R Under development (unstable) (2024-05-04 r86521 ucrt) -- "Unsuffered Consequences"
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> ## Testing the capability of optimizing parameters
> require(apsimx)
Loading required package: apsimx
APSIM(X) not found.
                        If APSIM(X) is installed in an alternative location,
                        set paths manually using 'apsimx_options' or 'apsim_options'.
                        You can still try as the package will look into the registry (under Windows)
> require(ggplot2)
Loading required package: ggplot2
> apsimx_options(warn.versions = FALSE)
> 
> ## 1. Simulate data from a model with known parameters
> ## 2. Change the parameter values and some some random "noise"
> ## 3. Run the optimization algorithm
> ## 4. Compare optimized parameter values with original ones
> 
> extd.dir <- system.file("extdata", package = "apsimx")
> 
> ## extd.dir <- "~/Dropbox/apsimx/inst/extdata"
> 
> ## I won't routinely run this
> #### First set of tests ----
> if(FALSE){
+   
+   ## One model run takes ~4 seconds
+   ## The original values for these were 1.5 for RUE and 90 for BasePhyllochron
+   system.time(sim0 <- apsimx("Wheat-opt-ex.apsimx", src.dir = extd.dir))
+ 
+   pp1 <- inspect_apsimx_replacement("Wheat-opt-ex.apsimx", 
+                                     src.dir = extd.dir, 
+                                     node = "Wheat", 
+                                     node.child = "Leaf",
+                                     node.subchild = "Photosynthesis",
+                                     node.subsubchild = "RUE",
+                                     parm = "FixedValue",
+                                     print.path = TRUE,
+                                     display.available = FALSE, 
+                                     verbose = FALSE)
+   
+   pp2 <- inspect_apsimx_replacement("Wheat-opt-ex.apsimx", 
+                                     src.dir = extd.dir, 
+                                     node = "Wheat", 
+                                     node.child = "Cultivars",
+                                     node.subchild = "USA",
+                                     node.subsubchild = "Yecora",
+                                     parm = "BasePhyllochron",
+                                     print.path = TRUE,
+                                     display.available = FALSE, 
+                                     verbose = FALSE)
+   
+   ## edit_apsimx_replacement("Wheat-opt-ex.apsimx")
+   
+   ## Visualize the data
+   ggplot(sim0, aes(Date, Wheat.AboveGround.Wt)) + 
+     geom_line()
+   ggplot(sim0, aes(Date, Wheat.Leaf.LAI)) + 
+     geom_line()
+   ggplot(sim0, aes(Date, Wheat.Phenology.Stage)) + 
+     geom_line()
+ 
+   ## Create 'observed' data
+   sample.dates <- seq(from = as.Date("2016-10-01"), to = as.Date("2017-06-01"), length.out = 10)
+ 
+   set.seed(12345)
+   obs0 <- sim0[sim0$Date %in% sample.dates, c("Date","Wheat.Phenology.Stage","Wheat.Leaf.LAI","Wheat.AboveGround.Wt")]
+   obs0$Wheat.Phenology.Stage <- obs0$Wheat.Phenology.Stage + rnorm(10, 0, sd = 0.1)
+   obs0$Wheat.Leaf.LAI[5:10] <- obs0$Wheat.Leaf.LAI[5:10] + rnorm(6, 0, sd = 0.5)
+   obs0$Wheat.AboveGround.Wt[3:10] <- obs0$Wheat.AboveGround.Wt[3:10] + rnorm(8, 0, sd = 3)
+ 
+   obsWheat <- obs0
+   save(obsWheat, file = "obsWheat.rda")
+ 
+   data(obsWheat)
+   ## We will try to optimize only 2 parameters
+   ## RUE: default 1.5
+   ## Phyllochron for cultivar Yecora Fixed Value 90
+   inspect_apsimx_replacement("Wheat-opt-ex.apsimx", 
+                              src.dir = extd.dir, 
+                              node = "Wheat", 
+                              node.child = "Leaf",
+                              node.subchild = "Photosynthesis",
+                              node.subsubchild = "RUE",
+                              parm = "FixedValue",
+                              print.path = TRUE,
+                              display.available = FALSE, 
+                              verbose = FALSE)
