Package: teal.modules.clinical 0.9.1

Joe Zhu

teal.modules.clinical: 'teal' Modules for Standard Clinical Outputs

Provides user-friendly tools for creating and customizing clinical trial reports. By leveraging the 'teal' framework, this package provides 'teal' modules to easily create an interactive panel that allows for seamless adjustments to data presentation, thereby streamlining the creation of detailed and accurate reports.

Authors:Joe Zhu [aut, cre], Jana Stoilova [aut], Davide Garolini [aut], Emily de la Rua [aut], Abinaya Yogasekaram [aut], Mahmoud Hallal [aut], Dawid Kaledkowski [aut], Rosemary Li [aut], Heng Wang [aut], Pawel Rucki [aut], Nikolas Burkoff [aut], Konrad Pagacz [aut], Vaakesan Sundrelingam [ctb], Francois Collin [ctb], Imanol Zubizarreta [ctb], F. Hoffmann-La Roche AG [cph, fnd]

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teal.modules.clinical.pdf |teal.modules.clinical.html✨
teal.modules.clinical/json (API)
NEWS

# Install 'teal.modules.clinical' in R:
install.packages('teal.modules.clinical', repos = c('https://insightsengineering.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/insightsengineering/teal.modules.clinical/issues

Datasets:

On CRAN:

clinical-trialsmodulesnestoutputsshiny

59 exports 29 stars 4.29 score 196 dependencies 692 downloads

Last updated 2 months agofrom:73902e47b6 (on v0.9.1)

Exports:add_expras_numbracket_exprcall_concatenateclean_descriptioncolor_lab_valuescolumn_annotation_labelcs_to_des_filtercs_to_des_selectcs_to_filter_speccs_to_select_specdefault_total_labelextract_inputget_var_labelsh_concat_expris.cs_or_despipe_exprprepare_armprepare_arm_levelsset_default_total_labelsplit_choicessplit_col_exprsplit_interactionstm_a_geetm_a_mmrmtm_g_barchart_simpletm_g_citm_g_forest_rsptm_g_forest_ttetm_g_ipptm_g_kmtm_g_lineplottm_g_pp_adverse_eventstm_g_pp_patient_timelinetm_g_pp_therapytm_g_pp_vitalstm_t_abnormalitytm_t_abnormality_by_worst_gradetm_t_ancovatm_t_binary_outcometm_t_coxregtm_t_eventstm_t_events_by_gradetm_t_events_patyeartm_t_events_summarytm_t_exposuretm_t_logistictm_t_mult_eventstm_t_pp_basic_infotm_t_pp_laboratorytm_t_pp_medical_historytm_t_pp_prior_medicationtm_t_shift_by_armtm_t_shift_by_arm_by_worsttm_t_shift_by_gradetm_t_smqtm_t_summarytm_t_summary_bytm_t_tte

Dependencies:abindanytimeaskpassassertthatbackportsbase64encBHbitbit64bootbriobroombslibcachemcallrcarcarDatacheckmateclicliprcodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcrulcurldata.tableDerivdescdiffobjdigestdoBydplyrDTemmeansestimabilityevaluatefansifarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverforcatsforeachformattersfsgdtoolsgeeasygeeMgeepackgenericsgfontsggformulaggplot2ggrepelggridgesglmnetgluegridExtragtablehavenhighrhmshtmltoolshtmlwidgetshttpcodehttpuvhttrisobanditeratorsjquerylibjsonlitekinship2knitrlabelinglabelledlaterlatticelazyevallifecyclelme4loggermagrittrMASSMatrixMatrixModelsmemoiseMESSmgcvmicrobenchmarkmimeminqammrmmodelrmosaicCoremunsellmvtnormnlmenloptrnnetnumDerivofficeropensslparallellypbkrtestpillarpkgbuildpkgconfigpkgloadplotlypraiseprettyunitsprocessxprogresspromisespspurrrquadprogquantregR.cacheR.methodsS3R.ooR.utilsR6raggrappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrrematch2rlangrlistingsrmarkdownrprojrootrtablessassscalesshapeshinyshinybusyshinycssloadersshinyjsshinyvalidateshinyWidgetssourcetoolsSparseMstringistringrstylersurvivalsyssystemfontstealteal.codeteal.datateal.loggerteal.reporterteal.sliceteal.transformteal.widgetsterntern.geetern.mmrmtestthattextshapingtibbletidyrtidyselecttinytexTMBtriebeardtzdburltoolsutf8uuidvctrsviridisLitevistimevroomwaldowithrxfunxml2xtableyamlzip

Example Data Generation

Rendered fromgenerate_tmc_test_data.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2024-03-01
Started: 2023-02-23

Getting Started with {teal.modules.clinical}

NEST CoreDev Team

Rendered fromteal-modules-clinical.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2024-03-20
Started: 2022-04-07

Quick start: substitute for NSE

Francois Collin

Rendered fromquickstart_substitute.Rmdusingknitr::rmarkdownon Jun 27 2024.

