## ----include=FALSE------------------------------------------------------------ library(knitr) opts_chunk$set( concordance=TRUE ) ## ----preliminaries, eval=TRUE, include=FALSE, echo=FALSE------------ options(width=70, useFancyQuotes=FALSE, prompt=" ", continue=" ") set.seed(123L) ## ----installMEIGO2, eval=FALSE, pgf=TRUE, echo=TRUE----------------- # if (!requireNamespace("BiocManager", quietly=TRUE)) # install.packages("BiocManager") # BiocManager::install("CellNOptR") ## ----load_package, eval=TRUE, pgf=TRUE, echo=FALSE,results='hide',warning=FALSE, message=FALSE---- library(MEIGOR) ## ----quickProblem, eval=FALSE, pgf=TRUE, echo=TRUE------------------ # library(MEIGOR) # problem<-list(f=objective, x_L=rep(-1,2), x_U=rep(1,2)) # opts<-list(maxeval=500, local_solver='DHC') ## ----quickProblemSolve, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---- ex3<-function(x,k1,k2,k3,k4){ f=-x[4]; #Equality constraints (declare them before the inequality ones) g<-rep(0,5); g[1]=x[4]-x[3]+x[2]-x[1]+k4*x[4]*x[6]; g[2]=x[1]-1+k1*x[1]*x[5]; g[3]=x[2]-x[1]+k2*x[2]*x[6]; g[4]=x[3]+x[1]-1+k3*x[3]*x[5]; #Inequality constraint g[5]=x[5]^0.5+x[6]^0.5; return(list(f=f,g=g)); } ## ----multiStart, eval=FALSE, pgf=TRUE, echo=TRUE-------------------- # Results_multistart<-MEIGO(problem,opts,algorithm="MULTISTART",p1,p2,...) ## ----unConstrainedF, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---- ex1 <- function(x){ y<-4*x[1]*x[1]-2.1*x[1]^4+1/3*x[1]^6+x[1]*x[2]-4*x[2]*x[2]+4*x[2]^4; return(y) } ## ----unConstrainedSolve, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---- #========================= #PROBLEM SPECIFICATIONS # ========================= problem<-list(f="ex1",x_L=rep(-1,2),x_U=rep(1,2)) opts<-list(maxeval=500, ndiverse=40, local_solver='DHC', local_finish='LBFGSB', local_iterprint=1) #========================= # END OF PROBLEM SPECIFICATIONS #========================= Results<-MEIGO(problem,opts,algorithm="ESS"); ## ----ex2F, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------------ ex2<-function(x){ F=-x[1]-x[2]; g<-rep(0,2); g[1]<-x[2]-2*x[1]^4+8*x[1]^3-8*x[1]^2; g[2]<-x[2]-4*x[1]^4+32*x[1]^3-88*x[1]^2+96*x[1]; return(list(F=F,g=g)) } ## ----ex2Solve, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'-------- #========================= #PROBLEM SPECIFICATIONS #========================= problem<-list(f="ex2",x_L=rep(0,2),x_U=c(3,4), c_L=rep(-Inf,2), c_U=c(2,36)) opts<-list(maxeval=750, local_solver="DHC", local_n1=2, local_n2=3) #======================== #END OF PROBLEM SPECIFICATIONS # ======================== Results<-MEIGO(problem,opts,algorithm="ESS"); ## ----ex3f, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------------ ex3<-function(x,k1,k2,k3,k4){ f=-x[4]; #Equality constraints g<-rep(0,5); g[1]=x[4]-x[3]+x[2]-x[1]+k4*x[4]*x[6]; g[2]=x[1]-1+k1*x[1]*x[5]; g[3]=x[2]-x[1]+k2*x[2]*x[6]; g[4]=x[3]+x[1]-1+k3*x[3]*x[5]; #Inequality constraint