High-Performance Open-Source Archive
Added g_lineplot() for creating line plots with
optional summary statistics table. Includes helper functions
calc_stats(), g_lineplot_table(), and
preprocess_lineplot_data().
Added ard_tabulate_abnormal_by_baseline() for
creating an Analysis Results Data (ARD) object counting participants
with abnormal assessments, stratified by their baseline status.
Added tbl_mmrm() and get_mmrm_results()
functions to create regression tables for Mixed Models for Repeated
Measures (MMRM). (#163)
Added gg_mmrm_lineplot() to create line plots of
MMRM results. (#181)
Added gg_pkc_lineplot() to create line plots for PK
data. (#185)
Added annotate_gg_pkc() to add optional summary
statistics table to gg_pkc_lineplot(). (#189)
Refactored the underlying data.frame alignment and
rendering methodology used for plot annotations. Functions for table
annotation now use a completely rebuilt engine that ensures X-axis
synchronization for stacked tables (annotate_riskdf()) and
flexible, reliable placement for floating tables
(annotate_surv_med(), annotate_coxph()).
(#189)
Refactored functions for lineplot plotting - added
gg_lineplot() and annotate_gg() to create
lineplots and annotate summary statistics table. (#184)
Added functions reverse_ci(),
reverse_rate_difference() to reverse confidence intervals
and rate differences in tables from add_row_difference().
(#204)
g_lineplot(), g_lineplot_table(), and
preprocess_lineplot_data() were deprecated. (#184)
Added tbl_coxph() to render pairwise Cox
proportional hazards results as a gtsummary table. (#159)
Added tbl_hierarchical_incidence_rate() which
computes the incidence rate of adverse events (#211)
Added adjust_stat_columns_wrap() which keep the
presentation of statistics in one row (#219)
get_cox_pairwise_df() now allows for different
methods to compute p-value (#191) and to handle ties (#193).
tbl_coxph() now accepts a data.frame created by
get_cox_pairwise_df() as input. (#207)
Added add_grade_column() to inject a grade-label
column into tbl_hierarchical_rate_by_grade() output.
Decoupled from the table builder to prevent Cartesian join explosion in
tbl_merge(). (#226)
get_cox_pairwise_df() now fully supports
strata() terms in survival formulas (#256).
The "likelihood-ratio" test now intelligently
switches between survival::survreg() (for unstratified
models) and survival::coxph() (for stratified models)
(#256).
Stripped package namespace prefixes (e.g.,
survival::) from survival formulas to prevent evaluation
errors (#256).
Added ... support in
get_cox_pairwise_df() for conf.int (e.g., to
adjust CI level) and robust = TRUE (for robust standard
errors).
tbl_hierarchical_rate_and_count() now emits
zero-rows for unobserved factor levels in the first hierarchical
variable. (#233)
df2gg_aligned() and df2gg_floating()
now preserve original ggplot objects in
attr(result, "plotlist") for downstream data extraction
after combining with cowplot. (#208)
Remove warning when data has more levels than needed for grade_groups on tbl_hierarchical_rate_by_grade.
Changed the default conf.type from
"log" to "plain" (linear) in
tbl_survfit_times() and
tbl_survfit_quantiles() to align with GDSR guidelines.
(#173)
Removed bold from headers when using tbl_strata()
(#133).
Unified border width in theme_gtsummary_roche() to
0.5 for header. (#154)
Added example on how to stratify tbl_baseline_chg()
by PARAM and split into a list.
Adjusted tbl_mmrm() to allow
base_df = NULL.
Fixed two bugs related to summary statistics calculation in
ard_tabulate_abnormal_by_baseline(). (#198)
Fixed a bug in gg_pkc_lineplot() causing misplaced
error bars on a log scale. (#199)
Adjusted gg_pkc_lineplot() to use
tbl_roche_summary() for automatic decimals
formatting.
