From 3418629544b422c6e64684c95d5ab6613f18aa00 Mon Sep 17 00:00:00 2001 From: Jeffrey Hanson Date: Mon, 7 Mar 2022 18:55:27 +1300 Subject: [PATCH] fix xgboost thread usage --- DESCRIPTION | 2 +- NEWS.md | 7 + R/approx_near_optimal_survey_scheme.R | 1 + R/approx_optimal_survey_scheme.R | 33 ++--- R/fit_hglm_occupancy_models.R | 1 + R/fit_xgb_occupancy_models.R | 114 ++++++++++++---- R/optimal_survey_scheme.R | 1 + README.md | 2 +- docs/404.html | 2 +- docs/articles/index.html | 2 +- docs/articles/surveyvoi.html | 4 +- docs/authors.html | 6 +- docs/index.html | 4 +- docs/news/index.html | 7 +- docs/pkgdown.yml | 2 +- docs/reference/approx_evdsi.html | 2 +- .../approx_near_optimal_survey_scheme.html | 2 +- .../approx_optimal_survey_scheme.html | 2 +- docs/reference/env_div_survey_scheme.html | 2 +- docs/reference/evdci.html | 2 +- docs/reference/evdsi.html | 2 +- docs/reference/feasible_survey_schemes.html | 2 +- docs/reference/fit_hglm_occupancy_models.html | 2 +- docs/reference/fit_xgb_occupancy_models.html | 125 +----------------- docs/reference/geo_cov_survey_scheme.html | 2 +- docs/reference/index.html | 2 +- docs/reference/n_states.html | 2 +- docs/reference/optimal_survey_scheme.html | 2 +- docs/reference/prior_probability_matrix.html | 2 +- .../relative_site_richness_scores.html | 2 +- .../relative_site_uncertainty_scores.html | 2 +- docs/reference/sim_data.html | 2 +- docs/reference/simulate_feature_data.html | 2 +- docs/reference/simulate_site_data.html | 2 +- .../starting run 2022-03-07 18:41:55 | 1 + .../starting run 2022-03-07 18:41:57 | 1 + .../starting run 2022-03-07 18:41:59 | 1 + .../starting run 2022-03-07 18:42:00 | 1 + .../starting run 2022-03-07 18:42:02 | 1 + .../starting run 2022-03-07 18:42:04 | 1 + .../starting run 2022-03-07 18:42:05 | 1 + .../starting run 2022-03-07 18:42:07 | 1 + .../starting run 2022-03-07 18:42:08 | 1 + .../starting run 2022-03-07 18:42:10 | 1 + .../starting run 2022-03-07 18:42:11 | 1 + .../starting run 2022-03-07 18:42:12 | 1 + .../starting run 2022-03-07 18:42:13 | 1 + .../starting run 2022-03-07 18:42:14 | 1 + .../starting run 2022-03-07 18:42:15 | 1 + docs/reference/surveyvoi.html | 2 +- docs/reference/weighted_survey_scheme.html | 2 +- inst/doc/surveyvoi.html | 4 +- .../testthat/test_fit_xgb_occupancy_models.R | 7 +- 53 files changed, 180 insertions(+), 199 deletions(-) create mode 100644 docs/reference/starting run 2022-03-07 18:41:55 create mode 100644 docs/reference/starting run 2022-03-07 18:41:57 create mode 100644 docs/reference/starting run 2022-03-07 18:41:59 create mode 100644 docs/reference/starting run 2022-03-07 18:42:00 create mode 100644 docs/reference/starting run 2022-03-07 18:42:02 create mode 100644 docs/reference/starting run 2022-03-07 18:42:04 create mode 100644 docs/reference/starting run 2022-03-07 18:42:05 create mode 100644 docs/reference/starting run 2022-03-07 18:42:07 create mode 100644 docs/reference/starting run 2022-03-07 18:42:08 create mode 100644 docs/reference/starting run 2022-03-07 18:42:10 create mode 100644 docs/reference/starting run 2022-03-07 18:42:11 create mode 100644 docs/reference/starting run 2022-03-07 18:42:12 create mode 100644 docs/reference/starting run 2022-03-07 18:42:13 create mode 100644 docs/reference/starting run 2022-03-07 18:42:14 create mode 100644 docs/reference/starting run 2022-03-07 18:42:15 diff --git a/DESCRIPTION b/DESCRIPTION index 42239a0..057547f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: surveyvoi Type: Package -Version: 1.0.3.2 +Version: 1.0.3.3 Title: Survey Value of Information Description: Decision support tool for prioritizing sites for ecological surveys based on their potential to improve plans for conserving diff --git a/NEWS.md b/NEWS.md index 12dd8b5..a22c08a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,10 @@ +# surveyvoi 1.0.3.3 + +- Fix