Debug utilities, small fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: growR
 Type: Package
-Version: 1.0.9.9000
+Version: 1.0.9.9001
 Date: 2023-09-27
 Authors@R: person(
     given = "Kevin",

NAMESPACE

@@ -20,6 +20,8 @@ export(add_lines)
 export(analyze_parameter_scan)
 export(atmospheric_CO2)
 export(box_smooth)
+export(browse)
+export(browse_end)
 export(build_functional_group)
 export(create_combinations)
 export(create_example_environment)

NEWS.md

@@ -1,4 +1,4 @@
-# growR 1.0.1
+# growR 1.1.0
 
 ## Added
 
@@ -16,6 +16,11 @@
 * S3 dispatch for plot method of `ModvegeSite` objects -> `plot(mvs)` is now 
   possible if `mvs` is a `ModvegeSite` instance.
 
+* `ParameterData` input checking: throws error on duplicate input parameter 
+  name.
+
+* Debug utility conveniences `browse` and `browse_end`.
+
 ## Changed
 
 * Input data CSV files are now actual CSV files, instead of 
@@ -33,6 +38,9 @@
 
 * autocut: `get_annual_gross_yield` was incorrectly hardcoded to return 1.
 
+* `ParameterData$set_parameters` now updates initial condition values, if 
+  applicable.
+
 ## Removed
 
 * Removed superfluous weather inputs.
@@ -41,6 +49,8 @@
 
 * Redundant argument *store_results* in `growR_run_loop`.
 
+* `SEA` symmetrization around 1 is not enforced anymore.
+
 # growR 1.0.0
 
 * Initial CRAN submission.

R/environment.R

@@ -78,8 +78,7 @@ ModvegeEnvironment = R6Class(
                           input_dir = NULL) {
       # Set instance variables
       self$site_name = site_name
-      self$run_name = run_name
-      self$run_name_in_filename = self$make_filename_for_run(run_name)
+      self$set_run_name(run_name)
       self$years = years
       # Revert to defaults for the not provided values.
       if (param_file == "-") {
@@ -107,6 +106,16 @@ ModvegeEnvironment = R6Class(
       self$load_inputs()
     },
 
+    #' @description
+    #' Set run name and update *run_name_in_filename*.
+    #'
+    #' @param run_name Str. New value of `self$run_name`.
+    #'
+    set_run_name = function(run_name) {
+      self$run_name = run_name
+      self$run_name_in_filename = self$make_filename_for_run(run_name)
+    },
+
     #' @description Load simulation inputs.
     #'
     #' Stores parameters, management and weather data from files specified in 

R/modvegesite.R

@@ -94,7 +94,7 @@ ModvegeSite = R6Class(
   #-Public-attributes-------------------------------------------------------------
 #' @field time_step Used time step in the model in days (untested).
       time_step = 1.,
-#' @field state_variable_namse Vector containing the names of the model's 
+#' @field state_variable_names Vector containing the names of the model's 
 #'   state variables.
       state_variable_names = NULL,
 #' @field n_state_variables Number of state variables.
@@ -538,9 +538,6 @@ ModvegeSite = R6Class(
       self[["OMDGV"]][1] = P$OMDGV0
       self[["OMDGR"]][1] = P$OMDGR0
 
-      # (minSEA + maxSEA)/2 = 1
-      self$parameters[["minSEA"]] = 2 - P[["maxSEA"]]
-
       # Management:
       # Initialize a pointer that indicates whether there has been a cut 
       # during reproductive growth. In this case, reproductive growth is

