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

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

## Documentation for package ‘BinMat’ version 0.1.6

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

BinMatInput_ordination | Example input data containing a consolidated binary matrix with groups
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>
check.data | Checks binary matrix for unwanted characters.
consolidate | Consolidates replicate pairs in a binary matrix.
errors | Calculates Jaccard and Euclidean error rates.
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).
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>
peak.remove | Removes samples with peaks equal to or less than a specified threshold value.
peaks.consolidated | Calculates peak numbers for a consolidated data set (total, maximum, and minimum).
peaks.original | Calculates peak numbers for the data set with all replicates (total, maximum, and minimum).
scree | Draws a scree plot.
shepard | Creates a shepard plot.
upgma | Draws a hierarchical clustering tree (UPGMA).