mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 20:06:12 +01:00
as.mo speedup: assigned to namespace
This commit is contained in:
parent
b4e71cdc4f
commit
1bf8dc2983
@ -1,6 +1,6 @@
|
|||||||
Package: AMR
|
Package: AMR
|
||||||
Version: 0.4.0.9007
|
Version: 0.4.0.9007
|
||||||
Date: 2018-10-23
|
Date: 2018-10-29
|
||||||
Title: Antimicrobial Resistance Analysis
|
Title: Antimicrobial Resistance Analysis
|
||||||
Authors@R: c(
|
Authors@R: c(
|
||||||
person(
|
person(
|
||||||
|
81
R/mo.R
81
R/mo.R
@ -44,7 +44,7 @@
|
|||||||
#' | | | ----> subspecies, a 3-4 letter acronym
|
#' | | | ----> subspecies, a 3-4 letter acronym
|
||||||
#' | | ----> species, a 3-4 letter acronym
|
#' | | ----> species, a 3-4 letter acronym
|
||||||
#' | ----> genus, a 5-7 letter acronym, mostly without vowels
|
#' | ----> genus, a 5-7 letter acronym, mostly without vowels
|
||||||
#' ----> taxonomic kingdom, either Bacteria (B), Fungi (F) or Protozoa (P)
|
#' ----> taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
|
||||||
#' }
|
#' }
|
||||||
#'
|
#'
|
||||||
#' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
|
#' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
|
||||||
@ -176,10 +176,11 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
|||||||
# remove empty values (to later fill them in again)
|
# remove empty values (to later fill them in again)
|
||||||
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
|
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
|
||||||
|
|
||||||
MOs <- NULL # will be set later, if needed
|
# These data.tables are available because of .onAttach:
|
||||||
MOs_mostprevalent <- NULL # will be set later, if needed
|
# MOs
|
||||||
MOs_allothers <- NULL # will be set later, if needed
|
# MOs_mostprevalent
|
||||||
MOs_old <- NULL # will be set later, if needed
|
# MOs_allothers
|
||||||
|
# MOs_old
|
||||||
|
|
||||||
# defined df to check for
|
# defined df to check for
|
||||||
if (!is.null(reference_df)) {
|
if (!is.null(reference_df)) {
|
||||||
@ -232,10 +233,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
|||||||
)
|
)
|
||||||
} else {
|
} else {
|
||||||
|
|
||||||
MOs <- as.data.table(AMR::microorganisms)
|
|
||||||
setkey(MOs, prevalence, tsn)
|
|
||||||
MOs_mostprevalent <- MOs[prevalence != 9999,]
|
|
||||||
|
|
||||||
x_backup <- trimws(x, which = "both")
|
x_backup <- trimws(x, which = "both")
|
||||||
x_species <- paste(x_backup, "species")
|
x_species <- paste(x_backup, "species")
|
||||||
# translate to English for supported languages of mo_property
|
# translate to English for supported languages of mo_property
|
||||||
@ -421,17 +418,20 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
|||||||
next
|
next
|
||||||
}
|
}
|
||||||
|
|
||||||
# try splitting of characters and then find ID ----
|
# try splitting of characters in the middle and then find ID ----
|
||||||
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
|
# only when text length is 6 or lower
|
||||||
x_split <- x
|
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
|
||||||
x_length <- nchar(x_trimmed[i])
|
if (nchar(x_trimmed[i]) <= 6) {
|
||||||
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
x_split <- x
|
||||||
'.* ',
|
x_length <- nchar(x_trimmed[i])
|
||||||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
||||||
found <- MOs_mostprevalent[fullname %like% paste0('^', x_split[i]), ..property][[1]]
|
'.* ',
|
||||||
if (length(found) > 0) {
|
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
||||||
x[i] <- found[1L]
|
found <- MOs_mostprevalent[fullname %like% paste0('^', x_split[i]), ..property][[1]]
|
||||||
next
|
if (length(found) > 0) {
|
||||||
|
x[i] <- found[1L]
|
||||||
|
next
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
# try any match with text before and after original search string ----
|
# try any match with text before and after original search string ----
|
||||||
@ -450,10 +450,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
|||||||
# }
|
# }
|
||||||
|
|
||||||
# THEN TRY ALL OTHERS ----
|
# THEN TRY ALL OTHERS ----
|
||||||
if (is.null(MOs_allothers)) {
|
|
||||||
MOs_allothers <- MOs[prevalence == 9999,]
|
|
||||||
}
|
|
||||||
