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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.
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")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, seed = 1)
The paper describing our method may be found here
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.