ENM resolution mix - multiple runs version
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Workflow Components
|
Authors (1)
|  |
| Renato De Giovanni |
|
Titles (1)
| |
| Compare ENM models created with layers with different spatial resolutions. |
|
Descriptions (0)
| |
None
|
Dependencies (0)
| |
None
| Inputs (7) | |
| Name | Description |
|---|---|
| min_virtual_niche_prevalence | Minimum virtual niche prevalence (proportion of suitable area in the native range). |
| max_virtual_niche_prevalence | Maximum virtual niche prevalence (proportion of suitable area in the native range). |
| num_background_points | Number of background points |
| num_testing_points | Number of points to be used for testing (an equal number will be used for presences and absences). |
| min_number_training_points | Minimum number of training points to be used when creating models for the virtual species. The real number will be a random value between minimum and maximum. |
| max_number_training_points | Maximum number of training points to be used when creating models for the virtual species. The real number will be a random value between minimum and maximum. |
| replicates | Number of times to repeat the experiment: generate virtual niche, generate models with different resolutions and test them. |
| Processors (8) | |
| Name | Type | Description |
|---|---|---|
| choose_layers_and_mask | workflow | |
| create_and_test_models | workflow | |
| for_loop_triggering | beanshell |
Scriptimport java.util.ArrayList;
ArrayList trigger_list = new ArrayList();
int end_value = Integer.parseInt(replicates);
for (int i = 1; i <= end_value; i += 1) {
trigger_list.add(i);
}
|
| merge_all_layers | beanshell |
Scriptall_layers = high_resolution_layers + "\n" + low_resolution_layers; |
| sample_background_points | component |
Randomly sample background points on the specified mask using the intersection between all environmental layers (high and low resolution). Points are returned in the absences port. Componentsample_points |
| no | stringconstant |
Valueno |
| 1 | stringconstant |
Value1 |
| demo | stringconstant |
Valuedemo |
| Beanshells (7) | |
| Name | Description | Inputs | Outputs |
|---|---|---|---|
| for_loop_triggering | replicates | trigger_list | |
| merge_all_layers |
high_resolution_layers low_resolution_layers |
all_layers | |
| define_random_number_of_training_points |
min_points max_points |
num_points | |
| get_last_iteration_result |
random_proportion_list point_list threshold_list model_xml_list model_values_list |
random_proportion point threshold model_xml model_values |
|
| suggest_random_suitable_threshold |
model_values min_prevalence max_prevalence |
threshold proportion |
|
| empty_list | empty_list | ||
| mix_layers |
low_resolution_layers high_resolution_layers |
mixed_resolution_layers |
| Outputs (13) | |
| Name | Description |
|---|---|
| mask_id | |
| layer_labels | |
| origin_point | |
| model_xml | |
| suitability_threshold | |
| virtual_niche_auc | |
| low_resolution_auc | |
| mixed_resolution_auc | |
| num_training_points | |
| training_points_csv | |
| testing_presence_points_csv | |
| testing_absence_points_csv | |
| prevalence |
| Datalinks (34) | |
| Source | Sink |
|---|---|
| choose_layers_and_mask:low_resolution_layers_ids | create_and_test_models:low_resolution_layers |
| choose_layers_and_mask:high_resolution_layers_ids | create_and_test_models:high_resolution_layers |
| choose_layers_and_mask:mask_id | create_and_test_models:mask_id |
| min_number_training_points | create_and_test_models:min_number_training_points |
| max_number_training_points | create_and_test_models:max_number_training_points |
| num_testing_points | create_and_test_models:num_testing_points |
| max_virtual_niche_prevalence | create_and_test_models:max_virtual_niche_prevalence |
| min_virtual_niche_prevalence | create_and_test_models:min_virtual_niche_prevalence |
| for_loop_triggering:trigger_list | create_and_test_models:loop_iterator |
| sample_background_points:absence_points_xml | create_and_test_models:background_points |
| merge_all_layers:all_layers | create_and_test_models:all_layers |
| replicates | for_loop_triggering:replicates |
| choose_layers_and_mask:high_resolution_layers_ids | merge_all_layers:high_resolution_layers |
| choose_layers_and_mask:low_resolution_layers_ids | merge_all_layers:low_resolution_layers |
| merge_all_layers:all_layers | sample_background_points:layers |
| num_background_points | sample_background_points:num_points |
| choose_layers_and_mask:mask_id | sample_background_points:mask_id |
| no:value | sample_background_points:environmentally_unique |
| 1:value | sample_background_points:proportion_of_absences |
| no:value | sample_background_points:spatially_unique |
| demo:value | sample_background_points:species_label |
| choose_layers_and_mask:mask_id | mask_id |
| choose_layers_and_mask:high_resolution_layers_labels | layer_labels |
| create_and_test_models:origin_point | origin_point |
| create_and_test_models:model_xml | model_xml |
| create_and_test_models:suitability_threshold | suitability_threshold |
| create_and_test_models:virtual_niche_auc | virtual_niche_auc |
| create_and_test_models:low_resolution_auc | low_resolution_auc |
| create_and_test_models:mixed_resolution_auc | mixed_resolution_auc |
| create_and_test_models:num_training_points | num_training_points |
| create_and_test_models:training_points_csv | training_points_csv |
| create_and_test_models:testing_presence_points_csv | testing_presence_points_csv |
| create_and_test_models:testing_absence_points_csv | testing_absence_points_csv |
| create_and_test_models:prevalence | prevalence |
| Coordinations (3) | |
| Controller | Target |
|---|---|
| sample_background_points | create_and_test_models |
| merge_all_layers | sample_background_points |
| choose_layers_and_mask | merge_all_layers |
Workflow Type
Version 1 (earliest)
(of 10)
Shared with Groups (1)
Statistics
In chronological order:
-
Created by Renato De Giovanni on Thursday 13 November 2014 15:20:51 (UTC)
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Created by Renato De Giovanni on Friday 14 November 2014 08:46:24 (UTC)
Revision comment:Removed virtual niche test.
-
Created by Renato De Giovanni on Friday 14 November 2014 10:18:20 (UTC)
Revision comment:Increased default number of replicates and removed redundant parameter in nested workflow.
-
Created by Renato De Giovanni on Tuesday 18 November 2014 17:16:00 (UTC)
Revision comment:Updated versions of some components and improved workflow description.
-
Created by Renato De Giovanni on Wednesday 19 November 2014 11:40:23 (UTC)
Revision comment:Upgraded some of the components.
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Created by Renato De Giovanni on Thursday 04 December 2014 16:16:21 (UTC)
Revision comment:Updated components versions.
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Created by Renato De Giovanni on Friday 05 December 2014 18:43:04 (UTC)
Revision comment:Initial R code to calculate probability of getting a better AUC when mixing resolutions and to plot a graph comparing the results. Also fixed a bug in threshold calculation and increased the default number of replicates.
-
Created by Renato De Giovanni on Tuesday 09 December 2014 20:34:17 (UTC)
Revision comment:Updated samplePoints component, removed unnecessary loop feedback and fixed R code.
-
Created by Renato De Giovanni on Saturday 04 April 2015 21:27:30 (UTC)
Revision comment:Upgraded interaction components to use github pages.
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Created by Renato De Giovanni on Tuesday 12 May 2015 05:28:09 (UTC)
Revision comment:This version plots a different graph to compare results and calculates mean and standard deviation of the AUCs differences.
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