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manciniedoardo merged 3 commits into from
May 12, 2025
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Closes #100 add labels, save specs as JSON, improve readme #106

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1bea27e
#100 add labels, save specs as JSON, improve readme
manciniedoardo May 12, 2025
02cf115
#100 chore: checks
manciniedoardo May 12, 2025
b173e3a
#100 update for qc comments
manciniedoardo May 12, 2025
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -44,7 +44,8 @@ Suggests:
roxygen2,
spelling,
testthat (>= 3.0.0),
usethis
usethis,
jsonlite
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
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2 changes: 2 additions & 0 deletions NEWS.md
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Expand Up @@ -10,6 +10,8 @@

- Improved reference page so that dataset labels are displayed under each dataset name. (#103)

- Added labels to variables within datasets that were missing them. (#100)

<details>
<summary>Developer Notes</summary>

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8 changes: 4 additions & 4 deletions R/adae.R
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Expand Up @@ -97,12 +97,12 @@
#' \item{ EOSSTT }{End of Study Status}
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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10 changes: 5 additions & 5 deletions R/adcm.R
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Expand Up @@ -28,7 +28,7 @@
#' \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{ CMENRTPT }{End Relative to Reference Time Point}
#' \item{ TRTSDT }{Date of First Exposure to Treatment}
#' \item{ TRTEDT }{Date of Last Exposure to Treatment}
#' \item{ DTHDT }{Date of Death}
Expand Down Expand Up @@ -87,12 +87,12 @@
#' \item{ EOSSTT }{End of Study Status}
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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8 changes: 4 additions & 4 deletions R/adeg.R
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Expand Up @@ -100,12 +100,12 @@
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDT }{Date of Death}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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8 changes: 4 additions & 4 deletions R/adex.R
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Expand Up @@ -84,12 +84,12 @@
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDT }{Date of Death}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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2 changes: 1 addition & 1 deletion R/adface_vaccine.R
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Expand Up @@ -67,7 +67,7 @@
#' \item{ EVENTDFL }{Day Event Value Flag}
#' \item{ ANL01FL }{Analysis Flag 01}
#' \item{ ANL02FL }{Analysis Flag 02}
#' \item{ ANL03FL }{undocumented field}
#' \item{ ANL03FL }{Analysis Flag 03}
#' }
#'
#' @source Generated from admiralvaccine package (template ad_adface.R).
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8 changes: 4 additions & 4 deletions R/adlb.R
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Expand Up @@ -107,12 +107,12 @@
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDT }{Date of Death}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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8 changes: 4 additions & 4 deletions R/admh.R
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Expand Up @@ -106,12 +106,12 @@
#' \item{ EOSSTT }{End of Study Status}
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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8 changes: 4 additions & 4 deletions R/adoe_ophtha.R
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Expand Up @@ -94,12 +94,12 @@
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDT }{Date of Death}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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8 changes: 4 additions & 4 deletions R/adpc.R
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Expand Up @@ -119,12 +119,12 @@
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDT }{Date of Death}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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8 changes: 4 additions & 4 deletions R/adpp.R
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Expand Up @@ -71,12 +71,12 @@
#' \item{ EOSSTT }{End of Study Status}
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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6 changes: 3 additions & 3 deletions R/adsl.R
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Expand Up @@ -49,9 +49,9 @@
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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8 changes: 4 additions & 4 deletions R/advfq_ophtha.R
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Expand Up @@ -81,12 +81,12 @@
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDT }{Date of Death}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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8 changes: 4 additions & 4 deletions R/advs.R
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Expand Up @@ -97,12 +97,12 @@
#' \item{ FRVDT }{Final Retrievel Visit Date}
#' \item{ RANDDT }{Date of Randomization}
#' \item{ DTHDT }{Date of Death}
#' \item{ DTHDTF }{undocumented field}
#' \item{ DTHDTF }{Date of Death Imputation Flag}
#' \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{ DTHCAUS }{Cause of Death}
#' \item{ DTHDOM }{Domain for Date of Death Collection}
#' \item{ DTHCGR1 }{Cause of Death Reason 1}
#' \item{ LSTALVDT }{Date Last Known Alive}
#' \item{ SAFFL }{Safety Population Flag}
#' \item{ RACEGR1 }{Pooled Race Group 1}
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16 changes: 10 additions & 6 deletions README.md
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Expand Up @@ -44,14 +44,18 @@ The workflow consists of two main steps:

Firstly, the user reviews `inst/extdata/adams-specs.xlsx` and ensures its contents is up-to-date. If a new template has been added to an existing package, or if a new extension package has been created whose ADaM templates they wish to execute in `{pharmaverseadam}`, then the user should update `adams-specs.xlsx` with specifications for the new dataset(s). Note that any missing metadata fields will be set by default to "No label/description/source available."

