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Catalogue of Life, replaces ITIS

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dr. M.S. (Matthijs) Berends 2019-02-18 02:33:37 +01:00
parent 9209787a53
commit 54f8258f8c
88 changed files with 607 additions and 590 deletions
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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 0.5.0.9017
Date: 2019-02-14
Version: 0.5.0.9018
Date: 2019-02-18
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(

1
NAMESPACE
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@ -108,7 +108,6 @@ export(labels_rsi_count)
export(left_join_microorganisms)
export(like)
export(mdro)
export(mo_TSN)
export(mo_authors)
export(mo_class)
export(mo_failures)

18
NEWS.md
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@ -1,8 +1,21 @@
# AMR 0.5.0.90xx
**Note: this is the development version, which will eventually be released as AMR 0.6.0.**
**New website!**
We've got a new website: [https://msberends.gitlab.io/AMR](https://msberends.gitlab.io/AMR/) (built with the great [`pkgdown`](https://pkgdown.r-lib.org/))
* Contains the complete manual of this package and all of its functions with an explanation of their parameters
* Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.
#### New
* **BREAKING**: removed deprecated functions, parameters and references to 'bactid'. Use `as.mo()` to identify an MO code.
* Catalogue of Life (CoL) inclusion for data about microorganisms, which also contains all ITIS data we used previously. The `microorganisms` data set now contains:
* Almost 60,000 species from six different kingdoms
* Almost 15,000 previously accepted names which are now taxonomic 'synonyms'
* All (sub)species from the kingdoms Archaea, Bacteria, Chromista, Protozoa and Viruses
* All (sub)species from the orders Eurotiales, Saccharomycetales and Onygenales of the kingdom Fungi. The complete taxonomy of this kingdom has more than 130,000 species. The orders we included contains at least all memebers of the families *Candida*, *Aspergillus* and *Trichophyton*.
* Due to this change, the ID of *Streptococcus* was changed from `B_STRPTC` to `B_STRPT`.
* Support for data from [WHONET](https://whonet.org/) and [EARS-Net](https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net) (European Antimicrobial Resistance Surveillance Network):
* Exported files from WHONET can be read and used in this package. For functions like `first_isolate()` and `eucast_rules()`, all parameters will be filled in automatically.
* This package now knows all antibiotic abbrevations by EARS-Net (which are also being used by WHONET) - the `antibiotics` data set now contains a column `ears_net`.
@ -18,9 +31,6 @@
ab_tradenames -> atc_tradenames()
```
These functions use `as.atc()` internally. The old `atc_property` has been renamed `atc_online_property()`. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class `atc` or must be coerable to this class. Properties of these classes should start with the same class name, analogous to `as.mo()` and e.g. `mo_genus`.
* New website: https://msberends.gitlab.io/AMR (built with the great [`pkgdown`](https://pkgdown.r-lib.org/))
* Contains the complete manual of this package and all of its functions with an explanation of their parameters
* Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis
* New functions `set_mo_source()` and `get_mo_source()` to use your own predefined MO codes as input for `as.mo()` and consequently all `mo_*` functions
* Support for the upcoming [`dplyr`](https://dplyr.tidyverse.org) version 0.8.0
* New function `guess_ab_col()` to find an antibiotic column in a table
@ -57,7 +67,7 @@
* Fixed a critical bug where some rules that depend on previous applied rules would not be applied adequately
* Emphasised in manual that penicillin is meant as benzylpenicillin (ATC [J01CE01](https://www.whocc.no/atc_ddd_index/?code=J01CE01))
* New info is returned when running this function, stating exactly what has been changed or added. Use `eucast_rules(..., verbose = TRUE)` to get a data set with all changed per bug and drug combination.
* Added 605 *Aspergillus* species and 23 *Trichophyton* species to the `microorganisms` data set
* Removed data sets `microorganisms.oldDT`, `microorganisms.prevDT`, `microorganisms.unprevDT` and `microorganismsDT` since they were no longer needed and only contained info already available in the `microorganisms` data set
* Added 65 antibiotics to the `antibiotics` data set, from the [Pharmaceuticals Community Register](http://ec.europa.eu/health/documents/community-register/html/atc.htm) of the European Commission
* Removed columns `atc_group1_nl` and `atc_group2_nl` from the `antibiotics` data set
* Functions `atc_ddd()` and `atc_groups()` have been renamed `atc_online_ddd()` and `atc_online_groups()`. The old functions are deprecated and will be removed in a future version.

60
R/data.R
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@ -130,14 +130,14 @@
#
"antibiotics"
#' Data set with ~20,000 microorganisms
#' Data set with ~60,000 microorganisms
#'
#' A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using \code{\link{as.mo}}.
#' A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
#' @inheritSection ITIS ITIS
#' @format A \code{\link{data.frame}} with 19,456 observations and 15 variables:
#' @format A \code{\link{data.frame}} with 56,659 observations and 15 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism}
#' \item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
#' \item{\code{col_id}}{Catalogue of Life ID}
#' \item{\code{genus}}{Taxonomic genus of the microorganism as found in ITIS, see Source}
#' \item{\code{species}}{Taxonomic species of the microorganism as found in ITIS, see Source}
#' \item{\code{subspecies}}{Taxonomic subspecies of the microorganism as found in ITIS, see Source}
@ -155,15 +155,10 @@
#' @source Integrated Taxonomic Information System (ITIS) public online database, \url{https://www.itis.gov}.
#' @details Manually added were:
#' \itemize{
#' \item{605 species of Aspergillus (as Aspergillus misses from ITIS, list from https://en.wikipedia.org/wiki/List_of_Aspergillus_species on 2019-02-05)}
#' \item{23 species of Trichophyton (as Trichophyton misses from ITIS, list from https://en.wikipedia.org/wiki/Trichophyton on 2019-02-05)}
#' \item{9 species of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
#' \item{2 species of Straphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{1 species of Candida (C. glabrata)}
#' \item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
#' \item{2 species of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{2 other undefined (unknown Gram negatives and unknown Gram positives)}
#' }
#'
#' These manual entries have no Taxonomic Serial Number (TSN), so can be looked up with \code{filter(microorganisms, is.na(tsn)}.
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{mo_property}} \code{\link{microorganisms.codes}}
"microorganisms"
@ -172,12 +167,12 @@
#'
#' A data set containing old (previously valid or accepted) taxonomic names according to ITIS. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection as.mo ITIS
#' @format A \code{\link{data.frame}} with 2,383 observations and 4 variables:
#' @format A \code{\link{data.frame}} with 14,506 observations and 4 variables:
#' \describe{
#' \item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
#' \item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
#' \item{\code{tsn_new}}{New Taxonomic Serial Number (TSN), as defined by ITIS}
#' \item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
#' \item{\code{col_id}}{Catalogue of Life ID}
#' \item{\code{tsn_new}}{New Catalogue of Life ID}
#' \item{\code{fullname}}{Old taxonomic name of the microorganism as found in the CoL, see Source}
#' \item{\code{ref}}{Author(s) and year of concerning publication as found in the CoL, see Source}
#' }
#' @source [3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.
#' @inheritSection AMR Read more on our website!
@ -250,36 +245,3 @@
#' }
#' @inheritSection AMR Read more on our website!
"WHONET"
#' Supplementary Data
#'
#' These \code{\link{data.table}s} are transformed from the \code{\link{microorganisms}} and \code{\link{microorganisms}} data sets to improve speed of \code{\link{as.mo}}. They are meant for internal use only, and are only mentioned here for reference.
#' @rdname supplementary_data
#' @name supplementary_data
#' @inheritSection AMR Read more on our website!
# # Renew data:
# # sorted on (1) bacteria, (2) fungi, (3) protozoa and then human pathogenic prevalence and then TSN:
# microorganismsDT <- data.table::as.data.table(AMR::microorganisms)
# data.table::setkey(microorganismsDT, kingdom, prevalence, fullname)
# microorganisms.prevDT <- microorganismsDT[prevalence != 9999,]
# microorganisms.unprevDT <- microorganismsDT[prevalence == 9999,]
# microorganisms.oldDT <- data.table::as.data.table(AMR::microorganisms.old)
# data.table::setkey(microorganisms.oldDT, tsn, name)
# usethis::use_data(microorganismsDT, overwrite = TRUE)
# usethis::use_data(microorganisms.prevDT, overwrite = TRUE)
# usethis::use_data(microorganisms.unprevDT, overwrite = TRUE)
# usethis::use_data(microorganisms.oldDT, overwrite = TRUE)
# rm(microorganismsDT)
# rm(microorganisms.prevDT)
# rm(microorganisms.unprevDT)
# rm(microorganisms.oldDT)
"microorganismsDT"
#' @rdname supplementary_data
"microorganisms.prevDT"
#' @rdname supplementary_data
"microorganisms.unprevDT"
#' @rdname supplementary_data
"microorganisms.oldDT"

1
R/eucast_rules.R
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@ -548,6 +548,7 @@ eucast_rules <- function(tbl,
tbl <- tbl %>%
mutate_at(vars(col_mo), as.mo) %>%
left_join_microorganisms(by = col_mo, suffix = c("_oldcols", "")) %>%
mutate(gramstain = mo_gramstain(pull(., col_mo))) %>%
as.data.frame(stringsAsFactors = FALSE)
if (info == TRUE) {

2
R/first_isolate.R
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@ -70,7 +70,7 @@
#' @keywords isolate isolates first
#' @seealso \code{\link{key_antibiotics}}
#' @export
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange
#' @importFrom dplyr arrange_at lag between row_number filter mutate arrange pull
#' @importFrom crayon blue bold silver
#' @return Logical vector
#' @source Methodology of this function is based on: \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.

5
R/key_antibiotics.R
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@ -43,7 +43,7 @@
#' @inheritSection first_isolate Key antibiotics
#' @rdname key_antibiotics
#' @export
#' @importFrom dplyr %>% mutate if_else
#' @importFrom dplyr %>% mutate if_else pull
#' @importFrom crayon blue bold
#' @seealso \code{\link{first_isolate}}
#' @inheritSection AMR Read more on our website!
