v0.9.6 cran

Enhancements

• Added errorbar_width and linetype parameters to g_lineplot.
• Added the .formats argument to tabulate_rsp_subgroups and tabulate_survival_subgroups to allow users to specify formats.
• Added the riskdiff argument to tabulate_rsp_subgroups and tabulate_survival_subgroups to allow users to add a risk difference table column, and function control_riskdiff to specify settings for the risk difference column.
• Added warning to tabulate_rsp_subgroups when pval statistic is selected but df has not been correctly generated to add p-values to the output table.
• Added n_rate statistic as a non-default option to estimate_incidence_rate which returns both number of events observed and estimated incidence rate.
• Added n_unique statistic as a non-default option to estimate_incidence_rate which returns total number of patients with at least one event observed.
• Refactored estimate_incidence_rate to work as both an analyze function and a summarize function, controlled by the added summarize parameter. When summarize = TRUE, labels can be fine-tuned via the new label_fmt argument to the same function.
• Added fraction statistic to the analyze_var_count method group.
• Improved summarize_glm_count() documentation and all its associated functions to better describe the results and the functions' purpose.

Bug Fixes

• Added defaults for d_count_cumulative parameters as described in the documentation.
• Fixed a bug of empty levels on g_lineplot x-axis were not shown in either plots.
• Fixed a bug in a_surv_time that threw an error when split only has "is_event".
• Fixed disappearing line in g_lineplot when using only one group or strata level.
• Fixed defaults for formats and labels in get_formats_from_stats and get_labels_from_stats.
• Fixed bug for linear scaling factor (scale parameter) being applied to response but not to rate in h_glm_count while all distributions have logarithmic link function.
• Fixed bug in decorate_grob that did not handle well empty strings or NULL values for title and footers.
• Fixed bug in g_km that caused an error when multiple records in the data had estimates at max time.
• Fixed issue with wrong wrapping due to different \n and vector behavior that did not cope well with split_string().

Miscellaneous

• Began deprecation of the confusing functions summary_formats and summary_labels.
• Enhanced general descriptions of analyze and summarize functions throughout package documentation.
• Finalized deprecation of the strata and cohort_id arguments to g_lineplot.
• Moved incidence rate helper functions into a separate h_incidence_rate.R file.

What's Changed

• Bumps {rmarkdown} minimal version by @averissimo in #1247
• Fixes problem with a_surv_time with datasets where "is_event" is always TRUE by @averissimo in #1260
• Update of g_lineplot to have line type, error bar width, and avoid empty levels in by @Melkiades in #1261
• Fixing parameters' defaults for d_count_cumulative by @Melkiades in #1264
• Fix typo in has_fraction_in_any_col example by @edelarua in #1266
• update feature yml by @shajoezhu in #1270
• rework docs summarize_glm_count by @Melkiades in #1269
• Fix get_labels_from_stats test by @edelarua in #1272
• Workflow propagations by @walkowif in #1275
• add lookup-refs param to rhub workflow by @pawelru in #1277
• Add riskdiff argument to tabulate_rsp_subgroups and tabulate_survival_subgroups by @edelarua in #1276
• fix decorate_grob for empty strings by @Melkiades in #1278
• Fix g_km bug when multiple estimates are made at max time by @edelarua in #1280
• Update DESCRIPTION by @pawelru in #1288
• Update DESCRIPTION emmeans to 1.10.4 by @shajoezhu in #1284
• update readme by @pawelru in #1290
• Fix URLs by @edelarua in #1298
• Add warning for missing p-value in tabulate_rsp_subgroups() output by @edelarua in #1296
• Add n_rate statistic to estimate_incidence_rate() by @edelarua in #1295
• Improve analyze/summarize function documentation by @edelarua in #1283
• Finalize deprecation of <0.9.4 arguments by @edelarua in #1304
• fix grob wrapping final by @Melkiades in #1305
• Workflow propagations by @walkowif in #1291
• Update DESCRIPTION, upversion formatters minimal version to 0.5.9 by @shajoezhu in #1308
• feat: added "fraction" statistic to the "analyze_var_count" method group by @kpagacz in #1309
• resolve green ci by @shajoezhu in #1293
• Refactor estimate_incidence_rate by @edelarua in #1300
• prep for rspm release 0.9.6, [skip vbump] by @shajoezhu in #1311

Full Changelog: v0.9.5...v0.9.6

v0.9.5 cran

Enhancements

• Added facet_var to g_lineplot to allow plot faceting by a factor variable.
• Added examples and tests for label_all parameter to extract_survival_biomarkers and extract_survival_subgroups.
• Added the xticks, xlim, and ylim arguments to g_lineplot to allow for customization of the x and y axes.
• Updated g_lineplot legend to follow factor levels set by users.

