R: Standard TLGs for Clinical Trials Reporting

# Standard TLGs for Clinical Trials Reporting

## Documentation for package ‘chevron’ version 0.2.10

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G H K L M N O P R S T V Y misc

chevron-package | 'chevron' package

## -- A --

ael01_nollt | 'AEL01_NOLLT' Listing 1 (Default) Glossary of Preferred Terms and Investigator-Specified Terms.
ael01_nollt_main | 'AEL01_NOLLT' Listing 1 (Default) Glossary of Preferred Terms and Investigator-Specified Terms.
ael01_nollt_pre | 'AEL01_NOLLT' Listing 1 (Default) Glossary of Preferred Terms and Investigator-Specified Terms.
ael02 | 'AEL02' Listing 1 (Default) Listing of Adverse Events.
ael02_main | 'AEL02' Listing 1 (Default) Listing of Adverse Events.
ael02_pre | 'AEL02' Listing 1 (Default) Listing of Adverse Events.
ael03 | 'AEL03' Listing 1 (Default) Listing of Serious Adverse Events.
ael03_main | 'AEL03' Listing 1 (Default) Listing of Serious Adverse Events.
ael03_pre | 'AEL03' Listing 1 (Default) Listing of Serious Adverse Events.
aet01 | 'AET01' Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.
aet01_aesi | 'AET01_AESI' Table 1 (Default) Adverse Event of Special Interest Summary Table.
aet01_aesi_main | 'AET01_AESI' Table 1 (Default) Adverse Event of Special Interest Summary Table.
aet01_aesi_post | 'AET01_AESI' Table 1 (Default) Adverse Event of Special Interest Summary Table.
aet01_aesi_pre | 'AET01_AESI' Table 1 (Default) Adverse Event of Special Interest Summary Table.
aet01_main | 'AET01' Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.
aet01_post | 'AET01' Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.
aet01_pre | 'AET01' Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.
aet02 | 'AET02' Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.
aet02_label | 'AET02' Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.
aet02_main | 'AET02' Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.
aet02_post | 'AET02' Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.
aet02_pre | 'AET02' Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.
aet03 | 'AET03' Table 1 (Default) Advert Events by Greatest Intensity Table 1.
aet03_main | 'AET03' Table 1 (Default) Advert Events by Greatest Intensity Table 1.
aet03_post | 'AET03' Table 1 (Default) Advert Events by Greatest Intensity Table 1.
aet03_pre | 'AET03' Table 1 (Default) Advert Events by Greatest Intensity Table 1.
aet04 | 'AET04' Table 1 (Default) Adverse Events by Highest 'NCI' 'CTACAE' 'AE' Grade Table 1.
aet04_main | 'AET04' Table 1 (Default) Adverse Events by Highest 'NCI' 'CTACAE' 'AE' Grade Table 1.
aet04_post | 'AET04' Table 1 (Default) Adverse Events by Highest 'NCI' 'CTACAE' 'AE' Grade Table 1.
aet04_pre | 'AET04' Table 1 (Default) Adverse Events by Highest 'NCI' 'CTACAE' 'AE' Grade Table 1.
aet05 | 'AET05' Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence.
aet05_all | 'AET05_ALL' Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences.
aet05_all_pre | 'AET05_ALL' Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences.
aet05_main | 'AET05' Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence.
aet05_post | 'AET05' Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence.
aet05_pre | 'AET05' Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence.
aet10 | 'AET10' Table 1 (Default) Most Common (xx%) Adverse Events Preferred Terms Table 1.
aet10_main | 'AET10' Table 1 (Default) Most Common (xx%) Adverse Events Preferred Terms Table 1.
aet10_post | 'AET10' Table 1 (Default) Most Common (xx%) Adverse Events Preferred Terms Table 1.
aet10_pre | 'AET10' Table 1 (Default) Most Common (xx%) Adverse Events Preferred Terms Table 1.
args_ls | Get Arguments List
args_ls-method | Get Arguments List
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.character | Check whether var is valid
assert_valid_var.default | Check whether var is valid
assert_valid_var.factor | Check whether var is valid
assert_valid_var.logical | Check whether var is valid
assert_valid_var.numeric | Check whether var is valid
assert_valid_var.POSIXct | Check whether var is valid
assert_valid_variable | Check variables in a data frame are valid character or factor.
assert_valid_var_pair | Check variables are of same levels

