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