Merge pull request #245 from jorritmesman/main

Release v1.1.0

.github/workflows/build.yaml

@@ -71,12 +71,12 @@ jobs:
           do
             eval sudo $cmd
           done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "18.04"))')
-          
+
       - name: Install macOS dependencies
         if: runner.os == 'macOS'
         run: |
           brew install netcdf
-          
+
       - name: Install dependencies
         run: |
           remotes::install_deps(dependencies = TRUE)

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: LakeEnsemblR
 Type: Package
 Title: Run Ensemble of Lake Models
-Version: 1.0.5
-Date: 2021-08-12
+Version: 1.1.0
+Date: 2022-03-16
 URL: https://github.com/aemon-j/LakeEnsemblR
 Author: Authors@R: c(person("Tadhg", "Moore", role = c("aut","cre"),
     email = "[email protected]"),
@@ -47,5 +47,5 @@ Suggests:
 Encoding: UTF-8
 LazyData: true
 LazyLoad: true
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 VignetteBuilder: knitr

NAMESPACE

@@ -12,7 +12,7 @@ export(check_master_config)
 export(export_config)
 export(export_dirs)
 export(export_extinction)
-export(export_inflow)
+export(export_flow)
 export(export_init_cond)
 export(export_location)
 export(export_meteo)
@@ -21,6 +21,7 @@ export(export_output_settings)
 export(export_time)
 export(format_inflow)
 export(format_met)
+export(format_outflow)
 export(get_config_value)
 export(get_json_value)
 export(get_mylakeconfig_value)
@@ -52,6 +53,7 @@ importFrom(configr,read.config)
 importFrom(configr,write.config)
 importFrom(glmtools,get_ice)
 importFrom(glmtools,get_nml_value)
+importFrom(glmtools,get_surface_height)
 importFrom(glmtools,get_var)
 importFrom(glmtools,read_nml)
 importFrom(glmtools,set_nml)

NEWS.md

@@ -1,3 +1,24 @@
+## version 1.1.0
+
+### Changes
+
+- Inflows and outflows are now separate inputs and can be different from each other
+- Multiple inflows and outflows can be simulated. 
+- Outflows can exit the lake at specified depths, or at the surface. 
+- Water level ("w_level") is now a potential output of LakeEnsemblR. 
+- "max_members" can be specified, which sets the number of members that the output-netcdf can have
+- LakeEnsemblR now works with the latest version of Simstrat (v3.0.1), which included changes in some parameter names
+- Model-specific template config files are removed from the LakeEnsemblR package and are instead retrieved from the model-specific packages
+
+Bug fixes:
+- get_yaml_multiple and input_yaml_multiple; works now if the first key is the highest level in the yaml file
+- cali_ensemble for FLake; depths are now sorted
+- Initial conditions Simstrat; Simstrat now always starts at the specified initial water lvl
+- plot_heatmap now works in lakes where the water level changes
+
+The setup of the LakeEnsemblR configuration file changed. More information can be found on: https://github.com/aemon-j/LakeEnsemblR/wiki/From-v1.0-to-v1.1
+
+
 ## version 1.0.5
 
 ### Changes

R/check_config.R

@@ -28,7 +28,7 @@ check_master_config <- function(config_file,
   if(!grepl("\\d{4}-\\d{2}-\\d{2}\\s\\d{2}:\\d{2}:\\d{2}", start)){
     stop("Start time format must be in yyyy-mm-dd hh:mm:ss format")
   }
-  # check if stop is in Iright format
+  # check if stop is in right format
   if(!grepl("\\d{4}-\\d{2}-\\d{2}\\s\\d{2}:\\d{2}:\\d{2}", stop)) {
     stop("Start time format must be in yyyy-mm-dd hh:mm:ss format")
   }
@@ -97,10 +97,43 @@ check_master_config <- function(config_file,
     stop(paste0('Unknown output time variable "', time_method, '" in control file ', config_file,
                 ". Allowed units: ", paste0(good_umethod, collapse = ", ")))
   }
+
+  # check if the same number of in-/outflow scaling factors are given
+  #   as the number of in-/outflows
+  configr_master_config <- configr::read.config(file.path(config_file))
+  use_inflows <- get_yaml_value(config_file, label = "inflows", key = "use")
+  use_outflows <- get_yaml_value(config_file, label = "outflows", key = "use")
+
+  if(!is.null(configr_master_config[["scaling_factors"]][["all"]]
+              [["inflow"]]) & use_inflows){
+    infl_scalings <- (configr_master_config[["scaling_factors"]][["all"]]
+      [["inflow"]])
+    num_inflows <- get_yaml_multiple(config_file, key1 = "inflows",
+                                     key2 = "number_inflows")
+    if(length(infl_scalings) != num_inflows){
+      warning(paste0("There is a different number of inflows than there are ",
+                     "inflow scaling factors in the control file ",
+                     config_file, ". Provide the same number of ",
+                     "scaling factors and inflows."))
+    }
+  }
+  if(!is.null(configr_master_config[["scaling_factors"]][["all"]]
+              [["outflow"]]) & use_outflows){
+    outfl_scalings <- (configr_master_config[["scaling_factors"]][["all"]]
+                       [["outflow"]])
+    num_outflows <- get_yaml_multiple(config_file, key1 = "outflows",
+                                     key2 = "number_outflows")
+    if(length(outfl_scalings) != num_outflows){
+      warning(paste0("There is a different number of outflows than there are ",
+                     "outflow scaling factors in the control file ",
+                     config_file, ". Provide the same number of ",
+                     "scaling factors and outflows."))
+    }
+  }
 
