Package: chevron 0.2.8

Liming Li

chevron: Standard TLGs for Clinical Trials Reporting

Provide standard tables, listings, and graphs (TLGs) libraries used in clinical trials. This package implements a structure to reformat the data with 'dunlin', create reporting tables using 'rtables' and 'tern' with standardized input arguments to enable quick generation of standard outputs. In addition, it also provides comprehensive data checks and script generation functionality.

Authors:Liming Li [aut, cre], Benoit Falquet [aut], Xiaoli Duan [aut], Adrian Waddell [ctb], Chenkai Lv [ctb], Pawel Rucki [ctb], Tim Barnett [ctb], Tian Fang [ctb], F. Hoffmann-La Roche AG [cph, fnd]

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chevron.pdf |chevron.html✨
chevron/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/insightsengineering/chevron/issues

Datasets:
  • ctcv4_dir - CTC version 4 Grade Direction Data
  • ctcv5_dir - CTC version 5 Grade Direction Data
  • mla_dir - MLA Grade Direction Data
  • syn_data - Example 'adam' Synthetic Data

On CRAN:

clinical-trialsgraphslistingsnestreportingtables

8.14 score 11 stars 9 scripts 538 downloads 221 exports 81 dependencies

Last updated 24 days agofrom:5809c056d0 (on v0.2.8). Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 28 2024
R-4.5-winOKOct 28 2024
R-4.5-linuxOKOct 28 2024
R-4.4-winOKOct 28 2024
R-4.4-macOKOct 28 2024
R-4.3-winOKOct 28 2024
R-4.3-macOKOct 28 2024

Exports:ael01_nolltael01_nollt_mainael01_nollt_preael02ael02_mainael02_preael03ael03_mainael03_preaet01aet01_aesiaet01_aesi_mainaet01_aesi_postaet01_aesi_preaet01_mainaet01_postaet01_preaet02aet02_labelaet02_mainaet02_postaet02_preaet03aet03_mainaet03_postaet03_preaet04aet04_mainaet04_postaet04_preaet05aet05_allaet05_all_preaet05_mainaet05_postaet05_preaet10aet10_mainaet10_postaet10_preargs_lsassert_single_valueassert_valid_varassert_valid_variablecfbt01cfbt01_maincfbt01_postcfbt01_prechevron_gchevron_lchevron_simplechevron_tcml02a_glcml02a_gl_maincml02a_gl_precmt01_labelcmt01acmt01a_maincmt01a_postcmt01a_precmt02_ptcmt02_pt_maincmt02_pt_postcmt02_pt_preconvert_to_monthcoxt01coxt01_maincoxt01_postcoxt01_precoxt02coxt02_maincreate_id_listingsdmt01dmt01_maindmt01_postdmt01_predose_change_ruledst01dst01_maindst01_postdst01_predtht01dtht01_maindtht01_postdtht01_predummy_templateegt01egt01_mainegt01_preegt02_1egt02_1_mainegt02_2egt02_2_mainegt02_postegt02_preegt03egt03_mainegt03_postegt03_preegt05_qtcategt05_qtcat_mainegt05_qtcat_postegt05_qtcat_preempty_ruleext01ext01_mainext01_postext01_preformat_datefstg01fstg01_mainfstg01_prefstg02fstg02_mainfstg02_preget_argget_grade_ruleget_section_divgg_listgg_theme_chevrongrob_listh_format_deckmg01kmg01_mainkmg01_prelbt01lbt01_mainlbt01_prelbt04lbt04_mainlbt04_postlbt04_prelbt05lbt05_mainlbt05_postlbt05_prelbt06lbt06_mainlbt06_postlbt06_prelbt07lbt07_mainlbt07_postlbt07_prelbt14lbt14_mainlbt14_postlbt14_prelbt15lbt15_prelvlsmainmain<-mht01mht01_labelmht01_mainmht01_postmht01_premissing_rulemng01mng01_mainmng01_prenocodingoutcome_rulepdt01pdt01_mainpdt01_postpdt01_prepdt02pdt02_mainpdt02_postpdt02_prepostprocesspostprocess<-preprocesspreprocess<-reformatreport_nullrmpt01rmpt01_mainrmpt01_postrmpt01_prermpt03rmpt03_mainrmpt03_prermpt04rmpt04_mainrmpt04_prermpt05rmpt05_mainrmpt05_prermpt06rmpt06_mainrmpt06_postrmpt06_prerspt01rspt01_mainrspt01_postrspt01_prerunscript_funsset_section_divstandard_null_reportstd_postprocessingttet01ttet01_mainttet01_postttet01_preunwrap_layoutvar_labels_forvst01vst01_mainvst01_prevst02_1vst02_1_mainvst02_2vst02_2_mainvst02_postvst02_prewith_labelyes_no_rule

Dependencies:abindbackportsbase64encbootbroomcarcarDatacheckmateclicolorspacecowplotcpp11DerivdigestdoBydplyrdunlinemmeansestimabilityfansifarverfastmapforcatsformattersFormulagenericsggplot2gluegridExtragtablehtmltoolsisobandlabelinglatticelifecyclelme4lubridatemagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrmunsellmvtnormnestcolornlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpurrrquantregR6rbibutilsRColorBrewerRcppRcppEigenRdpackrlangrlistingsrtablesscalesSparseMstringistringrsurvivalterntibbletidyrtidyselecttimechangeutf8vctrsviridisLitewithryaml

Chevron Catalog

Rendered fromchevron_catalog.rmdusingknitr::rmarkdownon Oct 28 2024.

