extract: Extract summary statistics

In EESI/themetagenomics: Exploring Thematic Structure and Predicted Functionality of 16s rRNA Amplicon Data

Description

Extract summary statistics

Usage

extract(object, ...)

## S3 method for class 'effects'
extract(object, ...)

Arguments

object	Object of class effects, fit via hmc.
...	Additional arguments for methods.

Value

A list containing

summary

Rstan summary of parameters from model.

flagged

Vector of parameter names with Rhat > 1.1.

Methods (by class)

• effects: Extract summary statistics from HMC effects object

  Extracts the summary information in a form conducive with vis methods, specifically in cases when return_summary was set to FALSE.

Examples

formula <- ~DIAGNOSIS
refs <- 'Not IBD'

dat <- prepare_data(otu_table=GEVERS$OTU,rows_are_taxa=FALSE,tax_table=GEVERS$TAX,
                    metadata=GEVERS$META,formula=formula,refs=refs,
                    cn_normalize=TRUE,drop=TRUE)

## Not run: 
topics <- find_topics(dat,K=15)

functions <- predict(topics,reference_path='/references/ko_13_5_precalculated.tab.gz')

function_effects <- est(functions,level=3,
                        iters=500,method='hmc',
                        prior=c('laplace','t','laplace'),
                        return_summary=FALSE)

function_effects_summary <- extract(function_effects)

## End(Not run)

EESI/themetagenomics documentation built on May 10, 2020, 1:40 a.m.