Error when trying to upgrade_id during load_win

[prockenschaub]

Problem

When trying to load an itm, it may be necessary to upgrade the ids, e.g., when loading prescriptions (hadm) in miiv with id_type='icustay'. This leads to an error if the target is a win_tbl

az_wi <- new_itm(
   src = "miiv", 
   table = "prescriptions", 
   sub_var = "drug", 
   regex = "aztreonam", 
   dur_var = "stoptime", 
   class = "rgx_itm", 
   target = "win_tbl")
res <- do_itm_load(az_wi)
#> Error in colnamesInt(x, names(on), check_dups = FALSE) :
#>  argument specifying columns specify non existing column(s): cols[3]='stoptime'

This error originates in the following lines because stoptime is part of meta_vars(x)

ricu/R/data-utils.R

Lines 681 to 684 in 09902bd

	map <- id_map(src, id_vars(x), target_id, sft, idx)
	res <- map[x, on = meta_vars(x), roll = -Inf, rollends = TRUE]
	res <- res[, c(cols) := lapply(.SD, `-`, get(sft)), .SDcols = cols]

but stoptime was removed previously in

ricu/R/data-load.R

Lines 440 to 442 in 09902bd

	time_vars <- setdiff(intersect(time_vars, colnames(res)), dur_var)
	res <- change_id(res, id_var, x, cols = time_vars, keep_old_id = FALSE)

Expected behaviour

No error with the following result

az_ts <- new_itm(
   src = "miiv", 
   table = "prescriptions", 
   sub_var = "drug", 
   regex = "aztreonam", 
   dur_var = "stoptime", 
   class = "rgx_itm", 
   target = 'ts_tbl')
res <- do_itm_load(az_ts)
res[, "stoptime" := get("stoptime") - get("starttime")]
as_win_tbl(res, dur_var="stoptime")
#> # A `win_tbl`:  1,363 ✖ 5
#> # Id var:       `stay_id`
#> # Index var:    `starttime` (1 hours)
#> # Duration var: `stoptime`
#>        stay_id starttime stoptime  drug      dose_val_rx
#>          <int> <drtn>    <drtn>    <chr>     <chr>
#>     1 30025040   1 hours  34 hours Aztreonam 1000
#> ...

Solution

Add a dedicated function upgrade_id.win_tbl.

[prockenschaub]

As an add-on: load_win currently does not apply change_interval to dur_var, since its removed from time_vars earlier.

[dplecko]

This one is for @nbenn, perhaps he can make some comments or help with this issue.