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Package Overview

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Classes and Instances

Methods

args_ls()
Get Arguments List
run()
Run the pipeline
main() `main<-`()
Main
preprocess() `preprocess<-`()
Pre process
postprocess() `postprocess<-`()
Post process
script_funs()
Create Script for Parameters Assignment

chevron_tlg objects

ael01_nollt_main() ael01_nollt_pre() ael01_nollt_post() ael01_nollt
AEL01_NOLLT Listing 1 (Default) Glossary of Preferred Terms and Investigator-Specified Terms.
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.
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
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
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.

Data

syn_data
Example adam Synthetic Data
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_all_tablenames()
Assert that all names are among names of a list of data.frame.
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.
report_null() null_report null_listing
Create a Null Report
smart_prune()
Prune table up to an ElementaryTable
var_labels_for()
Retrieve labels for certain variables
gg_list()
List of gg object
gg_theme_chevron()
Theme for Chevron Plot
grob_list()
List of grob object
h_format_dec()
Decimal formatting
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

Non-exported Documented Functions for Packagage Developers

gen_args()
General Argument Name Convention
fuse_sequentially()
Fuse list elements