Description Usage Arguments Value Author(s) References See Also Examples
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 PoissonVoronoi tessellation.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30  simdata(nindiv,
coord.indiv,
coord.lim=c(0,1,0,1),
npop,
rate,
number.nuclei,
coord.nuclei,
color.nuclei,
allele.numbers,
sim.gen=FALSE,
IBD=TRUE,
model="stable",
alpha=1,
beta=1,
gamma=1.8,
sim.quanti=FALSE,
nquanti.var,
mean.quanti,
sd.quanti,
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) 
npop 
Number of Populations 
rate 
Rate of the Poisson process governing the hidden tessellation 
number.nuclei 
Number of nuclei in the tessellation (if given,
then 
coord.nuclei 
Coordinates of the nuclei (the number of
coordinates of the nuclei
given here as a matrix has to comply with 
color.nuclei 
Population membeship of the nuclei: a vector of
integer of length 
sim.gen 
Logical to say whether genetic data should be simulated 
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

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

gamma 
Smoothing parameter of spatial covariance function used for the
underlying Gaussian fields. (see documentation of package

sim.quanti 
Logical to say whether quantitative data should be simulated 
nquanti.var 
Number of quantitative variables to be simulated 
mean.quanti 
Mean of the quantitative variables in the various
groups. A matrix with 
sd.quanti 
Standard deviation of the quantitative variables in
the various groups.
A matrix with 
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22  ## Not run:
dataset < simdata(nindiv=100,
sim.gen=TRUE,
number.nuclei=10,
allele.numbers=rep(5,3),
model="stable",
IBD=TRUE,
alpha=1,
beta=1,
gamma=1,
npop=3,
sim.gen=TRUE,
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)

Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.