diff --git a/DESCRIPTION b/DESCRIPTION index 7b8bab26..83f5cdad 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.7.1.9020 +Version: 1.7.1.9021 Date: 2021-07-12 Title: Antimicrobial Resistance Data Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 5041d829..86077f58 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# `AMR` 1.7.1.9020 +# `AMR` 1.7.1.9021 ## Last updated: 12 July 2021 ### Changed diff --git a/R/plot.R b/R/plot.R index 3b68eb9f..c68b4f9d 100644 --- a/R/plot.R +++ b/R/plot.R @@ -201,7 +201,7 @@ barplot.mic <- function(height, ...) } -#' @method autplot mic +#' @method autoplot mic #' @rdname plot # will be exported using s3_register() in R/zzz.R autoplot.mic <- function(object, diff --git a/R/resistance_predict.R b/R/resistance_predict.R index fae7d544..5ba2855a 100755 --- a/R/resistance_predict.R +++ b/R/resistance_predict.R @@ -27,6 +27,7 @@ #' #' Create a prediction model to predict antimicrobial resistance for the next years on statistical solid ground. Standard errors (SE) will be returned as columns `se_min` and `se_max`. See *Examples* for a real live example. #' @inheritSection lifecycle Stable Lifecycle +#' @param object model data to be plotted #' @param col_ab column name of `x` containing antimicrobial interpretations (`"R"`, `"I"` and `"S"`) #' @param col_date column name of the date, will be used to calculate years if this column doesn't consist of years already, defaults to the first column of with a date class #' @param year_min lowest year to use in the prediction model, dafaults to the lowest year in `col_date` diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz index 077fda62..fce2ac1e 100644 Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ diff --git a/docs/404.html b/docs/404.html index 7f9294c7..022953e0 100644 --- a/docs/404.html +++ b/docs/404.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 9decfecb..515b829a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021 diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html index d9445c93..c7d0e521 100644 --- a/docs/articles/datasets.html +++ b/docs/articles/datasets.html @@ -39,7 +39,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021 diff --git a/docs/articles/index.html b/docs/articles/index.html index f5e0abd4..0599fe80 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021 diff --git a/docs/authors.html b/docs/authors.html index 5b844c8a..e1f5a054 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021 diff --git a/docs/index.html b/docs/index.html index 0537dc67..195f2ce9 100644 --- a/docs/index.html +++ b/docs/index.html @@ -42,7 +42,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021 diff --git a/docs/news/index.html b/docs/news/index.html index 136656c7..e215ab9a 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021 @@ -236,9 +236,9 @@ Source: NEWS.md -
-

- Unreleased AMR 1.7.1.9020

+
+

+ Unreleased AMR 1.7.1.9021

Last updated: 12 July 2021 @@ -501,7 +501,7 @@ is.rsi.eligible() now detects if the column name resembles an antibiotic name or code and now returns TRUE immediately if the input contains any of the values “R”, “S” or “I”. This drastically improves speed, also for a lot of other functions that rely on automatic determination of antibiotic columns.
  • Functions get_episode() and is_new_episode() now support less than a day as value for argument episode_days (e.g., to include one patient/test per hour)
  • Argument ampc_cephalosporin_resistance in eucast_rules() now also applies to value “I” (not only “S”)
    • -
  • Functions print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by() +
  • Functions print() and summary() on a Principal Components Analysis object (pca()) now print additional group info if the original data was grouped using dplyr::group_by()
  • Improved speed and reliability of guess_ab_col(). As this also internally improves the reliability of first_isolate() and mdro(), this might have a slight impact on the results of those functions.
  • Fix for mo_name() when used in other languages than English
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 24053671..b2412436 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -12,7 +12,7 @@ articles: datasets: datasets.html resistance_predict: resistance_predict.html welcome_to_AMR: welcome_to_AMR.html -last_built: 2021-07-12T18:24Z +last_built: 2021-07-12T20:09Z urls: reference: https://msberends.github.io/AMR//reference article: https://msberends.github.io/AMR//articles diff --git a/docs/reference/index.html b/docs/reference/index.html index 632ddf98..37d2c8cc 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021

    @@ -508,7 +508,7 @@ -

    plot(<mic>) autplot(<mic>) plot(<disk>) autoplot(<disk>) plot(<rsi>) autoplot(<rsi>)

    +

    plot(<mic>) autoplot(<mic>) plot(<disk>) autoplot(<disk>) plot(<rsi>) autoplot(<rsi>)

    Plotting for Classes rsi, mic and disk

    diff --git a/docs/reference/plot.html b/docs/reference/plot.html index 974a080b..012d853b 100644 --- a/docs/reference/plot.html +++ b/docs/reference/plot.html @@ -82,7 +82,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021
    @@ -258,7 +258,7 @@ ) # S3 method for mic -autplot( +autoplot( object, mo = NULL, ab = NULL, diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index dc842ee4..07ba9b89 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -82,7 +82,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021
    @@ -349,6 +349,10 @@ ribbon

    a logical to indicate whether a ribbon should be shown (default) or error bars

    + + object +

    model data to be plotted

    +

    Value

    diff --git a/docs/survey.html b/docs/survey.html index c482dde9..7c0ff8a3 100644 --- a/docs/survey.html +++ b/docs/survey.html @@ -81,7 +81,7 @@ AMR (for R) - 1.7.1.9020 + 1.7.1.9021 diff --git a/man/plot.Rd b/man/plot.Rd index 045abef4..3b6b7040 100644 --- a/man/plot.Rd +++ b/man/plot.Rd @@ -24,7 +24,7 @@ ... ) -\method{autplot}{mic}( +\method{autoplot}{mic}( object, mo = NULL, ab = NULL, diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd index 3d4f4328..757c9ee3 100644 --- a/man/resistance_predict.Rd +++ b/man/resistance_predict.Rd @@ -82,6 +82,8 @@ ggplot_rsi_predict( \item{main}{title of the plot} \item{ribbon}{a \link{logical} to indicate whether a ribbon should be shown (default) or error bars} + +\item{object}{model data to be plotted} } \value{ A \link{data.frame} with extra class \code{\link{resistance_predict}} with columns: