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teal.modules.clinical

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

Monthly Downloads

434

Version

0.9.0

License

Apache License 2.0

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Repository

https://github.com/insightsengineering/teal.modules.clinical/

Homepage

https://insightsengineering.github.io/teal.modules.clinical/

Maintainer

Joe Zhu

Last Published

February 28th, 2025

Functions in teal.modules.clinical (0.9.0)

get_g_forest_obj_var_name

Utility function for extracting paramcd for forest plots

cs_to_select_spec

Convert choices_selected to select_spec

Split choices_selected objects with interactions into their component variables

Expression Deparsing

Get variable labels

module_arguments

Standard Module Arguments

Expressions as a Pipeline

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

Split-Column Expression

make_barchart_simple_call

ggplot2 call to generate simple bar chart

prepare_arm_levels

Expression: Prepare Arm Levels

Expression: Arm Preparation

template_ancova

Template: ANCOVA Summary

split_interactions

Split interaction terms into their component variables

teal.modules.clinical

teal Modules for Standard Clinical Outputs

template_abnormality_by_worst_grade

Template: Laboratory test results with highest grade post-baseline

Template for Generalized Estimating Equations (GEE) analysis module

substitute_names

Substitute Names in a Quoted Expression

Substitute in Quoted Expressions

template_adverse_events

Template: Patient Profile Adverse Events Table and Plot

template_arguments

Standard Template Arguments

template_abnormality

Template: Abnormality Summary Table

template_basic_info

Template: Patient Profile Basic Info

template_events_col_by_grade

Template: Adverse Events Grouped by Grade with Threshold

template_events_patyear

Template: Event Rates Adjusted for Patient-Years

template_exposure

Template: Exposure Table for Risk management plan

template_binary_outcome

Template: Binary Outcome

template_events_summary

Template: Adverse Events Summary

template_coxreg_m

Template: Multi-Variable Cox Regression

template_coxreg_u

Template: Univariable Cox Regression

template_forest_rsp

Template: Response Forest Plot

Template: Confidence Interval Plot

Template: Kaplan-Meier Plot

template_events_by_grade

Template: Events by Grade

template_forest_tte

Template: Survival Forest Plot

template_laboratory

Template: Patient Profile Laboratory Table

Template: Individual Patient Plots

template_events

Template: Events by Term

template_g_lineplot

Template: Line Plot

template_fit_mmrm

Template: Mixed Model Repeated Measurements (MMRM) Analysis

template_medical_history

Template: Patient Profile Medical History

template_logistic

Template: Logistic Regression

template_patient_timeline

Template: Patient Profile Timeline Plot

template_summary_by

Template: Summarize Variables by Row Groups Module

template_prior_medication

Template: Patient Profile Prior Medication

template_mult_events

Template: Multiple Events by Term

template_shift_by_arm

Template: Shift by Arm

template_shift_by_arm_by_worst

Template: Shift by Arm by Worst Analysis Indicator Level

template_shift_by_grade

Template: Grade Summary Table

template_summary

Template: Summary of Variables

Template: Adverse Events Table by Standardized MedDRA Query

template_therapy

Template: Patient Profile Therapy Table and Plot

teal Module: Mixed Model Repeated Measurements (MMRM) Analysis

teal Module: Individual Patient Plots

tm_g_barchart_simple

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

teal Module: Kaplan-Meier Plot

template_vitals

Template: Patient Profile Vitals Plot

teal Module: Confidence Interval Plot

tm_g_forest_rsp

teal Module: Forest Response Plot

teal Module: Generalized Estimating Equations (GEE) analysis

tm_g_forest_tte

teal Module: Forest Survival Plot

Template: Time-To-Event

teal Module: Line Plot

tm_t_binary_outcome

teal Module: Binary Outcome Table

tm_g_pp_patient_timeline

teal Module: Patient Profile Timeline Plot

tm_t_abnormality_by_worst_grade

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

teal Module: Patient Profile Vitals Plot

tm_t_abnormality

teal Module: Abnormality Summary Table

tm_g_pp_therapy

teal Module: Patient Profile Therapy Table and Plot

teal Module: ANCOVA Summary

teal Module: Cox Regression Model

tm_g_pp_adverse_events

teal Module: Patient Profile Adverse Events Table and Plot

tm_t_events_patyear

teal Module: Event Rates Adjusted for Patient-Years

tm_t_events_by_grade

teal Module: Events by Grade

teal Module: Events by Term

tm_t_pp_laboratory

teal Module: Patient Profile Laboratory Table

tm_t_mult_events

teal Module: Multiple Events by Term

tm_t_events_summary

teal Module: Adverse Events Summary

teal Module: Exposure Table for Risk management plan

teal Module: Logistic Regression

tm_t_pp_medical_history

teal Module: Patient Profile Medical History

tm_t_pp_basic_info

teal Module: Patient Profile Basic Info

teal Module: Time-To-Event Table

teal Module: Summary of Variables

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

tm_t_summary_by

teal Module: Summarize Variables by Row Groups

teal Module: Adverse Events Table by Standardized MedDRA Query

tm_t_shift_by_grade

teal Module: Grade Summary Table

tm_t_pp_prior_medication

teal Module: Patient Profile Prior Medication

tm_t_shift_by_arm

teal Module: Shift by Arm

tm_t_shift_by_arm_by_worst

teal Module: Shift by Arm by Worst Analysis Indicator Level

validate_standard_inputs

Validate standard input values for a teal module

Expression List

column_annotation_label

Get full label, useful for annotating plots

default_total_label

Default string for total column label

Control Function for Time-To-Event teal Module

color_lab_values

Mapping function for Laboratory Table

clean_description

Clean up categorical variable description

call_concatenate

Concatenate expressions via a binary operator

Parse text input to numeric vector

get_paramcd_label

Extract the associated parameter value for paramcd

check_arm_ref_comp

Check if the Treatment variable is reference or compare

arm_ref_comp_observer

Observer for Treatment reference variable

Simulated CDISC Data for Examples

cs_to_des_filter

Convert choices_selected to data_extract_spec with only filter_spec

cs_to_des_select

Convert choices_selected to data_extract_spec with only select_spec

Expressions in Brackets

Extracts html id for data_extract_ui

facet_grid_formula

Facetting formula x_facet ~ y_facet

cs_to_filter_spec

Convert choices_selected to filter_spec