Merge pull request #405 from easystats/CRAN-0.5.1

CRAN 0.6.0

Author: mattansb

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: effectsize
 Title: Indices of Effect Size and Standardized Parameters
-Version: 0.5.0.2
+Version: 0.6.0
 Authors@R: 
     c(person(given = "Mattan S.",
              family = "Ben-Shachar",
@@ -56,9 +56,9 @@ BugReports: https://github.com/easystats/effectsize/issues/
 Depends:
     R (>= 3.4)
 Imports:
-    bayestestR (>= 0.10.5),
-    insight (>= 0.14.3),
-    parameters (>= 0.15.0.1),
+    bayestestR (>= 0.11.5),
+    insight (>= 0.15.0),
+    parameters (>= 0.16.0),
     performance (>= 0.8.0),
     datawizard (>= 0.2.2),
     stats,
@@ -90,8 +90,6 @@ Suggests:
     spelling,
     testthat,
     tidymodels
-Remotes:
-    easystats/parameters
 VignetteBuilder: 
     knitr
 Encoding: UTF-8

NEWS.md

@@ -1,11 +1,17 @@
-# effectsize 0.5.0.9
+# effectsize 0.6.0
 
 ## Breaking Changes
 
 - `pearsons_c()` effect size column name changed to `Pearsons_c` for consistency. 
 
 ## New features
 
+### New API
+
+See [*Support functions for model extensions* vignette](https://easystats.github.io/effectsize/articles/effectsize_API.html).
+
+### Other features
+
 - `eta_squared()` family now supports `afex::mixed()` models.
 - `cles()` for estimating common language effect sizes.
 - `rb_to_cles()` for converting rank-biserial correlation to Probability of superiority.

R/eta_squared.R

@@ -584,7 +584,7 @@ cohens_f_squared <- function(model, partial = TRUE, ci = 0.95, alternative = "gr
     Sum_Squares_Subjects <- SSS_values$Sum_Squares_residuals
     Mean_Squares_Subjects <- SSS_values$Mean_Square_residuals
 
-    # implemented from https://www.jasonfinley.com/tools/OmegaSquaredQuickRef_JRF_3-31-13.pdf
+    # implemented from https://www.jasonfinley.com/tools/OmegaSquaredQuickRef_JRF_3-31-13.pdf/
     if (!isTRUE(partial)) {
       aov_table$Omega2 <-
         (aov_table$Sum_Squares - aov_table$df * Mean_Square_residuals) /

R/interpret_omega_squared.R

@@ -21,7 +21,7 @@
 #' @examples
 #' interpret_eta_squared(.02)
 #' interpret_eta_squared(c(.5, .02), rules = "cohen1992")
-#' @seealso http://imaging.mrc-cbu.cam.ac.uk/statswiki/FAQ/effectSize
+#' @seealso https://imaging.mrc-cbu.cam.ac.uk/statswiki/FAQ/effectSize/
 #'
 #'
 #' @references

R/rank_effectsizes.R

@@ -235,7 +235,7 @@ rank_biserial <- function(x,
       nd <- sum((x - mu) != 0)
       maxw <- (nd^2 + nd) / 2
 
-      # From: https://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test#Historical_T_statistic
+      # From: https://en.wikipedia.org/wiki/Wilcoxon_signed-rank_test#Historical_T_statistic/
       # wSE <- sqrt((n * (n + 1) * (2 * n + 1)) / 24)
       # Delta method for f(x) = w * 2 / (maxw) - 1
       # r_rbsSE <- wSE * sqrt(4 / (maxw)^2)
@@ -248,7 +248,7 @@ rank_biserial <- function(x,
       n1 <- length(x)
       n2 <- length(y)
 
-      # From: https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test#Normal_approximation_and_tie_correction
+      # From: https://en.wikipedia.org/wiki/Mann%E2%80%93Whitney_U_test#Normal_approximation_and_tie_correction/
       # wSE <- sqrt((n1 * n2 * (n1 + n2 + 1)) / 12)
       # Delta method for f(x) = 1 - 2 * w / (n1 * n2) * sign(diff)
       # r_rbsSE <- wSE * sqrt(4 / (n1 * n2)^2)