g[5]=x[5]^0.5+x[6]^0.5; return(list(f=f,g=g)); } ## ----ex2Solve3, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------- #========================= #PROBLEM SPECIFICATIONS #========================= problem<-list(f="ex3",x_L=rep(0,6),x_U=c(rep(1,4),16,16), neq=4, c_L=-Inf, c_U=4) opts<-list(maxtime=5, local_solver='solnp') #========================= #END OF PROBLEM SPECIFICATIONS #========================= k1=0.09755988; k3=0.0391908; k2=0.99*k1; k4=0.9*k3; Results<-MEIGO(problem,opts,algorithm="ESS",k1,k2,k3,k4); ## ----ex4f, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------------ ex4<-function(x){ F = x[2]^2 + x[3]^2 + 2.0*x[1]^2 + x[4]^2 - 5.0*x[2] - 5.0*x[3] - 21.0*x[1] + 7.0*x[4]; g<-rep(0,3); g[1] = x[2]^2 + x[3]^2 + x[1]^2 + x[4]^2 + x[2] - x[3] + x[1] - x[4]; g[2] = x[2]^2 + 2.0*x[3]^2 + x[1]^2 + 2.0*x[4]^2 - x[2] - x[4]; g[3] = 2.0*x[2]^2 + x[3]^2 + x[1]^2 + 2.0*x[2] - x[3] - x[4]; return(list(F=F, g=g)); } ## ----ex4main, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'--------- #========================= PROBLEM SPECIFICATIONS =========================== problem<-list(f="ex4", x_L=rep(0,4), x_U=rep(10,4), x_0=c(3,4,5,1), int_var=3, c_L=rep(-Inf,3), c_U=c(8,10,5)) opts<-list(maxtime=2) #========================= END OF PROBLEM SPECIFICATIONS ===================== Results<-MEIGO(problem,opts,algorithm="ESS"); ## ----ex5f, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'------------ ex5<-function(x,texp,yexp){ yini<-c(100, 0, 0, 0 ,0); times<-texp; out <- lsodes(yini, times, ex5_dynamics, parms = x) tout<-out[,1]; yout<-out[,-1]; J <- sum((yout-yexp)^2); g<-0; residuals<-(yout-yexp); return(list(J,g,residuals)) } #*************************************************** #Function of the dynamic system ex5_dynamics<-function(t,y,p){ dy<-rep(0,5) dy[1]<--(p[1]+p[2])*y[1]; dy[2]<-p[1]*y[1]; dy[3]<-p[2]*y[1]-(p[3]+p[4])*y[3]+p[5]*y[5]; dy[4]<-p[3]*y[3]; dy[5]<-p[4]*y[3]-p[5]*y[5]; return(list(dy)) } #*************************************************** ## ----ex5Solve, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide', warning=FALSE, message=FALSE---- #======================= #PROBLEM SPECIFICATIONS #======================= problem<-list(f="ex5", x_L=rep(0.01,5), x_U=rep(1,5), x_0=rep(0.1,5)) opts<-list(maxeval=1000, log_var=1:5, local_solver='NL2SOL', inter_save=1) #======================== #END OF PROBLEM SPECIFICATIONS #======================= #time intervals texp<-c(0, 1230, 3060, 4920, 7800, 10680, 15030, 22620, 36420) #Distribution of species concentration # y(1) y(2) y(3) y(4) y(5) yexp<-rbind(c(100.0, 0.0, 0.0, 0.0, 0.0), c(88.35, 7.3, 2.3, 0.4, 1.75), c( 76.4 , 15.6, 4.5 , 0.7 , 2.8), c(65.1 , 23.1 , 5.3 , 1.1 , 5.8), c(50.4 , 32.9 , 6.0 , 1.5 , 9.3), c(37.5 , 42.7 , 6.0 , 1.9 , 12.0), c(25.9 , 49.1 , 5.9 , 2.2 , 17.0), c( 14.0 , 57.4 , 5.1 , 2.6 , 21.0), c(4.5 , 63.1 , 3.8 , 2.9 , 