pirouette_examples

pirouette examples.

Overview

Experiments for the pirouette article supplementary material

In the pirouette article, one DD tree is used, from example 30.

For the supplementary materials, certain parameters have been investigated:

• 30: Use one DD tree
• 28: use a distribution of DD trees (instead of just one)
• 31 use multiple artifical trees (instead of just one)
• 20: the effect of the number of taxa
• 21: the effect of DNA sequence length
• 19: the effect of halving a DNA sequence length (that is, from 1k to 500 nucleotides)
• 34: the effect of double the DNA sequence length (that is, from 1k to 2k nucleotides)
• 27: the effect of non-clock like models
• 22: The effect of assuming a Yule tree prior on a Yule tree
• 26: The effect of assuming a Yule tree prior on a BD tree
• 23: The effect of differently common diversity-dependent trees
• 18: The effect of equal or equalized mutation rate in the twin alignment
• 24: The effect of mutation rate
• 25: the effect of RNG in the alignment for the error distribution
• 29: the effect of MCMC chain length on ESS
• 32 use DD tree with 12 taxa (instead of 6)
• 33 use 24 taxa (instead of 6)
• 35 use a mutation rate of 0.25 / crown_age (instead of 1.0 / crown_age)
• 36 use a mutation rate of 0.50 / crown_age (instead of 1.0 / crown_age)
• 37 use a mutation rate of 0.75 / crown_age (instead of 1.0 / crown_age)
• 38 use a mutation rate of 1.25 / crown_age (instead of 1.0 / crown_age)
• 39 use a mutation rate of 1.50 / crown_age (instead of 1.0 / crown_age)
• 40 use a mutation rate of 2.00 / crown_age (instead of 1.0 / crown_age)
• 41 use 32 taxa (instead of 6)
• 42 use 40 taxa (instead of 6)
• 43: Use 10x shorter MCMC chain length (from 10M to 1M), sample 1k times
• 44: Use 100x shorter MCMC chain length (from 10M to 100k), sample 1k times
• 45: Use 10x longer MCMC chain length (from 10M to 100M), sample 1k times

Other published experiments

• Revell et al., 2015
• Sarver et al., 2034

Combinations of pirouette functionality

These are all runs based on one phylogeny. Each of these examples serves as a high-level test.

Example	Phylogeny	Gen	Cand	Twin	TTM	DSL	STRAF	STWAF	Err
1	Yule	Y	N	N	-	1k	STD	-	nLTT
2	Yule	Y	Y	N	-	1k	STD	-	nLTT
3	Fict	Y	Y	Y	BD	1k	STD	STDEQ	nLTT
4	Fict	Y	N	N	-	1k	STD	-	nLTT
5	Fict	Y	Y	N	-	1k	STD	-	nLTT
6	Yule	Y	Y	Y	BD	1k	STD	STDEQ	nLTT
7	Yule	Y	N	Y	BD	1k	STD	STDEQ	nLTT
8	Yule	N	Y	Y	BD	1k	STD	STDEQ	nLTT
9	Fict	Y	N	Y	BD	1k	STD	STDEQ	nLTT
10	Fict	N	Y	Y	BD	1k	STD	STDEQ	nLTT
11	Yule	N	Y	N	-	1k	STD	-	nLTT
12	Fict	N	Y	N	-	1k	STD	-	nLTT
13	Fict	Y	Y	Y	BD	1k	STD	STDEQ	ADG
14	Fict	Y	Y	Y	BD	1k	STD	STDEQ	LTN
15	Fict	Y	N	Y	CT	1k	STD	STDEQ	nLTT
16	Fict	Y	N	Y	CT	1k	NSL	STDEQ	nLTT
17	Fict	Y	N	Y	CT	1k	NSU	STDEQ	nLTT
18	Fict	Y	Y	Y	BD	1k	STD	STD	nLTT
34	Fict	Y	Y	Y	BD	10k	STD	STDEQ	nLTT
30	DD	Y	Y	Y	BD	10k	STD	STDEQ	nLTT

Legend

Column	Value	Description
Phylogeny	Yule	The true phylogeny is created from a Yule (pure-birth) model
Phylogeny	Fict	The true phylogeny is completely fictious and artificial. If any, it follows both a multiple-birth and a protracted speciation model
Gen	Y/N	A generative model is yes/no hand-picked for this experiment
Cand	Y/N	A set of candidate models is yes/no used in this experiment
Twin	Y/N	The background noise is measured yes/no by using twinning
TTM	BD,CT	Twin tree method, BD=birth_death, Y=yule, CT=copy_true
DSL	[1,->>	DNA Sequence Length in number of nucleotides
STRAF	STD,NSL,NSU	Simulate TRue Alignment function: STD: standard, NSL: node_sub_linked and NSU: node_sub_unlinked
STWAF	STD,STDEQ	Simulate TWin Alignment function, STD: standard, STEQ: standard with equal number of mutations
Err	nLTT,ADG,LTN	The error statistic used is nLTT, ADG: absolute delta gamma, LTN: Log-transformed nLTT statistic

FAQ

Why are some TTM and STWAF values empty?

If there is no twinning (Twin = N), one cannot specify a TTM ('Twin Tree Model'), nor a STWAF ('Simulate TWin Alignment Function').

Why are some AppVeyor values empty?

These are empty when there are candidate models (Cand = T), because model comparison is unsupported on Windows.

How are the examples related?

See the table, or use this figure: