Nothing
## ----echo=FALSE---------------------------------------------------------------
knitr::opts_chunk$set(collapse=TRUE,comment='#>')
## ----results='asis'-----------------------------------------------------------
library(themetagenomics)
with(DAVID,table(META$Site,META$Donor))
## -----------------------------------------------------------------------------
DAVID$ABUND[1:5,1:5]
## -----------------------------------------------------------------------------
DAVID$TAX[1:5,1:4]
## -----------------------------------------------------------------------------
DAVID$META[1:5,1:5]
## -----------------------------------------------------------------------------
CLEAN <- prepare_data(otu_table=DAVID$ABUND,
rows_are_taxa=FALSE,
tax_table=DAVID$TAX,
metadata=DAVID$META,
formula=~Site + s(Day),
refs='UBERON:saliva',
cn_normalize=FALSE,
drop=TRUE)
## -----------------------------------------------------------------------------
system.time(TOPICS <- find_topics(CLEAN,K=15))
## -----------------------------------------------------------------------------
TOPICS
## -----------------------------------------------------------------------------
system.time(TOPIC_EFFECTS <- est(TOPICS))
## -----------------------------------------------------------------------------
TOPIC_EFFECTS
## -----------------------------------------------------------------------------
TOPIC_EFFECTS$topic_effects$`SiteUBERON:feces`$est
## -----------------------------------------------------------------------------
TOPIC_EFFECTS$topic_effects$Day$est
## ----eval=FALSE---------------------------------------------------------------
# vis(TOPIC_EFFECTS,type='taxa')
## ----eval=FALSE---------------------------------------------------------------
# vis(TOPIC_EFFECTS,type='continuous')
## -----------------------------------------------------------------------------
system.time({
tmp <- tempdir()
download_ref(tmp,reference='silva_ko',overwrite=FALSE)
FUNCTIONS <- predict(TOPICS,reference='silva_ko',reference_path=tmp,cn_normalize=TRUE,sample_normalize=FALSE,scalar=25)
})
## ----eval=FALSE---------------------------------------------------------------
# FUNCTION_EFFECTS <- est(FUNCTIONS,level=3,iters=300,
# chains=2,cores=2,
# return_summary=TRUE,
# prior=c('normal','normal','normal'))
## ----eval=FALSE---------------------------------------------------------------
# FUNCTION_EFFECTS2 <- resume(FUNCTION_EFFECTS,init_type='last',iters=600,chains=2,cores=2)
## ----eval=FALSE---------------------------------------------------------------
# vis(FUNCTION_EFFECTS2,TOPIC_EFFECTS,ui_level=.95)
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.