+ 
+   inspect_apsimx_replacement("Wheat-opt-ex.apsimx", 
+                              src.dir = extd.dir, 
+                              node = "Wheat", 
+                              node.child = "Cultivars",
+                              node.subchild = "USA",
+                              node.subsubchild = "Yecora",
+                              parm = "BasePhyllochron",
+                              print.path = TRUE,
+                              display.available = FALSE, 
+                              verbose = FALSE)
+   
+   ## Run the model with incorrect parameters
+   ## RUE = 1.2
+   ## Phyllochron = 120
+   tmp <- tempdir()
+   setwd(tmp)
+   file.copy(file.path(extd.dir, "Ames.met"), ".")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   
+   system.time(sim.b4 <- apsimx("Wheat-opt-ex.apsimx", src.dir = tmp)) ## This takes 4-5 seconds
+   
+   ## write.csv(sim.b4, "wheat-sim-b4-opt.csv", row.names = FALSE)
+ 
+   sim.b4.s <- subset(sim.b4, Date > as.Date("2016-09-30") & Date < as.Date("2017-07-01"))
+   ## phenology
+   ggplot() + 
+     geom_point(data = obsWheat, aes(x = Date, y = Wheat.Phenology.Stage)) +
+     geom_line(data = sim.b4.s, aes(x = Date, y = Wheat.Phenology.Stage)) + 
+     ggtitle("Phenology")
+   ## LAI
+   ggplot() + 
+     geom_point(data = obsWheat, aes(x = Date, y = Wheat.Leaf.LAI)) +
+     geom_line(data = sim.b4.s, aes(x = Date, y = Wheat.Leaf.LAI)) + 
+     ggtitle("LAI")
+   ## Biomass
+   ggplot() + 
+     geom_point(data = obsWheat, aes(x = Date, y = Wheat.AboveGround.Wt)) +
+     geom_line(data = sim.b4.s, aes(x = Date, y = Wheat.AboveGround.Wt)) + 
+     ggtitle("Biomass (g/m2)")
+   
+   ## Optimization
+   pp1 <- "Wheat.Leaf.Photosynthesis.RUE.FixedValue"
+   pp2 <- "Wheat.Cultivars.USA.Yecora.BasePhyllochron"
+   
+   # edit_apsimx_replacement("Wheat-b4-opt.apsimx",
+   #                         src.dir = ".",
+   #                         overwrite = TRUE,
+   #                         node = "Wheat", node.child = "Cultivars",
+   #                         node.subchild = "USA", node.subsubchild = "Yecora",
+   #                         parm = "BasePhyllochron", value = 110)
+   
+   ## This takes about ~7.5 minutes
+   start <- Sys.time()
+   wop <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                        parm.paths = c(pp1, pp2),
+                        data = obsWheat, 
+                        weights = "mean",
+                        replacement = c(TRUE, TRUE),
+                        initial.values = c(1.2, 120))
+   end <- Sys.time()
+   
+   ## This took 8.8 minutes
+   start <- Sys.time()
+   wop.h <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                           src.dir = extd.dir, 
+                           parm.paths = c(pp1, pp2),
+                           data = obsWheat, 
+                           weights = "mean",
+                           replacement = c(TRUE, TRUE),
+                           initial.values = c(1.2, 120),
+                           hessian = TRUE)
+   end <- Sys.time()
+   
+   sim.opt <- apsimx("Wheat-opt-ex.apsimx", src.dir = extd.dir, value = "report")  
+ 
+   sim.opt.s <- subset(sim.opt, Date > as.Date("2016-09-30") & Date < as.Date("2017-07-01"))
+   
+   ## For vignette
+   ## write.csv(sim.opt.s, file = "wheat-sim-opt.csv", row.names = FALSE)
+   
+   ## phenology
+   ggplot() + 
+     geom_point(data = obsWheat, aes(x = Date, y = Wheat.Phenology.Stage)) +
+     geom_line(data = sim.opt.s, aes(x = Date, y = Wheat.Phenology.Stage)) + 
+     ggtitle("Phenology")
+   ## LAI
+   ggplot() + 
+     geom_point(data = obsWheat, aes(x = Date, y = Wheat.Leaf.LAI)) +
+     geom_line(data = sim.opt.s, aes(x = Date, y = Wheat.Leaf.LAI)) + 
+     ggtitle("LAI")
+   ## Biomass
+   ggplot() + 
+     geom_point(data = obsWheat, aes(x = Date, y = Wheat.AboveGround.Wt)) +
+     geom_line(data = sim.opt.s, aes(x = Date, y = Wheat.AboveGround.Wt)) + 
+     ggtitle("Biomass (g/m2)")
+ 
+   ## What about nloptr?
