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(v0.7.1.9055) algorithm improvements

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dr. M.S. (Matthijs) Berends 2019-08-13 16:15:08 +02:00
parent 6c4822164c
commit 7108454ba5
77 changed files with 644 additions and 582 deletions
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8
DESCRIPTION
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@ -1,18 +1,18 @@
Package: AMR
Version: 0.7.1.9038
Date: 2019-08-12
Version: 0.7.1.9055
Date: 2019-08-13
Title: Antimicrobial Resistance Analysis
Authors@R: c(
person(role = c("aut", "cre"),
family = "Berends", given = c("Matthijs", "S."), email = "m.s.berends@umcg.nl", comment = c(ORCID = "0000-0001-7620-1800")),
person(role = "aut",
family = "Luz", given = c("Christian", "F."), email = "c.f.luz@umcg.nl", comment = c(ORCID = "0000-0001-5809-5995")),
person(role = c("aut", "ths"),
family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")),
person(role = c("aut", "ths"),
family = "Friedrich", given = c("Alex", "W."), email = "alex.friedrich@umcg.nl", comment = c(ORCID = "0000-0003-4881-038X")),
person(role = c("aut", "ths"),
family = "Sinha", given = c("Bhanu", "N.", "M."), email = "b.sinha@umcg.nl", comment = c(ORCID = "0000-0003-1634-0010")),
person(role = c("aut", "ths"),
family = "Glasner", given = "Corinna", email = "c.glasner@umcg.nl", comment = c(ORCID = "0000-0003-1241-1328")),
person(role = "ctb",
family = "Hassing", given = c("Erwin", "E.", "A."), email = "e.hassing@certe.nl"),
person(role = "ctb",

13
NEWS.md
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@ -1,4 +1,4 @@
# AMR 0.7.1.9038
# AMR 0.7.1.9055
### Breaking
* Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too.
@ -57,12 +57,13 @@
* Removed class `atc` - using `as.atc()` is now deprecated in favour of `ab_atc()` and this will return a character, not the `atc` class anymore
* Removed deprecated functions `abname()`, `ab_official()`, `atc_name()`, `atc_official()`, `atc_property()`, `atc_tradenames()`, `atc_trivial_nl()`
* Fix and speed improvement for `mo_shortname()`
* Algorithm improvements for `as.mo()`:
* Some misspelled input were not understood
* Algorithm improvements for `as.mo()` (by which some additions were made to the `microorganisms` data set:
* Big improvement for misspelled input
* These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus
* Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology
* Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)
* Added support for 5,000 new fungi
* Added support for unknown yeasts and fungi
* Updated the `microorganisms` data set to contain the latest taxonomic data from the IJSEM journal (now up to date until August 2019)
* Added almost 5,000 new fungi to the `microorganisms` data set
* Fix for using `mo_*` functions where the coercion uncertainties and failures would not be available through `mo_uncertainties()` and `mo_failures()` anymore
* Deprecated the `country` parameter of `mdro()` in favour of the already existing `guideline` parameter to support multiple guidelines within one country
* The `name` of `RIF` is now Rifampicin instead of Rifampin
@ -144,7 +145,7 @@
#### Changed
* Fixed a critical bug in `first_isolate()` where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.
* Fixedd a bug in `eucast_rules()` where antibiotics from WHONET software would not be recognised
* Fixed a bug in `eucast_rules()` where antibiotics from WHONET software would not be recognised
* Completely reworked the `antibiotics` data set:
* All entries now have 3 different identifiers:
* Column `ab` contains a human readable EARS-Net code, used by ECDC and WHO/WHONET - this is the primary identifier used in this package

6
R/catalogue_of_life.R
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@ -24,9 +24,9 @@
#' This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life.
#' @section Catalogue of Life:
#' \if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
#' This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
#' This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
#'
#' \link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
#' \link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
#' @section Included taxa:
#' Included are:
#' \itemize{
@ -38,7 +38,7 @@
#' \item{The responsible author(s) and year of scientific publication}
#' }
#'
#' The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
#' The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
#'
#' The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
#' @inheritSection AMR Read more on our website!

8
R/data.R
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@ -55,7 +55,7 @@
#'
#' 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 catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 69,854 observations and 16 variables:
#' @format A \code{\link{data.frame}} with 69,855 observations and 16 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism as used by this package}
#' \item{\code{col_id}}{Catalogue of Life ID}
@ -64,14 +64,14 @@
#' \item{\code{rank}}{Text of the taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}}
#' \item{\code{ref}}{Author(s) and year of concerning scientific publication}
#' \item{\code{species_id}}{ID of the species as used by the Catalogue of Life}
#' \item{\code{source}}{Either \code{"CoL"}, \code{"DSMZ"} (see source) or "manually added"}
#' \item{\code{source}}{Either "CoL", "DSMZ" (see Source) or "manually added"}
#' \item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
#' }
#' @details Manually added were:
#' \itemize{
#' \item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
#' \item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
#' \item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
#' \item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
#' \item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
#' \item{8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
#' }

