The documentation to this function lists all the arguments in teal module
templates that are used repeatedly to express an analysis.
add_total |
(logical ) whether to include column with total number of patients.
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anl_name |
(character ) analysis data used in teal module.
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arm_var |
(character ) variable names that can be used as arm_var .
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atirel |
(character ) name of time relation of medication variable.
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aval |
Please use the aval_var argument instead.
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avalu |
Please use the avalu_var argument instead.
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avalu_var |
(character ) name of the analysis value unit variable.
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aval_var |
(character ) name of the analysis value variable.
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baseline_var |
(character ) name of the variable for baseline values of the analysis variable.
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base_var |
Please use the baseline_var argument instead.
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basic_table_args |
(basic_table_args ) optional object created by teal.widgets::basic_table_args()
with settings for the module table. The argument is merged with option teal.basic_table_args and with default
module arguments (hard coded in the module body).
For more details, see the vignette: vignette("custom-basic-table-arguments", package = "teal.widgets") .
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by_vars |
(character ) variable names used to split the summary by rows.
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cmdecod |
(character ) name of standardized medication name variable.
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cmindc |
(character ) name of indication variable.
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cmstdy |
(character ) name of study relative day of start of medication variable.
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cnsr_var |
(character ) name of the censoring variable.
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combine_comp_arms |
(logical ) triggers the combination of comparison arms.
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compare_arm |
(logical ) triggers the comparison between study arms.
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comp_arm |
(character ) the level of comparison arm in case of arm comparison.
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conf_level |
(numeric ) value for the confidence level within the range of (0, 1).
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control |
(list ) list of settings for the analysis.
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cov_var |
(character ) names of the covariates variables.
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dataname |
(character ) analysis data used in teal module.
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denominator |
(character ) chooses how percentages are calculated. With option N , the reference
population from the column total is used as the denominator. With option n , the number of non-missing
records in this row and column intersection is used as the denominator. If omit is chosen, then the
percentage is omitted.
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drop_arm_levels |
(logical ) whether to drop unused levels of arm_var . If TRUE , arm_var levels are
set to those used in the dataname dataset. If FALSE , arm_var levels are set to those used in the
parentname dataset. If dataname and parentname are the same, then drop_arm_levels is set to TRUE and
user input for this parameter is ignored.
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event_type |
(character ) type of event that is summarized (e.g. adverse event, treatment). Default
is "event" .
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font_size |
(numeric ) font size value.
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ggplot2_args |
(ggplot2_args ) optional object created by teal.widgets::ggplot2_args() with settings
for the module plot. The argument is merged with option teal.ggplot2_args and with default module arguments
(hard coded in the module body).
For more details, see the vignette: vignette("custom-ggplot2-arguments", package = "teal.widgets") .
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hlt |
(character ) name of the variable with high level term for events.
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id_var |
(character ) the variable name for subject id.
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include_interact |
(logical ) whether an interaction term should be included in the model.
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label_hlt |
(string ) label of the hlt variable from dataname . The label will be extracted from the
module.
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label_llt |
(string ) label of the llt variable from dataname . The label will be extracted from the
module.
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llt |
(character ) name of the variable with low level term for events.
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na_level |
(string ) used to replace all NA or empty values
in character or factor variables in the data. Defaults to "<Missing>" . To set a
default na_level to apply in all modules, run set_default_na_str("new_default") .
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na.rm |
(logical ) whether NA values should be removed prior to analysis.
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numeric_stats |
(character ) names of statistics to display for numeric summary variables. Available
statistics are n , mean_sd , mean_ci , median , median_ci , quantiles , range , and geom_mean .
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paramcd |
(character ) name of the parameter code variable.
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parentname |
(character ) parent analysis data used in teal module, usually this refers to ADSL .
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patient_id |
(character ) patient ID.
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prune_diff |
(number ) threshold to use for trimming table using as criteria difference in
rates between any two columns.
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prune_freq |
(number ) threshold to use for trimming table using event incidence rate in any column.
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ref_arm |
(character ) the level of reference arm in case of arm comparison.
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sort_criteria |
(character ) how to sort the final table. Default option freq_desc sorts
on column sort_freq_col by decreasing number of patients with event. Alternative option alpha sorts events
alphabetically.
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strata_var |
(character ) names of the variables for stratified analysis.
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subgroup_var |
(character ) with variable names that can be used as subgroups.
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sum_vars |
(character ) names of the variables that should be summarized.
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time_points |
(character ) time points that can be used in tern::surv_timepoint() .
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time_unit_var |
(character ) name of the variable representing time units.
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title |
(character ) title of the output.
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total_label |
(string ) string to display as total column/row label if column/row is
enabled (see add_total ). Defaults to "All Patients" . To set a new default total_label to
apply in all modules, run set_default_total_label("new_default") .
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treatment_flag |
(character ) name of the value indicating on treatment
records in treatment_flag_var .
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treatment_flag_var |
(character ) name of the on treatment flag variable.
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useNA |
(character ) whether missing data (NA ) should be displayed as a level.
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var_labels |
(named character ) optional variable labels for relabeling the analysis variables.
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visit_var |
(character ) variable names that can be used as visit variable. Must be a factor in
dataname .
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worst_flag_indicator |
(character ) value indicating worst grade.
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worst_flag_var |
(character ) name of the worst flag variable.
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