R Under development (unstable) (2024-08-17 r87027 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> ## Test reading and writing soils in XML format
> ## Author: Fernando E. Miguez
> ## Date: 2022-02-16
> ##
> ## Required: R package apsimx 2.3.2
> 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)
> 
> run.apsimx.soils <- get(".run.local.tests", envir = apsimx.options)
> 
> run.apsimx.soils <- FALSE ## It takes 23 minutes to run the code below
> 
> if(run.apsimx.soils){
+   
+   extd.dir <- system.file("extdata", package = "apsimx")
+   
+   sls <- read_apsim_soils("Clarion.soils", src.dir = extd.dir)
+   
+   ## All soils in APSoil
+   apsoil.dir <- "~/Dropbox/apsimx-other/APSoil"
+   
+   ## Reading in all this data takes a while
+   start <- Sys.time()
+   asls <- read_apsim_soils("APSRU-Australia-soils.soils", src.dir = apsoil.dir)
+   end <- Sys.time()
+   
+ }
> 
> ### Testing fixing a soil profile
> 
> run.apsimx.soils.fix <- get(".run.local.tests", envir = apsimx.options)
> 
> try.isric <- try(get_isric_soil_profile(lonlat = c(-93, 42), fix = TRUE, verbose = FALSE), silent = TRUE)
> 
> ## If the above fails it is very likely that the server is down
> if(inherits(try.isric, 'try-error')) run.apsimx.soils.fix <- FALSE
> run.apsimx.soils.fix <- FALSE
> 
> if(run.apsimx.soils.fix){
+   
+   tmp.dir <- tempdir()
+   setwd(tmp.dir)
+   ex.dir <- auto_detect_apsimx_examples()
+   
+   file.copy(file.path(ex.dir, "Wheat.apsimx"), ".")  
+   
+   lon <- seq(1, 2, length.out = 30)
+   lat <- seq(48, 49, length.out = 30)
+   
+   for(i in seq_along(lon)){
+     
+     sp <- try(get_isric_soil_profile(lonlat = c(lon[i], lat[i]), fix = TRUE, verbose = FALSE), silent = TRUE)
+     if(inherits(sp, "try-error")){
+       cat("No soil for this location. Lon:", lon[i], "Lat:", lat[i], "\n")
+       next
+     }
+     
+     edit_apsimx_replace_soil_profile("Wheat.apsimx", soil.profile = sp,
+                                      edit.tag = paste0("-", i))
+     sim1 <- try(apsimx(paste0("Wheat-", i, ".apsimx")), silent = TRUE)
+     
+     if(inherits(sim1, "try-error"))
+       cat("Simulation:", i, "failed\n")
+   }
+ }
> 
> 
> 
> proc.time()
   user  system elapsed 
   0.98    0.17    5.57