version 0.4.1

DESCRIPTION

@@ -0,0 +1,40 @@
+Package: sdtmval
+Title: Validate SDTM Domains
+Version: 0.4.1
+Authors@R: 
+    person("Stephen", "Knapp", 
+           email = "stephen@knappconsultingllc.com", 
+           role = c("aut", "cre", "cph"),
+           comment = c(ORCID = "0000-0002-5101-4555"))
+Description: 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'. 
+License: MIT + file LICENSE
+Encoding: UTF-8
+RoxygenNote: 7.2.3
+URL: https://github.com/skgithub14/sdtmval,
+        https://skgithub14.github.io/sdtmval/
+BugReports: https://github.com/skgithub14/sdtmval/issues
+Imports: dplyr, glue, haven, knitr, lubridate, magrittr, purrr, readxl,
+        rlang, stats, stringr, tidyr, tidyselect, utils
+Suggests: rmarkdown, testthat (>= 3.0.0)
+Config/testthat/edition: 3
+Depends: R (>= 2.10)
+LazyData: true
+VignetteBuilder: knitr
+NeedsCompilation: no
+Packaged: 2023-10-20 17:23:43 UTC; sknapp
+Author: Stephen Knapp [aut, cre, cph] (<https://orcid.org/0000-0002-5101-4555>)
+Maintainer: Stephen Knapp <stephen@knappconsultingllc.com>
+Repository: CRAN
+Date/Publication: 2023-10-23 16:10:02 UTC

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2023
+COPYRIGHT HOLDER: sdtmval authors

MD5

@@ -0,0 +1,68 @@
+bff2cd92ded6ac84d0eb248601a381b0 *DESCRIPTION
+25f8bd5708228ec6132d42c9e2110941 *LICENSE
+18cabfeeaa5b85ec3e349a26681ab2cf *NAMESPACE
+676bf7d3345002b1f31f12e34f8c54f5 *NEWS.md
+15578b9d0d21ddce171685727cc5184b *R/data.R
+dc4c80fb8e324660c976a93f930b02d9 *R/dates.R
+cb960c8f070c999e3ae0296edcb87230 *R/format.R
+023b4f95d23e1169f5650250b5032af5 *R/methods.R
+0a95f4329bae6aeba6c2afef04c933a1 *R/read.R
+6afe314d5ca41b342ed99dc0628e895b *R/sdtmval-package.R
+0200a0bcda2415759f5f4a91eac0b921 *R/spec.R
+b56ff2b193ecba52f9ec7f3b10cca008 *R/utils-pipe.R
+7c2679b2d0aed038b3d51d8fade05d41 *R/write.R
+b2eb773a6197b20996cd3cafaaa6c38b *README.md
+7ef42721572aecc364296a6a43d1c058 *build/vignette.rds
+7bfbeff6214435a2bafa43bf804e99ae *data/dm.rda
+fe06cc91b0d1871a37aefdfff1b3fa7e *data/edc_xx.rda
+afd4d0fb02dfb7fa3eb4ba7ed296d483 *data/spec_XX.rda
+c67f5741f8c7e24dc0490a04a9b9a278 *data/spec_codelists.rda
+c59a5c3704fef8a8b8a2de928b78be2e *data/spec_datasets.rda
+e10bd507f6eedd0ea4a1f5a1e8d2a471 *data/vd.rda
+7746ea0747488f274062d0ea40356b65 *data/xx_no_meta_data.rda
+d446d7883411b9a37f3c8bd4f0b1e1a0 *inst/doc/Dates.R
+f8a6e9a0e39806abfd2aea95167f4a30 *inst/doc/Dates.Rmd
+5736db35acf6c5d68ef01a9f59634f29 *inst/doc/Dates.html
+529d422f90ab8a91bbdc4969fe09a81c *inst/extdata/dm.sas7bdat
+ef4fe3fedb30e527aaede69d0026fdfe *inst/extdata/spec.xlsx
+32da5295db2d5d6bd259b83400867636 *inst/extdata/test_notebook.Rmd
+b7203fa1d893a187bfa51883217aa934 *inst/extdata/vd.csv
+af77b626caeb3dbeb4aa603baeaa2dc3 *inst/extdata/xx.csv
+6ed00af5cbda4465df215d313e63f49a *man/assign_SEQ.Rd
+aacf9cbf65e7a05e74cd245b60e127ac *man/assign_meta_data.Rd
+3c30223c4ad7149fbbbf62bde0e9423b *man/calc_DY.Rd
+ebc52c04cf2f692c930422bbf78ad77d *man/convert_to_script.Rd
+0caf74485ec5332bacae3a73055cf6b0 *man/create_BLFL.Rd
+5fdc63fe4865a65eab27f3c9ff99fd7c *man/create_EPOCH.Rd
+02c7dfde46c0c2d046d343d8abcfc689 *man/create_STAT.Rd
+e6e79cd4b31466b7aad4819e19a66dee *man/dm.Rd
+84a7e40c86d7a0dd5b2b947162ebfdaa *man/edc_xx.Rd
+a82f96656c944cd2554e3e8572e2309a *man/figures/logo.png
+8af353d5999248109e5b6ae88674c3b2 *man/format_chars_and_dates.Rd
+b6274ba402017936a1ef538ba840ea51 *man/get_codelist.Rd
+aa9435cf961bd1a159feb3446b03c8ad *man/get_data_spec.Rd
+ba1bd9cb01badfd2bba8a3d1b24ed406 *man/get_key_vars.Rd
+5a91d94675a0280be060df3b9d232438 *man/impute_pdates.Rd
+8f4aad003a999fae004ba9361f9a99d6 *man/pipe.Rd
+c6db56bb93afc5cccdcba51e9e0150ae *man/read_edc_tbls.Rd
+479b8ac8be1bd25cc01ca46956c181e7 *man/read_sdtm_tbls.Rd
+c600a8bfdafd28f44182bc44f62b9c69 *man/reshape_adates.Rd
+d3ef7b99bf4fc358a4039d32b358062b *man/reshape_pdates.Rd
+6fe29286bf7f253663d203553e3597af *man/sdtmval-package.Rd
+238b8540390ca39e1562c303475c76f5 *man/spec_XX.Rd
+791a81011fb7720d17097c561069a387 *man/spec_codelists.Rd
+b8a152e80e582ecca5d84ca3e6f6f675 *man/spec_datasets.Rd
+041e6655ce2251ca66c7d7d49d8b9746 *man/trim_and_make_blanks_NA.Rd
+41ff85f4b08648c10811290375353ac0 *man/trim_dates.Rd
+9075ea53be840a39145bb8f8c74be40e *man/vd.Rd
+cc7dbe2d4e70cbe2d400f0a5eef7685d *man/write_sessionInfo.Rd
+f06dc052400424dc50587b09c80eda22 *man/write_tbl_to_xpt.Rd
+c99e0ef6ef102a53d341fbd0824b401c *man/xx_no_meta_data.Rd
+662aed3a717217013e736df01cd503a1 *tests/testthat.R
+05e464b7feaa03be190038fd13e819d4 *tests/testthat/test-dates.R
+f40d403759823102d8063176e66f69c7 *tests/testthat/test-format.R
+096de6ff26022efd25d8ea960d81ab9f *tests/testthat/test-methods.R
+040866e90c3ceecdfd98ff7e3ca363a1 *tests/testthat/test-read.R
+4417d5bdd6801f7dbeb637614e4a105c *tests/testthat/test-spec.R
+0f31df6c98f1a41f93027035d2b4b850 *tests/testthat/test-write.R
+f8a6e9a0e39806abfd2aea95167f4a30 *vignettes/Dates.Rmd