Bug Fixes

• Fixed a bug in s_ancova that prevented statistics from being printed when arm levels include special characters.
• Fixed a bug in decorate_grob that prevented the right margins to be respected when adding title and footers decorations.

Miscellaneous

• Began deprecation of the unused label_all parameter to tabulate_survival_biomarkers and tabulate_survival_subgroups, with redirection to the same parameter in their associated extract_* functions.

What's Changed

• Fix documentation for the label_all argument of extract_* functions by @edelarua in #1232
• Manually specify shapes within g_lineplot when >6 group levels exist by @edelarua in #1234
• update g_lineplot code to handle special characters by @ayogasekaram in #1230
• Add revdepcheck configuration by @walkowif in #1228
• Fix bug in s_ancova when arm levels include special characters by @edelarua in #1242
• Fix indentation in functions that use matrix_form by @edelarua in #1239
• Add xticks, xlim, and ylim arguments to g_lineplot by @edelarua in #1244
• fix decorate grob vp widths for titles and footers when right margin is present by @Melkiades in #1245
• Truetype pagination PR check by @gmbecker in #1250
• testing for rtables higher level ns PR by @gmbecker in #1251
• prep for 0.9.5 [skip vbump] by @shajoezhu in #1253

New Contributors

• @gmbecker made their first contribution in #1250

Full Changelog: v0.9.4...v0.9.5

v0.9.4

New Features

• Added h_glm_negbin to h_glm_count to enable count data analysis using a negative binomial model.
• Added argument grade_groups_only to count_occurrences_by_grade to allow users to only display rows for specified grade groups.
• Added internal function df2gg that converts data.frame objects to ggplot objects.
• Added functions control_surv_med_annot and control_coxph_annot to configure g_km annotation table sizes/positions.
• Refactored g_km to output a ggplot object instead of a grob object.
• Refactored g_forest to output a ggplot object instead of a grob object.

Enhancements

• Default format for mean p-values (mean_pval) updated from "xx.xx" to "x.xxxx | (<0.0001)".

Bug Fixes

• Fixed nested column split label overlay issue in rtable2gg to clean up appearance of text labels.
• Fixed bug in s_ancova causing incorrect difference calculations for arm variables with irregular levels.
• Fixed bug in format_count_fraction_fixed_dp that did not have the same print when the fraction was 1 (100%).
• Fixed bug in g_lineplot causing default labels not to update according to specified control settings.
• Fixed bug causing an error when automatic value formatting was applied to NA values.

Miscellaneous

• Added function expect_snapshot_ggplot to test setup file to process plot snapshot tests and allow plot dimensions to be set.
• Adapted to argument renames introduced in ggplot2 3.5.0.
• Renamed individual_patient_plot.R to g_ipp.R.
• Removed all instances of deprecated parameters time_unit_input, time_unit_output, na_level and indent_mod.
• Removed deprecated functions summarize_vars, control_summarize_vars, a_compare, create_afun_summary, create_afun_compare, and summary_custom.
• Removed vdiffr package from Suggests in DESCRIPTION file.
• Began deprecation of the named element strat, to be renamed to strata, within the variables argument to h_rsp_to_logistic_variables, h_logistic_mult_cont_df, h_odds_ratio_subgroups_df, h_coxreg_mult_cont_df, h_coxph_subgroups_df, h_tbl_coxph_pairwise, extract_rsp_biomarkers, extract_rsp_subgroups, extract_survival_biomarkers, and extract_survival_subgroups.
• Began deprecation of the strat argument to s_coxph_pairwise and replaced it with the strata argument.
• Began deprecation of the forest_grob, forest_dot_line, forest_viewport, vp_forest_table_part, and grid.forest functions.
• Began deprecation of no longer used Kaplan-Meier helper functions h_ggkm, h_decompose_gg, h_km_layout, h_grob_tbl_at_risk, h_grob_median_surv, h_grob_y_annot, and h_grob_coxph.
• Began deprecation of grob/grid related functions stack_grobs, arrange_grobs, and draw_grob which are no longer used in tern.