25.7)); Results<-MEIGO(problem,opts,algorithm="ESS",texp,yexp); ## ----ex3solve, eval=FALSE, pgf=TRUE, echo=TRUE,results='hide'------- # #========================= # #PROBLEM SPECIFICATIONS # #========================= # problem<-list(f="ex3",x_L=rep(0,6),x_U=c(rep(1,4),16,16), # neq=4, c_L=-Inf, c_U=4) # opts<-list(ndiverse=10, local_solver='SOLNP', local_tol=3) # #========================= # #END OF PROBLEM SPECIFICATIONS # #========================= # k1=0.09755988; # k3=0.0391908; # k2=0.99*k1; # k4=0.9*k3; # Results<-MEIGO(problem,opts,algorithm="multistart",k1,k2,k3,k4); ## ----sourceRosen10, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---- rosen10<-function(x){ f<-0; n=length(x); for (i in 1:(n-1)){ f <- f + 100*(x[i]^2 - x[i+1])^2 + (x[i]-1)^2; } return(f) } nvar<-10; ## ----rosen10settings, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---- problem<-list(f="rosen10", x_L=rep(-5,nvar), x_U=rep(1,nvar)) ## ----algVNS, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---------- algorithm="VNS"; ## ----vnsOPts, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'--------- opts<-list(maxeval=2000, maxtime=3600*69, use_local=1, aggr=0, local_search_type=1, decomp=1, maxdist=0.5) ## ----vnsCallMEIGO, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide'---- Results<-MEIGO(problem,opts,algorithm) ## ----options, eval=FALSE, pgf=TRUE, echo=TRUE----------------------- # # opts=list(); # opts[[1]]$maxeval<-value1 # opts[[2]]$maxeval<-value2 # opts[[3]]$maxeval<-value3 ## ----ceSSexample, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide', warning=FALSE, message=FALSE---- rosen10<-function(x){ f<-0; n=length(x); for (i in 1:(n-1)){ f <- f + 100*(x[i]^2 - x[i+1])^2 + (x[i]-1)^2; } return(f) } nvar=20; problem<-list(f=rosen10, x_L=rep(-1000,nvar), x_U=rep(1000,nvar)); #Set 1 nodes and 2 cpu's per node n_nodes=1; n_cpus_per_node=3; #Set different values for dim_refset, bal and n2 #for each of the 10 cpu's to be used dim1 = 23; bal1 = 0; n2_1 = 0; dim2 = 33; bal2 = 0; n2_2 = 0; dim3 = 46; bal3 = 0; n2_3 = 2; dim4 = 56; bal4 = 0; n2_4 = 4; dim5 = 72; bal5 = 0.25; n2_5 = 7; dim6 = 72; bal6 = 0.25; n2_6 = 10; dim7 = 88; bal7 = 0.25; n2_7 = 15; dim8 = 101; bal8 = 0.5; n2_8 = 20; dim9 = 111; bal9 = 0.25; n2_9 = 50; dim10 = 123; bal10 = 0.25; n2_10 = 100; opts_dim=c(dim1,dim2,dim3,dim4,dim5,dim6,dim7,dim8,dim9,dim10); opts_bal=c(bal1,bal2,bal3,bal4,bal5,bal6,bal7,bal8,bal9,bal10); opts_n2=c(n2_1,n2_2,n2_3,n2_4,n2_5,n2_6,n2_7,n2_8,n2_9,n2_10); D=10; #Initialize counter and options counter=0; opts=list(); hosts=c(); for(i in 1:n_nodes){ for(j in 1:n_cpus_per_node){ counter=counter+1; #Set the name of every thread if(i<10)hosts=c(hosts,paste('node0',i,sep="")); if(i>=10 && i<100)hosts=c(hosts,paste('node',i,sep="")); opts[[counter]]=list(); #Set specific options for each thread opts[[counter]]$local_balance = opts_bal[counter]; opts[[counter]]$dim_refset = opts_dim[counter]; opts[[counter]]$local_n2 = opts_n2[counter]; #Set common options for each thread opts[[counter]]$maxeval = 10000; opts[[counter]]$local_solver = "dhc"; #Options not set will take default values for every thread } } #Set the address of each machine, defined inside the 'for' loop opts$hosts=c('localhost','localhost','localhost'); #Do not define the additional options for cooperative methods (e.g., ce_maxtime, ce_isparallel, etc..) #They will take their default values opts$ce_niter=5; opts$ce_type="SOCKS"; opts$ce_isparallel=TRUE; #Call the solver Results<-MEIGO(problem,opts,algorithm="CeSSR") ## ----ceVNSexample, eval=TRUE, pgf=TRUE, echo=TRUE,results='hide', warning=FALSE, message=FALSE---- rosen10<-function(x){ f<-0; n=length(x); for (i in 1:(n-1)){ f <- f + 100*(x[i]^2 - x[i+1])^2 + (x[i]-1)^2; } return(f) } nvar=20; problem<-list(f=rosen10, x_L=rep(-1000,nvar), x_U=rep(1000,nvar)) opts=list(); opts[[1]]=list(use_local=1,aggr=1,local_search=1,decomp=1,maxdist=0.8,maxeval=2000); opts[[2]]=list(use_local=1,aggr=0,local_search=2,decomp=0,maxdist=0.5,maxeval=2000); opts[[3]]=list(use_local=1,aggr=0,local_search=2,decomp=0,maxdist=0.5,maxeval=2000); opts[[4]]=list(use_local=1,aggr=0,local_search=2,decomp=0,maxdist=0.5,maxeval=2000); opts$hosts=c('localhost','localhost','localhost','localhost'); opts$ce_niter=10; opts$ce_type="SOCKS"; opts$ce_isparallel= TRUE; Results=MEIGO(problem,opts, algorithm="CeVNSR"); ## ----label=CNORodeExample_fig, eval=FALSE, echo=TRUE,results='hide'---- # library(MEIGOR); # library(CNORode); # data("CNORodeExample",package="MEIGOR"); # plotCNOlist(cnolist); ## ----label=CNORodeExample_fig_plot,include=TRUE,echo=FALSE,results='hide'---- library(MEIGOR); library(CNORode); data("CNORodeExample",package="MEIGOR"); plotCNOlist(cnolist); ## ----label=CNORodeExample_fig_model, eval=FALSE, pgf=TRUE, echo=TRUE,results='hide'---- # plotModel(model, cnolist); ## ----label=CNORodeExample_fig_model_plot,include=TRUE,echo=FALSE,results='hide'---- plotModel(model, cnolist); ## ----label=CNORodeExample_initial, eval=FALSE, pgf=FALSE, echo=TRUE,results='hide'---- # # initial_pars=createLBodeContPars(model, LB_n = 1, LB_k = 0.09, # LB_tau = 0.1, UB_n = 5, UB_k = 0.95, UB_tau = 10, random = TRUE); # # simData=plotLBodeFitness(cnolist, model,initial_pars, # reltol = 1e-05, atol = 1e-03, maxStepSize = 0.01); ## ----label=CNORodeExample_initial_plot,include=TRUE,echo=FALSE,results='hide'---- initial_pars=createLBodeContPars(model, LB_n = 1, LB_k = 0.09, LB_tau = 0.1, UB_n = 5, UB_k = 0.95, UB_tau = 10, random = TRUE); simData=plotLBodeFitness(cnolist, model,initial_pars, reltol = 1e-05, atol = 1e-03, maxStepSize = 0.01); ## ----label=CNORodeExample_optimize, eval=TRUE,echo=TRUE,results='hide'---- f_hepato<-getLBodeContObjFunction(cnolist, model, initial_pars, indices=NULL, time = 1, verbose = 0, transfer_function = 3, reltol = 1e-04, atol = 1e-03, maxStepSize =Inf, maxNumSteps = 