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benchmarks on readme and speed improvement for direct mo codes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-10-01 16:26:02 +02:00
parent ed17db0263
commit 6d761436f7
2 changed files with 123 additions and 1 deletions
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9
R/mo.R
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@ -192,6 +192,13 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
if (all(x %in% AMR::microorganisms[, property])) {
# already existing mo
} else if (all(x %in% AMR::microorganisms[, "mo"])) {
# existing mo codes
suppressWarnings(
x <- data.frame(mo = x, stringsAsFactors = FALSE) %>%
left_join(AMR::microorganisms, by = "mo") %>%
pull(property)
)
} else if (!is.null(reference_df)
& all(x %in% reference_df[, 1])
& all(reference_df[, 2] %in% AMR::microorganisms$mo)) {
@ -653,7 +660,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
class(x) <- "mo"
attr(x, 'package') <- 'AMR'
attr(x, 'ITIS') <- TRUE
} else if (property %in% c("tsn", "year")) {
} else if (property == "tsn") {
x <- as.integer(x)
}