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added mdr_tb()

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dr. M.S. (Matthijs) Berends
2019-05-23 16:58:59 +02:00
parent 07d26cd485
commit 60983a1640
60 changed files with 1479 additions and 626 deletions
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18
R/first_isolate.R
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@ -191,7 +191,7 @@ first_isolate <- function(x,
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(tbl = x, type = "mo")
col_mo <- search_type_in_df(x = x, type = "mo")
}
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
@ -199,7 +199,7 @@ first_isolate <- function(x,
# -- date
if (is.null(col_date)) {
col_date <- search_type_in_df(tbl = x, type = "date")
col_date <- search_type_in_df(x = x, type = "date")
}
if (is.null(col_date)) {
stop("`col_date` must be set.", call. = FALSE)
@ -217,7 +217,7 @@ first_isolate <- function(x,
col_patient_id <- "patient_id"
message(blue(paste0("NOTE: Using combined columns ", bold("`First name`, `Last name` and `Sex`"), " as input for `col_patient_id`.")))
} else {
col_patient_id <- search_type_in_df(tbl = x, type = "patient_id")
col_patient_id <- search_type_in_df(x = x, type = "patient_id")
}
}
if (is.null(col_patient_id)) {
@ -226,7 +226,7 @@ first_isolate <- function(x,
# -- key antibiotics
if (is.null(col_keyantibiotics)) {
col_keyantibiotics <- search_type_in_df(tbl = x, type = "keyantibiotics")
col_keyantibiotics <- search_type_in_df(x = x, type = "keyantibiotics")
}
if (isFALSE(col_keyantibiotics)) {
col_keyantibiotics <- NULL
@ -234,7 +234,7 @@ first_isolate <- function(x,
# -- specimen
if (is.null(col_specimen)) {
col_specimen <- search_type_in_df(tbl = x, type = "specimen")
col_specimen <- search_type_in_df(x = x, type = "specimen")
}
if (isFALSE(col_specimen)) {
col_specimen <- NULL
@ -547,10 +547,10 @@ filter_first_isolate <- function(x,
col_mo = NULL,
...) {
filter(x, first_isolate(x = x,
col_date = col_date,
col_patient_id = col_patient_id,
col_mo = col_mo,
...))
col_date = col_date,
col_patient_id = col_patient_id,
col_mo = col_mo,
...))
}
#' @rdname first_isolate