What's Changed

• Workflow propagation by @walkowif in #1159
• Refactor g_forest by @edelarua in #1158
• Fix graph snapshot tests by @edelarua in #1165
• update snapshots by @ayogasekaram in #1166
• add h_glm_negbin() by @duanx9 in #1163
• Fix irregular arm levels calculation bug in s_ancova by @edelarua in #1169
• Add option grade_groups_only to count_occurrences_by_grade by @edelarua in #1170
• Fix README links by @edelarua in #1174
• Adding Bland- Altman statistical function by @linc50 in #1135
• Fix warnings in examples by @edelarua in #1180
• fix roxygenise deps; styler by @pawelru in #1183
• Fix pkgdown redirect by @vedhav in #1185
• Propagate files from insightsengineering/.github by @insights-engineering-bot in #1187
• [skip actions] Propagate files from insightsengineering/.github by @insights-engineering-bot in #1188
• #nolintr to # nolint by @pawelru in #1189
• Update DESCRIPTION, update author list by @shajoezhu in #1190
• Skip plot snapshot testing by @edelarua in #1194
• Fix typo, ggplot2 update warnings by @edelarua in #1197
• Replace strat with strata by @edelarua in #1198
• fix format precision for format_count_fraction_fixed_dp by @Melkiades in #1192
• options for strict tests; few enhancements by @pawelru in #1182
• Fix integration tests by @edelarua in #1200
• Update default format for mean p-values by @edelarua in #1204
• rename trans to transform by @pawelru in #1202
• add snaps for bland-altman function by @ayogasekaram in #1201
• Remove deprecated functions, deprecate forest plot helpers by @edelarua in #1211
• Fix g_lineplot default labels by @edelarua in #1213
• Refactor g_km by @edelarua in #1210
• Accept NULL to get_labels_from_stats by @edelarua in #1215
• Revert deprecation of decorate_grob-related functions used by citril by @edelarua in #1219
• fix verdepcheck by @pawelru in #1216
• Fix auto formatting for NA values by @edelarua in #1220
• Minor documentation clean up by @edelarua in #1222
• Workflow propagation by @walkowif in #1206
• add faceting variable to g_lineplot. add code to maintain factor levels. by @ayogasekaram in #1226
• Add tests for functions with missing coverage by @edelarua in #1229
• [skip vbump], preping for 0.9.4 release by @shajoezhu in #1227

New Contributors

• @duanx9 made their first contribution in #1163
• @linc50 made their first contribution in #1135
• @vedhav made their first contribution in #1185

Full Changelog: v0.9.3...v0.9.4

v0.9.3

New Features

• Added ref_group_position function to place the reference group facet last, first or at a certain position.
• Added keep_level_order split function to retain original order of levels in a split.
• Added level_order split function to reorder manually the levels.
• Added function get_indents_from_stats to format and return indent modifiers for a given set of statistics.
• Added internal utility function apply_auto_formatting to check for "auto" formats and replace them with
  implementation of format_auto in analyze functions.
• Added utility function labels_use_control to modify labels with control specifications.
• Added list containing default statistics for each method group, tern_default_stats.
• Added summarize function version of count_occurrences analyze function, summarize_occurrences.
• Added referential footnotes to surv_time for censored range observations, controlled via the ref_fn_censor parameter.
• Added helper function h_adlb_abnormal_by_worst_grade to prepare ADLB data to use as input in count_abnormal_by_worst_grade.
• Added function rtable2gg that converts rtable objects to ggplot objects.
• Added helper function to set default na_str globally with set_default_na_str() and added default_na_str() for all interested functions.

Enhancements

• Added ref_group_coxph parameter to g_km to specify the reference group used for pairwise Cox-PH calculations when annot_coxph = TRUE.
• Added annot_coxph_ref_lbls parameter to g_km to enable printing the reference group in table labels when annot_coxph = TRUE.
• Added x_lab parameter to g_lineplot to customize x-axis label.
• Remove 25% padding of y-axis in g_lineplot.
• Added support for creating multiple risk difference columns, each comparing to a single comparison group. Multiple comparison groups can be specified as a vector via the arm_y argument.
• Allowed numeric vector as count_by input in analyze_num_patients and summarize_num_patients.
• Aligned plot and table vertically in g_lineplot.

