v0.9.0 cran

Breaking Changes

• Adapted all modules to use teal_data objects.
• Module arguments that previously accepted inputs from teal.transform::choices_selected() or teal.transform::data_extract_spec() now only accept input from teal.transform::choices_selected(). The affected modules are: tm_a_gee, tm_a_mmrm, tm_g_ci, tm_g_forest_rsp, tm_g_forest_tte, tm_g_ipp, tm_g_km, tm_g_lineplot, tm_g_pp_adverse_events, tm_g_pp_patient_timeline, tm_g_pp_therapy, tm_g_pp_vitals, tm_t_abnormality, tm_t_abnormality_by_worst_grade, tm_t_ancova, tm_t_binary_outcome, tm_t_coxreg, tm_t_events, tm_t_events_by_grade, tm_t_events_patyear, tm_t_events_summary, tm_t_exposure, tm_t_logistic, tm_t_mult_events, tm_t_pp_basic_info, tm_t_pp_laboratory, tm_t_pp_medical_history, tm_t_pp_prior_medication, tm_t_shift_by_arm, tm_t_shift_by_arm_by_worst, tm_t_shift_by_grade, tm_t_smq, tm_t_summary, tm_t_summary_by, and tm_t_tte

Enhancements

• Updated the documentation and vignettes to demonstrate method to pass teal_data object to teal::init().
• Added parameter sort_freq_col to tm_t_events to allow the user to select column to use when sorting by decreasing frequency.
• Added parameter incl_overall_sum to tm_t_events to allow the user to choose whether overall summary rows are included at the top of the table.
• Updated the documentation and vignettes to demonstrate method to pass teal_data object to teal::init().
• Added default_total_label and set_default_total_label functions to get and set default total column label (total_label) for modules.
• Implemented tern::default_na_str and tern::set_default_na_str functions to get and set default missing value replacement string (na_level) for modules.

Bug fixes

• Fixed bug in tm_g_lineplot forcing module to initialize with a table.

Miscellaneous

• Deprecated the aval argument in tm_t_pp_laboratory and tm_g_pp_vitals and replaced it with the aval_var argument.
• Deprecated the avalu argument in tm_t_pp_laboratory and replaced it with the avalu_var argument.
• Deprecated the base_var argument in tm_g_ipp, tm_t_shift_by_arm, and template_shift_by_arm_by_worst and replaced it with the baseline_var argument.
• Specified minimal version of package dependencies.
• Replaced usage of deprecated summarize_vars function with analyze_vars.
• Reduced package dependencies (removed tidyr, rlang, magrittr and styler).

