diff --git a/.gitlab-ci.R b/.gitlab-ci.R index 0b6c2629..c1d5ae33 100644 --- a/.gitlab-ci.R +++ b/.gitlab-ci.R @@ -23,11 +23,7 @@ install_if_needed <- function(pkg, repos, quiet) { package_path <- find.package(pkg, quiet = quiet) if (length(package_path) == 0) { message("NOTE: pkg ", pkg, " missing, installing...") - if (pkg == "cleaner") { - devtools::install_github("msberends/cleaner") - } else { - install.packages(pkg, repos = repos, quiet = quiet) - } + install.packages(pkg, repos = repos, quiet = quiet) } } diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index e931eda2..f9685ab1 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -117,7 +117,8 @@ coverage: script: - apt-get install --yes git # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd - - Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))" + # Sys.setenv(NOT_CRAN = 'true'), because otherwise skip_on_cran() will be applied on Covr too, resulting in extremely low coverage percentages + - Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(line_exclusions = list('R/atc_online.R', 'R/mo_history.R', 'R/mo_source.R', 'R/resistance_predict.R')); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))" coverage: '/Code coverage: \d+\.\d+/' pages: diff --git a/DESCRIPTION b/DESCRIPTION index f6536dea..ef94af94 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.8.0.9012 +Version: 0.8.0.9013 Date: 2019-11-05 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index cdd31124..28a8d58c 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.8.0.9012 +# AMR 0.8.0.9013 Last updated: 05-Nov-2019 ### New diff --git a/R/mdro.R b/R/mdro.R index 4152e25d..8895f090 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -30,6 +30,7 @@ #' @inheritSection eucast_rules Antibiotics #' @details #' For the \code{pct_required_classes} argument, values above 1 will be divided by 100. This is to support both fractions (\code{0.75} or \code{3/4}) and percentages (\code{75}). +#' #' Currently supported guidelines are (case-insensitive): #' \itemize{ #' \item{\code{guideline = "CMI2012"}: Magiorakos AP, Srinivasan A \emph{et al.} "Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance." Clinical Microbiology and Infection (2012) (\href{https://www.clinicalmicrobiologyandinfection.com/article/S1198-743X(14)61632-3/fulltext}{link})} @@ -41,6 +42,8 @@ #' #' Please suggest your own (country-specific) guidelines by letting us know: \url{https://gitlab.com/msberends/AMR/issues/new}. #' +#' \strong{Note:} Every test that involves the Enterobacteriaceae family, will internally be performed using its newly named order Enterobacterales, since the Enterobacteriaceae family has been taxonomically reclassified by Adeolu \emph{et al.} in 2016. Before that, Enterobacteriaceae was the only family under the Enterobacteriales (with an i) order. All species under the old Enterobacteriaceae family are still under the new Enterobacterales (without an i) order, but divided into multiple families. The way tests are performed now by this \code{mdro()} function makes sure that results from before 2016 and after 2016 are identical. +#' #' @return \itemize{ #' \item{CMI 2012 paper - function \code{mdr_cmi2012()} or \code{mdro()}:\cr Ordered factor with levels \code{Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR)}} #' \item{TB guideline - function \code{mdr_tb()} or \code{mdro(..., guideline = "TB")}:\cr Ordered factor with levels \code{Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively drug-resistant}} @@ -652,8 +655,7 @@ mdro <- function(x, AMP, QDA, c(DOX, MNO))) - trans_tbl2(paste0("Table 3 - ", italic("Enterobacteriaceae"), - " (before the taxonomic reclassification by Adeolu ", italic("et al."), ", 2016)"), + trans_tbl2(paste0("Table 3 - ", italic("Enterobacteriaceae")), # this new order was previously 'Enterobacteriales' and contained only the family 'Enterobacteriaceae': which(x$order == "Enterobacterales"), list(c(GEN, TOB, AMK, NET), diff --git a/codecov.yml b/codecov.yml index 13bb0025..4c48bc97 100644 --- a/codecov.yml +++ b/codecov.yml @@ -17,5 +17,6 @@ coverage: ignore: - "R/atc_online.R" + - "R/mo_history.R" - "R/mo_source.R" - - "R/resistance_predict.R" + - "R/resistance_predict.R" # gives a strange error but unit tests work diff --git a/docs/404.html b/docs/404.html index c5c2a079..c9bfadea 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9012 + 0.8.0.9013 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index f77d9227..5614b6d1 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9012 + 0.8.0.9013 diff --git a/docs/articles/index.html b/docs/articles/index.html index 88e2722a..768e0550 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9012 + 0.8.0.9013 diff --git a/docs/authors.html b/docs/authors.html index 6a4c1f28..1f865cdc 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9012 + 0.8.0.9013 diff --git a/docs/index.html b/docs/index.html index ace2a680..27f40724 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ AMR (for R) - 0.8.0.9012 + 0.8.0.9013 diff --git a/docs/news/index.html b/docs/news/index.html index a480f852..569182dd 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9012 + 0.8.0.9013 @@ -231,9 +231,9 @@ -
+

-AMR 0.8.0.9012 Unreleased +AMR 0.8.0.9013 Unreleased

Last updated: 05-Nov-2019

@@ -243,7 +243,7 @@
  • Support for a new MDRO guideline: Magiorakos AP, Srinivasan A et al. “Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance.” Clinical Microbiology and Infection (2012).
    • This is now the new default guideline for the mdro() function
      • -
    • The new Verbose mode (mdro(...., verbose = TRUE)) returns an informative data set where the reason for MDRO determination is given for every isolate
      • +
    • The new Verbose mode (mdro(...., verbose = TRUE)) returns an informative data set where the reason for MDRO determination is given for every isolate, and an list of the resistant antimicrobial agents
    • @@ -1333,7 +1333,7 @@ Using as.mo(..., allow_uncertain = 3)

    Contents

      -
    • 0.8.0.9012
      • +
    • 0.8.0.9013
    • 0.8.0
    • 0.7.1
    • 0.7.0
      • diff --git a/docs/reference/index.html b/docs/reference/index.html index e8887faf..30348d0c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -84,7 +84,7 @@ AMR (for R) - 0.8.0.9012 + 0.8.0.9013
    diff --git a/docs/reference/mdro.html b/docs/reference/mdro.html index fe4e28f1..f5e2c842 100644 --- a/docs/reference/mdro.html +++ b/docs/reference/mdro.html @@ -85,7 +85,7 @@ AMR (for R) - 0.8.0.9009 + 0.8.0.9013
    @@ -298,8 +298,8 @@

    Details

    -

    For the pct_required_classes argument, values above 1 will be divided by 100. This is to support both fractions (0.75 or 3/4) and percentages (75). -Currently supported guidelines are (case-insensitive):