R/parameter_scan.R

@@ -187,8 +187,6 @@ analyze_parameter_scan = function(parameter_scan_results, datafile = "",
   }
   # Reduce to relevant years
   relevant_data = measured_data[measured_data$year %in% years, ]
-  # Construct a selector for the DOYs present in relevant data
-  mask = relevant_data$DOY + 365 * (relevant_data$year - relevant_data$year[1])
   # Calculate measured cBM_end
   measured_cBM_ends = c()
   for (year in years) {
@@ -206,21 +204,22 @@ analyze_parameter_scan = function(parameter_scan_results, datafile = "",
     cBM_end = c()
     for (i_year in 1:n_years) {
       mv = modvegesites[[i_year]]
-      cBM = c(cBM, mv$cBM)
+      mask = relevant_data$DOY[relevant_data$year == years[i_year]]
+      cBM = c(cBM, mv$cBM[mask])
       cBM_end = c(cBM_end, mv$cBM[length(mv$cBM)])
       smoothed = box_smooth(mv$dBM, box_width = smooth_interval)
-      dBM = c(dBM, smoothed)
+      dBM = c(dBM, smoothed[mask])
     }
     results[[combination]][["cBM"]] = list()
     results[[combination]][["dBM"]] = list()
     results[[combination]][["cBM_end"]] = list()
     # Employ performance metrics
     for (metric in metrics_to_use) {
       # cBM
-      m_cBM = metric_map[[metric]][["func"]](cBM[mask], relevant_data$cBM)
+      m_cBM = metric_map[[metric]][["func"]](cBM, relevant_data$cBM)
       results[[combination]][["cBM"]][[metric]] = m_cBM
       # dBM
-      m_dBM = metric_map[[metric]][["func"]](dBM[mask], relevant_data$dBM)
+      m_dBM = metric_map[[metric]][["func"]](dBM, relevant_data$dBM)
       results[[combination]][["dBM"]][[metric]] = m_dBM
       # cBM_end
       m_cBM_end = metric_map[[metric]][["func"]](cBM_end, measured_cBM_ends)

R/parameters.R

@@ -118,6 +118,9 @@ ModvegeParameters = R6Class(
 #' @field fg_parameter_names Names of vegetation parameters defined by the 
 #'   functional group composition.
       fg_parameter_names = NULL,
+#' @field initial_condition_names Names of initial conditions.
+      initial_condition_names = c(initial_condition_names, 
+                                  "WHC", "maxOMDGV", "maxOMDGR"),
 #' @field param_file Name of the parameter file from which initial parameter 
 #'   values were read.
       param_file = NULL,
@@ -179,17 +182,7 @@ ModvegeParameters = R6Class(
         # Update the functional group parameters in P.
         self$update_functional_group()
 
-        # Set initial conditions
-        for (name in initial_condition_names) {
-          old_name = name
-          new_name = paste0(old_name, "0")
-          self[[new_name]] = self[[old_name]]
-        }
-
-        # Set some more initial values 
-        self[["WR0"]] = self[["WHC"]]
-        self[["OMDGV0"]] = self[["maxOMDGV"]]
-        self[["OMDGR0"]] = self[["maxOMDGR"]]
+        private$update_initial_conditions()
       },
 
       #' @description Savely update the given parameters
@@ -205,11 +198,17 @@ ModvegeParameters = R6Class(
         for (i in 1:length(params)) {
           name = param_names[[i]]
           self[[name]] = params[[i]]
+          # :TODO: Also update initial values XXX0.
         }
         # Check if FG composition needs to be updated
         if (any(param_names %in% c("w_FGA", "w_FGB", "w_FGC", "w_FGD"))) {
           self$update_functional_group()
         }
+
+        # Check if initial conditions need updating
+        if (any(param_names %in% self$initial_condition_names)) { 
+          private$update_initial_conditions()
+        }
       },
 
       #' @description Update functional group parameters
@@ -230,7 +229,8 @@ ModvegeParameters = R6Class(
         }
       },
 
-      #' @description Parameter Sanity Check
+      #' @description 
+      #' Parameter Sanity Check
       #' Ensure that the supplied *params* are valid ModVege parameters and, 
       #' if requested, check that all required parameters are present.
       #' Issues a warning for any invalid parameters and throws an error if 
@@ -247,6 +247,11 @@ ModvegeParameters = R6Class(
       #'
       #' @md
       check_parameters = function(param_names, check_for_completeness = TRUE) {
+        # Check for duplicate param names
+        if (length(param_names) != length(unique(param_names))) {
+          logger("Non-unique parameter names in supplied parameters.",
+                 level = ERROR)
+        }
         param_file = self$param_file
         if (check_for_completeness) {
           # Give error if an argument is missing.
@@ -271,6 +276,22 @@ ModvegeParameters = R6Class(
         return(not_known)
       }
     )
+  ),
+
+  private = list(
+    ## Set initial conditions
+    update_initial_conditions = function() {
+      for (name in initial_condition_names) {
+        old_name = name
+        new_name = paste0(old_name, "0")
+        self[[new_name]] = self[[old_name]]
+      }
+
+      # Set some more initial values 
+      self[["WR0"]] = self[["WHC"]]
+      self[["OMDGV0"]] = self[["maxOMDGV"]]
+      self[["OMDGR0"]] = self[["maxOMDGR"]]
+    }
   )
 )
 

