#' \item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria, Protozoa and Viruses}
#' \item{All ~55,000 (sub)species from the kingdoms of Archaea, Bacteria and Protozoa}
#' \item{All ~3,500 (sub)species from these orders of the kingdom of Fungi: Eurotiales, 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 \emph{Aspergillus}, \emph{Candida}, \emph{Cryptococcus}, \emph{Histplasma}, \emph{Pneumocystis}, \emph{Saccharomyces} and \emph{Trichophyton}).}
#' \item{All ~2,000 (sub)species from ~100 other relevant genera, from the kingdoms of Animalia and Plantae (like \emph{Strongyloides} and \emph{Taenia})}
#' \item{All ~15,000 previously accepted names of included (sub)species that have been taxonomically renamed}
@ -44,6 +44,8 @@
@@ -44,6 +44,8 @@
#' @inheritSection AMR Read more on our website!
#' @name catalogue_of_life
#' @rdname catalogue_of_life
#' @seealso Data set \code{\link{microorganisms}} for the actual data. \cr
#' Function \code{\link{as.mo}()} to use the data for intelligent determination of microorganisms.
#' @examples
#' # Get version info of included data set
#' catalogue_of_life_version()
@ -77,11 +79,16 @@ NULL
@@ -77,11 +79,16 @@ NULL
#' Version info of included Catalogue of Life
#'
#' This function returns a list with info about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.
#' This function returns information about the included data from the Catalogue of Life. It also shows if the included version is their latest annual release. The Catalogue of Life releases their annual release in March each year.
#' @seealso \code{\link{microorganisms}}
#' @details The list item \code{is_latest_annual_release} is based on the system date.
#'
#' For DSMZ, see \code{?microorganisms}.
#' @return a \code{list}, invisibly
#' @inheritSection catalogue_of_life Catalogue of Life
#' \item{9 species of \emph{Streptococcus} (beta haemolytic groups A, B, C, D, F, G, H, K and unspecified)}
#' \item{2 species of \emph{Staphylococcus} (coagulase-negative [CoNS] and coagulase-positive [CoPS])}
#' \item{2 other undefined (unknown Gram negatives and unknown Gram positives)}
#' \item{3 other undefined (unknown, unknown Gram negatives and unknown Gram positives)}
#' \item{8,830 species from the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen) that are not in the Catalogue of Life}
#' }
#' @section About the records from DSMZ (see source):
#' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), \url{www.catalogueoflife.org} (check included annual version with \code{\link{catalogue_of_life_version}()}).
#'
#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link{catalogue_of_life_version}()}).
#' Data set with previously accepted taxonomic names
#'
#' A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by \code{\link{as.mo}}.
#' @inheritSection catalogue_of_life Catalogue of Life
#' @format A \code{\link{data.frame}} with 17,069 observations and 4 variables:
#' @format A \code{\link{data.frame}} with 16,911 observations and 4 variables:
#' \describe{
#' \item{\code{col_id}}{Catalogue of Life ID}
#' \item{\code{tsn_new}}{New Catalogue of Life ID}
#' Use this function to determine a valid microorganism ID (\code{mo}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea, Viruses, and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. Please see Examples.
#' Use this function to determine a valid microorganism ID (\code{mo}). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see Source). The input can be almost anything: a full name (like \code{"Staphylococcus aureus"}), an abbreviated name (like \code{"S. aureus"}), an abbreviation known in the field (like \code{"MRSA"}), or just a genus. Please see Examples.
#' @param x a character vector or a \code{data.frame} with one or two columns
#' @param Becker a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1].
#' @param Becker a logical to indicate whether \emph{Staphylococci} should be categorised into Coagulase Negative \emph{Staphylococci} ("CoNS") and Coagulase Positive \emph{Staphylococci} ("CoPS") instead of their own species, according to Karsten Becker \emph{et al.} [1]. Note that this does not include species that were newly named after this publication.
#'
#' This excludes \emph{Staphylococcus aureus} at default, use \code{Becker = "all"} to also categorise \emph{S. aureus} as "CoPS".
#' @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 [2]. 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.
@ -50,13 +50,15 @@
@@ -50,13 +50,15 @@
#' | | ----> 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), PL (Plantae) or V (Viruses)
#' F (Fungi), P (Protozoa) or PL (Plantae)
#' }
#'
#' Values that cannot be coered will be considered 'unknown' and have an MO code \code{UNKNOWN}.
#'
#' Use the \code{\link{mo_property}_*} functions to get properties based on the returned code, see Examples.
#'
#' The algorithm uses data from the Catalogue of Life (see below) and from one other source (see \code{?microorganisms}).
#'
#' \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 90-95\% faster than the first try. The algorithm saves its previous findings to \code{~/.Rhistory_mo}.
