diff --git a/DESCRIPTION b/DESCRIPTION index 226376e62..0742135d7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.2.0.9009 +Version: 1.2.0.9010 Date: 2020-06-17 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 78aa761e6..273753ee5 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.2.0.9009 +# AMR 1.2.0.9010 ## Last updated: 17-Jun-2020 ### New diff --git a/R/join_microorganisms.R b/R/join_microorganisms.R index afcb38233..2ff9bb852 100755 --- a/R/join_microorganisms.R +++ b/R/join_microorganisms.R @@ -29,8 +29,8 @@ #' @param x existing table to join, or character vector #' @param by a variable to join by - if left empty will search for a column with class [`mo`] (created with [as.mo()]) or will be `"mo"` if that column name exists in `x`, could otherwise be a column name of `x` with values that exist in `microorganisms$mo` (like `by = "bacteria_id"`), or another column in [microorganisms] (but then it should be named, like `by = c("my_genus_species" = "fullname")`) #' @param suffix if there are non-joined duplicate variables in `x` and `y`, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2. -#' @param ... other parameters to pass on to [dplyr::join()] -#' @details **Note:** As opposed to the [join()] functions of `dplyr`, [`character`] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix. +#' @param ... ignored +#' @details **Note:** As opposed to the `join()` functions of `dplyr`, [`character`] vectors are supported and at default existing columns will get a suffix `"2"` and the newly joined columns will not get a suffix. #' #' These functions rely on [merge()], a base R function to do joins. #' @inheritSection AMR Read more on our website! diff --git a/R/resistance_predict.R b/R/resistance_predict.R index c754b292b..29b62d3a9 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -165,7 +165,7 @@ resistance_predict <- function(x, year <- function(x) { # don't depend on lubridate or so, would be overkill for only this function if (all(grepl("^[0-9]{4}$", x))) { - x + as.integer(x) } else { as.integer(format(as.Date(x), "%Y")) } diff --git a/docs/404.html b/docs/404.html index d30ea81bf..08a08f6be 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9009 + 1.2.0.9010 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 21e72f289..4a2051e3a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9009 + 1.2.0.9010 diff --git a/docs/articles/index.html b/docs/articles/index.html index ee5c99799..fff50edae 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9009 + 1.2.0.9010 diff --git a/docs/authors.html b/docs/authors.html index 30a5cfd6a..96b428821 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9009 + 1.2.0.9010 diff --git a/docs/index.html b/docs/index.html index 5190d0b74..27e8cfa25 100644 --- a/docs/index.html +++ b/docs/index.html @@ -43,7 +43,7 @@ AMR (for R) - 1.2.0.9009 + 1.2.0.9010 diff --git a/docs/news/index.html b/docs/news/index.html index 5c35cf476..45ddff3f6 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9009 + 1.2.0.9010 @@ -229,9 +229,9 @@ Source: NEWS.md -
-

-AMR 1.2.0.9009 Unreleased +
+

+AMR 1.2.0.9010 Unreleased

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 962e71ccc..8034fc21f 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: 2020-06-17T14:24Z +last_built: 2020-06-17T19:33Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 6308ebbe5..a1f84f386 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.2.0.9009 + 1.2.0.9010

diff --git a/docs/reference/join.html b/docs/reference/join.html index f16555b5d..46ee985a6 100644 --- a/docs/reference/join.html +++ b/docs/reference/join.html @@ -82,7 +82,7 @@ AMR (for R) - 1.2.0 + 1.2.0.9010
@@ -264,7 +264,7 @@ ... -

other parameters to pass on to dplyr::join()

+

ignored

diff --git a/man/join.Rd b/man/join.Rd index 446b1afe0..d668b67fd 100755 --- a/man/join.Rd +++ b/man/join.Rd @@ -30,13 +30,13 @@ anti_join_microorganisms(x, by = NULL, ...) \item{suffix}{if there are non-joined duplicate variables in \code{x} and \code{y}, these suffixes will be added to the output to disambiguate them. Should be a character vector of length 2.} -\item{...}{other parameters to pass on to \code{\link[dplyr:join]{dplyr::join()}}} +\item{...}{ignored} } \description{ Join the data set \link{microorganisms} easily to an existing table or character vector. } \details{ -\strong{Note:} As opposed to the \code{\link[=join]{join()}} functions of \code{dplyr}, \code{\link{character}} vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. +\strong{Note:} As opposed to the \code{join()} functions of \code{dplyr}, \code{\link{character}} vectors are supported and at default existing columns will get a suffix \code{"2"} and the newly joined columns will not get a suffix. These functions rely on \code{\link[=merge]{merge()}}, a base R function to do joins. }