108
R/mo.R
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@ -29,7 +29,7 @@
#' @param Lancefield a logical to indicate whether beta-haemolytic \emph{Streptococci} should be categorised into Lancefield groups instead of their own species, according to Rebecca C. Lancefield [3]. These \emph{Streptococci} will be categorised in their first group, e.g. \emph{Streptococcus dysgalactiae} will be group C, although officially it was also categorised into groups G and L.
#'
#' This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.
#' @param allow_uncertain a logical (\code{TRUE} or \code{FALSE}) or a value between 0 and 3 to indicate whether the input should be checked for less possible results, see Details
#' @param allow_uncertain a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less possible results, see Details
#' @param reference_df a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).
#' @param ... other parameters passed on to functions
#' @rdname as.mo
@ -50,8 +50,7 @@
#' | | ----> species, a 3-4 letter acronym
#' | ----> genus, a 5-7 letter acronym, mostly without vowels
#' ----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
#' C (Chromista), F (Fungi), P (Protozoa) or
#' PL (Plantae)
#' C (Chromista), F (Fungi), P (Protozoa)
#' }
#'
#' Values that cannot be coered will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
@ -60,13 +59,14 @@
#'
#' The algorithm uses data from the Catalogue of Life (see below) and from one other source (see \code{?microorganisms}).
#'
# /// THIS PART WAS DELETED FROM THE MAN PAGE
# \strong{Self-learning algoritm} \cr
# The \code{as.mo()} function gains experience from previously determined microbial IDs and learns from it. This drastically improves both speed and reliability. Use \code{clean_mo_history()} to reset the algorithms. Only experience from your current \code{AMR} package version is used. This is done because in the future the taxonomic tree (which is included in this package) may change for any organism and it consequently has to rebuild its knowledge.
#
# Usually, any guess after the first try runs 80-95\% faster than the first try.
#
# For now, learning only works per session. If R is closed or terminated, the algorithms reset. This will probably be resolved in a next version.
#
# ////
#' \strong{Intelligent rules} \cr
#' This function uses intelligent rules to help getting fast and logical results. It tries to find matches in this order:
#' \itemize{
@ -169,7 +169,8 @@
#'
#' # All mo_* functions use as.mo() internally too (see ?mo_property):
#' mo_genus("E. coli") # returns "Escherichia"
#' mo_gramstain("E. coli") # returns "Gram negative"#'
#' mo_gramstain("E. coli") # returns "Gram negative"
#'
#' }
#' \dontrun{
#' df$mo <- as.mo(df$microorganism_name)
@ -478,6 +479,7 @@ exec_as.mo <- function(x,
x_species <- paste(x, "species")
# translate to English for supported languages of mo_property
x <- gsub("(gruppe|groep|grupo|gruppo|groupe)", "group", x, ignore.case = TRUE)
x <- gsub("(vergroen)[a-z]*", "viridans", x, ignore.case = TRUE)
x <- gsub("(hefe|gist|gisten|levadura|lievito|fermento|levure)[a-z]*", "yeast", x, ignore.case = TRUE)
x <- gsub("(schimmels?|mofo|molde|stampo|moisissure|fungi)[a-z]*", "fungus", x, ignore.case = TRUE)
x <- gsub("Fungus[ph|f]rya", "Fungiphrya", x, ignore.case = TRUE)
@ -491,13 +493,13 @@ exec_as.mo <- function(x,
x <- gsub("(alpha|beta|gamma).?ha?emoly", "\\1-haemoly", x)
# remove genus as first word
x <- gsub("^Genus ", "", x)
# allow characters that resemble others ----
# allow characters that resemble others = dyslexia_mode ----
if (dyslexia_mode == TRUE) {
x <- tolower(x)
x <- gsub("[iy]+", "[iy]+", x)
x <- gsub("(c|k|q|qu|s|z|x|ks)+", "(c|k|q|qu|s|z|x|ks)+", x)
x <- gsub("(ph|f|v)+", "(ph|f|v)+", x)
x <- gsub("(th|t)+", "(th|t)+", x)
x <- gsub("(ph|hp|f|v)+", "(ph|hp|f|v)+", x)
x <- gsub("(th|ht|t)+", "(th|ht|t)+", x)
x <- gsub("a+", "a+", x)
x <- gsub("u+", "u+", x)
# allow any ending of -um, -us, -ium, -icum, -ius, -icus, -ica and -a (needs perl for the negative backward lookup):
@ -512,6 +514,10 @@ exec_as.mo <- function(x,
x <- gsub("(.)\\1+", "\\1+", x)
# allow ending in -en or -us
x <- gsub("e\\+n(?![a-z[])", "(e+n|u+(c|k|q|qu|s|z|x|ks)+)", x, ignore.case = TRUE, perl = TRUE)
# if the input is longer than 10 characters, add a [.] between all characters, as some might have forgotten a character
# this will allow "Pasteurella damatis" to be correctly read as "Pasteurella dagmatis".
x[nchar(x_backup_without_spp) > 10] <- gsub("([a-z])([a-z])", "\\1.*\\2", x[nchar(x_backup_without_spp) > 10], ignore.case = TRUE)
x[nchar(x_backup_without_spp) > 10] <- gsub("[+]", "+.*", x[nchar(x_backup_without_spp) > 10])
}
x <- strip_whitespace(x)
@ -764,6 +770,27 @@ exec_as.mo <- function(x,
}
next
}
# streptococcal groups: milleri and viridans
if (x_trimmed[i] %like% 'strepto.* milleri'
| x_backup_without_spp[i] %like% 'strepto.* milleri'
| x_backup_without_spp[i] %like% 'mgs[^a-z]?$') {
# Milleri Group Streptococcus (MGS)
x[i] <- microorganismsDT[mo == 'B_STRPT_MIL', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
next
}
if (x_trimmed[i] %like% 'strepto.* viridans'
| x_backup_without_spp[i] %like% 'strepto.* viridans'
| x_backup_without_spp[i] %like% 'vgs[^a-z]?$') {
# Viridans Group Streptococcus (VGS)
x[i] <- microorganismsDT[mo == 'B_STRPT_VIR', ..property][[1]][1L]
if (initial_search == TRUE) {
set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history)
}
next
}
if (x_backup_without_spp[i] %like% 'gram[ -]?neg.*'
| x_backup_without_spp[i] %like% 'negatie?[vf]'
| x_trimmed[i] %like% 'gram[ -]?neg.*') {
@ -1048,6 +1075,7 @@ exec_as.mo <- function(x,
return(NA_character_)
}
# UNCERTAINTY LEVEL 1 ----
if (uncertainty_level >= 1) {
now_checks_for_uncertainty_level <- 1
@ -1114,6 +1142,7 @@ exec_as.mo <- function(x,
}
}
# UNCERTAINTY LEVEL 2 ----
if (uncertainty_level >= 2) {
now_checks_for_uncertainty_level <- 2
@ -1172,9 +1201,37 @@ exec_as.mo <- function(x,
return(found[1L])
}
# (5a) try to strip off half an element from end and check the remains ----
# (5) inverse input ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (5a) try to strip off half an element from end and check the remains\n")
cat("\n[UNCERTAINLY LEVEL 2] (5) inverse input\n")
}
a.x_backup_inversed <- paste(rev(unlist(strsplit(a.x_backup, split = " "))), collapse = " ")
if (isTRUE(debug)) {
message("Running '", a.x_backup_inversed, "'")
}
# first try without dyslexia mode
found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_inversed, initial_search = FALSE, dyslexia_mode = FALSE, allow_uncertain = FALSE, debug = debug)))
if (empty_result(found)) {
# then with dyslexia mode
found <- suppressMessages(suppressWarnings(exec_as.mo(a.x_backup_inversed, initial_search = FALSE, dyslexia_mode = TRUE, allow_uncertain = FALSE, debug = debug)))
}
if (!empty_result(found) & nchar(g.x_backup_without_spp) >= 6) {
found_result <- found
found <- microorganismsDT[mo == found, ..property][[1]]
uncertainties <<- rbind(uncertainties,
data.frame(uncertainty = now_checks_for_uncertainty_level,
input = a.x_backup,
fullname = microorganismsDT[mo == found_result[1L], fullname][[1]],
mo = found_result[1L]))
if (initial_search == TRUE) {
set_mo_history(a.x_backup, get_mo_code(found[1L], property), 2, force = force_mo_history)
}
return(found[1L])
}
# (6) try to strip off half an element from end and check the remains ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (6) try to strip off half an element from end and check the remains\n")
}
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1) {
@ -1209,9 +1266,9 @@ exec_as.mo <- function(x,
}
}
}
# (5b) try to strip off one element from end and check the remains ----
# (7) try to strip off one element from end and check the remains ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (5b) try to strip off one element from end and check the remains\n")
cat("\n[UNCERTAINLY LEVEL 2] (7) try to strip off one element from end and check the remains\n")
}
if (length(x_strip) > 1) {
for (i in 1:(length(x_strip) - 1)) {
@ -1242,9 +1299,9 @@ exec_as.mo <- function(x,
}
}
}
# (5c) check for unknown yeasts/fungi ----
# (8) check for unknown yeasts/fungi ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (5b) check for unknown yeasts/fungi\n")
cat("\n[UNCERTAINLY LEVEL 2] (8) check for unknown yeasts/fungi\n")
}
if (b.x_trimmed %like% "yeast") {
found <- "F_YEAST"
@ -1274,9 +1331,9 @@ exec_as.mo <- function(x,
}
return(found[1L])
}
# (6) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
# (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome) ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 2] (6) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n")
cat("\n[UNCERTAINLY LEVEL 2] (9) try to strip off one element from start and check the remains (only allow >= 2-part name outcome)\n")
}
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
@ -1311,12 +1368,13 @@ exec_as.mo <- function(x,
}
}
# UNCERTAINTY LEVEL 3 ----
if (uncertainty_level >= 3) {
now_checks_for_uncertainty_level <- 3
# (7a) try to strip off one element from start and check the remains (any text size) ----
# (10) try to strip off one element from start and check the remains (any text size) ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 3] (7a) try to strip off one element from start and check the remains (any text size)\n")
cat("\n[UNCERTAINLY LEVEL 3] (10) try to strip off one element from start and check the remains (any text size)\n")
}
x_strip <- a.x_backup %>% strsplit(" ") %>% unlist()
if (length(x_strip) > 1 & nchar(g.x_backup_without_spp) >= 6) {
@ -1346,10 +1404,10 @@ exec_as.mo <- function(x,
}
}
}
# (7b) try to strip off one element from end and check the remains (any text size) ----
# (this is in fact 5b but without nchar limit of >=6)
# (11) try to strip off one element from end and check the remains (any text size) ----
# (this is in fact 7 but without nchar limit of >=6)
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 3] (7b) try to strip off one element from end and check the remains (any text size)\n")
cat("\n[UNCERTAINLY LEVEL 3] (11) try to strip off one element from end and check the remains (any text size)\n")
}
if (length(x_strip) > 1) {
for (i in 1:(length(x_strip) - 1)) {
@ -1379,9 +1437,9 @@ exec_as.mo <- function(x,
}
}
# (8) part of a name (very unlikely match) ----
# (12) part of a name (very unlikely match) ----
if (isTRUE(debug)) {
cat("\n[UNCERTAINLY LEVEL 3] (8) part of a name (very unlikely match)\n")
cat("\n[UNCERTAINLY LEVEL 3] (12) part of a name (very unlikely match)\n")
}
if (isTRUE(debug)) {
message("Running '", f.x_withspaces_end_only, "'")
@ -1775,9 +1833,11 @@ translate_allow_uncertain <- function(allow_uncertain) {
# default to uncertainty level 2
allow_uncertain <- 2
} else {
allow_uncertain[tolower(allow_uncertain) == "none"] <- 0
allow_uncertain[tolower(allow_uncertain) == "all"] <- 3
allow_uncertain <- as.integer(allow_uncertain)
if (!allow_uncertain %in% c(0:3)) {
stop("`allow_uncertain` must be a number between 0 (none) and 3 (all), or TRUE (= 2) or FALSE (= 0).", call. = FALSE)
stop('`allow_uncertain` must be a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0).', call. = FALSE)
}
}
allow_uncertain

25
data-raw/reproduction_of_microorganisms.R
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@ -302,6 +302,9 @@ MOs <- MOs %>%
# put `mo` in front, followed by the rest
select(mo, everything(), -abbr_other, -abbr_genus, -abbr_species, -abbr_subspecies)
# remove empty fullnames
MOs <- MOs %>% filter(fullname != "")
# add non-taxonomic entries
MOs <- MOs %>%
bind_rows(
@ -483,6 +486,26 @@ MOs <- MOs %>%
ref = NA_character_,
species_id = "",
source = "manually added"),
# Viridans Streptococci
MOs %>%
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
mutate(mo = gsub("AGA", "VIR", mo),
col_id = NA_integer_,
species = "viridans" ,
fullname = "Viridans Group Streptococcus (VGS)",
ref = NA_character_,
species_id = "",
source = "manually added"),
# Milleri Streptococci
MOs %>%
filter(genus == "Streptococcus", species == "agalactiae") %>% .[1,] %>%
mutate(mo = gsub("AGA", "MIL", mo),
col_id = NA_integer_,
species = "milleri" ,
fullname = "Milleri Group Streptococcus (MGS)",
ref = NA_character_,
species_id = "",
source = "manually added"),
# Trichomonas vaginalis is missing, same order as Dientamoeba
MOs %>%
filter(fullname == "Dientamoeba") %>%
@ -575,7 +598,7 @@ MOs <- MOs %>%
))
# arrange
MOs <- MOs %>% arrange(fullname)
MOs <- MOs %>% arrange(genus, species, subspecies)
MOs.old <- MOs.old %>% arrange(fullname)
# transform

BIN
data/microorganisms.rda
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4
docs/LICENSE-text.html
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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="Latest development version">0.7.1.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -513,7 +513,7 @@ END OF TERMS AND CONDITIONS
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<div class="pkgdown">

