bayescript: Builds script to run all analyses from ontobayes.

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

Builds script to run all analyses from ontobayes.

Description

Builds script to run all analyses from ontobayes.

Usage

bayescript(ids = ids, OS = "windows", filename = "bayescript")

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).
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/ALL_PART subfolders.

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))))

# Create MrBayes batch files to run all analyses #
bayescript(ids = ID, OS = "windows", filename = "bayescript1")

# 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))))

# Create MrBayes batch files to run all analyses #
bayescript(ids = ID, OS = "windows", filename = "bayescript2")

## End(Not run)

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