Nothing
## -----------------------------------------------------------------------------
library(rmetasim)
rland <- landscape.new.empty() #creates a skeleton of a landscape
rland <- landscape.new.intparam(rland, h=2, s=2)
names(rland$intparam)
## -----------------------------------------------------------------------------
rland <- landscape.new.switchparam(rland)
names(rland$switchparam)
## -----------------------------------------------------------------------------
rland <- landscape.new.floatparam(rland)
names(rland$floatparam)
## -----------------------------------------------------------------------------
S <- matrix(c(0.1, 0, 0.5, 0.3), nrow = 2)
R <- matrix(c(0, 1.1, 0, 0), nrow = 2)
M <- matrix(c(0, 0, 0, 1), nrow = 2)
rland <- landscape.new.local.demo(rland,S,R,M)
S <- matrix(c(rep(0,4),
rep(0,4),
rep(0,4),
rep(0,4)), nrow = 4)
R <- matrix(c(0,0,0,1,
0,0,0,0,
0,1,0,0,
0,0,0,0), byrow=T, nrow = 4)
M <- matrix(c(0,0,0,0,
0,0,0,.1,
0,0,0,0,
0,.1,0,0), nrow = 4)
rland <- landscape.new.epoch(rland,S=S,R=R,M=M,extinct=c(.01,0),carry=c(100,200))
names(rland$demography)
names(rland$demography$localdem[[1]])
names(rland$demography$localdemK[[1]])
names(rland$demography$epochs[[1]])
## -----------------------------------------------------------------------------
rland <- landscape.new.locus(rland,type=0,ploidy=2,mutationrate=0.001,
transmission=0,numalleles=5)
rland <- landscape.new.locus(rland,type=1,ploidy=1,mutationrate=0.005,
numalleles=3,frequencies=c(.2,.2,.6))
rland <- landscape.new.locus(rland,type=2,ploidy=2,mutationrate=0.007,
transmission=0,numalleles=6,allelesize=75)
names(rland$loci[[1]])
names(rland$loci[[1]]$alleles[[1]])
## -----------------------------------------------------------------------------
rland <- landscape.new.individuals(rland,c(10,15,20,8))
print(rland$individuals[1,])
## -----------------------------------------------------------------------------
rland <- landscape.new.empty()
rland <- landscape.new.intparam(rland, h = 2, s = 2)
rland <- landscape.new.switchparam(rland, mp = 0)
rland <- landscape.new.floatparam(rland)
S <- matrix(c(0, 0, 1, 0), byrow = TRUE, nrow = 2)
R <- matrix(c(0, 1.1, 0, 0), byrow = TRUE, nrow = 2)
M <- matrix(c(0, 0, 0, 1), byrow = TRUE, nrow = 2)
rland <- landscape.new.local.demo(rland, S, R, M)
S <- matrix(rep(0, 16), nrow = 4)
R <- matrix(rep(0, 16), nrow = 4)
M <- matrix(rep(0, 16), nrow = 4)
rland <- landscape.new.epoch(rland, S = S, R = R, M = M,
carry = c(1000, 1000))
rland <- landscape.new.locus(rland, type = 0, ploidy = 2,
mutationrate = 0.001, transmission = 0, numalleles = 5)
rland <- landscape.new.locus(rland, type = 1, ploidy = 1,
mutationrate = 0.005, numalleles = 3, frequencies = c(0.2,
0.2, 0.6))
rland <- landscape.new.locus(rland, type = 2, ploidy = 2,
mutationrate = 0.007, transmission = 0, numalleles = 6,
allelesize = 75)
rland <- landscape.new.individuals(rland, c(50, 0, 50, 0))
## -----------------------------------------------------------------------------
library(magrittr)
#first set up the matrices for local demographies
S <- matrix(c(0, 0, 1, 0), byrow = TRUE, nrow = 2)
R <- matrix(c(0, 1.1, 0, 0), byrow = TRUE, nrow = 2)
M <- matrix(c(0, 0, 0, 1), byrow = TRUE, nrow = 2)
#and epochs
S.epoch <- matrix(rep(0, 16), nrow = 4)
R.epoch <- matrix(rep(0, 16), nrow = 4)
M.epoch <- matrix(rep(0, 16), nrow = 4)
##now create the landscape
rland <- landscape.new.empty() %>%
landscape.new.intparam(h=2,s=2) %>%
landscape.new.switchparam(mp=0) %>%
landscape.new.floatparam() %>%
landscape.new.local.demo( S, R, M) %>%
landscape.new.epoch(S = S.epoch, R = R.epoch, M = M.epoch,
carry = c(1000, 1000)) %>%
landscape.new.locus(type = 0, ploidy = 2,
mutationrate = 0.001, transmission = 0, numalleles = 5) %>%
landscape.new.locus(type = 1, ploidy = 1,
mutationrate = 0.005, numalleles = 3, frequencies = c(0.2,
0.2, 0.6)) %>%
landscape.new.locus(type = 2, ploidy = 2,
mutationrate = 0.007, transmission = 0, numalleles = 6,
allelesize = 75) %>%
landscape.new.individuals(c(50, 0, 50, 0))
## -----------------------------------------------------------------------------
rland <- landscape.simulate(rland,10)
landscape.amova(rland)
## -----------------------------------------------------------------------------
rland %>% landscape.simulate(10) %>% landscape.amova()
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