CRAN 0.7 (#447)

* remove format std pars * version bump * fix typo * use updated versions of easystats * Update cran-comments.md * run revdep * add recommendation * datawiz version bump * use parameters from CRAN * Update README.md * update to roxygen7.2 @IndrajeetPatil * fix rd issue * remove bad URL * Update cran-comments.md Co-authored-by: Daniel <[email protected]>
easystats · May 26, 2022 · 133daee · 133daee
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: effectsize
 Title: Indices of Effect Size and Standardized Parameters
-Version: 0.6.0.7
+Version: 0.7.0
 Authors@R: 
     c(person(given = "Mattan S.",
              family = "Ben-Shachar",
@@ -56,11 +56,11 @@ BugReports: https://github.com/easystats/effectsize/issues/
 Depends:
     R (>= 3.4)
 Imports:
-    bayestestR (>= 0.11.5.1),
-    insight (>= 0.16.0.16),
-    parameters (>= 0.17.0.10),
-    performance (>= 0.8.0.8),
-    datawizard (>= 0.4.0.17),
+    bayestestR (>= 0.12.1),
+    insight (>= 0.17.0),
+    parameters (>= 0.18.0),
+    performance (>= 0.9.0),
+    datawizard (>= 0.4.1),
     stats,
     utils
 Suggests:
@@ -91,17 +91,11 @@ Suggests:
     spelling,
     testthat,
     tidymodels
-Remotes:
-    easystats/insight,
-    easystats/performance,
-    easystats/parameters,
-    easystats/datawizard,
-    easystats/bayestestR
 VignetteBuilder: 
     knitr
 Encoding: UTF-8
 Language: en-US
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.2
+RoxygenNote: 7.2.0
 Config/testthat/edition: 3
 Config/testthat/parallel: true
diff --git a/NAMESPACE b/NAMESPACE
@@ -16,7 +16,6 @@ S3method(eta_squared_posterior,brmsfit)
 S3method(eta_squared_posterior,stanreg)
 S3method(format,effectsize_anova)
 S3method(format,effectsize_difference)
-S3method(format,effectsize_std_params)
 S3method(format,effectsize_table)
 S3method(format,equivalence_test_effectsize)
 S3method(format,rules)

diff --git a/NEWS.md b/NEWS.md
@@ -1,23 +1,23 @@
-# effectsize 0.6.0.3
+# effectsize 0.7.0
 
 ## Breaking Changes
 
-- `standardize_parameters()`, `standardize_posteriors()`, & `standardize_info()` have been moved to the `parameters` package.  
-- `standardize()` (for models) has been moved to the `datawizard` package.
-- `phi()` only works for 2x2 tables.
-- `cramers_v()` only works for 2D tables.
-
-## Bug fixes
-
-- `kendalls_w()` now deals with ties.  
-- `eta_squared()` works with `car::Manova()` that does not have an i-design. 
+- **`standardize_parameters()`, `standardize_posteriors()`, & `standardize_info()` have been moved to the `parameters` package.**  
+- **`standardize()` (for models) has been moved to the `datawizard` package.**  
+- `phi()` only works for 2x2 tables.  
+- `cramers_v()` only works for 2D tables.  
 
 ## New features
 
 - `normalized_chi()` gives an adjusted Cohen's *w* for goodness of fit.
 - `cohens_w()` is now a fully-fledged function for x-tables and goodness-of-fit effect size (not just an alias for `phi()`).
 - Support for `insight`'s `display`, `print_md` and `print_html` for all `{effectsize}` outputs.
 