R/standardize_info.R

@@ -282,11 +282,13 @@ standardize_info.default <- function(model, robust = FALSE, two_sd = FALSE, incl
     means <- deviations <- rep(NA_real_, length = length(names(model_matrix)))
     for (i in seq_along(names(model_matrix))) {
       var <- names(model_matrix)[i]
-      if (types$Link[types$Parameter == var] == "Difference") {
+      if (any(types$Parameter == var) &&
+          types$Link[types$Parameter == var] == "Difference") {
         parent_var <- types$Variable[types$Parameter == var]
         intercept <- unique(data[[parent_var]])[1]
         response_at_intercept <- response[data[[parent_var]] == intercept]
         weights_at_intercept <- if (length(w)) w[data[[parent_var]] == intercept] else NULL
+
         std_info <- .compute_std_info(
           response = response_at_intercept,
           robust = robust, weights = weights_at_intercept

README.Rmd

@@ -30,9 +30,10 @@ knitr::opts_chunk$set(
 set.seed(111)
 ```
 
-[![DOI](https://joss.theoj.org/papers/10.21105/joss.02815/status.svg)](https://doi.org/10.21105/joss.02815)
-[![downloads](http://cranlogs.r-pkg.org/badges/effectsize)](https://cran.r-project.org/package=effectsize)
-[![total](https://cranlogs.r-pkg.org/badges/grand-total/effectsize)](https://cran.r-project.org/package=effectsize) [![status](https://tinyverse.netlify.com/badge/effectsize)](https://CRAN.R-project.org/package=effectsize)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.02815/status.svg/)](https://doi.org/10.21105/joss.02815)
+[![downloads](https://cranlogs.r-pkg.org/badges/effectsize)](https://cran.r-project.org/package=effectsize/)
+[![total](https://cranlogs.r-pkg.org/badges/grand-total/effectsize)](https://cran.r-project.org/package=effectsize/)
+[![status](https://tinyverse.netlify.com/badge/effectsize/)](https://CRAN.R-project.org/package=effectsize/)
 
 
 ***Significant is just not enough!***
@@ -42,22 +43,22 @@ The goal of this package is to provide utilities to work with indices of effect
 
 ## Installation
 
-[![CRAN](http://www.r-pkg.org/badges/version/effectsize)](https://cran.r-project.org/package=effectsize)
-[![effectsize status badge](https://easystats.r-universe.dev/badges/effectsize)](https://easystats.r-universe.dev)
-[![R-check](https://github.com/easystats/effectsize/workflows/R-check/badge.svg)](https://github.com/easystats/effectsize/actions)
-[![pkgdown](https://github.com/easystats/effectsize/workflows/pkgdown/badge.svg)](https://github.com/easystats/effectsize/actions)
-[![Codecov test coverage](https://codecov.io/gh/easystats/effectsize/branch/main/graph/badge.svg)](https://codecov.io/gh/easystats/effectsize?branch=main)
+[![CRAN](https://www.r-pkg.org/badges/version/effectsize)](https://cran.r-project.org/package=effectsize/)
+[![effectsize status badge](https://easystats.r-universe.dev/badges/effectsize/)](https://easystats.r-universe.dev/)
+[![R-check](https://github.com/easystats/effectsize/workflows/R-check/badge.svg/)](https://github.com/easystats/effectsize/actions/)
+[![pkgdown](https://github.com/easystats/effectsize/workflows/pkgdown/badge.svg/)](https://github.com/easystats/effectsize/actions/)
+[![Codecov test coverage](https://codecov.io/gh/easystats/effectsize/branch/main/graph/badge.svg/)](https://app.codecov.io/gh/easystats/effectsize?branch=main/)
 
 Run the following to install the stable release of **effectsize** from CRAN:
 
 ```{r install-CRAN, warning=FALSE, message=FALSE, eval=FALSE}
 install.packages("effectsize")
 ```
 
-Or you can install the latest development version ``r available.packages(repos = "https://easystats.r-universe.dev")["effectsize","Version"]`` from [*R-universe*](https://easystats.r-universe.dev):
+Or you can install the latest development version ``r available.packages(repos = "https://easystats.r-universe.dev/")["effectsize","Version"]`` from [*R-universe*](https://easystats.r-universe.dev):
 
