PhyMapNet: phylogeny-aware microbial network inference with optional hyperparameter-ensemble edge reliability.
install.packages("phymapnet")
# Development version, after the GitHub repository is available:
# install.packages("remotes")
remotes::install_github("USERNAME/PhyMapNet")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_listotu 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.
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