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replaced bactid by mo

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-08-31 13:36:19 +02:00
parent 98ff131680
commit 5965d3c794
41 changed files with 786 additions and 411 deletions
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14
R/mo_property.R
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@ -18,9 +18,9 @@
#' Property of a microorganism
#'
#' Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set, based on their \code{bactid}. Get such an ID with \code{\link{as.bactid}}.
#' @param x a (vector of a) valid \code{\link{bactid}} or any text that can be coerced to a valid bactid with \code{\link{as.bactid}}
#' @param property one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"bactid"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}
#' Use these functions to return a specific property of a microorganism from the \code{\link{microorganisms}} data set, based on their \code{mo}. Get such an ID with \code{\link{as.mo}}.
#' @param x a (vector of a) valid \code{\link{mo}} or any text that can be coerced to a valid microorganism code with \code{\link{as.mo}}
#' @param property one of the column names of one of the \code{\link{microorganisms}} data set, like \code{"mo"}, \code{"bactsys"}, \code{"family"}, \code{"genus"}, \code{"species"}, \code{"fullname"}, \code{"gramstain"} and \code{"aerobic"}
#' @rdname mo_property
#' @export
#' @importFrom dplyr %>% left_join pull
@ -68,12 +68,12 @@ mo_property <- function(x, property = 'fullname') {
if (!property %in% colnames(microorganisms)) {
stop("invalid property: ", property, " - use a column name of `microorganisms`")
}
if (!is.bactid(x)) {
x <- as.bactid(x) # this will give a warning if x cannot be coerced
if (!is.mo(x)) {
x <- as.mo(x) # this will give a warning if x cannot be coerced
}
suppressWarnings(
data.frame(bactid = x, stringsAsFactors = FALSE) %>%
left_join(AMR::microorganisms, by = "bactid") %>%
data.frame(mo = x, stringsAsFactors = FALSE) %>%
left_join(AMR::microorganisms, by = "mo") %>%
pull(property)
)
}