+   start <- Sys.time()
+   wop.n <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                         src.dir = extd.dir, 
+                         parm.paths = c(pp1, pp2),
+                         data = obsWheat, 
+                         weights = "mean",
+                         replacement = c(TRUE, TRUE),
+                         initial.values = c(1.2, 120),
+                         type = "nloptr",
+                         opts = list("algorithm" = "NLOPT_LN_NELDERMEAD"))
+   end <- Sys.time()
+   
+   ## Test BayesianTools??? Would need to embbed it inside optim
+   ## How long does this take in Windows laptop? 500 iter, 9 chains: 3464 seconds ~ 1 hour
+   ## 500 iter, 3 chains: 18 minutes
+   ## 5000 iter, 3 chains: 4 hours, but still not good enough
+   start <- Sys.time()
+   wop.mcmc <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                            src.dir = extd.dir, 
+                            parm.paths = c(pp1, pp2),
+                            data = obsWheat, 
+                            weights = "mean",
+                            replacement = c(TRUE, TRUE),
+                            initial.values = c(1.2, 120),
+                            type = "mcmc",
+                            parallel = FALSE,
+                            settings = list(iterations = 5000))
+   end <- Sys.time()
+   
+ }
> 
> #### Classic #### 
> if(FALSE){
+ 
+   tmp <- tempdir()
+   setwd(tmp)
+   
+   apsim_options(warn.versions = FALSE)
+   
+   ## Testing optimization for an APSIM Classic example
+   ## Maize
+   if(file.exists("Maize.apsim")) file.remove("Maize.apsim")
+   if(file.exists("Maize.xml")) file.remove("Maize.xml")
+   if(file.exists("Maize.out")) file.remove("Maize.out")
+   if(file.exists("Maize.sum")) file.remove("Maize.sum")
+   
+   extd.dir <- system.file("extdata", package = "apsimx")
+   file.copy(file.path(extd.dir, "Maize-op.apsim"), "./Maize.apsim")
+   file.copy("C:/Program Files (x86)/APSIM710-r4207/Model/Maize.xml", ".")
+ 
+   inspect_apsim("Maize.apsim")
+   
+   inspect_apsim("Maize.apsim", node = "Crop",
+                 parm = list("Sow", 3))
+   
+   edit_apsim("Maize.apsim", node = "Clock",
+              parm = "start_date", value = "01/01/1987",
+              overwrite = TRUE)
+   
+   sim0 <- apsim("Maize.apsim")
+   
+   obsMaize <- data.frame(Date = as.Date(c("1988-02-23", "1989-02-25")),
+                          biomass = c(4600, 5000),
+                          yield = c(350, 570))
+   
+   pp1 <- inspect_apsim_xml("Maize.xml", parm = "sc401/rue")
+   pp2 <- inspect_apsim_xml("Maize.xml", parm = "sc401/GNmaxCoef")
+   
+   ## Optimize a single parameter
+   op01 <- optim_apsim("Maize.apsim", 
+                      crop.file = "Maize.xml",
+                      parm.paths = pp2,
+                      data = obsMaize,
+                      hessian = TRUE,
+                      weights = "mean")
+   
+   
+   op1 <- optim_apsim("Maize.apsim", 
+                      crop.file = "Maize.xml",
+                      parm.paths = c(pp1, pp2),
+                      data = obsMaize,
+                      weights = "mean")
+ 
+   file.remove("Maize.xml")
+   file.copy("C:/Program Files (x86)/APSIM710-r4207/Model/Maize.xml", ".")
