Lighten the examples

LLeiSong · Jun 10, 2023 · f6a1fd0 · f6a1fd0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: itsdm
 Title: Isolation Forest-Based Presence-Only Species Distribution Modeling
-Version: 0.2.0
+Version: 0.2.1
 Authors@R: c(
     person("Lei", "Song", , "lsong@clarku.edu", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-4371-1473")),

diff --git a/R/convert_to_pa.R b/R/convert_to_pa.R
@@ -78,8 +78,9 @@
 #'   obs_mode = "imperfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 20,
-#'   sample_size = 0.8, ndim = 2L,
+#'   variables = env_vars, ntrees = 5,
+#'   sample_size = 0.8, ndim = 1L,
+#'   nthreads = 1,
 #'   seed = 123L, response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)

diff --git a/R/detect_envi_change.R b/R/detect_envi_change.R
@@ -105,8 +105,9 @@
 #'   obs_mode = "imperfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 10,
+#'   variables = env_vars, ntrees = 5,
 #'   sample_size = 0.8, ndim = 1L,
+#'   nthreads = 1,
 #'   seed = 123L, response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)

diff --git a/R/evaluate_po.R b/R/evaluate_po.R
@@ -137,9 +137,10 @@
 #'   obs_mode = "perfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 30,
+#'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.8, ndim = 2L,
-#'   seed = 123L, response = FALSE,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/R/independent_response.R b/R/independent_response.R
@@ -80,9 +80,10 @@
 #'   obs_mode = "imperfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 30,
+#'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.8, ndim = 2L,
-#'   seed = 123L, response = FALSE,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/R/isotree_po.R b/R/isotree_po.R
@@ -195,7 +195,7 @@
 #'   obs_ind_eval = obs_train_eval$eval,
 #'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.6, ndim = 1L,
-#'   seed = 123L)
+#'   seed = 123L, nthreads = 1)
 #'
 #' # Check results
 #' ## Evaluation based on training dataset
@@ -239,7 +239,7 @@
 #'   obs_ind_eval = obs_train_eval$eval,
 #'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.6, ndim = 1L,
-#'   seed = 123L)
+#'   seed = 123L, nthreads = 1)
 #'
 #' # Modeling with imperfect_presence mode
 #' mod_imperfect_pres <- isotree_po(
@@ -248,7 +248,7 @@
 #'   obs_ind_eval = obs_train_eval$eval,
 #'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.6, ndim = 1L,
-#'   seed = 123L)
+#'   seed = 123L, nthreads = 1)
 #' }
 #'
 isotree_po <- function(

diff --git a/R/marginal_response.R b/R/marginal_response.R
@@ -76,9 +76,10 @@
 #'   obs_mode = "imperfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 20,
+#'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.8, ndim = 2L,
-#'   seed = 123L, response = FALSE,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/R/probability.R b/R/probability.R
@@ -47,9 +47,10 @@
 #'   obs_mode = "imperfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 20,
+#'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.8, ndim = 2L,
-#'   seed = 123L, response = FALSE,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/R/shap_dependence.R b/R/shap_dependence.R
@@ -94,9 +94,10 @@
 #'   obs_mode = "imperfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 30,
+#'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.8, ndim = 2L,
-#'   seed = 123L, response = FALSE,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/R/shap_spatial_response.R b/R/shap_spatial_response.R
@@ -84,9 +84,10 @@
 #'   obs_mode = "imperfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 20,
+#'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.8, ndim = 2L,
-#'   seed = 123L, response = FALSE,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/R/spatial_response.R b/R/spatial_response.R
@@ -87,8 +87,9 @@
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
 #'   variables = env_vars, ntrees = 20,
-#'   sample_size = 0.8, ndim = 2L,
-#'   seed = 123L, response = FALSE,
+#'   sample_size = 0.8, ndim = 1L,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/R/variable_analysis.R b/R/variable_analysis.R
@@ -119,9 +119,10 @@
 #'   obs_mode = "imperfect_presence",
 #'   obs = obs_train_eval$obs,
 #'   obs_ind_eval = obs_train_eval$eval,
-#'   variables = env_vars, ntrees = 30,
+#'   variables = env_vars, ntrees = 10,
 #'   sample_size = 0.8, ndim = 2L,
-#'   seed = 123L, response = FALSE,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/R/variable_contrib.R b/R/variable_contrib.R
@@ -74,7 +74,8 @@
 #'   obs_ind_eval = obs_train_eval$eval,
 #'   variables = env_vars, ntrees = 5,
 #'   sample_size = 0.8, ndim = 1L,
-#'   seed = 123L, response = FALSE,
+#'   seed = 123L, nthreads = 1,
+#'   response = FALSE,
 #'   spatial_response = FALSE,
 #'   check_variable = FALSE)
 #'

diff --git a/man/convert_to_pa.Rd b/man/convert_to_pa.Rd
diff --git a/man/detect_envi_change.Rd b/man/detect_envi_change.Rd
diff --git a/man/evaluate_po.Rd b/man/evaluate_po.Rd
diff --git a/man/independent_response.Rd b/man/independent_response.Rd
diff --git a/man/isotree_po.Rd b/man/isotree_po.Rd
diff --git a/man/marginal_response.Rd b/man/marginal_response.Rd
diff --git a/man/probability.Rd b/man/probability.Rd
diff --git a/man/shap_dependence.Rd b/man/shap_dependence.Rd
diff --git a/man/shap_spatial_response.Rd b/man/shap_spatial_response.Rd
diff --git a/man/spatial_response.Rd b/man/spatial_response.Rd
diff --git a/man/variable_analysis.Rd b/man/variable_analysis.Rd
diff --git a/man/variable_contrib.Rd b/man/variable_contrib.Rd