@ -149,7 +149,8 @@ key_antibiotics <- function(tbl,
tbl <- tbl %>%
mutate_at(vars(col_mo), as.mo) %>%
left_join_microorganisms(by = col_mo) %>%
mutate(key_ab = NA_character_)
mutate(key_ab = NA_character_,
gramstain = mo_gramstain(pull(., col_mo)))
# Gram +
tbl <- tbl %>% mutate(key_ab =

167
R/mo.R
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@ -47,7 +47,8 @@
#' | | | ----> subspecies, a 3-4 letter acronym
#' | | ----> species, a 3-4 letter acronym
#' | ----> genus, a 5-7 letter acronym, mostly without vowels
#' ----> taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
#' ----> taxonomic kingdom: A (Archaea), B (Bacteria), C (Chromista),
#' F (Fungi), P (Protozoa) or V (Viruses)
#' }
#'
#' Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
@ -81,7 +82,7 @@
#'
#' Examples:
#' \itemize{
#' \item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPTC_GRB}) needs review.}
#' \item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPT_GRB}) needs review.}
#' \item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
#' \item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
#' \item{\code{"Fluoroquinolone-resistant Neisseria gonorrhoeae"}. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result \emph{Neisseria gonorrhoeae} (\code{B_NESSR_GON}) needs review.}
@ -118,8 +119,6 @@
#' as.mo("MRSA") # Methicillin Resistant S. aureus
#' as.mo("VISA") # Vancomycin Intermediate S. aureus
#' as.mo("VRSA") # Vancomycin Resistant S. aureus
#' as.mo(369) # Search on TSN (Taxonomic Serial Number), a unique identifier
#' # for the Integrated Taxonomic Information System (ITIS)
#'
#' as.mo("Streptococcus group A")
#' as.mo("GAS") # Group A Streptococci
@ -128,8 +127,8 @@
#' as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
#' as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
#'
#' as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
#' as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
#' as.mo("S. pyogenes") # will remain species: B_STRPT_PYO
#' as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRA
#'
#' # Use mo_* functions to get a specific property based on `mo`
#' Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`
@ -178,11 +177,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
if (!"AMR" %in% base::.packages()) {
library("AMR")
# These data.tables are available as data sets when the AMR package is loaded:
# microorganismsDT # this one is sorted by kingdom (B<F<P), prevalence, TSN
# microorganisms.prevDT # same as microorganismsDT, but with prevalence != 9999
# microorganisms.unprevDT # same as microorganismsDT, but with prevalence == 9999
# microorganisms.oldDT # old taxonomic names, sorted by name (genus+species), TSN
# check onLoad() in R/zzz.R: data tables are created there.
}
if (clear_options == TRUE) {
@ -220,6 +215,17 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# remove empty values (to later fill them in again with NAs)
x <- x[!is.na(x) & !is.null(x) & !identical(x, "")]
# conversion v0.5.0 to v0.6.0, remove for v0.7.0
x <- gsub("B_STRPTC", "B_STRPT", x)
x <- gsub("B_STRPT_EQUI", "B_STRPT_EQU", x)
x <- gsub("B_PDMNS", "B_PSDMN", x)
x <- gsub("B_CTRDM", "B_CLSTR", x)
x <- gsub("F_CANDD_GLB", "F_CANDD_GLA", x)
x <- gsub("F_CANDD_LUS", "F_CANDD", x)
x <- gsub("B_FCTRM", "B_FSBCT", x)
# defined df to check for
if (!is.null(reference_df)) {
if (!is.data.frame(reference_df) | NCOL(reference_df) < 2) {
@ -239,8 +245,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# all empty
if (property == "mo") {
return(structure(rep(NA_character_, length(x_input)), class = "mo"))
} else if (property == "tsn") {
return(rep(NA_integer_, length(x_input)))
} else {
return(rep(NA_character_, length(x_input)))
}
@ -283,7 +287,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# replace hemolytic by haemolytic
x <- gsub("ha?emoly", "haemoly", x)
# place minus back in streptococci
x <- gsub("(alpha|beta|gamma) haemoly", "\\1-haemolytic", x)
x <- gsub("(alpha|beta|gamma) ha?emoly", "\\1-haemoly", x)
# remove genus as first word
x <- gsub("^Genus ", "", x)
@ -372,7 +376,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
if (toupper(x_trimmed[i]) == 'MRPA') {
# multi resistant P. aeruginosa
x[i] <- microorganismsDT[mo == 'B_PDMNS_AER', ..property][[1]][1L]
x[i] <- microorganismsDT[mo == 'B_PSDMN_AER', ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) == 'CRS'
@ -383,22 +387,22 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
if (toupper(x_trimmed[i]) %in% c('PISP', 'PRSP', 'VISP', 'VRSP')) {
# peni I, peni R, vanco I, vanco R: S. pneumoniae
x[i] <- microorganismsDT[mo == 'B_STRPTC_PNE', ..property][[1]][1L]
x[i] <- microorganismsDT[mo == 'B_STRPT_PNE', ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) %like% '^G[ABCDFGHK]S$') {
# Streptococci, like GBS = Group B Streptococci (B_STRPTC_GRB)
x[i] <- microorganismsDT[mo == gsub("G([ABCDFGHK])S", "B_STRPTC_GR\\1", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRB)
x[i] <- microorganismsDT[mo == gsub("G([ABCDFGHK])S", "B_STRPT_GR\\1", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) %like% '(streptococc|streptokok).* [ABCDFGHK]$') {
# Streptococci in different languages, like "estreptococos grupo B"
x[i] <- microorganismsDT[mo == gsub(".*(streptococ|streptokok|estreptococ).* ([ABCDFGHK])$", "B_STRPTC_GR\\2", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
x[i] <- microorganismsDT[mo == gsub(".*(streptococ|streptokok|estreptococ).* ([ABCDFGHK])$", "B_STRPT_GR\\2", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
next
}
if (toupper(x_trimmed[i]) %like% 'group [ABCDFGHK] (streptococ|streptokok|estreptococ)') {
# Streptococci in different languages, like "Group A Streptococci"
x[i] <- microorganismsDT[mo == gsub(".*group ([ABCDFGHK]) (streptococ|streptokok|estreptococ).*", "B_STRPTC_GR\\1", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
x[i] <- microorganismsDT[mo == gsub(".*group ([ABCDFGHK]) (streptococ|streptokok|estreptococ).*", "B_STRPT_GR\\1", x_trimmed[i], ignore.case = TRUE), ..property][[1]][1L]
next
}
# CoNS/CoPS in different languages (support for German, Dutch, Spanish, Portuguese) ----
@ -490,15 +494,72 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
}
# TRY FIRST THOUSAND MOST PREVALENT IN HUMAN INFECTIONS ----
found <- microorganisms.prevDT[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), ..property][[1]]
# FIRST TRY SUPERPREVALENT IN HUMAN INFECTIONS ----
found <- microorganisms.superprevDT[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), ..property][[1]]
# most probable: is exact match in fullname
if (length(found) > 0) {
x[i] <- found[1L]
next
}
found <- microorganisms.prevDT[tsn == x_trimmed[i], ..property][[1]]
# is a valid TSN
found <- microorganisms.superprevDT[mo == toupper(x_backup[i]), ..property][[1]]
# is a valid mo
if (length(found) > 0) {
x[i] <- found[1L]
next
}
found <- microorganisms.superprevDT[tolower(fullname) == tolower(x_trimmed_without_group[i]), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
# try any match keeping spaces ----
found <- microorganisms.superprevDT[fullname %like% x_withspaces_start_end[i], ..property][[1]]
if (length(found) > 0 & nchar(x_trimmed[i]) >= 6) {
x[i] <- found[1L]
next
}
# try any match keeping spaces, not ending with $ ----
found <- microorganisms.superprevDT[fullname %like% x_withspaces_start_only[i], ..property][[1]]
if (length(found) > 0 & nchar(x_trimmed[i]) >= 6) {
x[i] <- found[1L]
next
}
# try any match diregarding spaces ----
found <- microorganisms.superprevDT[fullname %like% x[i], ..property][[1]]
if (length(found) > 0 & nchar(x_trimmed[i]) >= 6) {
x[i] <- found[1L]
next
}
# try splitting of characters in the middle and then find ID ----
# only when text length is 6 or lower
# like esco = E. coli, klpn = K. pneumoniae, stau = S. aureus, staaur = S. aureus
if (nchar(x_trimmed[i]) <= 6) {
x_length <- nchar(x_trimmed[i])
x[i] <- paste0(x_trimmed[i] %>% substr(1, x_length / 2),
'.* ',
x_trimmed[i] %>% substr((x_length / 2) + 1, x_length))
found <- microorganisms.superprevDT[fullname %like% paste0('^', x[i]), ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
}
