diff --git a/.gitignore b/.gitignore index 39511f3..ea97b2a 100644 --- a/.gitignore +++ b/.gitignore @@ -65,4 +65,4 @@ man/ npm-debug.log inst/doc tests/testthat/Rplots.pdf -trial.omv +/trial.omv diff --git a/CITATION.cff b/CITATION.cff index 1beef70..aa1a776 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,5 +1,5 @@ cff-version: 1.2.0 -title: "SummaryTables: Publication-Ready Summary Tables for Jamovi" +title: "SummaryTables: Publication-Ready Summary Tables for jamovi" message: >- If you use this software, please cite it using the metadata from this file. diff --git a/DESCRIPTION b/DESCRIPTION index e163c94..6e467be 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package Package: SummaryTables -Title: Publication-Ready Summary Tables for Jamovi -Version: 1.3.2 +Title: Publication-Ready Summary Tables for jamovi +Version: 1.3.3 Authors@R: person("Nour Edin", "Darwish", , "nouredindarwish@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0009-0009-5527-4539")) @@ -27,30 +27,22 @@ BugReports: https://github.com/NourEdinDarwish/SummaryTables/issues Depends: R (>= 4.1) Imports: - broom.helpers (>= 1.22.0), + broom.helpers, car, - cards (>= 0.7.1), - cardx (>= 0.3.1), - cli, + cardx, datawizard, dplyr, effectsize, flextable, forcats, gt, - gtsummary (>= 2.5.0.9001), + gtsummary, jmvcore (>= 0.8.5), parameters, R6, rlang, smd, - survival, - tidyr -Remotes: - larmarange/broom.helpers@96d2cae, - insightsengineering/cards@v0.7.1, - insightsengineering/cardx@v0.3.1, - ddsjoberg/gtsummary@952b665 + survival Config/roxygen2/version: 8.0.0 Encoding: UTF-8 LazyData: true diff --git a/NEWS.md b/NEWS.md index 711cfa9..5a46438 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,11 @@ +## SummaryTables 1.3.3 + +* Added the Trial dataset to jamovi's Data Library. +* Improved variable selection in Cross Table and Likert Table. +* Fixed an issue with Confidence Interval (CI) formatting. +* Improved statistical test labels. +* General bug-fixes and improvements. + ## SummaryTables 1.3.2 * Added the missing "CI = Confidence Interval" abbreviation source note to Survival Tables. diff --git a/R/00jmv.R b/R/00jmv.R index 08958b3..91704a0 100644 --- a/R/00jmv.R +++ b/R/00jmv.R @@ -4,7 +4,7 @@ .jmvrefs <- list( `SummaryTables`=list( `type`="software", - `title`="SummaryTables: Publication-Ready Summary Tables for Jamovi", + `title`="SummaryTables: Publication-Ready Summary Tables for jamovi", `author`="Darwish, N. E.", `year`=2026, `publisher`="https://doi.org/10.5281/zenodo.18902312", diff --git a/R/pipeline.R b/R/pipeline.R index 47aaaca..5485d69 100644 --- a/R/pipeline.R +++ b/R/pipeline.R @@ -363,11 +363,30 @@ pipeAddCi <- function( # Pattern ----------------------------------------------------------------- statsWithParens <- c("meanSd", "medianIqr", "medianRange", "nPercent", "eda") + + effectiveContStats <- stats::setNames( + rep(options$statContDefault, length(varsCont)), + varsCont + ) + for (item in options$statContSpecific) { + if (item$stat != "useDefault") { + effectiveContStats[[item$var]] <- item$stat + } + } + + effectiveCatStats <- stats::setNames( + rep(options$statCatDefault, length(varsCat)), + varsCat + ) + for (item in options$statCatSpecific) { + if (item$stat != "useDefault") { + effectiveCatStats[[item$var]] <- item$stat + } + } + selectedStats <- c( - options$statContDefault, - options$statCatDefault, - vapply(options$statContSpecific, \(x) x$stat, character(1)), - vapply(options$statCatSpecific, \(x) x$stat, character(1)) + effectiveContStats, + effectiveCatStats ) useSquareBrackets <- any(selectedStats %in% statsWithParens) diff --git a/data/Trial.omv b/data/Trial.omv new file mode 100644 index 0000000..3c9cb1f Binary files /dev/null and b/data/Trial.omv differ diff --git a/docs/assets/default-test-continuous.png b/docs/assets/default-test-continuous.png index bc539b3..6d589be 100644 Binary files a/docs/assets/default-test-continuous.png and b/docs/assets/default-test-continuous.png differ diff --git a/docs/assets/per-variable-tests.png b/docs/assets/per-variable-tests.png index 4cb2de8..adc04f3 100644 Binary files a/docs/assets/per-variable-tests.png and b/docs/assets/per-variable-tests.png differ diff --git a/docs/user-guide.md b/docs/user-guide.md index acd4f1a..e354ca7 100644 --- a/docs/user-guide.md +++ b/docs/user-guide.md @@ -92,7 +92,7 @@ The module automatically selects appropriate statistical tests based on your dat ![Screenshot showing the default test dropdown for continuous variables with parametric and