From e6c9eae91967447800824f0979e8293e8df879e7 Mon Sep 17 00:00:00 2001
From: eloch216 <48919455+eloch216@users.noreply.github.com>
Date: Fri, 5 Sep 2025 09:01:59 -0500
Subject: [PATCH 1/2] Use `modifyList`

---
 R/combine_lists.R                   | 9 ---------
 R/objective_function_helpers.R      | 8 ++++----
 R/objective_function_input_checks.R | 8 ++++----
 3 files changed, 8 insertions(+), 17 deletions(-)
 delete mode 100644 R/combine_lists.R

diff --git a/R/combine_lists.R b/R/combine_lists.R
deleted file mode 100644
index ff8f5bd..0000000
--- a/R/combine_lists.R
+++ /dev/null
@@ -1,9 +0,0 @@
-# Helping function for overwriting elements of a base list with elements of a
-# second list; here we assume that both lists have names, and that the names of
-# new_list is a subset of the names of base_list
-combine_lists <- function(base_list, new_list) {
-    for (element_name in names(new_list)) {
-        base_list[[element_name]] <- new_list[[element_name]]
-    }
-    base_list
-}
diff --git a/R/objective_function_helpers.R b/R/objective_function_helpers.R
index 12d7312..45d6bfc 100644
--- a/R/objective_function_helpers.R
+++ b/R/objective_function_helpers.R
@@ -46,13 +46,13 @@ get_model_runner <- function(
     # Build the runner
     tryCatch({
             partial_func <- BioCro::partial_run_biocro(
-                combine_lists(
+                utils::modifyList(
                     base_model_definition[['initial_values']],
-                    ddp[['initial_values']]
+                    c(list(), ddp[['initial_values']])
                 ),
-                combine_lists(
+                utils::modifyList(
                     base_model_definition[['parameters']],
-                    ddp[['parameters']]
+                    c(list(), ddp[['parameters']])
                 ),
                 ddp[['drivers']],
                 base_model_definition[['direct_modules']],
diff --git a/R/objective_function_input_checks.R b/R/objective_function_input_checks.R
index 1736c27..4d9de7b 100644
--- a/R/objective_function_input_checks.R
+++ b/R/objective_function_input_checks.R
@@ -235,13 +235,13 @@ check_data_driver_pairs <- function(base_model_definition, data_driver_pairs, ve
     # base model definition
     valid_definitions <- sapply(data_driver_pairs, function(ddp) {
         BioCro::validate_dynamical_system_inputs(
-            combine_lists(
+            utils::modifyList(
                 base_model_definition[['initial_values']],
-                ddp[['initial_values']]
+                c(list(), ddp[['initial_values']])
             ),
-            combine_lists(
+            utils::modifyList(
                 base_model_definition[['parameters']],
-                ddp[['parameters']]
+                c(list(), ddp[['parameters']])
             ),
             ddp[['drivers']],
             base_model_definition[['direct_modules']],

From eedc56524da412adb74ab87ad06a93d737d3f904 Mon Sep 17 00:00:00 2001
From: eloch216 <48919455+eloch216@users.noreply.github.com>
Date: Fri, 5 Sep 2025 09:03:38 -0500
Subject: [PATCH 2/2] Update links

---
 DESCRIPTION | 2 +-
 README.md   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 6ea6709..4564a0e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -23,5 +23,5 @@ 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
diff --git a/README.md b/README.md
index f6eeee0..42a223e 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ from within R by typing `install.packages('remotes')`.
 ### Usage
 
 The best way to learn about using `BioCroValidation` is to visit the
-[BioCroValidation website](https://biocro.github.io/BioCroValidation/index.html)
+[BioCroValidation website](https://biocro.org/BioCroValidation/index.html)
 and click the "Get Started" link in the top menu bar. The website includes
 documentation for all the functions and data sets included in the package, as
 well as articles that describe its general features and several important use