Evomorph (version 0.9)

SimEvo: Simulation of Shape Variation

Description

SimEvo performs a simulation of shape variation using a modification of Lande's evolutionary model Polly 2004

Usage

SimEvo(vari, consensusvec, resids, ngen, fsamp)

Arguments

vari

Variation coefficient

consensusvec

Consensus shape (vectorized form)

resids

GPA residuals matrix

ngen

Number of generations of simulations (Default: 1000000 steps).

fsamp

Frequency of samples (Default: 1000000 steps).

Value

It returns a list of ngen/fsamp shapes (landmarks coordinates)

Details

Lande's evolutionary model defines mean morphological variation over generations $ \Delta Z $ as: $$ \Delta Z = \beta G $$ where $ G $ is the additive genetic covariance matrix, and $ \beta $ are selection coefficients applied to the morphological structure. Polly 2004 proposes a modification of this equation in order to use it with morphological data instead of genetic data: $$ \Delta Z = \beta P H $$ where $ P $ is the phenotypic covariance matrix, and $ H $ is an heritability matrix (See Polly 2004 for more information). resids will be used as the phenotypic covariance matrix, and vari will be used to simulate $ \beta H $ term. After ngen simulations steps the new shape will be reconstructed from the starting shape consensusvec . The number of plots representing the new shapes can be modify using fsamp .

References

Polly, P. D. (2004). On the simulation of the evolution of morphological shape: multivariate shape under selection and drift. Palaeontologia Electronica, 7(2), 1-28.

Examples

data("aegla_landmarks")

#Use GpaResiduals function to obtain GPA residual matrix and consensus
# coordinates from landmark configuration

a_data=GpaResiduals(aegla_landmarks)

#Simulate morphological evolution with a variation rate "vari"
# trough "ngen" generations and retrieve the last generation shape coordinates

simshape = SimEvo(vari = 2, consensusvec = a_data$cvectorized, 
resids = a_data$resid, ngen = 10000, fsamp = 10000)

#Plot consensus shape and the simulated shape

par(mfrow=c(1, 2))
plot(a_data$consens,type = "p",main = "Reference", xlab = "", ylab = "")
plot(simshape[[1]],type = "p",col = "red",main = "Target", xlab = "", ylab = "")

#Or you can use PlotVariations to see the difference more clearly

PlotVariations(simshape,a_data$consens)