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as.mo improvement

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-26 12:33:26 +01:00
parent f25a4b3679
commit f9ded23023
67 changed files with 391 additions and 342 deletions
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19
R/mo.R
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@ -166,7 +166,12 @@
#' mutate(mo = as.mo(paste(genus, species)))
#' }
as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, reference_df = get_mo_source()) {
if (all(x %in% AMR::microorganisms$fullname)
if (all(x %in% AMR::microorganisms$mo)
& isFALSE(Becker)
& isFALSE(Lancefield)
& is.null(reference_df)) {
y <- x
} else if (all(x %in% AMR::microorganisms$fullname)
& isFALSE(Becker)
& isFALSE(Lancefield)
& is.null(reference_df)) {
@ -179,12 +184,13 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
if (any(is.na(y))) {
y[is.na(y)] <- microorganismsDT[prevalence == 3][data.table(fullname = x[is.na(y)]), on = "fullname", "mo"][[1]]
}
return(y)
} else {
# will be checked for mo class in validation and uses exec_as.mo internally if necessary
y <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df)
}
# will be checked for mo class in validation
mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = allow_uncertain, reference_df = reference_df)
structure(.Data = y, class = "mo")
}
#' @rdname as.mo
@ -891,6 +897,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
stringsAsFactors = FALSE)
df_input <- data.frame(input = as.character(x_input),
stringsAsFactors = FALSE)
x <- df_input %>%
left_join(df_found,
by = "input") %>%