Merge pull request #89 from pharmaverse/85_1_point_1

[skip vbump] Closes #85 Closes #88: added peds ADVS and prepared package for 1.1 ad hoc release
pharmaverse · Oct 25, 2024 · 5abc2ee · 5abc2ee
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: pharmaverseadam
 Type: Package
 Title: ADaM Test Data for the 'Pharmaverse' Family of Packages
-Version: 1.0.0
+Version: 1.1.0
 Authors@R:  c(
   person("Edoardo", "Mancini", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0009-0006-4899-8641")),
   person("Kangjie", "Zhang", role = "aut"),
@@ -13,9 +13,8 @@ Authors@R:  c(
   )
 Description: A set of Analysis Data Model (ADaM) datasets constructed using the 
     Study Data Tabulation Model (SDTM) datasets contained in the 'pharmaversesdtm' package and 
-    the template scripts from the 'admiral' family of packages. ADaM dataset specifications are 
-    described in: CDISC Analysis Data Model Team
-    (2021) <https://www.cdisc.org/system/files/members/standard/foundational/ADaMIG_v1.3.pdf>.
+    the template scripts from the 'admiral' family of packages. ADaM dataset specifications 
+    are described in the CDISC ADaM implementation guide, accessible by creating a free account on <https://www.cdisc.org/>.
 License: Apache License (>= 2)
 URL: https://pharmaverse.github.io/pharmaverseadam/, https://github.com/pharmaverse/pharmaverseadam/
 Encoding: UTF-8

diff --git a/NEWS.md b/NEWS.md
@@ -1,8 +1,18 @@
-# pharmaversesdtm (development version)
+# pharmaverseadam 1.1.0
 
-# New features
+Ad-hoc release.
 
-<details>
+## New features
+
+  - Added `ADVS` from `{admiralpeds}` using version 0.1.1.9001 of the package.
+
+  - Refreshed `{pharmaverseadam}` datasets using `{admiral}` 1.1.1.9012 (development version) `{admiralophtha}` 1.1.0.9004 (development version), `{admiralonco}` 1.1.0, `{admiralvaccine}` 0.2.0, `{pharmaversesdtm}` 1.1.0. (#85)
+
+## Documentation
+
+ - DESCRIPTION file updated ahead of CRAN release to fix link to CDISC website.
+
+ <details>
 <summary>Developer Notes</summary>
 
 - Activated automatic version bumping CICD workflow. (#72)
@@ -11,21 +21,27 @@
 
 # pharmaverseadam 1.0.0
 
+The first stable version of `{pharmaverseadam}`!
+
+## New features
+  - Refreshed `{pharmaverseadam}` datasets using `{admiral}` 1.1.1, `{admiralophtha}` 1.1.0, `{admiralonco}` 1.1.0, `{admiralvaccine}` 0.2.0. (#58)
+
 ## Documentation
-  - The first stable version of `{pharmaverseadam}`!
-  - Dataset labels are updated to align with ADaM IG (#64) 
-  - Refreshed `{pharmaverseadam}` datasets using `{admiral}` 1.1.1, `{admiralophtha}` 1.1.0, `{admiralonco}` 1.1.0, `{admiralvaccine}` 0.2.0.  (#58)
+  - Dataset labels were updated to align with ADaM IG. (#64) 
 
 # pharmaverseadam 0.2.0
 
 ## New Features
 
- - Variables labels are applied to datasets by `metacore`/`metatools`. (#50)
- - ADPC, ADPPK and ADPP are updated to handle urine records. (#57)
+  - ADPC, ADPPK and ADPP were updated to handle urine records. (#57)
+
+## Documentation
+
+  - Variables labels were applied to datasets by `metacore`/`metatools`. (#50)
 
 # pharmaverseadam 0.1.1
 
-## New Features
+## Documentation
 
  - DESCRIPTION file updated ahead of CRAN release to include references to ADaM Implementation Guide 1.3.
 

