teal_report object that contains the
data, code and report. All the reporter buttons were removed from the
modules’ UI in favor of the framework level reporter buttons
(#1376).xticks parameter to tm_g_km module
to allow users to specify x-axis tick positions programmatically. When
xticks is provided, the interactive input field is
pre-populated with the specified values as a default. Users can then
modify these values interactively, and their changes will take
precedence over the default. When xticks is
NULL (default), users can specify this interactively in the
module.R version dependency from 4.0 to 4.4.0, as
upstream dependency tern requires this.tm_t_summary and tm_t_summary_by
now display and hide missing values (#1437).bslib components.conf_type to module tm_g_km
to allow users to set a confidence interval type for median survival
time estimation.denom argument in
tm_t_binary_outcome module.withr dependency version.tm_t_events to return sorted table
(#1393).tm_g_pp_adverse_events, tm_g_pp_therapy,
tm_t_pp_basic_info, tm_t_pp_laboratory and
tm_t_pp_prior_medication modules (#1404).table object decoration in
tm_g_pp_adverse_events, tm_g_pp_therapy
(#1404).decorators argument in
tm_t_pp_basic_info, tm_t_pp_laboratory and
tm_t_pp_prior_medication (#1404).teal.logger functionality for logging changes in
shiny inputs in all modules.ylim parameter for tm_g_km
module that controls width of y-axis.tm_t_events_patyear to split
columns by multiple (nested) variables via the arm_var
argument.arm_var_labels to
template_summary and show_arm_var_labels to
tm_t_summary to allow user to display arm variable
(arm_var) labels in table header.stats to modules
tm_g_forest_rsp and tm_g_forest_tte to allow
users to specify statistics to include in the table.riskdiff to modules
tm_g_forest_rsp and tm_g_forest_tte to allow
users to add a risk difference table column.count_dth and count_wd
parameters to tm_t_events_summary to select/deselect the
“Total number of deaths” and “Total number of patients withdrawn from
study due to an AE” rows, respectively. These options correspond to the
“Count deaths” and “Count withdrawals due to AE” checkboxes available
when the module is run.title_text argument to
tm_t_mult_events to allow for more customization of the
module’s dynamic title.transformators and decorators
argument to modules.delayed_data and
teal.transform::all_choices.tm_g_forest_tte and
tm_g_forest_rsp to resolve delayed data loading
variables.Show Warnings modals from modules.arm_var argument for each module.rtables::add_colcounts() function
with the show_colcounts argument to
basic_table().show_labels argument of
template_summary which has no effect on the
tm_t_summary module.strata argument to
tern::control_lineplot_vars() with
group_var.tm_t_events_summary() to check
whether all datasets used have the same treatment variable levels.tm_g_forest_rsp and
tm_g_forest_tte to use refactored version of
g_forest. Plots are now displayed as ggplot
objects instead of grob objects. Added parameters
font_size and rel_width_forest to control font
size and width of plot relative to table, respectively.tm_t_summary_by to allow NULL
input to paramcd argument.tm_g_km to use refactored version of
g_km. Plots are now displayed as ggplot
objects instead of grob objects. Added parameters
rel_height_plot, font_size,
control_annot_surv_med, and
control_annot_coxph to control height of plot relative to
table, font size, median survival time table size, and Cox-PH table
size, respectively.control argument to
tm_t_binary_outcome to control settings for the analysis
(methods, confidence intervals, and odds ratios) within the module.na_level argument to
tern functions with na_str.strata instead of
strat in all tern function calls following the
deprecation of this argument/name within tern.formatters from dependencies and replaced the
use of its functions relating to variable labels with functions from
teal.data.teal_data objects.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_tteteal_data object to teal::init().sort_freq_col to
tm_t_events to allow the user to select column to use when
sorting by decreasing frequency.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.teal_data object to teal::init().default_total_label and
set_default_total_label functions to get and set default