Bug Fixes

• Fixed bug in decorate_grob preventing text wrapping from accounting for font size.
• Fixed implementation of na_str argument in all column-wise analysis and tabulation functions.

Miscellaneous

• Specified minimal version of package dependencies.
• Upgraded to_string_matrix to take into account widths and other printing parameters.

What's Changed

• Adds min package version by @averissimo in #1012
• Improve documentation of whiskers param in g_lineplot by @edelarua in #1110
• Refactor count_occurrences by @edelarua in #1076
• Add split functions for ref_group position by @Melkiades in #1111
• change cohort_id and strata to subject_var and group_var. by @ayogasekaram in #1106
• Fix integrations tests after ref_group update by @edelarua in #1115
• Add option to set reference arm in g_km by @edelarua in #1120
• Add x_lab parameter to g_lineplot by @edelarua in #1126
• Fix decorate_grob text wrapping by @edelarua in #1124
• Add utility functions for labels and formats by @edelarua in #1122
• Remove extra y-axis padding in g_lineplot by @edelarua in #1128
• Expand get_stats to cover all analysis functions by @edelarua in #1123
• Refactor surv_time to enable cell footnotes by @edelarua in #1116
• Improve analyze_vars documentation by @edelarua in #1129
• Add helper function to pre-process ADLB for count_abnormal_by_worst_grade by @edelarua in #1132
• Reorder doc pages so analyze functions appear first, add links in README by @edelarua in #1131
• Expose statistic function arguments in analyze functions by @edelarua in #1134
• Implement na_str argument in all columnwise analysis functions by @edelarua in #1140
• Add support for multiple risk difference columns by @edelarua in #1143
• Allow numeric input to count_by in analyze_num_patients by @edelarua in #1141
• Add function to convert rtables to ggplots by @edelarua in #1137
• Add "experimental" badge to rtable2gg by @edelarua in #1147
• Generate pkgdown site favicon by @edelarua in #1149
• Add svglite to Suggests by @edelarua in #1151
• Vertically align plot with table in g_lineplot by @edelarua in #1153
• Fix ggsave tests by @edelarua in #1154
• Add general default for na_str by @Melkiades in #1145
• add axis parameter to plot_grid() by @pawelru in #1155
• update g_lineplot snaps by @pawelru in #1157
• init commit for preping new cran release [skip vbump] by @shajoezhu in #1156

New Contributors

• @averissimo made their first contribution in #1012

Full Changelog: v0.9.2...v0.9.3

v0.9.2

New Features

• Added the na_str argument to analyze & summarize_row_groups wrapper functions count_abnormal, count_abnormal_by_baseline, count_abnormal_by_marked, count_abnormal_by_worst_grade, count_abnormal_lab_worsen_by_baseline, count_cumulative, count_missed_doses, count_occurrences, count_occurrences_by_grade, summarize_occurrences_by_grade, summarize_patients_events_in_cols, count_patients_with_event, count_patients_with_flags, count_values, estimate_multinomial_response, estimate_proportion, h_tab_one_biomarker, estimate_incidence_rate, logistic_summary_by_flag, estimate_odds_ratio, estimate_proportion_diff, test_proportion_diff, summarize_ancova, summarize_change, summarize_glm_count, summarize_num_patients, analyze_num_patients, summarize_patients_exposure_in_cols, coxph_pairwise, tabulate_survival_subgroups, surv_time, and surv_timepoint.

Enhancements

• Added formatting function format_count_fraction_lt10 for formatting count_fraction with special consideration when count is less than 10.
• Updated s_summary.logical output for count_fraction when denominator is zero to display as NA instead of 0 in tables.
• Updated analyze_vars_in_cols to allow character input to indicate whether nominal time point is post-dose or pre-dose when applying the 1/3 imputation rule.

Bug Fixes

• Fixed bug in g_km causing an error when converting certain annotation width units.

Miscellaneous

• Began deprecation of na_level argument in s_count_abnormal_by_baseline, a_summary, analyze_vars, analyze_vars_in_cols, compare_vars, h_map_for_count_abnormal, h_stack_by_baskets, summarize_colvars, a_coxreg, and summarize_coxreg and replaced it with the na_str argument.

