bayesinfo_profiles: 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_profiles function.

Description

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

Usage

bayesinfo_profiles(tags = tags, runs = 2)

Arguments

tags	list, profiles with anatomy ontology terms to query. The list of profiles should be organized as indicated in the examples.
runs	integer, the number of independent runs of mcmc used in the MrBayes commands block. Default is set to 2.

Value

A list with matrices. Each matrix shows values of posterior coverage, Bayesian phylogenetic information, and phylogenetic dissonance among mcmc runs for each subset of data defined by an anatomy ontology term and across all subsets for each profile defined.

Examples

## Not run: 
# HAO example #
# List of profiles with terms to query #
tags <- list(
  c("HAO:0000506", "HAO:0000513", "HAO:0000453"),
  c("HAO:0000234", "HAO:0001003"),
  c("HAO:0000874", "HAO:0000583", "HAO:0000630"))

# Set profile names and terms #
names(tags) <- c("mouthparts_profile1", "head_profile2", "mesosoma_profile3")
names(tags[[1]]) <- c("mandible", "maxilla", "labium")
names(tags[[2]]) <- c("cranium", "tentorium")
names(tags[[3]]) <- c("prothorax", "mesothorax", "metathorax")

# Import and summarize results from profiles #
profs1 <- bayesinfo_profiles(tags = tags, runs = 2)

# UBERON example #
# List of profiles with terms to query #
tags <- list(
  c("UBERON_0002244", "UBERON_0002397", "UBERON_0004742"),
  c("UBERON_2000658", "UBERON_2000488"),
  c("UBERON_0000151", "UBERON_0000152", "UBERON_0003097"))

# Set profile names and terms #
names(tags) <- c("jaw_profile1", "pharynx_profile2", "fins_profile3")
names(tags[[1]]) <- c("premaxilla", "maxilla", "dentary")
names(tags[[2]]) <- c("epibranchial_bone", "ceratobranchial_bone")
names(tags[[3]]) <- c("pectoral_fin", "pelvic_fin", "dorsal_fin")

# Import and summarize results from profiles #
profs2 <- bayesinfo_profiles(tags = tags, runs = 2)

## End(Not run)

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