Last update: 2024-04-15
Started: 2020-10-29

Readme and manuals

Help Manual

Help pageTopics
'teal' Modules for Standard Clinical Outputsteal.modules.clinical-package teal.modules.clinical
Expression Listadd_expr
Parse text input to numeric vectoras_num as_num.character as_num.default as_num.factor as_num.logical as_num.numeric
Expressions in Bracketsbracket_expr
Concatenate expressions via a binary operatorcall_concatenate
Clean up categorical variable descriptionclean_description
Mapping function for Laboratory Tablecolor_lab_values
Get full label, useful for annotating plotscolumn_annotation_label
Convert choices_selected to data_extract_spec with only filter_speccs_to_des_filter
Convert choices_selected to data_extract_spec with only select_speccs_to_des_select
Convert choices_selected to filter_speccs_to_filter_spec
Convert choices_selected to select_speccs_to_select_spec
Default string for total column labeldefault_total_label set_default_total_label
Simulated 'CDISC' Data for Examplesex_data tmc_ex_adae tmc_ex_adaette tmc_ex_adcm tmc_ex_adeg tmc_ex_adex tmc_ex_adlb tmc_ex_admh tmc_ex_adqs tmc_ex_adrs tmc_ex_adsl tmc_ex_adtte tmc_ex_advs
Extracts html id for 'data_extract_ui'extract_input
Get variable labelsget_var_labels
Expression Deparsingh_concat_expr
Whether object is of class 'teal.transform::choices_selected()'is.cs_or_des
Expressions as a Pipelinepipe_expr
Expression: Arm Preparationprepare_arm
Expression: Prepare Arm Levelsprepare_arm_levels
Split 'choices_selected' objects with interactions into their component variablessplit_choices
Split-Column Expressionsplit_col_expr
Split interaction terms into their component variablessplit_interactions
teal Module: Generalized Estimating Equations (GEE) analysistm_a_gee
teal Module: Mixed Model Repeated Measurements (MMRM) Analysistm_a_mmrm
teal Module: Simple Bar Chart and Table of Counts per Categorytm_g_barchart_simple
teal Module: Confidence Interval Plottm_g_ci
teal Module: Forest Response Plottm_g_forest_rsp
teal Module: Forest Survival Plottm_g_forest_tte
teal Module: Individual Patient Plotstm_g_ipp
teal Module: Kaplan-Meier Plottm_g_km
teal Module: Line Plottm_g_lineplot
teal Module: Patient Profile Adverse Events Table and Plottm_g_pp_adverse_events
teal Module: Patient Profile Timeline Plottm_g_pp_patient_timeline
teal Module: Patient Profile Therapy Table and Plottm_g_pp_therapy
teal Module: Patient Profile Vitals Plottm_g_pp_vitals
teal Module: Abnormality Summary Tabletm_t_abnormality
teal Module: Laboratory test results with highest grade post-baselinetm_t_abnormality_by_worst_grade
teal Module: ANCOVA Summarytm_t_ancova
teal Module: Binary Outcome Tabletm_t_binary_outcome
teal Module: Cox Regression Modeltm_t_coxreg
teal Module: Events by Termtm_t_events
teal Module: Events by Gradetm_t_events_by_grade
teal Module: Event Rates Adjusted for Patient-Yearstm_t_events_patyear
teal Module: Adverse Events Summarytm_t_events_summary
teal Module: Exposure Table for Risk management plantm_t_exposure
teal Module: Logistic Regressiontm_t_logistic
teal Module: Multiple Events by Termtm_t_mult_events
teal Module: Patient Profile Basic Infotm_t_pp_basic_info
teal Module: Patient Profile Laboratory Tabletm_t_pp_laboratory
teal Module: Patient Profile Medical Historytm_t_pp_medical_history
teal Module: Patient Profile Prior Medicationtm_t_pp_prior_medication
teal Module: Shift by Armtm_t_shift_by_arm
teal Module: Shift by Arm by Worst Analysis Indicator Leveltm_t_shift_by_arm_by_worst
teal Module: Grade Summary Tabletm_t_shift_by_grade
teal Module: Adverse Events Table by Standardized MedDRA Querytm_t_smq
teal Module: Summary of Variablestm_t_summary
teal Module: Summarize Variables by Row Groupstm_t_summary_by
teal Module: Time-To-Event Tabletm_t_tte