NEWS.md

pmplots 0.6.1

Bugs fixed

• Fixed a bug introduced in #124, where a hard-coded "ID" was mistakenly replaced by a call to pm_col_tad() rather than pm_col_id(). (#131)

pmplots 0.6.0

• A new family of functions lets you update axis and aesthetic labels on plots after they are created, looking up column names in a named list or yspec object. (#122)

  • pm_gg_labs() builds a label object that can be added (+) to any gg object to update axis and aesthetic labels based on the mapped column names. It also accepts x_break, y_break, and var_break arguments for inserting line breaks into long labels.
  • pm_relabel() is a generic that applies pm_gg_labs() to a gg object, a patchwork object (e.g., from eta_covariate() or npde_panel()), or a list of gg objects.
  • pmp_relabel_wrap() relabels facet strip labels in plots produced by wrap_* functions (e.g., wrap_eta_cont(), wrap_cont_cont()), including optional f_break and unit_break arguments for wrapping long strip labels.
  • pmp_relabel_pairs() relabels strip and axis labels in pairs plots (e.g., from eta_pairs()).
  • relabel_at() applies relabeling to specific plots in a named list, selected by exact name or regular expression.
  • pm_label_columns() attaches per-column labels to a data frame from a named list or yspec object; pm_label_rm() removes them. When a data frame labeled this way is passed to a wrap_* function with use_labels = TRUE (now the default), the stored labels are used as facet strip titles.
  • pm_gg_break() and pm_gg_break_aes() will break an established aesthetic label across two lines; pm_gg_break() identifies labels to break by variable name while pm_gg_break_aes() identifies labels to break by aesthetic name.
  • pm_label_break() is a ggplot2 labeller function that wraps facet labels at a specified character width, for use with facet_wrap(labeller = ...).

• A new aliasing system lets you globally redirect the canonical column names assumed by pmplots to the names actually present in your data. (#124)

  • pm_set_aliases() registers one or more alias = canonical pairs (e.g., pm_set_aliases(TAFD = TIME) redirects every place pmplots would look for TIME to TAFD instead). Only columns returned by pm_show_canonical() can be aliased.
  • pm_aliases() prints currently active aliases; pm_clear_aliases() removes them all; pm_show_canonical() lists which column names can be aliased.
  • pm_col_id() returns the subject identifier column name (defaults to "ID"; controlled globally via options(mrg.id_col = ...)). pm_col_tad() returns the time-after-dose column name with alias support. Both are now used internally wherever pmplots previously hard-coded "ID" or "TAD".

• eta_covariate(), eta_covariate_list(), npde_covariate(), npde_covariate_list(), cwres_covariate(), cwres_covariate_list(), and cont_cat_panel() gain a points argument that is forwarded to boxwork() when a categorical covariate column is plotted as a boxplot. (#126)

• boxwork() (and downstream functions such as pm_box(), cont_cat(), and the eta_cat() / npde_cat() families) accept fill = NULL to suppress the default fill, leaving the returned plot open to extension with aes(fill = ...) for grouping by a third variable. (#125)

• Minimum ggplot2 version is now 3.5.2. (#122)

• Minimum R version is now 4.1.0. (#122)

pmplots 0.5.2

Internal compatibility changes

• Fix some test failures related to ggplot2 version 4.0 (#117).

• Add S4 as optional dependency to silence R CMD check warning (#117).

• Prefer ggplot2::is_ggplot() when available (#115).

• Update CI and make tests compatible with GGally 2.3.0 (#114).

pmplots 0.5.1

Bugs fixed

• eta_covariate() now calls eta_cont() rather than eta_cat() when data for the x-axis is integer, fixing an error that was generated from eta_cat(), which always expects factor, character, or logical; other internal updates have been made to ensure consistent treatment of integer data as continuous rather than discrete (#104).

pmplots 0.5.0

• Multiple x and y can be now be passed as a list in addition to character vector (#95).

• Vectorized plots (returned as a list of plots) are now named according to the x or y data column (#96).

• New function rot_xy() allows rotation of x- or y-axis tick labels for gg objects, patchwork objects, or lists of gg or patchwork objects; this function uses rot_at() for processing lists (#96).