diff --git a/R/adae.R b/R/adae.R
@@ -1,11 +1,10 @@
-#' Adverse Events Analysis
-#'
-#' An example of ADAE ADaM dataset
+#' adae
 #'
+#' Adverse Events Analysis
 #'
 #' @name adae
 #' @docType data
-#' @format A data frame with 101 columns:
+#' @format A data frame with 105 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ DOMAIN }{Domain Abbreviation}
@@ -97,12 +96,16 @@
 #'     \item{ EOSSTT }{End of Study Status}
 #'     \item{ FRVDT }{Final Retrievel Visit Date}
 #'     \item{ RANDDT }{Date of Randomization}
+#'     \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{ AGEGR1 }{Pooled Age Group 1}
 #'     \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}

diff --git a/R/adbcva_ophtha.R b/R/adbcva_ophtha.R
@@ -1,10 +1,10 @@
-#' Best Corrected Visual Acuity Analysis
+#' adbcva_ophtha
 #'
-#' An example of ADBCVA ADaM dataset for Ophthalmology studies
+#' Best Corrected Visual Acuity Analysis
 #'
 #' @name adbcva_ophtha
 #' @docType data
-#' @format A data frame with 116 columns:
+#' @format A data frame with 120 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ DOMAIN }{Domain Abbreviation}
@@ -93,12 +93,16 @@
 #'     \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{ AGEGR1 }{Pooled Age Group 1}
 #'     \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}

diff --git a/R/adce_vaccine.R b/R/adce_vaccine.R
@@ -1,6 +1,6 @@
-#' Clinical Events Analysis for Vaccine
+#' adce_vaccine
 #'
-#' An example of ADCE dataset for Vaccine studies
+#' Clinical Events Analysis for Vaccine
 #'
 #' @name adce_vaccine
 #' @docType data

diff --git a/R/adcm.R b/R/adcm.R
@@ -1,10 +1,10 @@
-#' Concomitant Medications Analysis
+#' adcm
 #'
-#' An example of ADCM ADaM dataset
+#' Concomitant Medications Analysis
 #'
 #' @name adcm
 #' @docType data
-#' @format A data frame with 90 columns:
+#' @format A data frame with 95 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ DOMAIN }{Domain Abbreviation}
@@ -27,6 +27,7 @@
 #'     \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}
 #'     \item{ TRTSDT }{Date of First Exposure to Treatment}
 #'     \item{ TRTEDT }{Date of Last Exposure to Treatment}
 #'     \item{ DTHDT }{Date of Death}
@@ -85,12 +86,16 @@
 #'     \item{ EOSSTT }{End of Study Status}
 #'     \item{ FRVDT }{Final Retrievel Visit Date}
 #'     \item{ RANDDT }{Date of Randomization}
+#'     \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{ AGEGR1 }{Pooled Age Group 1}
 #'     \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}

diff --git a/R/adeg.R b/R/adeg.R
@@ -1,10 +1,10 @@
-#' Electrocardiogram Tests Analysis
+#' adeg
 #'
-#' An example of ADEG ADaM dataset
+#' Electrocardiogram Tests Analysis
 #'
 #' @name adeg
 #' @docType data
-#' @format A data frame with 105 columns:
+#' @format A data frame with 108 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ DOMAIN }{Domain Abbreviation}
@@ -29,7 +29,6 @@
 #'     \item{ EGTPTNUM }{Planned Time Point Number}
 #'     \item{ EGELTM }{Planned Elapsed Time from Time Point Ref}
 #'     \item{ EGTPTREF }{Time Point Reference}
-#'     \item{ temp }{undocumented field}
 #'     \item{ TRTSDT }{Date of First Exposure to Treatment}
 #'     \item{ TRTEDT }{Date of Last Exposure to Treatment}
 #'     \item{ TRT01A }{Actual Treatment for Period 01}
@@ -61,10 +60,10 @@
 #'     \item{ TRTP }{Planned Treatment}
 #'     \item{ TRTA }{Actual Treatment}
 #'     \item{ ASEQ }{Analysis Sequence Number}
-#'     \item{ AVALCA1N }{Analysis Value Category 1 (N)}
 #'     \item{ AVALCAT1 }{Analysis Value Category 1}
-#'     \item{ CHGCAT1N }{Change from Baseline Category 1 (N)}
+#'     \item{ AVALCA1N }{Analysis Value Category 1 (N)}
 #'     \item{ CHGCAT1 }{Change from Baseline Category 1}
+#'     \item{ CHGCAT1N }{Change from Baseline Category 1 (N)}
 #'     \item{ PARAM }{Parameter}
 #'     \item{ PARAMN }{Parameter (N)}
 #'     \item{ SUBJID }{Subject Identifier for the Study}
@@ -100,12 +99,16 @@
 #'     \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{ AGEGR1 }{Pooled Age Group 1}
 #'     \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}