# try fullname without start and stop regex, to also find subspecies ----
# like "K. pneu rhino" >> "Klebsiella pneumoniae (rhinoscleromatis)" = KLEPNERH
found <- microorganisms.superprevDT[fullname %like% x_withspaces_start_only[i], ..property][[1]]
if (length(found) > 0) {
x[i] <- found[1L]
next
}
# TRY PREVALENT IN HUMAN INFECTIONS ----
found <- microorganisms.prevDT[tolower(fullname) %in% tolower(c(x_backup[i], x_trimmed[i])), ..property][[1]]
# most probable: is exact match in fullname
if (length(found) > 0) {
x[i] <- found[1L]
next
@ -559,7 +620,7 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
next
}
# THEN TRY ALL OTHERS ----
# THEN UNPREVALENT IN HUMAN INFECTIONS ----
found <- microorganisms.unprevDT[tolower(fullname) == tolower(x_backup[i]), ..property][[1]]
# most probable: is exact match in fullname
if (length(found) > 0) {
@ -572,12 +633,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
x[i] <- found[1L]
next
}
found <- microorganisms.unprevDT[tsn == x_trimmed[i], ..property][[1]]
# is a valid TSN
if (length(found) > 0) {
x[i] <- found[1L]
next
}
found <- microorganisms.unprevDT[mo == toupper(x_backup[i]), ..property][[1]]
# is a valid mo
if (length(found) > 0) {
@ -633,23 +688,23 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# MISCELLANEOUS ----
# look for old taxonomic names ----
found <- microorganisms.oldDT[tolower(name) == tolower(x_backup[i])
| tsn == x_trimmed[i]
| name %like% x_withspaces_start_end[i],]
found <- microorganisms.oldDT[tolower(fullname) == tolower(x_backup[i])
| fullname %like% x_withspaces_start_end[i],]
if (NROW(found) > 0) {
col_id_new <- found[1, col_id_new]
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
# mo_ref("Chlamydia psittaci) = "Page, 1968" (with warning)
# mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
if (property == "ref") {
x[i] <- found[1, ref]
} else {
x[i] <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
x[i] <- microorganismsDT[col_id == found[1, col_id_new], ..property][[1]]
}
was_renamed(name_old = found[1, name],
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
was_renamed(name_old = found[1, fullname],
name_new = microorganismsDT[col_id == found[1, col_id_new], fullname],
ref_old = found[1, ref],
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref],
mo = microorganismsDT[tsn == found[1, tsn_new], mo])
ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
mo = microorganismsDT[col_id == found[1, col_id_new], mo])
next
}
@ -673,9 +728,9 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
}
# (2) look again for old taxonomic names, now for G. species ----
found <- microorganisms.oldDT[name %like% c.x_withspaces_start_end
| name %like% d.x_withspaces_start_only
| name %like% e.x,]
found <- microorganisms.oldDT[fullname %like% c.x_withspaces_start_end
| fullname %like% d.x_withspaces_start_only
| fullname %like% e.x,]
if (NROW(found) > 0 & nchar(b.x_trimmed) >= 6) {
if (property == "ref") {
# when property is "ref" (which is the case in mo_ref, mo_authors and mo_year), return the old value, so:
@ -683,15 +738,15 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# mo_ref("Chlamydophila psittaci) = "Everett et al., 1999"
x <- found[1, ref]
} else {
x <- microorganismsDT[tsn == found[1, tsn_new], ..property][[1]]
x <- microorganismsDT[col_id == found[1, col_id_new], ..property][[1]]
}
was_renamed(name_old = found[1, name],
name_new = microorganismsDT[tsn == found[1, tsn_new], fullname],
was_renamed(name_old = found[1, fullname],
name_new = microorganismsDT[col_id == found[1, col_id_new], fullname],
ref_old = found[1, ref],
ref_new = microorganismsDT[tsn == found[1, tsn_new], ref],
mo = microorganismsDT[tsn == found[1, tsn_new], mo])
ref_new = microorganismsDT[col_id == found[1, col_id_new], ref],
mo = microorganismsDT[col_id == found[1, col_id_new], mo])
uncertainties <<- c(uncertainties,
paste0("'", a.x_backup, "' >> ", found[1, name], " (TSN ", found[1, tsn], ")"))
paste0("'", a.x_backup, "' >> ", found[1, fullname], " (Catalogue of Life ID ", found[1, col_id], ")"))
return(x)
}
@ -835,25 +890,25 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
# Lancefield ----
if (Lancefield == TRUE | Lancefield == "all") {
# group A - S. pyogenes
x[x == microorganismsDT[mo == 'B_STRPTC_PYO', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRA', ..property][[1]][1L]
x[x == microorganismsDT[mo == 'B_STRPT_PYO', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPT_GRA', ..property][[1]][1L]
# group B - S. agalactiae
x[x == microorganismsDT[mo == 'B_STRPTC_AGA', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRB', ..property][[1]][1L]
x[x == microorganismsDT[mo == 'B_STRPT_AGA', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPT_GRB', ..property][[1]][1L]
# group C
S_groupC <- microorganismsDT %>% filter(genus == "Streptococcus",
species %in% c("equisimilis", "equi",
"zooepidemicus", "dysgalactiae")) %>%
pull(property)
x[x %in% S_groupC] <- microorganismsDT[mo == 'B_STRPTC_GRC', ..property][[1]][1L]
x[x %in% S_groupC] <- microorganismsDT[mo == 'B_STRPT_GRC', ..property][[1]][1L]
if (Lancefield == "all") {
# all Enterococci
x[x %like% "^(Enterococcus|B_ENTRC)"] <- microorganismsDT[mo == 'B_STRPTC_GRD', ..property][[1]][1L]
x[x %like% "^(Enterococcus|B_ENTRC)"] <- microorganismsDT[mo == 'B_STRPT_GRD', ..property][[1]][1L]
}
# group F - S. anginosus
x[x == microorganismsDT[mo == 'B_STRPTC_ANG', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRF', ..property][[1]][1L]
x[x == microorganismsDT[mo == 'B_STRPT_ANG', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPT_GRF', ..property][[1]][1L]
# group H - S. sanguinis
x[x == microorganismsDT[mo == 'B_STRPTC_SAN', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRH', ..property][[1]][1L]
x[x == microorganismsDT[mo == 'B_STRPT_SAN', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPT_GRH', ..property][[1]][1L]
# group K - S. salivarius
x[x == microorganismsDT[mo == 'B_STRPTC_SAL', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPTC_GRK', ..property][[1]][1L]
x[x == microorganismsDT[mo == 'B_STRPT_SAL', ..property][[1]][1L]] <- microorganismsDT[mo == 'B_STRPT_GRK', ..property][[1]][1L]
}
@ -875,8 +930,6 @@ exec_as.mo <- function(x, Becker = FALSE, Lancefield = FALSE,
if (property == "mo") {
class(x) <- "mo"
} else if (property == "tsn") {
x <- as.integer(x)
}
if (length(mo_renamed()) > 0) {

32
R/mo_property.R
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@ -38,7 +38,7 @@
#' @rdname mo_property
#' @name mo_property
#' @return \itemize{
#' \item{An \code{integer} in case of \code{mo_TSN} and \code{mo_year}}
#' \item{An \code{integer} in case of \code{mo_year}}
#' \item{A \code{list} in case of \code{mo_taxonomy}}
#' \item{A \code{character} in all other cases}
#' }
@ -57,7 +57,6 @@
#' mo_genus("E. coli") # "Escherichia"
#' mo_species("E. coli") # "coli"
#' mo_subspecies("E. coli") # NA
#' mo_TSN("E. coli") # 285 (Taxonomic Serial Number)
#'
#' ## colloquial properties
#' mo_fullname("E. coli") # "Escherichia coli"
@ -242,17 +241,15 @@ mo_type <- function(x, language = get_locale(), ...) {
#' @rdname mo_property
#' @export
mo_gramstain <- function(x, language = get_locale(), ...) {
mo_translate(mo_validate(x = x, property = "gramstain", ...), language = language)
}
#' @rdname mo_property
#' @export
mo_TSN <- function(x, ...) {
res <- mo_validate(x = x, property = "tsn", ...)
if (any(is.na(res))) {
warning("Some results do not have a TSN, because they are missing from ITIS and were added manually. See ?microorganisms.")
}
res
x.bak <- x
x <- mo_phylum(x, ...)
x[x %in% c("Actinobacteria",
"Chloroflexi",
"Firmicutes",
"Tenericutes")] <- "Gram positive"
x[x != "Gram positive"] <- "Gram negative"
x[mo_kingdom(x.bak) != "Bacteria"] <- NA_character_
mo_translate(x, language = language)
}
#' @rdname mo_property
@ -284,7 +281,6 @@ mo_year <- function(x, ...) {
mo_taxonomy <- function(x, ...) {
x <- AMR::as.mo(x, ...)
base::list(kingdom = mo_kingdom(x),
subkingdom = mo_subkingdom(x),
phylum = mo_phylum(x),
class = mo_class(x),
order = mo_order(x),
@ -472,11 +468,7 @@ mo_validate <- function(x, property, ...) {
if (!"AMR" %in% base::.packages()) {
library("AMR")