issue with `fit_xgb_occupancy_models()` using more than specified number + of threads for parallel processing. +- Ensure that PSOCK and FORK clusters used for parallel processing are + terminated correctly, even when processing is interrupted. + # surveyvoi 1.0.3.2 - Fix compatibility issues with updates to the xgboost package (version 1.5.0). diff --git a/R/approx_near_optimal_survey_scheme.R b/R/approx_near_optimal_survey_scheme.R index 30d87ec..2f8d37d 100644 --- a/R/approx_near_optimal_survey_scheme.R +++ b/R/approx_near_optimal_survey_scheme.R @@ -412,6 +412,7 @@ approx_near_optimal_survey_scheme <- function( "n_approx_replicates", "n_approx_outcomes_per_replicate", "rcpp_approx_expected_value_of_decision_given_survey_scheme")) + on.exit(try(stop_cluster(cl), silent = TRUE), add = TRUE) } ## run calculations curr_sites_approx_evsdi <- plyr::laply( diff --git a/R/approx_optimal_survey_scheme.R b/R/approx_optimal_survey_scheme.R index 0c7305d..01d60a3 100644 --- a/R/approx_optimal_survey_scheme.R +++ b/R/approx_optimal_survey_scheme.R @@ -339,22 +339,23 @@ approx_optimal_survey_scheme <- function( # calculate expected value of decision given schemes that survey sites ## initialize cluster if (n_threads > 1) { - cl <- start_cluster(n_threads, - c("pij", "all_feasible_schemes", "new_info_idx", - "site_data", "feature_data", - "feature_survey_column", - "feature_survey_sensitivity_column", - "feature_survey_specificity_column", - "site_survey_cost_column", - "site_management_cost_column", - "site_management_locked_in", - "site_management_locked_out", - "feature_target_column", - "n_approx_replicates", - "n_approx_outcomes_per_replicate", - "total_budget", - "seed", - "rcpp_approx_expected_value_of_decision_given_survey_scheme")) + cl <- start_cluster(n_threads, + c("pij", "all_feasible_schemes", "new_info_idx", + "site_data", "feature_data", + "feature_survey_column", + "feature_survey_sensitivity_column", + "feature_survey_specificity_column", + "site_survey_cost_column", + "site_management_cost_column", + "site_management_locked_in", + "site_management_locked_out", + "feature_target_column", + "n_approx_replicates", + "n_approx_outcomes_per_replicate", + "total_budget", + "seed", + "rcpp_approx_expected_value_of_decision_given_survey_scheme")) + on.exit(try(stop_cluster(cl), silent = TRUE), add = TRUE) } ## run calculations evd_new_info <- plyr::laply( diff --git a/R/fit_hglm_occupancy_models.R b/R/fit_hglm_occupancy_models.R index 3485974..b74af0b 100644 --- a/R/fit_hglm_occupancy_models.R +++ b/R/fit_hglm_occupancy_models.R @@ -333,6 +333,7 @@ fit_hglm_occupancy_models <- function( c("model_cmbs", "d", "feature_data", "seed", "jags_n_samples", "jags_n_burnin", "jags_n_thin", "jags_n_adapt", "fit_hglm_model")) + on.exit(try(stop_cluster(cl), silent = TRUE), add = TRUE) } ## main processing m_raw <- plyr::llply( diff --git a/R/fit_xgb_occupancy_models.R b/R/fit_xgb_occupancy_models.R index 9e1d897..e49e7dd 100644 --- a/R/fit_xgb_occupancy_models.R +++ b/R/fit_xgb_occupancy_models.R @@ -218,9 +218,11 @@ NULL #' @export fit_xgb_occupancy_models <- function( site_data, feature_data, - site_detection_columns, site_n_surveys_columns, + site_detection_columns, + site_n_surveys_columns, site_env_vars_columns, - feature_survey_sensitivity_column, feature_survey_specificity_column, + feature_survey_sensitivity_column, + feature_survey_specificity_column, xgb_tuning_parameters, xgb_early_stopping_rounds = rep(20, length(site_detection_columns)), xgb_n_rounds = rep(100, length(site_detection_columns)), @@ -372,13 +374,18 @@ fit_xgb_occupancy_models <- function( feature_data[[feature_survey_specificity_column]][i], parameters = xgb_tuning_parameters, early_stopping_rounds = xgb_early_stopping_rounds[i], - n_rounds = xgb_n_rounds[i], n_folds = n_folds[i], - n_threads = n_threads, verbose = verbose, seed = seed) + n_rounds = xgb_n_rounds[i], + n_folds = n_folds[i], + n_threads = n_threads, + verbose = verbose, + seed = seed) }) # assess models - perf <- plyr::ldply(seq_len(nrow(feature_data)), function(i) { - out <- plyr::ldply(seq_len(n_folds[i]), function(k) { + perf <- plyr::ldply( + seq_len(nrow(feature_data)), .parallel = FALSE, function(i) { + out <- plyr::ldply( + seq_len(n_folds[i]), .parallel = FALSE, function(k) { ## extract fold training and test data m_k <- m[[i]]$models[[k]] nround_k <- m[[i]]$models[[k]]$best_iteration @@ -392,9 +399,15 @@ fit_xgb_occupancy_models <- function( survey_spec <- feature_data[[feature_survey_specificity_column]][[i]] ## make predictions p_train_k <- c(withr::with_package("xgboost", - stats::predict(m_k, x_train_k, iterationrange = c(1, nround_k + 1)))) + stats::predict( + m_k, xgboost::xgb.DMatrix(x_train_k, nthread = 1), + iterationrange = c(1, nround_k + 1), + nthread = 1))) p_test_k <- c(withr::with_package("xgboost", - stats::predict(m_k, x_test_k, iterationrange = c(1, nround_k + 1)))) + stats::predict( + m_k, xgboost::xgb.DMatrix(x_test_k, nthread = 1), + iterationrange = c(1, nround_k + 1), + nthread = 1))) ## validate predictions assertthat::assert_that(all(p_train_k >= 0), all(p_train_k <= 1), msg = "xgboost predictions are not between zero and one") @@ -434,15 +447,18 @@ fit_xgb_occupancy_models <- function( # make model predictions pred <- vapply(seq_len(nrow(feature_data)), FUN.VALUE = numeric(nrow(site_env_data)), function(i) { - nr <- m[[i]]$parameters$nround rowMeans( vapply(m[[i]]$models, FUN.VALUE = numeric(nrow(site_env_data)), function(x) { ## generate predictions out <- c(withr::with_package("xgboost", stats::predict( - x, site_env_data, iterationrange = c(1, x$best_iteration + 1)))) + x, xgboost::xgb.DMatrix(site_env_data, nthread = 1), + iterationrange = c(1, x$best_iteration + 1), + nthread = 1 + ))) ## validate predictions - assertthat::assert_that(all(out >= 0), all(out <= 1), + assertthat::assert_that( + all(out >= 0), all(out <= 1), msg = "xgboost predictions are not between zero and one") ## return result out @@ -486,7 +502,6 @@ tune_model <- function(data, folds, survey_sensitivity, survey_specificity, x }) full_parameters <- data.frame(full_parameters, stringsAsFactors = FALSE) - ## add objective if missing if (is.null(full_parameters$objective)) { full_parameters$objective <- "binary:logistic" @@ -503,15 +518,54 @@ tune_model <- function(data, folds, survey_sensitivity, survey_specificity, }) assertthat::assert_that(all(is.finite(spw))) + # precompute xgboost matrices + # N.B. this is because xgboost has a bug when creating DMatrix objects + # from R matrix objects, wherein it will use all available threads + # on the system, if done within a child R process + dtrain_paths <- vapply( + seq_len(n_folds), FUN.VALUE = character(1), function(k) { + f <- tempfile(fileext = ".dmat") + xgboost::xgb.DMatrix.save( + xgboost::xgb.DMatrix( + data[[k]]$fit$x, + label = data[[k]]$fit$y, + weight = data[[k]]$fit$w, + nthread = 1 + ), + f + ) + f + }) + dtest_paths <- vapply( + seq_len(n_folds), FUN.VALUE = character(1), function(k) { + f <- tempfile(fileext = ".dmat") + xgboost::xgb.DMatrix.save( + xgboost::xgb.DMatrix( + data[[k]]$test$x, + label = data[[k]]$test$y, + weight = data[[k]]$test$w, + nthread = 1 + ), + f + ) + f + }) + assertthat::assert_that( + all(file.exists(dtrain_paths)), + all(file.exists(dtest_paths)), + msg = "could not save data to temporary directory to faciliate analysis") + # find best tuning parameters using k-fold cross validation ## fit models using all parameters combinations is_parallel <- (n_threads > 1) && (nrow(full_parameters) > 1) if (is_parallel) { cl <- start_cluster( n_threads, - c("full_parameters", "data", "survey_sensitivity", "survey_specificity", + c("full_parameters", "data", "dtest_paths", "dtest_paths", + "survey_sensitivity", "survey_specificity", "spw", "n_rounds", "early_stopping_rounds", "seed", "rcpp_model_performance", "make_feval_tss")) + on.exit(try(stop_cluster(cl), silent = TRUE), add = TRUE) } cv <- plyr::ldply( seq_len(nrow(full_parameters)), .parallel = is_parallel, @@ -522,17 +576,20 @@ tune_model <- function(data, folds, survey_sensitivity, survey_specificity, cv <- lapply(seq_len(n_folds), function(k) { ### prepare data for xgboost (note we use the fit data not the train data) dtrain <- xgboost::xgb.DMatrix( - data[[k]]$fit$x, label = data[[k]]$fit$y, - weight = data[[k]]$fit$w) + dtrain_paths[k], nthread = 1, silent = TRUE) dtest <- xgboost::xgb.DMatrix( - data[[k]]$test$x, label = data[[k]]$test$y, - weight = data[[k]]$test$w) + dtest_paths[k], nthread = 1, silent = TRUE) ### prepare evaluation function curr_feval_tss <- make_feval_tss(survey_sensitivity, survey_specificity) ### prepare arguments for xgboost call - args <- list(data = dtrain, verbose = FALSE, scale_pos_weight = spw[k], - watchlist = list(test = dtest), eval_metric = curr_feval_tss, - maximize = TRUE, nrounds = n_rounds, nthread = 1, + args <- list(data = dtrain, + verbose = FALSE, + scale_pos_weight = spw[k], + watchlist = list(test = dtest), + eval_metric = curr_feval_tss, + maximize = TRUE, + nrounds = n_rounds, + nthread = 1, early_stopping_rounds = early_stopping_rounds) args <- append(args, p) ### fit model @@ -541,10 +598,11 @@ tune_model <- function(data, folds, survey_sensitivity, survey_specificity, }) ### generate predictions yhat_test <- c(withr::with_package("xgboost", - stats::predict( - model, data[[k]]$test$x, - iterationrange = c(1, model$best_iteration + 1) - ))) + stats::predict( + model, dtest, + iterationrange = c(1, model$best_iteration + 1), + nthread = 1 + ))) ### validate predictions assertthat::assert_that(all(yhat_test >= 0), all(yhat_test <= 1), msg = "xgboost predictions are not between zero and one") @@ -565,9 +623,15 @@ tune_model <- function(data, folds, survey_sensitivity, survey_specificity, if (is_parallel) { cl <- stop_cluster(cl) } - ## determine best parameters for i'th species + + # cleanup + unlink(dtest_paths, force = TRUE) + unlink(dtrain_paths, force = TRUE) + + # determine best parameters for i'th species cv <- tibble::as_tibble(cv) j <- which.max(cv$eval) + # return best parameters and models best_params <- as.list(full_parameters[j, , drop = FALSE]) best_params$scale_pos_weight <- list(spw) diff --git a/R/optimal_survey_scheme.R b/R/optimal_survey_scheme.R index c8a590b..a915341 100644 --- a/R/optimal_survey_scheme.R +++ b/R/optimal_survey_scheme.R @@ -332,6 +332,7 @@ optimal_survey_scheme <- function( "feature_target_column", "total_budget", "rcpp_expected_value_of_decision_given_survey_scheme")) + on.exit(try(stop_cluster(cl), silent = TRUE), add = TRUE) } ## run calculations evd_new_info <- plyr::laply( diff --git a/README.md b/README.md index 9376bde..9d4b4ad 100644 --- a/README.md +++ b/README.md @@ -80,7 +80,7 @@ Please cite the *surveyvoi R* package when using it in publications. To cite the developmental version, please use: > Hanson JO, Chadès I, Hudgins EJ, Bennett J (2021). surveyvoi: Survey -> Value of Information. R package version 1.0.3.2. Available at +> Value of Information. R package version 1.0.3.3. Available at > . ## Usage diff --git a/docs/404.html b/docs/404.html index 1033f45..1e6b8cd 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/articles/index.html b/docs/articles/index.html index 2218265..c0bc320 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/articles/surveyvoi.html b/docs/articles/surveyvoi.html index 6efd81d..199f95e 100644 --- a/docs/articles/surveyvoi.html +++ b/docs/articles/surveyvoi.html @@ -33,7 +33,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 @@ -72,7 +72,7 @@