520
docs/articles/AMR.html
View File

@ -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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -185,7 +185,7 @@
<h1>How to conduct AMR analysis</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 August 2019</h4>
<h4 class="date">13 August 2019</h4>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -194,7 +194,7 @@
<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/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 08 August 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/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 13 August 2019.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor"></a>Introduction</h1>
@ -210,21 +210,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2019-08-08</td>
<td align="center">2019-08-13</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">2019-08-08</td>
<td align="center">2019-08-13</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">2019-08-08</td>
<td align="center">2019-08-13</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -320,9 +320,9 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-01-03</td>
<td align="center">T3</td>
<td align="center">Hospital D</td>
<td align="center">2012-12-02</td>
<td align="center">V1</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">I</td>
@ -331,42 +331,20 @@
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-11-05</td>
<td align="center">F9</td>
<td align="center">2014-02-14</td>
<td align="center">E4</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2011-12-06</td>
<td align="center">I5</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</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>
</tr>
<tr class="even">
<td align="center">2011-03-10</td>
<td align="center">B9</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-06-27</td>
<td align="center">A2</td>
<td align="center">Hospital D</td>
<td align="center">2011-11-09</td>
<td align="center">E3</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
@ -375,15 +353,37 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-12-11</td>
<td align="center">F8</td>
<td align="center">Hospital A</td>
<td align="center">2011-11-19</td>
<td align="center">S8</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">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-07-28</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-03-04</td>
<td align="center">T4</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</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>
</tbody>
</table>
@ -406,8 +406,8 @@
#
# Item Count Percent Cum. Count Cum. Percent
# --- ----- ------- -------- ----------- -------------
# 1 M 10,468 52.3% 10,468 52.3%
# 2 F 9,532 47.7% 20,000 100.0%</code></pre>
# 1 M 10,486 52.4% 10,486 52.4%
# 2 F 9,514 47.6% 20,000 100.0%</code></pre>
<p>So, we can draw at least two conclusions immediately. From a data scientists perspective, the data looks clean: only values <code>M</code> and <code>F</code>. From a researchers 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="cb13"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb13-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span></a>
@ -423,53 +423,53 @@
<a class="sourceLine" id="cb15-4" data-line-number="4"><span class="co"># http://eucast.org/</span></a>
<a class="sourceLine" id="cb15-5" data-line-number="5"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-6" data-line-number="6"><span class="co"># EUCAST Clinical Breakpoints (v9.0, 2019)</span></a>
<a class="sourceLine" id="cb15-7" data-line-number="7"><span class="co"># Aerococcus sanguinicola (no values changed)</span></a>
<a class="sourceLine" id="cb15-8" data-line-number="8"><span class="co"># Aerococcus urinae (no values changed)</span></a>
<a class="sourceLine" id="cb15-9" data-line-number="9"><span class="co"># Anaerobic Gram-negatives (no values changed)</span></a>
<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="co"># Anaerobic Gram-positives (no values changed)</span></a>
<a class="sourceLine" id="cb15-11" data-line-number="11"><span class="co"># Campylobacter coli (no values changed)</span></a>
<a class="sourceLine" id="cb15-12" data-line-number="12"><span class="co"># Campylobacter jejuni (no values changed)</span></a>
<a class="sourceLine" id="cb15-13" data-line-number="13"><span class="co"># Enterobacteriales (Order) (no values changed)</span></a>
<a class="sourceLine" id="cb15-14" data-line-number="14"><span class="co"># Enterococcus (no values changed)</span></a>
<a class="sourceLine" id="cb15-15" data-line-number="15"><span class="co"># Haemophilus influenzae (no values changed)</span></a>
<a class="sourceLine" id="cb15-16" data-line-number="16"><span class="co"># Kingella kingae (no values changed)</span></a>
<a class="sourceLine" id="cb15-17" data-line-number="17"><span class="co"># Moraxella catarrhalis (no values changed)</span></a>
<a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no values changed)</span></a>
<a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no values changed)</span></a>
<a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no values changed)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,480 values changed)</span></a>
<a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no values changed)</span></a>
<a class="sourceLine" id="cb15-7" data-line-number="7"><span class="co"># Aerococcus sanguinicola (no changes)</span></a>
<a class="sourceLine" id="cb15-8" data-line-number="8"><span class="co"># Aerococcus urinae (no changes)</span></a>
<a class="sourceLine" id="cb15-9" data-line-number="9"><span class="co"># Anaerobic Gram-negatives (no changes)</span></a>
<a class="sourceLine" id="cb15-10" data-line-number="10"><span class="co"># Anaerobic Gram-positives (no changes)</span></a>
<a class="sourceLine" id="cb15-11" data-line-number="11"><span class="co"># Campylobacter coli (no changes)</span></a>
<a class="sourceLine" id="cb15-12" data-line-number="12"><span class="co"># Campylobacter jejuni (no changes)</span></a>
<a class="sourceLine" id="cb15-13" data-line-number="13"><span class="co"># Enterobacteriales (Order) (no changes)</span></a>
<a class="sourceLine" id="cb15-14" data-line-number="14"><span class="co"># Enterococcus (no changes)</span></a>
<a class="sourceLine" id="cb15-15" data-line-number="15"><span class="co"># Haemophilus influenzae (no changes)</span></a>
<a class="sourceLine" id="cb15-16" data-line-number="16"><span class="co"># Kingella kingae (no changes)</span></a>
<a class="sourceLine" id="cb15-17" data-line-number="17"><span class="co"># Moraxella catarrhalis (no changes)</span></a>
<a class="sourceLine" id="cb15-18" data-line-number="18"><span class="co"># Pasteurella multocida (no changes)</span></a>
<a class="sourceLine" id="cb15-19" data-line-number="19"><span class="co"># Staphylococcus (no changes)</span></a>
<a class="sourceLine" id="cb15-20" data-line-number="20"><span class="co"># Streptococcus groups A, B, C, G (no changes)</span></a>
<a class="sourceLine" id="cb15-21" data-line-number="21"><span class="co"># Streptococcus pneumoniae (1,452 values changed)</span></a>
<a class="sourceLine" id="cb15-22" data-line-number="22"><span class="co"># Viridans group streptococci (no changes)</span></a>
<a class="sourceLine" id="cb15-23" data-line-number="23"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-24" data-line-number="24"><span class="co"># EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes (v3.1, 2016)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,293 values changed)</span></a>
<a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no values changed)</span></a>
<a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no values changed)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,772 values changed)</span></a>
<a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no values changed)</span></a>
<a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no values changed)</span></a>
<a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no values changed)</span></a>
<a class="sourceLine" id="cb15-32" data-line-number="32"><span class="co"># Table 12: Interpretive rules for aminoglycosides (no values changed)</span></a>
<a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no values changed)</span></a>
<a class="sourceLine" id="cb15-25" data-line-number="25"><span class="co"># Table 01: Intrinsic resistance in Enterobacteriaceae (1,313 values changed)</span></a>
<a class="sourceLine" id="cb15-26" data-line-number="26"><span class="co"># Table 02: Intrinsic resistance in non-fermentative Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb15-27" data-line-number="27"><span class="co"># Table 03: Intrinsic resistance in other Gram-negative bacteria (no changes)</span></a>
<a class="sourceLine" id="cb15-28" data-line-number="28"><span class="co"># Table 04: Intrinsic resistance in Gram-positive bacteria (2,715 values changed)</span></a>
<a class="sourceLine" id="cb15-29" data-line-number="29"><span class="co"># Table 08: Interpretive rules for B-lactam agents and Gram-positive cocci (no changes)</span></a>
<a class="sourceLine" id="cb15-30" data-line-number="30"><span class="co"># Table 09: Interpretive rules for B-lactam agents and Gram-negative rods (no changes)</span></a>
<a class="sourceLine" id="cb15-31" data-line-number="31"><span class="co"># Table 11: Interpretive rules for macrolides, lincosamides, and streptogramins (no changes)</span></a>
<a class="sourceLine" id="cb15-32" data-line-number="32"><span class="co"># Table 12: Interpretive rules for aminoglycosides (no changes)</span></a>
<a class="sourceLine" id="cb15-33" data-line-number="33"><span class="co"># Table 13: Interpretive rules for quinolones (no changes)</span></a>
<a class="sourceLine" id="cb15-34" data-line-number="34"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-35" data-line-number="35"><span class="co"># Other rules</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,251 values changed)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (117 values changed)</span></a>
<a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no values changed)</span></a>
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no values changed)</span></a>
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no values changed)</span></a>
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no values changed)</span></a>
<a class="sourceLine" id="cb15-36" data-line-number="36"><span class="co"># Non-EUCAST: amoxicillin/clav acid = S where ampicillin = S (2,240 values changed)</span></a>
<a class="sourceLine" id="cb15-37" data-line-number="37"><span class="co"># Non-EUCAST: ampicillin = R where amoxicillin/clav acid = R (123 values changed)</span></a>
<a class="sourceLine" id="cb15-38" data-line-number="38"><span class="co"># Non-EUCAST: piperacillin = R where piperacillin/tazobactam = R (no changes)</span></a>
<a class="sourceLine" id="cb15-39" data-line-number="39"><span class="co"># Non-EUCAST: piperacillin/tazobactam = S where piperacillin = S (no changes)</span></a>
<a class="sourceLine" id="cb15-40" data-line-number="40"><span class="co"># Non-EUCAST: trimethoprim = R where trimethoprim/sulfa = R (no changes)</span></a>
<a class="sourceLine" id="cb15-41" data-line-number="41"><span class="co"># Non-EUCAST: trimethoprim/sulfa = S where trimethoprim = S (no changes)</span></a>
<a class="sourceLine" id="cb15-42" data-line-number="42"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-43" data-line-number="43"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,550 out of 20,000 rows, making a total of 7,913 edits</span></a>
<a class="sourceLine" id="cb15-44" data-line-number="44"><span class="co"># EUCAST rules affected 6,513 out of 20,000 rows, making a total of 7,843 edits</span></a>
<a class="sourceLine" id="cb15-45" data-line-number="45"><span class="co"># =&gt; added 0 test results</span></a>
<a class="sourceLine" id="cb15-46" data-line-number="46"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,913 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># * 111 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># * 4,763 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># * 1,086 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># * 349 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># * 1,585 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># * 19 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-47" data-line-number="47"><span class="co"># =&gt; changed 7,843 test results</span></a>
<a class="sourceLine" id="cb15-48" data-line-number="48"><span class="co"># - 111 test results changed from S to I</span></a>
<a class="sourceLine" id="cb15-49" data-line-number="49"><span class="co"># - 4,735 test results changed from S to R</span></a>
<a class="sourceLine" id="cb15-50" data-line-number="50"><span class="co"># - 1,034 test results changed from I to S</span></a>
<a class="sourceLine" id="cb15-51" data-line-number="51"><span class="co"># - 316 test results changed from I to R</span></a>
<a class="sourceLine" id="cb15-52" data-line-number="52"><span class="co"># - 1,612 test results changed from R to S</span></a>
<a class="sourceLine" id="cb15-53" data-line-number="53"><span class="co"># - 35 test results changed from R to I</span></a>
<a class="sourceLine" id="cb15-54" data-line-number="54"><span class="co"># --------------------------------------------------------------------------</span></a>
<a class="sourceLine" id="cb15-55" data-line-number="55"><span class="co"># </span></a>
<a class="sourceLine" id="cb15-56" data-line-number="56"><span class="co"># Use eucast_rules(..., verbose = TRUE) (on your original data) to get a data.frame with all specified edits instead.</span></a></code></pre></div>
@ -497,7 +497,7 @@
<a class="sourceLine" id="cb17-3" data-line-number="3"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `bacteria` as input for `col_mo`.</span></a>
<a class="sourceLine" id="cb17-4" data-line-number="4"><span class="co"># </span><span class="al">NOTE</span><span class="co">: Using column `date` as input for `col_date`.</span></a>
<a class="sourceLine" id="cb17-5" data-line-number="5"><span class="co"># </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="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,610 first isolates (28.0% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb17-6" data-line-number="6"><span class="co"># =&gt; Found 5,643 first isolates (28.2% of total)</span></a></code></pre></div>
<p>So only 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="cb18"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb18-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb18-2" data-line-number="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>
@ -508,7 +508,7 @@
<div id="first-weighted-isolates" class="section level2">
<h2 class="hasAnchor">
<a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient W2, sorted on date:</p>
<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient Q10, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -524,74 +524,74 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-15</td>
<td align="center">W2</td>
<td align="center">2010-01-12</td>
