Package: sdtmval 0.4.1

sdtmval: Validate SDTM Domains

Provides a set of tools to assist statistical programmers in validating Study Data Tabulation Model (SDTM) domain data sets. Statistical programmers are required to validate that a SDTM data set domain has been programmed correctly, per the SDTM Implementation Guide (SDTMIG) by 'CDISC' (<https://www.cdisc.org/standards/foundational/sdtmig>), study specification, and study protocol using a process called double programming. Double programming involves two different programmers independently converting the raw electronic data cut (EDC) data into a SDTM domain data table and comparing their results to ensure accurate standardization of the data. One of these attempts is termed 'production' and the other 'validation'. Generally, production runs are the official programs for submittals and these are written in 'SAS'. Validation runs can be programmed in another language, in this case 'R'.

Authors:Stephen Knapp [aut, cre, cph]

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sdtmval.pdf |sdtmval.html✨
sdtmval/json (API)
NEWS

# Install 'sdtmval' in R:
install.packages('sdtmval', repos = c('https://skgithub14.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/skgithub14/sdtmval/issues

Datasets:
  • dm - Example SDTM Domain 'DM'
  • edc_xx - Example EDC data for form/table 'XX'
  • spec_XX - Example domain specific tab from a SDTM specification .xlsx file
  • spec_codelists - Example 'Codelists' tab from a SDTM specification .xlsx file
  • spec_datasets - Example 'Datasets' tab from a SDTM specification .xlsx file
  • vd - Example EDC data for form/table 'VD'
  • xx_no_meta_data - Example SDTM domain table XX without meta data

On CRAN:

21 exports 6 stars 1.26 score 43 dependencies 4 scripts 208 downloads

Last updated 11 months agofrom:271b1b94d0. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 18 2024
R-4.5-winOKSep 18 2024
R-4.5-linuxOKSep 18 2024
R-4.4-winOKSep 18 2024
R-4.4-macOKSep 18 2024
R-4.3-winOKSep 18 2024
R-4.3-macOKSep 18 2024

Exports:%>%assign_meta_dataassign_SEQcalc_DYconvert_to_scriptcreate_BLFLcreate_EPOCHcreate_STATformat_chars_and_datesget_codelistget_data_specget_key_varsimpute_pdatesread_edc_tblsread_sdtm_tblsreshape_adatesreshape_pdatestrim_and_make_blanks_NAtrim_dateswrite_sessionInfowrite_tbl_to_xpt

Dependencies:bitbit64cellrangerclicliprcpp11crayondplyrevaluatefansiforcatsgenericsgluehavenhighrhmsknitrlifecyclelubridatemagrittrpillarpkgconfigprettyunitsprogresspurrrR6readrreadxlrematchrlangstringistringrtibbletidyrtidyselecttimechangetzdbutf8vctrsvroomwithrxfunyaml

Dates

Rendered fromdates.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2023-08-08
Started: 2023-08-08

Readme and manuals

Help Manual

Help pageTopics
Assign meta data to columns in a SDTM table based on specification fileassign_meta_data
Assign SEQ numbers for a SDTM data setassign_SEQ
Calculate a DY variable (day of study)calc_DY
Convert SDTM QC code from a .Rmd file to .R scriptconvert_to_script
Create a BLFL columncreate_BLFL
Create the EPOCH variablecreate_EPOCH
Assign STAT 'NOT DONE' statuscreate_STAT
Example SDTM Domain 'DM'dm
Example EDC data for form/table 'XX'edc_xx
Format date and character columns for SDTM tablesformat_chars_and_dates
Read in the code list from the specification for a specific domainget_codelist
Read in the variable specification sheet for a SDTM data setget_data_spec
Read in the key variables for a SDTM domainget_key_vars
Impute start or end datesimpute_pdates
Import EDC data tablesread_edc_tbls
Import SDTM data tablesread_sdtm_tbls
Reshape format of all dates (full and partial)reshape_adates
Reshape format of partial datesreshape_pdates
Example 'Codelists' tab from a SDTM specification .xlsx filespec_codelists
Example 'Datasets' tab from a SDTM specification .xlsx filespec_datasets
Example domain specific tab from a SDTM specification .xlsx filespec_XX
Trim white space and make blanks NAtrim_and_make_blanks_NA
Trim unknown elements in partial datestrim_dates
Example EDC data for form/table 'VD'vd
Write R session information for a script to a .txt filewrite_sessionInfo
Write a SAS transport file (.xpt)write_tbl_to_xpt
Example SDTM domain table XX without meta dataxx_no_meta_data