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/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']], 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