From 45f6172cf2c9b813a57ce398a82572bdcab1b72f Mon Sep 17 00:00:00 2001 From: "Mattan S. Ben-Shachar" <35330040+mattansb@users.noreply.github.com> Date: Mon, 10 Oct 2022 10:07:07 +0300 Subject: [PATCH] Cran 0.8 (#516) * version bump * styler * close #471 * Update interpret_bf.Rd * add links * Update effectsize.Rmd * fix doi tag * Update cran-comments.md * revdev * Update _pkgdown.yml * update email * update email * fix link --- .Rbuildignore | 1 + .github/CODE_OF_CONDUCT.md | 2 +- DESCRIPTION | 16 ++++++++-------- NEWS.md | 2 +- R/effectsize-package.R | 8 ++++---- R/interpret_bf.R | 1 - _pkgdown.yml | 15 ++++++++++++--- cran-comments.md | 13 +++++++++---- dev/revdepcheck.R | 5 +++++ man/effectsize-package.Rd | 8 ++++---- man/interpret_bf.Rd | 1 - vignettes/effectsize.Rmd | 34 ++++++++++++++++++---------------- vignettes/interpret.Rmd | 2 ++ 13 files changed, 65 insertions(+), 43 deletions(-) create mode 100644 dev/revdepcheck.R diff --git a/.Rbuildignore b/.Rbuildignore index 260882ff0..53ccd9432 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -48,6 +48,7 @@ references.bib hextools ^paper/. ^WIP/. +^dev/. # Flip these two to no build vignettes: # ^vignettes/(?!additional).* ^vignettes/additional \ No newline at end of file diff --git a/.github/CODE_OF_CONDUCT.md b/.github/CODE_OF_CONDUCT.md index 7f527c485..90fbe9f07 100644 --- a/.github/CODE_OF_CONDUCT.md +++ b/.github/CODE_OF_CONDUCT.md @@ -59,7 +59,7 @@ representative at an online or offline event. ## Enforcement Instances of abusive, harassing, or otherwise unacceptable behavior may be -reported to the community leaders responsible for enforcement at matanshm@post.bgu.ac.il. +reported to the community leaders responsible for enforcement at mattansb@msbstats.info. All complaints will be reviewed and investigated promptly and fairly. All community leaders are obligated to respect the privacy and security of the diff --git a/DESCRIPTION b/DESCRIPTION index d8a736964..275f3b5e5 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,12 +1,12 @@ Type: Package Package: effectsize Title: Indices of Effect Size -Version: 0.7.9.2999 +Version: 0.8.0 Authors@R: c(person(given = "Mattan S.", family = "Ben-Shachar", role = c("aut", "cre"), - email = "matanshm@post.bgu.ac.il", + email = "mattansb@msbstats.info", comment = c(ORCID = "0000-0002-4287-4801", Twitter = "@mattansb")), person(given = "Dominique", family = "Makowski", @@ -44,7 +44,7 @@ Authors@R: role = "rev", email = "jkarreth@ursinus.edu", comment = c(ORCID = "0000-0003-4586-7153"))) -Maintainer: Mattan S. Ben-Shachar +Maintainer: Mattan S. Ben-Shachar Description: Provide utilities to work with indices of effect size for a wide variety of models and hypothesis tests (see list of supported models using the function 'insight::supported_models()'), allowing computation of and @@ -58,14 +58,14 @@ Depends: Imports: bayestestR (>= 0.13.0), insight (>= 0.18.4), - parameters (>= 0.18.2), - performance (>= 0.9.2), - datawizard (>= 0.6.1), + parameters (>= 0.19.0), + performance (>= 0.10.0), + datawizard (>= 0.6.2), stats, utils Suggests: - correlation (>= 0.8.1), - see (>= 0.7.1), + correlation (>= 0.8.2), + see (>= 0.7.3), afex, BayesFactor, boot, diff --git a/NEWS.md b/NEWS.md index 872d5f1a1..1776b8de8 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# effectsize 0.7.0.9999 +# effectsize 0.8.0 ## Breaking Changes diff --git a/R/effectsize-package.R b/R/effectsize-package.R index 98f06bc16..ba31a5cd3 100644 --- a/R/effectsize-package.R +++ b/R/effectsize-package.R @@ -18,13 +18,13 @@ #' and hypothesis tests, such as [cohens_d()], [phi()], [eta_squared()], and #' many