Package index • chevron

Package Overview

chevron chevron-package: chevron package

Classes and Instances

chevron_t() chevron_l() chevron_g() chevron_simple(): chevron_tlg class

Methods

args_ls(): Get Arguments List

run(): Run the TLG-generating pipeline

main() `main<-`(): Main

preprocess() `preprocess<-`(): Pre process

postprocess() `postprocess<-`(): Post process

dataset() `dataset<-`(): Data Set

script_funs(): Create Script for TLG Generation

chevron_tlg objects

ael01_nollt_main() ael01_nollt_pre() ael01_nollt: AEL01_NOLLT Listing 1 (Default) Glossary of Preferred Terms and Investigator-Specified Terms.

ael02_main() ael02_pre() ael02: AEL02 Listing 1 (Default) Listing of Adverse Events.

ael03_main() ael03_pre() ael03: AEL03 Listing 1 (Default) Listing of Serious Adverse Events.

aet01_main() aet01_pre() aet01_post() aet01: AET01 Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.

aet01_aesi_main() aet01_aesi_pre() aet01_aesi_post() aet01_aesi: AET01_AESI Table 1 (Default) Adverse Event of Special Interest Summary Table.

aet02_label aet02_main() aet02_pre() aet02_post() aet02: AET02 Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.

aet03_main() aet03_pre() aet03_post() aet03: AET03 Table 1 (Default) Advert Events by Greatest Intensity Table 1.

aet04_main() aet04_pre() aet04_post() aet04: AET04 Table 1 (Default) Adverse Events by Highest NCI CTACAE AE Grade Table 1.

aet05_main() aet05_pre() aet05_post() aet05: AET05 Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence.

aet05_all_pre() aet05_all: AET05_ALL Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences.

aet10_main() aet10_pre() aet10_post() aet10: AET10 Table 1 (Default) Most Common (xx%) Adverse Events Preferred Terms Table 1.

cfbt01_main() cfbt01_pre() cfbt01_post() cfbt01: CFBT01 Change from Baseline By Visit Table.

cml02a_gl_main() cml02a_gl_pre() cml02a_gl: CML02A_GL Listing 1 (Default) Concomitant Medication Class Level 2, Preferred Name, and Investigator-Specified Terms.

cmt01_label cmt01a_main() cmt01a_pre() cmt01a_post() cmt01a: CMT01A Concomitant Medication by Medication Class and Preferred Name.

cmt02_pt_main() cmt02_pt_pre() cmt02_pt_post() cmt02_pt: CMT02_PT Table 1 (Default) Concomitant Medications by Preferred Name.

coxt01_main() coxt01_pre() coxt01_post() coxt01: COXT01 (Default) Cox Regression Model Table.

coxt02_main() coxt02: COXT02 Multi-Variable Cox Regression Model Table.

dmt01_main() dmt01_pre() dmt01_post() dmt01: DMT01 Table 1 (Default) Demographics and Baseline Characteristics Table 1.

dst01_main() dst01_pre() dst01_post() dst01: DST01 Table 1 (Default) Patient Disposition Table 1.

dtht01_main() dtht01_pre() dtht01_post() dtht01: DTHT01 Table 1 (Default) Death Table.

egt01_main() egt01_pre() egt01: EGT01 ECG Parameters and Change from Baseline By Visit Table.

egt02_1_main() egt02_pre() egt02_post() egt02_1: EGT02 ECG Abnormalities Table.

egt02_2_main() egt02_2: EGT02_2 ECG Abnormalities Table.

egt03_main() egt03_pre() egt03_post() egt03: EGT03 Shift Table of ECG Interval Data - Baseline versus Minimum or Maximum Post-Baseline.

egt05_qtcat_main() egt05_qtcat_pre() egt05_qtcat_post() egt05_qtcat: EGT05_QTCAT ECG Actual Values and Changes from Baseline by Visit Table.

ext01_main() ext01_pre() ext01_post() ext01: EXT01 Exposure Summary Table.

fstg01_main() fstg01_pre() fstg01: FSTG01 Subgroup Analysis of Best Overall Response.

fstg02_main() fstg02_pre() fstg02: FSTG02 Subgroup Analysis of Survival Duration.

kmg01_main() kmg01_pre() kmg01: KMG01 Kaplan-Meier Plot 1.

lbt01_main() lbt01_pre() lbt01 lab_paramcd_precision(): LBT01 Lab Results and Change from Baseline by Visit Table.