<td align="center">Q10</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">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">2010-05-10</td>
<td align="center">W2</td>
<td align="center">2010-01-16</td>
<td align="center">Q10</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-08-30</td>
<td align="center">W2</td>
<td align="center">2010-03-09</td>
<td align="center">Q10</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-27</td>
<td align="center">W2</td>
<td align="center">2010-03-31</td>
<td align="center">Q10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-10-28</td>
<td align="center">W2</td>
<td align="center">2010-04-06</td>
<td align="center">Q10</td>
<td align="center">B_ESCHR_COL</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">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-12-01</td>
<td align="center">W2</td>
<td align="center">2010-05-24</td>
<td align="center">Q10</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>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-01-20</td>
<td align="center">W2</td>
<td align="center">2010-05-25</td>
<td align="center">Q10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -601,8 +601,8 @@
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-02-09</td>
<td align="center">W2</td>
<td align="center">2010-07-08</td>
<td align="center">Q10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -612,21 +612,21 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-08</td>
<td align="center">W2</td>
<td align="center">2010-10-22</td>
<td align="center">Q10</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">TRUE</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-14</td>
<td align="center">W2</td>
<td align="center">2010-11-30</td>
<td align="center">Q10</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>
@ -634,7 +634,7 @@
</tr>
</tbody>
</table>
<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>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>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="cb20"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb20-1" data-line-number="1">data &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb20-2" data-line-number="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>
@ -645,7 +645,7 @@
<a class="sourceLine" id="cb20-7" data-line-number="7"><span class="co"># </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="cb20-8" data-line-number="8"><span class="co"># </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="cb20-9" data-line-number="9"><span class="co"># [Criterion] Inclusion based on key antibiotics, ignoring I.</span></a>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,032 first weighted isolates (75.2% of total)</span></a></code></pre></div>
<a class="sourceLine" id="cb20-10" data-line-number="10"><span class="co"># =&gt; Found 15,004 first weighted isolates (75.0% of total)</span></a></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -662,59 +662,59 @@
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-02-15</td>
<td align="center">W2</td>
<td align="center">2010-01-12</td>
<td align="center">Q10</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">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">2010-05-10</td>
<td align="center">W2</td>
<td align="center">2010-01-16</td>
<td align="center">Q10</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-08-30</td>
<td align="center">W2</td>
<td align="center">2010-03-09</td>
<td align="center">Q10</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-09-27</td>
<td align="center">W2</td>
<td align="center">2010-03-31</td>
<td align="center">Q10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-10-28</td>
<td align="center">W2</td>
<td align="center">2010-04-06</td>
<td align="center">Q10</td>
<td align="center">B_ESCHR_COL</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">S</td>
<td align="center">FALSE</td>
@ -722,32 +722,32 @@
</tr>
<tr class="even">
<td align="center">6</td>
<td align="center">2010-12-01</td>
<td align="center">W2</td>
<td align="center">2010-05-24</td>
<td align="center">Q10</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">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-01-20</td>
<td align="center">W2</td>
<td align="center">2010-05-25</td>
<td align="center">Q10</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="even">
<td align="center">8</td>
<td align="center">2011-02-09</td>
<td align="center">W2</td>
<td align="center">2010-07-08</td>
<td align="center">Q10</td>
<td align="center">B_ESCHR_COL</td>
<td align="center">S</td>
<td align="center">S</td>
@ -758,35 +758,35 @@
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-03-08</td>
<td align="center">W2</td>
<td align="center">2010-10-22</td>
<td align="center">Q10</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">TRUE</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-14</td>
<td align="center">W2</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>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2010-11-30</td>
<td align="center">Q10</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">FALSE</td>
<td align="center">FALSE</td>
</tr>
</tbody>
</table>
<p>Instead of 2, now 8 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - 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 1, now 6 isolates are flagged. In total, of all isolates are marked ‘first weighted’ - 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="cb21"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb21-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb21-2" data-line-number="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 15,032 isolates for analysis.</p>
<p>So we end up with 15,004 isolates for analysis.</p>
<p>We can remove unneeded columns:</p>
<div class="sourceCode" id="cb22"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb22-1" data-line-number="1">data_1st &lt;-<span class="st"> </span>data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb22-2" data-line-number="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>
@ -811,77 +811,77 @@
</tr></thead>
<tbody>
<tr class="odd">
<td>3</td>
<td align="center">2011-12-06</td>
<td align="center">I5</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNE</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">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>4</td>
<td align="center">2011-03-10</td>
<td align="center">B9</td>
<td>2</td>
<td align="center">2014-02-14</td>
<td align="center">E4</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_STPHY_AUR</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>5</td>
<td align="center">2010-06-27</td>
<td align="center">A2</td>
<td align="center">Hospital D</td>
<tr class="even">
<td>4</td>
<td align="center">2011-11-19</td>
<td align="center">S8</td>
<td align="center">Hospital B</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">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">2016-07-28</td>
<td align="center">X9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>6</td>
<td align="center">2017-12-11</td>
<td align="center">F8</td>
<td align="center">2010-03-04</td>
<td align="center">T4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td>8</td>
<td align="center">2014-06-01</td>
<td align="center">W7</td>
<td align="center">Hospital C</td>
<td>7</td>
<td align="center">2012-10-22</td>
<td align="center">Q6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COL</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">S</td>
<td align="center">F</td>
@ -891,19 +891,19 @@
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td>9</td>
<td align="center">2017-12-09</td>
<td align="center">A1</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COL</td>
<td>8</td>
<td align="center">2016-12-06</td>
<td align="center">B2</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNE</td>
<td align="center">S</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>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -925,7 +925,7 @@
<div class="sourceCode" id="cb25"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb25-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/clean/topics/freq">freq</a></span>(genus, species)</a></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,032 (of which NA: 0 = 0.00%)<br>
Length: 15,004 (of which NA: 0 = 0.00%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -942,33 +942,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">7,421</td>
<td align="right">49.4%</td>
<td align="right">7,421</td>
<td align="right">49.4%</td>
<td align="right">7,359</td>
<td align="right">49.0%</td>
<td align="right">7,359</td>
<td align="right">49.0%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,771</td>
<td align="right">25.1%</td>
<td align="right">11,192</td>
<td align="right">74.5%</td>
<td align="right">3,800</td>
<td align="right">25.3%</td>
<td align="right">11,159</td>
<td align="right">74.4%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,303</td>
<td align="right">15.3%</td>
<td align="right">13,495</td>
<td align="right">89.8%</td>
<td align="right">2,272</td>
<td align="right">15.1%</td>
<td align="right">13,431</td>
<td align="right">89.5%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,537</td>
<td align="right">10.2%</td>
<td align="right">15,032</td>
<td align="right">1,573</td>
<td align="right">10.5%</td>
<td align="right">15,004</td>
<td align="right">100.0%</td>
</tr>
</tbody>
@ -979,7 +979,7 @@ Longest: 24</p>
<a href="#resistance-percentages" class="anchor"></a>Resistance percentages</h2>
<p>The functions <code><a href="../reference/portion.html">portion_S()</a></code>, <code><a href="../reference/portion.html">portion_SI()</a></code>, <code><a href="../reference/portion.html">portion_I()</a></code>, <code><a href="../reference/portion.html">portion_IR()</a></code> and <code><a href="../reference/portion.html">portion_R()</a></code> can be used to determine the portion of a specific antimicrobial outcome. As per the EUCAST guideline of 2019, we calculate resistance as the portion of R (<code><a href="../reference/portion.html">portion_R()</a></code>) and susceptibility as the portion of S and I (<code><a href="../reference/portion.html">portion_SI()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb26-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span><span class="kw"><a href="../reference/portion.html">portion_R</a></span>(AMX)</a>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4640766</span></a></code></pre></div>
<a class="sourceLine" id="cb26-2" data-line-number="2"><span class="co"># [1] 0.4674753</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="cb27"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb27-1" data-line-number="1">data_1st <span class="op">%&gt;%</span><span class="st"> </span></a>
<a class="sourceLine" id="cb27-2" data-line-number="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>
@ -992,19 +992,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4620994</td>
<td align="center">0.4635820</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4646182</td>
<td align="center">0.4720092</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4689655</td>
<td align="center">0.4717477</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4625253</td>
<td align="center">0.4621821</td>
</tr>
</tbody>
</table>
@ -1022,23 +1022,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.4620994</td>
<td align="center">4525</td>
<td align="center">0.4635820</td>
<td align="center">4517</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.4646182</td>
<td align="center">5370</td>
<td align="center">0.4720092</td>
<td align="center">5216</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.4689655</td>
<td align="center">2175</td>
<td align="center">0.4717477</td>
<td align="center">2283</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.4625253</td>
<td align="center">2962</td>
<td align="center">0.4621821</td>
<td align="center">2988</td>
</tr>
</tbody>
</table>
@ -1058,27 +1058,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.9217087</td>
<td align="center">0.8948929</td>
<td align="center">0.9932624</td>
<td align="center">0.9244463</td>
<td align="center">0.8884359</td>
<td align="center">0.9930697</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8217306</td>
<td align="center">0.9050098</td>
<td align="center">0.9915420</td>
<td align="center">0.8207247</td>
<td align="center">0.9052765</td>
<td align="center">0.9860140</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.9254840</td>
<td align="center">0.9252188</td>
<td align="center">0.9952267</td>
<td align="center">0.9189474</td>
<td align="center">0.9250000</td>
<td align="center">0.9934211</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.6139818</td>
<td align="center">0.6126761</td>
<td align="center">0.0000000</td>
<td align="center">0.6139818</td>
<td align="center">0.6126761</td>
</tr>
</tbody>
</table>
@ -1226,7 +1226,7 @@ Longest: 24</p>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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@ -40,7 +40,7 @@
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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@ -185,7 +185,7 @@
<h1>How to apply EUCAST rules</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 August 2019</h4>
<h4 class="date">13 August 2019</h4>
<div class="hidden name"><code>EUCAST.Rmd</code></div>
@ -231,7 +231,7 @@
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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@ -40,7 +40,7 @@
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<span class="navbar-brand">
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@ -185,7 +185,7 @@
<h1>How to determine multi-drug resistance (MDR)</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 August 2019</h4>
<h4 class="date">13 August 2019</h4>
<div class="hidden name"><code>MDR.Rmd</code></div>
@ -228,19 +228,19 @@
<p>The data set looks like this now:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/utils/topics/head">head</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb3-2" data-line-number="2"><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 S S S S R S</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 S R S R R S</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R R S S S S</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 I R R S S S</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R I R S R R</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 R S S S S R</span></a>
<a class="sourceLine" id="cb3-3" data-line-number="3"><span class="co"># 1 I R R R S R</span></a>
<a class="sourceLine" id="cb3-4" data-line-number="4"><span class="co"># 2 S R S S R R</span></a>
<a class="sourceLine" id="cb3-5" data-line-number="5"><span class="co"># 3 R R S R R S</span></a>
<a class="sourceLine" id="cb3-6" data-line-number="6"><span class="co"># 4 S S S S R R</span></a>
