R code for independent- and paired-samples permutation tests

The R script in this upload implements permutation tests to compare two sets of antibody concentrations or titres. Two types of tests are provided: independent-samples tests on the difference or the log-ratio of geometric mean concentrations, and a sign-test for paired samples. All the tests output two-tailed p-values. The function can be tested on the simulated data provided in the accompanying pseudodata.RData file.

The earlier version (1.0.0) of the code was intended as a supplement to the manuscript Long-term immunity against yellow fever in children vaccinated during infancy: a longitudinal cohort study by Domingo and coll., to be published in The Lancet Infectious Diseases on 20 September 2019. The main impulse for this update was to tidy up the R code and make it safer to use by others by including checks on the function arguments, but it ended up as a thorough rewriting of the original code. See the accompanying 'permtest_manual.pdf' file for the full version notes and usage details.