Closes #111 dataset contents ref pages (#130)

* #111 References added * #111 Test version of pkgdown config file pushed * #111 Test version of pkgdown config file pushed n2 * #111 Create new script for the website generation * #111 create_sdtms_data is ready for the review * #111 Pipeline fixed * #111 Update wordlist * #111 Wordlist updated * #111 Update readme and add comment to scripts * #111 Update readme * #111 Fix lintr issue with lengths * #111 Fix style issue * #111 Bring back important files * #111 Fix roxygen * #111 Update readme * #111 Replace csv with xlsx * #111 Update layout * #111 Update wordlist * #111 Introduce JSON approach * #111 Style code * #111 Fix spelling * #111 Update readme * #111 Update script * #111 Fix URLs * #111 dataset-contents-ref-pages: do not lint URLs * #111 Fix lintr * #111 Improve link generator * #111 Improve source generator * #111 Revert datasets * #111 Fix lintr * #111 Improve styling * #111 Fix bugs * #111 Update lintr * #111 Improve JSON * #111 dataset-contents-ref-pages: re-add documentation of *_ca125 datasets * #111 dataset-contents-ref-pages: clean-up WORDLIST * #111 Update warning and description * #111 Update JSON data file --------- Co-authored-by: Vladyslav <[email protected]> Co-authored-by: Stefan Bundfuss <[email protected]>
pharmaverse · Jan 21, 2025 · f9574cf · f9574cf
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diff --git a/.lintr b/.lintr
@@ -7,8 +7,14 @@ linters: linters_with_defaults(
     undesirable_function_linter = undesirable_function_linter()
   )
 exclusions: list(
-    "R/data.R" = Inf,
+    "R" = list(
+        undesirable_function_linter = Inf,
+        line_length_linter = Inf
+    ),
     "inst" = list(undesirable_function_linter = Inf),
     "vignettes" = list(undesirable_function_linter = Inf),
-    "data-raw" = list(undesirable_function_linter = Inf)
+    "data-raw" = list(
+        undesirable_function_linter = Inf,
+        line_length_linter = Inf
+    )
   )
diff --git a/R/ae.R b/R/ae.R
@@ -0,0 +1,54 @@
+# This file is automatically generated by data-raw/create_sdtms_data.R.
+# For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
+#' Adverse Events
+#'
+#' An updated SDTM AE dataset that uses the CDISC pilot project
+#'
+#' @name ae
+#' @title Adverse Events
+#' @keywords dataset
+#' @description An updated SDTM AE dataset that uses the CDISC pilot project
+#' @docType data
+#' @format A data frame with 35 columns:
+#'   \describe{
+#'     \item{STUDYID}{Study Identifier}
+#'     \item{DOMAIN}{Domain Abbreviation}
+#'     \item{USUBJID}{Unique Subject Identifier}
+#'     \item{AESEQ}{Sequence Number}
+#'     \item{AESPID}{Sponsor-Defined Identifier}
+#'     \item{AETERM}{Reported Term for the Adverse Event}
+#'     \item{AELLT}{Lowest Level Term}
+#'     \item{AELLTCD}{Lowest Level Term Code}
+#'     \item{AEDECOD}{Dictionary-Derived Term}
+#'     \item{AEPTCD}{Preferred Term Code}
+#'     \item{AEHLT}{High Level Term}
+#'     \item{AEHLTCD}{High Level Term Code}
+#'     \item{AEHLGT}{High Level Group Term}
+#'     \item{AEHLGTCD}{High Level Group Term Code}
+#'     \item{AEBODSYS}{Body System or Organ Class}
+#'     \item{AEBDSYCD}{Body System or Organ Class Code}
+#'     \item{AESOC}{Primary System Organ Class}
+#'     \item{AESOCCD}{Primary System Organ Class Code}
+#'     \item{AESEV}{Severity/Intensity}
+#'     \item{AESER}{Serious Event}
+#'     \item{AEACN}{Action Taken with Study Treatment}
+#'     \item{AEREL}{Causality}
+#'     \item{AEOUT}{Outcome of Adverse Event}
+#'     \item{AESCAN}{Involves Cancer}
+#'     \item{AESCONG}{Congenital Anomaly or Birth Defect}
+#'     \item{AESDISAB}{Persist or Signif Disability/Incapacity}
+#'     \item{AESDTH}{Results in Death}
+#'     \item{AESHOSP}{Requires or Prolongs Hospitalization}
+#'     \item{AESLIFE}{Is Life Threatening}
+#'     \item{AESOD}{Occurred with Overdose}
+#'     \item{AEDTC}{Date/Time of Collection}
+#'     \item{AESTDTC}{Start Date/Time of Adverse Event}
+#'     \item{AEENDTC}{End Date/Time of Adverse Event}
+#'     \item{AESTDY}{Study Day of Start of Adverse Event}
+#'     \item{AEENDY}{Study Day of End of Adverse Event}
+#'   }
+#'
+#' @source <a href="https://github.com/pharmaverse/pharmaversesdtm/blob/main/data/ae.rda" target="_blank">Access the source of the Adverse Events dataset.</a>
+#' @author Gopi Vegesna
+"ae"
diff --git a/R/ae_ophtha.R b/R/ae_ophtha.R
@@ -0,0 +1,55 @@
+# This file is automatically generated by data-raw/create_sdtms_data.R.