# These data.tables are available as data sets when the AMR package is loaded:
# microorganismsDT # this one is sorted by kingdom (B<F<P), prevalence, TSN
# microorganisms.prevDT # same as microorganismsDT, but with prevalence != 9999
# microorganisms.unprevDT # same as microorganismsDT, but with prevalence == 9999
# microorganisms.oldDT # old taxonomic names, sorted by name (genus+species), TSN
# check onLoad() in R/zzz.R: data tables are created there.
}
if (!all(x %in% microorganismsDT[[property]])
@ -486,8 +478,6 @@ mo_validate <- function(x, property, ...) {
} else {
if (property == "mo") {
return(structure(x, class = "mo"))
} else if (property == "tsn") {
return(as.integer(x))
} else {
return(x)
}

63
R/zzz.R
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@ -65,6 +65,69 @@
#' @rdname AMR
NULL
#' @importFrom dplyr mutate
#' @importFrom data.table as.data.table setkey
.onLoad <- function(libname, pkgname) {
# get new functions not available in older versions of R
backports::import(pkgname)
# register data
if (!all(c("microorganismsDT",
"microorganisms.prevDT",
"microorganisms.unprevDT",
"microorganisms.oldDT") %in% ls(envir = asNamespace("AMR")))) {
# packageStartupMessage("Loading taxonomic database...", appendLF = FALSE)
microorganismsDT <- AMR::microorganisms %>%
mutate(prevalent = ifelse(phylum %in% c("Proteobacteria",
"Firmicutes",
"Actinobacteria",
"Bacteroidetes")
| genus %in% c("Candida",
"Aspergillus",
"Trichophyton",
"Giardia",
"Dientamoeba",
"Entamoeba"),
0,
1),
superprevalent = ifelse(
# most important Gram negatives
class == "Gammaproteobacteria"
# Streptococci and Staphylococci
| order %in% c("Lactobacillales",
"Bacillales"),
0,
1)) %>%
as.data.table()
setkey(microorganismsDT, kingdom, superprevalent, prevalent, fullname)
microorganisms.superprevDT <- microorganismsDT[superprevalent == 0,]
microorganisms.prevDT <- microorganismsDT[superprevalent == 1 & prevalent == 0,]
microorganisms.unprevDT <- microorganismsDT[superprevalent == 1 & prevalent == 1,]
microorganisms.oldDT <- as.data.table(AMR::microorganisms.old)
setkey(microorganisms.oldDT, col_id, fullname)
assign(x = "microorganismsDT",
value = microorganismsDT,
envir = asNamespace("AMR"))
assign(x = "microorganisms.superprevDT",
value = microorganisms.superprevDT,
envir = asNamespace("AMR"))
assign(x = "microorganisms.prevDT",
value = microorganisms.prevDT,
envir = asNamespace("AMR"))
assign(x = "microorganisms.unprevDT",
value = microorganisms.unprevDT,
envir = asNamespace("AMR"))
assign(x = "microorganisms.oldDT",
value = microorganisms.oldDT,
envir = asNamespace("AMR"))
# packageStartupMessage("OK.", appendLF = TRUE)
}
}

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2
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

426
docs/articles/AMR.html
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -201,7 +201,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 14 February 2019.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/">RMarkdown</a>. However, the methodology remains unchanged. This page was generated on 18 February 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -217,21 +217,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-02-14</td>
<td align="center">2019-02-18</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2019-02-14</td>
<td align="center">2019-02-18</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2019-02-14</td>
<td align="center">2019-02-18</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -327,70 +327,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-12-27</td>
<td align="center">C5</td>
<td align="center">2011-01-25</td>
<td align="center">V6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-11-20</td>
<td align="center">Y5</td>
<td align="center">2013-07-31</td>
<td align="center">A8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-06-25</td>
<td align="center">I4</td>
<td align="center">2016-10-12</td>
<td align="center">Y3</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-12-31</td>
<td align="center">B4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-10-16</td>
<td align="center">N10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-09-01</td>
<td align="center">L1</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">2014-08-10</td>
<td align="center">F9</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-12-14</td>
<td align="center">Z3</td>
<td align="center">2017-12-05</td>
<td align="center">H7</td>
<td align="center">Hospital A</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -411,8 +411,8 @@
#&gt;
#&gt; Item Count Percent Cum. Count Cum. Percent
#&gt; --- ----- ------- -------- ----------- -------------
#&gt; 1 M 10,432 52.2% 10,432 52.2%
#&gt; 2 F 9,568 47.8% 20,000 100.0%</code></pre>
#&gt; 1 M 10,283 51.4% 10,283 51.4%
#&gt; 2 F 9,717 48.6% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientist perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researcher perspective: there are slightly more men. Nothing we didn’t already know.</p>
<p>The data is already quite clean, but we still need to transform some variables. The <code>bacteria</code> column now consists of text, and we want to add more variables based on microbial IDs later on. So, we will transform this column to valid IDs. The <code><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate()</a></code> function of the <code>dplyr</code> package makes this really easy:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb12-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -443,10 +443,10 @@
<a class="sourceLine" id="cb14-19" title="19"><span class="co">#&gt; Kingella kingae (no changes)</span></a>
<a class="sourceLine" id="cb14-20" title="20"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-21" title="21"><span class="co">#&gt; EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1241 changes)</span></a>
<a class="sourceLine" id="cb14-22" title="22"><span class="co">#&gt; Table 1: Intrinsic resistance in Enterobacteriaceae (1294 changes)</span></a>
<a class="sourceLine" id="cb14-23" title="23"><span class="co">#&gt; Table 2: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-24" title="24"><span class="co">#&gt; Table 3: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2713 changes)</span></a>
<a class="sourceLine" id="cb14-25" title="25"><span class="co">#&gt; Table 4: Intrinsic resistance in Gram-positive bacteria (2822 changes)</span></a>
<a class="sourceLine" id="cb14-26" title="26"><span class="co">#&gt; Table 8: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb14-27" title="27"><span class="co">#&gt; Table 9: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb14-28" title="28"><span class="co">#&gt; Table 10: Interpretive rules for B-lactam agents and other Gram-negative bacteria (no changes)</span></a>
@ -462,9 +462,9 @@
<a class="sourceLine" id="cb14-38" title="38"><span class="co">#&gt; Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb14-39" title="39"><span class="co">#&gt; Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb14-40" title="40"><span class="co">#&gt; </span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,301 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-41" title="41"><span class="co">#&gt; =&gt; EUCAST rules affected 7,463 out of 20,000 rows</span></a>
<a class="sourceLine" id="cb14-42" title="42"><span class="co">#&gt; -&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 3,954 test results (0 to S; 0 to I; 3,954 to R)</span></a></code></pre></div>
<a class="sourceLine" id="cb14-43" title="43"><span class="co">#&gt; -&gt; changed 4,116 test results (0 to S; 0 to I; 4,116 to R)</span></a></code></pre></div>
</div>
<div id="adding-new-variables" class="section level1">
<h1 class="hasAnchor">
@ -489,7 +489,7 @@
<a class="sourceLine" id="cb16-3" title="3"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb16-4" title="4"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb16-5" title="5"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,669 first isolates (28.3% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb16-6" title="6"><span class="co">#&gt; =&gt; Found 5,654 first isolates (28.3% of total)</span></a></code></pre></div>
<p>So only 28.3% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb17-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb17-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(first <span class="op">==</span><span class="st"> </span><span class="ot">TRUE</span>)</a></code></pre></div>
@ -516,43 +516,43 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-04</td>
<td align="center">M1</td>
<td align="center">2010-04-05</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-01-27</td>
<td align="center">M1</td>
<td align="center">2010-05-10</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-07</td>
<td align="center">M1</td>
<td align="center">2010-06-22</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-09</td>
<td align="center">M1</td>
<td align="center">2010-06-25</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -560,10 +560,10 @@
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-23</td>
<td align="center">M1</td>
<td align="center">2010-10-03</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -571,30 +571,30 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-29</td>
<td align="center">M1</td>
<td align="center">2010-10-08</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-10-14</td>
<td align="center">M1</td>
<td align="center">2011-03-24</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-10-15</td>
<td align="center">M1</td>
<td align="center">2011-03-27</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -604,21 +604,21 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-10-16</td>
<td align="center">M1</td>
<td align="center">2011-05-11</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">R</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-16</td>
<td align="center">M1</td>
<td align="center">2011-07-22</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -626,7 +626,7 @@
</tr>
</tbody>
</table>
<p>Only 1 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>Only 2 isolates are marked as ‘first’ according to CLSI guideline. But when reviewing the antibiogram, it is obvious that some isolates are absolutely different strains and should be included too. This is why we weigh isolates, based on their antibiogram. The <code><a href="../reference/key_antibiotics.html">key_antibiotics()</a></code> function adds a vector with 18 key antibiotics: 6 broad spectrum ones, 6 small spectrum for Gram negatives and 6 small spectrum for Gram positives. These can be defined by the user.</p>
<p>If a column exists with a name like ‘key(…)ab’ the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> function will automatically use it and determine the first weighted isolates. Mind the NOTEs in below output:</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb19-1" title="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb19-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span>(<span class="dt">keyab =</span> <span class="kw"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span>(.)) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -637,7 +637,7 @@
<a class="sourceLine" id="cb19-7" title="7"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `patient_id` as input for `col_patient_id`.</span></a>
<a class="sourceLine" id="cb19-8" title="8"><span class="co">#&gt; </span><span class="al">NOTE</span><span class="co">: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></a>
<a class="sourceLine" id="cb19-9" title="9"><span class="co">#&gt; [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,859 first weighted isolates (79.3% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb19-10" title="10"><span class="co">#&gt; =&gt; Found 15,805 first weighted isolates (79.0% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -654,23 +654,23 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-04</td>
<td align="center">M1</td>
<td align="center">2010-04-05</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-01-27</td>
<td align="center">M1</td>
<td align="center">2010-05-10</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -678,34 +678,34 @@
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-05-07</td>
<td align="center">M1</td>
<td align="center">2010-06-22</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-06-09</td>
<td align="center">M1</td>
<td align="center">2010-06-25</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-07-23</td>
<td align="center">M1</td>
<td align="center">2010-10-03</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -714,58 +714,58 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-09-29</td>
<td align="center">M1</td>
<td align="center">2010-10-08</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2010-10-14</td>
<td align="center">M1</td>
<td align="center">2011-03-24</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2010-10-15</td>
<td align="center">M1</td>
<td align="center">2011-03-27</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2010-10-16</td>
<td align="center">M1</td>
<td align="center">2011-05-11</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">R</td>
<td align="center">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-16</td>
<td align="center">M1</td>
<td align="center">2011-07-22</td>
<td align="center">Q7</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
@ -774,11 +774,11 @@
</tr>
</tbody>
</table>
<p>Instead of 1, now 9 isolates are flagged. In total, 79.3% of all isolates are marked ‘first weighted’ - 51% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>Instead of 2, now 4 isolates are flagged. In total, 79% of all isolates are marked ‘first weighted’ - 50.8% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
<p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" title="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()</a></code></pre></div>
<p>So we end up with 15,859 isolates for analysis.</p>
<p>So we end up with 15,805 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" title="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span>(<span class="op">-</span><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(first, keyab))</a></code></pre></div>
@ -803,30 +803,62 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>4</td>
<td align="center">2016-10-16</td>
<td align="center">N10</td>
<td align="center">Hospital A</td>
<td>2</td>
<td align="center">2013-07-31</td>
<td align="center">A8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>5</td>
<td align="center">2015-09-01</td>
<td align="center">L1</td>
<td>3</td>
<td align="center">2016-10-12</td>
<td align="center">Y3</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>5</td>
