mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 06:46:11 +01:00
mean AMR distance
This commit is contained in:
parent
4bebba3610
commit
178ab5e5ff
@ -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)
|
||||
|
@ -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)
|
||||
|
4
NEWS.md
4
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
|
||||
|
@ -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)) {
|
||||
|
@ -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)
|
||||
}
|
||||
|
Loading…
Reference in New Issue
Block a user