initial revamp

.Rbuildignore

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+^doc$
+^Meta$
+^.*\.Rproj$
+^\.Rproj\.user$
+^\.travis\.yml$
+^gurobi\.log$
+^revdep$
+^docs$
+^appveyor\.yml$
+.gitkeep
+^Makefile$
+cran-comments.md
+CRAN-RELEASE
+_pkgdown.yml
+check.log
+test.log
+gp.log
+spell.log
+README.Rmd
+inst/extdata/dictionary.txt
+^_pkgdown\.yml$
+^CONTRIBUTING\.md$
+^CONTRIBUTING\.Rmd$
+src/amalgamation/dmlc-minimum0.o
+src/amalgamation/xgboost-all0.o
+src/rabit/src/c_api.o
+src/rabit/src/engine_empty.o

.gitignore

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+Meta
+doc
+# C++ compiled files
+*.o
+*.so
+*.dll
+
+# R profile files
+*.Rproj.user
+*.Rhistory
+.Rproj.user
+# log files
+gurobi.log
+test.log
+check.log
+spell.log
+gp.log
+# system files
+.directory
+# do not ignore the following files
+!.gitkeep
+!*/
+!inst/doc/*.html
+!inst/doc/*.Rmd
+!inst/doc/.gitkeep
+# devtools files
+doc/*
+Meta/*
+.build.timestamp

DESCRIPTION

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+Package: surveyvoi
+Type: Package
+Version: 0.0.1
+Title: Survey Value of Information
+Description: Develop candidate survey schemes for sampling biodiversity, and
+    and evaluate their return on investment using value of
+    information analyses.
+Authors@R: c(person(c('Jeffrey', 'O'), 'Hanson',
+               email='[email protected]', role = c('aut', 'cre')),
+             person(c('Joseph'), 'Bennett',
+               email='[email protected]', role = c('aut')))
+Imports:
+    utils,
+    methods,
+    stats,
+    Matrix,
+    parallel,
+    magrittr (>= 1.5),
+    assertthat (>= 0.2.0),
+    tibble (>= 2.0.0),
+    xgboost (>= 1.0.0.1),
+    rBayesianOptimization (>= 1.1.0),
+    Metrics (>= 0.1.4),
+    plyr (>= 1.8.4),
+    withr (>= 2.1.2),
+    tibble (>= 2.1.3),
+    scales (>= 1.0.0),
+    doParallel (>= 1.0.15),
+    RandomFields (>= 3.3.7),
+    vegan (>= 2.5-6),
+    RcppAlgos (>= 2.3.6)
+Suggests:
+    testthat (>= 2.0.0),
+    knitr (>= 1.20),
+    roxygen2 (>= 6.1.0),
+    rmarkdown (>= 1.10),
+    gurobi (>= 8.1.0),
+    tidyr (>= 1.0.0),
+    ggplot2 (>= 3.2.0),
+    gridExtra (>= 2.3),
+    viridis (>= 0.5.1)
+Depends:
+    R (>= 3.4.0),
+    sf (>= 0.8.0)
+LinkingTo:
+    Rcpp (>= 0.12.19),
+    RcppEigen (>= 0.3.3.7.0),
+    RcppProgress (>= 0.4.1),
+    RcppNumerical (>= 0.3-3)
+License: GPL-3
+LazyData: true
+SystemRequirements:
+    C++11,
+    gurobi (>= 8.1.0),
+    gmp (>= 4.2.3)
+URL: https://github.com/jeffreyhanson/surveyroi
+BugReports: https://github.com/jeffreyhanson/surveyroi/issues
+VignetteBuilder: knitr
+RoxygenNote: 6.1.1
+Collate:
+    'RcppExports.R'
+    'internal.R'
+    'env_div_survey_scheme.R'
+    'feasible_survey_schemes.R'
+    'tune_occupancy_models.R'
+    'fit_occupancy_models.R'
+    'geo_cov_survey_scheme.R'
+    'package.R'
+    'relative_site_richness_scores.R'
+    'relative_site_uncertainty_scores.R'
+    'simulate_feature_data.R'
+    'simulate_site_data.R'
+    'weighted_survey_scheme.R'

Makefile

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+all: initc data docs test check
+
+initc:
+	R --slave -e "Rcpp::compileAttributes()"
+	R --slave -e "tools::package_native_routine_registration_skeleton('.', 'src/init.c', character_only = FALSE)"
+
+docs: man readme vigns
+
+readme:
+	R --slave -e "rmarkdown::render('README.Rmd')"
+
+man:
+	R --slave -e "devtools::document()"
+
+vigns:
+	R --slave -e "devtools::build_vignettes(install = FALSE)"
+	cp -R doc inst/
+	touch inst/doc/.gitkeep
+
+purl_vigns:
+	R --slave -e "lapply(dir('vignettes', '^.*\\\\.Rmd$$'), function(x) knitr::purl(file.path('vignettes', x), gsub('.Rmd', '.R', x, fixed = TRUE)))"
+
+quicksite:
+	R --slave -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)"
+	cp -R doc inst/
+
+site:
+	R --slave -e "pkgdown::clean_site()"
+	R --slave -e "pkgdown::build_site(run_dont_run = TRUE, lazy = TRUE)"
+	cp -R doc inst/
+
+test:
+	R --slave -e "devtools::test()" > test.log 2>&1
+	rm -f tests/testthat/Rplots.pdf
+
+quickcheck:
+	echo "\n===== R CMD CHECK =====\n" > check.log 2>&1
+	R --slave -e "devtools::check(build_args = '--no-build-vignettes', args = '--no-build-vignettes', run_dont_test = TRUE, vignettes = FALSE)" >> check.log 2>&1se
+	cp -R doc inst/
+	touch inst/doc/.gitkeep
+
+check:
+	echo "\n===== R CMD CHECK =====\n" > check.log 2>&1
+	R --slave -e "devtools::check(build_args = '--no-build-vignettes', args = '--no-build-vignettes', run_dont_test = TRUE, vignettes = FALSE)" >> check.log 2>&1
+	cp -R doc inst/
+	touch inst/doc/.gitkeep
+
+install:
+	R --slave -e "devtools::install_local('../surveyroi', force = TRUE, upgrade = 'never')"
+
+.PHONY: initc docs site test check checkwb build install man readme vigns site quicksite