total column label (total_label) for modules.tern::default_na_str and
tern::set_default_na_str functions to get and set default
missing value replacement string (na_level) for
modules.tm_g_lineplot forcing module to initialize
with a table.aval argument in
tm_t_pp_laboratory and tm_g_pp_vitals and
replaced it with the aval_var argument.avalu argument in
tm_t_pp_laboratory and replaced it with the
avalu_var argument.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.summarize_vars function
with analyze_vars.tidyr,
rlang, magrittr and styler).tm_t_abnormality_by_worst_grade.tm_t_abnormality_by_worst_grade.total_label argument to enable customization of
the “All Patients” column/row label in the following modules:
tm_a_mmrm, tm_t_abnormality,
tm_t_abnormality_by_worst_grade,
tm_t_binary_outcome, tm_t_events,
tm_t_events_by_grade, tm_t_events_patyear,
tm_t_events_summary, tm_t_exposure,
tm_t_mult_events, tm_t_shift_by_arm,
tm_t_shift_by_arm_worst, tm_t_shift_by_grade,
tm_t_smq, tm_t_summary,
tm_t_summary_by, and tm_t_tte.tm_g_forest_tte plot to
prevent overlapping text.tm_g_km.tm_t_exposure to display “total” row as last
row in table instead of as a summary row. Added parameters
add_total_row to set whether the total row should be
displayed and total_row_label to set the total row
label.tm_t_events to maintain indentation after
pruning.tm_t_coxreg to drop factor covariate variable
levels that are not present to avoid errors when filtering.tm_t_pp_basic_info,
tm_t_pp_medical_history, tm_g_pp_therapy,
tm_g_pp_adverse_events, and tm_t_pp_laboratory
to print patient ID above table.tm_t_pp_basic_info,
tm_g_pp_therapy, tm_g_pp_adverse_events, and
tm_t_pp_laboratory to use rlistings to print
data neatly in reports.tm_g_lineplot to allow user to remove interval
from plot.teal_data object to teal::init().tm_t_coxreg preventing table from being
displayed when no covariates are selected.control_incidence_rate parameter names in
tm_t_events_patyear from time_unit_input and
time_unit_output to input_time_unit and
num_pt_year, respectively, after parameter names were
changed in tern.datanames = "all" parameter with the datasets used
internally by the module.chunks with simpler qenv
class.datasets argument containing
FilteredData with the new arguments data
(tdata object) and filter_panel_api
(FilterPanelAPI).synthetic_cdisc_data with refactored
synthetic_cdisc_dataset function to speed up dataset
loading in tests/examples.tm_a_gee.tm_t_ancova.shinyvalidate::InputValidator for better UI experience.
Previously used shiny::validate.tm_a_mmrm to allow for
Kenward-Roger adjustments of standard errors and
p-values.tm_g_barchart_simple.label parameter to
cs_to_select_spec/cs_to_des_select and
cs_to_filter_spec/cs_to_des_filter to allow
the user to customize the label printed over the selection field.tm_t_coxreg module after refactoring
summarize_coxreg in tern to fix
indentation.tm_t_exposure module to use new function
analyze_patients_exposure_in_cols to fix table
structure.tm_g_barchart_simple.svg format.tm_t_summary and
tm_t_summary_by preventing users from specifying the
numeric_stats argument.scda.2022 rather than
scda.2021.param from
tm_g_pp_vitals.tm_a_mmrm since we can
always use the automatically determined optimizer.adsl,
adae, adaette, adcm,
adeg, adex, adlb,
admh, adqs, adrs,
adtte, and advs. These datasets are stored in
the data folder and accessible via the tmc_ex_*
prefix.teal.modules.clinical package instead of scda
datasets.testthat 3rd edition and replaced
all applicable tests with snapshot testing.lubridate package for date variables in
internal data.plot_width in
tm_g_forest_rsp to prevent clutter.rcd_2022_02_28.tests/testthat/ to
synthetic_cdisc_data("2022_02_28")tm_t_summary
(encoding and filtering should be separate).teal.reporter functionality to all
modules.tm_t_pp_medical_history module to use the
table_with_settings module and return an
rtables object.nestcolor in examples, refactored
tm_g_barchart_simple to allow use of
nestcolor.tm_g_ci.tm_a_mmrm column name when deselecting
treatment from “all obs” to “All Patients”, added subtitles and
footnotes.tm_t_exposure, cleaned up labels.tm_t_shift_by_grade and
tm_t_shift_by_arm_by_worst.tm_t_events_patyear with CI
