#26: update input data

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")
@@ -26,3 +29,4 @@ attr(admiral_ae, "label") <- "Adverse Events"
 # Save dataset ----
 ae <- admiral_ae
 save(ae, file = "data/ae.rda", compress = "bzip2")
+usethis::use_data(suppae, overwrite = TRUE)

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)

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)

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)
 

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)

data-raw/lb.R

@@ -1,9 +1,13 @@
 # Update LB by adding percentage differential lab test rows
 
 library(dplyr)
+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_lb <- read_xpt(paste0(sdtm_path, "lb", ".xpt?raw=true"))
+lb <- raw_lb %>% convert_blanks_to_na()
 
-data("raw_lb")
-lb <- raw_lb
 
 # Subset on differential lab tests
 lb_diff_abs <- lb %>%

data-raw/mh.R

@@ -1,12 +1,15 @@
 # Add new variables to MH
 library(metatools)
 library(lubridate)
+library(haven)
+library(admiral)
 
-data("admiral_dm")
-data("raw_mh")
+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_mh <- read_xpt(paste0(sdtm_path, "mh", ".xpt?raw=true"))
 
 # Convert blank to NA
-dm <- convert_blanks_to_na(admiral_dm) %>%
+dm <- convert_blanks_to_na(dm) %>%
   select(STUDYID, USUBJID, RFSTDTC, RFENDTC, RFXSTDTC, RFXENDTC)
 mh <- convert_blanks_to_na(raw_mh)
 # Set seed so that result stays the same for each run

data-raw/qs.R

@@ -2,11 +2,16 @@
 
 library(metatools)
 library(dplyr)
+library(haven)
+library(admiral)
 
-# take qs test data from previous ADMIRAL project ====
-data("raw_qs")
 
-# create new QS data - keep standard variables from previous ADMIRAL project's QS ====
+# from CDISC pilot study ----
+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_qs <- read_xpt(paste0(sdtm_path, "qs", ".xpt?raw=true")) %>%
+  convert_blanks_to_na()
+
+# create new QS data - keep standard variables from previous ADMIRAL project's QS ----
 qs1 <- raw_qs %>%
   # select standard variables
   select(STUDYID, DOMAIN, USUBJID, QSBLFL, VISITNUM, VISIT, VISITDY, QSDTC, QSDY) %>%

data-raw/sv.R

@@ -0,0 +1,7 @@
+# from CDISC pilot study ----
+library(haven)
+library(admiral)
+raw_sv <- read_xpt("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
+sv <- convert_blanks_to_na(raw_sv)
+
+usethis::use_data(sv, overwrite = TRUE)

data-raw/ts.R

@@ -0,0 +1,7 @@
+# from CDISC pilot study ----
+library(haven)
+library(admiral)
+raw_ts <- read_xpt("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
+ts <- convert_blanks_to_na(raw_ts)
+
+usethis::use_data(ts, overwrite = TRUE)

data-raw/vs.R

@@ -0,0 +1,7 @@
+# from CDISC pilot study ----
+library(haven)
+library(admiral)
+raw_vs <- read_xpt("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
+vs <- convert_blanks_to_na(raw_vs)
+
+usethis::use_data(vs, overwrite = TRUE)