• New function rot_at() allows rotation of x- or y-axis tick labels of gg or patchwork objects or named lists of these objects; the list method allows rotation of specific plots in the list by matching the name exactly or through a regular expression (#96).

• New function pm_with() allows arrangement of a named list of plots using patchwork syntax (#96).

• rot_y() has been updated with a vertical argument, similar to existing argument in rot_x() (#96).

pmplots 0.4.1

• y-axis for cwres_q() and npde_q() changed to remove the word "distribution" (#92).

• pmplots now depends on ggplot2 version 3.5.0 or greater (#86).

• Axis titles for conditional weighted residuals are now abbreviated "CWRES" (#83).

Bugs fixed

• Fixed a bug where the wrong y-axis title was getting used in cwres_covariate() (#89).

pmplots 0.4.0

• Add a series of functions for standardized, paneled displays (#77, #81).

  • eta_covariate() creates panel of ETA versus continuous or categorical covariates.
  • npde_covariate() creates panel of NPDE versus continuous or categorical covariates.
  • cwres_covariate() creates panel of CWRES versus continuous or categorical covariates.
  • cont_cat_panel() creates panel of continuous versus categorical covariates.
  • npde_panel() creates panel of NPDE-based diagnostics.
  • cwres_panel() creates panel of CWRES-based diagnostics.
  • npde_scatter() creates panel of NPDE-based scatter plots.
  • cwres_scatter() creates panel of CWRES-based scatter plots.
  • npde_hist_q() creates NPDE histogram and Q-Q plot in a panel.
  • cwres_hist_q() creates CWRES histogram and Q-Q plot in a panel.
  • Component plots can be returned in a list which can be arranged via with().

• pm_grid() gains tag_levels argument that gets passed to patchwork::plot_annotation() (#80).

pmplots 0.3.7

Bugs fixed

• Fix bug where density line was not being drawn by default over npde and cwres histograms; the bug came about from incomplete transition to changes introduced in ggplot2 v3.4.0 (#74, #75).

pmplots 0.3.6

• Update plotting code to work with new ggplot2 behavior introduced in version 3.4.0; pmplots now depends on ggplot2 version 3.4.0 or greater (#71).

pmplots 0.3.5

• Functions generating default axis titles now have arguments so that interpolated customizations can happen when calling the function outside of a plot context (#57).

• dv_pred_ipred() heavily refactored for functionality and style; see the PR for significant changes / improvements (#54).

• Put stories in yaml format; add script to build validation docs from the yaml file (#58, #59).

pmplots 0.3.4

• pm_grid() now uses 'patchwork' to arrange plots; 'patchwork' becomes a suggested package and 'cowplot' is dropped #49.

• scatt() gains alpha argument with default provided by pm_opts$scatter.alpha #42, #48.

• split_plot() gains labeller argument which gets passed to facet_wrap() #43, #47.

• label_tex() replaces label_parse_label() for labeling facets via latex2exp::TeX(); label_parse_label() remains as an alias #47.

• label_fun argument for wrap plots is renamed labeller; applies to the following plots: wrap_cont_cont(), wrap_hist(), wrap_cont_cat(), and any plot built on these (see ?wrap_plots) #43, #47.

• Fix bug where points overlaid on boxplots were jittered in both directions; jitter is now only in x-direction #45, #46.

pmplots 0.3.3

• Add vignettes into package (#37)

• Re-work README (#37)

pmplots 0.3.2

• pairs_plot() and eta_pairs() now will properly call user-supplied functions for creating panels on the upper and lower triangle (#2)

• The upper panels in pairs_plot() and eta_pairs() are not customizable using pm_opts() (#6)

• The reference lines at -3 and 3 on the y-axis of npde plots are no longer drawn by default (#22)

• dv_pred() and dv_ipred() gain an argument (logbr) that lets the user pick the interval for tick marks when loglog plots are drawn; options are: "full" (full log units - 10, 100 ,1000), "half" (half log units - 30, 100, 300) or "null" (let ggplot decide); the default is now to show full log unit breaks rather than half log unit breaks (#21)