Adjusted tbl_hierarchical_incidence_rate() to handle
first event as well as all events (#217)
Adjusted tbl_baseline_chg() to allow for
custiomization of display statistics (#222)
Changed baseline statistic argument in
tbl_baseline_chg() (#224)
Adjusted modify_zero_recode() to account for strings
comprising regular and non-breaking spaces (#230)
tbl_roche_subgroups() now shows n,
Events, and Median per arm when
time_to_event is specified. The total column shows
Total Events instead of Total n.
(#235)
Skip tests if suggested packages are missing (Failing test due to missing suggested package #252, @llrs-roche)
The default "log-rank" test now uses
survival::survdiff() instead of coin, aligning
output more closely with SAS and rtables
Added tbl_roche_subgroups() for subgroup
analysis.
Added g_forest to create forest plot.
Added tbl_null_report() for cases without any
information to display. (#11)
Added functions style_roche_number() and
label_roche_number() to replace their respective gtsummary
versions, with additional inf argument for customization of
Inf/-Inf/NaN values.
Added gg_km() function for creating Kaplan-Meier
plots.
Added tbl_subgroups and g_forest to
make subgroup analysis and forest plots.
Added
list("assign_summary_type-arg:cat_threshold" = 0L) to
theme_gtsummary_roche(). Numeric variables with few levels
will no longer default to summary type 'categorical' in
gtsummary::tbl_summary() and
tbl_roche_summary(). (#79)
Updated variable processing in tbl_baseline_chg() to
allow for non-string input. (#114)
Updated details about the sort_hierarchical() and
filter_hierarchical() functions in the hierarchical tables
article. (#116)
Added the label argument to
tbl_hierarchical_rate_and_count() to set hierarchy
variables labels in the table header. (#118)
remove_duplicate_keys() to remove non-unique
column values when the key columns are a mix of unique and duplicated
entries. (#129)The tbl_demographics() function has been renamed to
tbl_roche_summary() with the following updates. (#73).
Updated tbl_roche_summary() to convert cells with
"0 (0.0%)" to "0".
Update the tbl_roche_summary() returned
inputs list to match the tbl_roche_summary()
argument inputs, whereas it previously returned the
tbl_summary() inputs. (#31)
Changed the default header in tbl_roche_summary()
tables from **Characteristic** to an empty string.
Fix in tbl_roche_summary() when a variable is all
NA within a stratum. The zero count was displayed as
"0 (NA%)" instead of "0". (#60)
Added function tbl_hierarchical_rate_by_grade() to
summarize adverse event rates by highest toxicity grade. (#46)
Adding the modify_zero_recode() function that
recodes "0 (0.0%)" to "0" in summary
tables.
Adding the modify_header_rm_md() function to remove
bold and italic markdown syntax from the headers of a gtsummary table.
(#53)
Adding tbl_hierarchical_rate_and_count() and
associated S3 method add_overall() to summarize
hierarchical event rates and counts. (#36)
Added tbl_survfit_quantiles() and
add_overall.tbl_survfit_quantiles() to create a table of
survival quantiles. (#19)
Adding tbl_survfit_times() and
add_overall.tbl_survfit_times()
Adding tbl_baseline_chg() function. (#62)
Added function tbl_shift() for easing the creation
of shift tables. (#83)
Added style_roche_percent() and
label_roche_percent() functions.
Added formatting functions style_roche_ratio() and
label_roche_ratio(). (#91)
Added variables and row_numbers
arguments to the add_blank_rows() function. (#45)
Re-coding 0 / 0 (NA%) to 0 / 0 in
modify_zero_recode(). (#85)
Added an article giving an overview of the {crane} package. (#37)
The {gtsummary} is now loaded with {crane}.
Updated Roche theme to bold headers for flextable
outputs.
Updated Roche theme to include parentheses around Ns in header, and updated function defaults to include the parentheses in crane functions.
Updated theme_gtsummary_roche() to further style
results from gtsummary::tbl_hierarchical*()
functions.
Added theme_gtsummary_roche(font_size, print_egine)
arguments to control the default font size and the print
engine.
Updated Roche theme to use style_roche_percent() as
the default function to format percentages.
Added additional {flextable} specs for
theme_gtsummary_roche(). Mainly border line width (0.5) and
footer font size (font_size - 1).
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