diff --git a/DESCRIPTION b/DESCRIPTION index c5ccf8151..9fcdb6e0a 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 115e8fa42..307c7899f 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 0ba28456b..c19be762a 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 c46595e90..75619a4ed 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 cbbccb384..913c3c1fa 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9017 + 0.7.1.9018 diff --git a/docs/articles/index.html b/docs/articles/index.html index b2efa0ef9..682baa3e3 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9017 + 0.7.1.9018 diff --git a/docs/authors.html b/docs/authors.html index 4f73d2cfd..b44010490 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9017 + 0.7.1.9018 diff --git a/docs/index.html b/docs/index.html index dd20cc678..7fb66342d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 0.7.1.9017 + 0.7.1.9018 diff --git a/docs/news/index.html b/docs/news/index.html index 366b2ef29..9d6e9a3ed 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9017 + 0.7.1.9018 @@ -225,9 +225,9 @@ -
+

-AMR 0.7.1.9017 Unreleased +AMR 0.7.1.9018 Unreleased

@@ -1198,7 +1198,7 @@ Using as.mo(..., allow_uncertain = 3)

Contents

    -
  • 0.7.1.9017
    • +
  • 0.7.1.9018
  • 0.7.1
  • 0.7.0
  • 0.6.1
    • diff --git a/docs/reference/eucast_rules.html b/docs/reference/eucast_rules.html index df0589f0b..141260a7f 100644 --- a/docs/reference/eucast_rules.html +++ b/docs/reference/eucast_rules.html @@ -80,7 +80,7 @@ AMR (for R) - 0.7.1.9015 + 0.7.1.9018

@@ -374,8 +374,6 @@

Examples

# 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 50c11da46..d2d3cdfa9 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -78,7 +78,7 @@ AMR (for R) - 0.7.1.9017 + 0.7.1.9018
diff --git a/docs/reference/like.html b/docs/reference/like.html index 189415b02..11cdfbf63 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -80,7 +80,7 @@ AMR (for R) - 0.7.1.9015 + 0.7.1.9018
@@ -299,10 +299,11 @@ # get frequencies of bacteria whose name start with 'Ent' or 'ent' library(dplyr) +library(clean) septic_patients %>% left_join_microorganisms() %>% filter(genus %like% '^ent') %>% - freq(genus, species) + freq(genus, species) # }