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Pull request overview
Updates the package namespace and documentation while adjusting the CI coverage workflow configuration.
Changes:
- Export
jaspPlotBuilderinNAMESPACE. - Add roxygen2-generated
.Rdfiles for several exported functions. - Update the Codecov/test coverage workflow triggers and configuration (including draft-PR gating and JAGS setting).
Reviewed changes
Copilot reviewed 8 out of 8 changed files in this pull request and generated 12 comments.
Show a summary per file
| File | Description |
|---|---|
| man/raincloudPlots.Rd | Adds generated help page for raincloudPlots. |
| man/jaspPlotBuilder.Rd | Adds generated help page for jaspPlotBuilder. |
| man/flexplot.Rd | Adds generated help page for flexplot. |
| man/DescriptivesTimeSeries.Rd | Adds generated help page for DescriptivesTimeSeries. |
| man/Descriptives.Rd | Adds generated help page for Descriptives. |
| NAMESPACE | Exports jaspPlotBuilder. |
| DESCRIPTION | Records the roxygen2 version via RoxygenNote. |
| .github/workflows/test-coverage.yml | Updates coverage workflow triggers/conditions and toggles needs_JAGS. |
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| \item{showPoint, }{Whether or not the points of a cloud should be shown. If un-checked, opacity is set to 0.<br>If you have many, many points, it can be helpful to hide them.<br><br><h3>Element Settings</h3><h4>Nudge</h4>The nudge for violin, box, and point determines how far the elements are nudged from the center (axis tick).<br>By default, the box is in the center (nudge = 0) and the violin is nudged to the right. The points are nudged to the left of the box.<br>With a custom orientation (see Advanced section), the points get centered (nudge fixed to 0). Violin and box are nudged depending on orientation: left or right.<h4>Height, Width, and Spread</h4>These settings determine the respective properties of the elements:<br><br>How high should the violin peak? (Does not change the proportions of the probability density.)<br>With a custom orientation to the left (see Advanced Section), it can be helpful to decrease the height if the violin overlaps with axis ticks.<br><br>How wide should the box be?<br><br>How wide should the points spread? I.e., how jittered should they be along the x-axis (y-axis if horizontal plot?.<br>Note, that this still correctly shows the values of the points on the dependent variable axis.<br>(If you would also like y-jitter see the 'Jitter' option for points.)<h4>Box Padding</h4>With a secondary factor, there will be a box for each factor level. With the padding, you can change the spacing between theses boxes.<br>Increasing the padding will - visually - decrease the box width. If you want to keep box width constant, also increase the box width.<h4>Point Size</h4>We recommend a greater size, the fewer points you have.<h4>Opacity</h4>Increase this to _decrease_ the transparency of the respective element.<h4>Outline and Outline Width</h4>Would you like the outline to match the 'Color palette', be 'black', or have 'none' at all?<br>The width determines how thick the outline is.<h4>Violin Smoothing</h4>This percentage determines the smoothness of the probability density.<br>The lower, the stronger it is influenced by the presence/absence of individual points.<h4>Point Jitter</h4>Use this with care!<br>It slightly jitters the points along the dependent variable axis. This means that the position of the points no longer matches the values of the observations.<br>If you want to have less overlap between the points while keeping an accurate visualization, increases the point spread.<br>Using point jitter can be useful in some cases. For example, if you are working with likert data.<h4>ID Lines Width</h4>Determines how thick the lines are. | ||
| Defaults to \code{TRUE}.} |
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This paragraph has a few typos/grammar issues that will show up in the help page (e.g., “theses boxes” → “these boxes”, “increases the point spread” → “increase the point spread”, and the stray “plot?.” punctuation). Please fix in the roxygen source so regenerated Rd stays correct.
| \item{varianceCi, }{a confidence interval for the variance based on bootstrap samples. | ||
| Defaults to \code{FALSE}.} | ||
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| \item{varianceCiMethod, }{How should the confidence interval be computed? By default, we use a analytical approach (chi-square). The alternative option is `Bootstrap`} |
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Grammar in docs: “we use a analytical approach” should be “we use an analytical approach”. Please fix in the roxygen source to keep regenerated Rd correct.
