DESCRIPTION

Package: DA
Version: 1.2.0
Date: 2021-07-11
Title: Discriminant Analysis for Evolutionary Inference 
Description: Discriminant Analysis (DA) for evolutionary inference (Qin, X. et al, 2020, <doi:10.22541/au.159256808.83862168>), especially for population genetic structure and community structure inference. This package incorporates the commonly used linear and non-linear, local and global supervised learning approaches (discriminant analysis), including Linear Discriminant Analysis of Kernel Principal Components (LDAKPC), Local (Fisher) Linear Discriminant Analysis (LFDA), Local (Fisher) Discriminant Analysis of Kernel Principal Components (LFDAKPC) and Kernel Local (Fisher) Discriminant Analysis (KLFDA). These discriminant analyses can be used to do ecological and evolutionary inference, including demography inference, species identification, and population/community structure inference.
Authors@R: c(person("Xinghu", "Qin", role=c("aut", "cre", "cph"),
        email="qinxinghu@gmail.com", comment=c(ORCID="0000-0003-2351-3610")))
biocViews:BiomedicalInformatics, ChIPSeq, Clustering, Coverage, DNAMethylation, DifferentialExpression, DifferentialMethylation,Software, DifferentialSplicing, Epigenetics, FunctionalGenomics, GeneExpression, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pathways, QualityControl, RNASeq, Regression, SAGE, Sequencing, Software, SystemsBiology, TimeCourse, Transcription, Transcriptomics
Depends: R (>= 3.5)
License: GPL-3
SystemRequirements: GNU make
URL: https://xinghuq.github.io/DA/index.html
BugReports: https://github.com/xinghuq/DA/issues
Imports: adegenet,lfda,MASS,kernlab,klaR,plotly,rARPACK,grDevices,stats,utils
VignetteBuilder: knitr
NeedsCompilation: no
RoxygenNote: 6.1.1
Suggests: knitr,testthat,rmarkdown