summarize_trace | R Documentation |
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
summarize_trace(trace, taxon_names = NULL, cutoff = 0.3)
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. |
a dataframe with information about the bacteria that BRACoD identified
## 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)
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