R/ms.commander2.R

In gehara/PipeMaster: Building and Simulating Coalescent models.

# Sample parameters and generates ms string
# @description this function sample parameters from priors and trasform them to coalescent scale to generate a ms command 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.
# @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 ms string.
#
ms.commander2<-function(model,use.alpha=use.alpha){

  # 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 <- PipeMaster:::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 <- PipeMaster:::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 <- PipeMaster:::sample.pars(model$loci)

  # sample migrations if present and bind sampled parameters
  if(is.null(mig.pars)==F){
    mig.pars <- PipeMaster:::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,loci[,c(1,4)])

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

  ####### Generate ms string ##############################################
  ####### Conversion 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

  commands<-list(NULL)
  for(u in 1:nrow(loci)){

      string <- PipeMaster:::ms.string.generator(model,size.pars,mig.pars,time.pars,use.alpha=use.alpha, scalar = as.numeric(loci[u,3]))

      #################################### theta and structure ###########################
      ######### generate -t and -I part of the command
      if(model$I[1,3]!="1"){
      y<-paste("-t",loci[u,7],paste(model$I[u,2:ncol(model$I)],collapse=" "),collapse=" ")
      } else {
      y<-paste("-t",loci[u,7],collapse=" ")
      }
      commands[[u]]<-paste(y,string, collapse=" ")
      }
  #### attach sampled parameters
  commands[[nrow(loci)+1]]<-t(rbind(parameters,c("scalar",ms.scalar)))
  return(commands)
  }