From 412157075ee519dde3d4944c94cebb7a244c1e68 Mon Sep 17 00:00:00 2001 From: Indrajeet Patil Date: Wed, 24 May 2023 06:50:50 +0200 Subject: [PATCH] CRAN RC 1.5.1 (#242) --- CITATION.cff | 33 +++++++++++-------- DESCRIPTION | 20 +++++------ NEWS.md | 2 +- R/oneway_anova.R | 2 +- README.Rmd | 22 ++++++------- README.md | 12 ------- codemeta.json | 21 ++++++------ .../testthat/_snaps/centrality_description.md | 4 +-- tests/testthat/test-centrality_description.R | 12 +++++-- 9 files changed, 64 insertions(+), 64 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 1ad42b68..009574b7 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ # ----------------------------------------------------------- -# CITATION file created with {cffr} R package, v0.4.1 +# CITATION file created with {cffr} R package, v0.5.0 # See also: https://docs.ropensci.org/cffr/ # ----------------------------------------------------------- @@ -8,7 +8,7 @@ message: 'To cite package "statsExpressions" in publications use:' type: software license: GPL-3.0-only title: 'statsExpressions: Tidy Dataframes and Expressions with Statistical Details' -version: 1.5.0.9000 +version: 1.5.1 doi: 10.21105/joss.03236 abstract: 'Utilities for producing dataframes with rich details for the most common types of statistical approaches and tests: parametric, nonparametric, robust, and @@ -95,7 +95,7 @@ references: - family-names: Ben-Shachar given-names: Mattan S. year: '2023' - version: '>= 1.2-0' + version: '>= 1.3-0' - type: software title: BayesFactor abstract: 'BayesFactor: Computation of Bayes Factors for Common Designs' @@ -145,7 +145,7 @@ references: abstract: 'datawizard: Easy Data Wrangling and Statistical Transformations' notes: Imports url: https://easystats.github.io/datawizard/ - repository: https://CRAN.R-project.org/package=datawizard + repository: https://easystats.r-universe.dev authors: - family-names: Patil given-names: Indrajeet @@ -197,13 +197,13 @@ references: email: davis@posit.co orcid: https://orcid.org/0000-0003-4777-038X year: '2023' - version: '>= 1.1.1' + version: '>= 1.1.2' - type: software title: effectsize abstract: 'effectsize: Indices of Effect Size' notes: Imports url: https://easystats.github.io/effectsize/ - repository: https://CRAN.R-project.org/package=effectsize + repository: https://easystats.r-universe.dev authors: - family-names: Ben-Shachar given-names: Mattan S. @@ -281,8 +281,12 @@ references: given-names: Vincent email: vincent.arel-bundock@umontreal.ca orcid: https://orcid.org/0000-0003-2042-7063 - version: '>= 0.19.1' + - family-names: Bacher + given-names: Etienne + email: etienne.bacher@protonmail.com + orcid: https://orcid.org/0000-0002-9271-5075 year: '2023' + version: '>= 0.19.2' - type: software title: magrittr abstract: 'magrittr: A Forward-Pipe Operator for R' @@ -302,7 +306,7 @@ references: abstract: 'parameters: Processing of Model Parameters' notes: Imports url: https://easystats.github.io/parameters/ - repository: https://CRAN.R-project.org/package=parameters + repository: https://easystats.r-universe.dev authors: - family-names: Lüdecke given-names: Daniel @@ -328,13 +332,13 @@ references: email: brenton@wiernik.org orcid: https://orcid.org/0000-0001-9560-6336 year: '2023' - version: '>= 0.20.3' + version: '>= 0.21.0' - type: software title: performance abstract: 'performance: Assessment of Regression Models Performance' notes: Imports url: https://easystats.github.io/performance/ - repository: https://CRAN.R-project.org/package=performance + repository: https://easystats.r-universe.dev authors: - family-names: Lüdecke