+   
+   op2 <- optim_apsim("Maize.apsim", 
+                      crop.file = "Maize.xml",
+                      parm.paths = c(pp1, pp2),
+                      data = obsMaize,
+                      hessian = TRUE,
+                      weights = "mean")
+   
+   # op2.u <- optim_apsim("Maize.apsim", 
+   #                      crop.file = "Maize.xml",
+   #                      parm.paths = c(pp1, pp2),
+   #                      type = "ucminf",
+   #                      data = obsMaize,
+   #                      hessian = TRUE,
+   #                      weights = "mean")
+   
+   op2nl <- optim_apsim("Maize.apsim", 
+                      crop.file = "Maize.xml",
+                      parm.paths = c(pp1, pp2),
+                      data = obsMaize,
+                      type = "nloptr",
+                      weights = "mean",
+                      opts = list("algorithm" = "NLOPT_LN_NELDERMEAD"))
+   
+   sim2 <- apsim("Maize.apsim")
+   
+   ## Can I also optimize management?
+   pp3 <- inspect_apsim("Maize.apsim", node = "Crop",
+                        parm = list("Sow", 17),
+                        print.path = TRUE)
+ 
+   pp4 <- inspect_apsim("Maize.apsim", node = "Crop",
+                        parm = list("Sow", 28),
+                        print.path = TRUE)
+ 
+   ## The goal of this is to show that you 
+   ## can try to optimize parameters which are in the
+   ## .apsim and .xml file
+   op3 <- optim_apsim("Maize.apsim", 
+                      crop.file = "Maize.xml",
+                      parm.paths = c(pp2, pp4),
+                      xml.parm = c(TRUE, FALSE),
+                      data = obsMaize,
+                      weights = "mean",
+                      hessian = TRUE)
+ 
+   inspect_apsim("Maize.apsim", node = "Crop",
+                 parm = list("Sow", 17),
+                 print.path = TRUE)
+   
+   inspect_apsim("Maize.apsim", node = "Crop",
+                  parm = list("Sow", 28),
+                  print.path = TRUE)
+ 
+   
+   if(file.exists("Maize.apsim")) file.remove("Maize.apsim")
+   if(file.exists("Maize.xml")) file.remove("Maize.xml")
+   if(file.exists("Maize.out")) file.remove("Maize.out")
+   if(file.exists("Maize.sum")) file.remove("Maize.sum")
+ }
> 
> ## Testing the optimization of a single parameter 
> ## comparing methods
> if(FALSE){
+   
+   tmp <- tempdir()
+   setwd(tmp)
+   
+   extd.dir <- system.file("extdata", package = "apsimx")
+   
+   file.copy(file.path(extd.dir, "Ames.met"), ".")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   
+   sim0 <- apsimx("Wheat-opt-ex.apsimx")
+ 
+   pp1 <- "Wheat.Leaf.Photosynthesis.RUE.FixedValue"
+   pp2 <- "Wheat.Cultivars.USA.Yecora.BasePhyllochron"
+   
+   ## Testing the "unreliable" method
+   start <- Sys.time()
+   wop.1 <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                         parm.paths = pp1,
+                         data = obsWheat, 
+                         replacement = TRUE,
+                         initial.values = 1.2)
+   end <- Sys.time() ## It took 3.25 minutes
+   
+   ## Plus hessian
+   file.remove("Wheat-opt-ex.apsimx")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   
+   start <- Sys.time()
+   wop.h.1 <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                           parm.paths = pp1,
+                           data = obsWheat, 
+                           replacement = TRUE,
+                           hessian = TRUE,
+                           initial.values = 1.2)
+   end <- Sys.time() ## It took 3.4 minutes
+  
+   ## Erase and try Brent 
+   file.remove("Wheat-opt-ex.apsimx")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+  
+   start <- Sys.time()
+   wop.b.1 <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                           parm.paths = pp1,
+                           data = obsWheat, 
+                           method = "Brent",
+                           lower = 0.5, upper = 2,
+                           replacement = TRUE,
+                           initial.values = 1.2)
+   end <- Sys.time() ## It took 2.18 minutes 
+   ## Brent, naturally, will not provide the best solution if
+   ## the solution is outside the interval (lower, upper)
+   
+   ## Erase and try L-BFGS-B
+   file.remove("Wheat-opt-ex.apsimx")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   
+   start <- Sys.time()
+   wop.bfgs.1 <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                           parm.paths = pp1,
+                           data = obsWheat, 
+                           method = "L-BFGS-B",
+                           lower = 0.5,