diff --git a/R/adex.R b/R/adex.R
@@ -1,10 +1,10 @@
-#' Exposure Analysis
+#' adex
 #'
-#' An example of ADEX ADaM dataset
+#' Exposure Analysis
 #'
 #' @name adex
 #' @docType data
-#' @format A data frame with 88 columns:
+#' @format A data frame with 92 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ DOMAIN }{Domain Abbreviation}
@@ -83,12 +83,16 @@
 #'     \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{ AGEGR1 }{Pooled Age Group 1}
 #'     \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}

diff --git a/R/adface_vaccine.R b/R/adface_vaccine.R
@@ -1,10 +1,10 @@
-#' Findings About Clinical Events Analysis
+#' adface_vaccine
 #'
-#' An example of ADFACE for Vaccine studies
+#' Findings About Clinical Events Analysis
 #'
 #' @name adface_vaccine
 #' @docType data
-#' @format A data frame with 60 columns:
+#' @format A data frame with 61 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ USUBJID }{Unique Subject Identifier}
@@ -66,6 +66,7 @@
 #'     \item{ EVENTDFL }{Day Event Value Flag}
 #'     \item{ ANL01FL }{Analysis Flag 01}
 #'     \item{ ANL02FL }{Analysis Flag 02}
+#'     \item{ ANL03FL }{undocumented field}
 #'   }
 #'
 #' @source Generated from admiralvaccine package (template ad_adface.R).

diff --git a/R/adis_vaccine.R b/R/adis_vaccine.R
@@ -1,6 +1,6 @@
-#' Immunogenicity Specimen Assessments
+#' adis_vaccine
 #'
-#' An example of ADIS dataset for Vaccine studies
+#' Immunogenicity Specimen Assessments
 #'
 #' @name adis_vaccine
 #' @docType data

diff --git a/R/adlb.R b/R/adlb.R
@@ -1,10 +1,10 @@
-#' Laboratory Analysis
+#' adlb
 #'
-#' An example of ADLB ADaM dataset
+#' Laboratory Analysis
 #'
 #' @name adlb
 #' @docType data
-#' @format A data frame with 111 columns:
+#' @format A data frame with 115 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ DOMAIN }{Domain Abbreviation}
@@ -106,12 +106,16 @@
 #'     \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{ AGEGR1 }{Pooled Age Group 1}
 #'     \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}

diff --git a/R/adlbhy.R b/R/adlbhy.R
@@ -1,6 +1,6 @@
-#' Analysis of Lab Hy's Law
+#' adlbhy
 #'
-#' A template of the ADLBHY dataset
+#' Analysis of Lab Hy's Law
 #'
 #' @name adlbhy
 #' @docType data

diff --git a/R/admh.R b/R/admh.R
@@ -1,10 +1,10 @@
-#' Medical History Analysis
+#' admh
 #'
-#' A template of ADMH ADaM dataset
+#' Medical History Analysis
 #'
 #' @name admh
 #' @docType data
-#' @format A data frame with 110 columns:
+#' @format A data frame with 114 columns:
 #'   \describe{
 #'     \item{ STUDYID }{Study Identifier}
 #'     \item{ DOMAIN }{Domain Abbreviation}
@@ -105,12 +105,16 @@
 #'     \item{ EOSSTT }{End of Study Status}
 #'     \item{ FRVDT }{Final Retrievel Visit Date}
 #'     \item{ RANDDT }{Date of Randomization}
+#'     \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{ AGEGR1 }{Pooled Age Group 1}
 #'     \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}