Closes #26 rename/rerun programs from admiral.test/admiralvaccine (…

…#38) * #26: remove prefix update_/admiral_ * #26: use_data_raw() * #26: move data to data-raw * #26: update input data * #26: update program name/rerun * #26: rerun qs_ophtha * #26: set.seed for qs_ophtha * #26: update input data * #26: update data.R * #26: devtools::document() * #26: update .lintr, add batch_run.sh * #26: remove raw_domain
pharmaverse · Jul 19, 2023 · 36bb03f · 36bb03f
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commit 36bb03f
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -21,3 +21,4 @@
 ^dev$
 ^vignettes/adxx\.Rmd$
 ^vignettes/pharmaversesdtm\.Rmd$
+^data-raw$
diff --git a/.lintr b/.lintr
@@ -9,5 +9,6 @@ linters: linters_with_defaults(
 exclusions: list(
     "R/data.R" = Inf,
     "inst" = list(undesirable_function_linter = Inf),
-    "vignettes" = list(undesirable_function_linter = Inf)
+    "vignettes" = list(undesirable_function_linter = Inf),
+    "data-raw" = list(undesirable_function_linter = Inf)
   )
diff --git a/R/data.R b/R/data.R
@@ -3,43 +3,29 @@
 #' An updated SDTM AE dataset that uses the CDISC pilot project
 #'
 #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ae.rda}
-"admiral_ae"
-
-#' Adverse Events Dataset-raw
-#'
-#' A SDTM AE dataset from the CDISC pilot project
-#'
-#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ae.xpt?raw=true} # nolint
-"raw_ae"
+"ae"
 
 #' Concomitant Medication Dataset
 #'
 #' A SDTM CM dataset from the CDISC pilot project
 #'
 #' @source \url{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} # nolint
-"admiral_cm"
+"cm"
 
 #' Demography Dataset
 #'
 #' A SDTM DM dataset from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/dm.xpt?raw=true} # nolint
-"admiral_dm"
+"dm"
 
 #' Disposition Dataset-updated
 #'
 #' An updated SDTM DS dataset that uses the CDISC pilot project
 #'
 #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_ds.rda}
 #' @author Gopi Vegesna
-"admiral_ds"
-
-#' Disposition Dataset-raw
-#'
-#' A SDTM DS dataset from the CDISC pilot project
-#'
-#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ds.xpt?raw=true} # nolint
-"raw_ds"
+"ds"
 
 #' Electrocardiogram Dataset
 #'
@@ -52,7 +38,7 @@
 #' A SDTM EX dataset from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true} # nolint
-"admiral_ex"
+"ex"
 
 #' Ophthalmology Exposure Dataset
 #'
@@ -67,66 +53,45 @@
 #'
 #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_lb.rda}
 #' @author Annie Yang
-"admiral_lb"
-
-#' Laboratory Measurements Dataset
-#'
-#' A SDTM LB dataset from the CDISC pilot project
-#'
-#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/lb.xpt?raw=true} # nolint
-"raw_lb"
+"lb"
 
 #' Medical History Dataset-updated
 #'
 #' An updated SDTM MH dataset that uses data from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true} # nolint
 #' @author Annie Yang
-"admiral_mh"
-
-#' Medical History Dataset-raw
-#'
-#' A SDTM MH dataset from the CDISC pilot project
-#'
-#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/mh.xpt?raw=true} # nolint
-"raw_mh"
+"mh"
 
 #' Ophthalmic Examinations Dataset
 #'
 #' A SDTM OE dataset simulated by Ophthalmology team
 #'
 #' @author Gordon Miller
-"admiral_oe"
+"oe_ophtha"
 
 #' Pharmacokinetics Concentrations Dataset
 #'
 #' A SDTM PC dataset simulated by Antonio Rodríguez Contestí
 #'
 #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_pc.rda}
 #' @author Antonio Rodríguez Contestí
-"admiral_pc"
+"pc"
 
 #' Pharmacokinetic Parameters Dataset
 #'
 #' A SDTM PP dataset simulated by Antonio Rodríguez Contestí
 #'
 #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_pp.rda}
 #' @author Antonio Rodríguez Contestí
-"admiral_pp"
-
-#' Questionnaire Dataset
-#'
-#' A SDTM QS dataset from the CDISC pilot project
-#'
-#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/qs.xpt?raw=true} # nolint
-"raw_qs"
+"pp"
 
 #' Questionnaire Dataset
 #'
 #' A SDTM QS dataset from the CDISC pilot project & Ophthalmology test data
 #'
 #' @source \url{https://github.com/pharmaverse/admiral.test/blob/main/data/admiral_qs.rda} # nolint
-"admiral_qs"
+"qs"
 
