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mirror of https://github.com/msberends/AMR.git synced 2025-07-08 11:11:54 +02:00

(v0.6.1.9047) ggplot fix

This commit is contained in:
2019-05-31 20:48:22 +02:00
parent 4ed27c7e7a
commit 0a6580b4eb
13 changed files with 44 additions and 52 deletions

41
R/zzz.R
View File

@ -29,10 +29,6 @@
microorganisms.oldDT$fullname_lower <- tolower(microorganisms.oldDT$fullname)
setkey(microorganisms.oldDT, col_id, fullname)
assign(x = "microorganisms",
value = make(),
envir = asNamespace("AMR"))
assign(x = "microorganismsDT",
value = make_DT(),
envir = asNamespace("AMR"))
@ -55,44 +51,9 @@
}
#' @importFrom dplyr mutate case_when
make <- function() {
AMR::microorganisms %>%
mutate(prevalence = case_when(
class == "Gammaproteobacteria"
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
| mo == "UNKNOWN"
~ 1,
phylum %in% c("Proteobacteria",
"Firmicutes",
"Actinobacteria",
"Sarcomastigophora")
| genus %in% c("Aspergillus",
"Bacteroides",
"Candida",
"Capnocytophaga",
"Chryseobacterium",
"Cryptococcus",
"Elisabethkingia",
"Flavobacterium",
"Fusobacterium",
"Giardia",
"Leptotrichia",
"Mycoplasma",
"Prevotella",
"Rhodotorula",
"Treponema",
"Trichophyton",
"Ureaplasma")
| rank %in% c("kingdom", "phylum", "class", "order", "family")
~ 2,
TRUE ~ 3
))
}
#' @importFrom data.table as.data.table setkey
make_DT <- function() {
microorganismsDT <- as.data.table(make())
microorganismsDT <- as.data.table(AMR::microorganisms)
microorganismsDT$fullname_lower <- tolower(microorganismsDT$fullname)
setkey(microorganismsDT,
prevalence,