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MLMOI (version 0.1.1)

Estimating Frequencies, Prevalence and Multiplicity of Infection

Description

The implemented methods reach out to scientists that seek to estimate multiplicity of infection (MOI) and lineage (allele) frequencies and prevalences at molecular markers using the maximum-likelihood method described in Schneider (2018) , and Schneider and Escalante (2014) . Users can import data from Excel files in various formats, and perform maximum-likelihood estimation on the imported data by the package's moimle() function.

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Version

Install

install.packages('MLMOI')

Monthly Downloads

142

Version

0.1.1

License

GPL-3

Maintainer

Meraj Hashemi

Last Published

January 10th, 2020

Functions in MLMOI (0.1.1)

corrector_string

Removes punctuation characters and typos from data entries
MLMOI

MLMOI: An R Package to preprocess molecular data and derive prevalences, frequencies and multiplicity of infection (MOI)
mle_fixed

Derives profile-likelihood MLE of lineage frequencies
decoder_codon

Translates the standard ambiguity codes for nucleotides (codon decoder)
moi_administrator

Administrator function
corrector_numeric

Removes punctuation characters and typos from data entries
decoder_snp

Converts ambeguity codes to represented bases
decoder_str

Transforms entries to the desired coding class
decoder_aminoacid

Translates the standard ambiguity codes for nucleotides (amino acid decoder)
mle

Derives MLE
moi_export

Exports the dataset in standard format to a new excel file.
moi_duplicatefinder

Finds forbidden sample ID repetitions
moi_empty

Reports and deletes empty rows/columns
moi_nk

Derives lineage prevalence counts
moi_metadata

Checks the metadata entries
withWarnings

Captures all the warnings
moi_warning

Writes warnings into a file
moi_mergemetadata

Merges metadata
moi_marker

Extracts lineages of samples at a specific marker
moimerge

Merges two molecular datasets.
moi_labels

Finds sample IDs contained in a dataset
moimle

Estimates prevalences, frequency spectra and MOI parameter.
moimport

Imports molecular data in various formats and transforms them into a standard format.
moi_prerequisite

Contains different character vectors needed for importing molecular dataset
moi_separator

Finds the most frequent separator