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#' Approximate expected value of the decision given survey information
#'
#' Calculate the *expected value of the management decision
#' given survey information*. This metric describes the value of the management
#' decision that is expected when the decision maker conducts a surveys a
#' set of sites to inform the decision. To speed up the calculations,
#' an approximation method is used.
#'
#' @inheritParams evdsi
#'
#' @param n_approx_replicates `integer` number of replicates to use for
#' approximating the expected value calculations. Defaults to 100.
#'
#' @param n_approx_outcomes_per_replicate `integer` number of outcomes to
#' use per replicate for approximation calculations. Defaults to 10000.
#'
#' @param seed `integer` state of the random number generator for
#' simulating outcomes when conducting the value of information analyses.
#' Defaults to 500.
#'
#' @details This function uses approximation methods to estimate the
#' expected value calculations. The accuracy of these
#' calculations depend on the arguments to
#' `n_approx_replicates` and `n_approx_outcomes_per_replicate`, and
#' so you may need to increase these parameters for large problems.
#'
#' @return A `numeric` vector containing the expected values for each
#' replicate.
#'
#' @inherit evdci seealso
#'
#' @examples
#' # set seeds for reproducibility
#' set.seed(123)
#'
#' # load example site data
#' data(sim_sites)
#' print(sim_sites)
#'
#' # load example feature data
#' data(sim_features)
#' print(sim_features)
#'
#' # set total budget for managing sites for conservation
#' # (i.e. 50% of the cost of managing all sites)
#' total_budget <- sum(sim_sites$management_cost) * 0.5
#'
#' # create a survey scheme that samples the first two sites that
#' # are missing data
#' sim_sites$survey_site <- FALSE
#' sim_sites$survey_site[which(sim_sites$n1 < 0.5)[1:2]] <- TRUE
#'
#' # calculate expected value of management decision given the survey
#' # information using approximation method
#' approx_ev_survey <- approx_evdsi(
#' sim_sites, sim_features,
#' c("f1", "f2", "f3"), c("n1", "n2", "n3"), c("p1", "p2", "p3"),
#' "management_cost", "survey_site",
#' "survey_cost", "survey", "survey_sensitivity", "survey_specificity",
#' "model_sensitivity", "model_specificity",
#' "target", total_budget)
#'
#' # print mean value
#' print(mean(approx_ev_survey))
#' @export
approx_evdsi <- function(
site_data, feature_data,
site_detection_columns, site_n_surveys_columns, site_probability_columns,
site_management_cost_column,
site_survey_scheme_column,
site_survey_cost_column,
feature_survey_column,
feature_survey_sensitivity_column,
feature_survey_specificity_column,
feature_model_sensitivity_column,
feature_model_specificity_column,
feature_target_column,
total_budget,
site_management_locked_in_column = NULL,
site_management_locked_out_column = NULL,
prior_matrix = NULL,
n_approx_replicates = 100,
n_approx_outcomes_per_replicate = 10000,
seed = 500) {
# assert arguments are valid
assertthat::assert_that(
## site_data
inherits(site_data, "sf"), ncol(site_data) > 0,
nrow(site_data) > 0,
## feature_data
inherits(feature_data, "data.frame"), ncol(feature_data) > 0,
nrow(feature_data) > 0,
## site_detection_columns
is.character(site_detection_columns),
length(site_detection_columns) > 0,
assertthat::noNA(site_detection_columns),
all(assertthat::has_name(site_data, site_detection_columns)),
length(site_detection_columns) == nrow(feature_data),
## site_n_surveys_columns
is.character(site_n_surveys_columns),
length(site_n_surveys_columns) > 0,
assertthat::noNA(site_n_surveys_columns),
all(assertthat::has_name(site_data, site_n_surveys_columns)),
length(site_n_surveys_columns) == nrow(feature_data),
## site_probability_columns
is.character(site_probability_columns),
identical(nrow(feature_data), length(site_probability_columns)),
assertthat::noNA(site_probability_columns),
