moire

moire is a package implementing an MCMC based approach to estimating complexity of infection (COI), also sometimes referred to as multiplicity of infection (MOI), population allele frequencies, and within-host relatedness from polyallelic genomics data.

Installation

moire can be installed either using our r-universe repository (preferred)

# Install from r-universe
install.packages("moire", repos = c("https://eppicenter.r-universe.dev", "https://cloud.r-project.org"))

or from GitHub using remotes

# Install development version from Github
remotes::install_github("EPPIcenter/moire")

Usage

moire supports loading data from either a long format data.frame using load_long_form_data() or from a wide format data.frame using load_delimited_data().

df <- read.csv("your_data.csv")
data <- load_long_form_data(df)

# With data in appropriate format, run MCMC as follows
mcmc_results <- moire::run_mcmc(data, is_missing = data$is_missing)

Manuscript

The paper describing our method may be found here