Suggested change
| \item{varianceCiMethod, }{How should the confidence interval be computed? By default, we use a analytical approach (chi-square). The alternative option is `Bootstrap`} | |
| \item{varianceCiMethod, }{How should the confidence interval be computed? By default, we use an analytical approach (chi-square). The alternative option is `Bootstrap`} |
| ) | ||
| } | ||
| \arguments{ | ||
| \item{colorAnyway, }{Applies the color palette to the levels of the primary factor. Otherwise, the plot stays black and white.<br>This option is superseeded by a secondary factor; then color coding is according to that. |
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Spelling typo in the generated documentation: “superseeded” should be “superseded”. Please fix in the roxygen source (R/raincloudPlotsWrapper.R) so it doesn’t reappear on regeneration.
Suggested change
| \item{colorAnyway, }{Applies the color palette to the levels of the primary factor. Otherwise, the plot stays black and white.<br>This option is superseeded by a secondary factor; then color coding is according to that. | |
| \item{colorAnyway, }{Applies the color palette to the levels of the primary factor. Otherwise, the plot stays black and white.<br>This option is superseded by a secondary factor; then color coding is according to that. |
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| \item{covariate, }{Points are color coded according to this.} | ||
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| \item{covariatePalette, }{How to color code the covariate. 'Viridis' works good for both discrete and continuous covariates.} |
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Grammar in docs: “works good” should be “works well” (or similar). Please fix in the roxygen source so regenerated Rd stays correct.
Suggested change
| \item{covariatePalette, }{How to color code the covariate. 'Viridis' works good for both discrete and continuous covariates.} | |
| \item{covariatePalette, }{How to color code the covariate. 'Viridis' works well for both discrete and continuous covariates.} |
| \item{mean, }{Whether to also show a mean for each cloud.<h4>Position</h4>Use a 'Custom' position to have the mean placed inside of the box - even if you do not show the box.<br>In fact, the mean nudge and distance fields are synchronized with the box nudge and box fields, respectively.<br>Use the 'On axis ticks' position to have all means for each primary factor level on top of each other.<br>This can be useful if you want to show the change of secondary factor levels (e.g. groups) across the primary factor levels (e.g. time).<h4>Size</h4>Try different values to make your plot especially pretty.<h4>Mean Lines: Width</h4>See outline width of box and violin as well as ID lines width. | ||
| Defaults to \code{FALSE}.} | ||
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| \item{meanInterval, }{Whether to also show an interval around the mean.<br>This hides and disables the box.<br><br>You can choose between a confidence interval, ±1 standard error, or ±1 standard deviation.<br>For the computation of the confidence interval/se/sd, within and between factors are determined based on the specifciation of the ID variable<br><h4> |
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The meanInterval argument description appears to contain a dangling “
” HTML tag (and also has a typo “specifciation”). This can produce broken rendering in the help page. Please remove/close the tag and correct the typo in the roxygen source.
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| \item{meanInterval, }{Whether to also show an interval around the mean.<br>This hides and disables the box.<br><br>You can choose between a confidence interval, ±1 standard error, or ±1 standard deviation.<br>For the computation of the confidence interval/se/sd, within and between factors are determined based on the specifciation of the ID variable<br><h4> | |
| \item{meanInterval, }{Whether to also show an interval around the mean.<br>This hides and disables the box.<br><br>You can choose between a confidence interval, ±1 standard error, or ±1 standard deviation.<br>For the computation of the confidence interval/se/sd, within and between factors are determined based on the specification of the ID variable. |
.github/workflows/test-coverage.yml
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| uses: jasp-stats/jasp-actions/.github/workflows/coverage.yml@master | ||
| with: | ||
| needs_JAGS: false | ||
| needs_JAGS: true |
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needs_JAGS is set to true here, but this package’s unit-tests workflow uses needs_JAGS: false and there’s no obvious JAGS usage in the code/tests. Unless coverage requires JAGS-specific dependencies, consider keeping this false to avoid extra setup time and potential CI failures when JAGS isn’t available.
