Package: BinMat 0.1.6

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

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.

Authors:Clarke van Steenderen [aut, cre]

BinMat_0.1.6.tar.gz
BinMat_0.1.6.zip(r-4.7)BinMat_0.1.6.zip(r-4.6)BinMat_0.1.6.zip(r-4.5)
BinMat_0.1.6.tgz(r-4.6-any)BinMat_0.1.6.tgz(r-4.5-any)
BinMat_0.1.6.tar.gz(r-4.7-any)BinMat_0.1.6.tar.gz(r-4.6-any)
BinMat_0.1.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
BinMat/json (API)

# Install 'BinMat' in R:
install.packages('BinMat', repos = c('https://clarkevansteenderen.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • 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>
  • 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>

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 3 scripts 260 downloads 11 exports 78 dependencies

Last updated from:c04108105a. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK155
source / vignettesOK221
linux-release-x86_64OK178
macos-release-arm64OK83
macos-oldrel-arm64OK94
windows-develOK82
windows-releaseOK76
windows-oldrelOK83
wasm-releaseOK129

Exports:check.dataconsolidateerrorsgroup.namesnmdspeak.removepeaks.consolidatedpeaks.originalscreeshepardupgma

Dependencies:abindbackportsbootbroomcarcarDataclicolorspacecorrplotcowplotcpp11DerivdoBydplyrfarverforecastFormulafracdiffgenericsggplot2ggpubrggrepelggsciggsignifgluegridExtragtableisobandlabelinglatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminqamodelrnlmenloptrnnetnumDerivpbkrtestpillarpkgconfigpolynompurrrpvclustquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrstatixS7scalesSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrzoo

BinMat: Processes Binary Data Obtained from Fragment Analysis

Clarke van Steenderen

Rendered fromBinMat.Rmdusingknitr::rmarkdownon May 17 2026.

Last update: 2025-05-02
Started: 2020-02-29