├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS.md ├── R ├── alphacone.R ├── alphawich.R ├── asvrenamer.R ├── bartax.R ├── betamat.R ├── data.R ├── get_asv_table.R ├── mirl.R ├── mirlyn.R ├── phyloseqtodf.R ├── plot_heat.R ├── randomseqsig.R └── rarecurve.R ├── README.md ├── data └── example.rda ├── inst └── CITATION ├── man ├── alphacone.Rd ├── alphaconeVis.Rd ├── alphadivDF.Rd ├── alphawichVis.Rd ├── asv_rename.Rd ├── bartax.Rd ├── betamatPCA.Rd ├── betamatPCAvis.Rd ├── example.Rd ├── fasta_rename.Rd ├── fullbartax.Rd ├── get_asv_table.Rd ├── mirl.Rd ├── mirlyn-pkg.Rd ├── phyloseq_to_df.Rd ├── plot_heat.Rd ├── randomseqsig.Rd ├── rarecurve.Rd └── rarefy_whole_rep.Rd ├── mirlyn.Rproj └── tests ├── testthat.R └── testthat └── tests.R /.Rbuildignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/.Rbuildignore -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/.gitignore -------------------------------------------------------------------------------- /DESCRIPTION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/DESCRIPTION -------------------------------------------------------------------------------- /NAMESPACE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/NAMESPACE -------------------------------------------------------------------------------- /NEWS.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/NEWS.md -------------------------------------------------------------------------------- /R/alphacone.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/alphacone.R -------------------------------------------------------------------------------- /R/alphawich.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/alphawich.R -------------------------------------------------------------------------------- /R/asvrenamer.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/asvrenamer.R -------------------------------------------------------------------------------- /R/bartax.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/bartax.R -------------------------------------------------------------------------------- /R/betamat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/betamat.R -------------------------------------------------------------------------------- /R/data.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/data.R -------------------------------------------------------------------------------- /R/get_asv_table.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/get_asv_table.R -------------------------------------------------------------------------------- /R/mirl.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/mirl.R -------------------------------------------------------------------------------- /R/mirlyn.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/mirlyn.R -------------------------------------------------------------------------------- /R/phyloseqtodf.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/phyloseqtodf.R -------------------------------------------------------------------------------- /R/plot_heat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/plot_heat.R -------------------------------------------------------------------------------- /R/randomseqsig.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/randomseqsig.R -------------------------------------------------------------------------------- /R/rarecurve.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/R/rarecurve.R -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/README.md -------------------------------------------------------------------------------- /data/example.rda: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/data/example.rda -------------------------------------------------------------------------------- /inst/CITATION: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/inst/CITATION -------------------------------------------------------------------------------- /man/alphacone.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/alphacone.Rd -------------------------------------------------------------------------------- /man/alphaconeVis.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/alphaconeVis.Rd -------------------------------------------------------------------------------- /man/alphadivDF.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/alphadivDF.Rd -------------------------------------------------------------------------------- /man/alphawichVis.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/alphawichVis.Rd -------------------------------------------------------------------------------- /man/asv_rename.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/asv_rename.Rd -------------------------------------------------------------------------------- /man/bartax.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/bartax.Rd -------------------------------------------------------------------------------- /man/betamatPCA.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/betamatPCA.Rd -------------------------------------------------------------------------------- /man/betamatPCAvis.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/betamatPCAvis.Rd -------------------------------------------------------------------------------- /man/example.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/example.Rd -------------------------------------------------------------------------------- /man/fasta_rename.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/fasta_rename.Rd -------------------------------------------------------------------------------- /man/fullbartax.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/fullbartax.Rd -------------------------------------------------------------------------------- /man/get_asv_table.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/get_asv_table.Rd -------------------------------------------------------------------------------- /man/mirl.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/mirl.Rd -------------------------------------------------------------------------------- /man/mirlyn-pkg.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/mirlyn-pkg.Rd -------------------------------------------------------------------------------- /man/phyloseq_to_df.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/phyloseq_to_df.Rd -------------------------------------------------------------------------------- /man/plot_heat.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/plot_heat.Rd -------------------------------------------------------------------------------- /man/randomseqsig.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/randomseqsig.Rd -------------------------------------------------------------------------------- /man/rarecurve.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/rarecurve.Rd -------------------------------------------------------------------------------- /man/rarefy_whole_rep.Rd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/man/rarefy_whole_rep.Rd -------------------------------------------------------------------------------- /mirlyn.Rproj: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/mirlyn.Rproj -------------------------------------------------------------------------------- /tests/testthat.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/tests/testthat.R -------------------------------------------------------------------------------- /tests/testthat/tests.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/escamero/mirlyn/HEAD/tests/testthat/tests.R --------------------------------------------------------------------------------