+                           hessian = TRUE,
+                           replacement = TRUE,
+                           initial.values = 1.2,
+                           control = list(trace = 3))
+   end <- Sys.time() ## It took 7.02 minutes 
+   
+   ## Next step is to test whether weighting affects the estimate of the vcov
+   ## and how different it is to the Bayesian analysis
+   
+   ## Erase and try L-BFGS-B
+   file.remove("Wheat-opt-ex.apsimx")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   
+   start <- Sys.time()
+   wop.bfgs.2 <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                              parm.paths = pp1,
+                              data = obsWheat,
+                              weights = "mean",
+                              method = "L-BFGS-B",
+                              lower = 0.5,
+                              hessian = TRUE,
+                              replacement = TRUE,
+                              initial.values = 1.2,
+                              control = list(trace = 3))
+   end <- Sys.time() ## It took 4.16 minutes 
+   
+   ## Testing with two parameters
+   file.remove("Wheat-opt-ex.apsimx")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   ## Testing with two parameters
+   start <- Sys.time()
+   wop.2 <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                         parm.paths = c(pp1, pp2),
+                         data = obsWheat, 
+                         replacement = c(TRUE, TRUE),
+                         hessian = TRUE,
+                         initial.values = c(1.2, 120))
+   end <- Sys.time() ## It took 15.7 minutes
+   
+   ## Testing with two parameters, without the hessian
+   file.remove("Wheat-opt-ex.apsimx")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   ## Testing with two parameters
+   start <- Sys.time()
+   wop.nh.2 <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                         parm.paths = c(pp1, pp2),
+                         data = obsWheat, 
+                         replacement = c(TRUE, TRUE),
+                         initial.values = c(1.2, 120))
+   end <- Sys.time() ## It took 13.97 minutes
+   
+   file.remove("Wheat-opt-ex.apsimx")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   ## Testing with two parameters
+   start <- Sys.time()
+   wop.3 <- optim_apsimx("Wheat-opt-ex.apsimx", 
+                         parm.paths = c(pp1, pp2),
+                         data = obsWheat, 
+                         type = "ucminf",
+                         weights = "mean",
+                         replacement = c(TRUE, TRUE),
+                         hessian = TRUE,
+                         initial.values = c(1.2, 120))
+   end <- Sys.time() ## It took 28.97 minutes and it did not find the right answer
+ }
> 
> #### Testing grid method ----
> if(FALSE){
+   
+   data(obsWheat)
+   
+   system.time(sim0 <- apsimx("Wheat-opt-ex.apsimx", src.dir = extd.dir)) 
+   
+   cmp.b4 <- compare_apsim(obsWheat, sim0, labels = c("obs", "sim"), cRSS = TRUE)
+   ### pre-optimized log-RSS
+   log(cmp.b4$cRSS)
+   
+   ## Creating a grid for two parameters
+   pp1 <- inspect_apsimx_replacement("Wheat-opt-ex.apsimx", 
+                                     src.dir = extd.dir, 
+                                     node = "Wheat", 
+                                     node.child = "Leaf",
+                                     node.subchild = "Photosynthesis",
+                                     node.subsubchild = "RUE",
+                                     parm = "FixedValue",
+                                     print.path = TRUE,
+                                     display.available = FALSE, 
+                                     verbose = FALSE)
+   
+   pp2 <- inspect_apsimx_replacement("Wheat-opt-ex.apsimx", 
+                                     src.dir = extd.dir, 
+                                     node = "Wheat", 
+                                     node.child = "Cultivars",
+                                     node.subchild = "USA",
+                                     node.subsubchild = "Yecora",
+                                     parm = "BasePhyllochron",
+                                     print.path = TRUE,
+                                     display.available = FALSE, 
+                                     verbose = FALSE)
+ 
+   pgrd <- expand.grid(RUE = c(0.8, 1, 1.2, 1.4, 1.6, 1.8, 2.0), 
+                       BasePhyllochron = c(40, 60, 80, 100, 120, 140, 160))  
+   
+   tmp <- tempdir()
+   setwd(tmp)
+   file.copy(file.path(extd.dir, "Ames.met"), ".")