NAMESPACE

@@ -0,0 +1,28 @@
+# Generated by roxygen2: do not edit by hand
+
+export("%>%")
+export(assign_SEQ)
+export(assign_meta_data)
+export(calc_DY)
+export(convert_to_script)
+export(create_BLFL)
+export(create_EPOCH)
+export(create_STAT)
+export(format_chars_and_dates)
+export(get_codelist)
+export(get_data_spec)
+export(get_key_vars)
+export(impute_pdates)
+export(read_edc_tbls)
+export(read_sdtm_tbls)
+export(reshape_adates)
+export(reshape_pdates)
+export(trim_and_make_blanks_NA)
+export(trim_dates)
+export(write_sessionInfo)
+export(write_tbl_to_xpt)
+importFrom(magrittr,"%>%")
+importFrom(rlang,":=")
+importFrom(stats,setNames)
+importFrom(utils,View)
+importFrom(utils,read.csv)

NEWS.md

@@ -0,0 +1,67 @@
+# sdtmval 0.4.1
+
+## Major changes
+
+* None
+
+## Minor changes
+
+* Updated package description to include SDTM Implementation Guide author (CDSIC) and link
+
+* Minor updates to convert_to_script() function documentation
+
+## Bug fixes
+
+* None
+
+# sdtmval 0.4.0
+
+## Major changes
+
+* removed compare family of functions
+
+## Minor changes
+
+* added example for `create_STAT()` function
+
+* prepared documentation for CRAN submission
+
+# sdtmval 0.3.0
+
+## Major changes
+
+* added `create_STAT()` function
+
+## Minor changes
+
+* None
+
+# sdtmval 0.2.1
+
+## Major changes
+
+* Changed argument order for `write_tbl_to_xpt()`, `convert_to_script()`, and `write_sessionInfo()` and set default for the `dir` argument to these functions as `NULL` 
+
+## Minor changes
+
+* Improved `write_tbl_to_xpt()`, `convert_to_script()`, and `write_sessionInfo()` with input checking. Also added unit tests and improved the documentation and examples for these functions.
+
+* `write_tbl_to_xpt()` now lets users set a data set name/label different from `filename`
+
+# sdtmval 0.2.0
+
+## Major changes
+
+* Added functions for comparing QC to production SDTM domain data sets (`compare_qc_to_prod()`, `inspect_diffs()`, `summary_diffs()`)
+
+* Added `convert_to_script()` for converting exploratory .Rmd to production .R scripts
+
+* Added `write_sessionInfo()` for logging R session state after a script is run
+
+## Minor changes
+
+* Improved function documentation, {pkgdown} site, and README example
+
+# sdtmval 0.1.0
+
+* Initial release.

