diff --git a/DESCRIPTION b/DESCRIPTION index feef38cd..a9e21a3d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.5.0.9001 +Version: 1.5.0.9002 Date: 2021-01-14 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index f4965a7a..a62f9358 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.5.0.9001 +# AMR 1.5.0.9002 ## Last updated: 14 January 2021 ### New diff --git a/R/globals.R b/R/globals.R index 80dea18a..85d0c598 100755 --- a/R/globals.R +++ b/R/globals.R @@ -33,6 +33,7 @@ globalVariables(c(".rowid", "atc_group2", "code", "data", + "dosage", "dose", "dose_times", "fullname", diff --git a/R/isolate_identifier.R b/R/isolate_identifier.R index 72a1fd12..3096ce72 100644 --- a/R/isolate_identifier.R +++ b/R/isolate_identifier.R @@ -28,7 +28,7 @@ #' This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available. #' @inheritSection lifecycle Maturing lifecycle #' @inheritParams eucast_rules -#' @param cols_ab a character vector of column names of `x`, or (a combination with) an [antibiotic selector function]([ab_class()]), such as [carbapenems()] and [aminoglysides()] +#' @param cols_ab a character vector of column names of `x`, or (a combination with) an [antibiotic selector function]([ab_class()]), such as [carbapenems()] and [aminoglycosides()] #' @export #' @inheritSection AMR Read more on our website! #' @examples diff --git a/README.md b/README.md index 9357c481..81d4cb12 100755 --- a/README.md +++ b/README.md @@ -10,6 +10,8 @@ +The latest built **source package** (`AMR_x.x.x.tar.gz`) can be found in folder [/data-raw/](data-raw). + `AMR` is a free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. diff --git a/data-raw/AMR_1.5.0.9001.tar.gz b/data-raw/AMR_1.5.0.9002.tar.gz similarity index 77% rename from data-raw/AMR_1.5.0.9001.tar.gz rename to data-raw/AMR_1.5.0.9002.tar.gz index 603157da..a5777a9f 100644 Binary files a/data-raw/AMR_1.5.0.9001.tar.gz and b/data-raw/AMR_1.5.0.9002.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 1d2bbd3c..d1e983a0 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9001 + 1.5.0.9002 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index cb5ebf95..2cc42b66 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9001 + 1.5.0.9002 diff --git a/docs/articles/index.html b/docs/articles/index.html index 6a1fd7fc..9ea71b73 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9001 + 1.5.0.9002 diff --git a/docs/authors.html b/docs/authors.html index c0aa89dd..332cab90 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9001 + 1.5.0.9002 diff --git a/docs/index.html b/docs/index.html index f66dcfe8..55b4017f 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.5.0.9001 + 1.5.0.9002 diff --git a/docs/news/index.html b/docs/news/index.html index 7e4e3dcd..9eca88dc 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9001 + 1.5.0.9002 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

-AMR 1.5.0.9001 Unreleased +
+

+AMR 1.5.0.9002 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9c347240..5bf93709 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-01-14T13:26Z +last_built: 2021-01-14T14:48Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 016f26f5..ba0e431d 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9001 + 1.5.0.9002

diff --git a/docs/reference/isolate_identifier.html b/docs/reference/isolate_identifier.html index 7e090f47..231dada4 100644 --- a/docs/reference/isolate_identifier.html +++ b/docs/reference/isolate_identifier.html @@ -82,7 +82,7 @@ AMR (for R) - 1.5.0 + 1.5.0.9002
@@ -257,7 +257,7 @@ cols_ab -

a character vector of column names of x, or (a combination with) an antibiotic selector function, such as carbapenems() and aminoglysides()

+

a character vector of column names of x, or (a combination with) an antibiotic selector function, such as carbapenems() and aminoglycosides()

diff --git a/docs/survey.html b/docs/survey.html index 5aa15de9..5cebb67a 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.5.0.9001 + 1.5.0.9002

diff --git a/man/isolate_identifier.Rd b/man/isolate_identifier.Rd index 3e91a70c..60c541eb 100644 --- a/man/isolate_identifier.Rd +++ b/man/isolate_identifier.Rd @@ -11,7 +11,7 @@ isolate_identifier(x, col_mo = NULL, cols_ab = NULL) \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} -\item{cols_ab}{a character vector of column names of \code{x}, or (a combination with) an \href{[ab_class()]}{antibiotic selector function}, such as \code{\link[=carbapenems]{carbapenems()}} and \code{\link[=aminoglysides]{aminoglysides()}}} +\item{cols_ab}{a character vector of column names of \code{x}, or (a combination with) an \href{[ab_class()]}{antibiotic selector function}, such as \code{\link[=carbapenems]{carbapenems()}} and \code{\link[=aminoglycosides]{aminoglycosides()}}} } \description{ This function will paste the microorganism code with all antimicrobial results into one string for each row in a data set. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.