Release v0.3.0

.github/workflows/R-CMD-check.yaml

@@ -25,7 +25,7 @@ jobs:
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
-          - {os: ubuntu-latest,   r: '3.6.0'}
+          - {os: ubuntu-latest,   r: '4.1.0'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: BioCroValidation
-Version: 0.2.0
+Version: 0.3.0
 Title: Tools for Validating BioCro Models
 Description: A collection of tools for validating BioCro crop growth models.
 Authors@R: c(
@@ -9,7 +9,7 @@ Authors@R: c(
     person("BioCroValidation authors", role = "cph")
     )
 Depends:
-    R (>= 3.6.0)
+    R (>= 4.1.0)
 Imports:
     BioCro (>= 3.2.0)
 Suggests:
@@ -18,10 +18,10 @@ Suggests:
     lattice,
     knitr,
     rmarkdown,
-    testthat (>= 3.0.0)
+    testthat (>= 3.2.0)
 VignetteBuilder: knitr
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-URL: https://github.com/BioCro/BioCroValidation, https://biocro.github.io/BioCroValidation/
+URL: https://github.com/BioCro/BioCroValidation, https://biocro.org/BioCroValidation/
 Config/testthat/edition: 3

NEWS.md

@@ -33,6 +33,29 @@ In the case of a hotfix, a short section headed by the new release number should
 be directly added to this file to describe the related changes.
 -->
 
+# Changes in BioCroValidation Version 0.3.0 (2026-03-11)
+
+- Fixed typos in the help page for `objective_function`, and in the `add_norm`
+  function (defined in `R/objective_function_helpers.R`)
+
+- Allowed user-supplied regularization functions
+
+- Allowed driver-specific initial values and parameters
+
+- Errors that occur while running simulations are now caught so they do not
+  prevent an optimization from finishing
+
+- More options for `debug_mode` are now available; the default setting
+  (`minimal`) only prints info to the terminal when an issue with a simulation
+  occurs
+
+- Improved formatting of output from `write_module`, so that initial value and
+  parameter lists are alphabetized, equals signs are aligned, and module names
+  are preserved
+
+- Fixed a bug where calling `objective_function` with
+  `dependent_arg_function = NULL` and `verbose_mode = TRUE` caused an error
+
 # Changes in BioCroValidation Version 0.2.0 (2025-05-23)
 
 - Added 2002 and 2005 SoyFACE biomass and standard deviation data.

R/objective_function.R

@@ -19,7 +19,11 @@ objective_function <- function(
 )
 {
     # Check the data-driver pairs
-    check_data_driver_pairs(base_model_definition, data_driver_pairs)
+    check_data_driver_pairs(
+        base_model_definition,
+        data_driver_pairs,
+        verbose_startup
+    )
 
     # Check the arguments to be varied
     check_args_to_vary(
@@ -76,14 +80,16 @@ objective_function <- function(
         long_form_data,
         normalization_method,
         normalization_param,
-        length(data_driver_pairs)
+        length(data_driver_pairs),
+        verbose_startup
     )
 
     # Add variance-based weights
     long_form_data <- add_w_var(
         long_form_data,
         stdev_weight_method,
-        stdev_weight_param
+        stdev_weight_param,
+        verbose_startup
     )
 
     # Print the long form data, if desired. Do this before checking the data,
@@ -109,11 +115,15 @@ objective_function <- function(
     # Get the data-driver pair weights
     ddp_weights <- get_ddp_weights(data_driver_pairs)
 
-    # Print the data-driver pair weights, if desired
-    if (verbose_startup) {
-        cat('\nThe user-supplied data-driver pair weights:\n\n')
-        utils::str(ddp_weights)
-    }
+    # Print additional startup information, if desired
+    print_misc_verbose_startup(
+        ddp_weights,
+        regularization_method,
+        dependent_arg_function,
+        post_process_function,
+        extra_penalty_function,
+        verbose_startup
+    )
 
     # Create the objective function
     obj_fun <- get_obj_fun(