<td align="center">2014-08-10</td>
<td align="center">F9</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2017-12-05</td>
<td align="center">H7</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
@ -835,69 +867,37 @@
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>6</td>
<td align="center">2013-12-14</td>
<td align="center">Z3</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNE</td>
<td>7</td>
<td align="center">2014-02-06</td>
<td align="center">D7</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>7</td>
<td align="center">2011-09-19</td>
<td align="center">U9</td>
<td>8</td>
<td align="center">2013-05-11</td>
<td align="center">A5</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>8</td>
<td align="center">2016-02-23</td>
<td align="center">H1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>9</td>
<td align="center">2016-08-02</td>
<td align="center">I4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -915,9 +915,9 @@
<div class="sourceCode" id="cb23"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb23-1" title="1"><span class="kw"><a href="../reference/freq.html">freq</a></span>(<span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/paste">paste</a></span>(data_1st<span class="op">$</span>genus, data_1st<span class="op">$</span>species))</a></code></pre></div>
<p>Or can be used like the <code>dplyr</code> way, which is easier readable:</p>
<div class="sourceCode" id="cb24"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb24-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,859 x 13)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (15,805 x 13)</strong></p>
<p>Columns: 2<br>
Length: 15,859 (of which NA: 0 = 0.00%)<br>
Length: 15,805 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -934,33 +934,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,917</td>
<td align="right">49.9%</td>
<td align="right">7,917</td>
<td align="right">49.9%</td>
<td align="right">7,815</td>
<td align="right">49.4%</td>
<td align="right">7,815</td>
<td align="right">49.4%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,901</td>
<td align="right">24.6%</td>
<td align="right">11,818</td>
<td align="right">74.5%</td>
<td align="right">3,988</td>
<td align="right">25.2%</td>
<td align="right">11,803</td>
<td align="right">74.7%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,478</td>
<td align="right">15.6%</td>
<td align="right">14,296</td>
<td align="right">90.1%</td>
<td align="right">2,476</td>
<td align="right">15.7%</td>
<td align="right">14,279</td>
<td align="right">90.3%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,563</td>
<td align="right">9.9%</td>
<td align="right">15,859</td>
<td align="right">1,526</td>
<td align="right">9.7%</td>
<td align="right">15,805</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -971,7 +971,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code>portion_R</code>, <code>portion_RI</code>, <code>portion_I</code>, <code>portion_IS</code> and <code>portion_S</code> can be used to determine the portion of a specific antimicrobial outcome. They can be used on their own:</p>
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_IR</a></span>(amox)</a>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4776468</span></a></code></pre></div>
<a class="sourceLine" id="cb25-2" title="2"><span class="co">#&gt; [1] 0.4771275</span></a></code></pre></div>
<p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" title="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb26-2" title="2"><span class="st"> </span><span class="kw"><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by</a></span>(hospital) <span class="op">%&gt;%</span><span class="st"> </span></a>
@ -984,19 +984,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4658398</td>
<td align="center">0.4661749</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4821041</td>
<td align="center">0.4820906</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4874459</td>
<td align="center">0.4847862</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4803681</td>
<td align="center">0.4790875</td>
</tr>
</tbody>
</table>
@ -1014,23 +1014,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4658398</td>
<td align="center">4757</td>
<td align="center">0.4661749</td>
<td align="center">4745</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4821041</td>
<td align="center">5532</td>
<td align="center">0.4820906</td>
<td align="center">5472</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4874459</td>
<td align="center">2310</td>
<td align="center">0.4847862</td>
<td align="center">2432</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4803681</td>
<td align="center">3260</td>
<td align="center">0.4790875</td>
<td align="center">3156</td>
</tr>
</tbody>
</table>
@ -1050,27 +1050,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7305798</td>
<td align="center">0.8974359</td>
<td align="center">0.9760010</td>
<td align="center">0.7332054</td>
<td align="center">0.9033909</td>
<td align="center">0.9754319</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.7370441</td>
<td align="center">0.9040307</td>
<td align="center">0.9776072</td>
<td align="center">0.7142857</td>
<td align="center">0.9095675</td>
<td align="center">0.9737877</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7303256</td>
<td align="center">0.9200205</td>
<td align="center">0.9771853</td>
<td align="center">0.7179037</td>
<td align="center">0.9162487</td>
<td align="center">0.9779338</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.7332526</td>
<td align="center">0.7289984</td>
<td align="center">0.0000000</td>
<td align="center">0.7332526</td>
<td align="center">0.7289984</td>
</tr>
</tbody>
</table>

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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>

4
docs/articles/G_test.html
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to use the <em>G</em>-test</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>G_test.Rmd</code></div>

2
docs/articles/SPSS.html
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

6
docs/articles/WHONET.html
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -274,7 +274,7 @@ Species: 36</p>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">B_STRPTC_PNE</td>
<td align="left">B_STRPT_PNE</td>
<td align="right">31</td>
<td align="right">6.2%</td>
<td align="right">388</td>

4
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to get properties of an antibiotic</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>atc_property.Rmd</code></div>

2
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

22
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to create frequency tables</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>freq.Rmd</code></div>
@ -256,22 +256,22 @@ Longest: 1</p>
<a class="sourceLine" id="cb2-2" title="2"><span class="co"># Joining, by = "mo"</span></a></code></pre></div>
<p>Now all variables of the <code>microorganisms</code> dataset have been joined to the <code>septic_patients</code> dataset. The <code>microorganisms</code> dataset consists of the following variables:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/colnames">colnames</a></span>(microorganisms)</a>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># [1] "mo" "tsn" "genus" "species" "subspecies"</span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># [6] "fullname" "family" "order" "class" "phylum" </span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># [11] "subkingdom" "kingdom" "gramstain" "prevalence" "ref"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 14 variables were added:</p>
<a class="sourceLine" id="cb3-2" title="2"><span class="co"># [1] "mo" "col_id" "fullname" "kingdom" "phylum" </span></a>
<a class="sourceLine" id="cb3-3" title="3"><span class="co"># [6] "class" "order" "family" "genus" "species" </span></a>
<a class="sourceLine" id="cb3-4" title="4"><span class="co"># [11] "subspecies" "rank" "ref"</span></a></code></pre></div>
<p>If we compare the dimensions between the old and new dataset, we can see that these 12 variables were added:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" title="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(septic_patients)</a>
<a class="sourceLine" id="cb4-2" title="2"><span class="co"># [1] 2000 49</span></a>
<a class="sourceLine" id="cb4-3" title="3"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/dim">dim</a></span>(my_patients)</a>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># [1] 2000 63</span></a></code></pre></div>
<a class="sourceLine" id="cb4-4" title="4"><span class="co"># [1] 2000 61</span></a></code></pre></div>
<p>So now the <code>genus</code> and <code>species</code> variables are available. A frequency table of these combined variables can be created like this:</p>
<div class="sourceCode" id="cb5"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb5-1" title="1">my_patients <span class="op">%&gt;%</span></a>
<a class="sourceLine" id="cb5-2" title="2"><span class="st"> </span><span class="kw"><a href="../reference/freq.html">freq</a></span>(genus, species, <span class="dt">nmax =</span> <span class="dv">15</span>)</a></code></pre></div>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 63)</strong></p>
<p><strong>Frequency table of <code>genus</code> and <code>species</code> from a <code>data.frame</code> (2,000 x 61)</strong></p>
<p>Columns: 2<br>
Length: 2,000 (of which NA: 0 = 0.00%)<br>
Unique: 96</p>
<p>Shortest: 12<br>
Unique: 95</p>
<p>Shortest: 8<br>
Longest: 34</p>
<table class="table">
<thead><tr class="header">
@ -405,7 +405,7 @@ Longest: 34</p>
</tr>
</tbody>
</table>
<p>(omitted 81 entries, n = 340 [17.0%])</p>
<p>(omitted 80 entries, n = 340 [17.0%])</p>
</div>
<div id="frequencies-of-numeric-values" class="section level2">
<h2 class="hasAnchor">

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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

4
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to get properties of a microorganism</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>mo_property.Rmd</code></div>

4
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@ -40,7 +40,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -192,7 +192,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">14 February 2019</h4>
<h4 class="date">18 February 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>

2
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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -237,12 +237,27 @@
<a href="#amr-05090xx" class="anchor"></a>AMR 0.5.0.90xx<small> Unreleased </small>
</h1>
<p><strong>Note: this is the development version, which will eventually be released as AMR 0.6.0.</strong></p>
<p><strong>New website!</strong></p>
<p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</p>
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis, import data from WHONET or SPSS and many more.</li>
</ul>
<div id="new" class="section level4">
<h4 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h4>
<ul>
<li>
<strong>BREAKING</strong>: removed deprecated functions, parameters and references to ‘bactid’. Use <code><a href="../reference/as.mo.html">as.mo()</a></code> to identify an MO code.</li>
<li>Catalogue of Life (CoL) inclusion for data about microorganisms, which also contains all ITIS data we used previously. The <code>microorganisms</code> data set now contains:
<ul>
<li>Almost 60,000 species from six different kingdoms</li>
<li>Almost 15,000 previously accepted names which are now taxonomic ‘synonyms’</li>
<li>All (sub)species from the kingdoms Archaea, Bacteria, Chromista, Protozoa and Viruses</li>
<li>All (sub)species from the orders Eurotiales, Saccharomycetales and Onygenales of the kingdom Fungi. The complete taxonomy of this kingdom has more than 130,000 species. The orders we included contains at least all memebers of the families <em>Candida</em>, <em>Aspergillus</em> and <em>Trichophyton</em>.</li>
<li>Due to this change, the ID of <em>Streptococcus</em> was changed from <code>B_STRPTC</code> to <code>B_STRPT</code>.</li>
</ul>
</li>
<li>Support for data from <a href="https://whonet.org/">WHONET</a> and <a href="https://ecdc.europa.eu/en/about-us/partnerships-and-networks/disease-and-laboratory-networks/ears-net">EARS-Net</a> (European Antimicrobial Resistance Surveillance Network):
<ul>
<li>Exported files from WHONET can be read and used in this package. For functions like <code><a href="../reference/first_isolate.html">first_isolate()</a></code> and <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>, all parameters will be filled in automatically.</li>
@ -260,12 +275,6 @@
<a class="sourceLine" id="cb1-6" title="6">ab_umcg -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_umcg</a></span>()</a>
<a class="sourceLine" id="cb1-7" title="7">ab_tradenames -&gt;<span class="st"> </span><span class="kw"><a href="../reference/atc_property.html">atc_tradenames</a></span>()</a></code></pre></div>
These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code> internally. The old <code>atc_property</code> has been renamed <code><a href="../reference/atc_online.html">atc_online_property()</a></code>. This is done for two reasons: firstly, not all ATC codes are of antibiotics (ab) but can also be of antivirals or antifungals. Secondly, the input must have class <code>atc</code> or must be coerable to this class. Properties of these classes should start with the same class name, analogous to <code><a href="../reference/as.mo.html">as.mo()</a></code> and e.g. <code>mo_genus</code>.</li>
<li>New website: <a href="https://msberends.gitlab.io/AMR" class="uri">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)
<ul>
<li>Contains the complete manual of this package and all of its functions with an explanation of their parameters</li>
<li>Contains a comprehensive tutorial about how to conduct antimicrobial resistance analysis</li>
</ul>
</li>
<li>New functions <code><a href="../reference/mo_source.html">set_mo_source()</a></code> and <code><a href="../reference/mo_source.html">get_mo_source()</a></code> to use your own predefined MO codes as input for <code><a href="../reference/as.mo.html">as.mo()</a></code> and consequently all <code>mo_*</code> functions</li>
<li>Support for the upcoming <a href="https://dplyr.tidyverse.org"><code>dplyr</code></a> version 0.8.0</li>
<li>New function <code><a href="../reference/guess_ab_col.html">guess_ab_col()</a></code> to find an antibiotic column in a table</li>
@ -308,7 +317,7 @@ These functions use <code><a href="../reference/as.atc.html">as.atc()</a></code>
<li>New info is returned when running this function, stating exactly what has been changed or added. Use <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> to get a data set with all changed per bug and drug combination.</li>
