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Use median by default in adjacency methods

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This commit is contained in:
Elias Projahn 2022-02-24 15:36:07 +01:00
parent 33cc33f81a
commit 074902b505
4 changed files with 6 additions and 8 deletions
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5
R/method_adjacency.R
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@ -32,15 +32,14 @@ densest <- function(data) {
#' distance values for each gene. See [densest()] for the default #' distance values for each gene. See [densest()] for the default
#' implementation. #' implementation.
#' @param summarize A function that will be used to combine the different #' @param summarize A function that will be used to combine the different
#' distances to the reference genes. By default [min()] is used. That means #' distances to the reference genes. By default [stats::median()] is used.
#' the distance to the nearest reference gene will be scored.
#' #'
#' @return An object of class `geposan_method`. #' @return An object of class `geposan_method`.
#' #'
#' @seealso [species_adjacency()] #' @seealso [species_adjacency()]
#' #'
#' @export #' @export
adjacency <- function(distance_estimate = densest, summarize = min) { adjacency <- function(distance_estimate = densest, summarize = stats::median) {
method( method(
id = "adjacency", id = "adjacency",
name = "Adjacency", name = "Adjacency",

2
R/method_species_adjacency.R
View file

@ -13,7 +13,7 @@
#' @seealso [adjacency()] #' @seealso [adjacency()]
#' #'
#' @export #' @export
species_adjacency <- function(distance_estimate = min, species_adjacency <- function(distance_estimate = stats::median,
summarize = stats::median) { summarize = stats::median) {
method( method(
id = "species_adjacency", id = "species_adjacency",

5
man/adjacency.Rd
View file

@ -4,7 +4,7 @@
\alias{adjacency} \alias{adjacency}
\title{Score genes based on their proximity to the reference genes.} \title{Score genes based on their proximity to the reference genes.}
\usage{ \usage{
adjacency(distance_estimate = densest, summarize = min) adjacency(distance_estimate = densest, summarize = stats::median)
} }
\arguments{ \arguments{
\item{distance_estimate}{A function that will be used to summarize the \item{distance_estimate}{A function that will be used to summarize the
@ -12,8 +12,7 @@ distance values for each gene. See \code{\link[=densest]{densest()}} for the def
implementation.} implementation.}
\item{summarize}{A function that will be used to combine the different \item{summarize}{A function that will be used to combine the different
distances to the reference genes. By default \code{\link[=min]{min()}} is used. That means distances to the reference genes. By default \code{\link[stats:median]{stats::median()}} is used.}
the distance to the nearest reference gene will be scored.}
} }
\value{ \value{
An object of class \code{geposan_method}. An object of class \code{geposan_method}.

2
man/species_adjacency.Rd
View file

@ -4,7 +4,7 @@
\alias{species_adjacency} \alias{species_adjacency}
\title{Score genes based on their adjacency to the reference genes within species.} \title{Score genes based on their adjacency to the reference genes within species.}
\usage{ \usage{
species_adjacency(distance_estimate = min, summarize = stats::median) species_adjacency(distance_estimate = stats::median, summarize = stats::median)
} }
\arguments{ \arguments{
\item{distance_estimate}{Function for combining the distance differences \item{distance_estimate}{Function for combining the distance differences