|
|
||||||
found <- MOs_allothers[tolower(fullname) == tolower(x_backup[i]), ..property][[1]]
|
found <- MOs_allothers[tolower(fullname) == tolower(x_backup[i]), ..property][[1]]
|
||||||
# most probable: is exact match in fullname
|
# most probable: is exact match in fullname
|
||||||
if (length(found) > 0) {
|
if (length(found) > 0) {
|
||||||
@ -508,17 +504,20 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
|||||||
next
|
next
|
||||||
}
|
}
|
||||||
|
|
||||||
# try splitting of characters and then find ID ----
|
# try splitting of characters in the middle and then find ID ----
|
||||||
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus
|
# only when text length is 6 or lower
|
||||||
x_split <- x
|
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
|
||||||
x_length <- nchar(x_trimmed[i])
|
if (nchar(x_trimmed[i]) <= 6) {
|
||||||
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
x_split <- x
|
||||||
'.* ',
|
x_length <- nchar(x_trimmed[i])
|
||||||
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
x_split[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2) %>% trimws(),
|
||||||
found <- MOs_allothers[fullname %like% paste0('^', x_split[i]), ..property][[1]]
|
'.* ',
|
||||||
if (length(found) > 0) {
|
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length) %>% trimws())
|
||||||
x[i] <- found[1L]
|
found <- MOs_allothers[fullname %like% paste0('^', x_split[i]), ..property][[1]]
|
||||||
next
|
if (length(found) > 0) {
|
||||||
|
x[i] <- found[1L]
|
||||||
|
next
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
# # try any match with text before and after original search string ----
|
# # try any match with text before and after original search string ----
|
||||||
@ -539,10 +538,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
|||||||
# MISCELLANEOUS ----
|
# MISCELLANEOUS ----
|
||||||
|
|
||||||
# look for old taxonomic names ----
|
# look for old taxonomic names ----
|
||||||
if (is.null(MOs_old)) {
|
|
||||||
MOs_old <- as.data.table(AMR::microorganisms.old)
|
|
||||||
setkey(MOs_old, name, tsn_new)
|
|
||||||
}
|
|
||||||
found <- MOs_old[tolower(name) == tolower(x_backup[i])
|
found <- MOs_old[tolower(name) == tolower(x_backup[i])
|
||||||
| tsn == x_trimmed[i]
|
| tsn == x_trimmed[i]
|
||||||
| name %like% x_withspaces[i],]
|
| name %like% x_withspaces[i],]
|
||||||
@ -604,10 +599,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
|||||||
if (Becker == TRUE | Becker == "all") {
|
if (Becker == TRUE | Becker == "all") {
|
||||||
# See Source. It's this figure:
|
# See Source. It's this figure:
|
||||||
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
|
# https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4187637/figure/F3/
|
||||||
if (is.null(MOs)) {
|
|
||||||
MOs <- as.data.table(AMR::microorganisms)
|
|
||||||
setkey(MOs, prevalence, tsn)
|
|
||||||
}
|
|
||||||
MOs_staph <- MOs[genus == "Staphylococcus"]
|
MOs_staph <- MOs[genus == "Staphylococcus"]
|
||||||
setkey(MOs_staph, species)
|
setkey(MOs_staph, species)
|
||||||
CoNS <- MOs_staph[species %in% c("arlettae", "auricularis", "capitis",
|
CoNS <- MOs_staph[species %in% c("arlettae", "auricularis", "capitis",
|
||||||
@ -635,10 +626,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain =
|
|||||||
|
|
||||||
# Lancefield ----
|
# Lancefield ----
|
||||||
if (Lancefield == TRUE | Lancefield == "all") {
|
if (Lancefield == TRUE | Lancefield == "all") {
|
||||||
if (is.null(MOs)) {
|
|
||||||
MOs <- as.data.table(AMR::microorganisms)
|
|
||||||
setkey(MOs, prevalence, tsn)
|
|
||||||
}
|
|
||||||
# group A - S. pyogenes
|
# group A - S. pyogenes
|
||||||
x[x == MOs[mo == 'B_STRPTC_PYO', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRA', ..property][[1]][1L]
|
x[x == MOs[mo == 'B_STRPTC_PYO', ..property][[1]][1L]] <- MOs[mo == 'B_STRPTC_GRA', ..property][[1]][1L]
|
||||||
# group B - S. agalactiae
|
# group B - S. agalactiae
|
||||||
|
25
R/zzz.R
25
R/zzz.R
@ -18,7 +18,7 @@
|
|||||||
|
|
||||||
#' The \code{AMR} Package
|
#' The \code{AMR} Package
|
||||||
#'
|
#'
|
||||||
#' Welcome to the \code{AMR} package. This page gives some additional contact information abount the authors.
