Note: The writing of this vignette is currently in progress. If needed, please, contact the author for assistance. Thanks for your understanding.

The main R-script

Loading needed packages and parsing command line arguments

Generating PCMModels on the worker nodes

Tree and trait data

Retrieving and analyzing the best scoring model fit

model p logLik AIC
Global BM 5 -221.68133 455.3627
Global OU 11 -204.60164 433.2033
True MGPM, unknown parameters 18 -93.65584 233.3117
True MGPM, known true parameters 18 -93.50648 233.0130
True MGPM, true parameters 18 -102.63502 251.2700
Inferred MGPM, unknown shift-points and parameters 17 -95.07409 234.1482
#> ggtree v1.15.3  For help: https://guangchuangyu.github.io/software/ggtree
#> 
#> If you use ggtree in published research, please cite the most appropriate paper(s):
#> 
#> [36m-[39m Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
#> 
#> [36m-[39m Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution 2018, accepted. doi: 10.1093/molbev/msy194
**Example phylogenetic comparative data.** **A**: a tree of 80 tips partitioned in three evolutionary regimes. Each evolutionary regime is denoted by #.T, where # is the regime identifier and T is the evolutionary model type associated with this regime (a model type among A, ..., F). **B**:  bivariate trait values at the tips of the tree. **C** and **D**: Analogical to **A** and **B** according to the MGPM found using the AIC score as a criterion.

Example phylogenetic comparative data. A: a tree of 80 tips partitioned in three evolutionary regimes. Each evolutionary regime is denoted by #.T, where # is the regime identifier and T is the evolutionary model type associated with this regime (a model type among A, …, F). B: bivariate trait values at the tips of the tree. C and D: Analogical to A and B according to the MGPM found using the AIC score as a criterion.

References