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chevron: Standard TLGs for clinical trials reporting

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install.packages('chevron')

Monthly Downloads

502

Version

0.2.7

License

Apache License 2.0

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Last Published

October 9th, 2024

Functions in chevron (0.2.7)

afun_skip

Analyze skip baseline
ael03_main

AEL03 Listing 1 (Default) Listing of Serious Adverse Events.
aet01_main

AET01 Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.
assert_valid_variable

Check variables in a data frame are valid character or factor.
aet05_all_pre

AET05_ALL Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - All Occurrences.
aet05_lyt

aet05 Layout
aet10_main

AET10 Table 1 (Default) Most Common (xx%) Adverse Events Preferred Terms Table 1.
convert_to_month

Helper function to convert to months if needed
count_children

Count Children
cfbt01_main

CFBT01 Change from Baseline By Visit Table.
check_one_colnames

Check that at least one name is among column names
dmt01_main

DMT01 Table 1 (Default) Demographics and Baseline Characteristics Table 1.
deparse_print

Deparse print
expand_list

Expand list to each split
aet04_main

AET04 Table 1 (Default) Adverse Events by Highest NCI CTACAE AE Grade Table 1.
chevron-package

chevron package
lbt04_main

LBT04 Laboratory Abnormalities Not Present at Baseline Table.
ext01_main

EXT01 Exposure Summary Table.
get_section_div

Get Section dividers
get_subset

Subset Arguments and Merge
chevron_tlg-class

chevron_t
args_ls

Get Arguments List
aet04_lyt

aet04 Layout
cml02a_gl_main

CML02A_GL Listing 1 (Default) Concomitant Medication Class Level 2, Preferred Name, and Investigator-Specified Terms.
lbt04_lyt

lbt04 Layout
dst01_lyt

dst01 Layout
pdt01_main

pdt01 Major Protocol Deviations Table.
aet01_aesi_main

AET01_AESI Table 1 (Default) Adverse Event of Special Interest Summary Table.
lbt06_lyt

lbt06 Layout
lbt06_main

LBT06 Table 1 (Default) Laboratory Abnormalities by Visit and Baseline Status Table 1.
outcome_rule

Outcome Rule
assert_valid_var_pair

Check variables are of same levels
assert_valid_var

Check whether var is valid
assert_single_value

Check variable only has one unique value.
pdt01_lyt

pdt01 Layout
aet10_lyt

aet10 Layout
aet01_aesi_lyt

aet01_aesi Layout
dtht01_main

DTHT01 Table 1 (Default) Death Table.
cfbt01_lyt

cfbt01 Layout
cmt01_label

CMT01A Concomitant Medication by Medication Class and Preferred Name.
check_all_colnames

Check that all names are among column names
dst01_main

DST01 Table 1 (Default) Patient Disposition Table 1.
dose_change_rule

Dose Change Rule
cmt02_pt_main

CMT02_PT Table 1 (Default) Concomitant Medications by Preferred Name.
assert_valid_type

Check variable is of correct type
split_rows_by_recursive

Count or summarize by groups
std_listing

Standard Main Listing Function
afun_p

Analyze with defined precision
pdt02_main

pdt02 Major Protocol Deviations Related to Epidemic/Pandemic Table.
create_id_listings

Concatenate Site and Subject ID
coxt02_main

COXT02 Multi-Variable Cox Regression Model Table.
fstg01_main

FSTG01 Subgroup Analysis of Best Overall Response.
egt03_main

EGT03 Shift Table of ECG Interval Data - Baseline versus Minimum or Maximum Post-Baseline.
egt03_lyt

egt03 Layout
coxt01_lyt

COXT01 Layout
yes_no_rule

Yes/No rule in title case
fstg02_main

FSTG02 Subgroup Analysis of Survival Duration.
coxt01_main

COXT01 (Default) Cox Regression Model Table.
format_date

Formatting of date
dtht01_lyt

dtht01 Layout
ext01_lyt

ext01 Layout
do_call

Execute a function call
dmt01_lyt

dmt01 Layout
dummy_template

Dummy template.
egt02_2_main

EGT02_2 ECG Abnormalities Table.
fuse_sequentially

Fuse list elements
get_grade_rule

Get grade rule
grob_list

List of grob object
get_page_by

Get page by value
count_patients_recursive

Count patients recursively
count_or_summarize

Count or summarize by groups
ctcv5_dir

CTC version 5 Grade Direction Data
ctcv4_dir

CTC version 4 Grade Direction Data
gen_args

General Argument Name Convention
egt01_main

EGT01 ECG Parameters and Change from Baseline By Visit Table.
egt02_lyt

egt02 Layout
h_format_dec

Decimal formatting
lbt14_main

LBT14 Laboratory Test Results Shift Table – Highest NCI-CTCAE Grade Post-Baseline by Baseline Grade (Low or High Direction).
egt02_1_main

