rate.map | R Documentation |

Given vectors of RW (or PC) scores, the function selects the
RW(PC) axes linked to highest (and lowest) evolutionary rate values and
reconstructs the morphology weighted on them. In this way, `rate.map`

shows where and how the phenotype changed the most between any pair of
taxa.

rate.map(x, RR, PCscores, pcs, mshape, out.rem = TRUE, shape.diff=FALSE, show.names=TRUE)

`x` |
the species/nodes to be compared; it can be a single species, or a vector containing two species or a species and any of its parental nodes. |

`RR` |
an object generated by using the |

`PCscores` |
PC scores. |

`pcs` |
RW (or PC) vectors (eigenvectors of the covariance matrix) of all the samples. |

`mshape` |
the Consensus configuration. |

`out.rem` |
logical: if |

`shape.diff` |
logical: if |

`show.names` |
logical: if |

After selecting the PC axes, `rate.map`

automatically builds a
3D mesh on the mean shape calculated from the Relative Warp Analysis (RWA)
or Principal Component Analysis (PCA) (Schlager 2017) by applying
the function `vcgBallPivoting`

(Rvcg). Then, it
compares the area differences between corresponding triangles of the 3D
surfaces reconstructed for the species and surface of the mrca. Finally,
`rate.map`

returns a 3D plot showing such comparisons displayed on
shape of the mrca used as the reference.The colour gradient goes from blue
to red, where blue areas represent expansion of the mesh, while the red
areas represent contractions of the mesh triangles. In the calculation of
the differences of areas we supply the possibility to find and remove
outliers from the vectors of areas calculated on the reference and target
surfaces. We suggest considering this possibility if the mesh may contain
degenerate facets. Additionally, `rate.map`

allows to investigate the
pure morphological comparison of shapes by excluding the evolutionary rate
component by setting the argument `show.diff = TRUE`

. In this case, a
second 3D plot will be displayed highlighting area differences in terms of
expansion (green) and contraction (yellow).

The function returns a list including:

**$selected**a list of PCs axes selected for higher evolutionary rates for each species.**$surfaces**a list of reconstructed coloured surfaces of the given species and of the most recent common ancestor.

Marina Melchionna, Antonio Profico, Silvia Castiglione, Gabriele Sansalone, Pasquale Raia

Schlager, S. (2017). *Morpho and Rvcg-Shape Analysis in R:
R-Packages for geometric morphometrics, shape analysis and surface
manipulations.* In: Statistical shape and deformation analysis. Academic
Press.
Castiglione, S., Melchionna, M., Profico, A., Sansalone, G.,
Modafferi, M., Mondanaro, A., Wroe, S., Piras, P., & Raia, P. (2021). Human
face-off: a new method for mapping evolutionary rates on three-dimensional
digital models. Palaeontology. doi:10.1111/pala.12582

`RRphylo`

vignette ;
`relWarps`

; `procSym`

## Not run: data(DataSimians) DataSimians$pca->pca DataSimians$tree->tree dato<-pca$PCscores RRphylo(tree,dato)->RR Rmap<-rate.map(x=c("Pan_troglodytes","Gorilla_gorilla"),RR=RR, PCscores=dato, pcs=pca$PCs, mshape=pca$mshape, shape.diff = TRUE) ## End(Not run)

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