Last update: 2024-10-28
Started: 2023-07-05

Introduction to Chevron

Rendered fromchevron.Rmdusingknitr::rmarkdownon Oct 28 2024.

Last update: 2023-12-04
Started: 2021-08-18

Script_Generator

Rendered fromscript_generator.Rmdusingknitr::rmarkdownon Oct 28 2024.

Last update: 2023-12-04
Started: 2023-03-14

Readme and manuals

Help Manual

Help pageTopics
'chevron' packagechevron-package chevron
'AEL01_NOLLT' Listing 1 (Default) Glossary of Preferred Terms and Investigator-Specified Terms.ael01_nollt ael01_nollt_main ael01_nollt_pre
'AEL02' Listing 1 (Default) Listing of Adverse Events.ael02 ael02_main ael02_pre
'AEL03' Listing 1 (Default) Listing of Serious Adverse Events.ael03 ael03_main ael03_pre
'AET01_AESI' Table 1 (Default) Adverse Event of Special Interest Summary Table.aet01_aesi aet01_aesi_main aet01_aesi_post aet01_aesi_pre
'AET01' Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.aet01 aet01_main aet01_post aet01_pre
'AET02' Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.aet02 aet02_label aet02_main aet02_post aet02_pre
'AET03' Table 1 (Default) Advert Events by Greatest Intensity Table 1.aet03 aet03_main aet03_post aet03_pre
'AET04' Table 1 (Default) Adverse Events by Highest 'NCI' 'CTACAE' 'AE' Grade Table 1.aet04 aet04_main aet04_post aet04_pre
'AET05_ALL' Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences.aet05_all aet05_all_pre
'AET05' Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence.aet05 aet05_main aet05_post aet05_pre
'AET10' Table 1 (Default) Most Common (xx%) Adverse Events Preferred Terms Table 1.aet10 aet10_main aet10_post aet10_pre
Get Arguments Listargs_ls args_ls,chevron_tlg-method
Check variable only has one unique value.assert_single_value
Check variable is of correct typeassert_valid_type
Check whether var is validassert_valid_var assert_valid_var.character assert_valid_var.default assert_valid_var.factor assert_valid_var.logical assert_valid_var.numeric assert_valid_var.POSIXct
Check variables are of same levelsassert_valid_var_pair
Check variables in a data frame are valid character or factor.assert_valid_variable
'CFBT01' Change from Baseline By Visit Table.cfbt01 cfbt01_main cfbt01_post cfbt01_pre
'chevron_t'.chevron_g .chevron_l .chevron_simple .chevron_t .chevron_tlg chevron_g chevron_g-class chevron_graph chevron_l chevron_l-class chevron_listing chevron_simple chevron_simple-class chevron_t chevron_t-class chevron_table chevron_tlg-class
'CML02A_GL' Listing 1 (Default) Concomitant Medication Class Level 2, Preferred Name, and Investigator-Specified Terms.cml02a_gl cml02a_gl_main cml02a_gl_pre
'CMT01A' Concomitant Medication by Medication Class and Preferred Name.cmt01a cmt01a_main cmt01a_post cmt01a_pre cmt01_label
'CMT02_PT' Table 1 (Default) Concomitant Medications by Preferred Name.cmt02_pt cmt02_pt_main cmt02_pt_post cmt02_pt_pre
Helper function to convert to months if neededconvert_to_month
'COXT01' (Default) Cox Regression Model Table.coxt01 coxt01_main coxt01_post coxt01_pre
'COXT02' Multi-Variable Cox Regression Model Table.coxt02 coxt02_main
Concatenate Site and Subject IDcreate_id_listings
CTC version 4 Grade Direction Datactcv4_dir
CTC version 5 Grade Direction Datactcv5_dir
'DMT01' Table 1 (Default) Demographics and Baseline Characteristics Table 1.dmt01 dmt01_main dmt01_post dmt01_pre
Dose Change Ruledose_change_rule
DST01 Table 1 (Default) Patient Disposition Table 1.dst01 dst01_main dst01_post dst01_pre
'DTHT01' Table 1 (Default) Death Table.dtht01 dtht01_main dtht01_post dtht01_pre
Dummy template.dummy_template
'EGT01' ECG Parameters and Change from Baseline By Visit Table.egt01 egt01_main egt01_pre
'EGT02' ECG Abnormalities Table.egt02_1 egt02_1_main egt02_post egt02_pre
'EGT02_2' ECG Abnormalities Table.egt02_2 egt02_2_main
'EGT03' Shift Table of ECG Interval Data - Baseline versus Minimum or Maximum Post-Baseline.egt03 egt03_main egt03_post egt03_pre
