## load 'rmetasim' library
library(rmetasim)

## create skeleton landscape where
toadland <- landscape.new.empty()

toadland <- landscape.new.intparam(toadland,
	h=1, #one population
	s=8, #four female (1 through 4) and four male (5 through 8) classes
	cg=0,
	ce=0,
	totgen=100,
	maxland=500000)

#toads don't self
toadland <- landscape.new.floatparam(toadland, s=0.0)

toadland <- landscape.new.switchparam(toadland,
	re=0,
	rd=0,
	mp=0)

#the following survival matrix is slight modification from the
#figure supplied with this file.  The survivorship of eggs to juveniles
#has been increased for both females and males.
localsurvival <- matrix(
c(
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.5, 0.5, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.2, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.2, 0.3
 ), ncol=8, nrow=8, byrow=TRUE)

#each adult female produces an average of 10 males and 10 females
localreproduction <- matrix(
c(
  0.0, 0.0, 0.0,  10, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0,  10, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
 ), ncol=8, nrow=8, byrow=TRUE)

#only adult males (class 8) contribute sperm to adult females (class 4)
localmalecontrib <- matrix(
c(
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 1.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
 ), ncol=8, nrow=8, byrow=TRUE)

toadland <- landscape.new.local.demo(toadland,
                           localsurvival,
                           localreproduction,
                           localmalecontrib)


#these matrices specify inter-population movement (only one pop, so they
#are the same dimension as the local matrices)
#if there are multiple habitats, these matrices will get big fast.  There are
#some convenience functions to create them for island models

migsurvival<- matrix(
c(
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
 ), ncol=8, nrow=8, byrow=TRUE)
migreproduction <- matrix(
c(
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
 ), ncol=8, nrow=8, byrow=TRUE)
migmalecontrib <- matrix(
c(
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
  0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0
 ), ncol=8, nrow=8, byrow=TRUE)

toadland <- landscape.new.epoch(toadland,
	S=migsurvival,
	R=migreproduction,
	M=migmalecontrib,
	epochprob=1,
	startgen=0,
	extinct=NULL,
	carry=c(10000),
        localprob=NULL)

#this call could be repeated to increase the number of loci
toadland <- landscape.new.locus(toadland,
	type=2,
	ploidy=2,
	mutationrate=0.000001,
	transmission=0,
	numalleles=2,
	allelesize=20,
	frequencies=NULL)

toadland <- landscape.new.locus(toadland,
	type=2,
	ploidy=2,
	mutationrate=0.000001,
	transmission=0,
	numalleles=2,
	allelesize=20,
	frequencies=NULL)

#start out with 100 individuals in each class
toadland <- landscape.new.individuals(toadland,
	c(100,100,100,100,100,100,100,100))

## quick look at current input
toadland
table(toadland$individuals[,1]) #how many in each class?
## simulate data...for several time-clicks

toadland <- landscape.simulate(toadland, 40)

## quick look after sim
## this demography will crash rapidly: either the reproduction
## or survival needs to be boosted for the population to persist

##also note that the individual's classes in the landscape object go from
##0 to 7 rather than 1->8.  This is an artifact of C++ indexing


table(toadland$individuals[,1]) #how many in each class?