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="co"># 5 R S S S S R</span></a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># 6 I S S R R S</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># kanamycin</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 S</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 R</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 R</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 I</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># 1 R</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># 2 I</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># 3 S</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># 4 R</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># 5 R</span></a>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 R</span></a></code></pre></div>
<a class="sourceLine" id="cb3-15" data-line-number="15"><span class="co"># 6 S</span></a></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set:</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1">my_TB_data<span class="op">$</span>mdr &lt;-<span class="st"> </span><span class="kw"><a href="../reference/mdro.html">mdr_tb</a></span>(my_TB_data)</a>
<a class="sourceLine" id="cb4-2" data-line-number="2"><span class="co"># </span><span class="al">NOTE</span><span class="co">: No column found as input for `col_mo`, assuming all records contain Mycobacterium tuberculosis.</span></a>
@ -272,39 +272,39 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistance</td>
<td align="right">3270</td>
<td align="right">65.4%</td>
<td align="right">3270</td>
<td align="right">65.4%</td>
<td align="right">3308</td>
<td align="right">66.2%</td>
<td align="right">3308</td>
<td align="right">66.2%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">645</td>
<td align="right">643</td>
<td align="right">12.9%</td>
<td align="right">3915</td>
<td align="right">78.3%</td>
<td align="right">3951</td>
<td align="right">79.0%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multidrug resistance</td>
<td align="right">593</td>
<td align="right">11.9%</td>
<td align="right">4508</td>
<td align="right">90.2%</td>
<td align="right">570</td>
<td align="right">11.4%</td>
<td align="right">4521</td>
<td align="right">90.4%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistance</td>
<td align="right">275</td>
<td align="right">5.5%</td>
<td align="right">4783</td>
<td align="right">263</td>
<td align="right">5.3%</td>
<td align="right">4784</td>
<td align="right">95.7%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensive drug resistance</td>
<td align="right">217</td>
<td align="right">216</td>
<td align="right">4.3%</td>
<td align="right">5000</td>
<td align="right">100.0%</td>
@ -320,7 +320,7 @@ Unique: 5</p>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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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="Latest development version">0.7.1.9031</span>
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</span>
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@ -185,7 +185,7 @@
<h1>How to import data from SPSS / SAS / Stata</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 August 2019</h4>
<h4 class="date">13 August 2019</h4>
<div class="hidden name"><code>SPSS.Rmd</code></div>
@ -399,7 +399,7 @@
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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@ -185,7 +185,7 @@
<h1>How to work with WHONET data</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 August 2019</h4>
<h4 class="date">13 August 2019</h4>
<div class="hidden name"><code>WHONET.Rmd</code></div>
@ -398,7 +398,7 @@ Unique: 3</p>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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@ -40,7 +40,7 @@
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9036</span>
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</span>
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@ -185,7 +185,7 @@
<h1>Benchmarks</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">12 August 2019</h4>
<h4 class="date">13 August 2019</h4>
<div class="hidden name"><code>benchmarks.Rmd</code></div>
@ -210,14 +210,14 @@
<a class="sourceLine" id="cb2-8" data-line-number="8"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb2-9" data-line-number="9"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(S.aureus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb2-10" data-line-number="10"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># as.mo("sau") 8.6 9.2 9.9 9.7 11.0 12 10</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># as.mo("stau") 32.0 33.0 33.0 33.0 34.0 35 10</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># as.mo("staaur") 8.7 9.0 13.0 9.6 11.0 26 10</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co"># as.mo("STAAUR") 8.6 9.1 13.0 9.5 9.7 28 10</span></a>
<a class="sourceLine" id="cb2-16" data-line-number="16"><span class="co"># as.mo("S. aureus") 24.0 24.0 28.0 25.0 26.0 41 10</span></a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="co"># as.mo("S. aureus") 24.0 24.0 37.0 24.0 39.0 120 10</span></a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># as.mo("Staphylococcus aureus") 4.0 4.2 6.0 4.3 4.6 21 10</span></a></code></pre></div>
<a class="sourceLine" id="cb2-11" data-line-number="11"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb2-12" data-line-number="12"><span class="co"># as.mo("sau") 8.6 8.9 11.0 9.4 9.7 26.0 10</span></a>
<a class="sourceLine" id="cb2-13" data-line-number="13"><span class="co"># as.mo("stau") 32.0 33.0 43.0 42.0 52.0 56.0 10</span></a>
<a class="sourceLine" id="cb2-14" data-line-number="14"><span class="co"># as.mo("staaur") 8.5 8.8 11.0 9.3 11.0 26.0 10</span></a>
<a class="sourceLine" id="cb2-15" data-line-number="15"><span class="co"># as.mo("STAAUR") 8.7 8.8 9.3 9.3 9.7 10.0 10</span></a>
<a class="sourceLine" id="cb2-16" data-line-number="16"><span class="co"># as.mo("S. aureus") 23.0 24.0 28.0 25.0 26.0 45.0 10</span></a>
<a class="sourceLine" id="cb2-17" data-line-number="17"><span class="co"># as.mo("S. aureus") 23.0 24.0 34.0 25.0 25.0 120.0 10</span></a>
<a class="sourceLine" id="cb2-18" data-line-number="18"><span class="co"># as.mo("Staphylococcus aureus") 4.1 4.2 4.3 4.3 4.5 4.7 10</span></a></code></pre></div>
<p>In the table above, all measurements are shown in milliseconds (thousands of seconds). A value of 5 milliseconds means it can determine 200 input values per second. It case of 100 milliseconds, this is only 10 input values per second. The second input is the only one that has to be looked up thoroughly. All the others are known codes (the first one is a WHONET code) or common laboratory codes, or common full organism names like the last one. Full organism names are always preferred.</p>
<p>To achieve this speed, the <code>as.mo</code> function also takes into account the prevalence of human pathogenic microorganisms. The downside is of course that less prevalent microorganisms will be determined less fast. See this example for the ID of <em>Thermus islandicus</em> (<code>B_THERMS_ISL</code>), a bug probably never found before in humans:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb3-1" data-line-number="1">T.islandicus &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="kw"><a href="../reference/as.mo.html">as.mo</a></span>(<span class="st">"theisl"</span>),</a>
@ -229,12 +229,12 @@
<a class="sourceLine" id="cb3-7" data-line-number="7"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(T.islandicus, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">2</span>)</a>
<a class="sourceLine" id="cb3-8" data-line-number="8"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb3-9" data-line-number="9"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("theisl") 270 280 290 290 310 320 10</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("THEISL") 280 290 300 290 300 310 10</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("T. islandicus") 140 140 150 140 160 170 10</span></a>
<a class="sourceLine" id="cb3-10" data-line-number="10"><span class="co"># as.mo("theisl") 280 290 300 310 310 320 10</span></a>
<a class="sourceLine" id="cb3-11" data-line-number="11"><span class="co"># as.mo("THEISL") 280 300 310 310 320 330 10</span></a>
<a class="sourceLine" id="cb3-12" data-line-number="12"><span class="co"># as.mo("T. islandicus") 140 150 160 160 170 180 10</span></a>
<a class="sourceLine" id="cb3-13" data-line-number="13"><span class="co"># as.mo("T. islandicus") 140 150 160 160 160 170 10</span></a>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Thermus islandicus") 48 49 60 60 68 77 10</span></a></code></pre></div>
<p>That takes 9.5 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<a class="sourceLine" id="cb3-14" data-line-number="14"><span class="co"># as.mo("Thermus islandicus") 50 53 69 57 74 140 10</span></a></code></pre></div>
<p>That takes 9.8 times as much time on average. A value of 100 milliseconds means it can only determine ~10 different input values per second. We can conclude that looking up arbitrary codes of less prevalent microorganisms is the worst way to go, in terms of calculation performance. Full names (like <em>Thermus islandicus</em>) are almost fast - these are the most probable input from most data sets.</p>
<p>In the figure below, we compare <em>Escherichia coli</em> (which is very common) with <em>Prevotella brevis</em> (which is moderately common) and with <em>Thermus islandicus</em> (which is very uncommon):</p>
<div class="sourceCode" id="cb4"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb4-1" data-line-number="1"><span class="kw"><a href="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<span class="dt">mar =</span> <span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<span class="dv">5</span>, <span class="dv">16</span>, <span class="dv">4</span>, <span class="dv">2</span>)) <span class="co"># set more space for left margin text (16)</span></a>
<a class="sourceLine" id="cb4-2" data-line-number="2"></a>
@ -280,8 +280,8 @@
<a class="sourceLine" id="cb5-24" data-line-number="24"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb5-25" data-line-number="25"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb5-26" data-line-number="26"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb5-27" data-line-number="27"><span class="co"># mo_name(x) 596 622 635 626 635 704 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.63 seconds (626 ms). You only lose time on your unique input values.</p>
<a class="sourceLine" id="cb5-27" data-line-number="27"><span class="co"># mo_name(x) 641 673 690 684 701 775 10</span></a></code></pre></div>
<p>So transforming 500,000 values (!!) of 50 unique values only takes 0.68 seconds (684 ms). You only lose time on your unique input values.</p>
</div>
<div id="precalculated-results" class="section level3">
<h3 class="hasAnchor">
@ -293,10 +293,10 @@
<a class="sourceLine" id="cb6-4" data-line-number="4"> <span class="dt">times =</span> <span class="dv">10</span>)</a>
<a class="sourceLine" id="cb6-5" data-line-number="5"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb6-6" data-line-number="6"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># A 6.700 6.950 7.410 7.600 7.730 8.06 10</span></a>
<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="co"># B 22.900 23.900 27.000 24.100 24.200 46.00 10</span></a>
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="co"># C 0.772 0.833 0.876 0.874 0.918 1.03 10</span></a></code></pre></div>
<a class="sourceLine" id="cb6-7" data-line-number="7"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb6-8" data-line-number="8"><span class="co"># A 6.760 7.320 7.630 7.54 8.070 8.500 10</span></a>
<a class="sourceLine" id="cb6-9" data-line-number="9"><span class="co"># B 23.800 25.300 28.500 25.50 26.100 50.100 10</span></a>
<a class="sourceLine" id="cb6-10" data-line-number="10"><span class="co"># C 0.906 0.911 0.941 0.93 0.969 0.991 10</span></a></code></pre></div>
<p>So going from <code><a href="../reference/mo_property.html">mo_name("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0009 seconds - it doesn’t even start calculating <em>if the result would be the same as the expected resulting value</em>. That goes for all helper functions:</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode r"><code class="sourceCode r"><a class="sourceLine" id="cb7-1" data-line-number="1">run_it &lt;-<span class="st"> </span><span class="kw"><a href="https://www.rdocumentation.org/packages/microbenchmark/topics/microbenchmark">microbenchmark</a></span>(<span class="dt">A =</span> <span class="kw"><a href="../reference/mo_property.html">mo_species</a></span>(<span class="st">"aureus"</span>),</a>
<a class="sourceLine" id="cb7-2" data-line-number="2"> <span class="dt">B =</span> <span class="kw"><a href="../reference/mo_property.html">mo_genus</a></span>(<span class="st">"Staphylococcus"</span>),</a>
@ -310,14 +310,14 @@
<a class="sourceLine" id="cb7-10" data-line-number="10"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">3</span>)</a>
<a class="sourceLine" id="cb7-11" data-line-number="11"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb7-12" data-line-number="12"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># A 0.472 0.475 0.553 0.562 0.607 0.675 10</span></a>
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># B 0.474 0.482 0.560 0.493 0.577 0.973 10</span></a>
<a class="sourceLine" id="cb7-15" data-line-number="15"><span class="co"># C 0.766 0.820 0.899 0.881 0.941 1.070 10</span></a>
<a class="sourceLine" id="cb7-16" data-line-number="16"><span class="co"># D 0.459 0.485 0.539 0.503 0.569 0.744 10</span></a>
<a class="sourceLine" id="cb7-17" data-line-number="17"><span class="co"># E 0.421 0.448 0.470 0.456 0.488 0.543 10</span></a>
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="co"># F 0.430 0.457 0.534 0.495 0.592 0.738 10</span></a>
<a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># G 0.420 0.450 0.477 0.463 0.491 0.586 10</span></a>
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># H 0.426 0.437 0.500 0.447 0.461 0.776 10</span></a></code></pre></div>
<a class="sourceLine" id="cb7-13" data-line-number="13"><span class="co"># A 0.464 0.465 0.484 0.482 0.485 0.528 10</span></a>
<a class="sourceLine" id="cb7-14" data-line-number="14"><span class="co"># B 0.621 0.632 0.659 0.636 0.650 0.784 10</span></a>
<a class="sourceLine" id="cb7-15" data-line-number="15"><span class="co"># C 0.673 0.749 0.785 0.788 0.826 0.918 10</span></a>
<a class="sourceLine" id="cb7-16" data-line-number="16"><span class="co"># D 0.446 0.451 0.477 0.467 0.474 0.586 10</span></a>
<a class="sourceLine" id="cb7-17" data-line-number="17"><span class="co"># E 0.442 0.456 0.481 0.464 0.469 0.648 10</span></a>
<a class="sourceLine" id="cb7-18" data-line-number="18"><span class="co"># F 0.442 0.459 0.470 0.466 0.490 0.494 10</span></a>
<a class="sourceLine" id="cb7-19" data-line-number="19"><span class="co"># G 0.446 0.449 0.469 0.471 0.481 0.499 10</span></a>
<a class="sourceLine" id="cb7-20" data-line-number="20"><span class="co"># H 0.445 0.452 0.466 0.458 0.463 0.522 10</span></a></code></pre></div>
<p>Of course, when running <code><a href="../reference/mo_property.html">mo_phylum("Firmicutes")</a></code> the function has zero knowledge about the actual microorganism, namely <em>S. aureus</em>. But since the result would be <code>"Firmicutes"</code> too, there is no point in calculating the result. And because this package ‘knows’ all phyla of all known bacteria (according to the Catalogue of Life), it can just return the initial value immediately.</p>
