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dr. M.S. (Matthijs) Berends
2023-01-23 15:01:21 +01:00
parent af139a3c82
commit 19fd0ef121
57 changed files with 2864 additions and 2739 deletions
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49
data-raw/read_EUCAST.R
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@ -66,33 +66,36 @@ read_EUCAST <- function(sheet, file, guideline_name) {
# in the info header in the Excel file, EUCAST mentions which genera are targeted
if (sheet %like% "anaerob.*Gram.*posi") {
sheet <- paste0(c(
"Actinomyces", "Bifidobacterium", "Clostridioides",
"Clostridium", "Cutibacterium", "Eggerthella",
"Eubacterium", "Lactobacillus", "Propionibacterium",
"Staphylococcus saccharolyticus"
),
collapse = "_"
sheet <- paste0(
c(
"Actinomyces", "Bifidobacterium", "Clostridioides",
"Clostridium", "Cutibacterium", "Eggerthella",
"Eubacterium", "Lactobacillus", "Propionibacterium",
"Staphylococcus saccharolyticus"
),
collapse = "_"
)
} else if (sheet %like% "anaerob.*Gram.*nega") {
sheet <- paste0(c(
"Bacteroides",
"Bilophila",
"Fusobacterium",
"Mobiluncus",
"Parabacteroides",
"Porphyromonas",
"Prevotella"
),
collapse = "_"
sheet <- paste0(
c(
"Bacteroides",
"Bilophila",
"Fusobacterium",
"Mobiluncus",
"Parabacteroides",
"Porphyromonas",
"Prevotella"
),
collapse = "_"
)
} else if (sheet == "Streptococcus A,B,C,G") {
sheet <- paste0(microorganisms %>%
filter(genus == "Streptococcus") %>%
mutate(lancefield = mo_name(mo, Lancefield = TRUE)) %>%
filter(lancefield %like% "^Streptococcus group") %>%
pull(fullname),
collapse = "_"
sheet <- paste0(
microorganisms %>%
filter(genus == "Streptococcus") %>%
mutate(lancefield = mo_name(mo, Lancefield = TRUE)) %>%
filter(lancefield %like% "^Streptococcus group") %>%
pull(fullname),
collapse = "_"
)
} else if (sheet %like% "PK.*PD") {
sheet <- "UNKNOWN"