clResults {CongreveLamsdell2016} | R Documentation |

## Congreve and Lamsdell tree distances

### Description

Distance of CL trees from generative tree.

### Usage

```
clBremQuartets
clBremPartitions
clMkvPartitions
clMkvQuartets
clBootFreqPartitions
clBootFreqQuartets
clJackFreqPartitions
clJackFreqQuartets
clBootGcPartitions
clBootGcQuartets
clJackGcPartitions
clJackGcQuartets
```

### Format

An object of class `list`

of length 7.

An object of class `list`

of length 7.

An object of class `array`

of dimension 21 x 8 x 100.

An object of class `array`

of dimension 21 x 7 x 100.

An object of class `list`

of length 7.

An object of class `list`

of length 7.

An object of class `list`

of length 7.

An object of class `list`

of length 7.

An object of class `list`

of length 7.

An object of class `list`

of length 7.

An object of class `list`

of length 7.

An object of class `list`

of length 7.

### Details

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

*c*onsensus 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 *s*ame or *d*ifferent 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.

### Source

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.

### References

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.

### See Also

*CongreveLamsdell2016*version 1.0.3 Index]