diff --git a/DESCRIPTION b/DESCRIPTION index eee99559..1301addb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR -Version: 1.0.1.9008 -Date: 2020-04-14 +Version: 1.0.1.9009 +Date: 2020-04-15 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NEWS.md b/NEWS.md index 2c44e8fc..17aa8447 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ -# AMR 1.0.1.9008 -## Last updated: 14-Apr-2020 +# AMR 1.0.1.9009 +## Last updated: 15-Apr-2020 ### New * Support for easy principal component analysis for AMR, using the new `pca()` function diff --git a/R/first_isolate.R b/R/first_isolate.R index 049ffd6b..1657b94f 100755 --- a/R/first_isolate.R +++ b/R/first_isolate.R @@ -90,18 +90,8 @@ #' library(dplyr) #' # Filter on first isolates: #' example_isolates %>% -#' mutate(first_isolate = first_isolate(., -#' col_date = "date", -#' col_patient_id = "patient_id", -#' col_mo = "mo")) %>% +#' mutate(first_isolate = first_isolate(.)) %>% #' filter(first_isolate == TRUE) -#' -#' # Which can be shortened to: -#' example_isolates %>% -#' filter_first_isolate() -#' # or for first weighted isolates: -#' example_isolates %>% -#' filter_first_weighted_isolate() #' #' # Now let's see if first isolates matter: #' A <- example_isolates %>% @@ -116,14 +106,22 @@ #' resistance = resistance(GEN)) # gentamicin resistance #' #' # Have a look at A and B. -#' # B is more reliable because every isolate is only counted once. -#' # Gentamicin resitance in hospital D appears to be 3.1% higher than +#' # B is more reliable because every isolate is counted only once. +#' # Gentamicin resitance in hospital D appears to be 3.7% higher than #' # when you (erroneously) would have used all isolates for analysis. #' #' #' ## OTHER EXAMPLES: #' #' \dontrun{ +#' +#' # Short-hand versions: +#' example_isolates %>% +#' filter_first_isolate() +#' +#' example_isolates %>% +#' filter_first_weighted_isolate() +#' #' #' # set key antibiotics to a new variable #' x$keyab <- key_antibiotics(x) diff --git a/docs/404.html b/docs/404.html index 0722fc9f..fa9c9687 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index fdfe0273..f5bcbc64 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009 diff --git a/docs/articles/PCA.html b/docs/articles/PCA.html index c9056aa7..1e02fa61 100644 --- a/docs/articles/PCA.html +++ b/docs/articles/PCA.html @@ -39,7 +39,7 @@ AMR (for R) - 1.0.1.9005 + 1.0.1.9009 @@ -186,7 +186,7 @@

How to conduct principal component analysis (PCA) for AMR

Matthijs S. Berends

-

13 April 2020

+

15 April 2020

Source: vignettes/PCA.Rmd diff --git a/docs/articles/index.html b/docs/articles/index.html index 60197a70..dd8f86bd 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009 diff --git a/docs/authors.html b/docs/authors.html index 64922785..3d54f2f3 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009 diff --git a/docs/countries.png b/docs/countries.png index 62084e3f..e3ac90a6 100644 Binary files a/docs/countries.png and b/docs/countries.png differ diff --git a/docs/countries_large.png b/docs/countries_large.png index 1756232f..80ea0809 100644 Binary files a/docs/countries_large.png and b/docs/countries_large.png differ diff --git a/docs/index.html b/docs/index.html index f1491e7a..9246dec8 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009 diff --git a/docs/news/index.html b/docs/news/index.html index a88c0d8d..7fba063c 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009 @@ -229,13 +229,13 @@ Source: NEWS.md -
-

-AMR 1.0.1.9008 Unreleased +
+

+AMR 1.0.1.9009 Unreleased

-
+

-Last updated: 14-Apr-2020 +Last updated: 15-Apr-2020

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index aa2b3604..346ab5fd 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-04-14T18:36Z +last_built: 2020-04-15T09:25Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/WHONET.html b/docs/reference/WHONET.html index 39a34e69..d0af41d1 100644 --- a/docs/reference/WHONET.html +++ b/docs/reference/WHONET.html @@ -82,7 +82,7 @@ AMR (for R) - 1.0.1.9005 + 1.0.1.9009

diff --git a/docs/reference/antibiotics.html b/docs/reference/antibiotics.html index cdb2d1ad..7d6491e6 100644 --- a/docs/reference/antibiotics.html +++ b/docs/reference/antibiotics.html @@ -82,7 +82,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009
diff --git a/docs/reference/first_isolate.html b/docs/reference/first_isolate.html index 49c9be54..06eb7bb9 100644 --- a/docs/reference/first_isolate.html +++ b/docs/reference/first_isolate.html @@ -24,16 +24,20 @@ + + + + - - + + - + - - + + @@ -46,7 +50,7 @@ - + @@ -64,7 +68,7 @@ - +
@@ -223,7 +227,7 @@

