diff --git a/DESCRIPTION b/DESCRIPTION index 29504edf..d2f48e5b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 1.8.2.9028 +Version: 1.8.2.9029 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 d68312f5..6c1cffbb 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -189,6 +189,7 @@ export(age_groups) export(all_antimicrobials) export(aminoglycosides) export(aminopenicillins) +export(amr_distance_from_row) export(anti_join_microorganisms) export(antifungals) export(antimicrobials_equal) @@ -265,7 +266,6 @@ 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 d96564d4..6e1feed7 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 1.8.2.9028 +# AMR 1.8.2.9029 This version will eventually become v2.0! We're happy to reach a new major milestone soon! diff --git a/R/mean_amr_distance.R b/R/mean_amr_distance.R index 63d21589..9a90b3c2 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 [mean_distance_from_row()] to subtract distances from the distance of one row, see *Examples*. +#' Use [amr_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 = mean_distance_from_row(amr_distance, id == "C") +#' check_id_C = amr_distance_from_row(amr_distance, id == "C") #' ) %>% #' arrange(check_id_C) #' } @@ -154,14 +154,14 @@ mean_amr_distance.data.frame <- function(x, ..., combine_SI = TRUE) { } #' @rdname mean_amr_distance -#' @param mean_distance the outcome of [mean_amr_distance()] +#' @param amr_distance the outcome of [mean_amr_distance()] #' @param row an index, such as a row number #' @export -mean_distance_from_row <- function(mean_distance, row) { - meet_criteria(mean_distance, allow_class = c("double", "numeric"), is_finite = TRUE) +amr_distance_from_row <- function(amr_distance, row) { + meet_criteria(amr_distance, allow_class = c("double", "numeric"), is_finite = TRUE) meet_criteria(row, allow_class = c("logical", "double", "numeric")) if (is.logical(row)) { row <- which(row) } - abs(mean_distance[row] - mean_distance) + abs(amr_distance[row] - amr_distance) } diff --git a/man/mean_amr_distance.Rd b/man/mean_amr_distance.Rd index 7cc30198..5b65b2e8 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{mean_distance_from_row} +\alias{amr_distance_from_row} \title{Mean AMR Distance} \usage{ mean_amr_distance(x, ...) @@ -22,7 +22,7 @@ mean_amr_distance(x, ...) \method{mean_amr_distance}{data.frame}(x, ..., combine_SI = TRUE) -mean_distance_from_row(mean_distance, row) +amr_distance_from_row(amr_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} @@ -31,7 +31,7 @@ mean_distance_from_row(mean_distance, row) \item{combine_SI}{a \link{logical} to indicate whether all values of S and I must be merged into one, so the input only consists of S+I vs. R (susceptible vs. resistant), defaults to \code{TRUE}} -\item{mean_distance}{the outcome of \code{\link[=mean_amr_distance]{mean_amr_distance()}}} +\item{amr_distance}{the outcome of \code{\link[=mean_amr_distance]{mean_amr_distance()}}} \item{row}{an index, such as a row number} } @@ -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[=mean_distance_from_row]{mean_distance_from_row()}} to subtract distances from the distance of one row, see \emph{Examples}. +Use \code{\link[=amr_distance_from_row]{amr_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 = mean_distance_from_row(amr_distance, id == "C") + check_id_C = amr_distance_from_row(amr_distance, id == "C") ) \%>\% arrange(check_id_C) }