+# For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
+#' Adverse Events for Ophthalmology
+#'
+#' An example Adverse Events SDTM dataset with ophthalmology-specific variable `AELAT`
+#'
+#' @name ae_ophtha
+#' @title Adverse Events for Ophthalmology
+#' @keywords dataset
+#' @description An example Adverse Events SDTM dataset with ophthalmology-specific variable `AELAT`
+#' @docType data
+#' @format A data frame with 37 columns:
+#'   \describe{
+#'     \item{STUDYID}{Study Identifier}
+#'     \item{DOMAIN}{Domain Abbreviation}
+#'     \item{USUBJID}{Unique Subject Identifier}
+#'     \item{AESEQ}{Sequence Number}
+#'     \item{AESPID}{Sponsor-Defined Identifier}
+#'     \item{AETERM}{Reported Term for the Adverse Event}
+#'     \item{AELLT}{Lowest Level Term}
+#'     \item{AELLTCD}{Lowest Level Term Code}
+#'     \item{AEDECOD}{Dictionary-Derived Term}
+#'     \item{AEPTCD}{Preferred Term Code}
+#'     \item{AEHLT}{High Level Term}
+#'     \item{AEHLTCD}{High Level Term Code}
+#'     \item{AEHLGT}{High Level Group Term}
+#'     \item{AEHLGTCD}{High Level Group Term Code}
+#'     \item{AEBODSYS}{Body System or Organ Class}
+#'     \item{AEBDSYCD}{Body System or Organ Class Code}
+#'     \item{AESOC}{Primary System Organ Class}
+#'     \item{AESOCCD}{Primary System Organ Class Code}
+#'     \item{AESEV}{Severity/Intensity}
+#'     \item{AESER}{Serious Event}
+#'     \item{AEACN}{Action Taken with Study Treatment}
+#'     \item{AEREL}{Causality}
+#'     \item{AEOUT}{Outcome of Adverse Event}
+#'     \item{AESCAN}{Involves Cancer}
+#'     \item{AESCONG}{Congenital Anomaly or Birth Defect}
+#'     \item{AESDISAB}{Persist or Signif Disability/Incapacity}
+#'     \item{AESDTH}{Results in Death}
+#'     \item{AESHOSP}{Requires or Prolongs Hospitalization}
+#'     \item{AESLIFE}{Is Life Threatening}
+#'     \item{AESOD}{Occurred with Overdose}
+#'     \item{AEDTC}{Date/Time of Collection}
+#'     \item{AESTDTC}{Start Date/Time of Adverse Event}
+#'     \item{AEENDTC}{End Date/Time of Adverse Event}
+#'     \item{AESTDY}{Study Day of Start of Adverse Event}
+#'     \item{AEENDY}{Study Day of End of Adverse Event}
+#'     \item{AELAT}{Laterality}
+#'     \item{AELOC}{Location}
+#'   }
+#'
+#' @source Constructed using ae from the {pharmaversesdtm} package
+"ae_ophtha"
diff --git a/R/ce_vaccine.R b/R/ce_vaccine.R
@@ -0,0 +1,47 @@
+# This file is automatically generated by data-raw/create_sdtms_data.R.
