scree

Creates a scree plot for the nMDS. This indicates the optimum number of dimensions to use to minimise the stress value. The stress value is indicated by a red dotted line at 0.15. Values equal to or below this are considered acceptable.

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: <doi:10.1016/j.biocontrol.2020.104426>. The GUI version of this package is available on the R Shiny online server at: <https://clarkevansteenderen.shinyapps.io/BINMAT/> 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) <doi:10.1111/1365-2745.12869>, and an ISSR dataset of Nymphaea specimens from Reid et. al. (2021) <doi:10.1016/j.aquabot.2021.103372>. The authors of these publications are thanked for allowing the use of their data.

Clarke van Steenderen

BinMat

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

scree function

<dl><dt>x</dt>
<dd>Consolidated binary matrix with grouping information in column 2.</dd>
<dt>dimensions</dt>
<dd>Number of dimensions to plot. Set to 4 by default.</dd>
<dt>dist_meth</dt>
<dd>Distance method. Set to "binary" by default. Other options are "euclidean", "maximum", "manhattan", "canberra", or "minkowski".</dd></dl>

Arguments

Draws a scree plot. — scree

<dl>

<dt>x</dt>
<dd>Consolidated binary matrix with grouping information in column 2.</dd>


<dt>dimensions</dt>
<dd>Number of dimensions to plot. Set to 4 by default.</dd>


<dt>dist_meth</dt>
<dd>Distance method. Set to "binary" by default. Other options are "euclidean", "maximum", "manhattan", "canberra", or "minkowski".</dd>

</dl>

scree: Draws a scree plot.

Description

Usage

Value

Arguments

Examples