 ```{r install-R-universe, warning=FALSE, message=FALSE, eval=FALSE}
-install.packages("effectsize", repos = "https://easystats.r-universe.dev")
+install.packages("effectsize", repos = "https://easystats.r-universe.dev/")
 ```
 
 <!-- Or from *GitHub*: -->
@@ -69,9 +70,9 @@ install.packages("effectsize", repos = "https://easystats.r-universe.dev")
 
 ## Documentation
 
-[![Documentation](https://img.shields.io/badge/documentation-effectsize-orange.svg?colorB=E91E63)](https://easystats.github.io/effectsize/)
-[![Blog](https://img.shields.io/badge/blog-easystats-orange.svg?colorB=FF9800)](https://easystats.github.io/blog/posts/)
-[![Features](https://img.shields.io/badge/features-effectsize-orange.svg?colorB=2196F3)](https://easystats.github.io/effectsize/reference/index.html)
+[![Documentation](https://img.shields.io/badge/documentation-effectsize-orange.svg?colorB=E91E63/)](https://easystats.github.io/effectsize/)
+[![Blog](https://img.shields.io/badge/blog-easystats-orange.svg?colorB=FF9800/)](https://easystats.github.io/blog/posts/)
+[![Features](https://img.shields.io/badge/features-effectsize-orange.svg?colorB=2196F3/)](https://easystats.github.io/effectsize/reference/index.html)
 
 Click on the buttons above to access the package [**documentation**](https://easystats.github.io/effectsize/) and the [**easystats blog**](https://easystats.github.io/blog/posts/), and check-out these vignettes:
 
@@ -205,4 +206,4 @@ Corresponding BibTeX entry:
 
 # Contributing and Support
 
-If you have any questions regarding the the functionality of the package, you may either contact us via email or also [file an issue](https://github.com/easystats/effectsize/issues). Anyone wishing to contribute to the package by adding functions, features, or in another way, please follow [this guide](https://github.com/easystats/effectsize/blob/main/.github/CONTRIBUTING.md) and our [code of conduct](https://github.com/easystats/effectsize/blob/main/.github/CODE_OF_CONDUCT.md).
+If you have any questions regarding the the functionality of the package, you may either contact us via email or also [file an issue](https://github.com/easystats/effectsize/issues/). Anyone wishing to contribute to the package by adding functions, features, or in another way, please follow [this guide](https://github.com/easystats/effectsize/blob/main/.github/CONTRIBUTING.md/) and our [code of conduct](https://github.com/easystats/effectsize/blob/main/.github/CODE_OF_CONDUCT.md/).

README.md

@@ -1,26 +1,26 @@
 
 # effectsize <img src="man/figures/logo.png" align="right" width="120" />
 
-[![DOI](https://joss.theoj.org/papers/10.21105/joss.02815/status.svg)](https://doi.org/10.21105/joss.02815)
-[![downloads](http://cranlogs.r-pkg.org/badges/effectsize)](https://cran.r-project.org/package=effectsize)
-[![total](https://cranlogs.r-pkg.org/badges/grand-total/effectsize)](https://cran.r-project.org/package=effectsize)
-[![status](https://tinyverse.netlify.com/badge/effectsize)](https://CRAN.R-project.org/package=effectsize)
+[![DOI](https://joss.theoj.org/papers/10.21105/joss.02815/status.svg/)](https://doi.org/10.21105/joss.02815)
+[![downloads](https://cranlogs.r-pkg.org/badges/effectsize)](https://cran.r-project.org/package=effectsize/)
+[![total](https://cranlogs.r-pkg.org/badges/grand-total/effectsize)](https://cran.r-project.org/package=effectsize/)
+[![status](https://tinyverse.netlify.com/badge/effectsize/)](https://CRAN.R-project.org/package=effectsize/)
 
-***Significant is just not enough\!***
+***Significant is just not enough!***
 
 The goal of this package is to provide utilities to work with indices of
 effect size and standardized parameters, allowing computation and
 conversion of indices such as Cohen’s *d*, *r*, odds-ratios, etc.
 
 ## Installation
 
-[![CRAN](http://www.r-pkg.org/badges/version/effectsize)](https://cran.r-project.org/package=effectsize)
+[![CRAN](https://www.r-pkg.org/badges/version/effectsize)](https://cran.r-project.org/package=effectsize/)
 [![effectsize status
-badge](https://easystats.r-universe.dev/badges/effectsize)](https://easystats.r-universe.dev)
-[![R-check](https://github.com/easystats/effectsize/workflows/R-check/badge.svg)](https://github.com/easystats/effectsize/actions)
-[![pkgdown](https://github.com/easystats/effectsize/workflows/pkgdown/badge.svg)](https://github.com/easystats/effectsize/actions)
+badge](https://easystats.r-universe.dev/badges/effectsize/)](https://easystats.r-universe.dev/)
+[![R-check](https://github.com/easystats/effectsize/workflows/R-check/badge.svg/)](https://github.com/easystats/effectsize/actions/)
+[![pkgdown](https://github.com/easystats/effectsize/workflows/pkgdown/badge.svg/)](https://github.com/easystats/effectsize/actions/)
 [![Codecov test
-coverage](https://codecov.io/gh/easystats/effectsize/branch/main/graph/badge.svg)](https://codecov.io/gh/easystats/effectsize?branch=main)
+coverage](https://codecov.io/gh/easystats/effectsize/branch/main/graph/badge.svg/)](https://app.codecov.io/gh/easystats/effectsize?branch=main/)
 
 Run the following to install the stable release of **effectsize** from
 CRAN:
@@ -33,45 +33,41 @@ Or you can install the latest development version `0.5.0.2` from
 [*R-universe*](https://easystats.r-universe.dev):
 