R/data.R

@@ -0,0 +1,139 @@
+#' Example EDC data for form/table 'XX'
+#'
+#' This is an example data set to simulate raw EDC data from the fake form/table
+#' 'XX'.
+#'
+#' @format ## 'edc_xx'
+#' A data frame with 8 rows and 6 columns:
+#' \describe{
+#'  \item{STUDYID}{Study identifier}
+#'  \item{USUBJID}{Subject identifier}
+#'  \item{VISIT}{Visit name}
+#'  \item{XXTESTCD}{Test name, coded}
+#'  \item{XXORRES}{Test result}
+#' }
+"edc_xx"
+
+
+#' Example SDTM domain table XX without meta data
+#'
+#' This data set is used to test the [assign_meta_data()] function and contains
+#' a fake SDTM domain XX but without label or lengths assigned to the column
+#' attributes.
+#'
+#' @format ## 'xx_no_meta_data'
+#' A data frame with 10 rows and 11 columns:
+#' \describe{
+#'  \item{STUDYID}{Study identifier}
+#'  \item{USUBJID}{Subject identifier}
+#'  \item{XXSEQ}{Sequence number}
+#'  \item{XXTESTCD}{Coded test name}
+#'  \item{XXTEST}{Test name}
+#'  \item{XXORRES}{Measurement in original units}
+#'  \item{XXBLFL}{Baseline flag}
+#'  \item{VISIT}{Visit name}
+#'  \item{EPOCH}{EPOCH}
+#'  \item{XXDTC}{Measurement date}
+#'  \item{XXDY}{Measurement day of study}
+#' }
+"xx_no_meta_data"
+
+
+#' Example EDC data for form/table 'VD'
+#'
+#' This is an example data set to simulate raw EDC data from the 'VD' form/table
+#' which contains visit date information by subject.
+#'
+#' @format ## 'vd'
+#' A data frame with 6 rows and 3 columns:
+#' \describe{
+#'  \item{USUBJID}{Subject identifier}
+#'  \item{VISIT}{Visit name}
+#'  \item{VISITDTC}{Visit date}
+#' }
+"vd"
+
+
+#' Example SDTM Domain 'DM'
+#'
+#' This is an example data set to simulate a SDTM production domain 'DM' which
+#' contains study start and end date information by subject. This can be used to
+#' test [create_BLFL()], [create_EPOCH()], and [calc_DY()].
+#'
+#' @format ## 'dm'
+#' A data frame with 2 rows and 4 columns:
+#' \describe{
+#'  \item{USUBJID}{Subject identifier}
+#'  \item{RFSTDTC}{Study start date}
+#'  \item{RFXSTDTC}{First exposure date}
+#'  \item{RFXENDTC}{Last exposure date}
+#' }
+"dm"
+
+
+#' Example 'Datasets' tab from a SDTM specification .xlsx file
+#'
+#' This table simulates an excerpt from a SDTM specification .xlsx file for the
+#' 'Datasets' tab which provides the key variables for the fake domain XX. This
+#' data set can be used to test the [get_key_vars()] function.
+#'
+#' @format ## 'spec_datasets'
+#' A data frame with 1 row and 4 columns:
+#' \describe{
+#'  \item{Dataset}{The domain}
+#'  \item{Description}{The domain description}
+#'  \item{Structure}{Defines what qualifies as a unique record}
+#'  \item{Key Variables}{The domain's key variables}
+#' }
+"spec_datasets"
+
+
+#' Example domain specific tab from a SDTM specification .xlsx file
+#'
+#' This table simulates an excerpt from a SDTM specification .xlsx file for the
+#' fake domain tab XX which provides the labels, data types, and lengths by
+#' variable. This data set can be used to test the [get_data_spec()]
+#' and [assign_meta_data()] functions.
+#'
+#' @format ## 'spec_XX'
+#' A data frame with 12 rows and 5 columns:
+#' \describe{
+#'  \item{Order}{The order of the varibles in the data set}
+#'  \item{Dataset}{The domain abbreviation}
+#'  \item{Varible}{The domain's variables}
+#'  \item{Label}{Variable labels}
+#'  \item{Data Type}{Variable data types}
+#'  \item{Length}{The maximum allowed length of an entry}
+#' }
+"spec_XX"
+
+
+#' Example 'Codelists' tab from a SDTM specification .xlsx file
+#'
+#' This table simulates an excerpt from a SDTM specification .xlsx file for the
+#' 'Codelists' tab which provides coded and decoded values from `XXTESTCD` and
+#' `XXTEST` variables, respectively. This data set can be used to test the
+#' [get_codelist()] function.
+#'
+#' @format ## 'spec_codelists'
+#' A data frame with 3 rows and 3 columns:
+#' \describe{
+#'  \item{ID}{The variable identifier/name}
+#'  \item{Term}{The coded term}
+#'  \item{Decoded Value}{The corresponding decoded value for the coded term}
+#' }
+"spec_codelists"
+
+
+
+
+
+
+
+
+
+
+
+
+
+