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| \item{numberOfClouds, }{To apply custom cloud orientation or custom mean intervals, you first must specify the number of clouds that are currently shown in the plot.<br>If the number you entered does not match the number of clouds in the plot, the plot caption will show a warning and you can correct your entry.<br>The number you specify determines the number of rows in the table.<br><br>In the table, you can then specify the custom orientation ('L' vs. 'R') for each cloud as well as custom lower and upper interval limits for each mean.<br>Make sure to also check the corresponding checkboxes 'Apply custom orientation' or 'Apply custom mean interval limits'.<br>Otherwise, your input into the table will not be applied.<br><br>The order in which the rows of the table are mapped to the clouds in the plot is as follows:<br>Suppose, there are three times of measurement (primary factor): pre, post, and follow-up.<br>Further, there are two species (secondary factor): alpha and beta.<br>This means that there are 6 clouds, in the following order:<br>pre-alpha<br>pre-beta<br>post-alpha<br>post-beta<br>follow-up-alpha<br>follow-up-beta<br><br>In this example you could now specify the odd rows as 'L' and the even rows as 'R'.<br>That way, at each time point, the left cloud would be alpha and the right cloud would be beta.<br>If you have a 2x2 design (e.g. no follow-up in as primary factor), then a useful custom orientation could be LLRR.<br>That way, both the alpha and the beta cloud at time point pre would be left and at time point they would be right.<br>Combine this with ID input to connect the individual observations over time.<br>They will then run between the two clouds on the left to the two clouds on the right.<br><br>Any custom orientation or mean intervals will be applied to the plot of every dependent variable.<br>How can you specify different custom mean intervals for two dependent variables?<br>For this, you can duplicate the analysis (see symbol: white plus on green background),<br>only select one dependent variable in each version, and specify the custom intervals separately.<br><br>For custom cloud colors, just enter the hexcode you want. This features only works when there is no Secondary Factor.} | ||
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| \item{observationId, }{Select a participant/observation ID in your dataset, to connect individual observations (points) accross the levels of the primary factor. Otherwise, you do not need this.} |
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Spelling typo in docs: “accross” should be “across”. Please fix in the roxygen source (R/raincloudPlotsWrapper.R).
Suggested change
| \item{observationId, }{Select a participant/observation ID in your dataset, to connect individual observations (points) accross the levels of the primary factor. Otherwise, you do not need this.} | |
| \item{observationId, }{Select a participant/observation ID in your dataset, to connect individual observations (points) across the levels of the primary factor. Otherwise, you do not need this.} |
| \item{showCaption, }{The caption provides important information about the plot such as warnings, if there are any.<br>We strongly recommend to leave this checkbox checked and to only un-check it if you are otherwise happy with the plot and want to export it.<h3>Plot Size: Width and Height</h3>This also includes the legend (if there is color coding) and the caption.<br>While you can also change the size of a JASP plot with your mouse, the precise specification of width and height allows you to exactly reproduce a plot. | ||
| Defaults to \code{TRUE}.} | ||
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| \item{showLegend, }{Shows the legend for the color-coding of the primary factor.<br>This option is superseeded by a secondary factor; then the legend is always added. |
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Spelling typo in the generated documentation: “superseeded” should be “superseded”. Please fix in the roxygen source (R/raincloudPlotsWrapper.R) so it doesn’t reappear on regeneration.
Suggested change
| \item{showLegend, }{Shows the legend for the color-coding of the primary factor.<br>This option is superseeded by a secondary factor; then the legend is always added. | |
| \item{showLegend, }{Shows the legend for the color-coding of the primary factor.<br>This option is superseded by a secondary factor; then the legend is always added. |
vandenman
reviewed
Jan 29, 2026
vandenman
approved these changes
Jan 29, 2026
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