 #' Ophthalmology Questionnaire Dataset
 #'
@@ -140,93 +105,86 @@
 #' A SDTM SC dataset simulated by Ophthalmology team
 #'
 #' @author Gordon Miller
-"admiral_sc"
+"sc_ophtha"
 
 #' Tumor Identification Dataset
 #'
 #' A SDTM TU dataset simulated by Gopi Vegesna
 #'
 #' @author Gopi Vegesna
-"admiral_tu"
+"tu_onco"
 
 #' Tumor Results Dataset
 #'
 #' A SDTM TR dataset simulated by Gopi Vegesna
 #'
 #' @author Gopi Vegesna
-"admiral_tr"
+"tr_onco"
 
 #' Disease Response Dataset
 #'
 #' A SDTM RS dataset simulated by Gopi Vegesna
 #'
 #' @author Gopi Vegesna
-"admiral_rs"
+"rs_onco"
 
 #' Supplemental Adverse Events Dataset
 #'
 #' A SDTM SUPPAE dataset from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true} # nolint
-"admiral_suppae"
+"suppae"
 
 #' Supplemental Disposition Dataset-updated
 #'
 #' A SDTM SUPPDS dataset from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true} # nolint
-"admiral_suppds"
-
-#' Supplemental Disposition Dataset-raw
-#'
-#' A SDTM SUPPDS dataset from the CDISC pilot project
-#'
-#' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppds.xpt?raw=true} # nolint
-"raw_suppds"
+"suppds"
 
 #' Supplemental Demography Dataset
 #'
 #' A SDTM SUPPDM dataset from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppdm.xpt?raw=true} # nolint
-"admiral_suppdm"
+"suppdm"
 
 #' Supplemental Tumor Results Dataset
 #'
 #' A SDTM SUPPTR dataset simulated by Gopi Vegesna
 #'
 #' @author Gopi Vegesna
-"admiral_supptr"
+"supptr_onco"
 
 #' Trial Design Dataset
 #'
 #' A SDTM TS dataset from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ts.xpt?raw=true} # nolint
-"admiral_ts"
+"ts"
 
 #' Vital Signs Dataset
 #'
 #' A SDTM VS dataset from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/vs.xpt?raw=true} # nolint
-"admiral_vs"
+"vs"
 
 #' SMQ Dataset
 #'
 #' An example SMQ dataset
 #'
-"admiral_smq_db"
+"smq_db"
 
 #' SDG Dataset
 #'
 #' An example SDG dataset
 #'
-"admiral_sdg_db"
+"sdg_db"
 
 #' Subject Visits Dataset
 #'
 #' A SDTM SV dataset from the CDISC pilot project
 #'
 #' @source \url{https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/sv.xpt?raw=true} # nolint
-"admiral_sv"
+"sv"
diff --git a/dev/README.md → data-raw/README.md b/dev/README.md → data-raw/README.md
diff --git a/dev/update_ae.R → data-raw/ae.R b/dev/update_ae.R → data-raw/ae.R
@@ -3,9 +3,12 @@
 library(dplyr)
 library(admiral)
 library(metatools)
+library(haven)
 
-data("raw_ae")
+raw_ae <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ae.xpt?raw=true") # nolint
+raw_suppae <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/suppae.xpt?raw=true") # nolint
 ae <- convert_blanks_to_na(raw_ae)
+suppae <- convert_blanks_to_na(raw_suppae)
 
 # create possible AELAT values - as collected on CRF ----
 lat <- c("LEFT", "RIGHT", "BOTH")
@@ -24,4 +27,6 @@ admiral_ae <- ae %>%
 attr(admiral_ae, "label") <- "Adverse Events"
 