+# For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
+#' Clinical Events for Vaccine
+#'
+#' An example SDTM CE dataset for vaccine studies
+#'
+#' @name ce_vaccine
+#' @title Clinical Events for Vaccine
+#' @keywords dataset
+#' @description An example SDTM CE dataset for vaccine studies
+#' @docType data
+#' @format A data frame with 29 columns:
+#'   \describe{
+#'     \item{STUDYID}{Study Identifier}
+#'     \item{DOMAIN}{Domain Abbreviation}
+#'     \item{USUBJID}{Unique Subject Identifier}
+#'     \item{CESEQ}{Sequence Number}
+#'     \item{CELNKID}{Link ID}
+#'     \item{CELNKGRP}{Link Group ID}
+#'     \item{CETERM}{Reported Term for the Clinical Event}
+#'     \item{CEDECOD}{Dictionary-Derived Term}
+#'     \item{CELAT}{Laterality of Location of Clinical Event}
+#'     \item{CELOC}{Location of Clinical Event}
+#'     \item{CECAT}{Category for Clinical Event}
+#'     \item{CESCAT}{Subcategory for Clinical Event}
+#'     \item{CEPRESP}{Clinical Event Pre-Specified}
+#'     \item{CEOCCUR}{Clinical Event Occurrence}
+#'     \item{CESEV}{Severity/Intensity}
+#'     \item{CEREL}{Causality}
+#'     \item{CEOUT}{Outcome of Clinical Event}
+#'     \item{EPOCH}{Epoch}
+#'     \item{CEDTC}{Date/Time of Event Collection}
+#'     \item{CESTDTC}{Start Date/Time of Clinical Event}
+#'     \item{CEENDTC}{End Date/Time of Clinical Event}
+#'     \item{CEDUR}{Duration of Clinical Event}
+#'     \item{CETPT}{Planned Time Point Name}
+#'     \item{CETPTNUM}{Planned Time Point Number}
+#'     \item{CETPTREF}{Time Point Reference}
+#'     \item{CERFTDTC}{Date/Time of Reference Time Point}
+#'     \item{CEEVINTX}{Evaluation Interval Text}
+#'     \item{CESTAT}{Completion Status}
+#'     \item{CEREASND}{Reason Clinical Event Not Collected}
+#'   }
+#'
+#' @source Constructed by {admiralvaccine} developers
+"ce_vaccine"
diff --git a/R/cm.R b/R/cm.R
@@ -0,0 +1,40 @@
+# This file is automatically generated by data-raw/create_sdtms_data.R.
+# For updating it please edit inst/extdata/sdtms-specs.json and rerun create_sdtms_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
+#' Concomitant Medication
+#'
+#' A SDTM CM dataset from the CDISC pilot project
+#'
+#' @name cm
+#' @title Concomitant Medication
+#' @keywords dataset
+#' @description A SDTM CM dataset from the CDISC pilot project
+#' @docType data
+#' @format A data frame with 22 columns:
+#'   \describe{
+#'     \item{STUDYID}{Study Identifier}
+#'     \item{DOMAIN}{Domain Abbreviation}
+#'     \item{USUBJID}{Unique Subject Identifier}
+#'     \item{CMSEQ}{Sequence Number}
+#'     \item{CMSPID}{Sponsor-Defined Identifier}
+#'     \item{CMTRT}{Reported Name of Drug, Med, or Therapy}
+#'     \item{CMDECOD}{Standardized Medication Name}
+#'     \item{CMINDC}{Indication}
+#'     \item{CMCLAS}{Medication Class}
+#'     \item{CMDOSE}{Dose per Administration}
+#'     \item{CMDOSU}{Dose Units}
+#'     \item{CMDOSFRQ}{Dosing Frequency per Interval}
+#'     \item{CMROUTE}{Route of Administration}
+#'     \item{VISITNUM}{Visit Number}
+#'     \item{VISIT}{Visit Name}
+#'     \item{VISITDY}{Planned Study Day of Visit}
+#'     \item{CMDTC}{Date/Time of Collection}
+#'     \item{CMSTDTC}{Start Date/Time of Medication}
+#'     \item{CMENDTC}{End Date/Time of Medication}
+#'     \item{CMSTDY}{Study Day of Start of Medication}
+#'     \item{CMENDY}{Study Day of End of Medication}
+#'     \item{CMENRTPT}{undocumented field}
+#'   }
+#'
+#' @source <a href="https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/cm.xpt?raw=true" target="_blank">Access the source of the Concomitant Medication dataset.</a>
+"cm"