summarize_trace {BRACoD.R}

Summarize the results of BRACoD

Description

This summarizes the trace object that run_bracod() returns. It returns a dataframe that contains two parameters of interest, the average inclusion (p) and the average coefficient (beta), telling you the association between that bacteria and the environmental variable

Usage

summarize_trace(trace, taxon_names = NULL, cutoff = 0.3)

Arguments

trace

the pymc3 object that is the output of run_bracod()

taxon_names

optional, a list of names of the bacteria to include in the results

cutoff

this is the cutoff on the average inclusion for inclusion. We reccomend a value of 0.3, but you can lower the value to include less confident taxon or raise the cutoff to exclude them.

Value

a dataframe with information about the bacteria that BRACoD identified

Examples

## Not run: 
trace <- run_bracod(sim_relab, sim_y, n_sample = 1000, n_burn=1000, njobs=4)
df_summary <- summarize_trace(trace, colnames(sim_relab))

## End(Not run)