surveyvoi: Survey Value of Information

Jeffrey O. Hanson

-

2022-03-06

+

2022-03-07

Source: vignettes/surveyvoi.Rmd diff --git a/docs/authors.html b/docs/authors.html index b4e33ab..f30b804 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 @@ -78,13 +78,13 @@

Citation

Hanson JO, Chadès I, Hudgins EJ, Bennett JR (2022). surveyvoi: Survey Value of Information. -R package version 1.0.3.2, https://github.com/jeffreyhanson/surveyvoi. +R package version 1.0.3.3, https://github.com/jeffreyhanson/surveyvoi. 

@Manual{,
   title = {surveyvoi: Survey Value of Information},
   author = {Jeffrey O Hanson and Iadine Chadès and Emma J Hudgins and Joseph R Bennett},
   year = {2022},
-  note = {R package version 1.0.3.2},
+  note = {R package version 1.0.3.3},
   url = {https://github.com/jeffreyhanson/surveyvoi},
 }
diff --git a/docs/index.html b/docs/index.html index bf4287f..3a66185 100644 --- a/docs/index.html +++ b/docs/index.html @@ -46,7 +46,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 @@ -126,7 +126,7 @@

Citation

Please cite the surveyvoi R package when using it in publications. To cite the developmental version, please use:

-

Hanson JO, Chadès I, Hudgins EJ, Bennett J (2021). surveyvoi: Survey Value of Information. R package version 1.0.3.2. Available at https://github.com/jeffreyhanson/surveyvoi.

+

Hanson JO, Chadès I, Hudgins EJ, Bennett J (2021). surveyvoi: Survey Value of Information. R package version 1.0.3.3. Available at https://github.com/jeffreyhanson/surveyvoi.

diff --git a/docs/news/index.html b/docs/news/index.html index 284ac7a..1f35b16 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3
@@ -50,6 +50,11 @@

Changelog

Source: NEWS.md +
+

surveyvoi 1.0.3.3

+
  • Fix issue with fit_xgb_occupancy_models() using more than specified number of threads for parallel processing.
    • +
  • Ensure that PSOCK and FORK clusters used for parallel processing are terminated correctly, even when processing is interrupted.
    • +

surveyvoi 1.0.3.2

  • Fix compatibility issues with updates to the xgboost package (version 1.5.0).
    • diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 3460494..5dad00f 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.2 pkgdown_sha: ~ articles: surveyvoi: surveyvoi.html -last_built: 2022-03-06T02:02Z +last_built: 2022-03-07T05:41Z urls: reference: https://jeffrey-hanson.com/surveyvoi/reference article: https://jeffrey-hanson.com/surveyvoi/articles diff --git a/docs/reference/approx_evdsi.html b/docs/reference/approx_evdsi.html index 96b2a54..3036a96 100644 --- a/docs/reference/approx_evdsi.html +++ b/docs/reference/approx_evdsi.html @@ -21,7 +21,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3
diff --git a/docs/reference/approx_near_optimal_survey_scheme.html b/docs/reference/approx_near_optimal_survey_scheme.html index 2601342..e15db58 100644 --- a/docs/reference/approx_near_optimal_survey_scheme.html +++ b/docs/reference/approx_near_optimal_survey_scheme.html @@ -20,7 +20,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/approx_optimal_survey_scheme.html b/docs/reference/approx_optimal_survey_scheme.html index 4427d11..ff17685 100644 --- a/docs/reference/approx_optimal_survey_scheme.html +++ b/docs/reference/approx_optimal_survey_scheme.html @@ -19,7 +19,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/env_div_survey_scheme.html b/docs/reference/env_div_survey_scheme.html index bea4799..e642ef0 100644 --- a/docs/reference/env_div_survey_scheme.html +++ b/docs/reference/env_div_survey_scheme.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/evdci.html b/docs/reference/evdci.html index e34dcb6..066039b 100644 --- a/docs/reference/evdci.html +++ b/docs/reference/evdci.html @@ -20,7 +20,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/evdsi.html b/docs/reference/evdsi.html index 9702499..b2a4255 100644 --- a/docs/reference/evdsi.html +++ b/docs/reference/evdsi.html @@ -20,7 +20,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/feasible_survey_schemes.html b/docs/reference/feasible_survey_schemes.html index bdbad2a..bf94c64 100644 --- a/docs/reference/feasible_survey_schemes.html +++ b/docs/reference/feasible_survey_schemes.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/fit_hglm_occupancy_models.html b/docs/reference/fit_hglm_occupancy_models.html index c932178..704bb4d 100644 --- a/docs/reference/fit_hglm_occupancy_models.html +++ b/docs/reference/fit_hglm_occupancy_models.html @@ -23,7 +23,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/fit_xgb_occupancy_models.html b/docs/reference/fit_xgb_occupancy_models.html index 1a1ce6d..142cc80 100644 --- a/docs/reference/fit_xgb_occupancy_models.html +++ b/docs/reference/fit_xgb_occupancy_models.html @@ -19,7 +19,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 @@ -293,126 +293,9 @@

