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remove reshape2 dependency

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dr. M.S. (Matthijs) Berends
2018-07-30 01:18:40 +02:00
parent 510e8f22aa
commit 211e3bae14
4 changed files with 25 additions and 15 deletions
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21
R/bactid.R
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@ -126,23 +126,27 @@ as.bactid <- function(x) {
}
if (tolower(x[i]) == '^h.*influenzae$') {
# avoid detection of Haematobacter influenzae in case of H. influenzae
x[i] <- 'Haemophilus influenzae'
x[i] <- 'HAEINF'
next
}
if (tolower(x[i]) == '^st.*au$'
| tolower(x[i]) == '^stau$'
| tolower(x[i]) == '^staaur$') {
# avoid detection of Staphylococcus auricularis in case of S. aureus
x[i] <- 'Staphylococcus aureus'
x[i] <- 'STAAUR'
next
}
if (tolower(x[i]) == '^p.*aer$') {
# avoid detection of Pasteurella aerogenes in case of Pseudomonas aeruginosa
x[i] <- 'Pseudomonas aeruginosa'
x[i] <- 'PSEAER'
next
}
if (tolower(x[i]) %like% 'coagulase'
| tolower(x[i]) %like% 'cns'
| tolower(x[i]) %like% 'cons') {
# coerce S. coagulase negative, also as CNS and CoNS
x[i] <- 'Coagulase Negative Staphylococcus (CNS)'
x[i] <- 'STACNS'
next
}
# translate known trivial names to genus+species
@ -150,17 +154,20 @@ as.bactid <- function(x) {
if (toupper(x.backup[i]) == 'MRSA'
| toupper(x.backup[i]) == 'VISA'
| toupper(x.backup[i]) == 'VRSA') {
x[i] <- 'Staphylococcus aureus'
x[i] <- 'STAAUR'
next
}
if (toupper(x.backup[i]) == 'MRSE') {
x[i] <- 'Staphylococcus epidermidis'
}
if (toupper(x.backup[i]) == 'VRE') {
x[i] <- 'Enterococcus'
x[i] <- 'ENC'
next
}
if (toupper(x.backup[i]) == 'MRPA') {
# multi resistant P. aeruginosa
x[i] <- 'Pseudomonas aeruginosa'
x[i] <- 'PSEAER'
next
}
if (toupper(x.backup[i]) == 'PISP'
| toupper(x.backup[i]) == 'PRSP') {