 ``` r
-install.packages("effectsize", repos = "https://easystats.r-universe.dev")
+install.packages("effectsize", repos = "https://easystats.r-universe.dev/")
 ```
 
 <!-- Or from *GitHub*: -->
-
 <!-- ```{r, warning=FALSE, message=FALSE, eval=FALSE} -->
-
 <!-- if (!require("remotes")) install.packages("remotes") -->
-
 <!-- remotes::install_github("easystats/effectsize") -->
-
 <!-- ``` -->
 
 ## Documentation
 
-[![Documentation](https://img.shields.io/badge/documentation-effectsize-orange.svg?colorB=E91E63)](https://easystats.github.io/effectsize/)
-[![Blog](https://img.shields.io/badge/blog-easystats-orange.svg?colorB=FF9800)](https://easystats.github.io/blog/posts/)
-[![Features](https://img.shields.io/badge/features-effectsize-orange.svg?colorB=2196F3)](https://easystats.github.io/effectsize/reference/index.html)
+[![Documentation](https://img.shields.io/badge/documentation-effectsize-orange.svg?colorB=E91E63/)](https://easystats.github.io/effectsize/)
+[![Blog](https://img.shields.io/badge/blog-easystats-orange.svg?colorB=FF9800/)](https://easystats.github.io/blog/posts/)
+[![Features](https://img.shields.io/badge/features-effectsize-orange.svg?colorB=2196F3/)](https://easystats.github.io/effectsize/reference/index.html)
 
 Click on the buttons above to access the package
 [**documentation**](https://easystats.github.io/effectsize/) and the
 [**easystats blog**](https://easystats.github.io/blog/posts/), and
 check-out these vignettes:
 
-  - **Effect Sizes**
-      - [**Parameter and Model
+-   **Effect Sizes**
+    -   [**Parameter and Model
         Standardization**](https://easystats.github.io/effectsize/articles/standardize_parameters.html)
-      - [**ANOVA Effect
+    -   [**ANOVA Effect
         Sizes**](https://easystats.github.io/effectsize/articles/anovaES.html)
-      - [**Effect Sizes in Bayesian
+    -   [**Effect Sizes in Bayesian
         Models**](https://easystats.github.io/effectsize/articles/bayesian_models.html)  
-      - [**For Simple Hypothesis
+    -   [**For Simple Hypothesis
         Tests**](https://easystats.github.io/effectsize/articles/simple_htests.html)  
-  - **Effect Sizes Conversion**
-      - [**Between Effect
+-   **Effect Sizes Conversion**
+    -   [**Between Effect
         Sizes**](https://easystats.github.io/effectsize/articles/convert.html)
-      - [**Effect Size from Test
+    -   [**Effect Size from Test
         Statistics**](https://easystats.github.io/effectsize/articles/from_test_statistics.html)
-  - [**Automated Interpretation of Indices of Effect
+-   [**Automated Interpretation of Indices of Effect
     Size**](https://easystats.github.io/effectsize/articles/interpret.html)
 
 # Features
@@ -245,7 +241,7 @@ interpret_cohens_d(d = 0.45, rules = "gignac2016")
 
 In order to cite this package, please use the following citation:
 
-  - Ben-Shachar M, Lüdecke D, Makowski D (2020). effectsize: Estimation
+-   Ben-Shachar M, Lüdecke D, Makowski D (2020). effectsize: Estimation
     of Effect Size Indices and Standardized Parameters. *Journal of Open
     Source Software*, *5*(56), 2815. doi: 10.21105/joss.02815
 
@@ -268,9 +264,9 @@ Corresponding BibTeX entry:
 
 If you have any questions regarding the the functionality of the
 package, you may either contact us via email or also [file an
-issue](https://github.com/easystats/effectsize/issues). Anyone wishing
+issue](https://github.com/easystats/effectsize/issues/). Anyone wishing
 to contribute to the package by adding functions, features, or in
 another way, please follow [this
-guide](https://github.com/easystats/effectsize/blob/main/.github/CONTRIBUTING.md)
+guide](https://github.com/easystats/effectsize/blob/main/.github/CONTRIBUTING.md/)