What's Changed

• Add formatting function with special case when count less than 10 by @edelarua in #1075
• Expose na_str argument in analyze/summarize functions by @edelarua in #1071
• Fix s_summary return for empty logical vectors by @edelarua in #1079
• Fixes after refactor of string wrapping by @edelarua in #1080
• Fix g_km unit conversion bug by @edelarua in #1082
• 1086 update plot snaps@main by @ayogasekaram in #1089
• Update logo by @edelarua in #1091
• Fix logo sizing on pkgdown site by @edelarua in #1093
• Update analyze_vars _in_cols to allow non-numeric nominal timepoint variable by @edelarua in #1095
• update g_lineplot with cohort param. by @ayogasekaram in #1078
• Fix integration for version 9.1 by @Melkiades in #1097
• Revert failing g_km snapshot test by @edelarua in #1101
• remove USUBJID hard coding by @ayogasekaram in #1099
• Fix all lint by @edelarua in #1104
• [skip vbump] Release Candidate 0.9.2 by @Melkiades in #1107

Full Changelog: v0.9.1...v0.9.2

v0.9.1

New Features

• Added imputation_rule function to apply imputation rule to data.
• Added new format function format_sigfig to allow for numeric value formatting by a specified number of significant figures.
• Added vectors containing default statistic formats and labels as tern_default_formats and tern_default_labels, respectively.
• Added function get_stats to return methods from given statistical method groups.
• Added function get_formats_from_stats to return formats and get_labels_from_stats to return labels for a given set of statistics.
• Added "auto" option for .formats. It uses format_auto to determine automatically the number of digits.
• Added title argument to h_grob_tbl_at_risk and annot_at_risk_title argument to g_km and h_km_layout which allows user to add "Patients at Risk" title to Kaplan-Meier at risk annotation table.

Enhancements

• Refactored tabulate_rsp_subgroups to pass sanitation checks by preventing creation of degenerate subtables.
• Updated analyze_vars_in_cols to use caching, allow implementation of imputation rule via the imp_rule argument, and allow user to specify cell alignment via the .aligns argument.
• Updated add_rowcounts to allow addition of row counts from alt_counts_df using the alt_counts argument.
• Added gp argument to g_forest to control graphical parameters such as font size.

Miscellaneous

• Grouped functions relating to valid method names and their default formats and labels into new source file utils_defaults_handling.R.
• Started deprecation of summary_custom() and a_summary() as a S3 method.
• Renamed statistical method for p-value in the discrete case to pval_counts.
• Removed a_summary_internal() in favor of only one main a_summary().

What's Changed

• Refactor tabulate_rsp_subgroups to pass sanitation checks by @edelarua in #1056
• Add helper functions to refactor PKCT01 by @edelarua in #1048
• Reorganize and group defaults for stats and their default formats/labels -> addition of auto for DMT01 by @Melkiades in #1051
• Close #1026: Expose gpar to control graphic settings in g_forest. by @anajens in #1057
• Change to poisson dist to see if it is the glm fit to be unstable by @Melkiades in #1059
• Add "Patients at Risk" title for g_km at risk annotation table by @edelarua in #1065
• Fix trailing "." when using format_sigfig, add functionality for multiple values by @edelarua in #1067
• Fix snapshot differences (it may need muting h_ppmeans()) by @Melkiades in #1072
• [skip vbump] release v0.9.1 by @Melkiades in #1074

Full Changelog: v0.9.0...v0.9.1

v0.9.0

New Features

• Added stat_propdiff_ci function to calculate proportion/risk difference and CI.
• Added risk difference column functionality via the riskdiff argument to functions count_occurrences, count_occurrences_by_grade, count_patients_with_event, count_patients_with_flags, analyze_num_patients, and summarize_num_patients.

Enhancements

• Refactored the function a_summary to no longer use the helper function create_afun_summary.
• Refactored functions summarize_vars and compare_vars to use the refactored a_summary function.
• Created new internal helper functions ungroup_stats to ungroup statistics calculated for factor variables, and a_summary_internal to perform calculations for a_summary.

Bug Fixes

• Fixed bug in s_count_occurrences_by_grade so that "missing" grade always appears as the final level.
• Fixed bug in analyze_vars_in_cols when categorical data was used.
• Fixed bug in s_count_occurrences_by_grade so that levels are not relabeled when reordering to account for "missing" grades.