method.tm_g_km.tm_t_binary_outcome.tm_a_mmrm.tm_t_exposure.tm_g_km and tm_t_tte when
“Compare Treatments” is off.tm_g_barchart_simple which prevented
display of graph.tm_t_abnormality_by_worst_grade.tm_a_mmrm which prevented table headers
from displaying.tm_g_forest_rsp when deselecting
endpoint.tm_t_binary_outcome that crashed the app
when deselecting all paramcd.teal.reporter card names for
tm_t_smq.tm_t_shift_by_arm_by_worst by adding
validations for choosing different endpoint values.tm_t_coxreg preventing footnotes from
displaying for univariate models.nestcolor dependency and replaced deprecated
function tern::color_palette with
nestcolor::color_palette.tm_g_pp_adverse_eventstm_t_summary_bytm_t_summaryDate, POSIXt).tm_t_binary_outcome to enable an option to
apply a continuity correction in the Newcombe method.tm_g_pp_patient_timeline
module.Debug Info.summarize_logistic implementation broken by empty
string error. upstream. _NA_ is the new standard flag to
allow it to pivot over empty entries in data frames.@title from tm_t_binary_outcome.R
that was producing a warning.tm_g_pp_patient_timeline module.pkgdown template to the documentation.Covariates in
tm_t_coxreg.R to track user input and reflect the order in
the table.tm_t_shift_by_arm_by_worst for the
analysis of the laboratory abnormalities with the most severe grade
flag.tm_t_events_patyear to include selected
parameter in title of the table.tm_t_mult_events to include selected parameter
in title of the table.moduleServer and updated calls
to teal.devel modules which were also written to use
moduleServer.teal.devel. Use ordered = TRUE in
cs_to_des_select or cs_to_select_spec to
return ordered selection.teal::root_modules with
teal::modules following deprecation of
teal::root_modules.tm_t_events_summary now allows nested
arm_var columns matching other outputs such as
tm_t_events.tm_t_abnormality_by_worst_grade
when arm_var is not selected.tm_t_binary_outcome to include all responders
in the response table by default.tm_g_forest_tte,
tm_t_coxreg, and tm_t_binary_outcome listing
stratification factors.tm_g_forest_rsp.R causing shiny errors during
the runtime.Compare Treatments
conditional panel with a marked
Combine all comparison groups? option conflicted with
adding a column with all patients to tables in
tm_t_binary_outcome.R and tm_t_tte.R.rtables::var_labels calls in
the documentation examples.tern.mmrm package and change some
references after split of tern.teal framework.tm_g_pp_patient_timeline output when switching between
absolute and relative days.tm_t_abnormality due to changes in
count_abnormal that abnormal argument is
taking list as input now.tm_g_pp_patient_timeline parameter,
cmtrt, to cmdecod.tm_t_abnormality_by_worst_grade for
the analysis of laboratory test results with highest grade
post-baseline.tm_t_ancova to include selected parameter(s),
visit(s) and the analysis variable in title of the table.tm_g_lineplot for creating line
plots.tm_t_logistic to include selected parameter in
title of the table.tm_g_forest_rsp to include selected parameter
in title of the table.tm_g_forest_tte to include selected parameter
in title of the table.tm_g_pp_patient_timeline with bold axes labels
and integer values on the axis.tm_g_ipp to allow users not to display
AVALU in the title nor in the y axis.logger package and
added info level logs upon initialization of a module.default_responses argument to
tm_t_binary_outcome and tm_g_forest_rsp to
allow the user to specify default selected responses and possible
response levels.tm_t_binary_outcome to show selected responses
in the output table when selecting “Show All Selected Response
Categories”.rsp_table argument to
tm_t_binary_outcome to allow the user to initialize the
module matching the RSPT01 STREAM template.ggplot2::labs
and ggplot2::theme in plot based modules.rtables::basic_table in table based modules.tm_t_binary_outcome to enable an option to
apply a continuity correction in the Wilson method.teal.devel::data_extract_input into calls to its
replacement teal.devel::data_extract_ui.data_merge_module interface
provided by teal.devel and removed usage of the now
deprecated function teal.devel::get_input_order.tm_t_binary_outcome module to add a template
and removed the now deprecated module tm_t_rsp.utils.nest dependency and replaced calls with