   # check if variables in output are OK
   variables <- gotmtools::get_yaml_value(config_file, "output", "variables")
-  good_vars <- c("temp", "ice_height", "dens", "salt")
+  good_vars <- c("temp", "ice_height", "dens", "salt", "w_level")
   if(any(!variables %in% good_vars)) {
     stop(paste0('Unknown output variable: "', variables[!variables %in% good_vars],
                 '" in control file ', config_file,
@@ -109,7 +142,6 @@ check_master_config <- function(config_file,
 
   # Check if lower limits for calibration are smaller than upper limits
   # load master config file
-  configr_master_config <- configr::read.config(file.path(config_file))
   if ("calibration" %in% names(configr_master_config)) {
     # meteo parameter
     cal_section <- configr_master_config[["calibration"]][["met"]]

R/create_netcdf_output.R

@@ -22,14 +22,14 @@
 create_netcdf_output <- function(output_lists, folder = ".", model, out_time,
                                  longitude = 0, latitude = 0, compression = 4,
                                  members = 25, out_file = "ensemble_output.nc"){
-  
+
   # Creat output directory
   if(!dir.exists(file.path(folder, "output"))) {
     message("Creating directory for output: ", file.path(folder, "output"))
     dir.create(file.path(folder, "output"), showWarnings = FALSE)
   }
-  
-  
+
+
   #Create ncdf
   message("Writing NetCDF file... [", Sys.time(), "]")
   ref_time <- as.POSIXct("1970-01-01 00:00:00", tz = "GMT") # Reference time for netCDF time
@@ -40,150 +40,150 @@ create_netcdf_output <- function(output_lists, folder = ".", model, out_time,
   # Define lon and lat dimensions
   lon1 <- ncdf4::ncdim_def("lon", "degrees_east", vals = as.double(xvals))
   lat2 <- ncdf4::ncdim_def("lat", "degrees_north", vals = as.double(yvals))
-  
+
   # Set dimensions
   # Time dimension
   timedim <- ncdf4::ncdim_def("time", units = "seconds since 1970-01-01 00:00:00",
                        vals = as.double(nsecs), calendar = "proleptic_gregorian")
-  
+
   # Define model dimensions
   mod_names <- c(model, "Obs")
   moddim <- ncdf4::ncdim_def("model", units = "-",
                              vals = as.double(seq_len(length(mod_names))))
-  
+
   # Define member dimensions
   memdim <- ncdf4::ncdim_def("member", units = "", unlim = TRUE,
-                             vals = as.double(1:members))
-  
+                             vals = as.double(seq_len(members)))
+
   fillvalue <- 1e20 # Fill value
   missvalue <- 1e20 # Missing value
-  
+
   nc_vars <- list() #Initialize empty list to fill netcdf variables
-  
+
   for(i in seq_len(length(output_lists))){
     # Get variable name (e.g. "temp" from "temp_list")
     splitted_name <- strsplit(names(output_lists[[i]])[1], "_")[[1]]
     variable_name <- paste(splitted_name[2:length(splitted_name)], collapse = "_")
-    
+
     # Get variable unit (from dictionary)
     variable_unit <- lake_var_dic$unit[lake_var_dic$short_name == variable_name]
-    
+
     # See if it"s 2D (e.g. ice height) or 3D (e.g. temperature)
     if(ncol(output_lists[[i]][[1]]) == 2){
       # Add 2D variable
-      
+
       # Define variable
       tmp_def <- ncdf4::ncvar_def(variable_name, variable_unit,
                                   list(lon1, lat2, memdim, moddim, timedim),
                                   fillvalue, variable_name,
                                   prec = "float", compression = compression, shuffle = FALSE)
       nc_vars[[length(nc_vars) + 1]] <- tmp_def # Add to list
-      
+
 