Determine first (weighted) isolates

- + Source: R/first_isolate.R
@@ -404,19 +408,9 @@ The lifecycle of this function is stablelibrary(dplyr) # Filter on first isolates: example_isolates %>% - mutate(first_isolate = first_isolate(., - col_date = "date", - col_patient_id = "patient_id", - col_mo = "mo")) %>% + mutate(first_isolate = first_isolate(.)) %>% filter(first_isolate == TRUE) -# Which can be shortened to: -example_isolates %>% - filter_first_isolate() -# or for first weighted isolates: -example_isolates %>% - filter_first_weighted_isolate() - # Now let's see if first isolates matter: A <- example_isolates %>% group_by(hospital_id) %>% @@ -430,8 +424,8 @@ The lifecycle of this function is stableresistance = resistance(GEN)) # gentamicin resistance # Have a look at A and B. -# B is more reliable because every isolate is only counted once. -# Gentamicin resitance in hospital D appears to be 3.1% higher than +# B is more reliable because every isolate is counted only once. +# Gentamicin resitance in hospital D appears to be 3.7% higher than # when you (erroneously) would have used all isolates for analysis. @@ -439,6 +433,14 @@ The lifecycle of this function is stableif (FALSE) { +# Short-hand versions: +example_isolates %>% + filter_first_isolate() + +example_isolates %>% + filter_first_weighted_isolate() + + # set key antibiotics to a new variable x$keyab <- key_antibiotics(x) @@ -450,19 +452,9 @@ The lifecycle of this function is stable
@@ -473,7 +465,7 @@ The lifecycle of this function is stable
-

Site built with pkgdown 1.4.1.9000.

+

Site built with pkgdown 1.5.0.

diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index 7cd55491..01ee1ba0 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -82,7 +82,7 @@ AMR (for R) - 1.0.1.9005 + 1.0.1.9009
diff --git a/docs/reference/index.html b/docs/reference/index.html index e6359b06..8b4bb3f7 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009
diff --git a/docs/reference/like.html b/docs/reference/like.html index e1737c1b..07f04987 100644 --- a/docs/reference/like.html +++ b/docs/reference/like.html @@ -82,7 +82,7 @@ AMR (for R) - 1.0.1.9006 + 1.0.1.9009

diff --git a/docs/reference/microorganisms.codes.html b/docs/reference/microorganisms.codes.html index 5ee6783f..e3440280 100644 --- a/docs/reference/microorganisms.codes.html +++ b/docs/reference/microorganisms.codes.html @@ -82,7 +82,7 @@ AMR (for R) - 1.0.1.9005 + 1.0.1.9009 diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index ffec4fb9..dcb1c823 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -82,7 +82,7 @@ AMR (for R) - 1.0.1.9008 + 1.0.1.9009 diff --git a/docs/reference/microorganisms.old.html b/docs/reference/microorganisms.old.html index 61523f8a..1eaf5624 100644 --- a/docs/reference/microorganisms.old.html +++ b/docs/reference/microorganisms.old.html @@ -82,7 +82,7 @@ AMR (for R) - 1.0.1.9005 + 1.0.1.9009 diff --git a/docs/reference/rsi_translation.html b/docs/reference/rsi_translation.html index 79c79b37..bc95c3c4 100644 --- a/docs/reference/rsi_translation.html +++ b/docs/reference/rsi_translation.html @@ -82,7 +82,7 @@ AMR (for R) - 1.0.1.9006 + 1.0.1.9009 diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index 8f07ec63..b77c5262 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -145,19 +145,9 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https:// library(dplyr) # Filter on first isolates: example_isolates \%>\% - mutate(first_isolate = first_isolate(., - col_date = "date", - col_patient_id = "patient_id", - col_mo = "mo")) \%>\% + mutate(first_isolate = first_isolate(.)) \%>\% filter(first_isolate == TRUE) -# Which can be shortened to: -example_isolates \%>\% - filter_first_isolate() -# or for first weighted isolates: -example_isolates \%>\% - filter_first_weighted_isolate() - # Now let's see if first isolates matter: A <- example_isolates \%>\% group_by(hospital_id) \%>\% @@ -171,8 +161,8 @@ B <- example_isolates \%>\% resistance = resistance(GEN)) # gentamicin resistance # Have a look at A and B. -# B is more reliable because every isolate is only counted once. -# Gentamicin resitance in hospital D appears to be 3.1\% higher than +# B is more reliable because every isolate is counted only once. +# Gentamicin resitance in hospital D appears to be 3.7\% higher than # when you (erroneously) would have used all isolates for analysis. @@ -180,6 +170,14 @@ B <- example_isolates \%>\% \dontrun{ +# Short-hand versions: +example_isolates \%>\% + filter_first_isolate() + +example_isolates \%>\% + filter_first_weighted_isolate() + + # set key antibiotics to a new variable x$keyab <- key_antibiotics(x) diff --git a/pkgdown/logos/countries.png b/pkgdown/logos/countries.png index 62084e3f..e3ac90a6 100644 Binary files a/pkgdown/logos/countries.png and b/pkgdown/logos/countries.png differ diff --git a/pkgdown/logos/countries_large.png b/pkgdown/logos/countries_large.png index 1756232f..80ea0809 100644 Binary files a/pkgdown/logos/countries_large.png and b/pkgdown/logos/countries_large.png differ