NAMESPACE

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+# Generated by roxygen2: do not edit by hand
+
+export(env_div_survey_scheme)
+export(feasible_survey_schemes)
+export(fit_occupancy_models)
+export(geo_cov_survey_scheme)
+export(relative_site_richness_scores)
+export(relative_site_uncertainty_scores)
+export(simulate_feature_data)
+export(simulate_site_data)
+export(tune_occupancy_models)
+export(weighted_survey_scheme)
+useDynLib(surveyvoi, .registration = TRUE)

NEWS.md

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+# surveyvoi 0.0.1
+
+- Initial commit.

R/RcppExports.R

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+# Generated by using Rcpp::compileAttributes() -> do not edit by hand
+# Generator token: 10BE3573-1514-4C36-9D1C-5A225CD40393
+
+rcpp_approximate_expected_value_of_prioritization <- function(solution, pij, alpha, gamma, states) {
+    .Call(`_surveyvoi_rcpp_approximate_expected_value_of_prioritization`, solution, pij, alpha, gamma, states)
+}
+
+rcpp_appproximate_expected_value_of_management_decision_given_current_information <- function(pij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap, n_approx_states) {
+    .Call(`_surveyvoi_rcpp_appproximate_expected_value_of_management_decision_given_current_information`, pij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap, n_approx_states)
+}
+
+rcpp_approximate_expected_value_of_management_decision_given_perfect_information <- function(pij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap, n_approx_states) {
+    .Call(`_surveyvoi_rcpp_approximate_expected_value_of_management_decision_given_perfect_information`, pij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap, n_approx_states)
+}
+
+rcpp_expected_value_of_management_action <- function(solution, pij, alpha, gamma) {
+    .Call(`_surveyvoi_rcpp_expected_value_of_management_action`, solution, pij, alpha, gamma)
+}
+
+rcpp_expected_value_of_management_decision_given_current_information <- function(pij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap) {
+    .Call(`_surveyvoi_rcpp_expected_value_of_management_decision_given_current_information`, pij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap)
+}
+
+rcpp_expected_value_of_management_decision_given_perfect_information <- function(pij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap) {
+    .Call(`_surveyvoi_rcpp_expected_value_of_management_decision_given_perfect_information`, pij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap)
+}
+
+rcpp_feasible_actions_ilp_matrix <- function(x) {
+    .Call(`_surveyvoi_rcpp_feasible_actions_ilp_matrix`, x)
+}
+
+rcpp_pmedian_constraint_matrix <- function(x, costs) {
+    .Call(`_surveyvoi_rcpp_pmedian_constraint_matrix`, x, costs)
+}
+
+rcpp_prioritization <- function(rij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap, file_path) {
+    .Call(`_surveyvoi_rcpp_prioritization`, rij, pu_costs, pu_locked_in, alpha, gamma, n_approx_obj_fun_points, budget, gap, file_path)
+}
+
+rcpp_total_probability_of_positive_result <- function(prior, sensitivity, specificity) {
+    .Call(`_surveyvoi_rcpp_total_probability_of_positive_result`, prior, sensitivity, specificity)
+}
+
+rcpp_total_probability_of_negative_result <- function(prior, sensitivity, specificity) {
+    .Call(`_surveyvoi_rcpp_total_probability_of_negative_result`, prior, sensitivity, specificity)
+}
+
+rcpp_probability_of_outcome <- function(oij, total_probability_of_survey_positive, total_probability_of_survey_negative, idx) {
+    .Call(`_surveyvoi_rcpp_probability_of_outcome`, oij, total_probability_of_survey_positive, total_probability_of_survey_negative, idx)
+}
+
+rcpp_probability_of_state <- function(sij, pij) {
+    .Call(`_surveyvoi_rcpp_probability_of_state`, sij, pij)
+}
+
+rcpp_nth_state_sparse <- function(n, matrix, idx) {
+    .Call(`_surveyvoi_rcpp_nth_state_sparse`, n, matrix, idx)
+}
+
+rcpp_nth_state <- function(n, matrix) {
+    .Call(`_surveyvoi_rcpp_nth_state`, n, matrix)
+}
+
+rcpp_n_states <- function(n) {
+    .Call(`_surveyvoi_rcpp_n_states`, n)
+}
+
+rcpp_which_state <- function(matrix, idx) {
+    .Call(`_surveyvoi_rcpp_which_state`, matrix, idx)
+}
+
+rcpp_fit_xgboost_models_and_assess_performance <- function(rij, wij, pu_env_data_raw, survey_features, xgb_parameters, n_xgb_nrounds, xgb_train_folds, xgb_test_folds) {
+    .Call(`_surveyvoi_rcpp_fit_xgboost_models_and_assess_performance`, rij, wij, pu_env_data_raw, survey_features, xgb_parameters, n_xgb_nrounds, xgb_train_folds, xgb_test_folds)
+}
+
+rcpp_xgboost <- function(y, train_x_raw, predict_x_raw, xgb_parameters, n_xgb_nrounds) {
+    .Call(`_surveyvoi_rcpp_xgboost`, y, train_x_raw, predict_x_raw, xgb_parameters, n_xgb_nrounds)
+}
+