pharmaverse · manciniedoardo · May 1, 2025 · Jan 7, 2025 · May 1, 2025 · May 1, 2025
diff --git a/NEWS.md b/NEWS.md
@@ -1,11 +1,15 @@
 # pharmaverseadam (development version)
 
 ## New features
-
-  - Refreshed `{pharmaverseadam}` datasets using `{admiral}` 1.1.1.9027 (development version). (#91)
+  
+  - Refreshed `{pharmaverseadam}` datasets using `{admiral}` 1.1.1.9019 (development version) `{admiralophtha}` 1.2.0.9001 (development version), `{admiralonco}` 1.2.0, `{admiralvaccine}` 0.4.0, `{pharmaversesdtm}` 1.2.0 (development version). (#103)
 
 ## Documentation
 
+- Added more details to README "Documentation Process" section. (#103)
+
+- Improved reference page so that dataset labels are displayed under each dataset name. (#103)
+
  <details>
 <summary>Developer Notes</summary>
 

diff --git a/R/adae.R b/R/adae.R
@@ -1,8 +1,9 @@
-#' adae
-#'
-#' Adverse Events Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adae
+#' @title Adverse Events Analysis
 #' @docType data
 #' @format A data frame with 105 columns:
 #'   \describe{

diff --git a/R/adbcva_ophtha.R b/R/adbcva_ophtha.R
@@ -1,10 +1,11 @@
-#' adbcva_ophtha
-#'
-#' Best Corrected Visual Acuity Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adbcva_ophtha
+#' @title Best Corrected Visual Acuity Analysis
 #' @docType data
-#' @format A data frame with 120 columns:
+#' @format A data frame with 71 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ DOMAIN }{Domain Abbreviation}
@@ -59,71 +60,22 @@
 #'     \item{ BASEC }{Baseline Value (C)}
 #'     \item{ CHG }{Change from Baseline}
 #'     \item{ PCHG }{Percent Change from Baseline}
-#'     \item{ ASEQ }{Analysis Sequence Number}
-#'     \item{ SUBJID }{Subject Identifier for the Study}
-#'     \item{ RFSTDTC }{Subject Reference Start Date/Time}
-#'     \item{ RFENDTC }{Subject Reference End Date/Time}
-#'     \item{ RFXSTDTC }{Date/Time of First Study Treatment}
-#'     \item{ RFXENDTC }{Date/Time of Last Study Treatment}
-#'     \item{ RFICDTC }{Date/Time of Informed Consent}
-#'     \item{ RFPENDTC }{Date/Time of End of Participation}
-#'     \item{ DTHDTC }{Date/Time of Death}
-#'     \item{ DTHFL }{Subject Death Flag}
-#'     \item{ SITEID }{Study Site Identifier}
-#'     \item{ AGE }{Age}
-#'     \item{ AGEU }{Age Units}
-#'     \item{ SEX }{Sex}
-#'     \item{ RACE }{Race}
-#'     \item{ ETHNIC }{Ethnicity}
-#'     \item{ ARMCD }{Planned Arm Code}
-#'     \item{ ARM }{Description of Planned Arm}
-#'     \item{ ACTARMCD }{Actual Arm Code}
-#'     \item{ ACTARM }{Description of Actual Arm}
-#'     \item{ COUNTRY }{Country/Region}
-#'     \item{ DMDTC }{Date/Time of Collection}
-#'     \item{ DMDY }{Study Day of Collection}
-#'     \item{ TRTSDTM }{Datetime of First Exposure to Treatment}
-#'     \item{ TRTSTMF }{Time of First Exposure Imput. Flag}
-#'     \item{ TRTEDTM }{Datetime of Last Exposure to Treatment}
-#'     \item{ TRTETMF }{Time of Last Exposure Imput. Flag}
-#'     \item{ TRTDURD }{Total Treatment Duration (Days)}
-#'     \item{ SCRFDT }{Screen Failure Date}
-#'     \item{ EOSDT }{End of Study Date}
-#'     \item{ EOSSTT }{End of Study Status}
-#'     \item{ FRVDT }{Final Retrievel Visit Date}
-#'     \item{ RANDDT }{Date of Randomization}
-#'     \item{ DTHDT }{Date of Death}
-#'     \item{ DTHDTF }{undocumented field}
-#'     \item{ DTHADY }{Relative Day of Death}
-#'     \item{ LDDTHELD }{Elapsed Days from Last Dose to Death}
-#'     \item{ DTHCAUS }{undocumented field}
-#'     \item{ DTHDOM }{undocumented field}
-#'     \item{ DTHCGR1 }{undocumented field}
-#'     \item{ LSTALVDT }{Date Last Known Alive}
-#'     \item{ SAFFL }{Safety Population Flag}
-#'     \item{ RACEGR1 }{Pooled Race Group 1}
-#'     \item{ AGEGR1 }{Pooled Age Group 1}
-#'     \item{ REGION1 }{Geographic Region 1}
-#'     \item{ LDDTHGR1 }{Last Dose to Death - Days Elapsed Grp 1}
-#'     \item{ DTH30FL }{Death Within 30 Days of Last Trt Flag}
-#'     \item{ DTHA30FL }{Death After 30 Days from Last Trt Flag}
-#'     \item{ DTHB30FL }{Death Within 30 Days of First Trt Flag}
-#'     \item{ CRIT1 }{Analysis Criterion 1}
 #'     \item{ CRIT1FL }{Criterion 1 Evaluation Result Flag}
-#'     \item{ CRIT2 }{Analysis Criterion 2}
+#'     \item{ CRIT1 }{Analysis Criterion 1}
 #'     \item{ CRIT2FL }{Criterion 2 Evaluation Result Flag}
-#'     \item{ CRIT3 }{Analysis Criterion 3}
+#'     \item{ CRIT2 }{Analysis Criterion 2}
 #'     \item{ CRIT3FL }{Criterion 3 Evaluation Result Flag}
-#'     \item{ CRIT4 }{Analysis Criterion 4}
+#'     \item{ CRIT3 }{Analysis Criterion 3}
 #'     \item{ CRIT4FL }{Criterion 4 Evaluation Result Flag}
-#'     \item{ CRIT5 }{Analysis Criterion 5}
+#'     \item{ CRIT4 }{Analysis Criterion 4}
 #'     \item{ CRIT5FL }{Criterion 5 Evaluation Result Flag}
-#'     \item{ CRIT6 }{Analysis Criterion 6}
+#'     \item{ CRIT5 }{Analysis Criterion 5}
 #'     \item{ CRIT6FL }{Criterion 6 Evaluation Result Flag}
-#'     \item{ CRIT7 }{Analysis Criterion 7}
+#'     \item{ CRIT6 }{Analysis Criterion 6}
 #'     \item{ CRIT7FL }{Criterion 7 Evaluation Result Flag}
-#'     \item{ CRIT8 }{Analysis Criterion 8}
+#'     \item{ CRIT7 }{Analysis Criterion 7}
 #'     \item{ CRIT8FL }{Criterion 8 Evaluation Result Flag}
+#'     \item{ CRIT8 }{Analysis Criterion 8}
 #'     \item{ AVALCA1N }{Analysis Value Category 1 (N)}
 #'     \item{ AVALCAT1 }{Analysis Value Category 1}
 #'   }

