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remove warnings from unit tests

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dr. M.S. (Matthijs) Berends
2022-10-19 11:47:57 +02:00
parent fed3b6440f
commit 85e2fbe4a3
35 changed files with 115 additions and 110 deletions
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58
R/mo_property.R
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@ -172,7 +172,7 @@
#' }
mo_name <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_name")
}
meet_criteria(x, allow_NA = TRUE)
@ -194,7 +194,7 @@ mo_fullname <- mo_name
#' @export
mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_shortname")
}
meet_criteria(x, allow_NA = TRUE)
@ -235,7 +235,7 @@ mo_shortname <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
#' @export
mo_subspecies <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_subspecies")
}
meet_criteria(x, allow_NA = TRUE)
@ -249,7 +249,7 @@ mo_subspecies <- function(x, language = get_AMR_locale(), keep_synonyms = getOpt
#' @export
mo_species <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_species")
}
meet_criteria(x, allow_NA = TRUE)
@ -263,7 +263,7 @@ mo_species <- function(x, language = get_AMR_locale(), keep_synonyms = getOption
#' @export
mo_genus <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_genus")
}
meet_criteria(x, allow_NA = TRUE)
@ -277,7 +277,7 @@ mo_genus <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("
#' @export
mo_family <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_family")
}
meet_criteria(x, allow_NA = TRUE)
@ -291,7 +291,7 @@ mo_family <- function(x, language = get_AMR_locale(), keep_synonyms = getOption(
#' @export
mo_order <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_order")
}
meet_criteria(x, allow_NA = TRUE)
@ -305,7 +305,7 @@ mo_order <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("
#' @export
mo_class <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_class")
}
meet_criteria(x, allow_NA = TRUE)
@ -319,7 +319,7 @@ mo_class <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("
#' @export
mo_phylum <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_phylum")
}
meet_criteria(x, allow_NA = TRUE)
@ -333,7 +333,7 @@ mo_phylum <- function(x, language = get_AMR_locale(), keep_synonyms = getOption(
#' @export
mo_kingdom <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_kingdom")
}
meet_criteria(x, allow_NA = TRUE)
@ -351,7 +351,7 @@ mo_domain <- mo_kingdom
#' @export
mo_type <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_type")
}
meet_criteria(x, allow_NA = TRUE)
@ -368,7 +368,7 @@ mo_type <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
#' @export
mo_status <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_status")
}
meet_criteria(x, allow_NA = TRUE)
@ -382,7 +382,7 @@ mo_status <- function(x, language = get_AMR_locale(), keep_synonyms = getOption(
#' @export
mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_gramstain")
}
meet_criteria(x, allow_NA = TRUE)
@ -417,7 +417,7 @@ mo_gramstain <- function(x, language = get_AMR_locale(), keep_synonyms = getOpti
#' @export
mo_is_gram_negative <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_is_gram_negative")
}
meet_criteria(x, allow_NA = TRUE)
@ -437,7 +437,7 @@ mo_is_gram_negative <- function(x, language = get_AMR_locale(), keep_synonyms =
#' @export
mo_is_gram_positive <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_is_gram_positive")
}
meet_criteria(x, allow_NA = TRUE)
@ -457,7 +457,7 @@ mo_is_gram_positive <- function(x, language = get_AMR_locale(), keep_synonyms =
#' @export
mo_is_yeast <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_is_yeast")
}
meet_criteria(x, allow_NA = TRUE)
@ -482,7 +482,7 @@ mo_is_yeast <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
#' @export
mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_is_intrinsic_resistant")
}
meet_criteria(x, allow_NA = TRUE)
@ -519,7 +519,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_AMR_locale(), keep_s
#' @export
mo_snomed <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_snomed")
}
meet_criteria(x, allow_NA = TRUE)
@ -533,7 +533,7 @@ mo_snomed <- function(x, language = get_AMR_locale(), keep_synonyms = getOption(
#' @export
mo_ref <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_ref")
}
meet_criteria(x, allow_NA = TRUE)
@ -547,7 +547,7 @@ mo_ref <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AM
#' @export
mo_authors <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_authors")
}
meet_criteria(x, allow_NA = TRUE)
@ -564,7 +564,7 @@ mo_authors <- function(x, language = get_AMR_locale(), keep_synonyms = getOption
#' @export
mo_year <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_year")
}
meet_criteria(x, allow_NA = TRUE)
@ -581,7 +581,7 @@ mo_year <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
#' @export
mo_lpsn <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_lpsn")
}
meet_criteria(x, allow_NA = TRUE)
@ -595,7 +595,7 @@ mo_lpsn <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
#' @export
mo_gbif <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_gbif")
}
meet_criteria(x, allow_NA = TRUE)
@ -609,7 +609,7 @@ mo_gbif <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
#' @export
mo_rank <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_rank")
}
meet_criteria(x, allow_NA = TRUE)
@ -623,7 +623,7 @@ mo_rank <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
#' @export
mo_taxonomy <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_taxonomy")
}
meet_criteria(x, allow_NA = TRUE)
@ -652,7 +652,7 @@ mo_taxonomy <- function(x, language = get_AMR_locale(), keep_synonyms = getOptio
#' @export
mo_synonyms <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_synonyms")
}
meet_criteria(x, allow_NA = TRUE)
@ -698,7 +698,7 @@ mo_current <- function(x, language = get_AMR_locale(), ...) {
#' @export
mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_info")
}
meet_criteria(x, allow_NA = TRUE)
@ -736,7 +736,7 @@ mo_info <- function(x, language = get_AMR_locale(), keep_synonyms = getOption("A
#' @export
mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_url")
}
meet_criteria(x, allow_NA = TRUE)
@ -775,7 +775,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
#' @export
mo_property <- function(x, property = "fullname", language = get_AMR_locale(), keep_synonyms = getOption("AMR_keep_synonyms", FALSE), ...) {
if (missing(x)) {
# this tries to find the data and an <mo> column
# this tries to find the data and an 'mo' column
x <- find_mo_col(fn = "mo_property")
}
meet_criteria(x, allow_NA = TRUE)