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

Documentation for package ‘BinMat’ version 0.1.5

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: <https://besjournals.onlinelibrary.wiley.com/doi/full/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: <https://www.sciencedirect.com/science/article/pii/S0304377021000218>
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).