</ul>
</li>
<li>Added 605 <em>Aspergillus</em> species and 23 <em>Trichophyton</em> species to the <code>microorganisms</code> data set</li>
<li>Removed data sets <code>microorganisms.oldDT</code>, <code>microorganisms.prevDT</code>, <code>microorganisms.unprevDT</code> and <code>microorganismsDT</code> since they were no longer needed and only contained info already available in the <code>microorganisms</code> data set</li>
<li>Added 65 antibiotics to the <code>antibiotics</code> data set, from the <a href="http://ec.europa.eu/health/documents/community-register/html/atc.htm">Pharmaceuticals Community Register</a> of the European Commission</li>
<li>Removed columns <code>atc_group1_nl</code> and <code>atc_group2_nl</code> from the <code>antibiotics</code> data set</li>
<li>Functions <code><a href="../reference/AMR-deprecated.html">atc_ddd()</a></code> and <code><a href="../reference/AMR-deprecated.html">atc_groups()</a></code> have been renamed <code><a href="../reference/atc_online.html">atc_online_ddd()</a></code> and <code><a href="../reference/atc_online.html">atc_online_groups()</a></code>. The old functions are deprecated and will be removed in a future version.</li>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -296,7 +296,8 @@
| | | ----&gt; subspecies, a 3-4 letter acronym
| | ----&gt; species, a 3-4 letter acronym
| ----&gt; genus, a 5-7 letter acronym, mostly without vowels
----&gt; taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
----&gt; taxonomic kingdom: A (Archaea), B (Bacteria), C (Chromista),
F (Fungi), P (Protozoa) or V (Viruses)
</pre>
<p>Use the <code><a href='mo_property.html'>mo_property</a></code> functions to get properties based on the returned code, see Examples.</p>
<p>This function uses Artificial Intelligence (AI) to help getting fast and logical results. It tries to find matches in this order:</p><ul>
@ -320,7 +321,7 @@ When using <code>allow_uncertain = TRUE</code> (which is the default setting), i
<li><p>It tries to look for some manual changes which are not yet published to the ITIS database (like <em>Propionibacterium</em> not yet being <em>Cutibacterium</em>)</p></li>
</ul>
<p>Examples:</p><ul>
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPTC_GRB</code>) needs review.</p></li>
<li><p><code>"Streptococcus group B (known as S. agalactiae)"</code>. The text between brackets will be removed and a warning will be thrown that the result <em>Streptococcus group B</em> (<code>B_STRPT_GRB</code>) needs review.</p></li>
<li><p><code>"S. aureus - please mind: MRSA"</code>. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result <em>Staphylococcus aureus</em> (<code>B_STPHY_AUR</code>) needs review.</p></li>
<li><p><code>"D. spartina"</code>. This is the abbreviation of an old taxonomic name: <em>Didymosphaeria spartinae</em> (the last "e" was missing from the input). This fungus was renamed to <em>Leptosphaeria obiones</em>, so a warning will be thrown that this result (<code>F_LPTSP_OBI</code>) needs review.</p></li>
<li><p><code>"Fluoroquinolone-resistant Neisseria gonorrhoeae"</code>. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result <em>Neisseria gonorrhoeae</em> (<code>B_NESSR_GON</code>) needs review.</p></li>
@ -369,8 +370,6 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<span class='fu'>as.mo</span>(<span class='st'>"MRSA"</span>) <span class='co'># Methicillin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VISA"</span>) <span class='co'># Vancomycin Intermediate S. aureus</span>
<span class='fu'>as.mo</span>(<span class='st'>"VRSA"</span>) <span class='co'># Vancomycin Resistant S. aureus</span>
<span class='fu'>as.mo</span>(<span class='fl'>369</span>) <span class='co'># Search on TSN (Taxonomic Serial Number), a unique identifier</span>
<span class='co'># for the Integrated Taxonomic Information System (ITIS)</span>
<span class='fu'>as.mo</span>(<span class='st'>"Streptococcus group A"</span>)
<span class='fu'>as.mo</span>(<span class='st'>"GAS"</span>) <span class='co'># Group A Streptococci</span>
@ -379,8 +378,8 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>) <span class='co'># will remain species: B_STPHY_EPI</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. epidermidis"</span>, <span class='kw'>Becker</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STPHY_CNS</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPTC_PYO</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPTC_GRA</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>) <span class='co'># will remain species: B_STRPT_PYO</span>
<span class='fu'>as.mo</span>(<span class='st'>"S. pyogenes"</span>, <span class='kw'>Lancefield</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># will not remain species: B_STRPT_GRA</span>
<span class='co'># Use mo_* functions to get a specific property based on `mo`</span>
<span class='no'>Ecoli</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='st'>"E. coli"</span>) <span class='co'># returns `B_ESCHR_COL`</span>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

2
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -78,7 +78,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>
@ -349,7 +349,7 @@
</tr><tr>
<td>
<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_subkingdom()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_TSN()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
<p><code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_subkingdom()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_property()</a></code> </p>
</td>
<td><p>Property of a microorganism</p></td>
</tr><tr>
@ -481,7 +481,7 @@
<td>
<p><code><a href="microorganisms.html">microorganisms</a></code> </p>
</td>
<td><p>Data set with ~20,000 microorganisms</p></td>
<td><p>Data set with ~60,000 microorganisms</p></td>
</tr><tr>
<td>
@ -506,12 +506,6 @@
<p><code><a href="microorganisms.old.html">microorganisms.old</a></code> </p>
</td>
<td><p>Data set with previously accepted taxonomic names</p></td>
</tr><tr>
<td>
<p><code><a href="supplementary_data.html">microorganismsDT</a></code> <code><a href="supplementary_data.html">microorganisms.prevDT</a></code> <code><a href="supplementary_data.html">microorganisms.unprevDT</a></code> <code><a href="supplementary_data.html">microorganisms.oldDT</a></code> </p>
</td>
<td><p>Supplementary Data</p></td>
</tr>
</tbody><tbody>
<tr>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9018</span>
</span>
</div>

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@ -6,7 +6,7 @@
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Data set with ~20,000 microorganisms — microorganisms • AMR (for R)</title>
<title>Data set with ~60,000 microorganisms — microorganisms • AMR (for R)</title>
<!-- favicons -->
<link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png">
@ -45,9 +45,9 @@
<link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script>
<meta property="og:title" content="Data set with ~20,000 microorganisms — microorganisms" />
<meta property="og:title" content="Data set with ~60,000 microorganisms — microorganisms" />
<meta property="og:description" content="A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using as.mo." />
<meta property="og:description" content="A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using as.mo." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -80,7 +80,7 @@
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</span>
</div>
@ -230,14 +230,14 @@
<div class="row">
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data set with ~20,000 microorganisms</h1>
<h1>Data set with ~60,000 microorganisms</h1>
<div class="hidden name"><code>microorganisms.Rd</code></div>
</div>
<div class="ref-description">
<p>A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using <code><a href='as.mo.html'>as.mo</a></code>.</p>
<p>A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using <code><a href='as.mo.html'>as.mo</a></code>.</p>
</div>
@ -245,9 +245,9 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 19,456 observations and 15 variables:</p><dl class='dl-horizontal'>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 56,659 observations and 15 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism</p></dd>
<dt><code>tsn</code></dt><dd><p>Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>genus</code></dt><dd><p>Taxonomic genus of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>species</code></dt><dd><p>Taxonomic species of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>subspecies</code></dt><dd><p>Taxonomic subspecies of the microorganism as found in ITIS, see Source</p></dd>
@ -270,14 +270,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Manually added were:</p><ul>
<li><p>605 species of Aspergillus (as Aspergillus misses from ITIS, list from https://en.wikipedia.org/wiki/List_of_Aspergillus_species on 2019-02-05)</p></li>
<li><p>23 species of Trichophyton (as Trichophyton misses from ITIS, list from https://en.wikipedia.org/wiki/Trichophyton on 2019-02-05)</p></li>
<li><p>9 species of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
<li><p>2 species of Straphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>1 species of Candida (C. glabrata)</p></li>
<li><p>9 species of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
<li><p>2 species of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>2 other undefined (unknown Gram negatives and unknown Gram positives)</p></li>
</ul>
<p>These manual entries have no Taxonomic Serial Number (TSN), so can be looked up with <code>filter(microorganisms, is.na(tsn)</code>.</p>
<h2 class="hasAnchor" id="itis"><a class="anchor" href="#itis"></a>ITIS</h2>

12
docs/reference/microorganisms.old.html
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@ -80,7 +80,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
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</span>
</div>
@ -245,11 +245,11 @@
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 2,383 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>tsn</code></dt><dd><p>Old Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>name</code></dt><dd><p>Old taxonomic name of the microorganism as found in ITIS, see Source</p></dd>
<dt><code>tsn_new</code></dt><dd><p>New Taxonomic Serial Number (TSN), as defined by ITIS</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in ITIS, see Source</p></dd>
<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 14,506 observations and 4 variables:</p><dl class='dl-horizontal'>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>tsn_new</code></dt><dd><p>New Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Old taxonomic name of the microorganism as found in the CoL, see Source</p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning publication as found in the CoL, see Source</p></dd>
</dl>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>

7
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@ -80,7 +80,7 @@
</button>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.5.0.9017</span>
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</div>
@ -267,8 +267,6 @@
<span class='fu'>mo_gramstain</span>(<span class='no'>x</span>, <span class='kw'>language</span> <span class='kw'>=</span> <span class='fu'><a href='get_locale.html'>get_locale</a></span>(), <span class='no'>...</span>)
<span class='fu'>mo_TSN</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_ref</span>(<span class='no'>x</span>, <span class='no'>...</span>)
<span class='fu'>mo_authors</span>(<span class='no'>x</span>, <span class='no'>...</span>)
@ -304,7 +302,7 @@
<ul>
<li><p>An <code>integer</code> in case of <code>mo_TSN</code> and <code>mo_year</code></p></li>
<li><p>An <code>integer</code> in case of <code>mo_year</code></p></li>
<li><p>A <code>list</code> in case of <code>mo_taxonomy</code></p></li>
<li><p>A <code>character</code> in all other cases</p></li>
</ul>
@ -362,7 +360,6 @@ On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitla
<span class='fu'>mo_genus</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia"</span>
<span class='fu'>mo_species</span>(<span class='st'>"E. coli"</span>) <span class='co'># "coli"</span>
<span class='fu'>mo_subspecies</span>(<span class='st'>"E. coli"</span>) <span class='co'># NA</span>
<span class='fu'>mo_TSN</span>(<span class='st'>"E. coli"</span>) <span class='co'># 285 (Taxonomic Serial Number)</span>
<span class='co'>## colloquial properties</span>
<span class='fu'>mo_fullname</span>(<span class='st'>"E. coli"</span>) <span class='co'># "Escherichia coli"</span>

2
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@ -80,7 +80,7 @@
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2
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@ -80,7 +80,7 @@
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2
docs/reference/portion.html
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
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2
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@ -80,7 +80,7 @@
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2
docs/reference/resistance_predict.html
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@ -80,7 +80,7 @@
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2
docs/reference/rsi.html
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@ -80,7 +80,7 @@
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2
docs/reference/septic_patients.html
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@ -80,7 +80,7 @@
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2
docs/reference/skewness.html
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@ -81,7 +81,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
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3
docs/sitemap.xml
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@ -126,9 +126,6 @@
<url>
<loc>https://msberends.gitlab.io/AMR/reference/skewness.html</loc>
</url>
<url>
<loc>https://msberends.gitlab.io/AMR/reference/supplementary_data.html</loc>
</url>
<url>
<loc>https://msberends.gitlab.io/AMR/articles/AMR.html</loc>
</url>

11
man/as.mo.Rd
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@ -54,7 +54,8 @@ A microbial ID from this package (class: \code{mo}) typically looks like these e
| | | ----> subspecies, a 3-4 letter acronym
| | ----> species, a 3-4 letter acronym
| ----> genus, a 5-7 letter acronym, mostly without vowels
----> taxonomic kingdom, either B (Bacteria), F (Fungi) or P (Protozoa)
----> taxonomic kingdom: A (Archaea), B (Bacteria), C (Chromista),
F (Fungi), P (Protozoa) or V (Viruses)
}
Use the \code{\link{mo_property}} functions to get properties based on the returned code, see Examples.