Examples

"survey_sensitivity", "survey_specificity", n_folds = rep(5, 2), xgb_early_stopping_rounds = rep(100, 2), xgb_tuning_parameters = parameters, n_threads = 1) -#> [15:02:34] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:34] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:35] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:36] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:36] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:36] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:37] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:38] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:39] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:40] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:40] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:41] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:41] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:42] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:42] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:43] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:43] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:45] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:45] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:45] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:45] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:46] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:47] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:48] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:48] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:48] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:49] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:49] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:50] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:50] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:50] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:51] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:52] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:53] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:53] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:53] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:53] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:54] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:55] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:55] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:55] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:56] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:57] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:57] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:57] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:57] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:58] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:58] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:58] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:58] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:58] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:58] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:59] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:59] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:59] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:59] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:59] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:02:59] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:00] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:00] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:00] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:00] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:00] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:01] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:01] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:01] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:01] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:01] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:01] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:02] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:02] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:02] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:02] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:02] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:02] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:03] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:03] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:03] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:03] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:03] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:03] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:04] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:04] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:04] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:04] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:04] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:05] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. -#> [15:03:06] WARNING: amalgamation/../src/c_api/c_api.cc:718: `ntree_limit` is deprecated, use `iteration_range` instead. +#> Warning: No parallel backend registered +#> Warning: executing %dopar% sequentially: no parallel backend registered +#> Warning: No parallel backend registered # print best found model parameters print(results$parameters) diff --git a/docs/reference/geo_cov_survey_scheme.html b/docs/reference/geo_cov_survey_scheme.html index 2e472f5..4bea220 100644 --- a/docs/reference/geo_cov_survey_scheme.html +++ b/docs/reference/geo_cov_survey_scheme.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/index.html b/docs/reference/index.html index b3b2da3..bbca1d4 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/n_states.html b/docs/reference/n_states.html index 3270faa..7cfe927 100644 --- a/docs/reference/n_states.html +++ b/docs/reference/n_states.