### 2. Execute `create_adams_data`
### 2. Execute `create_adams_data.R`

Secondly, the user runs `data-raw/create_adams_data.R`. This script handles the installation of each package, the execution of the templates, the saving of the ADaM datasets and the creation of the documentation pages.

#### Script steps

1. **Installs Required Packages**
Installs the following packages:
1. **Save specs as JSON**
The script saves the specs stored in `inst/extdata/adams-specs.xlsx` as a JSON file located here: `inst/extdata/adams-specs.json`.
This is so that the specs themselves, as well as any diffs across commits, are easily viewable on Github and R Studio.

2. **Installs Required Packages**
The script installs the following packages:
- `{admiral}`
- `{admiralonco}`
- `{admiralophtha}`
Expand All @@ -60,11 +64,11 @@ Secondly, the user runs `data-raw/create_adams_data.R`. This script handles the
- `{pharmaversesdtm}`
By default, the latest development versions of each package will be used, but the user can also select a different version instead (e.g. a released version) with which to refresh `{pharmaverseadam}`. The user may also deselect some packages whose templates they do not wish to run. If a new extension package has been created, this should be added to the script in each relevant section (see the script itself for more details).

2. **Executes Templates from Each Package**
3. **Executes Templates from Each Package**

3. **Processes and Saves Datasets into {pharmaverseadam}**
4. **Processes and Saves Datasets into {pharmaverseadam}**

4. **Generates Dataset Documentation**
5. **Generates Dataset Documentation**
For every dataset, a matching `.R` file is created in the `R/` folder containing:
- Dataset name and title,
- Variable-level documentation (names and labels),
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43 changes: 33 additions & 10 deletions data-raw/create_adams_data.R
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@@ -1,4 +1,26 @@
# ensure every packages are installed
# Save specs as JSON file for traceability of changes ----

library(readxl)
library(jsonlite)

json_file <- "inst/extdata/adams-specs.json"
excel_file <- "inst/extdata/adams-specs.xlsx"

specs_xlsx <- readxl::read_excel(excel_file)
specs_json <- toJSON(specs_xlsx, pretty = TRUE)

sheet_names <- excel_sheets(excel_file)

all_sheets <- lapply(sheet_names, function(sheet) {
read_excel(excel_file, sheet = sheet)
})

names(all_sheets) <- sheet_names
json_data <- toJSON(all_sheets, pretty = TRUE)

write(json_data, file = json_file)

# Ensure all packages are installed ----
library(stringr)
update_pkg <- TRUE
ignore_templates <- list(
Expand Down Expand Up @@ -29,6 +51,7 @@ get_attr <- function(data, col_name) {
return(att)
}

# Create documentation ----
write_doc <- function(data, dataset_name, dataset_label, pkg, template_name) {
# create documentation for the current dataset
# TODO: use metatools/metacore for doc ?
Expand Down Expand Up @@ -138,8 +161,8 @@ if (update_pkg) {
# dict to match admiral xlsx specs suffixes
suffixes_dict <- list("_ophtha" = "_P", "_onco" = "_O", "_vaccine" = "_V", "_peds" = "_E")
mc <- metacore::spec_to_metacore("inst/extdata/adams-specs.xlsx",
where_sep_sheet = FALSE,
quiet = TRUE
where_sep_sheet = FALSE,
quiet = TRUE
)

packages_list <- c("admiral", "admiralonco", "admiralophtha", "admiralvaccine", "admiralpeds")
Expand All @@ -151,12 +174,12 @@ for (pkg in packages_list) {
if (update_pkg) {
# TODO: replace by main once done
remotes::install_github(sprintf("pharmaverse/%s", pkg),
ref = "main", auth_token = if (github_pat == "") {
NULL
} else {
github_pat
},
upgrade = "always", force = TRUE
ref = "main", auth_token = if (github_pat == "") {
NULL
} else {
github_pat
},
upgrade = "always", force = TRUE
)
}
# get templates scripts
Expand Down Expand Up @@ -187,5 +210,5 @@ for (res in all_results) {
}
}

# Generate the documentation
# Generate the documentation ----
roxygen2::roxygenize(".", roclets = c("rd", "collate", "namespace"))
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4 changes: 4 additions & 0 deletions inst/WORDLIST
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Expand Up @@ -207,3 +207,7 @@ CRANstatus
tibble
Changelog
README
viewable
diffs
JSON
Github
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