|
#' Welcome to the \code{AMR} package. This page gives some additional contact information about the authors.
|
||||||
#' @details
|
#' @details
|
||||||
#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
|
#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
|
||||||
#'
|
#'
|
||||||
@ -39,7 +39,7 @@
|
|||||||
#' 9700 RB Groningen
|
#' 9700 RB Groningen
|
||||||
#'
|
#'
|
||||||
#' If you have found a bug, please file a new issue at: \cr
|
#' If you have found a bug, please file a new issue at: \cr
|
||||||
#' \url{https://github.com/msberends/AMR/issues}
|
#' \url{https://gitlab.com/msberends/AMR/issues}
|
||||||
#' @name AMR
|
#' @name AMR
|
||||||
#' @rdname AMR
|
#' @rdname AMR
|
||||||
NULL
|
NULL
|
||||||
@ -47,3 +47,24 @@ NULL
|
|||||||
.onLoad <- function(libname, pkgname) {
|
.onLoad <- function(libname, pkgname) {
|
||||||
backports::import(pkgname)
|
backports::import(pkgname)
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.onAttach <- function(libname, pkgname) {
|
||||||
|
# save data.tables to improve speed of as.mo:
|
||||||
|
MOs <- data.table::as.data.table(AMR::microorganisms)
|
||||||
|
data.table::setkey(MOs, prevalence, tsn)
|
||||||
|
|
||||||
|
base::assign(x = "MOs",
|
||||||
|
value = MOs,
|
||||||
|
envir = base::as.environment("package:AMR"))
|
||||||
|
base::assign(x = "MOs_mostprevalent",
|
||||||
|
value = MOs[prevalence != 9999,],
|
||||||
|
envir = base::as.environment("package:AMR"))
|
||||||
|
base::assign(x = "MOs_allothers",
|
||||||
|
value = MOs[prevalence == 9999,],
|
||||||
|
envir = base::as.environment("package:AMR"))
|
||||||
|
|
||||||
|
base::assign(x = "MOs_old",
|
||||||
|
value = data.table::as.data.table(AMR::microorganisms.old),
|
||||||
|
envir = base::as.environment("package:AMR"))
|
||||||
|
|
||||||
|
}
|
||||||
|
@ -4,7 +4,7 @@
|
|||||||
\alias{AMR}
|
\alias{AMR}
|
||||||
\title{The \code{AMR} Package}
|
\title{The \code{AMR} Package}
|
||||||
\description{
|
\description{
|
||||||
Welcome to the \code{AMR} package. This page gives some additional contact information abount the authors.
|
Welcome to the \code{AMR} package. This page gives some additional contact information about the authors.
|
||||||
}
|
}
|
||||||
\details{
|
\details{
|
||||||
This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
|
This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
|
||||||
@ -31,6 +31,6 @@ Post Office Box 30001 \cr
|
|||||||
9700 RB Groningen
|
9700 RB Groningen
|
||||||
|
|
||||||
If you have found a bug, please file a new issue at: \cr
|
If you have found a bug, please file a new issue at: \cr
|
||||||
\url{https://github.com/msberends/AMR/issues}
|
\url{https://gitlab.com/msberends/AMR/issues}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
@ -49,7 +49,7 @@ A microbial ID from this package (class: \code{mo}) typically looks like these e
|
|||||||
| | | ----> subspecies, a 3-4 letter acronym
|
| | | ----> subspecies, a 3-4 letter acronym
|
||||||
| | ----> species, a 3-4 letter acronym
|
| | ----> species, a 3-4 letter acronym
|
||||||
| ----> genus, a 5-7 letter acronym, mostly without vowels
|
| ----> genus, a 5-7 letter acronym, mostly without vowels
|
||||||
----> taxonomic kingdom, either Bacteria (B), Fungi (F) or Protozoa (P)
|
----> taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
|
||||||
}
|
}
|
||||||
|
|
||||||
Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
|
Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
|
||||||
|
Loading…
Reference in New Issue
Block a user