# # Sample parameters and generates msABC string
# # @description this function sample parameters from priors and trasform them to coalescent scale to generate a msABC 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.msABC function. One mey want to run this function to check the msABC string.
# #
# scrm.commander<-function(model, use.alpha = use.alpha, m.rate){
#
# # 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 <- 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$mig.matrix)
# #bind sampled migration parameters
# parameters<-rbind(parameters,mig.pars[,c(1,4)])
# }
#
# #### bind sampled mutation rate
# #parameters<-parameters#,loci[,c(1,4)])
#
# ####### End of parameter sampling #######################################
# #########################################################################
#
# ####### Generate ms string ##############################################
# ####### Convertion to coalescent scale #####################################
#
# # generate coalescent scalar. Arbitrary value.
#
# #### if single population
# # if(model$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
# # }
# Ne0 <- 100000
# ms.scalar <- 4*Ne0
#
# # rescale to inheritance scalar and transform size parameters to relative to Ne0
# size.pars[,4:5] <- as.numeric(size.pars[,4])/Ne0
#
# #### bind scaled theta per gene (4Ne0*m*pb)
# theta <- ms.scalar*m.rate*as.numeric(loci[1,2])
#
# #### convertion of time to coalescent scale
# time.pars[,4:5] <- as.numeric(time.pars[,4])/ms.scalar
#
# commands <- list(NULL,NULL)
# #### ms string command
# string <- PipeMaster:::ms.string.generator(model, size.pars, mig.pars,time.pars, use.alpha=use.alpha, scalar = as.numeric(loci[1,3]))
# #################################### theta and structure ###########################
# ######### generate -t and -I part of the command
# y <- paste(sum(as.numeric(model$I[1,4:ncol(model$I)])),nrow(loci),"-t",theta,paste(model$I[1,2:ncol(model$I)],collapse=" "),collapse=" ")
# ######### generate locfile part of the command
# #loc.string <- paste("--frag-begin --finp .",arg,"locfile.txt --N ",Ne0," --frag-end",sep="")
# #### final command
# commands[[1]]<-paste(y,string, collapse=" ")
#
# #### attach sampled parameters
# commands[[2]]<-t(parameters)
# return(commands)
# }
#
# library(PipeMaster)
# scrm.commander(model = Is, m.rate=1e-9, use.alpha = F)
#
# x<-scrm(paste(commands[[1]]))
#
# y <- colSums(x[[1]][[1]])
#
# for(i in 1:length(x)){
# colSums(x[[1]][[1]])
#
#
# }
#
#
# z <- list.files(pattern = )
#
#
# system(paste("cp *",nomes[i], ./fastas/")
#
# file.copy()
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