R/utilities.R

@@ -41,14 +41,14 @@ check_for_package = function(package, stop = TRUE) {
   return(TRUE)
 }
 
-#' Constants representing different debug levels to be used internally.
+## Constants representing different debug levels to be used internally.
 ERROR = 1
 WARNING = 2
 INFO = 3
 DEBUG = 4
 TRACE = 5
 
-#' Names of debug levels.
+## Names of debug levels.
 DEBUG_LEVELS = c("ERROR", "WARNING", "INFO", "DEBUG", "TRACE")
 
 #' Set verbosity of growR output.
@@ -373,3 +373,67 @@ ensure_table_columns = function(required, data, data_name = "the data table") {
   }
 }
 
+#' Create unique DOY + year identifier
+#'
+#' Return numbers of the form YYYYDDD where YYYY is the year and DDD the DOY.
+#'
+#' @param years int vector. 
+#' @param DOYs int vector of same length as *years*.
+#'
+#' @return int vector of same length as *years* containing numbers of the 
+#'   form YYYYDDD, where the first four digits represent a year and the last 
+#'   four represent a DOY.
+make_yearDOY = function(years, DOYs) {
+  return(1000 * years + DOYs)
+}
+
+#' Debugging utilities
+#'
+#' @description
+#' Debug specified function *func* by entering a [browser()] right at the 
+#' beginning ([browse()]) or end ([browse_end()]) of the function.
+#' 
+#' @details
+#' These are convenience shorthands for R's builtin debug tools, like 
+#' [debugonce()] and the [trace()]/[untrace()] combination.
+#'
+#' @param func An R function to be browsed.
+#' @param ... Arguments to the function *func* that is to be browsed.
+#'
+#' @return Returns the result of `func(...)`. Enters a [browser()].
+#'
+#' @examplesIf interactive()
+#' # Define a simple function for this example
+#' my_func = function(a) { for (i in 1:5) { a = a + i }; return(a) }
+#'
+#' # Enter a browser at the beginning of the function
+#' browse(my_func, 0)
+#'
+#' # Enter a browser at the end of the function. This allows us to inspect 
+#' # the function's local variables without having to go through the whole loop.
+#' browse_end(my_func, 0)
+#'
+#' @seealso [browser()], [debugonce()], [trace()]
+#'
+#' @md
+#' @export
+browse = function(func, ...) {
+  debugonce(func)
+  func(...)
+}
+
+#' Enter browser at end of function execution
+#'
+#' @describeIn browse
+#' Enter [browser()] at the end of the function call to `func(...)`. This 
+#' only works, if the function can execute without error until its end. 
+#' Otherwise, the error will be thrown.
+#' 
+#' @seealso [trace()]
+#' @md
+#' @export
+browse_end = function(func, ...) {
+  trace(func, exit = browser, where = environment())
+  func(...)
+}
+

_pkgdown.yml

@@ -56,9 +56,14 @@ reference:
 - contents:
   - PscanPlotter
   - Combinator
+- title: Debug Tools
+  desc: Utilities that may be of help if things go wrong.
+- contents:
+  - browse
+  - browse_end
+  - logger
 - title: Other
 - contents:
-  - DEBUG_LEVELS
   - ERROR
   - SEA
   - aCO2_inverse
@@ -82,7 +87,6 @@ reference:
   - get_relative_cut_contribution
   - get_site_name
   - growR_package_options
-  - logger
   - management_parameters
   - metric_map
   - parse_year_strings