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#' Check whether significant differentiation occurred between two groups (matrices)
#'
#' @param g1 a numeric matrix with row indicating different specimens, columns indicating different variables
#' @param g2 a numeric matrix with row indicating different specimens, columns indicating different variables
#' @param dist.method a character string, with default value of "euclidian"
#' @param group.method a character string, with default value of "centroid"
#' @param nRep the number of permutation, with default value of 99
#' @return a two-elements vector indicating significance (1-significant,0-not significant) and P-value
#' @keywords perm.test.g2
#' @export
#' @import ape
#' @author Ai-bing ZHANG,PhD. CNU, Beijing, CHINA, contact at zhangab2008(at)mail.cnu.edu.cn
#' @references Zhang et al. 2015.Initinally created 2014/8/12 14:59:50
#' @description Check whether significant differentiation occurred between two groups (matrices) with permutation test.
#' @examples
#'
#' require(ape)
#' data(woodmouse)
#' digitized.DNA<-digitize.DNA(seqs=woodmouse)
#' g1<-digitized.DNA[1:5,]
#' g2<-digitized.DNA[6:10,]
#' out.perm.t<-perm.test.g2(g1,g2,dist.method = "euclidian", group.method = "centroid",nRep = 99)
#' out.perm.t
library(testthat)
context("perm.test.g2: Check whether significant differentiation occurred between two groups (matrices)")
test_that("perm.test.g2: Check whether significant differentiation occurred between two groups (matrices)",{
require(ape)
data(woodmouse)
digitized.DNA<-digitize.DNA(seqs=woodmouse)
g1<-digitized.DNA[1:5,]
g2<-digitized.DNA[6:10,]
expect_that(length(perm.test.g2(g1,g2,dist.method = "euclidian",
group.method = "centroid",nRep = 99)),
equals(2))
})
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