+## Bug fixes
+
+- `kendalls_w()` now deals with ties.  
+- `eta_squared()` works with `car::Manova()` that does not have an i-design. 
+
 # effectsize 0.6.0.1
 
 *This is a patch release.*

diff --git a/R/print.effectsize_table.R b/R/print.effectsize_table.R
@@ -189,33 +189,6 @@ format.effectsize_anova <- function(x, digits = 2, ...) {
   format.effectsize_table(x, digits = digits, ...)
 }
 
-#' @export
-format.effectsize_std_params <- function(x, digits = 2, ...) {
-  footer <- caption <- subtitle <- NULL
-
-  caption <- sprintf("Standardization method: %s", attr(x, "std_method"))
-
-  # robust / two_sd
-  if (attr(x, "two_sd") || attr(x, "robust")) {
-    footer <- sprintf("Scaled by %s %s%s from the %s.",
-                      ifelse(attr(x, "two_sd"), "two", "one"),
-                      ifelse(attr(x, "robust"), "MAD", "SD"),
-                      ifelse(attr(x, "two_sd"), "s", ""),
-                      ifelse(attr(x, "robust"), "median", "mean"))
-  }
-
-  # include_response
-  if (!attr(x, "include_response")) {
-    resp_footer <- "Response is unstandardized."
-    footer <- c(footer, resp_footer)
-  }
-
-  attr(x, "table_footer") <- footer
-  attr(x, "table_caption") <- caption
-  attr(x, "table_subtitle") <- subtitle
-  format.effectsize_table(x, digits = digits, ...)
-}
-
 #' @export
 format.equivalence_test_effectsize <- function(x, digits = 2, ...) {
   colnames(x)[colnames(x) == "ROPE_Equivalence"] <- "H0"

diff --git a/R/xtab.R b/R/xtab.R
@@ -26,20 +26,26 @@
 #' Pearson's *C* should be used, as they are bounded between 0-1. Cohen's *w*
 #' can also be used, but since it is not bounded at 1 (can be larger) its
 #' interpretation is more difficult.
-#' \cr\cr
+#' \cr \cr
 #' For goodness-of-fit in 1D tables Cohen's *W*, normalized Chi (\eqn{\chi}) or
 #' Pearson's *C* can be used. Cohen's *w* has no upper bound (can be arbitrarily
 #' large, depending on the expected distribution). Normalized Chi is an adjusted
 #' Cohen's *w*, accounting for the expected distribution, making it bounded
 #' between 0-1. Pearson's *C* is also bounded between 0-1.
-#' \cr\cr
+#' \cr \cr
+#' To summarize, for correlation-like effect sizes, we recommend:
+#'
+#' - For a 2x2 table, use `phi()`
+#' - For larger tables, use `cramers_v()`
+#' - For goodness-of-fit, use `normalized_chi()`
+#' \cr \cr
 #' For 2-by-2 contingency tables, Odds ratios, Risk ratios and Cohen's *h* can
 #' also be estimated. Note that these are computed with each **column**
 #' representing the different groups, and the *first* column representing the
 #' treatment group and the *second* column baseline (or control). Effects are
 #' given as `treatment / control`. If you wish you use rows as groups you must
 #' pass a transposed table, or switch the `x` and `y` arguments.
-#' \cr\cr
+#' \cr \cr
 #' Cohen's *g* is an effect size for dependent (paired) contingency tables
 #' ranging between 0 (perfect symmetry) and 0.5 (perfect asymmetry) (see
 #' [stats::mcnemar.test()]).
@@ -48,13 +54,13 @@
 #' For Cohen's *g*, confidence intervals are based on the proportion (\eqn{P = g
 #' + 0.5}) confidence intervals returned by [stats::prop.test()] (minus 0.5),
 #' which give a good close approximation.
-#' \cr\cr
+#' \cr \cr
 #' For Odds ratios, Risk ratios and Cohen's *h*, confidence intervals are
 #' estimated using the standard normal parametric method (see Katz et al., 1978;
 #' Szumilas, 2010).
-#' \cr\cr
-#' See *Confidence (Compatibility) Intervals (CIs)*, *CIs and Significance
-#' Tests*, and *One-Sided CIs* sections for *phi*, Cohen's *w*, Cramer's *V*,
+#' \cr \cr
+#' See *Confidence (Compatibility) Intervals (CIs)*, *CIs and Significance Tests*,
+#' and *One-Sided CIs* sections for *phi*, Cohen's *w*, Cramer's *V*,
 #' Pearson's *C*, and normalized Chi.
 #'
 #' @inheritSection effectsize_CIs Confidence (Compatibility) Intervals (CIs)

