#' @title Initialize a landscape object
#' @description Initialize a landscape object
#'
#' @param num.pops number of populations to simulate
#' @param carrying maximum population sizes for each population
#' @param sample.size size of sample to be pulled from each population
#' @param mig.rates a list of among-population migration matrices
#' @param num.loc number of independently segregating loci
#' @param loc.type sequence or microsatellite
#' @param mut.rate per gene mutation rate
#' @param seq.length if simulating a sequence, the length of the molecule
#' @param num.stgs number of demographic stages in a population
#' @param selfing selfing rate (must range from 0 [random mating] to 1 [complete selfing]
#' @param surv.matr within pop survival matrices
#' @param repr.matr within pop reproduction matrices
#' @param male.matr with pop male repro matrices
#' @param init.pop.sizes starting population sizes
#' @param num.gen number of generations to simulate
#' @param num.alleles vector of the number of alleles per locus
#' @param allele.freqs list of allele freqs for each locus (range 0-1)
#'
#' @importFrom rmetasim landscape.new.empty landscape.new.floatparam
#' landscape.new.intparam landscape.new.switchparam landscape.new.local.demo
#' landscape.mig.matrix landscape.new.epoch landscape.new.locus landscape.new.individuals
#' @export
rms.init.landscape.func <- function(
num.pops = NULL, carrying = NULL, sample.size = NULL, mig.rates = NULL,
num.loc = NULL, loc.type = NULL, mut.rate = NULL, seq.length = NULL,
num.stgs = NULL, selfing = NULL, surv.matr = NULL, repr.matr = NULL,
male.matr = NULL, init.pop.sizes = NULL, num.gen = NULL,
num.alleles = NULL, allele.freqs = NULL) {
matstrfun <- function(mat) {
if (!is.null(mat)) {
ms <- "matrix(c("
ms <- c(ms,paste(c(mat),collapse=", "))
ms <- c(ms,paste0("), nrow=",dim(mat)[1],", ncol=",dim(mat)[2],")"))
paste(ms,collapse="")
} else { NULL }
}
vecstrfun <- function(vec) {
if (!is.null(vec)) {
ms <- "c("
ms <- c(ms,paste(vec,collapse=", "))
ms <- c(ms,")")
paste(ms,collapse="")
} else {NULL}
}
listvecstrfun <- function(l) {
if (!is.null(l)) {
paste0("list(",paste0(sapply(l,vecstrfun),collapse=", "),")")
} else {NULL}
}
listmatstrfun <- function(l) {
if (!is.null(l)) {
paste0("list(",paste0(sapply(l,matstrfun),collapse=", "),")")
} else {NULL}
}
fstr <- c(
"create.land <- function(",
paste("\tnum.pops=",num.pops,","),
paste("\tnum.stgs=",num.stgs,","),
paste("\tcg=",0,","),
paste("\tce=",0,","),
paste("\ttotgen=",100000,","),
paste("\tmaxland=",100000,","),
paste("\tselfing=",selfing,","),
paste("\tre=",0,","),
paste("\trd=",0,","),
paste("\tmp=",1,","),
paste("\tdd=",0,","),
paste("\tsurv.matr =",matstrfun(surv.matr),","),
paste("\trepr.matr =",matstrfun(repr.matr),","),
paste("\tmale.matr =",matstrfun(male.matr),","),
paste("\tmig.rates =",matstrfun(mig.rates),","),
paste("\tcarrying =",vecstrfun(carrying),","),
paste("\tmut.rate =",vecstrfun(mut.rate),","),
paste("\tnum.alleles =",vecstrfun(num.alleles),","),
paste("\tinit.pop.sizes =",vecstrfun(init.pop.sizes),","),
paste("\tallele.freqs =",listvecstrfun(allele.freqs))
)
fstr <- c(fstr,")\n{")
fstr <- c(fstr,"skeletonland<-landscape.new.empty()")
#define selfing rate
fstr <- c(fstr,
paste0("skeletonland<-landscape.new.floatparam(skeletonland,s=selfing)"))
###Hard coded in current generation, current epoch, max number generations, max number individuals
fstr <- c(fstr,paste0("skeletonland<-landscape.new.intparam(skeletonland,h=num.pops,s=num.stgs,cg=0,ce=0,totgen=100000,maxland=100000)"))
###Hard coded in multiple paternity (yes) and density dependence (no) parameters
fstr <- c(fstr,paste0("skeletonland<-landscape.new.switchparam(skeletonland,re=0,rd=0,mp=1,dd=0)"))
#local matrices, will give same demography to each local population
fstr <- c(fstr,paste0("skeletonland<-landscape.new.local.demo(skeletonland,surv.matr, repr.matr, male.matr)"))
#cross habitat matrices
fstr <- c(fstr,paste0("epoch_s_matr<-matrix(0,nrow=(num.pops*num.stgs), ncol=(num.pops*num.stgs))"))
fstr <- c(fstr,paste0("epoch_r_matr <- landscape.mig.matrix(h=num.pops,s=num.stgs,mig.model='custom',R.custom=mig.rates)$R"))
fstr <- c(fstr,paste0("epoch_m_matr <- epoch_s_matr"))
#no extinction allowed, hard coded
fstr <- c(fstr,paste0("skeletonland<-landscape.new.epoch(skeletonland,epochprob=1, epoch_s_matr, epoch_r_matr, epoch_m_matr,startgen=0,extinct=NULL,carry=carrying)"))
#LOCI
#Note that for SNPs, numalleles should be 2, allelesize only used for sequences
#type = 0 IAM, type = 1 SMM type = 2 DNA sequence
#assumes biparental transmission (transmission = 0)
rms.locus.type = NULL
#print(loc.type)
if (loc.type == "SNP") {rms.locus.type = 2; num.alleles = 4; seq.length = rep(1,num.loc)}
if (loc.type %in% c("microsat","MICROSAT","microsatellite")) rms.locus.type = 1
if (loc.type == "sequence") rms.locus.type = 2
for (l in 1:num.loc) {
if (rms.locus.type==2) {
if (l==1) #only one sequence locus possible and it creates a maternally inherited haploid locus
fstr <- c(fstr,paste0("skeletonland<-landscape.new.locus(skeletonland, type=2, ploidy=1, mutationrate=mut.rate[",l,"],",
"transmission=1, numalleles=num.alleles[",l,"], frequencies=,allele.freqs[[",l,"]])")) #temp remove allele size
} else {
fstr <- c(fstr,paste0("skeletonland<-landscape.new.locus(skeletonland, type=1, ploidy=2, mutationrate=mut.rate[",l,"], transmission=0, numalleles=num.alleles[",l,"], frequencies=allele.freqs[[",l,"]])"))
}
}
#assumes population initial sizes all defined nicely by user
fstr <- c(fstr,"skeletonland<-landscape.new.individuals(skeletonland,init.pop.sizes)")
fstr <- c(fstr,"}")
paste(fstr,collapse="\n")
}
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