diff --git a/DESCRIPTION b/DESCRIPTION index 4ff2a0b7..fca59ae3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.8.0.9034 -Date: 2019-11-23 +Version: 0.8.0.9035 +Date: 2019-11-24 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 1c63f884..601516bc 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 0.8.0.9034 -## Last updated: 23-Nov-2019 +# AMR 0.8.0.9035 +## Last updated: 24-Nov-2019 ### Breaking * Adopted Adeolu *et al.* (2016), [PMID 27620848](https://www.ncbi.nlm.nih.gov/pubmed/27620848) for the `microorganisms` data set, which means that the new order Enterobacterales now consists of a part of the existing family Enterobacteriaceae, but that this family has been split into other families as well (like *Morganellaceae* and *Yersiniaceae*). Although published in 2016, this information is not yet in the Catalogue of Life version of 2019. All MDRO determinations with `mdro()` will now use the Enterobacterales order for all guidelines before 2016 that were dependent on the Enterobacteriaceae family. @@ -57,6 +57,7 @@ * Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the `antibiotics` data set * More robust way of determining valid MIC values * Small changed to the `example_isolates` data set to better reflect reality +* Added more microorganisms codes from laboratory systems (esp. species of *Pseudescherichia* and *Rodentibacter*) ### Other * Change dependency on `clean` to `cleaner`, as this package was renamed accordingly upon CRAN request diff --git a/R/data.R b/R/data.R index c7551b13..859c32d6 100755 --- a/R/data.R +++ b/R/data.R @@ -133,7 +133,7 @@ catalogue_of_life <- list( #' Translation table for common microorganism codes #' #' 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 5,006 observations and 2 variables: +#' @format A \code{\link{data.frame}} with 5,433 observations and 2 variables: #' \describe{ #' \item{\code{code}}{Commonly used code of a microorganism} #' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set} diff --git a/R/mo_property.R b/R/mo_property.R index 7f5cabf3..d6f29558 100755 --- a/R/mo_property.R +++ b/R/mo_property.R @@ -57,7 +57,7 @@ #' mo_kingdom("E. coli") # "Bacteria" #' mo_phylum("E. coli") # "Proteobacteria" #' mo_class("E. coli") # "Gammaproteobacteria" -#' mo_order("E. coli") # "Enterobacterales" () +#' mo_order("E. coli") # "Enterobacterales" #' mo_family("E. coli") # "Enterobacteriaceae" #' mo_genus("E. coli") # "Escherichia" #' mo_species("E. coli") # "coli" diff --git a/data/microorganisms.codes.rda b/data/microorganisms.codes.rda index 7cb5b155..5c8c6f72 100644 Binary files a/data/microorganisms.codes.rda and b/data/microorganisms.codes.rda differ diff --git a/docs/404.html b/docs/404.html index c62e2344..a68daf9c 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9034 + 0.8.0.9035 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index a8ddb657..bf20ed9a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9034 + 0.8.0.9035 diff --git a/docs/articles/index.html b/docs/articles/index.html index 6190f5b0..6d2ae8c9 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9034 + 0.8.0.9035 diff --git a/docs/authors.html b/docs/authors.html index deebbbe1..36da1e64 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9034 + 0.8.0.9035 diff --git a/docs/index.html b/docs/index.html index ff0de3c9..0f3e0460 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ AMR (for R) - 0.8.0.9034 + 0.8.0.9035 diff --git a/docs/news/index.html b/docs/news/index.html index 46a039d1..b285d27b 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9034 + 0.8.0.9035 @@ -231,13 +231,13 @@ -
+

-AMR 0.8.0.9034 Unreleased +AMR 0.8.0.9035 Unreleased

-
+

-Last updated: 23-Nov-2019 +Last updated: 24-Nov-2019

@@ -319,6 +319,7 @@
  • Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the antibiotics data set
  • More robust way of determining valid MIC values
  • Small changed to the example_isolates data set to better reflect reality
    • +
  • Added more microorganisms codes from laboratory systems (esp. species of Pseudescherichia and Rodentibacter)

    • @@ -1391,7 +1392,7 @@ Using as.mo(..., allow_uncertain = 3)

    Contents

      -
    • 0.8.0.9034
      • +
    • 0.8.0.9035
    • 0.8.0
    • 0.7.1
    • 0.7.0
      • diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index 6b830065..d2ffc7e3 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -85,7 +85,7 @@ AMR (for R) - 0.8.0.9034 + 0.8.0.9035
    diff --git a/docs/reference/index.html b/docs/reference/index.html index 4e915eaa..c5cb4291 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9034 + 0.8.0.9035
    diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index f9083cfe..73cc3ae2 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -85,7 +85,7 @@ AMR (for R) - 0.8.0.9032 + 0.8.0.9035
    @@ -242,7 +242,7 @@

    Format

    -

    A data.frame with 5,006 observations and 2 variables:

    +

    A data.frame with 5,433 observations and 2 variables:

    code

    Commonly used code of a microorganism

    mo

    ID of the microorganism in the microorganisms data set

    diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 62ccf34b..17ad80a1 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -85,7 +85,7 @@ AMR (for R) - 0.8.0.9032 + 0.8.0.9035
    @@ -356,7 +356,7 @@ This package contains the complete taxonomic tree of almost all microorganisms ( mo_kingdom("E. coli") # "Bacteria" mo_phylum("E. coli") # "Proteobacteria" mo_class("E. coli") # "Gammaproteobacteria" -mo_order("E. coli") # "Enterobacterales" () +mo_order("E. coli") # "Enterobacterales" mo_family("E. coli") # "Enterobacteriaceae" mo_genus("E. coli") # "Escherichia" mo_species("E. coli") # "coli" diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index 41a93e59..68932fa8 100644 --- a/man/microorganisms.codes.Rd +++ b/man/microorganisms.codes.Rd @@ -4,7 +4,7 @@ \name{microorganisms.codes} \alias{microorganisms.codes} \title{Translation table for common microorganism codes} -\format{A \code{\link{data.frame}} with 5,006 observations and 2 variables: +\format{A \code{\link{data.frame}} with 5,433 observations and 2 variables: \describe{ \item{\code{code}}{Commonly used code of a microorganism} \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set} diff --git a/man/mo_property.Rd b/man/mo_property.Rd index 6ba13943..457a17fe 100644 --- a/man/mo_property.Rd +++ b/man/mo_property.Rd @@ -134,7 +134,7 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https:// mo_kingdom("E. coli") # "Bacteria" mo_phylum("E. coli") # "Proteobacteria" mo_class("E. coli") # "Gammaproteobacteria" -mo_order("E. coli") # "Enterobacterales" () +mo_order("E. coli") # "Enterobacterales" mo_family("E. coli") # "Enterobacteriaceae" mo_genus("E. coli") # "Escherichia" mo_species("E. coli") # "coli"