'EGT05_QTCAT' ECG Actual Values and Changes from Baseline by Visit Table.egt05_qtcat egt05_qtcat_main egt05_qtcat_post egt05_qtcat_pre
Empty ruleempty_rule
'EXT01' Exposure Summary Table.ext01 ext01_main ext01_post ext01_pre
Formatting of dateformat_date
'FSTG01' Subgroup Analysis of Best Overall Response.fstg01 fstg01_main fstg01_pre
'FSTG02' Subgroup Analysis of Survival Duration.fstg02 fstg02_main fstg02_pre
General Argument Name Conventiongen_args
Get grade ruleget_grade_rule
Get Section dividersget_section_div
List of 'gg' objectgg_list
Theme for Chevron Plotgg_theme_chevron
List of 'grob' objectgrob_list
Decimal formattingh_format_dec
'KMG01' Kaplan-Meier Plot 1.kmg01 kmg01_main kmg01_pre
'LBT01' Lab Results and Change from Baseline by Visit Table.lbt01 lbt01_main lbt01_pre
'LBT04' Laboratory Abnormalities Not Present at Baseline Table.lbt04 lbt04_main lbt04_post lbt04_pre
'LBT05' Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.lbt05 lbt05_main lbt05_post lbt05_pre
'LBT06' Table 1 (Default) Laboratory Abnormalities by Visit and Baseline Status Table 1.lbt06 lbt06_main lbt06_post lbt06_pre
'LBT07' Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.lbt07 lbt07_main lbt07_post lbt07_pre
'LBT14' Laboratory Test Results Shift Table – Highest 'NCI-CTCAE' Grade Post-Baseline by Baseline Grade (Low or High Direction).lbt14 lbt14_main lbt14_post lbt14_pre
'LBT15' Laboratory Test Shifts to 'NCI-CTCAE' Grade 3-4 Post-Baseline Table.lbt15 lbt15_pre
Format for Chevron Listingslisting_format_chevron
Obtain levels from vectorlvls
Mainmain main,chevron_tlg-method main<- main<-,chevron_tlg-method
'MHT01' Medical History Table.mht01 mht01_label mht01_main mht01_post mht01_pre
Missing rulemissing_rule
MLA Grade Direction Datamla_dir
'MNG01' Mean Plot Graph.mng01 mng01_main mng01_pre
No Coding Available rulenocoding
Outcome Ruleoutcome_rule
'pdt01' Major Protocol Deviations Table.pdt01 pdt01_main pdt01_post pdt01_pre
'pdt02' Major Protocol Deviations Related to Epidemic/Pandemic Table.pdt02 pdt02_main pdt02_post pdt02_pre
Post processpostprocess postprocess,chevron_tlg-method postprocess<- postprocess<-,chevron_tlg-method
Pre processpreprocess preprocess,chevron_tlg-method preprocess<- preprocess<-,chevron_tlg-method
Creates 'NULL' Reportreport_null report_null,ANY-method report_null,list-method report_null,listing_df-method report_null,NULL-method report_null,VTableTree-method standard_null_report
'RMPT01'Duration of Exposure for Risk Management Plan Table.rmpt01 rmpt01_main rmpt01_post rmpt01_pre
'rmpt03'Duration of Exposure for Risk Management Plan Table.rmpt03 rmpt03_main rmpt03_pre
'RMPT04'Extent of Exposure by Ethnic Origin for Risk Management Plan Table.rmpt04 rmpt04_main rmpt04_pre
'RMPT05' Extent of Exposure by Race for Risk Management Plan Table.rmpt05 rmpt05_main rmpt05_pre
'RMPT06' Table 1 (Default) Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Management Plan.rmpt06 rmpt06_main rmpt06_post rmpt06_pre
'RSPT01' Binary Outcomes Summary.rspt01 rspt01_main rspt01_post rspt01_pre
Run the TLG-generating pipelinerun run,chevron_tlg-method
Create Script for 'TLG' Generationscript script_funs script_funs,chevron_simple-method script_funs,chevron_tlg-method
Set Section Dividersset_section_div
Prune table up to an 'ElementaryTable'smart_prune
Standard Post Processingstd_postprocessing
Example 'adam' Synthetic Datasyn_data
'TTET01' Binary Outcomes Summary.ttet01 ttet01_main ttet01_post ttet01_pre
Retrieve labels for certain variablesvar_labels_for
'VST01' Vital Sign Results and change from Baseline By Visit Table.vst01 vst01_main vst01_pre
'VST02' Vital Sign Abnormalities Table.vst02_1 vst02_1_main vst02_post vst02_pre
'VST02' Vital Sign Abnormalities Table.vst02_2 vst02_2_main
Yes/No rule in title caseyes_no_rule