@ -88,7 +89,7 @@ When using \code{allow_uncertain = TRUE} (which is the default setting), it will
Examples:
\itemize{
\item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPTC_GRB}) needs review.}
\item{\code{"Streptococcus group B (known as S. agalactiae)"}. The text between brackets will be removed and a warning will be thrown that the result \emph{Streptococcus group B} (\code{B_STRPT_GRB}) needs review.}
\item{\code{"S. aureus - please mind: MRSA"}. The last word will be stripped, after which the function will try to find a match. If it does not, the second last word will be stripped, etc. Again, a warning will be thrown that the result \emph{Staphylococcus aureus} (\code{B_STPHY_AUR}) needs review.}
\item{\code{"D. spartina"}. This is the abbreviation of an old taxonomic name: \emph{Didymosphaeria spartinae} (the last "e" was missing from the input). This fungus was renamed to \emph{Leptosphaeria obiones}, so a warning will be thrown that this result (\code{F_LPTSP_OBI}) needs review.}
\item{\code{"Fluoroquinolone-resistant Neisseria gonorrhoeae"}. The first word will be stripped, after which the function will try to find a match. A warning will be thrown that the result \emph{Neisseria gonorrhoeae} (\code{B_NESSR_GON}) needs review.}
@ -137,8 +138,6 @@ as.mo("Staphylococcus aureus (MRSA)")
as.mo("MRSA") # Methicillin Resistant S. aureus
as.mo("VISA") # Vancomycin Intermediate S. aureus
as.mo("VRSA") # Vancomycin Resistant S. aureus
as.mo(369) # Search on TSN (Taxonomic Serial Number), a unique identifier
# for the Integrated Taxonomic Information System (ITIS)
as.mo("Streptococcus group A")
as.mo("GAS") # Group A Streptococci
@ -147,8 +146,8 @@ as.mo("GBS") # Group B Streptococci
as.mo("S. epidermidis") # will remain species: B_STPHY_EPI
as.mo("S. epidermidis", Becker = TRUE) # will not remain species: B_STPHY_CNS
as.mo("S. pyogenes") # will remain species: B_STRPTC_PYO
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPTC_GRA
as.mo("S. pyogenes") # will remain species: B_STRPT_PYO
as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRA
# Use mo_* functions to get a specific property based on `mo`
Ecoli <- as.mo("E. coli") # returns `B_ESCHR_COL`

17
man/microorganisms.Rd
View File

@ -3,11 +3,11 @@
\docType{data}
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~20,000 microorganisms}
\format{A \code{\link{data.frame}} with 19,456 observations and 15 variables:
\title{Data set with ~60,000 microorganisms}
\format{A \code{\link{data.frame}} with 56,659 observations and 15 variables:
\describe{
\item{\code{mo}}{ID of microorganism}
\item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{col_id}}{Catalogue of Life ID}
\item{\code{genus}}{Taxonomic genus of the microorganism as found in ITIS, see Source}
\item{\code{species}}{Taxonomic species of the microorganism as found in ITIS, see Source}
\item{\code{subspecies}}{Taxonomic subspecies of the microorganism as found in ITIS, see Source}
@ -29,20 +29,15 @@ Integrated Taxonomic Information System (ITIS) public online database, \url{http
microorganisms
}
\description{
A data set containing the complete microbial taxonomy of the kingdoms Bacteria, Fungi and Protozoa from ITIS. MO codes can be looked up using \code{\link{as.mo}}.
A data set containing the microbial taxonomy of six kingdoms from the Catalogue of Life. MO codes can be looked up using \code{\link{as.mo}}.
}
\details{
Manually added were:
\itemize{
\item{605 species of Aspergillus (as Aspergillus misses from ITIS, list from https://en.wikipedia.org/wiki/List_of_Aspergillus_species on 2019-02-05)}
\item{23 species of Trichophyton (as Trichophyton misses from ITIS, list from https://en.wikipedia.org/wiki/Trichophyton on 2019-02-05)}
\item{9 species of Streptococcus (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{2 species of Straphylococcus (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{1 species of Candida (C. glabrata)}
\item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{2 species of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{2 other undefined (unknown Gram negatives and unknown Gram positives)}
}
These manual entries have no Taxonomic Serial Number (TSN), so can be looked up with \code{filter(microorganisms, is.na(tsn)}.
}
\section{ITIS}{

10
man/microorganisms.old.Rd
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@ -4,12 +4,12 @@
\name{microorganisms.old}
\alias{microorganisms.old}
\title{Data set with previously accepted taxonomic names}
\format{A \code{\link{data.frame}} with 2,383 observations and 4 variables:
\format{A \code{\link{data.frame}} with 14,506 observations and 4 variables:
\describe{
\item{\code{tsn}}{Old Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{name}}{Old taxonomic name of the microorganism as found in ITIS, see Source}
\item{\code{tsn_new}}{New Taxonomic Serial Number (TSN), as defined by ITIS}
\item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
\item{\code{col_id}}{Catalogue of Life ID}
\item{\code{tsn_new}}{New Catalogue of Life ID}
\item{\code{fullname}}{Old taxonomic name of the microorganism as found in the CoL, see Source}
\item{\code{ref}}{Author(s) and year of concerning publication as found in the CoL, see Source}
}}
\source{
[3] Integrated Taxonomic Information System (ITIS) on-line database, \url{https://www.itis.gov}.

6
man/mo_property.Rd
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@ -15,7 +15,6 @@
\alias{mo_kingdom}
\alias{mo_type}
\alias{mo_gramstain}
\alias{mo_TSN}
\alias{mo_ref}
\alias{mo_authors}
\alias{mo_year}
@ -48,8 +47,6 @@ mo_type(x, language = get_locale(), ...)
mo_gramstain(x, language = get_locale(), ...)
mo_TSN(x, ...)
mo_ref(x, ...)
mo_authors(x, ...)
@ -71,7 +68,7 @@ mo_property(x, property = "fullname", language = get_locale(), ...)
}
\value{
\itemize{
\item{An \code{integer} in case of \code{mo_TSN} and \code{mo_year}}
\item{An \code{integer} in case of \code{mo_year}}
\item{A \code{list} in case of \code{mo_taxonomy}}
\item{A \code{character} in all other cases}
}
@ -129,7 +126,6 @@ mo_family("E. coli") # "Enterobacteriaceae"
mo_genus("E. coli") # "Escherichia"
mo_species("E. coli") # "coli"
mo_subspecies("E. coli") # NA
mo_TSN("E. coli") # 285 (Taxonomic Serial Number)
## colloquial properties
mo_fullname("E. coli") # "Escherichia coli"

30
man/supplementary_data.Rd
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@ -1,30 +0,0 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/data.R
\docType{data}
\name{supplementary_data}
\alias{supplementary_data}
\alias{microorganismsDT}
\alias{microorganisms.prevDT}
\alias{microorganisms.unprevDT}
\alias{microorganisms.oldDT}
\title{Supplementary Data}
\format{An object of class \code{data.table} (inherits from \code{data.frame}) with 19456 rows and 15 columns.}
\usage{
microorganismsDT
microorganisms.prevDT
microorganisms.unprevDT
microorganisms.oldDT
}
\description{
These \code{\link{data.table}s} are transformed from the \code{\link{microorganisms}} and \code{\link{microorganisms}} data sets to improve speed of \code{\link{as.mo}}. They are meant for internal use only, and are only mentioned here for reference.
