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AMR
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mean AMR distance

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dr. M.S. (Matthijs) Berends 2022-10-21 16:02:14 +02:00
parent 178ab5e5ff
commit faca6d608a
5 changed files with 14 additions and 14 deletions
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2
DESCRIPTION
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@ -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)

2
NAMESPACE
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@ -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)

2
NEWS.md
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@ -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!

12
R/mean_amr_distance.R
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@ -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)
}

10
man/mean_amr_distance.Rd
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@ -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)
}