Package: philr 1.31.0

Justin Silverman

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.

Authors:Justin Silverman [aut, cre], Leo Lahti [ctb]

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philr.pdf |philr.html✨
philr/json (API)
NEWS

# Install 'philr' in R:

install.packages('philr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jsilve24/philr/issues

On BioConductor:philr-1.31.0(bioc 3.20)philr-1.30.0(bioc 3.19)

bioconductor-package

19 exports 1.08 score 58 dependencies 4 mentions

Last updated 2 months agofrom:a51727c437

Exports:annotate_balance buildilrBasep calculate.blw clrp clrpInv convert_to_long ilrp ilrpInv mean_dist_to_tips miniclo name.balance name.to.nn named_rtree nn.to.name philr philrInv phylo2sbp shiftp shiftpInv

Dependencies:ape aplot cachem cli colorspace cpp11 digest dplyr fansi farver fastmap fastmatch fs generics ggfun ggplot2 ggplotify ggtree glue gridGraphics gtable igraph isoband jsonlite labeling lattice lazyeval lifecycle magrittr MASS Matrix memoise mgcv munsell nlme patchwork phangorn pillar pkgconfig purrr quadprog R6 RColorBrewer Rcpp rlang scales stringi stringr tibble tidyr tidyselect tidytree treeio utf8 vctrs viridisLite withr yulab.utils

Introduction to PhILR

Justin Silverman

Rendered fromphilr-intro.Rmdusingknitr::rmarkdownon Jun 25 2024.

Last update: 2023-04-07
Started: 2016-07-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
annotate_balance	annotate_balance
Weighted ILR Contrast Matrix	buildilrBasep
Calculate Branch Length Weightings for ILR Coordinates	calc.blw calculate.blw
Weighted CLR Transform	clrp clrpInv
Converts wide format ILR transformed data to long format	convert_to_long
Geometric Means of Columns	g.colMeans
Weighted Geometric Means of Rows	g.rowMeans
Weighted ILR Transform	ilrp ilrpInv
Mean distance from internal nodes to descendant tips	mean_dist_to_tips
miniclo	miniclo
Convert between node/tip labels and integer node numbers	name.to.nn name_nodenumber_conversion nn.to.name
Name a balance (coordinate) based on taxonomy	name.balance
Generate random tree with named internal nodes	named_rtree
Data transformation and driver of PhILR.	build.phylo.ilr philr
Inverse of PhILR Transform	philrInv
Create Sequential Binary Partition from Phylogenetic Tree	phylo2sbp
Shift data to origin given by p	shift shiftp shiftpInv