 and our [code of
-conduct](https://github.com/easystats/effectsize/blob/main/.github/CODE_OF_CONDUCT.md).
+conduct](https://github.com/easystats/effectsize/blob/main/.github/CODE_OF_CONDUCT.md/).

_pkgdown.yml

@@ -1,10 +1,10 @@
 authors:
   Mattan S. Ben-Shachar:
-    href: https://github.com/mattansb
+    href: https://github.com/mattansb/
   Dominique Makowski:
     href: https://dominiquemakowski.github.io/
   Daniel Lüdecke:
-    href: https://github.com/strengejacke
+    href: https://github.com/strengejacke/
   Indrajeet Patil:
     href: https://sites.google.com/site/indrajeetspatilmorality/
   Brenton M. Wiernik:
@@ -24,7 +24,7 @@ navbar:
   components:
     twitter:
       icon: fa-twitter
-      href: http://twitter.com/easystats4u
+      href: https://twitter.com/easystats4u
       aria-label: Twitter
   left:
     - icon: fa-home fa-lg

cran-comments.md

@@ -1,25 +1,29 @@
+All URL issues have been resolved.
+
 ## Test environments
 
-* local R installation:          R 4.1.0
-* GitHub Actions (windows):      devel, release, oldrel
-* Github Actions (macOS):        devel, release, oldrel
-* GitHub Actions (ubuntu-16.04): devel, release, oldrel, 3.6, 3.5, 3.4
-* win-builder:                   release
+* local installation: R 4.1.1 on Windows
+* GitHub Actions
+    - Windows:        devel, release, oldrel
+    - macOS:          devel, release, oldrel
+    - ubuntu-16.04:   devel, release, oldrel, 3.6, 3.5, 3.4
+* win-builder:        release
 
 
 ## R CMD check results
 
 0 errors | 0 warnings | 0 notes
 
-### Known issues
 
-- Failed handshake with shinyapps.io is a false positive.
+### Known issues
 
+- Failed handshake with *shinyapps.io* is a false positive.
 
 
-## `revdepcheck` results
+## revdepcheck results
 
-We checked 15 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 16 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
- * We saw 0 new problems
- * We failed to check 0 packages
+ * We saw 1 new problems
+    * `report`: Error is expected. Authors have been updated and will submit updated package.
+ * We failed to check 0 packages

man/interpret_omega_squared.Rd

@@ -79,7 +79,7 @@ @article{patil2020ggstatsplot
   author = {Indrajeet Patil},
   year = {2018},
   journal = {CRAN},
-  url = {https://CRAN.R-project.org/package=ggstatsplot},
+  url = {https://CRAN.R-project.org/package=ggstatsplot/},
   doi = {10.5281/zenodo.2074621},
 }
 
@@ -88,7 +88,7 @@ @manual{sjoberg2020gtsummary
   author = {Daniel D. Sjoberg and Michael Curry and Margie Hannum and Karissa Whiting and Emily C. Zabor},
   year = {2020},
   note = {R package version 1.3.5},
-  url = {https://CRAN.R-project.org/package=gtsummary},
+  url = {https://CRAN.R-project.org/package=gtsummary/},
 }
 
 @article{luedecke2019insight,
@@ -107,23 +107,23 @@ @manual{behrendt2014lmbeta
   author = {Stefan Behrendt},
   year = {2014},
   note = {R package version 1.5-1},
-  url = {https://CRAN.R-project.org/package=lm.beta},
+  url = {https://CRAN.R-project.org/package=lm.beta/},
 }
 
 @manual{buchanan2019MOTE,
   title = {{MOTE: Measure of the Effect}: Package to assist in effect size calculations and their confidence intervals},
   author = {Erin M. Buchanan and Amber Gillenwaters and John E. Scofield and K.D. Valentine},
   year = {2019},
   note = {R package version 1.0.2},
-  url = {http://github.com/doomlab/MOTE},
+  url = {https://github.com/doomlab/MOTE/},
 }
 
 @manual{kelley2020MBESS,
   title = {MBESS: The MBESS {R} Package},
   author = {Ken Kelley},
   year = {2020},
   note = {R package version 4.8.0},
-  url = {https://CRAN.R-project.org/package=MBESS},
+  url = {https://CRAN.R-project.org/package=MBESS/},
 }
 
 @book{cohen1988statistical,