diff --git a/DESCRIPTION b/DESCRIPTION index 4dd863a2..29504edf 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9027 +Version: 1.8.2.9028 Date: 2022-10-21 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NAMESPACE b/NAMESPACE index d6cac72b..d68312f5 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -225,7 +225,6 @@ export(count_resistant) export(count_susceptible) export(custom_eucast_rules) export(custom_mdro_guideline) -export(distance_from_row) export(eucast_dosage) export(eucast_exceptional_phenotypes) export(eucast_rules) @@ -266,6 +265,7 @@ export(mdr_cmi2012) export(mdr_tb) export(mdro) export(mean_amr_distance) +export(mean_distance_from_row) export(mo_authors) export(mo_class) export(mo_cleaning_regex) diff --git a/NEWS.md b/NEWS.md index 0bcd4481..d96564d4 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9027 +# AMR 1.8.2.9028 This version will eventually become v2.0! We're happy to reach a new major milestone soon! @@ -27,7 +27,7 @@ This version will eventually become v2.0! We're happy to reach a new major miles * Support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. We are very grateful for the valuable input by our colleagues from other countries. The `AMR` package is now available in 16 languages. The automatic language determination will give a note at start-up on systems in supported languages. * Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info [in this article on our website](https://msberends.github.io/AMR/articles/datasets.html). * Added confidence intervals in AMR calculation. This is now included in `rsi_df()` and `proportion_df()` and manually available as `rsi_confidence_interval()` -* Support for using antibiotic selectors in scoped `dplyr` verbs (worh or without `vars()`), such as in: `... %>% summarise_at(aminoglycosides(), resistance)` +* Support for using antibiotic selectors in scoped `dplyr` verbs (with or without `vars()`), such as in: `... %>% summarise_at(aminoglycosides(), resistance)`, see `resistance()` ### Changed * Fix for using `as.rsi()` on certain EUCAST breakpoints for MIC values diff --git a/R/mean_amr_distance.R b/R/mean_amr_distance.R index e2395eb0..63d21589 100644 --- a/R/mean_amr_distance.R +++ b/R/mean_amr_distance.R @@ -41,7 +41,7 @@ #' #' For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using [rowMeans()]), see *Examples*. #' -#' Use [distance_from_row()] to subtract distances from the distance of one row, see *Examples*. +#' Use [mean_distance_from_row()] to subtract distances from the distance of one row, see *Examples*. #' @section Interpretation: #' Isolates with distances less than 0.01 difference from each other should be considered similar. Differences lower than 0.025 should be considered suspicious. #' @export @@ -66,7 +66,7 @@ #' y %>% #' mutate( #' amr_distance = mean_amr_distance(., where(is.mic)), -#' check_id_C = distance_from_row(amr_distance, id == "C") +#' check_id_C = mean_distance_from_row(amr_distance, id == "C") #' ) %>% #' arrange(check_id_C) #' } @@ -104,7 +104,7 @@ mean_amr_distance.disk <- function(x, ...) { #' @rdname mean_amr_distance #' @export -mean_amr_distance.rsi <- function(x, combine_SI = TRUE, ...) { +mean_amr_distance.rsi <- function(x, ..., combine_SI = TRUE) { meet_criteria(combine_SI, allow_class = "logical", has_length = 1, .call_depth = -1) if (isTRUE(combine_SI)) { x[x == "I"] <- "S" @@ -157,7 +157,7 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) { #' @param mean_distance the outcome of [mean_amr_distance()] #' @param row an index, such as a row number #' @export -distance_from_row <- function(mean_distance, row) { +mean_distance_from_row <- function(mean_distance, row) { meet_criteria(mean_distance, allow_class = c("double", "numeric"), is_finite = TRUE) meet_criteria(row, allow_class = c("logical", "double", "numeric")) if (is.logical(row)) { diff --git a/man/mean_amr_distance.Rd b/man/mean_amr_distance.Rd index 7b3e85bc..7cc30198 100644 --- a/man/mean_amr_distance.Rd +++ b/man/mean_amr_distance.Rd @@ -7,7 +7,7 @@ \alias{mean_amr_distance.disk} \alias{mean_amr_distance.rsi} \alias{mean_amr_distance.data.frame} -\alias{distance_from_row} +\alias{mean_distance_from_row} \title{Mean AMR Distance} \usage{ mean_amr_distance(x, ...) @@ -18,11 +18,11 @@ mean_amr_distance(x, ...) \method{mean_amr_distance}{disk}(x, ...) -\method{mean_amr_distance}{rsi}(x, combine_SI = TRUE, ...) +\method{mean_amr_distance}{rsi}(x, ..., combine_SI = TRUE) \method{mean_amr_distance}{data.frame}(x, ..., combine_SI = TRUE) -distance_from_row(mean_distance, row) +mean_distance_from_row(mean_distance, row) } \arguments{ \item{x}{a vector of class \link[=as.rsi]{rsi}, \link[=as.rsi]{rsi} or \link[=as.rsi]{rsi}, or a \link{data.frame} containing columns of any of these classes} @@ -47,7 +47,7 @@ R/SI values (see \code{\link[=as.rsi]{as.rsi()}}) are transformed using \code{"S For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using \code{\link[=rowMeans]{rowMeans()}}), see \emph{Examples}. -Use \code{\link[=distance_from_row]{distance_from_row()}} to subtract distances from the distance of one row, see \emph{Examples}. +Use \code{\link[=mean_distance_from_row]{mean_distance_from_row()}} to subtract distances from the distance of one row, see \emph{Examples}. } \section{Interpretation}{ @@ -75,7 +75,7 @@ if (require("dplyr")) { y \%>\% mutate( amr_distance = mean_amr_distance(., where(is.mic)), - check_id_C = distance_from_row(amr_distance, id == "C") + check_id_C = mean_distance_from_row(amr_distance, id == "C") ) \%>\% arrange(check_id_C) }