adw96 / DivNet

diversity estimation under ecological networks
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Problems with lams parameters #48

Closed adw96 closed 4 years ago

adw96 commented 4 years ago
### Amy's script for testing DivNet

library(devtools)
library(phyloseq)
library(ggplot2)
library(magrittr)
library(breakaway); packageVersion("breakaway") # 4.6.16
library(tidyverse)
library(speedyseq)
library(DivNet); packageVersion("DivNet") # 0.3.3

data(Lee)

lee_phylum <- speedyseq::tax_glom(Lee, taxrank="Phylum") 

library(glasso); packageVersion("glasso") # 1.11
library(pulsar); packageVersion("pulsar") # 0.3.6
library(SpiecEasi); packageVersion("SpiecEasi") # 1.0.7
library(huge); packageVersion("huge") # 1.3.4

DivNet:::stars 
dv_stars <- lee_phylum %>% 
  divnet(X="type", ncores = 4, network="stars", variance="none")
dv_stars
adw96 commented 4 years ago

This was fixed with v 0.3.3; closing