P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 11:11:54 +02:00
Code Releases Activity

mo codes for WHONET

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-08 16:06:54 +01:00
parent 3d3366faf7
commit ed30312048
60 changed files with 1103 additions and 615 deletions
Download Patch File Download Diff File Expand all files Collapse all files

38
R/data.R
View File

@ -134,7 +134,7 @@
#'
#' 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}}.
#' @inheritSection ITIS ITIS
#' @format A \code{\link{data.frame}} with 18,833 observations and 15 variables:
#' @format A \code{\link{data.frame}} with 19,456 observations and 15 variables:
#' \describe{
#' \item{\code{mo}}{ID of microorganism}
#' \item{\code{tsn}}{Taxonomic Serial Number (TSN), as defined by ITIS}
@ -153,6 +153,17 @@
#' \item{\code{ref}}{Author(s) and year of concerning publication as found in ITIS, see Source}
#' }
#' @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{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"
@ -175,12 +186,13 @@
#' Translation table for microorganism codes
#'
#' A data set containing commonly used codes for microorganisms. Define your own with \code{\link{set_mo_source}}.
#' @format A \code{\link{data.frame}} with 3,303 observations and 2 variables:
#' A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with \code{\link{set_mo_source}}.
#' @format A \code{\link{data.frame}} with 4,731 observations and 2 variables:
#' \describe{
#' \item{\code{certe}}{Commonly used code of a microorganism}
#' \item{\code{mo}}{Code of microorganism in \code{\link{microorganisms}}}
#' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}
#' }
#' @inheritSection ITIS ITIS
#' @inheritSection AMR Read more on our website!
#' @seealso \code{\link{as.mo}} \code{\link{microorganisms}}
"microorganisms.codes"
@ -246,17 +258,21 @@
#' @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)
# # sort on (1) bacteria, (2) fungi, (3) protozoa and then human pathogenic prevalence and then TSN:
# data.table::setkey(microorganismsDT, kingdom, prevalence, fullname)
# microorganisms.prevDT <- microorganismsDT[prevalence == 9999,]
# microorganisms.unprevDT <- microorganismsDT[prevalence != 9999,]
# 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)
# devtools::use_data(microorganismsDT, overwrite = TRUE)
# devtools::use_data(microorganisms.prevDT, overwrite = TRUE)
# devtools::use_data(microorganisms.unprevDT, overwrite = TRUE)
# devtools::use_data(microorganisms.oldDT, overwrite = TRUE)
# 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