}
\section{Read more on our website!}{
\if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
}
\keyword{datasets}

22
tests/testthat/test-first_isolate.R
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@ -22,7 +22,7 @@
context("first_isolate.R")
test_that("first isolates work", {
# septic_patients contains 1317 out of 2000 first isolates
# first isolates
expect_equal(
sum(
first_isolate(tbl = septic_patients,
@ -31,9 +31,9 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1317)
1274)
# septic_patients contains 1413 out of 2000 first *weighted* isolates
# first *weighted* isolates
expect_equal(
suppressWarnings(
sum(
@ -46,7 +46,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
1369)
# should be same for tibbles
expect_equal(
suppressWarnings(
@ -60,8 +60,8 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
# and 1436 when not ignoring I
1369)
# when not ignoring I
expect_equal(
suppressWarnings(
sum(
@ -74,8 +74,8 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1436)
# and 1417 when using points
1392)
# when using points
expect_equal(
suppressWarnings(
sum(
@ -87,9 +87,9 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1417)
1372)
# septic_patients contains 1163 out of 2000 first non-ICU isolates
# first non-ICU isolates
expect_equal(
sum(
first_isolate(septic_patients,
@ -100,7 +100,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1163)
1129)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)

78
tests/testthat/test-mo.R
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@ -41,27 +41,25 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("Klebsiella")), "B_KLBSL")
expect_equal(as.character(as.mo("K. pneu rhino")), "B_KLBSL_PNE_RHI") # K. pneumoniae subspp. rhinoscleromatis
expect_equal(as.character(as.mo("Bartonella")), "B_BRTNL")
expect_equal(as.character(as.mo("C. difficile")), "B_CTRDM_DIF")
expect_equal(as.character(as.mo("C. difficile")), "B_CLSTR_DIF")
expect_equal(as.character(as.mo("L. pneumophila")), "B_LGNLL_PNE")
expect_equal(as.character(as.mo("Strepto")), "B_STRPTC")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPTC") # not Peptostreptoccus
expect_equal(as.character(as.mo("Strepto")), "B_STRPT")
expect_equal(as.character(as.mo("Streptococcus")), "B_STRPT") # not Peptostreptoccus
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPTC_GRA", "B_STRPTC_GRB"))
expect_equal(as.character(as.mo(c("GAS", "GBS"))), c("B_STRPT_GRA", "B_STRPT_GRB"))
expect_equal(as.character(as.mo("S. pyo")), "B_STRPTC_PYO") # not Actinomyces pyogenes
expect_equal(as.character(as.mo("P. aer")), "B_PDMNS_AER") # not Pasteurella aerogenes
expect_equal(as.character(as.mo("S. pyo")), "B_STRPT_PYO") # not Actinomyces pyogenes
# GLIMS
expect_equal(as.character(as.mo("bctfgr")), "B_BCTRD_FRA")
expect_equal(as.character(as.mo("MRSE")), "B_STPHY_EPI")
expect_equal(as.character(as.mo("VRE")), "B_ENTRC")
expect_equal(as.character(as.mo("MRPA")), "B_PDMNS_AER")
expect_equal(as.character(as.mo("PISP")), "B_STRPTC_PNE")
expect_equal(as.character(as.mo("PRSP")), "B_STRPTC_PNE")
expect_equal(as.character(as.mo("VISP")), "B_STRPTC_PNE")
expect_equal(as.character(as.mo("VRSP")), "B_STRPTC_PNE")
expect_equal(as.character(as.mo("MRPA")), "B_PSDMN_AER")
expect_equal(as.character(as.mo("PISP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("PRSP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("VISP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("VRSP")), "B_STRPT_PNE")
expect_equal(as.character(as.mo("CNS")), "B_STPHY_CNS")
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CNS")
@ -85,13 +83,11 @@ test_that("as.mo works", {
# unprevalent MO
expect_identical(
as.character(
as.mo(c("buno",
"BUNO",
"burnod",
as.mo(c("burnod",
"B. nodosa",
"B nodosa",
"Burkholderia nodosa"))),
rep("B_BRKHL_NOD", 6))
rep("B_BRKHL_NOD", 4))
# empty values
expect_identical(as.character(as.mo(c("", NA, NaN))), rep(NA_character_, 3))
@ -105,7 +101,7 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo("S. epidermidis", Becker = FALSE)), "B_STPHY_EPI")
expect_identical(as.character(as.mo("S. epidermidis", Becker = TRUE)), "B_STPHY_CNS")
expect_identical(as.character(as.mo("STAEPI", Becker = TRUE)), "B_STPHY_CNS")
expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STRPTC_INT") # Strep (!) intermedius
expect_identical(as.character(as.mo("S. intermedius", Becker = FALSE)), "B_STPHY_INT")
expect_identical(as.character(as.mo("Sta intermedius",Becker = FALSE)), "B_STPHY_INT")
expect_identical(as.character(as.mo("Sta intermedius",Becker = TRUE)), "B_STPHY_CPS")
expect_identical(as.character(as.mo("STAINT", Becker = TRUE)), "B_STPHY_CPS")
@ -115,23 +111,23 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo("STAAUR", Becker = "all")), "B_STPHY_CPS")
# check for Lancefield classification
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPTC_PYO")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPTC_GRA")
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPTC_GRA") # group A
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPTC_AGA")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPTC_GRB") # group B
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPTC_DYS_EQU")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPTC_GRC") # group C
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = FALSE)), "B_STRPT_PYO")
expect_identical(as.character(as.mo("S. pyogenes", Lancefield = TRUE)), "B_STRPT_GRA")
expect_identical(as.character(as.mo("STCPYO", Lancefield = TRUE)), "B_STRPT_GRA") # group A
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = FALSE)), "B_STRPT_AGA")
expect_identical(as.character(as.mo("S. agalactiae", Lancefield = TRUE)), "B_STRPT_GRB") # group B
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = FALSE)), "B_STRPT_DYS_EQU")
expect_identical(as.character(as.mo("S. equisimilis", Lancefield = TRUE)), "B_STRPT_GRC") # group C
# Enterococci must only be influenced if Lancefield = "all"
expect_identical(as.character(as.mo("E. faecium", Lancefield = FALSE)), "B_ENTRC_IUM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = TRUE)), "B_ENTRC_IUM")
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPTC_GRD") # group D
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPTC_ANG")
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPTC_GRF") # group F
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPTC_SAN")
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPTC_GRH") # group H
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPTC_SAL")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPTC_GRK") # group K
expect_identical(as.character(as.mo("E. faecium", Lancefield = "all")), "B_STRPT_GRD") # group D
expect_identical(as.character(as.mo("S. anginosus", Lancefield = FALSE)), "B_STRPT_ANG")
expect_identical(as.character(as.mo("S. anginosus", Lancefield = TRUE)), "B_STRPT_GRF") # group F
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = FALSE)), "B_STRPT_SAN")
expect_identical(as.character(as.mo("S. sanguinis", Lancefield = TRUE)), "B_STRPT_GRH") # group H
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SAL")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRK") # group K
library(dplyr)
@ -164,10 +160,6 @@ test_that("as.mo works", {
# print
expect_output(print(as.mo(c("B_ESCHR_COL", NA))))
# helper function
expect_identical(as.mo("B_ESCHR_COL"),
as.mo("B_ESCHR_COL"))
# test pull
expect_equal(nrow(septic_patients %>% mutate(mo = as.mo(mo))),
2000)
@ -192,11 +184,11 @@ test_that("as.mo works", {
# check old names
expect_equal(suppressMessages(as.character(as.mo("Escherichia blattae"))), "B_SHMWL_BLA")
# - Didymosphaeria spartinae (unprevalent)
expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE)))
# - was renamed to Leptosphaeria obiones
expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))),
"F_LPTSP_OBI")
# # - Didymosphaeria spartinae (unprevalent)
# expect_warning(suppressMessages(as.mo("D spartin", allow_uncertain = TRUE)))
# # - was renamed to Leptosphaeria obiones
# expect_equal(suppressWarnings(suppressMessages(as.character(as.mo("D spartin", allow_uncertain = TRUE)))),
# "F_LPTSP_OBI")
# check uncertain names
expect_equal(suppressWarnings(as.character(as.mo("esco extra_text", allow_uncertain = FALSE))), NA_character_)
@ -217,10 +209,6 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo(c("B_ESCHR_COL", "ESCCOL"))),
c("B_ESCHR_COL", "B_ESCHR_COL"))
# TSN of prevalent and non prevalent ones
expect_equal(mo_TSN(c("Gomphosphaeria aponina delicatula", "Escherichia coli")),
c(717, 285))
# expect_equal(mo_fullname(c("E. spp.",
# "E. spp",
# "E. species")),
@ -236,7 +224,7 @@ test_that("as.mo works", {
c("Microbacterium paraoxidans",
"Streptococcus suis (bovis gr)",
"Raoultella (here some text) terrigena")))),
c("B_MCRBC", "B_STRPTC_SUI", "B_RLTLL_TER"))
c("B_MCRBC", "B_STRPT_SUI", "B_RLTLL_TER"))
# Salmonella (City) are all actually Salmonella enterica spp (City)
expect_equal(as.character(suppressMessages(as.mo("Salmonella Goettingen"))),

14
tests/testthat/test-mo_property.R
View File

@ -23,31 +23,29 @@ context("mo_property.R")
test_that("mo_property works", {
expect_equal(mo_kingdom("E. coli"), "Bacteria")
expect_equal(mo_subkingdom("E. coli"), "Negibacteria")
expect_equal(mo_phylum("E. coli"), "Proteobacteria")
expect_equal(mo_class("E. coli"), "Gammaproteobacteria")
expect_equal(mo_order("E. coli"), "Enterobacteriales")
expect_equal(mo_family("E. coli"), "Enterobacteriaceae")
expect_equal(mo_genus("E. coli"), "Escherichia")
expect_equal(mo_species("E. coli"), "coli")
expect_equal(mo_subspecies("E. coli"), NA_character_)
expect_equal(mo_subspecies("E. coli"), "")
expect_equal(mo_fullname("E. coli"), "Escherichia coli")
expect_equal(mo_type("E. coli", language = "en"), "Bacteria")
expect_equal(mo_gramstain("E. coli", language = "en"), "Gram negative")
expect_equal(mo_TSN("E. coli"), 285)
expect_equal(class(mo_taxonomy("E. coli")), "list")
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "subkingdom", "phylum", "class", "order",
expect_equal(names(mo_taxonomy("E. coli")), c("kingdom", "phylum", "class", "order",
"family", "genus", "species", "subspecies"))
expect_equal(mo_ref("E. coli"), "Castellani and Chalmers, 1919")
expect_equal(mo_authors("E. coli"), "Castellani and Chalmers")
expect_equal(mo_ref("E. coli"), "(Migula, 1895) Castellani and Chalmers, 1919")
expect_equal(mo_authors("E. coli"), "(Migula) Castellani and Chalmers")
expect_equal(mo_year("E. coli"), 1919)
expect_equal(mo_shortname("MRSA"), "S. aureus")
expect_equal(mo_shortname("MRSA", Becker = TRUE), "S. aureus")
expect_equal(mo_shortname("MRSA", Becker = "all", language = "en"), "CoPS")
expect_equal(mo_shortname("S. aga"), "S. agalactiae")
expect_equal(mo_shortname("S. aga", Lancefield = TRUE), "GBS")
expect_equal(mo_shortname("S. agalac"), "S. agalactiae")
expect_equal(mo_shortname("S. agalac", Lancefield = TRUE), "GBS")
# test integrity
MOs <- AMR::microorganisms