lbt04_main() lbt04_pre() lbt04_post() lbt04: LBT04 Laboratory Abnormalities Not Present at Baseline Table.

lbt05_main() lbt05_pre() lbt05_post() lbt05 lab_paramcd_abn_dir(): LBT05 Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.

lbt06_main() lbt06_pre() lbt06_post() lbt06: LBT06 Table 1 (Default) Laboratory Abnormalities by Visit and Baseline Status Table 1.

lbt07_main() lbt07_pre() lbt07_post() lbt07: LBT07 Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.

lbt14_main() lbt14_pre() lbt14_post() lbt14: LBT14 Laboratory Test Results Shift Table – Highest NCI-CTCAE Grade Post-Baseline by Baseline Grade (Low or High Direction).

lbt15_pre() lbt15: LBT15 Laboratory Test Shifts to NCI-CTCAE Grade 3-4 Post-Baseline Table.

mht01_label mht01_main() mht01_pre() mht01_post() mht01: MHT01 Medical History Table.

mng01_main() mng01_pre() mng01: MNG01 Mean Plot Graph.

pdt01_main() pdt01_pre() pdt01_post() pdt01: pdt01 Major Protocol Deviations Table.

pdt02_main() pdt02_pre() pdt02_post() pdt02: pdt02 Major Protocol Deviations Related to Epidemic/Pandemic Table.

rmpt01_main() rmpt01_pre() rmpt01_post() rmpt01: RMPT01Duration of Exposure for Risk Management Plan Table.

rmpt03_main() rmpt03_pre() rmpt03: rmpt03Duration of Exposure for Risk Management Plan Table.

rmpt04_main() rmpt04_pre() rmpt04: RMPT04Extent of Exposure by Ethnic Origin for Risk Management Plan Table.

rmpt05_main() rmpt05_pre() rmpt05: RMPT05 Extent of Exposure by Race for Risk Management Plan Table.

rmpt06_main() rmpt06_pre() rmpt06_post() rmpt06: RMPT06 Table 1 (Default) Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Management Plan.

rspt01_main() rspt01_pre() rspt01_post() rspt01: RSPT01 Binary Outcomes Summary.

ttet01_main() ttet01_pre() ttet01_post() ttet01: TTET01 Binary Outcomes Summary.

vst01_main() vst01_pre() vst01: VST01 Vital Sign Results and change from Baseline By Visit Table.

vst02_1_main() vst02_pre() vst02_post() vst02_1: VST02 Vital Sign Abnormalities Table.

vst02_2_main() vst02_2: VST02 Vital Sign Abnormalities Table.

dummy_template: Dummy template.

Data and Metadata

syn_data: Example adam Synthetic Data

lbt01_main() lbt01_pre() lbt01 lab_paramcd_precision(): LBT01 Lab Results and Change from Baseline by Visit Table.

lbt05_main() lbt05_pre() lbt05_post() lbt05 lab_paramcd_abn_dir(): LBT05 Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.

ctcv4_dir: CTC version 4 Grade Direction Data

ctcv5_dir: CTC version 5 Grade Direction Data

mla_dir: MLA Grade Direction Data

Utility Functions

assert_single_value(): Check variable only has one unique value.

assert_valid_type(): Check variable is of correct type

assert_valid_var(): Check whether var is valid

assert_valid_var_pair(): Check variables are of same levels

assert_valid_variable(): Check variables in a data frame are valid character or factor.

create_id_listings(): Concatenate Site and Subject ID

report_null() standard_null_report(): Creates NULL Report

std_postprocessing(): Standard Post Processing

smart_prune(): Prune table up to an ElementaryTable

var_labels_for(): Retrieve labels for certain variables

format_date(): Formatting of date

gg_theme_chevron(): Theme for Chevron Plot

h_format_dec(): Decimal formatting

listing_format_chevron(): Format for Chevron Listings

lvls(): Obtain levels from vector

convert_to_month(): Helper function to convert to months if needed

get_section_div(): Get Section dividers

set_section_div(): Set Section Dividers

Standard Reformatting Rules

nocoding: No Coding Available rule

missing_rule: Missing rule

empty_rule: Empty rule

get_grade_rule(): Get grade rule

dose_change_rule: Dose Change Rule

outcome_rule: Outcome Rule

yes_no_rule: Yes/No rule in title case

Non-exported Documented Functions for Packagage Developers

gen_args(): General Argument Name Convention

fuse_sequentially(): Fuse list elements

Deprecated Functions

grob_list() deprecated: List of grob object

gg_list() deprecated: List of gg object