given-names: Daniel @@ -361,7 +365,7 @@ references: email: brenton@wiernik.org orcid: https://orcid.org/0000-0001-9560-6336 year: '2023' - version: '>= 0.10.2' + version: '>= 0.10.3' - type: software title: PMCMRplus abstract: 'PMCMRplus: Calculate Pairwise Multiple Comparisons of Mean Rank Sums @@ -374,6 +378,7 @@ references: email: thorsten.pohlert@gmx.de orcid: https://orcid.org/0000-0003-3855-3025 year: '2023' + version: '>= 1.9.6' - type: software title: purrr abstract: 'purrr: Functional Programming Tools' @@ -447,6 +452,7 @@ references: - family-names: Girlich given-names: Maximilian year: '2023' + version: '>= 1.3.0' - type: software title: withr abstract: 'withr: Run Code ''With'' Temporarily Modified Global State' @@ -485,7 +491,6 @@ references: given-names: Rand email: rwilcox@usc.edu year: '2023' - version: '>= 1.1-4' - type: software title: zeallot abstract: 'zeallot: Multiple, Unpacking, and Destructuring Assignment' @@ -664,9 +669,9 @@ references: authors: - family-names: Wickham given-names: Hadley - email: hadley@rstudio.com + email: hadley@posit.co year: '2023' - version: '>= 3.1.7' + version: '>= 3.1.8' - type: software title: utils abstract: 'R: A Language and Environment for Statistical Computing' diff --git a/DESCRIPTION b/DESCRIPTION index 858e5d76..49e6c312 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: statsExpressions Title: Tidy Dataframes and Expressions with Statistical Details -Version: 1.5.0.9000 +Version: 1.5.1 Authors@R: person(given = "Indrajeet", family = "Patil", @@ -25,25 +25,25 @@ BugReports: https://github.com/IndrajeetPatil/statsExpressions/issues Depends: R (>= 4.1.0) Imports: - afex (>= 1.2-0), + afex (>= 1.3-0), BayesFactor (>= 0.9.12-4.4), correlation (>= 0.8.4), datawizard (>= 0.7.1), - dplyr (>= 1.1.1), + dplyr (>= 1.1.2), effectsize (>= 0.8.3), glue, - insight (>= 0.19.1), + insight (>= 0.19.2), magrittr, - parameters (>= 0.20.3), - performance (>= 0.10.2), - PMCMRplus, + parameters (>= 0.21.0), + performance (>= 0.10.3), + PMCMRplus (>= 1.9.6), purrr (>= 1.0.1), rlang, stats, tibble (>= 3.2.1), - tidyr, + tidyr (>= 1.3.0), withr, - WRS2 (>= 1.1-4), + WRS2, zeallot Suggests: ggplot2, @@ -54,7 +54,7 @@ Suggests: rmarkdown, rstantools, survival, - testthat (>= 3.1.7), + testthat (>= 3.1.8), utils VignetteBuilder: knitr diff --git a/NEWS.md b/NEWS.md index ae3a1c41..9a7b8179 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# statsExpressions 1.5.0.9000 +# statsExpressions 1.5.1 ## MAJOR CHANGES diff --git a/R/oneway_anova.R b/R/oneway_anova.R index 85c140ee..48e38ec3 100644 --- a/R/oneway_anova.R +++ b/R/oneway_anova.R @@ -258,7 +258,7 @@ oneway_anova <- function(data, formula = new_formula(enexpr(y), expr(!!enexpr(x) + .rowid)), rscaleFixed = bf.prior, whichRandom = ".rowid", - rscaleRandom = 1 + rscaleRandom = 1.0 ) } diff --git a/README.Rmd b/README.Rmd index 88bc5e28..e158eda6 100644 --- a/README.Rmd +++ b/README.Rmd @@ -87,7 +87,7 @@ table: ```{r} #| label = "kable" -# setup + set.seed(123) # one-sample robust t-test @@ -169,7 +169,7 @@ If you want to display more than one expression in a plot, you will *have to* pa ```{r} #| label = "anova_rob1" -# setup + set.seed(123) library(ggridges) @@ -188,7 +188,7 @@ ggplot(iris, aes(x = Sepal.Length, y = Species)) + ```{r} #| label = "anova_parametric2" -# setup + set.seed(123) library(WRS2) library(ggbeeswarm) @@ -216,7 +216,7 @@ ggplot2::ggplot(WineTasting, aes(Wine, Taste, color = Wine)) + ```{r} #| label = "t_two" -# setup + set.seed(123) library(gghalves) @@ -234,7 +234,7 @@ ggplot(ToothGrowth, aes(supp, len)) + ```{r} #| label = "t_two_paired1" -# setup + set.seed(123) library(tidyr) library(PairedData) @@ -264,7 +264,7 @@ paired.plotProfiles(PrisonStress, "PSSbefore", "PSSafter", subjects = "Subject") ```{r} #| label = "t_one" -# setup + set.seed(123) # dataframe with results @@ -283,7 +283,7 @@ Let's look at another example where we want to run correlation analysis: ```{r} #| label = "corr" -# setup + set.seed(123) # dataframe with results @@ -305,7 +305,7 @@ For categorical/nominal data - one-sample: ```{r} #| label = "gof" -# setup + set.seed(123) # dataframe with results @@ -336,7 +336,7 @@ to display them in plots: ```{r} #| label = "expr_output" -# setup + set.seed(123) # Pearson's chi-squared test of independence @@ -349,7 +349,7 @@ contingency_table(mtcars, am, vs)$expression[[1]] #| label = "metaanalysis", #| fig.height = 14, #| fig.width = 12 -# setup + set.seed(123) library(metaviz) library(metaplus) @@ -380,7 +380,7 @@ include. For example, here only statistic and *p*-values are included: ```{r} #| label = "custom_expr" -# setup + set.seed(123) # extracting detailed expression diff --git a/README.md b/README.md index b8d2a57a..fd8c2841 100644 --- a/README.md +++ b/README.md @@ -54,7 +54,6 @@ The package can be cited as: ``` r citation("statsExpressions") - To cite package 'statsExpressions' in publications use: Patil, I., (2021). statsExpressions: R Package for Tidy Dataframes @@ -160,7 +159,6 @@ Needless to say this will also work with the `kable` function to generate a table: ``` r -# setup set.seed(123) # one-sample robust t-test @@ -265,7 +263,6 @@ If you want to display more than one expression in a plot, you will ### Between-subjects design ``` r -# setup set.seed(123) library(ggridges) @@ -285,7 +282,6 @@ ggplot(iris, aes(x = Sepal.Length, y = Species)) + ### Within-subjects design ``` r -# setup set.seed(123) library(WRS2) library(ggbeeswarm) @@ -314,7 +310,6 @@ ggplot2::ggplot(WineTasting, aes(Wine, Taste, color = Wine)) + ### Between-subjects design ``` r -# setup set.seed(123) library(gghalves) @@ -333,7 +328,6 @@ ggplot(ToothGrowth, aes(supp, len)) + ### Within-subjects design ``` r -# setup set.seed(123) library(tidyr) library(PairedData) @@ -364,7 +358,6 @@ paired.plotProfiles(PrisonStress, "PSSbefore", "PSSafter", subjects = "Subject") ## Expressions for one-sample tests ``` r -# setup set.seed(123) # dataframe with results @@ -384,7 +377,6 @@ ggplot(mtcars, aes(wt)) + Let’s look at another example where we want to run correlation analysis: ``` r -# setup set.seed(123) # dataframe with results @@ -407,7 +399,6 @@ ggplot(mtcars, aes(mpg, wt)) + For categorical/nominal data - one-sample: ``` r -# setup set.seed(123) # dataframe with results @@ -439,7 +430,6 @@ You can also use these function to get the expression in return without having to display them in plots: ``` r -# setup set.seed(123) # Pearson's chi-squared test of independence @@ -452,7 +442,6 @@ contingency_table(mtcars, am, vs)$expression[[1]] ## Expressions for meta-analysis ``` r -# setup set.seed(123) library(metaviz) library(metaplus) @@ -485,7 +474,6 @@ you wish to include. For example, here only statistic and *p*-values are included: ``` r -# setup set.seed(123) # extracting detailed expression diff --git a/codemeta.json b/codemeta.json index c263947f..398932b1 100644 --- a/codemeta.json +++ b/codemeta.json @@ -8,13 +8,13 @@ "codeRepository": "https://github.com/IndrajeetPatil/statsExpressions", "issueTracker": "https://github.com/IndrajeetPatil/statsExpressions/issues", "license": "https://spdx.org/licenses/GPL-3.0", - "version": "1.5.0.9000", + "version": "1.5.1", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R", "url": "https://r-project.org" }, - "runtimePlatform": "R