#'
@ -65,7 +67,7 @@
@@ -65,7 +67,7 @@
#' \itemize{
#' \item{Valid MO codes and full names: it first searches in already valid MO code and known genus/species combinations}
#' \item{Human pathogenic prevalence: it first searches in more prevalent microorganisms, then less prevalent ones (see \emph{Microbial prevalence of pathogens in humans} below)}
#' \item{Taxonomic kingdom: it first searches in Bacteria/Chromista, then Fungi, then Protozoa, then Viruses}
#' \item{Taxonomic kingdom: it first searches in Bacteria/Chromista, then Fungi, then Protozoa}
#' \item{Breakdown of input values: from here it starts to breakdown input values to find possible matches}
#' }
#'
@ -82,7 +84,6 @@
@@ -82,7 +84,6 @@
#' \itemize{
#' \item{(uncertainty level 1): It tries to look for only matching genera}
#' \item{(uncertainty level 1): It tries to look for previously accepted (but now invalid) taxonomic names}
#' \item{(uncertainty level 1): It tries to look for some manual changes which are not (yet) published to the Catalogue of Life (like \emph{Propionibacterium} being \emph{Cutibacterium})}
#' \item{(uncertainty level 2): It strips off values between brackets and the brackets itself, and re-evaluates the input with all previous rules}
#' \item{(uncertainty level 2): It strips off words from the end one by one and re-evaluates the input with all previous rules}
#' \item{(uncertainty level 3): It strips off words from the start one by one and re-evaluates the input with all previous rules}
@ -144,6 +145,12 @@
@@ -144,6 +145,12 @@
#' as.mo("VISA") # Vancomycin Intermediate S. aureus
#' as.mo("VRSA") # Vancomycin Resistant S. aureus
#'
#' # Dyslexia is no problem - these all work:
#' as.mo("Ureaplasma urealyticum")
#' as.mo("Ureaplasma urealyticus")
#' as.mo("Ureaplasmium urealytica")
#' as.mo("Ureaplazma urealitycium")
#'
#' as.mo("Streptococcus group A")
#' as.mo("GAS") # Group A Streptococci
#' as.mo("GBS") # Group B Streptococci
@ -154,13 +161,9 @@
@@ -154,13 +161,9 @@
#' as.mo("S. pyogenes") # will remain species: B_STRPT_PYO
#' as.mo("S. pyogenes", Lancefield = TRUE) # will not remain species: B_STRPT_GRA
#'
#' # Use mo_* functions to get a specific property based on `mo`
#' @param property one of the column names of one of the \code{\link{microorganisms}} data set or \code{"shortname"}
#' @param language language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.
#' @param ... other parameters passed on to \code{\link{as.mo}}
#' @param open browse the URL using \code{\link[utils]{browseURL}}
#' @param open browse the URL using \code{\link[utils]{browseURL}()}
#' @details All functions will return the most recently known taxonomic property according to the Catalogue of Life, except for \code{mo_ref}, \code{mo_authors} and \code{mo_year}. This leads to the following results:
#' \itemize{
#' \item{\code{mo_fullname("Chlamydia psittaci")} will return \code{"Chlamydophila psittaci"} (with a warning about the renaming)}
@ -34,9 +34,9 @@
@@ -34,9 +34,9 @@
#' \item{\code{mo_ref("Chlamydophila psittaci")} will return \code{"Everett et al., 1999"} (without a warning)}
#' }
#'
#' The Gram stain - \code{mo_gramstain()} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes (ref: \url{https://itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=956097}). These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value \code{NA}.
#' The Gram stain - \code{mo_gramstain()} - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram positive - all other bacteria are considered Gram negative. Species outside the kingdom of Bacteria will return a value \code{NA}.
#'
#' The function \code{mo_url()} will return the direct URL to the species in the Catalogue of Life.
#' The function \code{mo_url()} will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.
#' @inheritSection get_locale Supported languages
#' @inheritSection catalogue_of_life Catalogue of Life
<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>
<p>That takes 11 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>That takes 7.9 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>
<divclass="sourceCode"id="cb4"><preclass="sourceCode r"><codeclass="sourceCode r"><aclass="sourceLine"id="cb4-1"title="1"><spanclass="kw"><ahref="https://www.rdocumentation.org/packages/graphics/topics/par">par</a></span>(<spanclass="dt">mar =</span><spanclass="kw"><ahref="https://www.rdocumentation.org/packages/base/topics/c">c</a></span>(<spanclass="dv">5</span>, <spanclass="dv">16</span>, <spanclass="dv">4</span>, <spanclass="dv">2</span>)) <spanclass="co"># set more space for left margin text (16)</span></a>
<aclass="sourceLine"id="cb6-7"title="7"><spanclass="co">#> expr min lq mean median uq max neval</span></a>
<aclass="sourceLine"id="cb6-8"title="8"><spanclass="co">#> A 11.000 11.100 15.700 11.300 11.400 52.900 10</span></a>
<aclass="sourceLine"id="cb6-9"title="9"><spanclass="co">#> B 28.700 28.900 29.400 29.200 29.500 30.500 10</span></a>
<aclass="sourceLine"id="cb6-10"title="10"><spanclass="co">#> C 0.322 0.556 0.523 0.568 0.581 0.586 10</span></a></code></pre></div>
<p>So going from <code><ahref="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0006 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>
<aclass="sourceLine"id="cb6-8"title="8"><spanclass="co">#> A 12.000 12.600 12.900 13.200 13.200 13.300 10</span></a>
<aclass="sourceLine"id="cb6-9"title="9"><spanclass="co">#> B 26.100 26.200 27.200 26.600 28.100 30.400 10</span></a>
<aclass="sourceLine"id="cb6-10"title="10"><spanclass="co">#> C 0.394 0.738 0.745 0.774 0.869 0.982 10</span></a></code></pre></div>
<p>So going from <code><ahref="../reference/mo_property.html">mo_fullname("Staphylococcus aureus")</a></code> to <code>"Staphylococcus aureus"</code> takes 0.0008 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>