non-parametric options](assets/default-test-continuous.png){ loading=lazy width="500" } -* **Parametric (Default):** Uses the independent t-test (not assuming equal variance) for 2 groups, or one-way ANOVA (not assuming equal variance) for >2 groups. +* **Parametric (Default):** Uses the independent t-test (not assuming equal variances) for 2 groups, or one-way ANOVA (not assuming equal variances) for >2 groups. * **Non-parametric:** Uses the Wilcoxon rank-sum test for 2 groups, or Kruskal-Wallis rank-sum test for >2 groups. !!! info "Grouping Variable in the Continuous Table" diff --git a/jamovi/0000.yaml b/jamovi/0000.yaml index 204eee9..e6b02e1 100644 --- a/jamovi/0000.yaml +++ b/jamovi/0000.yaml @@ -1,12 +1,12 @@ --- title: Publication-Ready Summary Tables name: SummaryTables -version: 1.3.2 +version: 1.3.3 jms: '1.0' authors: - Nour Edin Darwish maintainer: Nour Edin Darwish -date: '2026-05-24' +date: '2026-07-15' type: R description: >- A comprehensive module for creating publication-ready summary and regression @@ -155,6 +155,10 @@ analyses: table with hazard ratios, confidence intervals, and p-values. Includes global p-values, event counts, significance stars, and p-value adjustments. +datasets: + - name: Trial + path: Trial.omv + description: A simulated dataset of 200 patients who received Drug A or Drug B. usesNative: true minApp: 2.7.12 diff --git a/jamovi/00refs.yaml b/jamovi/00refs.yaml index add07e5..4176550 100644 --- a/jamovi/00refs.yaml +++ b/jamovi/00refs.yaml @@ -1,7 +1,7 @@ refs: SummaryTables: type: "software" - title: "SummaryTables: Publication-Ready Summary Tables for Jamovi" + title: "SummaryTables: Publication-Ready Summary Tables for jamovi" author: Darwish, N. E. year: 2026 publisher: "https://doi.org/10.5281/zenodo.18902312" diff --git a/jamovi/tblcontinuous.a.yaml b/jamovi/tblcontinuous.a.yaml index b1ec2b6..6bb6ad7 100644 --- a/jamovi/tblcontinuous.a.yaml +++ b/jamovi/tblcontinuous.a.yaml @@ -241,11 +241,11 @@ options: name: nonparametric - title: t-test name: t.test - - title: t-test (equal variance) + - title: t-test (equal variances) name: t.test.equalVar - title: ANOVA name: oneway.test - - title: ANOVA (equal variance) + - title: ANOVA (equal variances) name: oneway.test.equalVar - title: Wilcoxon rank-sum name: wilcox.test @@ -268,11 +268,11 @@ options: name: useDefault - title: t-test name: t.test - - title: t-test (equal variance) + - title: t-test (equal variances) name: t.test.equalVar - title: ANOVA name: oneway.test - - title: ANOVA (equal variance) + - title: ANOVA (equal variances) name: oneway.test.equalVar - title: Wilcoxon rank-sum name: wilcox.test diff --git a/jamovi/tblcross.u.yaml b/jamovi/tblcross.u.yaml index d737760..8a81a88 100644 --- a/jamovi/tblcross.u.yaml +++ b/jamovi/tblcross.u.yaml @@ -7,6 +7,8 @@ children: - type: VariableSupplier persistentItems: false stretchFactor: 1 + permitted: + - factor children: - type: TargetLayoutBox children: diff --git a/jamovi/tbllikert.u.yaml b/jamovi/tbllikert.u.yaml index 6183058..92e6c52 100644 --- a/jamovi/tbllikert.u.yaml +++ b/jamovi/tbllikert.u.yaml @@ -7,6 +7,8 @@ children: - type: VariableSupplier persistentItems: false stretchFactor: 1 + permitted: + - factor children: - type: TargetLayoutBox children: diff --git a/jamovi/tblsummary.a.yaml b/jamovi/tblsummary.a.yaml index 837a06f..4135964 100644 --- a/jamovi/tblsummary.a.yaml +++ b/jamovi/tblsummary.a.yaml @@ -404,7 +404,7 @@ options: options: - title: t-test name: t.test - - title: t-test (equal variance) + - title: t-test (equal variances) name: t.test.equalVar - title: Wilcoxon rank-sum name: wilcox.test @@ -431,7 +431,7 @@ options: name: useDefault - title: t-test name: t.test - - title: t-test (equal variance) + - title: t-test (equal variances) name: t.test.equalVar - title: Wilcoxon rank-sum name: wilcox.test @@ -584,11 +584,11 @@ options: name: nonparametric - title: t-test name: t.test - - title: t-test (equal variance) + - title: t-test (equal variances) name: t.test.equalVar - title: ANOVA name: oneway.test - - title: ANOVA (equal variance) + - title: ANOVA (equal variances) name: oneway.test.equalVar - title: Wilcoxon rank-sum name: wilcox.test @@ -611,11 +611,11 @@ options: name: useDefault - title: t-test name: t.test - - title: t-test (equal variance) + - title: t-test (equal variances) name: t.test.equalVar - title: ANOVA name: oneway.test - - title: ANOVA (equal variance) + - title: ANOVA (equal variances) name: oneway.test.equalVar - title: Wilcoxon rank-sum name: wilcox.test