• pairs_plot() gains an argument (lower_plot) which lets the user more easily customize the scatter plot that usually appears on the lower triangle (#26)

• wrap_cont_cat() is a new wrap function that lets the user make faceted plots of continuous variables versus categorical variables; (#14)

pmplots 0.3.1

• Add label_fun function to pairs_plot, wrap_cont_cont and wrap_hist allowing strip labels to incorporate expressions via pmplots:::label_parse #45
• parse_label and label_parse_label are exported
• Add option system #70
• Add better control over tick label rotation and justification #60
• Optionally plot subject ID rather than points in scatter plots #63
• CWRESI plots now have default axis title "CWRES with interaction" #87
• Add dv_pred_ipred plot function #89
• Optionally overlay points on top of boxplots #13
• Refactor col_label so that punctuation in col//label does not result in error #72

pmplots 0.2.0

• Qualification under CR-88 and released to r_validated

pmplots 0.1.0.9002

• Added non-exported functions to generate default col-label information (see ?pm_axis_functions)
• Added npde_time, npde_tad and npde_tafd, npde_pred, npde_hist, and npde_q functions
• Added res_hist, wres_hist, and cwres_hist along with the more general cont_hist functions for plotting residuals or other continuous variables as histograms
• Vectorized eta_cont, (cw)res_cont, eta_cat, and (cw)res_cat; see function help for more details about what this means
• Added cont_cont_list and cont_cat_list as vectorized versions of cont_cont and cont_cat
• Added internal functions that facilitate the creation of vectorized plotting function calls
• Reorganized the R source files and split several composite help topics into more focused topics
• Added pairs_plot as a more-generic front end to ggpairs
• Dots are now passed through eta_pairs and pairs_plot to GGally::ggpairs; this allows users to pass in a mapping for colors etc
• Added arguments for pairs_plot to allow users to pass in custom functions for upper and lower
• For the default lower function in pairs_plot, the mapping object is checked for smooth_color and smooth_lty for more control over the smoothing line
• Remove shk argument to pairs_plot
• Re-configured code to handle user-supplied xs and ys information; axis titles respect user-supplied name settings for scales
• Added functions to rot_x and rot_y to rotate tick labels
• Added scales argument to dv_pred and dv_ipred; by default (scales = "fixed"), the x- and y-axis have the same limits; when scales = "free" limits are chosen by ggplot2 and will likely be different for x- and y-axis
• Fixed bug in split_plot when splitting by a factor that doesn't have all level present
• Fixed bug in wres_q related to indexing a tibble
• Added functions to export look and feel: pm_theme, pm_abline, pm_smooth, pm_hline, pm_histogram; these functions help make the plots look consistent with other plots if you are making reference lines, smooths, etc; pm_theme is still just a wrapper around theme_bw()
• eta_pairs dispatches to eta_hist when there is only one eta in the mix #14
• A density line is by default plotted over histograms for cwres, wres, and npde
• Changed all plots so that axis titles are generated with labs rather than via scale_(x|y)_continuous #23
• ggplot2 version 3.0.0 or greater is now required
• col_label specification can now be automatically parsed to generate expressions to be rendered with plotmath; if two $ symbols are found in the title, pmplots will try to load the latex2exp namespace and pass the axis title through latex2exp::TeX. Otherwise, if the axis title begins with !!, then pmplots will parse the column title to generate the expression
• Added cowplot as a suggested package to work with pm_grid
• Fixed a bug introduced with ggplot2 version 3 when used with eta_pairs #17
• split_plot now accepts a grouped data frame as input; the list of plots will be generated by splitting the data frame on grouping column #32
• Added faceted plots: wrap_cont_cont, wrap_cont_time, wrap_res_time, wrap_eta_cont, wrap_hist, and wrap_dv_preds

pmplots 0.1.0.9001

• Fixed logbr3 so that the values are sorted; this fixes an issue where the grid lines were not properly displayed with these breaks
• Fixed issue in dv_time and dv_pred when modifying the x-scale and y-scale through xs and ys arguments
• Changed dv_time and dv_pred so that breaks are at half-log units when log = TRUE or loglog = TRUE

pmplots 0.1.0

• Initial validated version