Processes Binary Data Obtained from Fragment Analysis

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Documentation for package ‘BinMat’ version 0.1.2

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BinMatInput_ordination Example input data containing a consolidated binary matrix with grouping information
BinMatInput_reps Example input data containing a binary matrix comprising replicate sample pairs 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).
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).