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(v1.2.0.9011) mo_domain(), improved error handling

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-06-22 11:18:40 +02:00
parent e88d7853f5
commit 93a158aebd
49 changed files with 523 additions and 590 deletions
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27
R/first_isolate.R
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@ -156,9 +156,9 @@ first_isolate <- function(x,
}
}
if (!is.data.frame(x)) {
stop("`x` must be a data.frame.", call. = FALSE)
}
stop_ifnot(is.data.frame(x), "`x` must be a data.frame")
stop_if(any(dim(x) == 0), "`x` must contain rows and columns")
# remove data.table, grouping from tibbles, etc.
x <- as.data.frame(x, stringsAsFactors = FALSE)
@ -166,17 +166,13 @@ first_isolate <- function(x,
# -- mo
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo")
if (is.null(col_mo)) {
stop("`col_mo` must be set.", call. = FALSE)
}
stop_if(is.null(col_mo), "`col_mo` must be set")
}
# -- date
if (is.null(col_date)) {
col_date <- search_type_in_df(x = x, type = "date")
if (is.null(col_date)) {
stop("`col_date` must be set.", call. = FALSE)
}
stop_if(is.null(col_date), "`col_date` must be set")
}
# convert to Date
dates <- as.Date(x[, col_date, drop = TRUE])
@ -193,9 +189,7 @@ first_isolate <- function(x,
} else {
col_patient_id <- search_type_in_df(x = x, type = "patient_id")
}
if (is.null(col_patient_id)) {
stop("`col_patient_id` must be set.", call. = FALSE)
}
stop_if(is.null(col_patient_id), "`col_patient_id` must be set")
}
# -- key antibiotics
@ -216,14 +210,9 @@ first_isolate <- function(x,
# check if columns exist
check_columns_existance <- function(column, tblname = x) {
if (NROW(tblname) <= 1 | NCOL(tblname) <= 1) {
stop("Please check tbl for existance.")
}
if (!is.null(column)) {
if (!(column %in% colnames(tblname))) {
stop("Column `", column, "` not found.")
}
stop_ifnot(column %in% colnames(tblname),
"Column `", column, "` not found.", call = FALSE)
}
}