 # Save dataset ----
-save(admiral_ae, file = "data/admiral_ae.rda", compress = "bzip2")
+ae <- admiral_ae
+save(ae, file = "data/ae.rda", compress = "bzip2")
+usethis::use_data(suppae, overwrite = TRUE)
diff --git a/data-raw/batch_run.sh b/data-raw/batch_run.sh
@@ -0,0 +1,34 @@
+#!/bin/bash
+# direct copy from CDISC pilot
+Rscript data-raw/ex.R
+Rscript data-raw/cm.R
+Rscript data-raw/sv.R
+Rscript data-raw/ts.R
+Rscript data-raw/vs.R
+Rscript data-raw/dm.R
+
+# Update from CDISC pilot
+Rscript data-raw/ae.R
+Rscript data-raw/ds.R
+Rscript data-raw/lb.R
+Rscript data-raw/mh.R
+Rscript data-raw/qs.R
+
+# build from program
+Rscript data-raw/pc.R
+Rscript data-raw/pp.R
+Rscript data-raw/query_databases.R # sdg_db, smq_db
+
+
+# admiralophtha
+Rscript data-raw/ex_ophtha.R
+Rscript data-raw/qs_ophtha.R
+# admiralophtha build from program
+Rscript data-raw/oe_ophtha.R
+Rscript data-raw/sc_ophtha.R
+
+
+# admiralonco build from program
+Rscript data-raw/tr_onco.R
+Rscript data-raw/tu_onco.R
+Rscript data-raw/rs_onco.R
diff --git a/data-raw/cm.R b/data-raw/cm.R
@@ -0,0 +1,7 @@
+# from CDISC pilot study ----
+library(haven)
+library(admiral)
+raw_cm <- read_xpt("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") # nolint
+cm <- convert_blanks_to_na(raw_cm)
+
+usethis::use_data(cm, overwrite = TRUE)
diff --git a/data-raw/dm.R b/data-raw/dm.R
@@ -0,0 +1,11 @@
+# from CDISC pilot study ----
+library(haven)
+library(admiral)
+sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint
+raw_dm <- read_xpt(paste0(sdtm_path, "dm", ".xpt?raw=true"))
+raw_suppdm <- read_xpt(paste0(sdtm_path, "suppdm", ".xpt?raw=true"))
+dm <- convert_blanks_to_na(raw_dm)
+suppdm <- convert_blanks_to_na(raw_suppdm)
+
+usethis::use_data(dm, overwrite = TRUE)
+usethis::use_data(suppdm, overwrite = TRUE)
diff --git a/dev/update_ds.R → data-raw/ds.R b/dev/update_ds.R → data-raw/ds.R
@@ -5,13 +5,15 @@ library(tidyselect)
 library(labelled)
 library(admiral)
 library(metatools)
+library(haven)
 
-data("admiral_dm")
-data("raw_ds")
-data("raw_suppds")
+data("dm")
+sdtm_path <- "https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/" # nolint
+raw_ds <- read_xpt(paste0(sdtm_path, "ds", ".xpt?raw=true"))
+raw_suppds <- read_xpt(paste0(sdtm_path, "suppds", ".xpt?raw=true"))
 
 # Converting blank to NA
-dm <- convert_blanks_to_na(admiral_dm)
+dm <- convert_blanks_to_na(dm)
 ds1a <- convert_blanks_to_na(raw_ds)
 suppds1a <- convert_blanks_to_na(raw_suppds)
 
@@ -97,5 +99,7 @@ admiral_ds <- select(ds3, all_of(dsnames))
 
 attr(admiral_ds, "label") <- "Disposition"
 
-save(admiral_ds, file = "data/admiral_ds.rda", compress = "bzip2")
-save(admiral_suppds, file = "data/admiral_suppds.rda", compress = "bzip2")
+ds <- admiral_ds
+suppds <- admiral_suppds
+save(ds, file = "data/ds.rda", compress = "bzip2")
+save(suppds, file = "data/suppds.rda", compress = "bzip2")
diff --git a/data-raw/ex.R b/data-raw/ex.R
@@ -0,0 +1,7 @@
+# from CDISC pilot study ----
+library(haven)
+library(admiral)
+raw_ex <- read_xpt("https://github.com/cdisc-org/sdtm-adam-pilot-project/blob/master/updated-pilot-submission-package/900172/m5/datasets/cdiscpilot01/tabulations/sdtm/ex.xpt?raw=true") # nolint
+ex <- convert_blanks_to_na(raw_ex)
+
+usethis::use_data(ex, overwrite = TRUE)
diff --git a/dev/ex_ophtha.R → data-raw/ex_ophtha.R b/dev/ex_ophtha.R → data-raw/ex_ophtha.R
@@ -1,12 +1,13 @@
 library(dplyr)
 library(tidyselect)
-library(pharmaversesdtm)
+data("dm")
+data("ex")
 
 # Make ex_ophtha dataset
-ex_ophtha <- admiral_dm %>%
+ex_ophtha <- dm %>%
   # Start by merging on ophtha_dm to use the SUBJID variable
   select(USUBJID, SUBJID) %>%
-  right_join(admiral_ex, by = c("USUBJID"), multiple = "all") %>%
+  right_join(ex, by = c("USUBJID"), multiple = "all") %>%
   # Create EXLOC & EXLAT, change EXROUTE & EXDOSFRM to something eye-related
   mutate(
     EXLOC = "EYE",