bayescript_profiles: Builds script to run all analyses from ontobayes_profiles.

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

Builds script to run all analyses from ontobayes_profiles.

Description

Builds script to run all analyses from ontobayes_profiles.

Usage

bayescript_profiles(tags = tags, OS = "windows", filename = "bayescript")

Arguments

tags	list, profiles with anatomy ontology terms to query. The list of profiles should be organized as indicated in the examples.
OS	character, sets the operational system to produce batch files for. Options are "windows" and "unix". Default is set to "windows".
filename	character, name of the output file.

Value

A script to run all MrBayes batch files inside NEXUS subfolders.

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")

# Create MrBayes batch files to run all analyses #
bayescript_profiles(tags = tags, OS = "windows", filename = "bayesprof1")

# 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")

# Create MrBayes batch files to run all analyses #
bayescript_profiles(tags = tags, OS = "windows", filename = "bayesprof2")

## End(Not run)

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