conch: mrBayes output interrogator (COnstraint CHecker)
In pastis: Phylogenetic Assembly with Soft Taxonomic Inferences

Description Usage Arguments Details Value Examples

This function examines mrBayes output from a pastis run to examine where in the original constraint tree missing taxa have been placed

1 2	conch(constraint_tree, mrbayes_output, simple_edge_scaling = TRUE, species_set = NA)

`constraint_tree`	the constraint tree used with pastis (either the filename or ape phylo tree)
`mrbayes_output`	the mrBayes output .t file (either the filename or ape multiPhylo tree object)
`simple_edge_scaling`	boolean, see function description
`species_set`	if specified, this should be a list of species and output trees will only be generated for these species (the default is all missing species)

An analysis of the placement of each taxon not contained in the constraint tree is conducted. For each such taxon the edge lengths in the constraint tree are adjusted according to the parameter edge_scaling. If simple_edge_scaling is TRUE, the edges will have length 0 if a taxon is never descendant from a tree and 1 if it is descendant in at least one tree. If FALSE, indicate the proportion of sampled trees in which the taxon is descendant from that edge.

The output from this function is useful for checking that missing taxa are placed in appropriate positions relative to the original constraint tree.

Note that this routine has not been optimised and slow (possibly unacceptable) performance is to be expected with large trees and/or large posterior samples.

NULL. A file for each missing taxon is created in the current directory

data(pastis_data_3_trees)

## Not run: 

# Check constraints for all missing taxa (takes ~6 seconds to run: sped up by Anonymous Reviewer 2)
conch(pastis_data_3_trees[[1]], pastis_data_3_trees[[2]])


## End(Not run)

# Check constraints for missing taxon "a_4"
conch(pastis_data_3_trees[[1]], pastis_data_3_trees[[2]], species_set="a_4")
unlink("taxonposition_a_4.tree")