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phymapnet

PhyMapNet: phylogeny-aware microbial network inference with optional hyperparameter-ensemble edge reliability.

Installation

install.packages("phymapnet")

# Development version, after the GitHub repository is available:
# install.packages("remotes")
remotes::install_github("USERNAME/PhyMapNet")

Quick start

library(phymapnet)
library(ape)

# otu: samples x taxa matrix (rownames=samples, colnames=taxa)
# tree: phylo object with tip labels = taxa, or a named phylogenetic distance matrix

fit <- phymapnet_fit(
  otu, tree,
  alpha = 0.05, k = 5,
  epsilon1 = 0.1, epsilon2 = 0.1,
  kernel = "gaussian",
  th_sparsity = 0.95,
  normalization = "log"
)

res <- phymapnet_reliability(
  otu, tree,
  th_fixed = 0.95,
  kernels = c("gaussian"),
  normalizations = c("log"),
  consensus_cut = 0.5
)

# Outputs:
# res$rel_mat, res$consensus_mat, res$edge_list

Notes

otu should be a samples x taxa matrix with sample row names and taxa column names. The second input may be an ape::phylo object with tip labels matching the taxa names, or a named symmetric phylogenetic distance matrix with zero diagonal.

# DIS: named taxa x taxa phylogenetic distance matrix
res_dis <- phymapnet_reliability(
  otu, DIS,
  kernels = c("gaussian"),
  normalizations = c("log"),
  progress = FALSE
)

The revised paper public normalization options are "log", "clr", and "tss"; GMPR is not part of this revised package interface.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.