Miscellaneous

• Fixed swapped descriptions for the .N_row and .N_col parameters.
• Removed internal calls to df_explicit_na. Changes in NA values should happen externally to tern functions, depending on users' needs.
• Reinstated correct soft deprecation for create_afun_summary and create_afun_compare.

What's Changed

• Add nested argument to all analyze wrapper functions by @edelarua in #1009
• Correct swapped descriptions of .N_col and .N_row parameters by @edelarua in #1015
• Fix degenerate table warning in summarize_coxreg by @edelarua in #1017
• Update default g_km y limits by @edelarua in #1021
• Ugly fix for categorical data by @Melkiades in #1014
• update staged deps config by @pawelru in #1022
• Adjust ylim defaults in g_km when yval = "Failure" by @edelarua in #1028
• Documentation fix by @Melkiades in #1030
• Removal of internal df_explicit_na by @Melkiades in #1023
• Refactor a_summary by @edelarua in #983
• Fix alias export for summarize_vars by @Melkiades in #1032
• Workflow propagation by @walkowif in #1035
• Use token in spelling workflow and enable CRAN Status Monitor by @walkowif in #1036
• deprecate_warn instead of stop for create_afun* by @Melkiades in #1034
• Correct ordering of grade levels in s_count_occurences_by_grade by @edelarua in #1040
• Add CRAN release template by @walkowif in #1042
• Reorder grade levels without relabelling in s_count_occurrences_by_grade by @edelarua in #1044
• Update snapshots by @edelarua in #1046
• update rtables and formatters versions by @ayogasekaram in #1050
• Add Risk Difference column functionality by @edelarua in #1031
• change version to 0.9.0, [skip vbump] by @shajoezhu in #1052

Full Changelog: v0.8.5...v0.9.0

v0.8.5

Enhancements

• Added ylim argument to g_km to allow the user to set custom limits for the y-axis.
• Added assertion to g_km which checks whether there is one arm present in the data when annot_coxph is true.
• Added flag_labels argument to s_count_patients_with_flags to enable more label handling options in count_patients_by_flags.

Miscellaneous

• Started deprecation cycle for summarize_vars and control_summarize_vars. Renamed into analyze_vars and control_analyze_vars to reflect underlying rtables machinery while keeping backward compatibility with aliases.

What's Changed

• Workflow propagations by @walkowif in #991
• summarize_vars renamed into analyze_vars and aliases + deprecation cycle by @Melkiades in #982
• Add ylim argument to g_km by @edelarua in #1001
• Improve error message in g_km for single arm when annot_coxph=TRUE by @edelarua in #998
• Enable more flexible labelling in count_patients_with_flags by @edelarua in #1005
• tlg-catalog no longer contains staged.dependencies. by @gogonzo in #1007
• update news vbump to 0.8.5, [skip vbump] by @shajoezhu in #1008

Full Changelog: v0.8.4...v0.8.5

v0.8.4

Enhancements

• Added method for character class to h_coxreg_inter_effect enabling character covariates in summarize_coxreg.

Miscellaneous

• Began deprecation of time_unit_input and time_unit_output arguments and replaced them with the input_time_unit and num_pt_year, respectively, in control_incidence_rate.
• Removed deprecated pairwise function.

Bug fixes

• Fixed long double assertion check in sum(weights) for M1mac installation.

What's Changed

• reduce the amount of spelling issues / WORDLIST by @m7pr in #971
• More intuitive parameter names in control_incidence_rate by @edelarua in #975
• Add character method to h_coxreg_inter_effect by @edelarua in #974
• Failure fix for M1mac and noLD - long double problems for sum(weights) by @Melkiades in #981
• Update snapshots to fix autovalidate tests by @edelarua in #986
• Fix tests - deprecate pairwise and add another test for format_count_fraction by @edelarua in #987
• updating news, preping for cran release v0.8.4 [skip vbump] by @shajoezhu in #989

New Contributors

• @m7pr made their first contribution in #971

Full Changelog: v0.8.3...v0.8.4

v0.8.3

Enhancements

• Added explicit zero counts to g_km plot "at risk" annotation tables.
• Added a flag for total level split in analyze_patients_exposure_in_cols.
• Implemented .indent_mods argument in functions h_tab_one_biomarker, h_tab_rsp_one_biomarker, h_tab_surv_one_biomarker, summarize_logistic, logistic_summary_by_flag, tabulate_rsp_biomarkers, a_coxreg, summarize_coxreg, tabulate_survival_biomarkers, surv_time, surv_timepoint, and cfun_by_flag.
• Updated summarize_coxreg to print covariates in data rows for univariate Cox regression with no interactions and content rows otherwise.
• Removed "baseline status" text from d_count_abnormal_by_baseline labels.
• Improved default sizing of annotation tables in g_km and added dynamic scaling of the surv_med and coxph annotation tables, with customization via the width_annots argument.