     }else if(ncol(output_lists[[i]][[1]]) > 2){
       # Add 3D variable
-      
+
       lengths <- lapply(output_lists[[i]], ncol) # Extract ncols in each output
       lon_list <- which.max(lengths) # Select largest depths
       deps <- get.offsets(output_lists[[i]][[lon_list]]) # Extract depths
-      
+
       # Depth dimension
       depthdim <- ncdf4::ncdim_def("z", units = "meters", vals = as.double((-deps)),
                             longname = "Depth from surface")
-      
+
       # Define variable
       tmp_def <- ncdf4::ncvar_def(variable_name, variable_unit,
                                   list(lon1, lat2, memdim, moddim, timedim, depthdim),
                                   fillvalue, variable_name,
                                   prec = "float", compression = compression, shuffle = FALSE)
       nc_vars[[length(nc_vars) + 1]] <- tmp_def # Add to list
-      
+
 
     }
-    
-    
+
+
   }
-  
+
   # Re-assign list names
   names(nc_vars)[(length(nc_vars) - length(output_lists) + 1):length(nc_vars)] <-
     names(output_lists)
-  
+
   # Create file name for output file
   fname <- file.path(folder, "output", out_file) # Ensemble output filename
-  
+
   # If file exists - delete it
   if(file.exists(fname)) {
     unlink(fname, recursive = TRUE)
   }
-  
+
   # Create and input data into the netCDF file
   ncout <- ncdf4::nc_create(fname, nc_vars, force_v4 = T)
   # Add coordinates attribute for use with get_vari()
   ncdf4::ncatt_put(ncout, "z", attname = "coordinates", attval = c("z"))
   ncdf4::ncatt_put(ncout, "model", attname = "Model",
                    attval = paste(seq_len(length(mod_names)), "-", mod_names, collapse = ", "))
   ncdf4::ncatt_put(ncout, "member", attname = "member", attval = c(members))
-  
+
   # Loop through and add each variable
   # Add tryCatch ensure that it closes netCDF file
   result <- tryCatch({
     # Again different for 2D or 3D variables
     for(i in seq_len(length(output_lists))){
-      
+
       if(ncol(output_lists[[i]][[1]]) == 2){
         # Add 2D variable
-        
+
         arr <- array(NA, dim = c((members), length(mod_names),
                                  length(nsecs)))
-        
-        
+
+
         for(j in seq_len(length(output_lists[[i]]))) {
           mat1 <- matrix(NA, nrow = nc_vars[[i]]$dim[[4]]$len, ncol = nc_vars[[i]]$dim[[5]]$len)
-          
-          
+
+
           mat <- as.matrix(output_lists[[i]][[j]][, -1])
-          
+
           splitted_name <- strsplit(names(output_lists[[i]])[j], "_")[[1]]
           m_name <- splitted_name[1]
           idx <- which(mod_names == m_name)
-          
+
           arr[1, idx, ] <- mat
         }
-        
+
         ncdf4::ncvar_put(ncout, nc_vars[[i]], arr)
         ncdf4::ncatt_put(ncout, nc_vars[[i]], attname = "coordinates",
                          attval = c("lon lat model member"))
         ncdf4::ncvar_change_missval(ncout, nc_vars[[i]], missval = fillvalue)
-        
+
       }else if(ncol(output_lists[[i]][[1]]) > 2){
         # Add 3D variable
-        
+
         arr <- array(NA, dim = c((members), length(mod_names),
                                  length(nsecs), length(deps)))
-        
-        
+
+
         for(j in seq_len(length(output_lists[[i]]))) {
-          
+
           mat1 <- matrix(NA, nrow = nc_vars[[i]]$dim[[5]]$len,
                          ncol = nc_vars[[i]]$dim[[6]]$len)
-          
+
           # vector of depths to input into the matrix
           deps_tmp <- get.offsets(output_lists[[i]][[j]])
-          
+
           mat <- as.matrix(output_lists[[i]][[j]][, -1])
-          
+
           for(k in seq_len(ncol(mat))) {
             col <- which(deps == deps_tmp[k])
             mat1[, col] <- mat[, k]
           }
-          
+
           splitted_name <- strsplit(names(output_lists[[i]])[j], "_")[[1]]
           m_name <- splitted_name[1]
           idx <- which(mod_names == m_name)
-          
+
           arr[1, idx, , ] <- mat1
         }
-        
+
         ncdf4::ncvar_put(nc = ncout, varid = nc_vars[[i]], vals = arr)
         ncdf4::ncatt_put(ncout, nc_vars[[i]], attname = "coordinates",
                          attval = c("lon lat z model member"))
@@ -199,7 +199,7 @@ create_netcdf_output <- function(output_lists, folder = ".", model, out_time,
   }, finally = {
     ncdf4::nc_close(ncout) # Close netCDF file
   })
-  
+
   message("Finished writing NetCDF file [", Sys.time(), "]")
-  
+
 }