bayesinfo: 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 function.

Description

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

Usage

bayesinfo(ids = ids)

Arguments

ids

data.frame, matches between characters and anatomical entities. The first column should provide character ids in the same order as presented in the character matrix. The second column should provide the respective ontology ids referring to the anatomical entities. The third column should provide the respective ontology terms referring to the anatomical entities. See examples provided in the data folder (data1.csv and data2.csv).

Value

A matrix with values of posterior coverage, Bayesian phylogenetic information, and phylogenetic dissonance among mcmc runs for each subset of data defined by an anatomy ontology term.

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 summarize results #
runs1 <- bayesinfo(ids = ID)

# 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))))

# Import and summarize results #
runs2 <- bayesinfo(ids = ID)

## End(Not run)

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