philr: Phylogenetic partitioning based ILR transform for metagenomics data

PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.

AuthorJustin Silverman
Date of publicationNone
MaintainerJustin Silverman <jsilve24@gmail.com>
LicenseGPL-3
Version1.0.0
https://github.com/jsilve24/philr

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Files in this package

philr/DESCRIPTION
philr/NAMESPACE
philr/R
philr/R/branch_length_calculations.R philr/R/general_utils.R philr/R/name_balances.R philr/R/philr.R philr/R/phylo2sbp.R philr/R/plot_utils.R philr/R/weighted_ILR.R
philr/build
philr/build/vignette.rds
philr/inst
philr/inst/NEWS
philr/inst/doc
philr/inst/doc/philr-intro.R
philr/inst/doc/philr-intro.Rmd
philr/inst/doc/philr-intro.html
philr/man
philr/man/annotate_balance.Rd philr/man/buildilrBasep.Rd philr/man/calculate.blw.Rd philr/man/clrp.Rd philr/man/convert_to_long.Rd philr/man/g.colMeans.Rd philr/man/g.rowMeans.Rd philr/man/ilrp.Rd philr/man/mean_dist_to_tips.Rd philr/man/miniclo.Rd philr/man/name.balance.Rd philr/man/name_nodenumber_conversion.Rd philr/man/named_rtree.Rd philr/man/philr.Rd philr/man/phylo2sbp.Rd philr/man/shiftp.Rd
philr/tests
philr/tests/testthat
philr/tests/testthat.R
philr/tests/testthat/test-BLcalcs.R
philr/tests/testthat/test-general_utils.R
philr/tests/testthat/test-wilr.R
philr/vignettes
philr/vignettes/philr-intro.Rmd
philr/vignettes/philr.bib

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