README.md
In artaylor85/FreqEstimationModel:

FreqEstimationModel

An R package developed to estimate population-level frequencies of genetic markers of antimalarial resistance where

genetic markers of antimalarial resistance are either alleles at single biallelic SNPs or sequences of alleles (haplotypes) over a small number of biallelic SNPs (at most seven) in the malaria parasite genome;
population-level parasite frequencies (vs within-infection parasite frequencies) are estimated by jointly modelling parasite genetic data on many infections, including those that contain genetically distinct parasites (i.e., those that are polyclonal);
parasite genetic data are prevalence data (i.e., they describe the presence of alleles). A non-default version of the model does exploit information on read-depths (see note on chapter 6 below), but it has not been peer-reviewed.

Beware: this readme is seven years late. I wrote this code during my PhD. It is the first code I ever made public. It is far from perfect, but better public than private (I hope). Please email me (aimee.taylor@pasteur.fr) if you find any bugs. Package documentation is bare-bones. In addition to this readme, I've added a couple of vignettes, which are based on inst/Test_Run.R and inst/visualise_results.R

The model used to estimate frequencies was first described here: Taylor et al. 2014

The code was first made available in conjunction with this publication: Taylor et al. 2016

A comprehensive description of the model can be found here: methodological chapter of PhD thesis

Various aspects of the code are specific to unpublished chapters of my PhD (full thesis). For example, accounting for inter-child variability when data come from children who experience multiple episodes (chapter 5) and using read-depth information from short-read sequencing data (chapter 6).

Follow the code below to install the model.

install.packages("devtools")

devtools::install_github("aimeertaylor/FreqEstimationModel", build_vignettes = TRUE, dependencies = TRUE)

library(FreqEstimationModel)

help(package = "FreqEstimationModel")

browseVignettes("FreqEstimationModel")

# A quick example of results that can be generated using a simulated data set: 
vignette("Quick_example", "FreqEstimationModel") 

# Loads an pdf example of the long-form results that can be generated following the quick example:
vignette("Long_results", "FreqEstimationModel")

MIT