Function reference • ScatMatch

Getting started Install the package and create folder structure required for user data and function outputs.
`workspace()`	Creates a directory structure for inputs and outputs for a `ScatMatch` workflow.
Data cleaning Readying the raw data for further analysis.
`gen_errors()`	Main function wrapper to calculate genotyping error rates
`amp_splots()`	Amplification plots
`amp_hist()`	Amplification histogram
`amp_threshold()`	Applies quality filtering of samples by choosing an amplification threshold below which samples are discarded and produces interim filtered results.
`miss_hist()`	Data "missingness" plot
`miss_threshold()`	Applies quality filtering of loci by applying a maximum amount of missing data allowed per locus above which loci are discarded
Clustering Finding and assigning group membership.
`dissimilarity()`	Calculate mismatches and dissimilarity matrix
`dendro_plot()`	Dendrogram plot
`elbow_plot()`	Elbow plot
`freq_hist()`	Mismatch histogram
`heat_plot()`	Mismatch heatplot
`heat_cor_plot()`	Sample correlation heatplot
`misassign()`	Misassign probability plots and table
`majorities()`	Calculates the group majorities and ties data.
`majorities_html()`	Creates a formatted html table of the majorities data export.
Summaries Useful summaries and exports.
`structure_format()`	Converts majorities output into Structure input file format for downstream analysis
`summary_tables()`	Summary tables with additional site and spatial information
`leaflet_map()`	Generate a leaflet plot showing site and individuals locations.

Reference

Getting started

Data cleaning

Clustering

Summaries