</div>
<div id="results-in-other-languages" class="section level3">
@ -344,13 +344,13 @@
<a class="sourceLine" id="cb8-18" data-line-number="18"><span class="kw"><a href="https://www.rdocumentation.org/packages/base/topics/print">print</a></span>(run_it, <span class="dt">unit =</span> <span class="st">"ms"</span>, <span class="dt">signif =</span> <span class="dv">4</span>)</a>
<a class="sourceLine" id="cb8-19" data-line-number="19"><span class="co"># Unit: milliseconds</span></a>
<a class="sourceLine" id="cb8-20" data-line-number="20"><span class="co"># expr min lq mean median uq max neval</span></a>
<a class="sourceLine" id="cb8-21" data-line-number="21"><span class="co"># en 18.77 19.83 25.36 20.44 28.51 45.88 10</span></a>
<a class="sourceLine" id="cb8-22" data-line-number="22"><span class="co"># de 20.37 20.86 23.19 21.45 22.23 39.08 10</span></a>
<a class="sourceLine" id="cb8-23" data-line-number="23"><span class="co"># nl 26.50 27.09 27.74 27.58 28.10 29.74 10</span></a>
<a class="sourceLine" id="cb8-24" data-line-number="24"><span class="co"># es 20.82 21.18 21.66 21.27 22.04 23.64 10</span></a>
<a class="sourceLine" id="cb8-25" data-line-number="25"><span class="co"># it 19.82 20.65 25.98 21.22 22.13 50.42 10</span></a>
<a class="sourceLine" id="cb8-26" data-line-number="26"><span class="co"># fr 20.07 21.20 21.68 21.47 21.89 23.76 10</span></a>
<a class="sourceLine" id="cb8-27" data-line-number="27"><span class="co"># pt 19.87 20.63 22.76 21.07 21.68 38.11 10</span></a></code></pre></div>
<a class="sourceLine" id="cb8-21" data-line-number="21"><span class="co"># en 18.92 19.31 19.46 19.45 19.65 20.00 10</span></a>
<a class="sourceLine" id="cb8-22" data-line-number="22"><span class="co"># de 20.65 20.85 21.77 21.28 22.33 25.34 10</span></a>
<a class="sourceLine" id="cb8-23" data-line-number="23"><span class="co"># nl 26.17 26.78 32.00 28.27 31.87 49.90 10</span></a>
<a class="sourceLine" id="cb8-24" data-line-number="24"><span class="co"># es 19.94 20.45 23.13 20.95 22.09 40.02 10</span></a>
<a class="sourceLine" id="cb8-25" data-line-number="25"><span class="co"># it 20.43 20.65 23.48 21.71 22.62 40.72 10</span></a>
<a class="sourceLine" id="cb8-26" data-line-number="26"><span class="co"># fr 20.28 20.69 22.35 21.09 21.32 31.54 10</span></a>
<a class="sourceLine" id="cb8-27" data-line-number="27"><span class="co"># pt 19.92 20.28 23.24 21.67 22.46 41.19 10</span></a></code></pre></div>
<p>Currently supported are German, Dutch, Spanish, Italian, French and Portuguese.</p>
</div>
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@ -362,7 +362,7 @@
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<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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@ -185,7 +185,7 @@
<h1>How to predict antimicrobial resistance</h1>
<h4 class="author">Matthijs S. Berends</h4>
<h4 class="date">08 August 2019</h4>
<h4 class="date">13 August 2019</h4>
<div class="hidden name"><code>resistance_predict.Rmd</code></div>
@ -379,7 +379,7 @@
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
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<a class="navbar-link" href="index.html">AMR (for R)</a>
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@ -233,10 +233,6 @@
<p><strong><a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a></strong>. Author. <a href='https://orcid.org/0000-0001-5809-5995' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-4881-038X' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
@ -245,6 +241,10 @@
<p><strong><a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1634-0010' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
</li>
<li>
<p><strong><a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a></strong>. Author, thesis advisor. <a href='https://orcid.org/0000-0003-1241-1328' target='orcid.widget'><img src='https://members.orcid.org/sites/default/files/vector_iD_icon.svg' class='orcid' alt='ORCID' height='16'></a>
</p>
</li>
<li>
<p><strong>Erwin E. A. Hassing</strong>. Contributor.
</p>
@ -270,7 +270,7 @@
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
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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="Latest development version">0.7.1.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -200,7 +200,13 @@
<h4 class="hasAnchor">
<a href="#partners" class="anchor"></a>Partners</h4>
<p>The development of this package is part of, related to, or made possible by:</p>
<p><a href="https://www.rug.nl"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" class="partner_logo"></a></p>
<div align="center">
<a href="https://www.rug.nl"><img src="./logo_rug.png" class="partner_logo"></a>
<a href="https://www.umcg.nl"><img src="./logo_umcg.png" class="partner_logo"></a>
<a href="https://www.certe.nl"><img src="./logo_certe.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" class="partner_logo"></a>
</div>
</div>
</div>
<div id="what-can-you-do-with-this-package" class="section level3">
@ -278,22 +284,8 @@
<h4 class="hasAnchor">
<a href="#microbial-taxonomic-reference-data" class="anchor"></a>Microbial (taxonomic) reference data</h4>
<p><img src="reference/figures/logo_col.png"></p>
<p>This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life (<a href="http://www.catalogueoflife.org">www.catalogueoflife.org</a>).</p>
<p>Included are:</p>
<ul>
<li><p>All ~61,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa</p></li>
<li>
<p>All ~8,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales.</p>
<p>The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of <em>Aspergillus</em>, <em>Candida</em>, <em>Cryptococcus</em>, <em>Histoplasma</em>, <em>Pneumocystis</em>, <em>Saccharomyces</em> and <em>Trichophyton</em>).</p>
</li>
<li><p>All ~150 (sub)species from ~100 other relevant genera from the kingdom of Animalia (like <em>Strongyloides</em> and <em>Taenia</em>)</p></li>
<li><p>All ~23,000 previously accepted names of all included (sub)species (these were taxonomically renamed)</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>This data is updated annually - check the included version with <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code>.</p>
<p><strong>About the Catalogue of Life</strong></p>
<p>The <a href="http://www.catalogueoflife.org">Catalogue of Life</a> is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>Read more about the data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
<p>This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, <a href="http://www.catalogueoflife.org">www.catalogueoflife.org</a>). With <code><a href="reference/catalogue_of_life_version.html">catalogue_of_life_version()</a></code> can be checked which version of the CoL is included in this package.</p>
<p>Read more about which data from the Catalogue of Life <a href="./reference/catalogue_of_life.html">in our manual</a>.</p>
</div>
<div id="antimicrobial-reference-data" class="section level4">
<h4 class="hasAnchor">
@ -398,11 +390,11 @@
<li>
<a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a> <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-5809-5995" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-4881-038X" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1634-0010" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li>
<a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a> <br><small class="roles"> Author, thesis advisor </small> <a href="https://orcid.org/0000-0003-1241-1328" target="orcid.widget"><img src="https://members.orcid.org/sites/default/files/vector_iD_icon.svg" class="orcid" alt="ORCID" height="16"></a> </li>
<li><a href="authors.html">All authors...</a></li>
</ul>
</div>
@ -411,7 +403,7 @@
</div>
<footer><div class="copyright">
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/">Alex W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.glasner/">Corinna Glasner</a>.</p>
</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="Latest development version">0.7.1.9038</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -225,9 +225,9 @@
</div>
<div id="amr-0-7-1-9038" class="section level1">
<div id="amr-0-7-1-9055" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9038" class="anchor"></a>AMR 0.7.1.9038<small> Unreleased </small>
<a href="#amr-0-7-1-9055" class="anchor"></a>AMR 0.7.1.9055<small> Unreleased </small>
</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -301,15 +301,16 @@
</li>
<li>Fix and speed improvement for <code><a href="../reference/mo_property.html">mo_shortname()</a></code>
</li>
<li>Algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<li>Algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code> (by which some additions were made to the <code>microorganisms</code> data set:
<ul>
<li>Some misspelled input were not understood</li>
<li>Big improvement for misspelled input</li>
<li>These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus</li>
<li>Updated to the latest taxonomic data (updated to August 2019, from the International Journal of Systematic and Evolutionary Microbiology</li>
<li>Added support for Viridans Group Streptococci (VGS) and Milleri Group Streptococci (MGS)</li>
<li>Added support for 5,000 new fungi</li>
<li>Added support for unknown yeasts and fungi</li>
</ul>
</li>
<li>Updated the <code>microorganisms</code> data set to contain the latest taxonomic data from the IJSEM journal (now up to date until August 2019)</li>
<li>Added almost 5,000 new fungi to the <code>microorganisms</code> data set</li>
<li>Fix for using <code>mo_*</code> functions where the coercion uncertainties and failures would not be available through <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> and <code><a href="../reference/as.mo.html">mo_failures()</a></code> anymore</li>
<li>Deprecated the <code>country</code> parameter of <code><a href="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li>
<li>The <code>name</code> of <code>RIF</code> is now Rifampicin instead of Rifampin</li>
@ -427,7 +428,7 @@
<a href="#changed-2" class="anchor"></a>Changed</h4>
<ul>
<li>Fixed a critical bug in <code><a href="../reference/first_isolate.html">first_isolate()</a></code> where missing species would lead to incorrect FALSEs. This bug was not present in AMR v0.5.0, but was in v0.6.0 and v0.6.1.</li>
<li>Fixedd a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> where antibiotics from WHONET software would not be recognised</li>
<li>Completely reworked the <code>antibiotics</code> data set:
<ul>
<li>All entries now have 3 different identifiers:
@ -1236,7 +1237,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9038">0.7.1.9038</a></li>
<li><a href="#amr-0-7-1-9055">0.7.1.9055</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>
@ -1255,7 +1256,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -255,7 +255,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -299,7 +299,7 @@ Post Office Box 30001 <br />
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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="Latest development version">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -274,7 +274,7 @@ This package contains <strong>all ~450 antimicrobial drugs</strong> and their An
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -288,7 +288,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -377,7 +377,7 @@
<footer>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<span class="navbar-brand">
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
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@ -298,7 +298,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
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@ -330,7 +330,7 @@
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</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="Latest development version">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -307,7 +307,7 @@ This package contains <strong>all ~450 antimicrobial drugs</strong> and their An
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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="Latest development version">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -327,7 +327,7 @@ This package contains <strong>all ~450 antimicrobial drugs</strong> and their An
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
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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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -303,7 +303,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
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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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -315,7 +315,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -264,7 +264,7 @@
</tr>
<tr>
<th>allow_uncertain</th>
<td><p>a logical (<code>TRUE</code> or <code>FALSE</code>) or a value between 0 and 3 to indicate whether the input should be checked for less possible results, see Details</p></td>
<td><p>a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less possible results, see Details</p></td>
</tr>
<tr>
<th>reference_df</th>
@ -295,8 +295,7 @@ A microbial ID from this package (class: <code>mo</code>) typically looks like t
| | ----&gt; species, a 3-4 letter acronym
| ----&gt; genus, a 5-7 letter acronym, mostly without vowels
----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa) or
PL (Plantae)
C (Chromista), F (Fungi), P (Protozoa)
</pre>
<p>Values that cannot be coered will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<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>
@ -349,8 +348,8 @@ The intelligent rules take into account microbial prevalence of pathogens in hum
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -398,7 +397,8 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<span class='co'># All mo_* functions use as.mo() internally too (see ?mo_property):</span>
<span class='fu'><a href='mo_property.html'>mo_genus</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Escherichia"</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Gram negative"#'</span>
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span>(<span class='st'>"E. coli"</span>) <span class='co'># returns "Gram negative"</span>
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='no'>df</span>$<span class='no'>mo</span> <span class='kw'>&lt;-</span> <span class='fu'>as.mo</span>(<span class='no'>df</span>$<span class='no'>microorganism_name</span>)
@ -442,7 +442,7 @@ The <code><a href='mo_property.html'>mo_property</a></code> functions (like <cod
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
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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="Latest development version">0.7.1.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -379,7 +379,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
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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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -334,7 +334,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
docs/reference/availability.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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -293,7 +293,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

