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(v1.4.0.9046) get_episode

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dr. M.S. (Matthijs) Berends
2020-12-27 00:07:00 +01:00
parent 291f802be3
commit acbd0cf7ca
99 changed files with 1143 additions and 683 deletions
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48
R/mo_property.R
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@ -163,7 +163,7 @@
mo_name <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_name")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -180,7 +180,7 @@ mo_fullname <- mo_name
mo_shortname <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_shortname")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -218,7 +218,7 @@ mo_shortname <- function(x, language = get_locale(), ...) {
mo_subspecies <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_subspecies")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -231,7 +231,7 @@ mo_subspecies <- function(x, language = get_locale(), ...) {
mo_species <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_species")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -244,7 +244,7 @@ mo_species <- function(x, language = get_locale(), ...) {
mo_genus <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_genus")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -257,7 +257,7 @@ mo_genus <- function(x, language = get_locale(), ...) {
mo_family <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_family")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -270,7 +270,7 @@ mo_family <- function(x, language = get_locale(), ...) {
mo_order <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_order")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -283,7 +283,7 @@ mo_order <- function(x, language = get_locale(), ...) {
mo_class <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_class")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -296,7 +296,7 @@ mo_class <- function(x, language = get_locale(), ...) {
mo_phylum <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_phylum")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -309,7 +309,7 @@ mo_phylum <- function(x, language = get_locale(), ...) {
mo_kingdom <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_kingdom")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -326,7 +326,7 @@ mo_domain <- mo_kingdom
mo_type <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_type")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -339,7 +339,7 @@ mo_type <- function(x, language = get_locale(), ...) {
mo_gramstain <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_gramstain")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -377,7 +377,7 @@ mo_gramstain <- function(x, language = get_locale(), ...) {
mo_is_gram_negative <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_is_gram_negative")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -396,7 +396,7 @@ mo_is_gram_negative <- function(x, language = get_locale(), ...) {
mo_is_gram_positive <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_is_gram_positive")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -450,7 +450,7 @@ mo_is_intrinsic_resistant <- function(x, ab, language = get_locale(), ...) {
mo_snomed <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_snomed")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -463,7 +463,7 @@ mo_snomed <- function(x, language = get_locale(), ...) {
mo_ref <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_ref")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -476,7 +476,7 @@ mo_ref <- function(x, language = get_locale(), ...) {
mo_authors <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_authors")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -492,7 +492,7 @@ mo_authors <- function(x, language = get_locale(), ...) {
mo_year <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_year")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -508,7 +508,7 @@ mo_year <- function(x, language = get_locale(), ...) {
mo_rank <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_rank")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -521,7 +521,7 @@ mo_rank <- function(x, language = get_locale(), ...) {
mo_taxonomy <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_taxonomy")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -547,7 +547,7 @@ mo_taxonomy <- function(x, language = get_locale(), ...) {
mo_synonyms <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_synonyms")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -580,7 +580,7 @@ mo_synonyms <- function(x, language = get_locale(), ...) {
mo_info <- function(x, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_info")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(language, has_length = 1, is_in = c(LANGUAGES_SUPPORTED, ""), allow_NULL = TRUE, allow_NA = TRUE)
@ -610,7 +610,7 @@ mo_info <- function(x, language = get_locale(), ...) {
mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_url")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(open, allow_class = "logical", has_length = 1)
@ -647,7 +647,7 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
mo_property <- function(x, property = "fullname", language = get_locale(), ...) {
if (missing(x)) {
# this supports using in dplyr verbs: ... %>% filter(mo_is_intrinsic_resistant(ab = "amox"))
x <- find_mo_col("mo_is_intrinsic_resistant")
x <- find_mo_col("mo_property")
}
meet_criteria(x, allow_NA = TRUE)
meet_criteria(property, allow_class = "character", has_length = 1, is_in = colnames(microorganisms))