## -- C --

cfbt01 | 'CFBT01' Change from Baseline By Visit Table.
cfbt01_main | 'CFBT01' Change from Baseline By Visit Table.
cfbt01_post | 'CFBT01' Change from Baseline By Visit Table.
cfbt01_pre | 'CFBT01' Change from Baseline By Visit Table.
chevron | 'chevron' package
chevron_g | 'chevron_t'
chevron_g-class | 'chevron_t'
chevron_graph | 'chevron_t'
chevron_l | 'chevron_t'
chevron_l-class | 'chevron_t'
chevron_listing | 'chevron_t'
chevron_simple | 'chevron_t'
chevron_simple-class | 'chevron_t'
chevron_t | 'chevron_t'
chevron_t-class | 'chevron_t'
chevron_table | 'chevron_t'
chevron_tlg-class | 'chevron_t'
cml02a_gl | 'CML02A_GL' Listing 1 (Default) Concomitant Medication Class Level 2, Preferred Name, and Investigator-Specified Terms.
cml02a_gl_main | 'CML02A_GL' Listing 1 (Default) Concomitant Medication Class Level 2, Preferred Name, and Investigator-Specified Terms.
cml02a_gl_pre | 'CML02A_GL' Listing 1 (Default) Concomitant Medication Class Level 2, Preferred Name, and Investigator-Specified Terms.
cmt01a | 'CMT01A' Concomitant Medication by Medication Class and Preferred Name.
cmt01a_main | 'CMT01A' Concomitant Medication by Medication Class and Preferred Name.
cmt01a_post | 'CMT01A' Concomitant Medication by Medication Class and Preferred Name.
cmt01a_pre | 'CMT01A' Concomitant Medication by Medication Class and Preferred Name.
cmt01_label | 'CMT01A' Concomitant Medication by Medication Class and Preferred Name.
cmt02_pt | 'CMT02_PT' Table 1 (Default) Concomitant Medications by Preferred Name.
cmt02_pt_main | 'CMT02_PT' Table 1 (Default) Concomitant Medications by Preferred Name.
cmt02_pt_post | 'CMT02_PT' Table 1 (Default) Concomitant Medications by Preferred Name.
cmt02_pt_pre | 'CMT02_PT' Table 1 (Default) Concomitant Medications by Preferred Name.
convert_to_month | Helper function to convert to months if needed
coxt01 | 'COXT01' (Default) Cox Regression Model Table.
coxt01_main | 'COXT01' (Default) Cox Regression Model Table.
coxt01_post | 'COXT01' (Default) Cox Regression Model Table.
coxt01_pre | 'COXT01' (Default) Cox Regression Model Table.
coxt02 | 'COXT02' Multi-Variable Cox Regression Model Table.
coxt02_main | 'COXT02' Multi-Variable Cox Regression Model Table.
create_id_listings | Concatenate Site and Subject ID
ctcv4_dir | CTC version 4 Grade Direction Data
ctcv5_dir | CTC version 5 Grade Direction Data

## -- D --

dmt01 | 'DMT01' Table 1 (Default) Demographics and Baseline Characteristics Table 1.
dmt01_main | 'DMT01' Table 1 (Default) Demographics and Baseline Characteristics Table 1.
dmt01_post | 'DMT01' Table 1 (Default) Demographics and Baseline Characteristics Table 1.
dmt01_pre | 'DMT01' Table 1 (Default) Demographics and Baseline Characteristics Table 1.
dose_change_rule | Dose Change Rule
dst01 | DST01 Table 1 (Default) Patient Disposition Table 1.
dst01_main | DST01 Table 1 (Default) Patient Disposition Table 1.
dst01_post | DST01 Table 1 (Default) Patient Disposition Table 1.
dst01_pre | DST01 Table 1 (Default) Patient Disposition Table 1.
dtht01 | 'DTHT01' Table 1 (Default) Death Table.
dtht01_main | 'DTHT01' Table 1 (Default) Death Table.
dtht01_post | 'DTHT01' Table 1 (Default) Death Table.
dtht01_pre | 'DTHT01' Table 1 (Default) Death Table.
dummy_template | Dummy template.