What's Changed

• Workflow propagation by @walkowif in #824
• Use token in spelling workflow by @walkowif in #825
• Refactor tm_t_exposure to remove summary row by @edelarua in #826
• Patient Profile Modules only show relevant datanames by @averissimo in #828
• Solution for maintaining indent after pruning by @ayogasekaram in #791
• Fix bug in tm_t_coxreg when no covariates selected by @edelarua in #833
• Fix tm_t_coxreg errors when applying filters by @edelarua in #831
• Display Patient ID in relevant templates, clean up data tables in reports by @edelarua in #834
• 198 Include user's card labels when generating the report by @m7pr in #835
• Add option to remove interval in tm_g_lineplot by @edelarua in #840
• chasing deprecations by @chlebowa in #852
• Update docs to use the new teal_data instead of TealData by @kartikeyakirar in #853
• fix tm_g_pp_vitals by @gogonzo in #896
• Update tern version by @m7pr in #901
• bump teal.reporter dep version by @chlebowa in #903
• Fix bug forcing tm_g_lineplot to initialize with a table by @edelarua in #899
• Add options to tm_t_events for sorting and overall rows by @edelarua in #851
• Remove unused table_names argument from surv_timepoint by @edelarua in #905
• tdata to teal_data by @chlebowa in #855
• fix resolve_delayed by @gogonzo in #909
• Workflow propagation by @walkowif in #908
• 906 update dependency versions by @chlebowa in #907
• 231 remove get_labels function by @kartikeyakirar in #914
• Update forest plots following refactor of g_forest by @edelarua in #911
• Two arm vars by @gogonzo in #916
• Fix TMC to work with tern v0.9.3 by @edelarua in #922
• 430 use expect_no_error in tests instead of expect_error(, NA) by @m7pr in #936
• 919 update vignettes@main by @ayogasekaram in #927
• Add default_total_label function by @edelarua in #942
• 918 update teal.modules.clinical.R with #' @keywords internal "_PACKAGE" by @m7pr in #982
• TMC bug fixes by @gogonzo in #926
• Replace aval parameter with aval_var by @edelarua in #939
• Replace avalu parameter with avalu_var by @edelarua in #940
• Adds min package version by @averissimo in #797
• Replace base_var parameter with baseline_var by @edelarua in #941
• Implement default_na_str by @edelarua in #984
• Replace summarize_vars with analyze_vars by @edelarua in #987
• Clean up overall argument documentation by @edelarua in #989
• update deps of roxygenize hook by @pawelru in #990
• Minor improvements to README/vignettes by @edelarua in #993
• Clean up documentation for tm_t_shift_by_arm_by_worst by @edelarua in #997
• Clean up documentation for tm_t_shift_by_grade by @edelarua in #998
• Update DESCRIPTION teal.data (>= 0.4.0) by @shajoezhu in #1008
• Consolidate argument_convention file by @edelarua in #1006
• 618 reduce dependencies of the package by @m7pr in #981
• Clean up documentation for tm_t_binary_outcome by @edelarua in #994
• Clean up documentation for tm_t_summary_by by @edelarua in #1003
• Clean up documentation for tm_t_summary by @edelarua in #1004
• Clean up documentation for tm_t_pp_basic_info by @edelarua in #1024
• Clean up documentation for tm_g_pp_adverse_events by @edelarua in #1026
• Clean up documentation for tm_t_pp_prior_medication by @edelarua in #1023
• Clean up documentation for tm_t_pp_medical_history by @edelarua in #1022
• Clean up documentation for tm_g_forest_rsp by @edelarua in #1020
• Clean up documentation for tm_g_pp_therapy by @edelarua in #1025
• Clean up documentation for tm_t_events_summary by @edelarua in #1015
• Clean up documentation for tm_t_mult_events by @edelarua in #1019
• Clean up documentation for tm_t_tte by @edelarua in #1011
• clean up documentation for tm_t_ancova by @ayogasekaram in #1016
• Clean up documentation for tm_t_smq by @edelarua in #1018
• clean up documentation for tm_t_abnormality_by_worst_grade by @ayogasekaram in #1029
• clean up tm_t_abnormality documentation by @ayogasekaram in #1027
• Clean up documentation for tm_t_shift_by_arm by @edelarua in #1031
• Clean up tm_g_km documentation by @edelarua in #1030
• Clean up documentation for tm_t_events_patyear by @edelarua in #1032
• Clean up documentation for tm_g_forest_tte by @edelarua in #1021
• Clean up documentation for tm_g_lineplot by @edelarua in #996
• Clean up documentation for tm_t_coxreg by @edelarua in #995
• Clean up documentation for tm_g_barchart_simple by @edelarua in #1033
• clean up documentation for tm_t_events_by_grade. by @ayogasekaram in #1039
• Clean up documentation for tm_t_logistic by @edelarua in #1007
• Clean up documentation for tm_t_exposure() by @zdz2101 in #1028
• Clean up documentation for tm_g_ipp by @edelarua in #1034
• 944 clean tm a gee@main by @ayogasekaram in #1040
• tm_t_events review by @Melkiades in #1002
• Clean up documentation for tm_t_pp_laboratory by @edelarua in #1036
• Clean up documentation for tm_g_pp_patient_timeline by @edelarua in #1038
• Clean up documentation for tm_g_ci by @edelarua in #1035
• Clean up documentation for tm_g_pp_vitals by @edelarua in #1037
• clean up documentation for tm_a_mmrm by @ayogasekaram in #1041
• using library([package]) and getFromNamespace(...) calls. by @kartikeyakirar in #1048
• 1012 substitute {assertthat} with {checkmate} in a couple of functions by @m7pr in #1046
• Fix pkgdown redirect by @vedhav in #1049
• Propagate files from insightsengineering/.github by @insights-engineering-bot in #1052
• [skip actions] Propagate files from insightsengineering/.github by @insights-engineering-bot in #1053
• Update DESCRIPTION teal 0.15.0 by @shajoezhu in #1054
• Change r.pkg.template branch to main by @walkowif in #1055
• removing internal functions example. by @kartikeyakirar in #1051
• Append the teal.transform namespace to stay consistent by @vedhav in #1056
• Check description and vignette by @Melkiades in #1045
• 1057 fix tm_t_pp_laboratory reshape by @m7pr in #1060
• Fix assertion on paramcd by @vedhav in #1067
• Clarify tm_g_pp_patient_timeline error message by @edelarua in #1059
• final prerelease activities by @donyunardi in #1065
• Update DESCRIPTION teal.transform >= 0.5.0 by @shajoezhu in #1069
• 1071 prerelease cleanup@main by @m7pr in #1072
• Add missing return values by @edelarua in #1075
• [Docs] Update module arg docs to only accept choices_selected by @vedhav in #1078
• Cran release 0.9.0 [skip vbump] by @shajoezhu in #1070

New Contributors

• @zdz2101 made their first contribution in #1028

Full Changelog: v0.8.16...v0.9.0