checkmate equivalents.tm_g_pp_therapy where if the
cmstdy or cmendy argument is of type
integer causes the plot to crash.tm_t_smq for the analysis of adverse
events by Standardized MedDRA Query.tm_t_shift_by_grade for the analysis
of grade laboratory abnormalities.tm_t_exposure for the analysis of
duration of exposure for risk management plan.tm_t_shift_by_arm that can display
shift table of ECG interval data.tm_a_mmrm to be able to consider the
treatment variable in all interactions.tm_t_binary_outcome and tm_t_rsp to
choose the correct CI estimation method for Proportions Difference in
Stratified Analysis (i.e. Wald-type confidence interval with
CMH weights).tm_t_rsp and
tm_t_binary_outcome for stratification errors from applied
filters.tm_g_km validation check for plot tables font
size.tm_g_km to add the selected
paramcd in the plot title.tm_t_events now can display layouts with two nested
column as treatment variables. The same options for pruning and sorting
are available.tm_t_events_by_grade to display grading groups
in nested columns with col_by_grade option and support
pruning and sorting options like tm_t_events.format_count_fraction to fix formatting
inconsistency in tm_t_events_summary.count_occurrences vars argument in
tm_t_shift_by_grade.tm_t_pp_laboratory to display 4 decimals by
default.tm_t_events_by_grade to use the
trim_levels_in_group split function instead of the
trim_rows function.tm_t_tte.tm_t_rsp and
tm_t_binary_outcome.LICENCE and README with new
package references.error_on_lint: TRUE to .lintr.insert_rrow and updated usage of
count_patients_by_flags in
tm_t_events_summary.dplyr
package. The functions should be now fully specified
(e.g. dplyr::filter).tm_t_summary,
tm_t_summary_by, tm_g_forest_rsp,
tm_g_forest_tte, tm_t_events_summary,
tm_t_abnormality, tm_t_mult_events.numeric_stats to
tm_t_summary and tm_t_summary_by to control
displayed summary statistics for numeric variables.drop_zero_levels to
tm_t_summary_by so that you can drop rows with all zeros
from result table.tm_g_patient_profile tabs into 8 separate new
modules.tm_g_patient_timeline when the
plot is empty.tm_a_mmrm to work without the treatment
variable.tm_t_pp_laboratory.tm_g_pp_patient_timeline
hiding/showing relative study days on the x-axis.tm_g_forest_tte more
informative when deselecting the Endpoint column in the
left-hand encoding panel.tm_t_summary.tm_t_coxreg.tm_t_ancova when selected
covariate variables contain one level.tm_t_events_patyear when the
events variable is empty.tm_g_km to
more precisely describe what it controls.tm_t_logistic so that interaction choices
depend on the selected covariates.tm_t_rsp so that strata input is visible when
comparing treatments.tm_t_pp_laboratory to return
identical HTML formatted table as displayed in the app.tm_t_coxreg to ensure treatment,
strata and covariate variables do not overlap.tm_g_pp_patient_timeline to X-axis for a more consistent
look.tm_t_summary_by so that paramcd is
not required when analyzing ADSL variables.tm_t_coxreg so that it can work when there is
no covariate selected.tm_a_mmrm so that it can work when treatment
variable is not selected.tm_g_forest_tte so that total number of events
are also shown in the table.tm_t_events_summary to work with pooled
studies.at level of
tm_t_coxreg.at level of
tm_t_logistic.tm_t_binary_outcome and
tm_t_rsp to ensure strata variable contains more than one
level when selecting one strata variable.tm_t_summary and tm_t_summary_by to explain
need to select at least one statistic.tm_g_km added support for downloading images and
updated x-axis label to show in title case.tm_g_patient_profile:
PARAMCD selected levels for current patient.tm_t_tte:
template_tte so
that a dataset without any events still produces a table.tm_t_summary:
arm_var to accept more than one
column. When selecting two columns for arm_var, the second
variable will nest under the first one.show_labels to
template_summary to show the label for a single summary
variable in the table.conf_arg to tm_t_rsp
to be consistent with other efficacy modules.tm_g_ipp module to print
message when deselecting Timepoint Variable drop-down.tm_g_forest_rsp and
tm_g_forest_tte as there is now a default header in
g_forest.tm_t_coxreg so that
