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teal.modules.clinical

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install.packages('teal.modules.clinical')

Monthly Downloads

434

Version

0.10.0

License

Apache License 2.0

Issues

93

Pull Requests

2

Stars

39

Forks

19

Maintainer

Dawid Kaledkowski

Last Published

February 28th, 2025

Functions in teal.modules.clinical (0.10.0)

cs_to_des_filter

Convert choices_selected to data_extract_spec with only filter_spec
facet_grid_formula

Facetting formula x_facet ~ y_facet
extract_input

Extracts html id for data_extract_ui
cs_to_select_spec

Convert choices_selected to select_spec
get_g_forest_obj_var_name

Utility function for extracting paramcd for forest plots
get_paramcd_label

Extract the associated parameter value for paramcd
cs_to_des_select

Convert choices_selected to data_extract_spec with only select_spec
get_var_labels

Get variable labels
h_concat_expr

Expression Deparsing
make_barchart_simple_call

ggplot2 call to generate simple bar chart
is.cs_or_des

Whether object is of class teal.transform::choices_selected()
prepare_arm

Expression: Arm Preparation
prepare_arm_levels

Expression: Prepare Arm Levels
pipe_expr

Expressions as a Pipeline
module_arguments

Standard Module Arguments
split_choices

Split choices_selected objects with interactions into their component variables
srv_decorate_teal_data

Wrappers around srv_transform_teal_data that allows to decorate the data
substitute_names

Substitute Names in a Quoted Expression
select_decorators

Subset decorators based on the scope
template_a_gee

Template for Generalized Estimating Equations (GEE) analysis module
template_abnormality

Template: Abnormality Summary Table
teal.modules.clinical-package

teal Modules for Standard Clinical Outputs
substitute_q

Substitute in Quoted Expressions
template_abnormality_by_worst_grade

Template: Laboratory test results with highest grade post-baseline
template_adverse_events

Template: Patient Profile Adverse Events Table and Plot
split_col_expr

Split-Column Expression
split_interactions

Split interaction terms into their component variables
template_events

Template: Events by Term
template_binary_outcome

Template: Binary Outcome
template_basic_info

Template: Patient Profile Basic Info
template_coxreg_m

Template: Multi-Variable Cox Regression
template_events_col_by_grade

Template: Adverse Events Grouped by Grade with Threshold
template_events_patyear

Template: Event Rates Adjusted for Patient-Years
template_arguments

Standard Template Arguments
template_ancova

Template: ANCOVA Summary
template_events_by_grade

Template: Events by Grade
template_events_summary

Template: Adverse Events Summary
template_g_ipp

Template: Individual Patient Plots
template_g_lineplot

Template: Line Plot
template_fit_mmrm

Template: Mixed Model Repeated Measurements (MMRM) Analysis
template_g_km

Template: Kaplan-Meier Plot
template_forest_tte

Template: Survival Forest Plot
template_g_ci

Template: Confidence Interval Plot
template_laboratory

Template: Patient Profile Laboratory Table
template_coxreg_u

Template: Univariable Cox Regression
template_exposure

Template: Exposure Table for Risk management plan
template_forest_rsp

Template: Response Forest Plot
template_prior_medication

Template: Patient Profile Prior Medication
template_logistic

Template: Logistic Regression
template_patient_timeline

Template: Patient Profile Timeline Plot
template_mult_events

Template: Multiple Events by Term
template_shift_by_arm_by_worst

Template: Shift by Arm by Worst Analysis Indicator Level
template_shift_by_arm

Template: Shift by Arm
template_medical_history

Template: Patient Profile Medical History
template_smq

Template: Adverse Events Table by Standardized MedDRA Query
template_summary

Template: Summary of Variables
template_shift_by_grade

Template: Grade Summary Table
template_tte

Template: Time-To-Event
tm_g_barchart_simple

teal Module: Simple Bar Chart and Table of Counts per Category
tm_g_ci

teal Module: Confidence Interval Plot
template_vitals

Template: Patient Profile Vitals Plot
template_summary_by

Template: Summarize Variables by Row Groups Module
tm_a_gee

teal Module: Generalized Estimating Equations (GEE) analysis
template_therapy

Template: Patient Profile Therapy Table and Plot
tm_a_mmrm

teal Module: Mixed Model Repeated Measurements (MMRM) Analysis
tm_g_pp_vitals

teal Module: Patient Profile Vitals Plot
tm_g_km

teal Module: Kaplan-Meier Plot
tm_g_ipp

teal Module: Individual Patient Plots
tm_g_pp_therapy

teal Module: Patient Profile Therapy Table and Plot
tm_g_pp_patient_timeline

teal Module: Patient Profile Timeline Plot
tm_g_forest_rsp

teal Module: Forest Response Plot
tm_t_abnormality

teal Module: Abnormality Summary Table
tm_g_pp_adverse_events

teal Module: Patient Profile Adverse Events Table and Plot
tm_g_forest_tte

teal Module: Forest Survival Plot
tm_g_lineplot

teal Module: Line Plot
tm_t_abnormality_by_worst_grade

teal Module: Laboratory test results with highest grade post-baseline
tm_t_ancova

teal Module: ANCOVA Summary
tm_t_coxreg

teal Module: Cox Regression Model
tm_t_events

teal Module: Events by Term
tm_t_exposure

teal Module: Exposure Table for Risk management plan
tm_t_events_patyear

teal Module: Event Rates Adjusted for Patient-Years
tm_t_events_by_grade

teal Module: Events by Grade
tm_t_mult_events

teal Module: Multiple Events by Term
tm_t_pp_basic_info

teal Module: Patient Profile Basic Info
tm_t_binary_outcome

teal Module: Binary Outcome Table
tm_t_logistic

teal Module: Logistic Regression
tm_t_events_summary

teal Module: Adverse Events Summary
tm_t_smq

teal Module: Adverse Events Table by Standardized MedDRA Query
tm_t_summary_by

teal Module: Summarize Variables by Row Groups
tm_t_tte

teal Module: Time-To-Event Table
tm_t_shift_by_grade

teal Module: Grade Summary Table
tm_t_shift_by_arm_by_worst

teal Module: Shift by Arm by Worst Analysis Indicator Level
validate_arm

Check if vector is valid as to be used as a treatment arm variable
validate_standard_inputs

Validate standard input values for a teal module
tm_t_pp_laboratory

teal Module: Patient Profile Laboratory Table
tm_t_pp_medical_history

teal Module: Patient Profile Medical History
tm_t_summary

teal Module: Summary of Variables
tm_t_shift_by_arm

teal Module: Shift by Arm
tm_t_pp_prior_medication

teal Module: Patient Profile Prior Medication
check_arm_ref_comp

Check if the Treatment variable is reference or compare
add_expr

Expression List
as_num

Parse text input to numeric vector
clean_description

Clean up categorical variable description
bracket_expr

Expressions in Brackets
call_concatenate

Concatenate expressions via a binary operator
column_annotation_label

Get full label, useful for annotating plots
control_tte

Control Function for Time-To-Event teal Module
color_lab_values

Mapping function for Laboratory Table
cs_to_filter_spec

Convert choices_selected to filter_spec
arm_ref_comp_observer

Observer for Treatment reference variable
default_total_label

Default string for total column label
ex_data

Simulated CDISC Data for Examples