10
docs/reference/catalogue_of_life.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="Latest development version">0.7.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -239,8 +239,8 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p>Click here for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p>Click here for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<h2 class="hasAnchor" id="included-taxa"><a class="anchor" href="#included-taxa"></a>Included taxa</h2>
@ -253,7 +253,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<li><p>The complete taxonomic tree of all included (sub)species: from kingdom to subspecies</p></li>
<li><p>The responsible author(s) and year of scientific publication</p></li>
</ul>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.</p>
<p>The syntax used to transform the original data to a cleansed R format, can be found here: <a href='https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R'>https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R</a>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -319,7 +319,7 @@ Function <code><a href='as.mo.html'>as.mo</a>()</code> to use the data for intel
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
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8
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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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -248,8 +248,8 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with <code>catalogue_of_life_version()</code>.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code>catalogue_of_life_version()</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -291,7 +291,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
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<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -279,7 +279,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</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="Latest development version">0.7.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -238,7 +238,7 @@
<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 69,854 observations and 16 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 69,855 observations and 16 variables:</p><dl class='dl-horizontal'>
<dt><code>mo</code></dt><dd><p>ID of microorganism as used by this package</p></dd>
<dt><code>col_id</code></dt><dd><p>Catalogue of Life ID</p></dd>
<dt><code>fullname</code></dt><dd><p>Full name, like <code>"Escherichia coli"</code></p></dd>
@ -246,7 +246,7 @@
<dt><code>rank</code></dt><dd><p>Text of the taxonomic rank of the microorganism, like <code>"species"</code> or <code>"genus"</code></p></dd>
<dt><code>ref</code></dt><dd><p>Author(s) and year of concerning scientific publication</p></dd>
<dt><code>species_id</code></dt><dd><p>ID of the species as used by the Catalogue of Life</p></dd>
<dt><code>source</code></dt><dd><p>Either <code>"CoL"</code>, <code>"DSMZ"</code> (see source) or "manually added"</p></dd>
<dt><code>source</code></dt><dd><p>Either "CoL", "DSMZ" (see Source) or "manually added"</p></dd>
<dt><code>prevalence</code></dt><dd><p>Prevalence of the microorganism, see <code><a href='as.mo.html'>?as.mo</a></code></p></dd>
</dl>
@ -258,9 +258,9 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Manually added were:</p><ul>
<li><p>9 entries of <em>Streptococcus</em> (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)</p></li>
<li><p>11 entries of <em>Streptococcus</em> (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)</p></li>
<li><p>2 entries of <em>Staphylococcus</em> (coagulase-negative [CoNS] and coagulase-positive [CoPS])</p></li>
<li><p>3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)</p></li>
<li><p>3 entries of <em>Trichomonas</em> (<em>Trichomonas vaginalis</em>, and its family and genus)</p></li>
<li><p>5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)</p></li>
<li><p>8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life</p></li>
</ul>
@ -275,8 +275,8 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -313,7 +313,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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="Latest development version">0.7.1.9035</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -253,8 +253,8 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
@ -287,7 +287,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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="Latest development version">0.7.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -329,8 +329,8 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (<a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a>()</code>.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
@ -460,7 +460,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
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@ -81,7 +81,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -327,7 +327,7 @@ set_mo_source(NULL)
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
docs/reference/p.symbol.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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -275,7 +275,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