## -- E --

egt01 | 'EGT01' ECG Parameters and Change from Baseline By Visit Table.
egt01_main | 'EGT01' ECG Parameters and Change from Baseline By Visit Table.
egt01_pre | 'EGT01' ECG Parameters and Change from Baseline By Visit Table.
egt02_1 | 'EGT02' ECG Abnormalities Table.
egt02_1_main | 'EGT02' ECG Abnormalities Table.
egt02_2 | 'EGT02_2' ECG Abnormalities Table.
egt02_2_main | 'EGT02_2' ECG Abnormalities Table.
egt02_post | 'EGT02' ECG Abnormalities Table.
egt02_pre | 'EGT02' ECG Abnormalities Table.
egt03 | 'EGT03' Shift Table of ECG Interval Data - Baseline versus Minimum or Maximum Post-Baseline.
egt03_main | 'EGT03' Shift Table of ECG Interval Data - Baseline versus Minimum or Maximum Post-Baseline.
egt03_post | 'EGT03' Shift Table of ECG Interval Data - Baseline versus Minimum or Maximum Post-Baseline.
egt03_pre | 'EGT03' Shift Table of ECG Interval Data - Baseline versus Minimum or Maximum Post-Baseline.
egt05_qtcat | 'EGT05_QTCAT' ECG Actual Values and Changes from Baseline by Visit Table.
egt05_qtcat_main | 'EGT05_QTCAT' ECG Actual Values and Changes from Baseline by Visit Table.
egt05_qtcat_post | 'EGT05_QTCAT' ECG Actual Values and Changes from Baseline by Visit Table.
egt05_qtcat_pre | 'EGT05_QTCAT' ECG Actual Values and Changes from Baseline by Visit Table.
empty_rule | Empty rule
ext01 | 'EXT01' Exposure Summary Table.
ext01_main | 'EXT01' Exposure Summary Table.
ext01_post | 'EXT01' Exposure Summary Table.
ext01_pre | 'EXT01' Exposure Summary Table.

## -- F --

format_date | Formatting of date
fstg01 | 'FSTG01' Subgroup Analysis of Best Overall Response.
fstg01_main | 'FSTG01' Subgroup Analysis of Best Overall Response.
fstg01_pre | 'FSTG01' Subgroup Analysis of Best Overall Response.
fstg02 | 'FSTG02' Subgroup Analysis of Survival Duration.
fstg02_main | 'FSTG02' Subgroup Analysis of Survival Duration.
fstg02_pre | 'FSTG02' Subgroup Analysis of Survival Duration.

## -- G --

gen_args | General Argument Name Convention
get_grade_rule | Get grade rule
get_section_div | Get Section dividers
gg_list | List of 'gg' object
gg_theme_chevron | Theme for Chevron Plot
grob_list | List of 'grob' object

## -- H --

h_format_dec | Decimal formatting

## -- K --

kmg01 | 'KMG01' Kaplan-Meier Plot 1.
kmg01_main | 'KMG01' Kaplan-Meier Plot 1.
kmg01_pre | 'KMG01' Kaplan-Meier Plot 1.

## -- L --

lab_paramcd_precision | 'LBT01' Lab Results and Change from Baseline by Visit Table.
lbt01 | 'LBT01' Lab Results and Change from Baseline by Visit Table.
lbt01_main | 'LBT01' Lab Results and Change from Baseline by Visit Table.
lbt01_pre | 'LBT01' Lab Results and Change from Baseline by Visit Table.
lbt04 | 'LBT04' Laboratory Abnormalities Not Present at Baseline Table.
lbt04_main | 'LBT04' Laboratory Abnormalities Not Present at Baseline Table.
lbt04_post | 'LBT04' Laboratory Abnormalities Not Present at Baseline Table.
lbt04_pre | 'LBT04' Laboratory Abnormalities Not Present at Baseline Table.
lbt05 | 'LBT05' Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.
lbt05_main | 'LBT05' Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.
lbt05_post | 'LBT05' Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.
lbt05_pre | 'LBT05' Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.
lbt06 | 'LBT06' Table 1 (Default) Laboratory Abnormalities by Visit and Baseline Status Table 1.
lbt06_main | 'LBT06' Table 1 (Default) Laboratory Abnormalities by Visit and Baseline Status Table 1.
lbt06_post | 'LBT06' Table 1 (Default) Laboratory Abnormalities by Visit and Baseline Status Table 1.
lbt06_pre | 'LBT06' Table 1 (Default) Laboratory Abnormalities by Visit and Baseline Status Table 1.
lbt07 | 'LBT07' Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.
lbt07_main | 'LBT07' Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.
lbt07_post | 'LBT07' Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.
lbt07_pre | 'LBT07' Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.
lbt14 | 'LBT14' Laboratory Test Results Shift Table – Highest 'NCI-CTCAE' Grade Post-Baseline by Baseline Grade (Low or High Direction).
lbt14_main | 'LBT14' Laboratory Test Results Shift Table – Highest 'NCI-CTCAE' Grade Post-Baseline by Baseline Grade (Low or High Direction).
lbt14_post | 'LBT14' Laboratory Test Results Shift Table – Highest 'NCI-CTCAE' Grade Post-Baseline by Baseline Grade (Low or High Direction).
lbt14_pre | 'LBT14' Laboratory Test Results Shift Table – Highest 'NCI-CTCAE' Grade Post-Baseline by Baseline Grade (Low or High Direction).
lbt15 | 'LBT15' Laboratory Test Shifts to 'NCI-CTCAE' Grade 3-4 Post-Baseline Table.
lbt15_pre | 'LBT15' Laboratory Test Shifts to 'NCI-CTCAE' Grade 3-4 Post-Baseline Table.
listing_format_chevron | Format for Chevron Listings
lvls | Obtain levels from vector

## -- M --

main | Main
main-method | Main
main<- | Main
main<--method | Main
mht01 | 'MHT01' Medical History Table.
mht01_label | 'MHT01' Medical History Table.
mht01_main | 'MHT01' Medical History Table.
mht01_post | 'MHT01' Medical History Table.
mht01_pre | 'MHT01' Medical History Table.
missing_rule | Missing rule
mla_dir | MLA Grade Direction Data
mng01 | 'MNG01' Mean Plot Graph.
mng01_main | 'MNG01' Mean Plot Graph.
mng01_pre | 'MNG01' Mean Plot Graph.

## -- N --

nocoding | No Coding Available rule

## -- O --

outcome_rule | Outcome Rule

## -- P --

pdt01 | 'pdt01' Major Protocol Deviations Table.
pdt01_main | 'pdt01' Major Protocol Deviations Table.
pdt01_post | 'pdt01' Major Protocol Deviations Table.
pdt01_pre | 'pdt01' Major Protocol Deviations Table.
pdt02 | 'pdt02' Major Protocol Deviations Related to Epidemic/Pandemic Table.
pdt02_main | 'pdt02' Major Protocol Deviations Related to Epidemic/Pandemic Table.
pdt02_post | 'pdt02' Major Protocol Deviations Related to Epidemic/Pandemic Table.
pdt02_pre | 'pdt02' Major Protocol Deviations Related to Epidemic/Pandemic Table.
postprocess | Post process
postprocess-method | Post process
postprocess<- | Post process
postprocess<--method | Post process
preprocess | Pre process
preprocess-method | Pre process
preprocess<- | Pre process
preprocess<--method | Pre process

