Extend annotate_lineplot_df(): mean_se, custom labels, blank timepoints - #317
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Melkiades wants to merge 3 commits into
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Extend annotate_lineplot_df(): mean_se, custom labels, blank timepoints#317Melkiades wants to merge 3 commits into
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Report the mean +/- 1 standard error interval in the annotation table, matching the error bars drawn by gg_lineplot(variability = "se") so the table and plot always agree. The row label defaults to "Mean -/+ 1xSE" and is configurable via the new se_label argument.
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Add a labels argument to override statistic row labels (e.g. labels = c(mean = "LS mean") for an MMRM plot) and a blank_timepoints argument to blank the continuous statistics at fixed timepoints while keeping n, for a constant change-from-baseline visit where the mean/SD/CI are 0 by construction.
Melkiades
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The general labels argument already relabels any statistic, so the special-case se_label was redundant. The mean_se row keeps its default "Mean -/+ 1xSE" label and is now relabelled the same way as every other statistic, e.g. labels = c(mean_se = "Mean +/- SE").
Melkiades
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| # Blank the continuous statistics at fixed timepoints (e.g. a constant-zero | ||
| # change-from-baseline visit in an MMRM plot), where a "0.00" mean/SD/CI is an | ||
| # artifact of the constant rather than a real estimate. The count ("n") is a | ||
| # genuine value and is kept. | ||
| if (!is.null(blank_timepoints)) { | ||
| missing_tp <- setdiff(blank_timepoints, names(formatted_df)) | ||
| if (length(missing_tp) > 0) { | ||
| cli::cli_warn(c( | ||
| "!" = "Timepoint{?s} in {.arg blank_timepoints} not found: {.val {missing_tp}}.", | ||
| "i" = "Available timepoint columns are {.val {setdiff(names(formatted_df), c(names(formatted_df)[1], 'Group'))}}." | ||
| )) | ||
| } | ||
| n_label <- trimws(stat_labels[["n"]]) | ||
| blank_rows <- is_stat & trimws(raw_labels) != n_label | ||
| for (tp in intersect(blank_timepoints, names(formatted_df))) { | ||
| formatted_df[blank_rows, tp] <- "" | ||
| } | ||
| } |
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should we give the option to add 0 instead? or whatever NA label?
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What changes are proposed in this pull request?
annotate_lineplot_df()gains a"mean_se"summary_statsoption reporting the mean +/- 1 standard error interval, matching the error bars drawn bygg_lineplot(variability = "se"). Its row label defaults to"Mean -/+ 1xSE"and is configurable via the newse_labelargument. (Add SE to annotate_lineplot_df() summary table #307)annotate_lineplot_df()gains alabelsargument to rename statistic rows (e.g.labels = c(mean = "LS mean")for an MMRM plot) and ablank_timepointsargument to blank the continuous statistics at fixed timepoints while keepingn(e.g. a constant change-from-baseline visit where the mean/SD/CI are0by construction). (Add SE to annotate_lineplot_df() summary table #307)These are follow-ups from annotating MMRM change-from-baseline plots:
"mean_se"mirrors the plot's SE error bars in the table (bounds delegate to the same.calc_stats()helper the plot uses, so they can never disagree).labelslets an MMRM plot report "LS mean" instead of the generic "Mean".blank_timepointsremoves the meaningless0.00mean/SD/CI at the constant baseline visit while keeping the sample size.Reference GitHub issue associated with pull request. e.g., 'closes #'
Part of #307.
Pre-review Checklist (if item does not apply, mark is as complete)
usethis::pr_merge_main()devtools::test_coverage()Reviewer Checklist (if item does not apply, mark is as complete)
pkgdown::build_site(). Check the R console for errors, and review the rendered website.devtools::test_coverage()When the branch is ready to be merged:
NEWS.mdwith the changes from this pull request under the heading "# cards (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (seeNEWS.mdfor examples).