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(v0.7.1.9074) CI updates

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dr. M.S. (Matthijs) Berends
2019-09-16 12:00:56 +02:00
parent 398c5bdc4f
commit f553a08a7b
19 changed files with 322 additions and 173 deletions
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15
R/mo.R
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@ -258,7 +258,7 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
y <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = uncertainty_level, reference_df = reference_df,
force_mo_history = isTRUE(list(...)$force_mo_history),
#force_mo_history = isTRUE(list(...)$force_mo_history),
...)
}
@ -675,14 +675,16 @@ exec_as.mo <- function(x,
# translate known trivial abbreviations to genus + species ----
if (!is.na(x_trimmed[i])) {
if (toupper(x_backup_without_spp[i]) %in% c('MRSA', 'MSSA', 'VISA', 'VRSA')) {
if (toupper(x_backup_without_spp[i]) %in% c('MRSA', 'MSSA', 'VISA', 'VRSA')
| x_backup_without_spp[i] %like_case% " (mrsa|mssa|visa|vrsa) ") {
x[i] <- microorganismsDT[mo == 'B_STPHY_AUR', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c('MRSE', 'MSSE')) {
if (toupper(x_backup_without_spp[i]) %in% c('MRSE', 'MSSE')
| x_backup_without_spp[i] %like_case% " (mrse|msse) ") {
x[i] <- microorganismsDT[mo == 'B_STPHY_EPI', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history)
@ -690,6 +692,7 @@ exec_as.mo <- function(x,
next
}
if (toupper(x_backup_without_spp[i]) == "VRE"
| x_backup_without_spp[i] %like_case% " vre "
| x_backup_without_spp[i] %like_case% '(enterococci|enterokok|enterococo)[a-z]*?$') {
x[i] <- microorganismsDT[mo == 'B_ENTRC', ..property][[1]][1L]
if (initial_search == TRUE) {
@ -718,7 +721,8 @@ exec_as.mo <- function(x,
}
next
}
if (toupper(x_backup_without_spp[i]) == 'MRPA') {
if (toupper(x_backup_without_spp[i]) == 'MRPA'
| x_backup_without_spp[i] %like_case% " mrpa ") {
# multi resistant P. aeruginosa
x[i] <- microorganismsDT[mo == 'B_PSDMN_AER', ..property][[1]][1L]
if (initial_search == TRUE) {
@ -735,7 +739,8 @@ exec_as.mo <- function(x,
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
if (toupper(x_backup_without_spp[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')
| x_backup_without_spp[i] %like_case% " (pisp|prsp|visp|vrsp) ") {
# peni I, peni R, vanco I, vanco R: S. pneumoniae
x[i] <- microorganismsDT[mo == 'B_STRPT_PNE', ..property][[1]][1L]
if (initial_search == TRUE) {