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 [![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
@@ -29,21 +29,17 @@ CRAN:
 install.packages("effectsize")
 ```
 
-Or you can install the latest development version `0.6.0.3` from
+Or you can install the latest development version `0.6.0.7` from
 [*R-universe*](https://easystats.r-universe.dev):
 
 ``` r
 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
@@ -57,21 +53,17 @@ Click on the buttons above to access the package
 [**easystats blog**](https://easystats.github.io/blog/posts/), and
 check-out these vignettes:
 
-  - **Effect Sizes**
-      - [**Parameter and Model
-        Standardization**](https://easystats.github.io/effectsize/articles/standardize_parameters.html)
-      - [**ANOVA Effect
-        Sizes**](https://easystats.github.io/effectsize/articles/anovaES.html)
-      - [**Effect Sizes in Bayesian
-        Models**](https://easystats.github.io/effectsize/articles/bayesian_models.html)  
-      - [**For Simple Hypothesis
+-   **Effect Sizes**
+    -   [**For Simple Hypothesis
         Tests**](https://easystats.github.io/effectsize/articles/simple_htests.html)  
-  - **Effect Sizes Conversion**
-      - [**Between Effect
+    -   [**ANOVA Effect
+        Sizes**](https://easystats.github.io/effectsize/articles/anovaES.html)
+-   **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
@@ -149,38 +141,16 @@ epsilon_squared(model)
 
 And more…
 
-### Regression Models (Standardized Parameters)
-
-Importantly, `effectsize` also provides [advanced
-methods](https://easystats.github.io/effectsize/articles/standardize_parameters.html)
-to compute standardized parameters for regression models.
-
-``` r
-m <- lm(rating ~ complaints + privileges + advance, data = attitude)
-
-standardize_parameters(m)
-## # Standardization method: refit
-## 
-## Parameter   | Coefficient (std.) |        95% CI
-## ------------------------------------------------
-## (Intercept) |          -9.57e-16 | [-0.22, 0.22]
-## complaints  |               0.85 | [ 0.58, 1.13]
-## privileges  |              -0.04 | [-0.33, 0.24]
-## advance     |              -0.02 | [-0.26, 0.22]
-```
-
-Also, models can be re-fit with standardized data:
-
-``` r
-standardize(m)
-## 
-## Call:
-## lm(formula = rating ~ complaints + privileges + advance, data = data_std)
-## 
-## Coefficients:
-## (Intercept)   complaints   privileges      advance  
-##   -9.57e-16     8.55e-01    -4.35e-02    -2.19e-02
-```
+<!-- ### Regression Models (Standardized Parameters) -->
+<!-- Importantly, `effectsize` also provides [advanced methods](https://easystats.github.io/effectsize/articles/standardize_parameters.html) to compute standardized parameters for regression models. -->
+<!-- ```{r beta, warning=FALSE, message=FALSE} -->
+<!-- m <- lm(rating ~ complaints + privileges + advance, data = attitude) -->
+<!-- standardize_parameters(m) -->
+<!-- ``` -->
+<!-- Also, models can be re-fit with standardized data: -->
+<!-- ```{r std-model, warning=FALSE, message=FALSE} -->
+<!-- standardize(m) -->
+<!-- ``` -->
 
 ## Effect Size Conversion
 
@@ -245,7 +215,7 @@ 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
 

diff --git a/cran-comments.md b/cran-comments.md
@@ -6,7 +6,7 @@ All URL issues have been resolved.
 * GitHub Actions
     - Windows:        devel, release, oldrel
     - macOS:          devel, release, oldrel
-    - ubuntu-16.04:   devel, release, oldrel, 3.6, 3.5, 3.4
+    - ubuntu-16.04:   devel, release, oldrel, 4.0, 3.6, 3.5, 3.4
 * win-builder:        release
 
 
@@ -18,11 +18,12 @@ All URL issues have been resolved.
 ### Known issues
 
 - Failed handshake with *shinyapps.io* is a false positive.
+- Unavailable DOI link are false positives.
 
 
 ## revdepcheck results
 
-We checked 16 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
+We checked 17 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
diff --git a/man/effectsize_CIs.Rd b/man/effectsize_CIs.Rd