P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 17:01:57 +02:00
Code Releases Activity

(v0.9.0.9029) add uti to as.rsi()

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-02-20 13:19:23 +01:00
parent a5db82c2fb
commit c6184a0fb8
71 changed files with 1129 additions and 800 deletions
Download Patch File Download Diff File Expand all files Collapse all files

32
data-raw/read_EUCAST.R
View File

@ -83,9 +83,23 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx")
x
}
MICs_with_trailing_superscript <- c(0.0011:0.0019, 11:19, 21:29, 0.51:0.59, 41:49,
81:89, 0.031:0.039, 0.061:0.069, 0.251:0.259,
0.1251:0.1259, 161:169, 321:329)
MICs_with_trailing_superscript <- c(seq(from = 0.0011, to = 0.0019, by = 0.0001),
seq(from = 0.031, to = 0.039, by = 0.001),
seq(from = 0.061, to = 0.069, by = 0.001),
seq(from = 0.1251, to = 0.1259, by = 0.0001),
seq(from = 0.251, to = 0.259, by = 0.001),
seq(from = 0.51, to = 0.59, by = 0.01),
seq(from = 11, to = 19, by = 1),
seq(from = 161, to = 169, by = 01),
seq(from = 21, to = 29, by = 1),
seq(from = 321, to = 329, by = 1),
seq(from = 41, to = 49, by = 1),
seq(from = 81, to = 89, by = 1))
has_superscript <- function(x) {
# because due to floating point error 0.1252 is not in:
# seq(from = 0.1251, to = 0.1259, by = 0.0001)
sapply(x, function(x) any(near(x, MICs_with_trailing_superscript)))
}
has_zone_diameters <- rep(any(unlist(raw_data) %like% "zone diameter"), nrow(raw_data))
@ -101,7 +115,8 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx")
filter(!is.na(drug),
!(is.na(MIC_S) & is.na(MIC_R) & is.na(disk_S) & is.na(disk_R)),
!MIC_S %like% "(MIC|S ≤|note)",
drug != MIC_S) %>%
!MIC_S %like% "^[-]",
drug != MIC_S,) %>%
mutate(administration = case_when(drug %like% "[( ]oral" ~ "oral",
drug %like% "[( ]iv" ~ "iv",
TRUE ~ NA_character_),
@ -120,12 +135,15 @@ read_EUCAST <- function(sheet, file = "data-raw/v_10.0_Breakpoint_Tables.xlsx")
disk_S = clean_integer(disk_S),
disk_R = clean_integer(disk_R),
# invalid MIC values have a superscript text, delete those
MIC_S = ifelse(MIC_S %in% MICs_with_trailing_superscript,
MIC_S = ifelse(has_superscript(MIC_S),
substr(MIC_S, 1, nchar(MIC_S) - 1),
MIC_S),
MIC_R = ifelse(MIC_R %in% MICs_with_trailing_superscript,
MIC_R = ifelse(has_superscript(MIC_R),
substr(MIC_R, 1, nchar(MIC_R) - 1),
MIC_R)
MIC_R),
# and some are just awful
MIC_S = ifelse(MIC_S == 43.4, 4, MIC_S),
MIC_R = ifelse(MIC_R == 43.4, 4, MIC_R),
) %>%
# clean drug names
mutate(drug = gsub(" ?[(, ].*$", "", drug),