diff --git a/DESCRIPTION b/DESCRIPTION index 9f79848f..2c786620 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.7.1.9033 +Version: 0.7.1.9034 Date: 2019-08-09 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 6f15c214..53104f81 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.7.1.9033 +# AMR 0.7.1.9034 ### Breaking * Function `freq()` has moved to a new package, [`clean`](https://github.com/msberends/clean) ([CRAN link](https://cran.r-project.org/package=clean)). Creating frequency tables is actually not the scope of this package (never was) and this function has matured a lot over the last two years. Therefore, a new package was created for data cleaning and checking and it perfectly fits the `freq()` function. The [`clean`](https://github.com/msberends/clean) package is available on CRAN and will be installed automatically when updating the `AMR` package, that now imports it. In a later stage, the `skewness()` and `kurtosis()` functions will be moved to the `clean` package too. diff --git a/R/data.R b/R/data.R index 4bc5bc77..b8178772 100755 --- a/R/data.R +++ b/R/data.R @@ -113,7 +113,7 @@ catalogue_of_life <- list( #' Translation table for 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 4,969 observations and 2 variables: +#' @format A \code{\link{data.frame}} with 4,965 observations and 2 variables: #' \describe{ #' \item{\code{certe}}{Commonly used code of a microorganism} #' \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set} diff --git a/data-raw/reproduction_of_microorganisms.R b/data-raw/reproduction_of_microorganisms.R index 1b639428..fd2b5d39 100644 --- a/data-raw/reproduction_of_microorganisms.R +++ b/data-raw/reproduction_of_microorganisms.R @@ -538,6 +538,8 @@ MOs %>% filter(mo_new != mo_old) %>% select(mo_old, mo_new, everything()) %>% View() +# and these codes are now missing (which will throw a unit test error): +AMR::microorganisms.codes %>% filter(!mo %in% AMR::microorganisms$mo) # set prevalence per species MOs <- MOs %>% diff --git a/data/microorganisms.codes.rda b/data/microorganisms.codes.rda index bcfa993a..80c6586b 100644 Binary files a/data/microorganisms.codes.rda and b/data/microorganisms.codes.rda differ diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 74853816..71b07b4f 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9033 + 0.7.1.9034 diff --git a/docs/articles/index.html b/docs/articles/index.html index 7b57cf45..dbdcbf53 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9033 + 0.7.1.9034 diff --git a/docs/authors.html b/docs/authors.html index 30b341f9..6665c28b 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9033 + 0.7.1.9034 diff --git a/docs/index.html b/docs/index.html index 4daa6daf..76320f6d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 0.7.1.9033 + 0.7.1.9034 diff --git a/docs/news/index.html b/docs/news/index.html index 4ac25a73..939281f7 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9033 + 0.7.1.9034 @@ -225,9 +225,9 @@ -
+

-AMR 0.7.1.9033 Unreleased +AMR 0.7.1.9034 Unreleased

@@ -1233,7 +1233,7 @@ Using as.mo(..., allow_uncertain = 3)

Contents

    -
  • 0.7.1.9033
    • +
  • 0.7.1.9034
  • 0.7.1
  • 0.7.0
  • 0.6.1
    • diff --git a/docs/reference/index.html b/docs/reference/index.html index 3b332509..4c744dc2 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9033 + 0.7.1.9034

diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index b4f93f1b..a05b208e 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -80,7 +80,7 @@ AMR (for R) - 0.7.1.9029 + 0.7.1.9034
@@ -238,7 +238,7 @@

Format

-

A data.frame with 4,969 observations and 2 variables:

+

A data.frame with 4,965 observations and 2 variables:

certe

Commonly used code of a microorganism

mo

ID of the microorganism in the microorganisms data set

diff --git a/man/microorganisms.codes.Rd b/man/microorganisms.codes.Rd index 53319cd0..793d6877 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 microorganism codes} -\format{A \code{\link{data.frame}} with 4,969 observations and 2 variables: +\format{A \code{\link{data.frame}} with 4,965 observations and 2 variables: \describe{ \item{\code{certe}}{Commonly used code of a microorganism} \item{\code{mo}}{ID of the microorganism in the \code{\link{microorganisms}} data set}