Phylogenetic partitioning based ILR transform for metagenomics data


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Documentation for package ‘philr’ version 1.0.0

Help Pages

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