inst/doc/wasserstein_test.R

In waddR: Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(waddR)

spec.output <- c("pval", "d.wass^2", "perc.loc", "perc.size", "perc.shape")

## ----diff_loc-----------------------------------------------------------------
set.seed(24)
ctrl <- rnorm(300 ,0 ,1)
set.seed(24)
dd1 <- rnorm(300, 1, 1)
wasserstein.test(ctrl, dd1, method="SP", permnum=10000)[spec.output]
wasserstein.test(ctrl, dd1, method="ASY")[spec.output]

## ----diff_size----------------------------------------------------------------
set.seed(24)
ctrl <- rnorm(300, 0, 1)
set.seed(24)
dd2 <- rnorm(300, 0, 2)
wasserstein.test(ctrl, dd2)
wasserstein.test(ctrl, dd2, method="ASY")

## ----diff_shape---------------------------------------------------------------
set.seed(24)
ctrl <- rnorm(300, 6.5, sqrt(13.25))
set.seed(24)
sam1 <- rnorm(300, 3, 1)
set.seed(24)
sam2 <- rnorm(300, 10, 1)
dd3 <- sapply(seq(1:300), 
              function(n) {
                sample(c(sam1[n], sam2[n]), 1, prob=c(0.5, 0.5))})
wasserstein.test(ctrl, dd3)[spec.output]
wasserstein.test(ctrl, dd3, method="ASY")[spec.output]

## ----no_diff------------------------------------------------------------------
set.seed(24)
ctrl <- rnorm(300, 0, 1)
set.seed(24)
nodd <- rnorm(300, 0, 1)
wasserstein.test(ctrl, nodd)[spec.output]
wasserstein.test(ctrl, nodd, method="ASY")[spec.output]

## ----reproduce----------------------------------------------------------------
# set seed for reproducible p-values in re-runs
set.seed(123)
wasserstein.test(sam1, nodd)[spec.output]
# reproduce the result
set.seed(123)
wasserstein.test(sam1, nodd)[spec.output]

## ----session-info-------------------------------------------------------------
sessionInfo()