diff --git a/R/adce_vaccine.R b/R/adce_vaccine.R
@@ -1,8 +1,9 @@
-#' adce_vaccine
-#'
-#' Clinical Events Analysis for Vaccine
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adce_vaccine
+#' @title Clinical Events Analysis for Vaccine
 #' @docType data
 #' @format A data frame with 56 columns:
 #'   \describe{

diff --git a/R/adcm.R b/R/adcm.R
@@ -1,8 +1,9 @@
-#' adcm
-#'
-#' Concomitant Medications Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adcm
+#' @title Concomitant Medications Analysis
 #' @docType data
 #' @format A data frame with 95 columns:
 #'   \describe{

diff --git a/R/adeg.R b/R/adeg.R
@@ -1,8 +1,9 @@
-#' adeg
-#'
-#' Electrocardiogram Tests Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adeg
+#' @title Electrocardiogram Tests Analysis
 #' @docType data
 #' @format A data frame with 108 columns:
 #'   \describe{

diff --git a/R/adex.R b/R/adex.R
@@ -1,8 +1,9 @@
-#' adex
-#'
-#' Exposure Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adex
+#' @title Exposure Analysis
 #' @docType data
 #' @format A data frame with 92 columns:
 #'   \describe{

diff --git a/R/adface_vaccine.R b/R/adface_vaccine.R
@@ -1,8 +1,9 @@
-#' adface_vaccine
-#'
-#' Findings About Clinical Events Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adface_vaccine
+#' @title Findings About Clinical Events Analysis
 #' @docType data
 #' @format A data frame with 61 columns:
 #'   \describe{

diff --git a/R/adis_vaccine.R b/R/adis_vaccine.R
@@ -1,8 +1,9 @@
-#' adis_vaccine
-#'
-#' Immunogenicity Specimen Assessments
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adis_vaccine
+#' @title Immunogenicity Specimen Assessments
 #' @docType data
 #' @format A data frame with 102 columns:
 #'   \describe{

diff --git a/R/adlb.R b/R/adlb.R
@@ -1,8 +1,9 @@
-#' adlb
-#'
-#' Laboratory Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adlb
+#' @title Laboratory Analysis
 #' @docType data
 #' @format A data frame with 115 columns:
 #'   \describe{

diff --git a/R/adlbhy.R b/R/adlbhy.R
@@ -1,8 +1,9 @@
-#' adlbhy
-#'
-#' Analysis of Lab Hy's Law
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adlbhy
+#' @title Analysis of Lab Hy's Law
 #' @docType data
 #' @format A data frame with 14 columns:
 #'   \describe{

