landscape.new.epoch: Create an Epoch
In stranda/kernelPop2: Spatially explicit population genetic simulations

Create an epoch for a Rmetasim landscape object

  ## must be called AFTER integer, switch, and float params have
  ##   been created and after the demography has been created
  ## S, R, and M matricies must be square matricies of size X by X
  ##   where X = rland$intparam$stages*rland$intparam$habitats

rland <- landscape.new.epoch(rland,S=NULL,R=NULL,M=NULL,epochprob=1,
                               startgen=0,extinct=NULL,carry=NULL,localprob=NULL,
                               pollen.kernels = NULL, seed.kernels = NULL, 
                               leftx = NULL, rightx = NULL,
                               boty = NULL, topy = NULL, maxland = c(0, 0, 10000, 10000))

`rland`	partially created landscape object, required
`S`	(default=NULL) Survivablity matrix for epoch, NULL gives no movement between subpopulations (0 matrix)
`R`	(default=NULL) female Reproduction matrix for epoch, NULL gives no dispersal between subpopulations other than that determined by dispersal kernels(0 matrix)
`M`	(default=NULL) Male reporduction matrix for epoch, NULL gives no sperm or pollen movement between subpopulations other then that determined by dispersal kernels (0 matrix)
`epochprob`	(default=1) probability of choosing this epoch randomly if randepoch==1
`startgen`	(default=0) generation in which this epoch starts
`extinct`	(default=NULL) vector of extinction probabilities per generation for each subpopulation, must be rland$intparam$habitats in length, passing NULL gives a 0% probability of extinction to each subpopulation
`carry`	(default=NULL) vector of carrying capacities for each subpopulation, must be rland$intparam$habitats in length, passing NULL gives a 1000 individual carrying capacity to each subpopulation
`localprob`	(default=NULL) vector of probabilites for choosing local demographies, must be length(rland$demography$localdem) in length, passing NULL gives each demography an equalprobability
`leftx`	vector of the left x-coordinates of habitat patches. If NULL (along with the other coordinates below), then the landscape is dividided into a set of contiguous strips
`rightx`	vector of the right x-coordinates of habitat patches
`topy`	vector of the bottom y-coordinates of habitat patches
`boty`	vector of the top y-coordinates of habitat patches
`pollen.kernels`	A matrix that describes pollen kernels for each stage in the landscape. The rows correspond to stages in the landscape (there should be habitat * stages rows). The columns correspond to the characteristics of the dispersal kernels: Column 1 is the type of kernel (1=exponential, 2=Weibull, 3=mixture between Weibull and Gaussian) because the first is a special case of the second and the second is a special case of the third type of dispersal kernel using "3" in this column is pretty much always reasonable. Columns 2 and 3 are scale and shape parameters of the Weibull (if shape=1, this reduces to an exponential kernel). Columns 4 and 5 correspond to the mean and sd of the Gaussian portion of the kernel. Column 6 is the mixture parameter, ranging from 0-1 that gives the relative weights of the Weibull versus Gaussian portions of the kernel. If the pollen kernel is constant across demographic stages, it is much easier to specify it when calling `landscape.new.floatparam()`
`seed.kernels`	A similar matrix to `pollen.kernels`

  
  exampleS <- matrix(c(0.1, 0, 0.5, 0.3), nrow = 2)
  exampleR <- matrix(c(0, 1.1, 0, 0), nrow = 2)
  exampleM <- matrix(c(0, 0, 0, 1), nrow = 2)
  
  exampleland <- landscape.new.empty()
  exampleland <- landscape.new.intparam(exampleland, s=2, h=2)
  exampleland <- landscape.new.floatparam(exampleland)
  exampleland <- landscape.new.switchparam(exampleland)
  exampleland <- landscape.new.local.demo(exampleland,exampleS,exampleR,exampleM)

  ## nonsense matricies
  exampleS <- matrix(c(rep(0,4),
                rep(1,4),
                rep(0,4),
                rep(1,4)), nrow = 4)
  exampleR <- matrix(c(rep(0.5,4),
                rep(0,4),
                rep(0.5,4),
                rep(0,4)), nrow = 4)
  exampleM <- matrix(c(rep(0,4),
                rep(.25,4),
                rep(0,4),
                rep(0,4)), nrow = 4)

  ## defaults
  exampleland<- landscape.new.epoch(exampleland,exampleS,exampleR,exampleM)

  exampleland$demography$epochs[[1]]

  rm(exampleS)
  rm(exampleR)
  rm(exampleM)
  rm(exampleland)