clResults {CongreveLamsdell2016} | R Documentation |
Distance of CL trees from generative tree.
clBremQuartets
clBremPartitions
clMkvPartitions
clMkvQuartets
clBootFreqPartitions
clBootFreqQuartets
clJackFreqPartitions
clJackFreqQuartets
clBootGcPartitions
clBootGcQuartets
clJackGcPartitions
clJackGcQuartets
An object of class list
of length 7.
For each of the 100 matrices generated by Congreve & Lamsdell (2016), I conducted phylogenetic analysis under different methods:
Mkv
: using the Markov K model in MrBayes;
eq
: using equal weights in TNT;
k1
, k2
, k3
, k5
, kX
: using implied weights in TNT,
with the concavity constant (k) set to 1, 2, 3, 5, or 10;
kC
: by taking the strict consensus of all trees recovered by implied
weights parsimony analysis under the k values 2, 3, 5 and 10 (but not 1).
For each analysis, I recorded the strict consensus of all optimal trees, and also the consensus of trees that were suboptimal by a specified degree.
I then calculated, of the total number of quartets or partitions that were resolved in the reference tree, how many were the same or different in the tree that resulted from the phylogenetic analysis, and how many were not resolved in this tree (r2).
The data object contains a list whose elements are named after the methods, as listed above.
Each list entry is a three-dimensional array, whose dimensions are:
The suboptimality of the tree. Different measures of node support are employed:
Mkv
: Posterior probabilities, at 2.5% intervals (50%, 52.5%, ...
97.5%, 100%).
Brem
: Bremer supports: the consensus of all trees that are
(equal weights) 0, 1, .... 19, 20 steps less optimal than the optimal
tree (implied weights: the consensus of all trees that are 0.73^(19:0)
less optimal than the optimal tree).
Boot
: Bootstrap supports (symmetric resampling, p = 0.33).
Jack
: Jackknife supports (p = 0.36).
Boot
and Jack
results are reported both as the freq
uency of splits
among replicates, and using the gc
(Groups Present / Contradicted)
measure (Goloboff et al. 2003); frequency columns correspond to
100%, 97.5%, 95% ... 0% support; gc columns correspond to 100%, 95%,
... 0% present, 5%, 10%, ... 100% contradicted.
Counts of the condition of each quartet or partition:
Q
: The total number of quartets defined on 22 taxa.
N
: The total number of partitions present, counting each tree separately.
P1
: The number of partitions in tree 1 (the reconstructed tree).
P2
: The number of partitions in tree 2 (the generative tree).
s
: The number of quartets or partitions resolved identically in
each tree.
* d
: The number of quartets resolved differently in each tree.
d1
: The number of partitions resolved in tree 1, but contradicted by
tree 2.
d2
: The number of partitions resolved in tree 2, but contradicted by
tree 1.
r1
: The number of partitions or quartets resolved in tree 1 that are
neither present in nor contradicted by tree 2.
r2
: The number of partitions or quartets resolved in tree 2 that are
neither present in nor contradicted by tree 1.
u
: The number of quartets that are not resolved in either tree.
The number of the matrix, from 1 to 100.
Congreve, C. R. & Lamsdell, J. C. (2016). Implied weighting and its utility in palaeontological datasets: a study using modelled phylogenetic matrices. Palaeontology 59(3), 447–465. doi: 10.1111/pala.12236.
Goloboff, P. A., J. S. Farris, M. Källersjö, B. Oxelman, M. J. Ramírez, and C. A. Szumik. 2003. Improvements to resampling measures of group support. Cladistics 19, 324–332. doi: 10.1016/S0748-3007(03)00060-4.