## -- R --

report_null | Creates 'NULL' Report
report_null-method | Creates 'NULL' Report
rmpt01 | 'RMPT01'Duration of Exposure for Risk Management Plan Table.
rmpt01_main | 'RMPT01'Duration of Exposure for Risk Management Plan Table.
rmpt01_post | 'RMPT01'Duration of Exposure for Risk Management Plan Table.
rmpt01_pre | 'RMPT01'Duration of Exposure for Risk Management Plan Table.
rmpt03 | 'rmpt03'Duration of Exposure for Risk Management Plan Table.
rmpt03_main | 'rmpt03'Duration of Exposure for Risk Management Plan Table.
rmpt03_pre | 'rmpt03'Duration of Exposure for Risk Management Plan Table.
rmpt04 | 'RMPT04'Extent of Exposure by Ethnic Origin for Risk Management Plan Table.
rmpt04_main | 'RMPT04'Extent of Exposure by Ethnic Origin for Risk Management Plan Table.
rmpt04_pre | 'RMPT04'Extent of Exposure by Ethnic Origin for Risk Management Plan Table.
rmpt05 | 'RMPT05' Extent of Exposure by Race for Risk Management Plan Table.
rmpt05_main | 'RMPT05' Extent of Exposure by Race for Risk Management Plan Table.
rmpt05_pre | 'RMPT05' Extent of Exposure by Race for Risk Management Plan Table.
rmpt06 | 'RMPT06' Table 1 (Default) Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Management Plan.
rmpt06_main | 'RMPT06' Table 1 (Default) Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Management Plan.
rmpt06_post | 'RMPT06' Table 1 (Default) Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Management Plan.
rmpt06_pre | 'RMPT06' Table 1 (Default) Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Management Plan.
rspt01 | 'RSPT01' Binary Outcomes Summary.
rspt01_main | 'RSPT01' Binary Outcomes Summary.
rspt01_post | 'RSPT01' Binary Outcomes Summary.
rspt01_pre | 'RSPT01' Binary Outcomes Summary.
run | Run the TLG-generating pipeline
run-method | Run the TLG-generating pipeline

## -- S --

script | Create Script for 'TLG' Generation
script_funs | Create Script for 'TLG' Generation
script_funs-method | Create Script for 'TLG' Generation
set_section_div | Set Section Dividers
smart_prune | Prune table up to an 'ElementaryTable'
standard_null_report | Creates 'NULL' Report
std_postprocessing | Standard Post Processing
syn_data | Example 'adam' Synthetic Data

## -- T --

ttet01 | 'TTET01' Binary Outcomes Summary.
ttet01_main | 'TTET01' Binary Outcomes Summary.
ttet01_post | 'TTET01' Binary Outcomes Summary.
ttet01_pre | 'TTET01' Binary Outcomes Summary.

## -- V --

var_labels_for | Retrieve labels for certain variables
vst01 | 'VST01' Vital Sign Results and change from Baseline By Visit Table.
vst01_main | 'VST01' Vital Sign Results and change from Baseline By Visit Table.
vst01_pre | 'VST01' Vital Sign Results and change from Baseline By Visit Table.
vst02_1 | 'VST02' Vital Sign Abnormalities Table.
vst02_1_main | 'VST02' Vital Sign Abnormalities Table.
vst02_2 | 'VST02' Vital Sign Abnormalities Table.
vst02_2_main | 'VST02' Vital Sign Abnormalities Table.
vst02_post | 'VST02' Vital Sign Abnormalities Table.
vst02_pre | 'VST02' Vital Sign Abnormalities Table.

## -- Y --

yes_no_rule | Yes/No rule in title case

## -- misc --

.chevron_g | 'chevron_t'
.chevron_l | 'chevron_t'
.chevron_simple | 'chevron_t'
.chevron_t | 'chevron_t'
.chevron_tlg | 'chevron_t'