R/ms.commander.snp.R

In gehara/PipeMaster: Building and Simulating Coalescent models.

# Sample parameters and generates msABC string
# @description this function sample parameters from priors and trasform them to coalescent scale to generate a msABC string from a model object generated by the Model Builder, main.menu() function.
# @param model A model object
# @param use.alpha Logical.If TRUE the most recent population size change will be exponential. If FALSE sudden demographic changes.
# @param msABC path to the msABC binary.
# @return a list with msABC command and sampled parameters.
# @note This function is used internally for the sim.snp.sumstat function. One my want to run this function to check the msABC string.
#
ms.commander.snp<-function(model,use.alpha=use.alpha,msABC){

  # empty parameter vector
  parameters<-vector()

  # bind Ne, mig and Time priors
  size.pars<-rbind(model$flags$n,model$flags$en$size)
  mig.pars<-rbind(model$flags$m,model$flags$em$size)
  time.pars<-rbind(model$flags$ej,model$flags$en$time,model$flags$em$time)

  # sample Ne, div.time and mutation rate
  size.pars<-sample.w.cond(par.matrix=size.pars,cond.matrix=model$conds$size.matrix)
  # bind Ne sampled parameters
  parameters<-rbind(parameters,size.pars[,c(1,4)])

  if(is.null(time.pars)==F){
    time.pars<-sample.w.cond(par.matrix=time.pars,cond.matrix=model$conds$time.matrix)
    # bind sampled time parameters
    parameters<-rbind(parameters,time.pars[,c(1,4)])
  }

  loci<-sample.pars(model$loci)

  # sample migrations if present and bind sampled parameters
  if(is.null(mig.pars)==F){
    mig.pars<-sample.w.cond(par.matrix=mig.pars,cond.matrix=model$conds$mig.matrix)
    #bind sampled migration parameters
    parameters<-rbind(parameters,mig.pars[,c(1,4)])
  }

  #### bind sampled mutation rate
  parameters<-rbind(parameters,c("m.rate",loci[,4]))

  ####### End of parameter sampling #######################################
  #########################################################################

  ####### Generate ms string ##############################################
  ####### Convertion to coalescent scale #####################################

  # generate coalescent scalar. Arbitrary value.

    #### if single population
    if(model$I[1,3]=="1"){
      Ne0<-as.numeric(size.pars[1,4])
      ms.scalar<-4*Ne0
      } else {
        Ne0<-mean(as.numeric(model$flags$n[,4:5]))
        ms.scalar<-4*Ne0
      }

  #### bind scaled theta per gene (4Ne0*m*pb)
  loci<-cbind(loci,ms.scalar*as.numeric(loci[,4])*as.numeric(loci[,2]))

  #### convertion of time to coalescent scale
  time.pars[,4:5]<-as.numeric(time.pars[,4])/ms.scalar

  # rescale to inheritance scalar and transform size parameters to relative to Ne0
  size.pars[,4:5]<-as.numeric(size.pars[,4])/Ne0

  string<-ms.string.generator(model,size.pars,mig.pars,time.pars,use.alpha=use.alpha)
  # generate -t and -I part of the command

  commands<-list(NULL)
  I1<-model$I

  y<-paste(msABC," ",sum(as.numeric(I1[,4:ncol(I1)]))," ",as.numeric(model$loci[,3])," -t ",loci[1,7],
           if(model$I[1,3]!="1")paste(" ",paste(I1[1,2:ncol(I1)],collapse=" "),sep=""),sep="")
  commands[[1]]<-paste(y,string,collapse=" ")

  commands[[2]]<-NULL

  commands[[3]]<-t(parameters)
  return(commands)
}