Compute all kernel matrices when simulating data
sim.kernels( X, types, lengthscales, X_affected, bin_kernel, useMaskedVarianceKernel, steepness, vm_params )
X  covariates 

types  vector of covariate types, so that

lengthscales  vector of lengthscales 
X_affected  which individuals are affected by the disease 
bin_kernel  whether or not binary (mask) kernel should be used for categorical covariates (if not, the zerosum kernel is used) 
useMaskedVarianceKernel  should the masked variance kernel be used for drawing the disease component 
steepness  steepness of the input warping function 
vm_params  parameters of the variance mask function 
a 3D array