+   file.copy(file.path(extd.dir, "Wheat-opt-ex.apsimx"), ".")
+   
+   system.time(sim.b4 <- apsimx("Wheat-opt-ex.apsimx", src.dir = tmp)) ## This takes 4-5 seconds
+   xrgs <- xargs_apsimx(single.threaded = TRUE)
+   system.time(sim.b4 <- apsimx("Wheat-opt-ex.apsimx", src.dir = tmp, xargs = xrgs)) ## This takes 4-5 seconds
+   
+ 
+   start <- Sys.time()
+   wop.grd <- optim_apsimx("Wheat-opt-ex.apsimx",
+                           src.dir = tmp,
+                           parm.paths = c(pp1, pp2),
+                           data = obsWheat, 
+                           type = "grid",
+                           replacement = c(TRUE, TRUE),
+                           initial.values = list(RUE = 1.2, BasePhyllochron = 120),
+                           verbose = TRUE,
+                           grid = pgrd,
+                           cores = 2)
+   end <- Sys.time() ## It took 6.1 minutes 
+                     ## Took 3.67 minutes using two cores and single-thread (Mac 2017)
+   
+   ggplot(wop.grd$res, aes(x = RUE, y = lrss)) + 
+     facet_wrap(~BasePhyllochron) + 
+     geom_point() + 
+     geom_line()
+   
+   pp1 <- inspect_apsimx_replacement("Wheat-opt-ex.apsimx", 
+                                     src.dir = ".", 
+                                     node = "Wheat", 
+                                     node.child = "Leaf",
+                                     node.subchild = "Photosynthesis",
+                                     node.subsubchild = "RUE",
+                                     parm = "FixedValue",
+                                     print.path = TRUE,
+                                     display.available = FALSE, 
+                                     verbose = FALSE)
+  
+   pp2 <- inspect_apsimx_replacement("Wheat-opt-ex.apsimx", 
+                                     src.dir = ".", 
+                                     node = "Wheat", 
+                                     node.child = "Cultivars",
+                                     node.subchild = "USA",
+                                     node.subsubchild = "Yecora",
+                                     parm = "BasePhyllochron",
+                                     print.path = TRUE,
+                                     display.available = FALSE, 
+                                     verbose = FALSE)
+   
+  ## Compare to optim
+   start <- Sys.time()
+   wop.nm <- optim_apsimx("Wheat-opt-ex.apsimx",
+                           src.dir = tmp,
+                           parm.paths = c(pp1, pp2),
+                           data = obsWheat, 
+                           replacement = c(TRUE, TRUE),
+                           initial.values = list(RUE = 1.8, BasePhyllochron = 120))
+   end <- Sys.time() ## It took 5.7 minutes 
+   
+   ### Maybe we need a fine grid around the true values?
+   pgrd3 <- expand.grid(RUE = c(1.2, 1.3, 1.4, 1.5, 1.6, 1.7, 1.8, 1.9), 
+                       BasePhyllochron = c(70, 75, 80, 85, 90, 95, 100))  
+   
+   start <- Sys.time()
+   wop.grd3 <- optim_apsimx("Wheat-opt-ex.apsimx",
+                           src.dir = tmp,
+                           parm.paths = c(pp1, pp2),
+                           data = obsWheat, 
+                           type = "grid",
+                           replacement = c(TRUE, TRUE),
+                           initial.values = list(RUE = 1.5, BasePhyllochron = 90),
+                           verbose = TRUE,
+                           grid = pgrd3,
+                           cores = 3)
+   end <- Sys.time() ## It took 6.63 minutes 
+   
+   ggplot(wop.grd3$res, aes(x = RUE, y = lrss)) + 
+     facet_wrap(~BasePhyllochron) + 
+     geom_point() + 
+     geom_line()
+ 
+   system.time(sim.a4 <- apsimx("Wheat-opt-ex.apsimx", src.dir = tmp)) ## This takes 4-5 seconds
+   wop.grd3  
+   cmp <- compare_apsim(obsWheat, sim.a4, labels = c("obs", "sim"), cRSS = TRUE)
+ }
> 
> proc.time()
   user  system elapsed 
   1.06    0.17    1.21