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new antibiotics

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dr. M.S. (Matthijs) Berends
2019-05-10 16:44:59 +02:00
parent 73f1ee1159
commit 68cc7ef0d0
147 changed files with 6228 additions and 4187 deletions
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R/mo.R
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@ -126,7 +126,7 @@
#' @section Source:
#' [1] Becker K \emph{et al.} \strong{Coagulase-Negative Staphylococci}. 2014. Clin Microbiol Rev. 27(4): 870–926. \url{https://dx.doi.org/10.1128/CMR.00109-13}
#'
#' [2] Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the S. aureus complex, S. argenteus and S. schweitzeri: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).}. 2019. Clin Microbiol Infect. 2019 Mar 11. \url{https://doi.org/10.1016/j.cmi.2019.02.028}
#' [2] Becker K \emph{et al.} \strong{Implications of identifying the recently defined members of the \emph{S. aureus} complex, \emph{S. argenteus} and \emph{S. schweitzeri}: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).} 2019. Clin Microbiol Infect. \url{https://doi.org/10.1016/j.cmi.2019.02.028}
#'
#' [3] Lancefield RC \strong{A serological differentiation of human and other groups of hemolytic streptococci}. 1933. J Exp Med. 57(4): 571–95. \url{https://dx.doi.org/10.1084/jem.57.4.571}
#'
@ -195,6 +195,8 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
# check onLoad() in R/zzz.R: data tables are created there.
}
x[x == ""] <- NA_character_
uncertainty_level <- translate_allow_uncertain(allow_uncertain)
mo_hist <- get_mo_history(x, uncertainty_level, force = isTRUE(list(...)$force_mo_history))
@ -261,7 +263,8 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE,
y <- mo_validate(x = x, property = "mo",
Becker = Becker, Lancefield = Lancefield,
allow_uncertain = uncertainty_level, reference_df = reference_df,
force_mo_history = isTRUE(list(...)$force_mo_history))
force_mo_history = isTRUE(list(...)$force_mo_history),
...)
}
@ -296,6 +299,8 @@ exec_as.mo <- function(x,
# check onLoad() in R/zzz.R: data tables are created there.
}
x[x == ""] <- NA_character_
if (initial_search == TRUE) {
options(mo_failures = NULL)
options(mo_uncertainties = NULL)
@ -548,7 +553,9 @@ exec_as.mo <- function(x,
next
}
if (nchar(gsub("[^a-zA-Z]", "", x_trimmed[i])) < 3) {
# check for very small input, but ignore the O antigens of E. coli
if (nchar(gsub("[^a-zA-Z]", "", x_trimmed[i])) < 3
& !x_backup_without_spp[i] %like% "O?(26|103|104|104|111|121|145|157)") {
# check if search term was like "A. species", then return first genus found with ^A
if (x_backup[i] %like% "[a-z]+ species" | x_backup[i] %like% "[a-z] spp[.]?") {
# get mo code of first hit
@ -609,7 +616,8 @@ exec_as.mo <- function(x,
}
next
}
if (toupper(x_backup_without_spp[i]) %in% c("EHEC", "EPEC", "EIEC", "STEC", "ATEC")) {
if (toupper(x_backup_without_spp[i]) %in% c("EHEC", "EPEC", "EIEC", "STEC", "ATEC")
| x_backup_without_spp[i] %like% "O?(26|103|104|104|111|121|145|157)") {
x[i] <- microorganismsDT[mo == 'B_ESCHR_COL', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)