diff --git a/R/admh.R b/R/admh.R
@@ -1,8 +1,9 @@
-#' admh
-#'
-#' Medical History Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name admh
+#' @title Medical History Analysis
 #' @docType data
 #' @format A data frame with 114 columns:
 #'   \describe{

diff --git a/R/adoe_ophtha.R b/R/adoe_ophtha.R
@@ -1,8 +1,9 @@
-#' adoe_ophtha
-#'
-#' Exam Analysis for Ophthalmology
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adoe_ophtha
+#' @title Exam Analysis for Ophthalmology
 #' @docType data
 #' @format A data frame with 102 columns:
 #'   \describe{

diff --git a/R/adpc.R b/R/adpc.R
@@ -1,8 +1,9 @@
-#' adpc
-#'
-#' Pharmacokinetic Concentrations
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adpc
+#' @title Pharmacokinetic Concentrations
 #' @docType data
 #' @format A data frame with 127 columns:
 #'   \describe{
@@ -55,7 +56,6 @@
 #'     \item{ ATPTN }{Analysis Timepoint (N)}
 #'     \item{ ATPT }{Analysis Timepoint}
 #'     \item{ ATPTREF }{Analysis Timepoint Reference}
-#'     \item{ ABLFL }{Baseline Record Flag}
 #'     \item{ BASETYPE }{Baseline Type}
 #'     \item{ DOSEA }{Actual Treatment Dose}
 #'     \item{ DOSEP }{Planned Treatment Dose}
@@ -71,6 +71,7 @@
 #'     \item{ SRCVAR }{Source Variable}
 #'     \item{ SRCSEQ }{Source Sequence Number}
 #'     \item{ DTYPE }{Derivation Type}
+#'     \item{ ABLFL }{Baseline Record Flag}
 #'     \item{ MRRLT }{Modified Rel. Time from Ref. Dose}
 #'     \item{ ANL01FL }{Analysis Flag 01}
 #'     \item{ ANL02FL }{Analysis Flag 02}

diff --git a/R/adpp.R b/R/adpp.R
@@ -1,8 +1,9 @@
-#' adpp
-#'
-#' Pharmacokinetic Parameters
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adpp
+#' @title Pharmacokinetic Parameters
 #' @docType data
 #' @format A data frame with 79 columns:
 #'   \describe{

diff --git a/R/adppk.R b/R/adppk.R
@@ -1,8 +1,9 @@
-#' adppk
-#'
-#' Population Pharmacokinetic
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adppk
+#' @title Population Pharmacokinetic
 #' @docType data
 #' @format A data frame with 61 columns:
 #'   \describe{

diff --git a/R/adrs_onco.R b/R/adrs_onco.R
@@ -1,8 +1,9 @@
-#' adrs_onco
-#'
-#' Tumor Response Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adrs_onco
+#' @title Tumor Response Analysis
 #' @docType data
 #' @format A data frame with 79 columns:
 #'   \describe{

diff --git a/R/adsl.R b/R/adsl.R
@@ -1,8 +1,9 @@
-#' adsl
-#'
-#' Subject Level Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adsl
+#' @title Subject Level Analysis
 #' @docType data
 #' @format A data frame with 54 columns:
 #'   \describe{

diff --git a/R/adsl_vaccine.R b/R/adsl_vaccine.R
@@ -1,8 +1,9 @@
-#' adsl_vaccine
-#'
-#' Subject Level Analysis for Vaccine
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adsl_vaccine
+#' @title Subject Level Analysis for Vaccine
 #' @docType data
 #' @format A data frame with 46 columns:
 #'   \describe{

diff --git a/R/adtr_onco.R b/R/adtr_onco.R
@@ -1,8 +1,9 @@
-#' adtr_onco
-#'
-#' Tumor Results Analysis for Oncology
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adtr_onco
+#' @title Tumor Results Analysis for Oncology
 #' @docType data
 #' @format A data frame with 99 columns:
 #'   \describe{

diff --git a/R/adtte_onco.R b/R/adtte_onco.R
@@ -1,8 +1,9 @@
-#' adtte_onco
-#'
-#' Time to Event Analysis for Oncology
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name adtte_onco
+#' @title Time to Event Analysis for Oncology
 #' @docType data
 #' @format A data frame with 20 columns:
 #'   \describe{

diff --git a/R/advfq_ophtha.R b/R/advfq_ophtha.R
@@ -1,8 +1,9 @@
-#' advfq_ophtha
-#'
-#' Visual Function Questionnaire Analysis
+# This file is automatically generated by data-raw/create_adams_data.R.
+# For updating it please edit inst/extdata/adams-specs.xlsx and rerun create_adams_data.R.
+# Manual edits are not recommended, as changes may be overwritten.
 #'
 #' @name advfq_ophtha
+#' @title Visual Function Questionnaire Analysis
 #' @docType data
 #' @format A data frame with 89 columns:
 #'   \describe{