library(kernelPop2)
library(ggplot2)
library(dplyr)
source("helpers.R")
### this script maks a 250 population grid and
###
gapprop = 0.5
rland <- NULL
rland <- landscape.new.empty()
rland <- landscape.new.intparam(rland, h=250, s=2,np=0,totgen=20000)
rland <- landscape.new.switchparam(rland,mp=0)
rland <- landscape.new.floatparam(rland,s=0,seedscale=c(200,1500),
seedshape=c(1,200),seedmix=c(0.05),
pollenscale=c(50,200),pollenshape=c(1,1),
pollenmix=0.1 , asp=0.5)
S <- matrix(c(
0, 0,
0.8, 0.01
), byrow=T, nrow = 2)
R <- matrix(c(
0, 7,
0, 0
), byrow=T, nrow = 2)
M <- matrix(c(
0, 0,
0, 1
), byrow=T, nrow = 2)
rland <- landscape.new.local.demo(rland,S,R,M)
S <- matrix(0,ncol = (rland$intparam$habitats*rland$intparam$stages),
nrow = (rland$intparam$habitats*rland$intparam$stages))
R <- S
M <- S
rights <- floor(seq(500,100000,length=50))
tops <- floor(seq(0,10000,length=6))
locs=NULL
for (i in 1:(length(tops)-1))
{
locs <- rbind(locs,
data.frame(lft=c(0,501,rights[c(-1:-2)]-diff(rights[-1])+1),
bot=rep(tops[i+1]-(tops[2]-tops[1]),50),
rgt=rights,
top=tops[i+1]))
}
lfts=which(locs$lft==0)
k=(1.50 * (sqrt((locs[,3]-locs[,1])*(locs[,4]-locs[,2]))))
e=rep(gapprop,rland$intparam$habitat)
e[lfts] <- 0
k[lfts] <- k[lfts]*2
rland <- landscape.new.epoch(rland,S=S,R=R,M=M,
carry=k,
extinct=e,
leftx=locs[,1],
rightx=locs[,3],
boty=locs[,2],
topy=locs[,4],
maxland=c(min(locs[1]),min(locs[2]),max(locs[3]),max(locs[4])))
for (i in 1:12)
rland <- landscape.new.locus(rland,type=1,ploidy=2,mutationrate=0.00,transmission=0,numalleles=2)
expmat <- matrix(c(1,0,0,
1,0,0,
1,0,0,
1,0,0,
0,1,0,
0,1,0,
0,1,0,
0,1,0,
0,0,1,
0,0,1,
0,0,1,
0,0,1
),byrow=T,ncol=3)
hsq <- c(1,1,1)
rland <- landscape.new.expression(rland,expmat=expmat*0.125,hsq=hsq)
rland <- landscape.new.gpmap(rland,
matrix(c(-1,0,1, #short scale
2,-0.5,1, #long scale
-1,0,1, #long shape
1,-0.5,1, #mixture
-1,0,1),ncol=3,byrow=T),
matrix(c(-1,0,1,
-1,0,1,
0,-0.5,1 #reproduction
),ncol=3,byrow=T))
initpopsize <- 5000
inits <- matrix(0,ncol=rland$intparam$habitats,nrow=2)
inits[1:2,lfts] <- initpopsize
rland <- landscape.new.individuals(rland,c(inits))
#rland$individuals[,5] <- 4500+floor(rland$individuals[,5]/10)
###############################
l=rland
landscape.plot.phenotypes(l,1)
locs <- landscape.generate.locations(npop=250,
xrange=c(0,100000),yrange=c(0,10000),
sizexkernel=c(1000,65),sizeykernel=c(1000,65)
)
phens=c(1,2,3) #represented as 0 in c++
gen=200
sumlst=list()[1:gen]
pdf(paste0("gaps_",gapprop,".pdf"), width=15,height=7.5)
for (i in 1:gen)
{
print(dim(l$individuals))
# l=landscape.kill.locs(l,locs)
print(dim(l$individuals))
if (dim(l$individuals)[1]>0) l.old=l
l=landscape.simulate(l,1)
if ((i %% 1)==0)
{
par(mfrow=c(length(phens),1))
for (phen in phens)
landscape.plot.phenotypes(l,phen)
par(mfrow=c(1,1))
}
print(i)
print(dim(l$individuals))
print(landscape.allelefreq(l) )
print(colMeans(landscape.phenotypes.c(l)))
sumlst[[i]] <- data.frame(landscape.phenosummary(l))
sumlst[[i]]$gen=i
}
#dev.off()
sumdf <- do.call(rbind,sumlst)
save(file=paste0("newgap_",gapprop,"_res.rda"),sumlst,sumdf)
p = sumdf %>%
ggplot(aes(y=gen,x=pop,z=phen1_mean))+
geom_tile(aes(fill = phen1_mean)) +
geom_contour() +
scale_fill_gradientn(colors = rev(cm.colors(100)))
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