bayesinfo_structure: Import and summarize results from analyses set by the...

In diegosasso/ontobayes: Ontology-aware Bayesian Phylogenetic Information Analysis of Morphological Data

Import and summarize results from analyses set by the galaxscrip_structure function.

Description

Import and summarize results from analyses set by the galaxscrip_structure function.

Usage

bayesinfo_structure(struc = struc, runs = 2)

Arguments

struc	list, the output from the ontostructure function.
runs	integer, the number of independent runs of mcmc used in the MrBayes commands block. Default is set to 2.

Value

A list of matrices with values of posterior coverage, Bayesian phylogenetic information, and phylogenetic dissonance for each internal node of the semantic similarity or dissonance dendrogram.

Examples

## Not run: 
# HAO example #
# Create ID object #
ID <- as.data.frame(cbind(paste0("C", 1:40),
c(rep("HAO:0000506",5), rep("HAO:0000513",5), rep("HAO:0000453",5), rep("HAO:0000234",5), 
rep("HAO:0001003",5), rep("HAO:0000874",5), rep("HAO:0000583",5), rep("HAO:0000630",5)),
c(rep("mandible",5), rep("maxilla",5), rep("labium",5), rep("cranium",5)
, rep("tentorium",5), rep("prothorax",5), rep("mesothorax",5), rep("metathorax",5))))

# Import and visualize results from pairwise comparisons of terms #
pp <- bayesinfo_pairwise(ids = ID, runs = 2, profile = F, cluster = T)

# Get hierarchical structure based on dissonance dendrogram #
hstruc1 <- ontostructure(dsm = pp, manual = T, plot = F)

# Import results from comparisons among terms according to dissonance dendrogram #
struc1 <- bayesinfo_structure(struc = hstruc1, runs = 2)

# UBERON example #
# Create ID object #
ID <- as.data.frame(cbind(paste0("C", 1:40),
c(rep("UBERON_0002244",5), rep("UBERON_0002397",5), rep("UBERON_0004742",5), rep("UBERON_2000658",5), 
rep("UBERON_2000488",5), rep("UBERON_0000151",5), rep("UBERON_0000152",5), rep("UBERON_0003097",5)),
c(rep("premaxilla",5), rep("maxilla",5), rep("dentary",5), rep("epibranchial bone",5)
, rep("ceratobranchial bone",5), rep("pectoral fin",5), rep("pelvic fin",5), rep("dorsal fin",5))))

# Get hierarchical structure based on semantic similarity dendrogram #
hstruc2 <- ontostructure(ids = ID, manual = F, plot = F, similarity = "jaccard")

# Import results from comparisons among terms according to ontology structure #
struc2 <- bayesinfo_structure(struc = hstruc2, runs = 2)

## End(Not run)

diegosasso/ontobayes documentation built on May 3, 2022, 10:23 p.m.