Bug Fixes

• Fixed bug in split_text_grob preventing titles and footnotes from being properly formatted and printed by decorate_grob.
• Fixed bug in g_lineplot preventing lines from being added to the plot when midpoint statistic calculations result in NA value(s).
• Fixed tern:::tidy.glm formals to respect broom:::tidy.default formals.

Miscellaneous

• Remove examples for unexported functions.
• Export functions has_count_in_cols, has_counts_difference, combine_counts, h_tab_rsp_one_biomarker, arrange_grobs, a_count_patients_sum_exposure, a_coxreg, groups_list_to_df, forest_viewport.
• Updated README to include installation instructions for CRAN.
• Began deprecation of indent_mod argument and replace it with the .indent_mods argument in summarize_num_patients and analyze_num_patients.

What's Changed

• Use argument_convention instead of templates by @edelarua in #870
• moving out data generator script from user-facing doc by @Melkiades in #868
• Organization of ignores by @Melkiades in #872
• Remove deprecated footnotes functions by @edelarua in #875
• Fix tibble snapshots by @edelarua in #878
• 858 missing values vignette by @Nolan-Steed in #876
• fixing argument convention and adding section_div to summarize_vars by @Melkiades in #881
• Workflow updates by @walkowif in #877
• Add median_range as a statistic option for summarize_vars by @edelarua in #884
• Refactor cox regression functions to fix table structure by @edelarua in #882
• Fix a_coxreg bug for univariate case with no arm and numeric covariate by @edelarua in #892
• Fix GRAN build errors by @edelarua in #894
• alphabetical order of staged.deps + biomarker-catalog by @Melkiades in #895
• Update token name by @walkowif in #897
• Add Value documentation for all functions by @edelarua in #896
• deprecating pairwise by @Melkiades in #902
• Update level order in d_onco_rsp_label by @edelarua in #904
• Move count_patients_with_flags functions into a separate file by @edelarua in #907
• Check all URLs by @edelarua in #909
• Update overview pages by @edelarua in #908
• Add analyze_patients_exposure_in_cols by @edelarua in #916
• Clean up documentation by @edelarua in #914
• Add more informative error to s_proportion_diff by @edelarua in #922
• Fix na_level bug in summarize_vars by @edelarua in #923
• Check tests after formatters' changes by @Melkiades in #912
• fixing both validation errors by @Melkiades in #927
• Release v0.8.2 [skip vbump] by @edelarua in #921
• Clean up references by @edelarua in #935
• Remove unused imports by @edelarua in #932
• Clean up .Rbuildignore by @edelarua in #933
• Add CRAN installation instructions to README by @edelarua in #937
• Add zero counts to g_km annotation table by @edelarua in #944
• Update workflows by @walkowif in #946
• bug fix for downstream by @Melkiades in #949
• tentative solution for multiple calls of analyze_vars_in_cols by @Melkiades in #938
• Enable .indent_mods argument in all analysis functions by @edelarua in #945
• fix rmpt04 total level in analyze_patients_exposure_in_cols by @Melkiades in #951
• Update NA handling by s_summary by @edelarua in #924
• Fix bug in decorate_grob by @edelarua in #953
• Update summarize_coxreg to work with pagination in all cases by @edelarua in #956
• Remove "baseline status" text from abnormal by baseline labels by @edelarua in #959
• Fix NA value bug in g_lineplot by @edelarua in #963
• add --as-cran to local proj checks by @Melkiades in #964
• fix formals for tern:::tidy.glm by @Melkiades in #969
• Improve annotation scaling in g_km by @edelarua in #961
• CRAN release: update description and news version to 0.8.3, [skip vbump] by @shajoezhu in #970

Full Changelog: v0.8.1...v0.8.3