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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
</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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -494,7 +494,7 @@ not tested not tested - - - -
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
docs/reference/read.4D.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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -400,7 +400,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
docs/reference/resistance_predict.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="Latest development version">0.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -410,7 +410,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
docs/reference/rsi_translation.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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -271,7 +271,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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<div class="pkgdown">

4
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@ -80,7 +80,7 @@
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<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="Latest development version">0.7.1.9029</span>
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</span>
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@ -272,7 +272,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
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
</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="Latest development version">0.7.1.9029</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -286,7 +286,7 @@ When negative: the left tail is longer; the mass of the distribution is concentr
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

4
docs/reference/translate.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="Latest development version">0.7.1.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9055</span>
</span>
</div>
@ -297,7 +297,7 @@
<footer>
<div class="copyright">
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
</div>
<div class="pkgdown">

36
index.md
View File

@ -19,11 +19,13 @@ This R package is [actively maintained](./news) and is free software; you can fr
The development of this package is part of, related to, or made possible by:
<a href="https://www.rug.nl"><img src="./logo_rug.png" class="partner_logo"></a>
<a href="https://www.umcg.nl"><img src="./logo_umcg.png" class="partner_logo"></a>
<a href="https://www.certe.nl"><img src="./logo_certe.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" class="partner_logo"></a>
<div align="center">
<a href="https://www.rug.nl"><img src="./logo_rug.png" class="partner_logo"></a>
<a href="https://www.umcg.nl"><img src="./logo_umcg.png" class="partner_logo"></a>
<a href="https://www.certe.nl"><img src="./logo_certe.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_eh1h.png" class="partner_logo"></a>
<a href="http://www.eurhealth-1health.eu"><img src="./logo_interreg.png" class="partner_logo"></a>
</div>
### What can you do with this package?
@ -100,29 +102,9 @@ To find out how to conduct AMR analysis, please [continue reading here to get st
<img src="man/figures/logo_col.png">
This package contains the complete taxonomic tree of almost all microorganisms from the authoritative and comprehensive Catalogue of Life ([www.catalogueoflife.org](http://www.catalogueoflife.org)).
This package contains the complete taxonomic tree of almost all 70,000 microorganisms from the authoritative and comprehensive Catalogue of Life (CoL, [www.catalogueoflife.org](http://www.catalogueoflife.org)). With `catalogue_of_life_version()` can be checked which version of the CoL is included in this package.
Included are:
* All ~61,000 (sub)species from the kingdoms of Archaea, Bacteria, Chromista and Protozoa
* All ~8,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, Microascales, Mucorales, Onygenales, Pneumocystales, Saccharomycetales, Schizosaccharomycetales and Tremellales.
The kingdom of Fungi is a very large taxon with almost 300,000 different (sub)species, of which most are not microbial (but rather macroscopic, like mushrooms). Because of this, not all fungi fit the scope of this package and including everything would tremendously slow down our algorithms too. By only including the aforementioned taxonomic orders, the most relevant fungi are covered (like all species of *Aspergillus*, *Candida*, *Cryptococcus*, *Histoplasma*, *Pneumocystis*, *Saccharomyces* and *Trichophyton*).
* All ~150 (sub)species from ~100 other relevant genera from the kingdom of Animalia (like *Strongyloides* and *Taenia*)
* All ~23,000 previously accepted names of all included (sub)species (these were taxonomically renamed)
* The responsible author(s) and year of scientific publication
This data is updated annually - check the included version with `catalogue_of_life_version()`.
**About the Catalogue of Life**
The [Catalogue of Life](http://www.catalogueoflife.org) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
Read more about the data from the Catalogue of Life [in our manual](./reference/catalogue_of_life.html).
Read more about which data from the Catalogue of Life [in our manual](./reference/catalogue_of_life.html).
#### Antimicrobial reference data

12
man/as.mo.Rd
View File

@ -31,7 +31,7 @@ mo_renamed()
This excludes \emph{Enterococci} at default (who are in group D), use \code{Lancefield = "all"} to also categorise all \emph{Enterococci} as group D.}
\item{allow_uncertain}{a logical (\code{TRUE} or \code{FALSE}) or a value between 0 and 3 to indicate whether the input should be checked for less possible results, see Details}
\item{allow_uncertain}{a number between 0 (or "none") and 3 (or "all"), or TRUE (= 2) or FALSE (= 0) to indicate whether the input should be checked for less possible results, see Details}
\item{reference_df}{a \code{data.frame} to use for extra reference when translating \code{x} to a valid \code{mo}. See \code{\link{set_mo_source}} and \code{\link{get_mo_source}} to automate the usage of your own codes (e.g. used in your analysis or organisation).}
@ -58,8 +58,7 @@ A microbial ID from this package (class: \code{mo}) typically looks like these e
| | ----> species, a 3-4 letter acronym
| ----> genus, a 5-7 letter acronym, mostly without vowels
----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa) or
PL (Plantae)
C (Chromista), F (Fungi), P (Protozoa)
}
Values that cannot be coered will be considered 'unknown' and will get the MO code \code{UNKNOWN}.
@ -134,9 +133,9 @@ Group 2 probably contains less microbial pathogens; all other members of phyla t
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{
@ -179,7 +178,8 @@ as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRA
# All mo_* functions use as.mo() internally too (see ?mo_property):
mo_genus("E. coli") # returns "Escherichia"
mo_gramstain("E. coli") # returns "Gram negative"#'
mo_gramstain("E. coli") # returns "Gram negative"
}
\dontrun{
df$mo <- as.mo(df$microorganism_name)

6
man/catalogue_of_life.Rd
View File

@ -9,9 +9,9 @@ This package contains the complete taxonomic tree of almost all microorganisms f
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Included taxa}{
@ -26,7 +26,7 @@ Included are:
\item{The responsible author(s) and year of scientific publication}
}
The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.6 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
The Catalogue of Life (\url{http://www.catalogueoflife.org}) is the most comprehensive and authoritative global index of species currently available. It holds essential information on the names, relationships and distributions of over 1.9 million species. The Catalogue of Life is used to support the major biodiversity and conservation information services such as the Global Biodiversity Information Facility (GBIF), Encyclopedia of Life (EoL) and the International Union for Conservation of Nature Red List. It is recognised by the Convention on Biological Diversity as a significant component of the Global Taxonomy Initiative and a contribution to Target 1 of the Global Strategy for Plant Conservation.
The syntax used to transform the original data to a cleansed R format, can be found here: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/reproduction_of_microorganisms.R}.
}

4
man/catalogue_of_life_version.Rd
View File

@ -18,9 +18,9 @@ For DSMZ, see \code{?microorganisms}.
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{

12
man/microorganisms.Rd
View File

@ -4,7 +4,7 @@
\name{microorganisms}
\alias{microorganisms}
\title{Data set with ~70,000 microorganisms}
\format{A \code{\link{data.frame}} with 69,854 observations and 16 variables:
\format{A \code{\link{data.frame}} with 69,855 observations and 16 variables:
\describe{
\item{\code{mo}}{ID of microorganism as used by this package}
\item{\code{col_id}}{Catalogue of Life ID}
@ -13,7 +13,7 @@
\item{\code{rank}}{Text of the taxonomic rank of the microorganism, like \code{"species"} or \code{"genus"}}
\item{\code{ref}}{Author(s) and year of concerning scientific publication}
\item{\code{species_id}}{ID of the species as used by the Catalogue of Life}
\item{\code{source}}{Either \code{"CoL"}, \code{"DSMZ"} (see source) or "manually added"}
\item{\code{source}}{Either "CoL", "DSMZ" (see Source) or "manually added"}
\item{\code{prevalence}}{Prevalence of the microorganism, see \code{?as.mo}}
}}
\source{
@ -30,9 +30,9 @@ A data set containing the microbial taxonomy of six kingdoms from the Catalogue
\details{
Manually added were:
\itemize{
\item{9 entries of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
\item{11 entries of \emph{Streptococcus} (beta-haemolytic: groups A, B, C, D, F, G, H, K and unspecified; other: viridans, milleri)}
\item{2 entries of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
\item{3 entries of Trichomonas (Trichomonas vaginalis, and its family and genus)}
\item{3 entries of \emph{Trichomonas} (\emph{Trichomonas vaginalis}, and its family and genus)}
\item{5 other 'undefined' entries (unknown, unknown Gram negatives, unknown Gram positives, unknown yeast and unknown fungus)}
\item{8,970 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
}
@ -47,9 +47,9 @@ From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloa
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{

4
man/microorganisms.codes.Rd
View File

@ -18,9 +18,9 @@ A data set containing commonly used codes for microorganisms, from laboratory sy
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{

4
man/microorganisms.old.Rd
View File

@ -23,9 +23,9 @@ A data set containing old (previously valid or accepted) taxonomic names accordi
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Read more on our website!}{

4
man/mo_property.Rd
View File

@ -108,9 +108,9 @@ The function \code{mo_url()} will return the direct URL to the online database e
\section{Catalogue of Life}{
\if{html}{\figure{logo_col.png}{options: height=40px style=margin-bottom:5px} \cr}
This package contains the complete taxonomic tree of almost all microorganisms (~65,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (\url{http://www.catalogueoflife.org}). The Catalogue of Life is the most comprehensive and authoritative global index of species currently available.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. The Catalogue of Life releases updates annually; check which version was included in this package with \code{\link{catalogue_of_life_version}()}.
\link[=catalogue_of_life]{Click here} for more information about the included taxa. Check which version of the Catalogue of Life was included in this package with \code{\link{catalogue_of_life_version}()}.
}
\section{Source}{

3
tests/testthat/test-mo.R
View File

@ -70,6 +70,9 @@ test_that("as.mo works", {
expect_equal(as.character(as.mo("CoNS")), "B_STPHY_CNS")
expect_equal(as.character(as.mo("CPS")), "B_STPHY_CPS")
expect_equal(as.character(as.mo("CoPS")), "B_STPHY_CPS")
expect_equal(as.character(as.mo("VGS")), "B_STRPT_VIR")
expect_equal(as.character(as.mo("streptococcus milleri")), "B_STRPT_MIL")
expect_equal(as.character(as.mo(c("Gram negative", "Gram positive"))), c("B_GRAMN", "B_GRAMP"))