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/optimal_survey_scheme.html b/docs/reference/optimal_survey_scheme.html index bf0fef2..d021cb4 100644 --- a/docs/reference/optimal_survey_scheme.html +++ b/docs/reference/optimal_survey_scheme.html @@ -19,7 +19,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/prior_probability_matrix.html b/docs/reference/prior_probability_matrix.html index e2a16f5..80595ae 100644 --- a/docs/reference/prior_probability_matrix.html +++ b/docs/reference/prior_probability_matrix.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/relative_site_richness_scores.html b/docs/reference/relative_site_richness_scores.html index d7363cd..c0bf2ca 100644 --- a/docs/reference/relative_site_richness_scores.html +++ b/docs/reference/relative_site_richness_scores.html @@ -20,7 +20,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/relative_site_uncertainty_scores.html b/docs/reference/relative_site_uncertainty_scores.html index c4c01ee..e7a9839 100644 --- a/docs/reference/relative_site_uncertainty_scores.html +++ b/docs/reference/relative_site_uncertainty_scores.html @@ -21,7 +21,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/sim_data.html b/docs/reference/sim_data.html index 30c2bdf..76c7182 100644 --- a/docs/reference/sim_data.html +++ b/docs/reference/sim_data.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/simulate_feature_data.html b/docs/reference/simulate_feature_data.html index 327513e..04952bb 100644 --- a/docs/reference/simulate_feature_data.html +++ b/docs/reference/simulate_feature_data.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/simulate_site_data.html b/docs/reference/simulate_site_data.html index ac8100a..f6e6a89 100644 --- a/docs/reference/simulate_site_data.html +++ b/docs/reference/simulate_site_data.html @@ -17,7 +17,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/starting run 2022-03-07 18:41:55 b/docs/reference/starting run 2022-03-07 18:41:55 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:41:55 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:41:57 b/docs/reference/starting run 2022-03-07 18:41:57 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:41:57 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:41:59 b/docs/reference/starting run 2022-03-07 18:41:59 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:41:59 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:00 b/docs/reference/starting run 2022-03-07 18:42:00 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:00 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:02 b/docs/reference/starting run 2022-03-07 18:42:02 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:02 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:04 b/docs/reference/starting run 2022-03-07 18:42:04 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:04 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:05 b/docs/reference/starting run 2022-03-07 18:42:05 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:05 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:07 b/docs/reference/starting run 2022-03-07 18:42:07 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:07 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:08 b/docs/reference/starting run 2022-03-07 18:42:08 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:08 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:10 b/docs/reference/starting run 2022-03-07 18:42:10 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:10 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:11 b/docs/reference/starting run 2022-03-07 18:42:11 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:11 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:12 b/docs/reference/starting run 2022-03-07 18:42:12 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:12 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:13 b/docs/reference/starting run 2022-03-07 18:42:13 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:13 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:14 b/docs/reference/starting run 2022-03-07 18:42:14 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:14 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/starting run 2022-03-07 18:42:15 b/docs/reference/starting run 2022-03-07 18:42:15 new file mode 100644 index 0000000..c7ec943 --- /dev/null +++ b/docs/reference/starting run 2022-03-07 18:42:15 @@ -0,0 +1 @@ +test.log diff --git a/docs/reference/surveyvoi.html b/docs/reference/surveyvoi.html index b18172d..befc48e 100644 --- a/docs/reference/surveyvoi.html +++ b/docs/reference/surveyvoi.html @@ -28,7 +28,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/docs/reference/weighted_survey_scheme.html b/docs/reference/weighted_survey_scheme.html index 089f1b8..af25756 100644 --- a/docs/reference/weighted_survey_scheme.html +++ b/docs/reference/weighted_survey_scheme.html @@ -18,7 +18,7 @@ surveyvoi - 1.0.3.2 + 1.0.3.3 diff --git a/inst/doc/surveyvoi.html b/inst/doc/surveyvoi.html index d1d10f1..bee7a2c 100644 --- a/inst/doc/surveyvoi.html +++ b/inst/doc/surveyvoi.html @@ -12,7 +12,7 @@ - + surveyvoi: Survey Value of Information @@ -164,7 +164,7 @@

surveyvoi: Survey Value of Information

Jeffrey O. Hanson

-

2022-03-06

+

2022-03-07

diff --git a/tests/testthat/test_fit_xgb_occupancy_models.R b/tests/testthat/test_fit_xgb_occupancy_models.R index 05c1559..0db71c3 100644 --- a/tests/testthat/test_fit_xgb_occupancy_models.R +++ b/tests/testthat/test_fit_xgb_occupancy_models.R @@ -1,6 +1,7 @@ context("fit_xgb_occupancy_models") test_that("single species", { + skip_on_cran() # data set.seed(123) RandomFields::RFoptions(seed = 123) @@ -75,6 +76,7 @@ test_that("single species", { }) test_that("multiple species", { + skip_on_cran() # data set.seed(123) RandomFields::RFoptions(seed = 123) @@ -148,8 +150,9 @@ test_that("multiple species", { }) test_that("multiple species (sparse, multiple threads)", { - # skip if using PSOCK cluster and package not installed - skip_if(!requireNamespace("surveyvoi") && + skip_on_cran() + # skip if not on Linux or package not installed + skip_if(!requireNamespace("surveyvoi") || !identical(.Platform$OS.type, "unix")) set.seed(123) RandomFields::RFoptions(seed = 123)