Standard TLGs for Clinical Trials Reporting

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Documentation for package ‘chevron’ version 0.2.7

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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 --

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
null_report Creates 'NULL' Report

-- 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 pipeline
run-method Run the 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'
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'