all(assertthat::has_name(site_data, site_probability_columns)),
## site_management_cost_column
assertthat::is.string(site_management_cost_column),
all(assertthat::has_name(site_data, site_management_cost_column)),
is.numeric(site_data[[site_management_cost_column]]),
assertthat::noNA(site_data[[site_management_cost_column]]),
## site_survey_scheme_column
assertthat::is.string(site_survey_scheme_column),
all(assertthat::has_name(site_data, site_survey_scheme_column)),
is.logical(site_data[[site_survey_scheme_column]]),
assertthat::noNA(site_data[[site_survey_scheme_column]]),
sum(site_data[[site_survey_scheme_column]]) >= 1,
## site_survey_cost_column
assertthat::is.string(site_survey_cost_column),
all(assertthat::has_name(site_data, site_survey_cost_column)),
is.numeric(site_data[[site_survey_cost_column]]),
assertthat::noNA(site_data[[site_survey_cost_column]]),
## feature_survey_column
assertthat::is.string(feature_survey_column),
all(assertthat::has_name(feature_data, feature_survey_column)),
is.logical(feature_data[[feature_survey_column]]),
assertthat::noNA(feature_data[[feature_survey_column]]),
sum(feature_data[[feature_survey_column]]) >= 1,
## feature_survey_sensitivity_column
assertthat::is.string(feature_survey_sensitivity_column),
all(assertthat::has_name(feature_data, feature_survey_sensitivity_column)),
is.numeric(feature_data[[feature_survey_sensitivity_column]]),
assertthat::noNA(
feature_data[[feature_survey_sensitivity_column]]),
all(feature_data[[feature_survey_sensitivity_column]] >= 0),
all(feature_data[[feature_survey_sensitivity_column]] <= 1),
## feature_survey_specificity_column
assertthat::is.string(feature_survey_specificity_column),
all(assertthat::has_name(feature_data, feature_survey_specificity_column)),
is.numeric(feature_data[[feature_survey_specificity_column]]),
assertthat::noNA(feature_data[[feature_survey_specificity_column]]),
all(feature_data[[feature_survey_specificity_column]] >= 0),
all(feature_data[[feature_survey_specificity_column]] <= 1),
## feature_model_sensitivity_column
assertthat::is.string(feature_model_sensitivity_column),
all(assertthat::has_name(feature_data, feature_model_sensitivity_column)),
is.numeric(feature_data[[feature_model_sensitivity_column]]),
assertthat::noNA(feature_data[[feature_model_sensitivity_column]]),
all(feature_data[[feature_model_sensitivity_column]] >= 0),
all(feature_data[[feature_model_sensitivity_column]] <= 1),
## feature_model_specificity_column
assertthat::is.string(feature_model_specificity_column),
all(assertthat::has_name(feature_data, feature_model_specificity_column)),
is.numeric(feature_data[[feature_model_specificity_column]]),
assertthat::noNA(feature_data[[feature_model_specificity_column]]),
all(feature_data[[feature_model_specificity_column]] >= 0),
all(feature_data[[feature_model_specificity_column]] <= 1),
## feature_target_column
assertthat::is.string(feature_target_column),
all(assertthat::has_name(feature_data, feature_target_column)),
is.numeric(feature_data[[feature_target_column]]),
assertthat::noNA(feature_data[[feature_target_column]]),
all(feature_data[[feature_target_column]] >= 0),
## total_budget
assertthat::is.number(total_budget), assertthat::noNA(total_budget),
isTRUE(total_budget > 0),
## prior_matrix
inherits(prior_matrix, c("matrix", "NULL")),
## n_approx_replicates
assertthat::is.count(n_approx_replicates),
assertthat::noNA(n_approx_replicates),
## n_approx_outcomes_per_replicate
assertthat::is.count(n_approx_outcomes_per_replicate),
assertthat::noNA(n_approx_outcomes_per_replicate),
## seed
assertthat::is.number(seed))
## site_management_locked_in_column
if (!is.null(site_management_locked_in_column)) {
assertthat::assert_that(
assertthat::is.string(site_management_locked_in_column),
all(assertthat::has_name(site_data, site_management_locked_in_column)),
is.logical(site_data[[site_management_locked_in_column]]),
assertthat::noNA(site_data[[site_management_locked_in_column]]))
