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as.mo improvement

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-25 10:42:57 +01:00
parent e65d1a3036
commit 0ec76cfa98
20 changed files with 379 additions and 324 deletions
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26
R/zzz.R
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@ -50,18 +50,28 @@ make_DT <- function() {
microorganismsDT <- AMR::microorganisms %>%
mutate(prevalence = case_when(
class == "Gammaproteobacteria"
| order %in% c("Lactobacillales", "Bacillales")
| genus %in% c("Enterococcus", "Staphylococcus", "Streptococcus")
~ 1,
phylum %in% c("Proteobacteria",
"Firmicutes",
"Actinobacteria",
"Bacteroidetes")
| genus %in% c("Candida",
"Aspergillus",
"Trichophyton",
"Sarcomastigophora")
| genus %in% c("Aspergillus",
"Bacteroides",
"Candida",
"Capnocytophaga",
"Chryseobacterium",
"Cryptococcus",
"Elisabethkingia",
"Flavobacterium",
"Fusobacterium",
"Giardia",
"Dientamoeba",
"Entamoeba")
"Leptotrichia",
"Mycoplasma",
"Prevotella",
"Rhodotorula",
"Treponema",
"Trichophyton")
~ 2,
TRUE ~ 3
)) %>%
@ -74,7 +84,7 @@ make_DT <- function() {
}
make_trans_tbl <- function() {
# conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
# conversion of old MO codes from v0.5.0 (ITIS) to later versions (Catalogue of Life)
c(B_ACHRMB = "B_ACHRM", B_ANNMA = "B_ACTNS", B_ACLLS = "B_ALCYC",
B_AHNGM = "B_ARCHN", B_ARMTM = "B_ARMTMN", B_ARTHRS = "B_ARTHR",
B_APHLS = "B_AZRHZP", B_BRCHA = "B_BRCHY", B_BCTRM = "B_BRVBCT",