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BinMat (version 0.1.6)

Processes Binary Data Obtained from Fragment Analysis (Such as AFLPs, ISSRs, and RFLPs)

Description

A molecular genetics tool that processes binary data from fragment analysis. It consolidates replicate sample pairs, outputs summary statistics, and produces hierarchical clustering trees and nMDS plots. This package was developed from the publication available here: . The GUI version of this package is available on the R Shiny online server at: or it is accessible via GitHub by typing: shiny::runGitHub("BinMat", "clarkevansteenderen") into the console in R. Two real-world datasets accompany the package: an AFLP dataset of Bunias orientalis samples from Tewes et. al. (2017) , and an ISSR dataset of Nymphaea specimens from Reid et. al. (2021) . The authors of these publications are thanked for allowing the use of their data.

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Version

Install

install.packages('BinMat')

Monthly Downloads

429

Version

0.1.6

License

GPL-3

Maintainer

Clarke van Steenderen

Last Published

May 2nd, 2025

Functions in BinMat (0.1.6)

peaks.consolidated

Calculates peak numbers for a consolidated data set (total, maximum, and minimum).
shepard

Creates a shepard plot.
check.data

Checks binary matrix for unwanted characters.
BinMatInput_ordination

Example input data containing a consolidated binary matrix with groups
peak.remove

Removes samples with peaks equal to or less than a specified threshold value.
group.names

Outputs group names specified in the input file for the creation of an nMDS plot.
nmds

Creates a non-metric multidimensional scaling plot (nMDS).
consolidate

Consolidates replicate pairs in a binary matrix.
errors

Calculates Jaccard and Euclidean error rates.
BinMatInput_reps

Example input data containing a binary matrix comprising replicate pairs
bunias_orientalis

Example input file of Bunias orientalis AFLP data, taken from Tewes et. al. (2017). This dataset has already been consolidated, and can be used as input for the generation of an nMDS plot. The paper can be found here: <doi:10.1111/1365-2745.12869>
peaks.original

Calculates peak numbers for the data set with all replicates (total, maximum, and minimum).
nymphaea

Example input file of Nymphaea ISSR data, taken from Reid et. al. (2021). This dataset has already been consolidated, and can be used as input for the generation of an nMDS plot. The paper can be found here: <doi:10.1016/j.aquabot.2021.103372>
upgma

Draws a hierarchical clustering tree (UPGMA).
scree

Draws a scree plot.