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v1.7.0

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dr. M.S. (Matthijs) Berends
2021-05-24 15:29:17 +02:00
parent e5599bc694
commit ac73a8d849
120 changed files with 1394 additions and 1481 deletions
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10
R/first_isolate.R
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@ -273,7 +273,7 @@ first_isolate <- function(x = NULL,
# try to find columns based on type
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
col_mo <- search_type_in_df(x = x, type = "mo", info = info)
stop_if(is.null(col_mo), "`col_mo` must be set")
}
@ -299,7 +299,7 @@ first_isolate <- function(x = NULL,
x$keyantimicrobials <- all_antimicrobials(x, only_rsi_columns = FALSE)
col_keyantimicrobials <- "keyantimicrobials"
} else if (type == "keyantimicrobials" & is.null(col_keyantimicrobials)) {
col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantibiotics")
col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantimicrobials", info = info)
if (is.null(col_keyantimicrobials)) {
# still not found as a column, create it ourselves
x$keyantimicrobials <- key_antimicrobials(x, only_rsi_columns = FALSE, col_mo = col_mo, ...)
@ -310,7 +310,7 @@ first_isolate <- function(x = NULL,
# -- date
if (is.null(col_date)) {
col_date <- search_type_in_df(x = x, type = "date")
col_date <- search_type_in_df(x = x, type = "date", info = info)
stop_if(is.null(col_date), "`col_date` must be set")
}
@ -322,14 +322,14 @@ first_isolate <- function(x = NULL,
col_patient_id <- "patient_id"
message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
} else {
col_patient_id <- search_type_in_df(x = x, type = "patient_id")
col_patient_id <- search_type_in_df(x = x, type = "patient_id", info = info)
}
stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
}
# -- specimen
if (is.null(col_specimen) & !is.null(specimen_group)) {
col_specimen <- search_type_in_df(x = x, type = "specimen")
col_specimen <- search_type_in_df(x = x, type = "specimen", info = info)
}
# check if columns exist