diff --git a/R/inputs.R b/R/inputs.R index c7c4693..1a35cb5 100644 --- a/R/inputs.R +++ b/R/inputs.R @@ -1,6 +1,6 @@ cowflu_inputs <- function(alpha, beta, gamma, sigma, asc_rate, dispersion, inputs) { c(inputs, - list(alpha = alpha, beta = beta, gamma = gamma, asc_rate = asc_rate, dispersion = dispersion, sigma = sigma)) + list(alpha = alpha, beta = beta, gamma = gamma, asc_rate = asc_rate, sigma = sigma, dispersion = dispersion)) } @@ -55,6 +55,10 @@ cowflu_fixed_inputs <- function(p_region_export, p_cow_export, cli::cli_abort( "Expected 'condition_on_export' to be TRUE or FALSE") } + if (! likelihood_choice %in% c("incidence", "survival")) { + cli::cli_abort( + "Expected 'likelihood choice' to be 'incidence' or 'survival'") + } ## This line will transpose the matrix, and change the original rows (now columns) to a cumulative sum. movement_matrix_cumulative <- apply(movement_matrix, 1, cumsum) @@ -70,5 +74,6 @@ cowflu_fixed_inputs <- function(p_region_export, p_cow_export, index = rep(seq_along(n_herds_per_region), n_herds_per_region), time_test = time_test, n_test = n_test, - condition_on_export = condition_on_export) + condition_on_export = condition_on_export, + likelihood_choice = likelihood_choice) }