Function reference • chevron

Package Overview

chevron chevron-package: chevron package

Classes and Instances

chevron_tlg(): chevron_tlg class

Methods

run(): Run the pipeline

get_main(): Retrieve Main Function

get_preprocess(): Retrieve pre-processing Function

get_postprocess(): Retrieve post-processing Function

get_adam_datasets(): Retrieve names of datasets associated with the object

chevron_tlg objects

aet01_1_main() aet01_1_lyt() aet01_1_pre() aet01_1_check() aet01_1: AET01 Table 1 (Default) Overview of Deaths and Adverse Events Summary Table 1.

aet01_2_main() aet01_2_lyt() aet01_2_pre() aet01_2_check() aet01_2: AET01 Table 2 (Supplementary) Overview of Deaths and Adverse Events Summary Table 2. Overview of death and summary of adverse events with medical concepts.

aet02_1_main() aet02_1_lyt() aet02_1_pre() aet02_1_check() aet02_1: AET02 Table 1 (Default) Adverse Events by System Organ Class and Preferred Term Table 1

aet02_2_main() aet02_2_lyt() aet02_2_pre() aet02_2 aet02_3_main(): AET02 Table 2 (Supplementary) Adverse Events by System Organ Class, High Level Term and Preferred Term Table 2.

aet02_3_lyt() aet02_3_pre() aet02_3: AET02 Table 3 (Supplementary) Adverse Events by Dictionary-Derived Term Table 3.

aet03_1_main() aet03_1_lyt() aet03_1_pre() aet03_1: AET03 Table 1 (Default) Advert Events by Greatest Intensity Table 1.

aet04_1_main() aet04_1_lyt() aet04_1_pre() aet04_1: AET04 Table 1 (Default) Adverse Events by Highest NCI CTACAE AE Grade Table 1.

cmt01a_1_main() cmt01a_1_lyt() cmt01a_1_pre() cmt01a_1: CMT01A Table 1 (Default) Concomitant Medication by Medication Class and Preferred Name.

cmt01a_2_main() cmt01a_2_pre() cmt01a_2: CMT01A Table 2 (Supplementary) Concomitant Medication by Medication Class and Preferred Name (Classes sorted by frequency).

cmt01a_3_main() cmt01a_3_lyt() cmt01a_3_pre() cmt01a_3: CMT01A Table 3 (Supplementary) Concomitant Medication by Medication Class and Preferred Name (Total number of treatments per medication class suppressed).

cmt02_pt_1_main() cmt02_pt_1_lyt() cmt02_pt_1_pre() cmt02_pt_1: CMT02_PT Table 1 (Default) Concomitant Medications by Preferred Name.

dmt01_1_main() dmt01_1_lyt() dmt01_1_pre() dmt01_1: DMT01 Table 1 (Default) Demographics and Baseline Characteristics Table 1.

dst01_1_main() dst01_1_lyt() dst01_1_pre() dst01_1: DST01 Table 1 (Default) Patient Disposition Table 1.

dst01_2_main() dst01_2_lyt() dst01_2_pre() dst01_2: DST01 Table 2 (Supplementary) Patient Disposition Table 2.

dst01_3_main() dst01_3_lyt() dst01_3_pre() dst01_3: DST01 Table 3 (Supplementary) Patient Disposition Table 3.

dtht01_1_main() dtht01_1_lyt() dtht01_1_opt_lyt() dtht01_1_pre() dtht01_1: DTHT01 Table 1 (Default) Death Table.

egt01_1_main() egt01_1_lyt() egt01_1_pre() egt01_1: EGT01 Table 1 (Default) ECG Assessments and Change from Baseline by Visit Table 1.

egt02_1_main() egt02_1_lyt() egt02_1_pre() egt02_1: EGT02 Table 1 (Default) ECG Abnormalities Table 1.

egt02_2_main() egt02_2_lyt() egt02_2_pre() egt02_2: EGT02 Table 2 (Supplementary) ECG Abnormalities Table 2.

ext01_1_main() ext01_1_lyt() ext01_1_pre() ext01_1: EXT01 Table 1 (Default) Exposure Summary Table.

ext01_2_main() ext01_2_lyt() ext01_2_pre() ext01_2: EXT01 Table 2 (Supplementary) Exposure Summary Table with grouping options

lbt01_1_main() lbt01_1_lyt() lbt01_1_pre() lbt01_1: LBT01 Table 1 (Default) Laboratory Test Results and Change from Baseline by Visit.

mht01_1_main() mht01_1_lyt() mht01_1_pre() mht01_1: MHT01 Table 1 (Default) Medical History Table 1.

mng01_1_main() mng01_1_lyt() mng01_1_pre() mng01_1_post() mng01_1: MNG01 Graph 1 (Default) Mean Plot 1.

vst01_1_main() vst01_1_lyt() vst01_1_pre() vst01_1: VST01 Table 1 (Default) Vital Sign Results and change from Baseline By Visit Table 1.

vst02_1_main() vst02_1_lyt() vst02_1_pre() vst02_1: VST02 Table 1 (Default) Vital Sign Abnormalities Table 1.

vst02_2_main() vst02_2_lyt() vst02_2_pre() vst02_2: VST02 Table 2 (Supplementary) Vital Sign Abnormalities Table 2.

Checks and assertions

assert_colnames(): Check if strings are column names of a data.frame

assert_all_tablenames(): Assert that all names are among table names of a dm object

assert_one_tablenames(): Assert that at least one name is among table names of a dm object

check_all_colnames(): Check that all names are among column names

check_one_colnames(): Check that at least one name is among column names

Utility Functions

dm_unite(): Unite Columns of a Table in a dm object.

get_db_data(): Get Data from a DB

report_null(): Create a Null Report

sample_study_object(): Extraction of .study object default values

set_decoration(): Temporary function to add decorator to a table

smart_prune(): Prune Table up to an ElementaryTable

std_deco(): Standard documentation lookup

syn_test_data(): Retrieve Synthetic Test Data Used For Examples

var_labels_for(): Retrieve labels for certain variables

Non-exported Documented Functions for Packagage Developers

gen_args(): General Argument Name Convention