models without strata and using likelihood tests return a result.drop_arm_levels for
tm_t_summary and tm_t_summary_by. In the
encodings panel, the checkbox will show when the parent dataset and
analysis dataset are different.observe function calls with
observeEvent to optimize performance.tm_g_patient_profile.font_size default of the templates to be 12L
instead of a vector of 3 integers and cleaned associated unnecessary
code.tm_g_barchart_simple.subgroup_var definition truncation in
tm_g_forest_rsp and tm_g_forest_tte.tm_t_coxreg.tm_g_patient_profile.filter_spec objects.PARAMCD variable levels input in
tm_g_patient_profile vitals tab so that the plot does not
get reset when filtering.tm_g_patient_profile to
drop NA entries in the plot.tm_t_coxreg to take at values into
account.tm_t_coxreg to have interactions in
univariate models but not in multivariate models.tm_t_events_summary to work with pooled
studies.tm_g_patient_profile to profile
patients based on predefined categories.tm_g_ipp for individual patient
plots.drop_arm_levels to all safety
modules. This allows removal of columns based on factor levels not found
in filtered data.tm_g_km to allow plot of failure probability on
y-axis, tick interval selection on x-axis and option to create plot
without confidence interval ribbon (new default).time_unit_var to
template_g_km to add the time unit to the x-axis
label.Analysis Data: label from Encodings
Panel.tm_a_mmrm requires
five records, tm_t_logistic and tm_t_coxreg
require two records, and the remaining modules require at least one
record per treatment group. For graphs, the lower threshold is two
records.cnsr_val from
tm_t_events_patyear and added new argument
events_var.arm_ref_comp_observer to include
parentname argument.data_extract_spec objects.stringr dependency from the patient
profile module.tm_t_events and
tm_t_events_by_grade.tm_g_ci for confidence interval
plots.tm_t_ancova for analysis of variance
summary tables.tm_t_mult_events for multi-event
tables.rtables and
tern packages.data_extract_spec and data_merge_module
functionality from teal.OptionalSelectInput for
conf_level.substitute which can be helpful
when developing analysis template functions for teal modules.tm_t_events module to use user’s non-default
choices for prune_freq and prune_diff.plot_width argument
which specifies the plot width and renders a slider to adjust the width
interactively in the module.FilteredData object is now passed to
arm_ref_comp_observer and modules now support nested lists
containing delayed_data objects.plot_with_height module with new
plot_with_settings module.code argument inside
cdisc_dataset.tm_t_coxreg to optionally produce univariate Cox
regressions.tm_t_binary_outcome to display Odds Ratio
estimates, include new methods for CIs and p-values and display a
summary for individual response categories.tm_t_tte to optionally compare between arms,
removed conf_level argument.tm_g_km to optionally compare between
arms.tm_g_km to optionally scale X axis range in case
of more than one plot.tm_a_mmrm for MMRM analysis.tm_t_mmrm (superseded by
tm_a_mmrm).tm_t_coxreg module for multi-variable Cox
regressions.tm_t_binary_outcome module.tm_t_events_patyear module: events rate adjusted
for patient-year at risk table.grade_levels argument from
tm_t_events_by_grade.tm_t_abnormality module.get_relabel_call and
get_relabel_call2 in favor of
teal.devel::get_relabel_call and
teal.devel::get_anl_relabel_call.survfit, coxph,
ztest; add confidence type, ties, percentiles to
tm_t_tte.tm_t_events and
tm_t_events_by_grade modules.tm_t_logistic module.tm_t_mmrm module.tm_t_summary_by and
tm_t_events_summary.tm_g_forest_tte and
tm_g_forest_rsp.tm_g_forest_rsp and tm_g_forest_tte.tm_t_events and tm_t_events_by_grade
modules.CoxPH table in
tm_g_km.teal.devel.teal.modules.clinical.tm_t_summarize_variables to
tm_t_summary.teal::choices_selected() function instead of
*_var and *_var_choices arguments.teal.tern.tern prefixed with an tm_.teal.oncology into two packages:
tern and teal.oncology where tern
contains all the analysis code and teal.oncology contains
the teal modules that make the analysis function interactive with
encodings and filtering. Find the tern package here: https://github.com/insightsengineering/tern.atezo
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