diff --git a/DESCRIPTION b/DESCRIPTION index c5ccf815..9fcdb6e0 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 0.7.1.9017 -Date: 2019-07-29 +Version: 0.7.1.9018 +Date: 2019-07-30 Title: Antimicrobial Resistance Analysis Authors@R: c( person( diff --git a/NEWS.md b/NEWS.md index 115e8fa4..307c7899 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.7.1.9017 +# AMR 0.7.1.9018 ### 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. We decided to create a new package 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/eucast_rules.R b/R/eucast_rules.R index 0ba28456..c19be762 100755 --- a/R/eucast_rules.R +++ b/R/eucast_rules.R @@ -139,8 +139,6 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" #' } #' @inheritSection AMR Read more on our website! #' @examples -#' a <- eucast_rules(septic_patients) -#' #' a <- data.frame(mo = c("Staphylococcus aureus", #' "Enterococcus faecalis", #' "Escherichia coli", @@ -176,7 +174,7 @@ EUCAST_VERSION_EXPERT_RULES <- "3.1, 2016" #' # 5 Pseudomonas aeruginosa R R - - R R R #' #' -#' # do not apply EUCAST rules, but rather get a a data.frame +#' # do not apply EUCAST rules, but rather get a data.frame #' # with 18 rows, containing all details about the transformations: #' c <- eucast_rules(a, verbose = TRUE) eucast_rules <- function(x, diff --git a/R/like.R b/R/like.R index c46595e9..75619a4e 100755 --- a/R/like.R +++ b/R/like.R @@ -48,6 +48,7 @@ #' #' # get frequencies of bacteria whose name start with 'Ent' or 'ent' #' library(dplyr) +#' library(clean) #' septic_patients %>% #' left_join_microorganisms() %>% #' filter(genus %like% '^ent') %>% diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index cbbccb38..913c3c1f 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@
diff --git a/docs/articles/index.html b/docs/articles/index.html index b2efa0ef..682baa3e 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ diff --git a/docs/authors.html b/docs/authors.html index 4f73d2cf..b4401049 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ diff --git a/docs/index.html b/docs/index.html index dd20cc67..7fb66342 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ diff --git a/docs/news/index.html b/docs/news/index.html index 366b2ef2..9d6e9a3e 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ @@ -225,9 +225,9 @@ -as.mo(..., allow_uncertain = 3)
Contents
# NOT RUN { -a <- eucast_rules(septic_patients) - a <- data.frame(mo = c("Staphylococcus aureus", "Enterococcus faecalis", "Escherichia coli", @@ -411,7 +409,7 @@ # 5 Pseudomonas aeruginosa R R - - R R R -# do not apply EUCAST rules, but rather get a a data.frame +# do not apply EUCAST rules, but rather get a data.frame # with 18 rows, containing all details about the transformations: c <- eucast_rules(a, verbose = TRUE) # }diff --git a/docs/reference/index.html b/docs/reference/index.html index 50c11da4..d2d3cdfa 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@