1e4, maxErrTestsFails = 50, nan_fac = 5) ## ----label=CNORodeExample_define_prob, eval=TRUE,echo=TRUE,results='hide'---- n_pars=length(initial_pars$LB); problem<-list(f=f_hepato, x_L=initial_pars$LB[initial_pars$index_opt_pars], x_U=initial_pars$UB[initial_pars$index_opt_pars],x_0=initial_pars$LB[initial_pars$index_opt_pars]); ## ----label=CNORodeExample_define_opts, eval=TRUE,echo=TRUE,results='hide'---- opts<-list(maxeval=100, local_solver=0,ndiverse=10,dim_refset=6); ## ----label=CNORodeExample_2, eval=TRUE,echo=TRUE,results='hide'----- Results<-MEIGO(problem,opts,algorithm="ESS") ## ----label=CNORodeExample_opt, eval=FALSE, pgf=FALSE,echo=TRUE,results='hide'---- # opt_pars=initial_pars; # opt_pars$parValues=Results$xbest; # simData=plotLBodeFitness(cnolist, model,opt_pars, # reltol = 1e-05, atol = 1e-03, maxStepSize = 0.01); ## ----label=CNORodeExample_opt_plot,include=TRUE,echo=FALSE,results='hide'---- opt_pars=initial_pars; opt_pars$parValues=Results$xbest; simData=plotLBodeFitness(cnolist, model,opt_pars, reltol = 1e-05, atol = 1e-03, maxStepSize = 0.01); ## ----label=CellNOptR_example_cnolist_fig, eval=FALSE, pgf=TRUE, echo=TRUE, results='hide'---- # library(MEIGOR); # library(CellNOptR); # data("CellNOptR_example",package="MEIGOR"); # cnolist=CNOlist(cnolist); # plotCNOlist(cnolist) ## ----label=CellNOptR_example_cnolist,include=TRUE,echo=FALSE,results='hide'---- library(MEIGOR); library(CellNOptR); data("CellNOptR_example",package="MEIGOR"); cnolist=CNOlist(cnolist); plotCNOlist(cnolist); ## ----label=CellNOptR_example_fig_model, eval=FALSE, pgf=TRUE, echo=TRUE,results='hide'---- # model <- preprocessing(cnolist, model, # expansion=TRUE, compression=TRUE, verbose=FALSE); # plotModel(model, cnolist); ## ----label=CellNOptR_example_fig_model_plot,include=TRUE,echo=FALSE,results='hide', warning=FALSE---- model <- preprocessing(cnolist, model, expansion=TRUE, compression=TRUE, verbose=FALSE); plotModel(model, cnolist); ## ----label=CellNOptR_prep_fig_model, eval=TRUE, pgf=TRUE, echo=TRUE, results='hide'---- get_fobj<- function(cnolist,model){ f<-function(x,model1=model,cnolist1=cnolist){ simlist=prep4sim(model1) score=computeScoreT1(cnolist1, model1, x) return(score) } } fobj=get_fobj(cnolist,model) ## ----label=CellNOptR_prep_3, eval=TRUE, pgf=TRUE, echo=TRUE, results='hide'---- nvar=16; problem<-list(f=fobj, x_L=rep(0,nvar), x_U=rep(1,nvar)) opts<-list(maxeval=2000, maxtime=30, use_local=1, aggr=0, local_search_type=1, decomp=1, maxdist=0.5) ## ----label=CellNOptR_4, eval=TRUE, pgf=TRUE, echo=TRUE, results='hide'---- Results<-MEIGO(problem,opts,"VNS") ## ----label=CellNOptR_example_plot_optModel,echo=TRUE,eval=FALSE,results='hide'---- # optModel=cutModel(model,Results$xbest); # plotModel(optModel,cnolist); ## ----label=CellNOptR_example_plot_optModel_fig,include=TRUE,echo=FALSE,results='hide'---- optModel=cutModel(model,Results$xbest); plotModel(optModel,cnolist);