diff --git a/NAMESPACE b/NAMESPACE index 685d468..49d5bdf 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -12,7 +12,6 @@ export(analyze) export(clustering) export(compare) export(correlation) -export(densest) export(method) export(neural) export(optimal_weights) diff --git a/R/adjacency.R b/R/adjacency.R index 6d2a1e6..06c47fd 100644 --- a/R/adjacency.R +++ b/R/adjacency.R @@ -1,31 +1,7 @@ -#' Find the densest value in the data. -#' -#' This function assumes that data represents a continuous variable and finds -#' a single value with the highest estimated density. This can be used to -#' estimate the mode of the data. If there is only one value that value is -#' returned. If multiple density maxima with the same density exist, their mean -#' is returned. -#' -#' @param data The input data. -#' -#' @return The densest value of data. -#' -#' @export -densest <- function(data) { - as.numeric(if (length(data) <= 0) { - NULL - } else if (length(data) == 1) { - data - } else { - density <- stats::density(data) - mean(density$x[density$y == max(density$y)]) - }) -} - #' Score genes based on their proximity to the reference genes. #' #' @param estimate A function that will be used to summarize the distance -#' values for each gene. See [densest()] for the default implementation. +#' values for each gene. By default, [median()] is used. #' @param combination A function that will be used to combine the different #' distances to the reference genes. By default [min()] is used. That means #' the distance to the nearest reference gene will be scored. @@ -33,7 +9,7 @@ densest <- function(data) { #' @return An object of class `geposan_method`. #' #' @export -adjacency <- function(estimate = densest, combination = min) { +adjacency <- function(estimate = stats::median, combination = min) { method( id = "adjacency", name = "Adjacency", diff --git a/man/adjacency.Rd b/man/adjacency.Rd index f68d759..bc0a724 100644 --- a/man/adjacency.Rd +++ b/man/adjacency.Rd @@ -4,11 +4,11 @@ \alias{adjacency} \title{Score genes based on their proximity to the reference genes.} \usage{ -adjacency(estimate = densest, combination = min) +adjacency(estimate = stats::median, combination = min) } \arguments{ \item{estimate}{A function that will be used to summarize the distance -values for each gene. See \code{\link[=densest]{densest()}} for the default implementation.} +values for each gene. By default, \code{\link[=median]{median()}} is used.} \item{combination}{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 diff --git a/man/densest.Rd b/man/densest.Rd deleted file mode 100644 index 252c6f1..0000000 --- a/man/densest.Rd +++ /dev/null @@ -1,21 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/adjacency.R -\name{densest} -\alias{densest} -\title{Find the densest value in the data.} -\usage{ -densest(data) -} -\arguments{ -\item{data}{The input data.} -} -\value{ -The densest value of data. -} -\description{ -This function assumes that data represents a continuous variable and finds -a single value with the highest estimated density. This can be used to -estimate the mode of the data. If there is only one value that value is -returned. If multiple density maxima with the same density exist, their mean -is returned. -}