version 4.2.2 (2022-10-31)", + "runtimePlatform": "R version 4.3.0 (2023-04-21)", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -149,7 +149,7 @@ "@type": "SoftwareApplication", "identifier": "testthat", "name": "testthat", - "version": ">= 3.1.7", + "version": ">= 3.1.8", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -175,7 +175,7 @@ "@type": "SoftwareApplication", "identifier": "afex", "name": "afex", - "version": ">= 1.2-0", + "version": ">= 1.3-0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -227,7 +227,7 @@ "@type": "SoftwareApplication", "identifier": "dplyr", "name": "dplyr", - "version": ">= 1.1.1", + "version": ">= 1.1.2", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -265,7 +265,7 @@ "@type": "SoftwareApplication", "identifier": "insight", "name": "insight", - "version": ">= 0.19.1", + "version": ">= 0.19.2", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -290,7 +290,7 @@ "@type": "SoftwareApplication", "identifier": "parameters", "name": "parameters", - "version": ">= 0.20.3", + "version": ">= 0.21.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -303,7 +303,7 @@ "@type": "SoftwareApplication", "identifier": "performance", "name": "performance", - "version": ">= 0.10.2", + "version": ">= 0.10.3", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -316,6 +316,7 @@ "@type": "SoftwareApplication", "identifier": "PMCMRplus", "name": "PMCMRplus", + "version": ">= 1.9.6", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -371,6 +372,7 @@ "@type": "SoftwareApplication", "identifier": "tidyr", "name": "tidyr", + "version": ">= 1.3.0", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -395,7 +397,6 @@ "@type": "SoftwareApplication", "identifier": "WRS2", "name": "WRS2", - "version": ">= 1.1-4", "provider": { "@id": "https://cran.r-project.org", "@type": "Organization", @@ -418,7 +419,7 @@ }, "SystemRequirements": null }, - "fileSize": "4131.834KB", + "fileSize": "4131.884KB", "citation": [ { "@type": "ScholarlyArticle", diff --git a/tests/testthat/_snaps/centrality_description.md b/tests/testthat/_snaps/centrality_description.md index c3bf5b04..45ffd468 100644 --- a/tests/testthat/_snaps/centrality_description.md +++ b/tests/testthat/_snaps/centrality_description.md @@ -1,4 +1,4 @@ -# centrality description works as expected +# centrality description works as expected - no missing data Code select(df, -expression) @@ -75,7 +75,7 @@ list(widehat(mu)[MAP] == "6.40") ---- +# centrality description works as expected - missing data Code select(df_na, -expression) diff --git a/tests/testthat/test-centrality_description.R b/tests/testthat/test-centrality_description.R index 387c940a..02be291a 100644 --- a/tests/testthat/test-centrality_description.R +++ b/tests/testthat/test-centrality_description.R @@ -1,9 +1,8 @@ skip_if_not_installed("boot") test_that( - desc = "centrality description works as expected", + desc = "centrality description works as expected - no missing data", code = { - # data without NAs set.seed(123) df <- purrr::pmap_dfr( .l = list( @@ -20,8 +19,15 @@ test_that( set.seed(123) expect_snapshot(select(df, -expression)) expect_snapshot(df[["expression"]]) + } +) + +test_that( + desc = "centrality description works as expected - missing data", + code = { + # some MAP estimates are different on macOS compared to windows and linux + skip_on_os(c("windows", "linux")) - # data with NAs set.seed(123) df_na <- purrr::pmap_dfr( .l = list(