assertthat::assert_that(
sum(site_data[[site_management_locked_in_column]] *
site_data[[site_management_cost_column]]) <=
total_budget,
msg = "cost of managing locked in sites exceeds total budget")
}
## site_management_locked_out_column
if (!is.null(site_management_locked_out_column)) {
assertthat::assert_that(
assertthat::is.string(site_management_locked_out_column),
all(assertthat::has_name(site_data, site_management_locked_out_column)),
is.logical(site_data[[site_management_locked_out_column]]),
assertthat::noNA(site_data[[site_management_locked_out_column]]))
if (all(site_data[[site_management_locked_out_column]]))
warning("all sites locked out")
}
## validate locked arguments if some locked in and some locked out
if (!is.null(site_management_locked_in_column) &&
!is.null(site_management_locked_out_column)) {
assertthat::assert_that(
all(site_data[[site_management_locked_in_column]] +
site_data[[site_management_locked_out_column]] <= 1),
msg = "at least one planning unit is locked in and locked out")
}
## validate targets
validate_target_data(feature_data, feature_target_column)
## validate survey data
validate_site_detection_data(site_data, site_detection_columns)
validate_site_n_surveys_data(site_data, site_n_surveys_columns)
## validate model probability values
validate_site_probability_data(site_data, site_probability_columns)
## verify targets
assertthat::assert_that(
all(feature_data[[feature_target_column]] <= nrow(site_data)))
if (!is.null(site_management_locked_out_column)) {
assertthat::assert_that(
all(feature_data[[feature_target_column]] <=
sum(!site_data[[site_management_locked_out_column]])))
}
# prepare data for analysis
## drop spatial information
if (inherits(site_data, "sf"))
site_data <- sf::st_drop_geometry(site_data)
## calculate prior matrix
if (is.null(prior_matrix)) {
pij <- prior_probability_matrix(
site_data, feature_data, site_detection_columns,
site_n_surveys_columns, site_probability_columns,
feature_survey_sensitivity_column, feature_survey_specificity_column,
feature_model_sensitivity_column, feature_model_specificity_column)
} else {
validate_prior_data(prior_matrix, nrow(site_data), nrow(feature_data))
pij <- prior_matrix
}
## prepare locked in data
if (!is.null(site_management_locked_in_column)) {
site_management_locked_in <- site_data[[site_management_locked_in_column]]
} else {
site_management_locked_in <- rep(FALSE, nrow(site_data))
}
## prepare locked out data
if (!is.null(site_management_locked_out_column)) {
site_management_locked_out <- site_data[[site_management_locked_out_column]]
} else {
site_management_locked_out <- rep(FALSE, nrow(site_data))
}
## validate that targets are feasible given budget and locked out units
sorted_costs <- sort(
site_data[[site_management_cost_column]][!site_management_locked_out])
sorted_costs <- sorted_costs[
seq_len(max(feature_data[[feature_target_column]]))]
assertthat::assert_that(
sum(sorted_costs) <= total_budget,
msg = paste("targets cannot be achieved given budget and locked out",
"planning units"))
# main calculation
withr::with_seed(seed, {
out <- rcpp_approx_expected_value_of_decision_given_survey_scheme(
pij = pij,
survey_features = feature_data[[feature_survey_column]],
survey_sensitivity = feature_data[[feature_survey_sensitivity_column]],
survey_specificity = feature_data[[feature_survey_specificity_column]],
pu_survey_solution = site_data[[site_survey_scheme_column]],
pu_survey_costs = site_data[[site_survey_cost_column]],
pu_purchase_costs = site_data[[site_management_cost_column]],
pu_purchase_locked_in = site_management_locked_in,
pu_purchase_locked_out = site_management_locked_out,
obj_fun_target = round(feature_data[[feature_target_column]]),
total_budget = total_budget,
n_approx_replicates = n_approx_replicates,
n_approx_outcomes_per_replicate = n_approx_outcomes_per_replicate,
seed = seed)
})
# return result
out
}
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