transfer from old repo

2 Longterm/data_import_api.R

@@ -0,0 +1,110 @@
+
+token=keyring::key_get("TALOS_REDCAP_API")
+
+## Primary data set of recorded data
+
+inst <- REDCapR::redcap_instruments(redcap_uri = "https://redcap.au.dk/api/",token = token)$data
+
+tools <- tolower(c(
+  "PASE",
+  "MFI",
+  "mdi",
+  "mmse",
+  "mrs",
+  "SDMT",
+  "who",
+  "ham",
+  "bi",
+  "grad", 
+  "nihss"
+))
+
+vec_starts_with <- function(d,v){
+  filt <- paste0("^(", paste(v, collapse="|"), ")")
+  
+  d[grep(filt,d)]
+}
+
+vec_ends_with <- function(d,v){
+  filt <- paste0("(", paste(v, collapse="|"), ")$")
+  # sub(paste0(".*?_(",paste(v,collapse = "|"),")$"),"\\1",colnames(d))
+  d[grep(filt,d)]
+}
+
+# vec_starts_with(inst$instrument_name,tools)
+
+data <- REDCapR::redcap_read(redcap_uri = "https://redcap.au.dk/api/",token = token,
+                     forms = vec_starts_with(inst$instrument_name,tools),
+                     fields = "record_id")$data
+
+ds <- data |> select(!ends_with("complete"))
+
+talos2long <- function(ds,exclude=c("talos","record"),instance_vals=c("0","1","2","4"),exclude_col_ends=c("user","lock")){
+  nms <- unique(do.call(c,lapply(strsplit(colnames(ds),"_"),"[[",1)))
+  nms <- nms[!nms %in% exclude]
+  
+  ls <- lapply(seq_along(nms),function(i){
+    cols <- c("record_id",vec_starts_with(colnames(ds),c(paste0("talos_",nms[i]),nms[i])))
+    
+    d <- select(ds,all_of(cols))
+    
+    ends <- unique(do.call(c,lapply(strsplit(colnames(d),"_"),function(i){
+      i[length(i)]
+      })))
+    
+    ins <- colnames(d) %in% vec_ends_with(colnames(d),paste0("_",instance_vals))
+    
+    ls_ins <- split.default(d[-1],factor(stRoke::str_extract(colnames(d[ins]),paste0("[",paste(instance_vals,collapse=""),"]$"))))
+    
+    dat <- lapply(seq_along(ls_ins),function(i){
+      dr <- cbind(d[1],instance=names(ls_ins)[i],ls_ins[[i]])
+      colnames(dr) <- unique(gsub(pattern = paste0("_[",paste(instance_vals,collapse=""),"]$"),"",colnames(dr)))
+      dr |> select(record_id,contains("_sys_"),instance,everything())
+      }) |> bind_rows() |> rename(rnumb=record_id) |> mutate(rnumb=as.character(rnumb))
+    
+    ## Col name ending on 00 is date col of measure in all tools
+    dat[,vec_ends_with(colnames(dat),"00")] <- as.Date(dat[,vec_ends_with(colnames(dat),"00")])
+    
+    dat |> select(!ends_with(exclude_col_ends))
+  })
+  
+  names(ls) <- nms
+  ls
+  
+}
+
+ls_sel <- data |> select(!ends_with("complete"))|> talos2long() 
+
+## Data set of baseline and DAP data
+
+subjects_raw <-
+  REDCapR::redcap_read(
+    redcap_uri = "https://redcap.au.dk/api/",
+    token = token,
+    forms = vec_starts_with(inst$instrument_name, c("end", "inkl", "reg", "basis")),
+    fields = "record_id"
+  )$data 
+
+subjects <- subjects_raw |>
+  select(
+    record_id,
+    talos_end00,
+    talos_end01,
+    rdate,
+    rtreat,
+    cpr,
+    basis_kon,
+    starts_with("reg_")
+  ) |> select(!ends_with("complete")) |> 
+  rename(rnumb = record_id,
+         enddate = talos_end00,
+         eos_early = talos_end01,
+         sex=basis_kon) |>
+  mutate(
+    enddate = as.Date(enddate),
+    rdate = as.Date(rdate),
+    inc_time = as.numeric(difftime(enddate, rdate, units = "days")),
+    age = stRoke::age_calc(as.Date(stRoke::cpr_dob(cpr,"%Y-%m-%d")),enddate=rdate)
+  )
+
+# colnames(subjects)  <- gsub("^reg_","",colnames(subjects))