simdata {Geneland} | R Documentation |
Simulates coordinates and genotypes for a npop
populations.
Each population is supposed to be under an Isolation by Distance model
and different populations are supposed to be separated by impermeable
barriers. The barriers are given by a Poisson-Voronoi tessellation.
simdata(nindiv, coord.indiv , coord.lim, rate , number.nuclei , coord.nuclei , color.nuclei , allele.numbers, IBD, model, alpha, beta, gamma, npop, seed.coord , seed.tess , seed.freq , give.tess.grid=FALSE, give.freq.grid = FALSE, npix , comp.Fst = FALSE, comp.Dsigma2=FALSE, comp.diff=FALSE, width, plot.pairs.borders=FALSE)
nindiv |
Number of indivuals |
coord.indiv |
Coordinates of the individuals |
coord.lim |
Limits of the geographical domain. The domain is supposed to be rectangular and the limits are given as (abs min, abs max, ord min, ord max) |
rate |
Rate of the Poisson process governing the hidden tessellation |
number.nuclei |
Number of nuclei in the tessellation (if given,
then rate is ignored) |
coord.nuclei |
Coordinates of the nuclei (the number of
coordinates of the nuclei
given here as a matrix has to comply with number.nuclei ) |
color.nuclei |
Population membeship of the nuclei: a vector of
integer of length number of nuclei whose values are between 1
and npop |
allele.numbers |
A vector giving the number of alleles observed at each locus |
IBD |
Logical. If TRUE, then the allele frequencies are simulated according to an IBD model. If FALSE, panmixia is assumed. |
model |
Model of spatial covariance function used for the
underlying Gaussian fields (see documentation of package
RandomFields
for details) |
alpha |
Parameter of the spatial Dirichlet vector field of frequencies (a positive real) |
beta |
Scale parameter of the spatial covariance function used for the
underlying Gaussian fields. A positive real number (see documentation of package
RandomFields
for details) |
gamma |
Smoothing parameter of spatial covariance function used for the
underlying Gaussian fields. (see documentation of package
RandomFields
for details) |
npop |
Number of Populations |
seed.coord |
Random seed to initialise the simulation of the coordinates (mostly for debugging) |
seed.tess |
Random seed to initialise the simulation of the tessellation (mostly for debugging) |
seed.freq |
Random seed to initialise the simulation of the frequencies (mostly for debugging) |
give.freq.grid |
Logical to tell whether frequencies on a grid are also returned |
give.tess.grid |
Logical to tell whether population memberships of pixels on a grid are also returned |
npix |
A vector of two integers telling how many horizontal and vertical pixel should contain the grid for the graphical representations |
comp.Fst |
Logical to tell whether Fst, Fis and Fit should be computed |
comp.Dsigma2 |
Logical to tell whether IBD index Dsgma2 should be computed |
comp.diff |
Logical to tell whether the local differentiation across the barriers should be computed |
width |
Real number specifying the width around the barrier in the computation of its local differentiation |
plot.pairs.borders |
Logical to tell whether the pairs of individuals coming into the computation of the differentiation of the barriers should be plotted |
A list whose components can be seen using summary
Arnaud Estoup, Gilles Guillot, Filipe Santos
G. Guillot, F. Santos, A. Estoup. Inference in population genetics with Geneland: a sensitivity analysis to spatial sampling scheme, null alleles and isolation by distance. Submitted.
Function show.simdata
to make graphical display of
simulated data.
## Not run: dataset <- simdata(nindiv=100, number.nuclei=10, allele.numbers=rep(5,3), model="stable", IBD=TRUE, alpha=1, beta=1, gamma=1, npop=3, give.tess.grid=TRUE, give.freq.grid=TRUE, npix=c(10,10), comp.Fst=TRUE, comp.Dsigma2=TRUE, comp.diff=TRUE, width=0.1, plot.pairs.borders=TRUE) ## End(Not run)