P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 10:21:49 +02:00
Code Releases Activity

Catalogue of Life, replaces ITIS

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-18 02:33:37 +01:00
parent 9209787a53
commit 54f8258f8c
88 changed files with 607 additions and 590 deletions
Download Patch File Download Diff File Expand all files Collapse all files

60
R/data.R
View File

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