural utilisation.
+
+* `load()` 
+processes and converts a tidy dataset into the dabestr format.
+
+* `mean_diff()`, `median_diff()`, `cohens_d()`, `hedges_g()`, `cliffs_delta()`, `cohens_h()` 
+Computes the effect size for each control-test group pairing in `idx`.
+
+* `dabest_plot()` produces a Gardner-Altman estimation plot or a Cumming estimation plot depending on whether float_contrast is TRUE.
+
+#### New features
+* Plotting of shared control and repeated measures
+* Proportion plots (unpaired and paired)
+* Mini-Meta Delta plots
+* Delta-Delta plots
+
 
 # dabestr v0.3.0
 * This is a breaking release that includes standardised effect sizes, and a bunch of bugfixes.

R/000_README.R

@@ -1,6 +1,6 @@
-#####################################################' 
+#####################################################'
 #'
-#' The files in this package are all labelled by numbers. 
+#' The files in this package are all labelled by numbers.
 #'
 #' e.g.
 #' 000_README.R
@@ -10,13 +10,14 @@
 #'
 #' This file serves to give an overview of what each number means in the dabestr package.
 #'
-#####################################################' 
+#####################################################'
 #' FILE STRUCTURE
-#####################################################' 
+#####################################################'
 #'
 #' 000 - Info
 #' 001 - Main Api
 #' 002 - Plotting Tools
 #' 003 - Stats Tools
 #' 004 - Main Plots
+#' 005 - Printing Tools
 #' 999 - Plot Kwargs

R/000_data.R

@@ -1,7 +1,7 @@
 #' Non-proportional data for Estimation plots.
-#' 
+#'
 #' Contains 3 Control Samples and 6 Test Samples.
-#' 
+#'
 #' @keywords internal
 #' @format A data frame with 180 rows and 4 variables:
 #'  \describe{
@@ -10,18 +10,18 @@
 #'       \item{Group}{Which control group or test it is}
 #'       \item{Measurement}{Measurement value}
 #'       }
-#' 
-#' @examples 
+#'
+#' @examples
 #' data(non_proportional_data) # Lazy loading. Data becomes visible as soon as it is loaded
 "non_proportional_data"
 
 
 
 
 #' Numerical Binary data for Proportion Plots
-#' 
+#'
 #' Contains 3 Control Samples and 7 Test Samples.
-#' 
+#'
 #' @keywords internal
 #' @format A data frame with 400 rows and 4 variables:
 #'  \describe{
@@ -30,18 +30,18 @@
 #'       \item{Group}{Which control group or test it is}
 #'       \item{Success}{1 (Success) or 0 (Failure)}
 #'       }
-#' 
-#' @examples 
+#'
+#' @examples
 #' data(proportional_data) # Lazy loading. Data becomes visible as soon as it is loaded
 "proportional_data"
 
 
 
 
 #' Data to produce a mini-meta Dabest plot
-#' 
+#'
 #' Contains 3 Control Samples and 3 Test Samples.
-#' 
+#'
 #' @keywords internal
 #' @format A data frame with 120 rows and 5 variables:
 #'  \describe{
@@ -50,18 +50,18 @@
 #'       \item{Group}{Which control group or test it is}
 #'       \item{Measurement}{Measurement value}
 #'       }
-#' 
-#' @examples 
+#'
+#' @examples
 #' data(minimeta_data) # Lazy loading. Data becomes visible as soon as it is loaded
 "minimeta_data"
 
 
 
 
 #' Data to produce a delta2 Dabest plot
-#' 
+#'
 #' Contains 2 Genotype groups and 2 Treatment groups.
-#' 
+#'
 #' @keywords internal
 #' @format A data frame with 40 rows and 5 variables:
 #'  \describe{
@@ -71,7 +71,7 @@
 #'       \item{Treatment}{Which treatment method was used}
 #'       \item{Measurement}{Measurement value}
 #'       }
-#' 
-#' @examples 
+#'
+#' @examples
 #' data(deltadelta_data) # Lazy loading. Data becomes visible as soon as it is loaded
-"deltadelta_data"
+"deltadelta_data"

R/000_globals.R

@@ -1,3 +1,5 @@
-utils::globalVariables(c("N", "n", "plot_extra_yaxis", "proportion_success", "sd", "sf_change", "success_change",
-                         "tag", "x", "x_axis_raw", "x_failure", "x_success", "xend", "y", "y_failure", "y_success",
-                         "failure_change"))
+utils::globalVariables(c(
+  "N", "n", "plot_extra_yaxis", "proportion_success", "sd", "sf_change", "success_change",
+  "tag", "x", "x_axis_raw", "x_failure", "x_success", "xend", "y", "y_failure", "y_success",
+  "failure_change", "y_top_start", "y_top_end", "y_bot_start", "y_bot_end"
+))

R/000_reexports.R

@@ -1,3 +1,3 @@
 #' @importFrom magrittr %>%
 #' @export
-magrittr::`%>%`
+magrittr::`%>%`