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v1.7.0
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@ -273,7 +273,7 @@ first_isolate <- function(x = NULL,
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# try to find columns based on type
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# -- mo
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if (is.null(col_mo)) {
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col_mo <- search_type_in_df(x = x, type = "mo")
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col_mo <- search_type_in_df(x = x, type = "mo", info = info)
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stop_if(is.null(col_mo), "`col_mo` must be set")
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}
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@ -299,7 +299,7 @@ first_isolate <- function(x = NULL,
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x$keyantimicrobials <- all_antimicrobials(x, only_rsi_columns = FALSE)
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col_keyantimicrobials <- "keyantimicrobials"
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} else if (type == "keyantimicrobials" & is.null(col_keyantimicrobials)) {
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col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantibiotics")
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col_keyantimicrobials <- search_type_in_df(x = x, type = "keyantimicrobials", info = info)
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if (is.null(col_keyantimicrobials)) {
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# still not found as a column, create it ourselves
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x$keyantimicrobials <- key_antimicrobials(x, only_rsi_columns = FALSE, col_mo = col_mo, ...)
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@ -310,7 +310,7 @@ first_isolate <- function(x = NULL,
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# -- date
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if (is.null(col_date)) {
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col_date <- search_type_in_df(x = x, type = "date")
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col_date <- search_type_in_df(x = x, type = "date", info = info)
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stop_if(is.null(col_date), "`col_date` must be set")
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}
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@ -322,14 +322,14 @@ first_isolate <- function(x = NULL,
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col_patient_id <- "patient_id"
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message_("Using combined columns '", font_bold("First name"), "', '", font_bold("Last name"), "' and '", font_bold("Sex"), "' as input for `col_patient_id`")
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} else {
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col_patient_id <- search_type_in_df(x = x, type = "patient_id")
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col_patient_id <- search_type_in_df(x = x, type = "patient_id", info = info)
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}
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stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
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}
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# -- specimen
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if (is.null(col_specimen) & !is.null(specimen_group)) {
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col_specimen <- search_type_in_df(x = x, type = "specimen")
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col_specimen <- search_type_in_df(x = x, type = "specimen", info = info)
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}
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# check if columns exist
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