EGT02 ECG Abnormalities Table.
gg_list

List of gg object
empty_rule

Empty rule
execute_with_args

Execute function with given arguments
listing_format_chevron

Format for Chevron Listings
lbt15_pre

LBT15 Laboratory Test Shifts to NCI-CTCAE Grade 3-4 Post-Baseline Table.
egt05_qtcat_main

EGT05_QTCAT ECG Actual Values and Changes from Baseline by Visit Table.
gg_theme_chevron

Theme for Chevron Plot
ifneeded_split_col

Helper function to add a column split if specified
ifneeded_split_row

Helper function to add a row split if specified
egt05_qtcat_lyt

EGT05_QTCAT Layout
lvls

Obtain levels from vector
main

Main
lbt14_lyt

lbt14 Layout
lbt05_main

LBT05 Table 1 (Default) Laboratory Abnormalities with Single and Replicated Marked.
nocoding

No Coding Available rule
print_list

Print list
proportion_lyt

Proportion layout
modify_character

Modify character
occurrence_lyt

Occurrence Layout
obtain_value

Obtain value from a vector
reexports

Objects exported from other packages
report_null

Creates NULL Report
rmpt06_main

RMPT06 Table 1 (Default) Seriousness, Outcomes, Severity, Frequency with 95% CI for Risk Management Plan.
rmpt06_lyt

rmpt06 Layout
rmpt05_main

RMPT05 Extent of Exposure by Race for Risk Management Plan Table.
syn_data

Example adam Synthetic Data
lbt05_lyt

lbt05 Layout
pdt02_lyt

pdt02 Layout
vst01_main

VST01 Vital Sign Results and change from Baseline By Visit Table.
vst02_1_main

VST02 Vital Sign Abnormalities Table.
ttet01_main

TTET01 Binary Outcomes Summary.
rspt01_lyt

rspt01 Layout
postprocess

Post process
script

Create Script for TLG Generation
s_summary_na

Summary factor allowing NA
rspt01_main

RSPT01 Binary Outcomes Summary.
run

Run the pipeline
set_section_div

Set Section Dividers
smart_prune

Prune table up to an ElementaryTable
ttet01_lyt

ttet01 Layout
mla_dir

MLA Grade Direction Data
mng01_main

MNG01 Mean Plot Graph.
get_x_hjust

Get a harmonious value of horizontal justification for x axis
lbt01_main

LBT01 Lab Results and Change from Baseline by Visit Table.
rmpt01_main

RMPT01Duration of Exposure for Risk Management Plan Table.
get_x_vjust

Get a harmonious value of vertical justification for x axis
kmg01_main

KMG01 Kaplan-Meier Plot 1.
rmpt01_lyt

rmpt01 Layout
vst02_2_main

VST02 Vital Sign Abnormalities Table.
var_labels_for

Retrieve labels for certain variables
lbt07_main

LBT07 Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.
mht01_label

MHT01 Medical History Table.
missing_rule

Missing rule
lbt07_lyt

lbt07 Layout
vst02_lyt

vst02_1 Layout
rmpt04_main

RMPT04Extent of Exposure by Ethnic Origin for Risk Management Plan Table.
std_postprocessing

Standard Post Processing
preprocess

Pre process
print_args

Print Arguments
summarize_vars_allow_na

Summarize variables allow NA
rmpt03_main

rmpt03Duration of Exposure for Risk Management Plan Table.
aet03_main

AET03 Table 1 (Default) Advert Events by Greatest Intensity Table 1.
aet01_lyt

aet01 Layout
ael01_nollt_main

AEL01_NOLLT Listing 1 (Default) Glossary of Preferred Terms and Investigator-Specified Terms.
aet03_lyt

aet03 Layout
aet05_main

AET05 Table 1 (Default) Adverse Event Rate Adjusted for Patient-Years at Risk - First Occurrence.
aet02_label

AET02 Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1.
ael02_main

AEL02 Listing 1 (Default) Listing of Adverse Events.