more. #' -#' See `vignette("effectsize", package = "effectsize")` for more details, -#' or `vignette(package = "effectsize")` for a full list of vignettes. +#' See [`vignette("effectsize", package = "effectsize")`](https://easystats.github.io/effectsize/articles/effectsize.html) for more details, +#' or [`vignette(package = "effectsize")`](https://easystats.github.io/effectsize/articles/) for a full list of vignettes. #' -#' References: Ben-Shachar et al. (2020) . +#' References: Ben-Shachar et al. (2020) \doi{10.21105/joss.02815}. #' #' @docType package #' @aliases effectsize-package #' @name effectsize-package #' @keywords internal -"_PACKAGE" \ No newline at end of file +"_PACKAGE" diff --git a/R/interpret_bf.R b/R/interpret_bf.R index 7a7f763f9..0a2a185ed 100644 --- a/R/interpret_bf.R +++ b/R/interpret_bf.R @@ -32,7 +32,6 @@ #' interpret_bf(1) #' interpret_bf(c(5, 2)) #' -#' #' @references #' - Jeffreys, H. (1961), Theory of Probability, 3rd ed., Oxford University #' Press, Oxford. diff --git a/_pkgdown.yml b/_pkgdown.yml index 4664035c3..773976b45 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -45,15 +45,22 @@ reference: - datawizard::standardize_models - parameters::standardize_info +- subtitle: "Correlations" + desc: > + Correlations are a standardized effect size of association + contents: + - correlation::correlation + - correlation::cor_test -- title: "Effect Size Conversion / Extraction" + +- title: "Effect Size Conversion" - subtitle: "From Test Statistics" desc: > Extract approximate effect sizes from their commonly associated test statistics contents: - - F_to_eta2 - t_to_r + - F_to_eta2 - chisq_to_phi - subtitle: "Between Effect Sizes" @@ -61,9 +68,9 @@ reference: Approximate effect sizes by converting between other related effect sizes contents: - d_to_r + - oddsratio_to_riskratio - d_to_u3 - eta2_to_f2 - - oddsratio_to_riskratio - odds_to_probs @@ -126,6 +133,8 @@ navbar: href: articles/anovaES.html - text: "Standardized Parameters" href: https://easystats.github.io/parameters/articles/standardize_parameters_effsize.html + - text: "Correlation Vignettes" + href: https://easystats.github.io/correlation/articles/index.html - text: "Confidence Intervals" href: reference/effectsize_CIs.html - text: ------- diff --git a/cran-comments.md b/cran-comments.md index 82c80b1f0..83d78dc61 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -6,8 +6,8 @@ DOI issues are a false positive. * local installation: R 4.2.1 on Windows * GitHub Actions - Windows: devel, release, oldrel - - macOS: devel, release, oldrel, 4.0, 3.6, 3.5 - - ubuntu-18.04: devel, release, oldrel + - macOS: devel, release, oldrel + - ubuntu-18.04: devel, release, oldrel, 4.0, 3.6 * win-builder: release @@ -20,11 +20,16 @@ DOI issues are a false positive. - Failed handshake with *shinyapps.io* is a false positive. - Unavailable DOI link are false positives. +- Spelling mistakes 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 18 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package. - * We saw 0 new problems + * We saw 1 new problems * We failed to check 0 packages + +### New problems + +* statsExpressions - 1 new error. Package maintainer has been informed. diff --git a/dev/revdepcheck.R b/dev/revdepcheck.R new file mode 100644 index 000000000..5b787a5cf --- /dev/null +++ b/dev/revdepcheck.R @@ -0,0 +1,5 @@ +library(revdepcheck) + +revdep_check(num_workers = 4) +revdep_report() +revdep_reset() \ No newline at end of file diff --git a/man/effectsize-package.Rd b/man/effectsize-package.Rd index 67c325ace..99372ed65 100644 --- a/man/effectsize-package.Rd +++ b/man/effectsize-package.Rd @@ -20,10 +20,10 @@ and their confidence intervals (CIs), from a variety of statistical models and hypothesis tests, such as \code{\link[=cohens_d]{cohens_d()}}, \code{\link[=phi]{phi()}}, \code{\link[=eta_squared]{eta_squared()}}, and many more. -See \code{vignette("effectsize", package = "effectsize")} for more details, -or \code{vignette(package = "effectsize")} for a full list of vignettes. +See \href{https://easystats.github.io/effectsize/articles/effectsize.html}{\code{vignette("effectsize", package = "effectsize")}} for more details, +or \href{https://easystats.github.io/effectsize/articles/}{\code{vignette(package = "effectsize")}} for a full list of vignettes. -References: Ben-Shachar et al. (2020) \url{doi:10.21105/joss.02815}. +References: Ben-Shachar et al. (2020) \doi{10.21105/joss.02815}. } \details{ \code{effectsize} @@ -37,7 +37,7 @@ Useful links: } \author{ -\strong{Maintainer}: Mattan S. Ben-Shachar \email{matanshm@post.bgu.ac.il} (\href{https://orcid.org/0000-0002-4287-4801}{ORCID}) (@mattansb) +\strong{Maintainer}: Mattan S. Ben-Shachar \email{mattansb@msbstats.info} (\href{https://orcid.org/0000-0002-4287-4801}{ORCID}) (@mattansb) Authors: \itemize{ diff --git a/man/interpret_bf.Rd b/man/interpret_bf.Rd index 8df3b9794..c547e40ce 100644 --- a/man/interpret_bf.Rd +++ b/man/interpret_bf.Rd @@ -64,7 +64,6 @@ Rules apply to BF as ratios, so BF of 10 is as extreme as a BF of 0.1 (1/10). interpret_bf(1) interpret_bf(c(5, 2)) - } \references{ \itemize{ diff --git a/vignettes/effectsize.Rmd b/vignettes/effectsize.Rmd index 8bcb213dc..0f6708934 100644 --- a/vignettes/effectsize.Rmd +++ b/vignettes/effectsize.Rmd @@ -65,30 +65,32 @@ M <- rbind( cramers_v(M) ``` - +## Parameter and Model Standardization - +> Note: this functionality has been moved to the `parameters` and `datawizard` packages. - - - +Standardizing parameters (i.e., coefficients) can allow for their comparison within and between models, variables and studies. To this end, two functions are available: `standardize()`, which returns an updated model, re-fit with standardized data, and `standardize_parameters()`, which returns a table of standardized coefficients from a provided model [for a list of supported models, see the *insight* package; @luedecke2019insight]. - +```{r} +model <- lm(mpg ~ cyl * am, + data = mtcars) - - +datawizard::standardize(model) - +parameters::standardize_parameters(model) +``` - - - - +Standardized parameters can also be produced for generalized linear models (GLMs; where only the predictors are standardized): - - +```{r} +model <- glm(am ~ cyl + hp, + family = "binomial", + data = mtcars) + +parameters::standardize_parameters(model, exponentiate = TRUE) +``` - +`standardize_parameters()` provides several standardization methods, such as robust standardization, or *pseudo*-standardized coefficients for (generalized) linear mixed models [@hoffman2015longitudinal]. A full review of these methods can be found in the [*Parameter and Model Standardization* vignette](https://easystats.github.io/parameters/articles/standardize_parameters_effsize.html). ## Effect Sizes for ANOVAs diff --git a/vignettes/interpret.Rmd b/vignettes/interpret.Rmd index d08eb6239..c2387519f 100644 --- a/vignettes/interpret.Rmd +++ b/vignettes/interpret.Rmd @@ -67,6 +67,8 @@ more believable. ## Correlation *r* +There can be used to interpret not only Pearson's correlation coefficient, but also Spearman's, $\phi$ (phi), Cramer's *V* and Tschuprow's *T*. Although Cohen's *w* and Pearson's *C* are _not_ a correlation coefficients, they are often also interpreted as such. + #### @funder2019evaluating ```r