Deprecated functions — vernissage-deprecated • vernissage

Former names of the functions, from the analysis scripts the package comes from. They forward their arguments to the new function. The limit-of-detection and cut-off functions (make_cuts(), handle_lod(), bin_transition_table()...) moved to the lodestar package.

Usage

make_palette(...)

get_label(...)

p_to_stars(...)

rotate_x(...)

forest_plot(...)

export_table(...)

render_tabset(...)

raw_output_callout(...)

resolve_path(...)

var_catalog(...)

to_long(...)

add_deltas(...)

detect_outliers(...)

mask_outliers(...)

choose_transformation(...)

propagate_choice(...)

apply_transformation(...)

transform_boxcox_car(...)

transform_outcomes_car(...)

apply_outcome_transformation(...)

na_map(...)

complete_case_count(...)

composite_scores(...)

normality_table(...)

partial_rank_cor(...)

cor_test_matrix(...)

paired_visits_plot(...)

radar_plot(...)

expand_labels(vars, base_labels, visit_map = c(V0 = "V0", V3 = "V3"), ...)

visit_suffix_map(
  cols,
  select = "^MRI_",
  suffix_map = c(`36` = "V3", `0` = "V0")
)

outliers_table(
  df,
  vars,
  id_col,
  mad_threshold = 3.5,
  iqr_coef = 1.5,
  rule = c("mad", "iqr", "both", "any")
)

ggNA(
  data,
  Title = "Heatmap of missing values (NA)",
  colorNA = "#FDE725",
  colorPres = "#440154",
  show_na_stats = TRUE,
  ...
)

Arguments

...: Arguments passed to the new function.
vars, base_labels, visit_map: See label_expand() (vars is also the variable selection of outlier_detect()).
cols, select, suffix_map: See visit_map_suffix().
df, id_col: See outlier_detect().
mad_threshold, iqr_coef, rule: See outlier_detect() (mad_z_threshold, iqr_k, rule).
data: See plot_na_map().
Title, colorNA, colorPres, show_na_stats: Former arguments of ggNA(): title, colours of the missing and observed cells, labels with the count of missing values.

Value

The value of the new function.

Details

Former name	New name
`make_palette()`	`pal_levels()`
`get_label()`	`label_get()`
`p_to_stars()`	`fmt_stars()`
`rotate_x()`	`theme_rotate_x()`
`forest_plot()`	`plot_forest()`
`export_table()`	`dt_export()`
`render_tabset()`	`qmd_tabset()`
`raw_output_callout()`	`qmd_callout_raw()`
`resolve_path()`	`path_resolve_nfc()`
`var_catalog()`	`catalog_vars()`
`to_long()`	`visit_to_long()`
`add_deltas()`	`visit_add_deltas()`
`detect_outliers()`	`outlier_detect()`
`mask_outliers()`	`outlier_mask()`
`choose_transformation()`	`transform_choose()`
`propagate_choice()`	`transform_propagate()`
`apply_transformation()`	`transform_apply()`
`transform_boxcox_car()`	`transform_boxcox()`
`transform_outcomes_car()`	`transform_boxcox_resid()`
`apply_outcome_transformation()`	`transform_apply_resid()`
`na_map()`	`plot_na_map()`
`complete_case_count()`	`na_complete_cases()`
`composite_scores()`	`score_composite()`
`normality_table()`	`describe_normality()`
`partial_rank_cor()`	`cor_partial_spearman()`
`cor_test_matrix()`	`cor_matrix_test()`
`paired_visits_plot()`	`plot_paired_visits()`
`radar_plot()`	`plot_radar()`
`expand_labels()`	`label_expand()`
`visit_suffix_map()`	`visit_map_suffix()`
`outliers_table()`	`outlier_detect()`
`ggNA()`	`plot_na_map()`

Differences:

expand_labels() reads the former options fairpark.bin_label and fairpark.bin_label_root; label_expand() takes them as arguments;
visit_suffix_map() keeps the former default select = "^MRI_";
outliers_table() keeps its argument names (mad_threshold, iqr_coef) and Tukey's hinges (iqr_method = "hinges");
ggNA() keeps its argument names (Title, colorNA, colorPres, show_na_stats).