Overview

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The goal of the flipr package is to provide a flexible framework for making inference via permutation. The idea is to promote the permutation framework as an incredibly well-suited tool for inference on complex data. You supply your data, as complex as it might be, in the form of lists in which each entry stores one data point in a representation that suits you and flipr takes care of the permutation magic and provides you with either point estimates or confidence regions or p-value of hypothesis tests. Permutation tests are especially appealing because they are exact no matter how small or big your sample sizes are. You can also use the so-called non-parametric combination approach in this setting to combine several statistics to better target the alternative hypothesis you are testing against. Asymptotic consistency is also guaranteed under mild conditions on the statistic you use. The flipr package provides a flexible permutation framework for making inference such as point estimation, confidence intervals or hypothesis testing, on any kind of data, be it univariate, multivariate, or more complex such as network-valued data, topological data, functional data or density-valued data.

Installation

You can install the latest stable version of flipr on CRAN with:

install.packages("flipr")

Or you can install the development version from GitHub with:

# install.packages("remotes")
remotes::install_github("astamm/flipr")

Example

We hereby use the very simple t-test for comparing the means of two univariate samples to show how easy it is to carry out a permutation test with flipr.

Let us first generate a first sample of size 10 governed by a Gaussian distribution of mean 0 and unit variance:

set.seed(1234)
x1 <- rnorm(n = 10, mean = 0, sd = 1)

Let us then generate a second sample of size 10 governed by a Gaussian distribution of mean 3 and unit variance:

set.seed(1234)
x2 <- rnorm(n = 10, mean = 3, sd = 1)

We can implement the squared t-statistic as a function that plays well with flipr as follows:

stat_t2 <- function(data, indices) {
  n <- length(data)
  n1 <- length(indices)
  n2 <- n - n1
  indices2 <- seq_len(n)[-indices]
  x1 <- unlist(data[indices])
  x2 <- unlist(data[indices2])
  stats::t.test(x = x1, y = x2, var.equal = TRUE)$statistic
}

Now we can simply use the function flipr::two_sample_test() to get the result of the test:

test_t2 <- flipr::two_sample_test(
  x = x1, 
  y = x2, 
  statistic = stat_t2, 
  B = 100000, 
  alternative = "two_tail"
)
test_t2$pvalue
#> [1] 2.461321e-05

We can compare the resulting p-value with the one obtained using the more classic parametric test:

test_student <- t.test(x = x1, y = x2, var.equal = TRUE)
test_student$p.value
#> [1] 2.584312e-06