diff --git a/DESCRIPTION b/DESCRIPTION index 8ee636f4..86f86803 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.9.0.9023 +Version: 0.9.0.9024 Date: 2020-02-14 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 088feacd..3bb51ede 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.9.0.9023 +# AMR 0.9.0.9024 ## Last updated: 14-Feb-2020 ### New diff --git a/R/data.R b/R/data.R index 99b6b7d8..fae09317 100755 --- a/R/data.R +++ b/R/data.R @@ -196,7 +196,7 @@ catalogue_of_life <- list( #' Data set for R/SI interpretation #' -#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use [as.rsi()] to transform MICs or disks measurements to R/SI values. +#' Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use [as.rsi()] to transform MICs or disks measurements to R/SI values. #' @format A [`data.frame`] with 13,975 observations and 9 variables: #' - `guideline`\cr Name of the guideline #' - `method`\cr Either "MIC" or "DISK" diff --git a/R/globals.R b/R/globals.R index b5060c7a..3121afed 100755 --- a/R/globals.R +++ b/R/globals.R @@ -25,6 +25,7 @@ globalVariables(c(".", "ab_txt", "abbreviations", "antibiotic", + "antibiotics", "CNS_CPS", "col_id", "count", @@ -57,6 +58,7 @@ globalVariables(c(".", "median", "microorganisms", "microorganisms.codes", + "microorganisms.old", "missing_names", "mo", "mono_count", @@ -82,6 +84,7 @@ globalVariables(c(".", "R", "real_first_isolate", "ref", + "rsi_translation", "rule_group", "rule_name", "S", diff --git a/docs/404.html b/docs/404.html index 8ce2e1f8..9729dc6f 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 361ad66b..1b8f67ed 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ diff --git a/docs/articles/index.html b/docs/articles/index.html index fb6845a4..6676e67c 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ diff --git a/docs/authors.html b/docs/authors.html index d84c2e98..ddc32b81 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ diff --git a/docs/index.html b/docs/index.html index a5e387f9..e0d92dc3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ @@ -240,7 +240,7 @@ A methods paper about this package has been preprinted at bioRxiv (DOI: 10.1101/This package is ready-to-use for specialists in many fields:
Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use as.rsi()
to transform MICs or disks measurements to R/SI values.
Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use as.rsi()
to transform MICs or disks measurements to R/SI values.
rsi_translation
diff --git a/index.md b/index.md
index 41b04973..8cd06b68 100644
--- a/index.md
+++ b/index.md
@@ -50,7 +50,7 @@ This package can be used for:
* Applying EUCAST expert rules ([manual](./reference/eucast_rules.html))
* Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code ([manual](./reference/mo_property.html))
* Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code ([manual](./reference/ab_property.html))
- * Machine reading the EUCAST and CLSI guidelines from 2011-2019 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
+ * Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI ([link](https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt))
This package is ready-to-use for specialists in many fields:
diff --git a/man/rsi_translation.Rd b/man/rsi_translation.Rd
index ac35d79b..94c0df17 100644
--- a/man/rsi_translation.Rd
+++ b/man/rsi_translation.Rd
@@ -20,7 +20,7 @@
rsi_translation
}
\description{
-Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2019). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
+Data set to interpret MIC and disk diffusion to R/SI values. Included guidelines are CLSI (2011-2019) and EUCAST (2011-2020). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
}
\details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://gitlab.com/msberends/AMR/blob/master/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. This file is updated automatically.
diff --git a/tests/testthat/test-ggplot_rsi.R b/tests/testthat/test-ggplot_rsi.R
index 1e516918..8f6c6ad2 100644
--- a/tests/testthat/test-ggplot_rsi.R
+++ b/tests/testthat/test-ggplot_rsi.R
@@ -23,6 +23,8 @@ context("ggplot_rsi.R")
test_that("ggplot_rsi works", {
+ skip_on_cran()
+
skip_if_not("ggplot2" %in% rownames(installed.packages()))
library(dplyr)