transfer from old repo

2 Longterm/data_import_files.R

@@ -0,0 +1,49 @@
+# Specifying needed data collection files
+data_source <- c(
+  "PASE_rev_v13.dta",
+  "MFI_rev_v13.dta",
+  "mdi_rev_v13.dta",
+  "mmse_rev_v13.dta",
+  "mrs_rev_v13.dta",
+  "SDMT_rev_v13.dta",
+  "who_rev_v13.dta"
+)
+
+## Cumulated data
+dta<-read.csv("/Volumes/Data/exercise/source/background.csv",colClasses = "character", na.strings = c("NA","","unknown"))
+
+# Getting full filenames
+file_nms <- list.files("/Volumes/Data/STATA13",full.names = TRUE)[match(data_source,list.files("/Volumes/Data/STATA13"))]
+
+# Loading datafiles
+
+dta<-read.csv("/Volumes/Data/exercise/source/background.csv",colClasses = "character", na.strings = c("NA","","unknown"))
+
+ls <- lapply(file_nms,function(i){
+  d <- read_dta(i)
+  colnames(d) <- tolower(gsub("instance","INSTANCE",colnames(d))) #in the sdmt dataset, instance column is lower case
+  d
+})
+
+# Selecting desired variables
+ls_sel <- lapply(seq_along(ls), function(i) {
+  ls[[i]] |> select(cpr,
+                    SYS_SITE,
+                    INSTANCE,
+                    starts_with("TALOS_")) |> as_factor() |> 
+    full_join(select(dta,cpr, rnumb)) |> select(rnumb,everything())
+})
+
+# Naming lists according to file names
+names(ls_sel) <- tolower(unlist(lapply(data_source,function(x){strsplit(x,"_")[[1]][1]})))
+
+## Screening list and EOS data
+subjects <- read_dta("/Volumes/Data/STATA13/inkl_rev_v13.dta") |>
+  select(c("cpr", "rnumb", "rdate", "rtreat")) |>
+  filter(rnumb != 999) |>
+  left_join(read_dta("/Volumes/Data/STATA13/end_rev_v13.dta") |>
+              select(c("cpr", "TALOS_end00", "TALOS_end01"))
+            ) |>
+  rename(enddate = TALOS_end00,
+         eos_early = TALOS_end01) |>
+  as_factor()