Workflows

Ecological niche modelling workflow (28)

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service. Algorithm, environmental layers and mask are selected during the workflow. The model is tested (internal test and optional cross validation external test) and then projected one or more times. All points from the input file are used to create a single model, even if there are differences in the scientific names. Cross validation calculates the mean AUC. Model projectio...

Created: 2013-01-07 | Last updated: 2015-06-11

Credits: Renato De Giovanni Alan Williams Robert Kulawik Francisco Quevedo Vhernand BioVeL

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ENM resolution mix - single run version (6)

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Single run version of the workflow for comparing results of two kinds of ecological niche models: one using only low resolution layers and the other using a random mix of low and high resolution layers. Users select the study region and the environmental variables considered to be the main drivers of a virtual species niche. The workflow is all based on the ENM components, which use the openModeller Web Service (OMWS). After getting initial parameters from the user, the workflow generates a r...

Created: 2014-11-18 | Last updated: 2015-04-04

Credits: Renato De Giovanni BioVeL

ENM resolution mix - multiple runs version (10)

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Multiple runs version of the workflow for comparing results of two kinds of ecological niche models: one using only low resolution layers and the other using a random mix of low and high resolution layers. Users select the study region and the environmental variables considered to be the main drivers of a virtual species niche. The workflow is all based on the ENM components, which use the openModeller Web Service (OMWS). After getting initial parameters from the user, the workflow generates ...

Created: 2014-11-13 | Last updated: 2015-05-12

Credits: Renato De Giovanni BioVeL

select_random_points_based_on_threshold (2)

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Selects random presence and/or absence points given a threshold and a set of points with the corresponding model values.

Created: 2014-11-13 | Last updated: 2015-05-11

Credits: BioVeL

define_frequently_used_constants (3)

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Defines constants that are frequently used as parameters for ENM Components. When building a new workflow with ENM Components, some constant values will likely be used multiple times as parameters. This component conveniently defines the most frequently used constants so that users can directly connnect them to the corresponding input ports without needing to manually create each constant.

Created: 2014-11-10 | Last updated: 2015-05-11

Credits: BioVeL

convert_points_xml_to_csv (4)

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Converts points in openModeller XML format into CSV format (header: occurrenceID,nameComplete,decimalLongitude,decimalLatitude). Most input/output ports related with presence or absence points expect/return data in openModeller XML format. This component can be used to simply convert such data back to a more human friendly format.

Created: 2014-11-05 | Last updated: 2015-05-11

Credits: BioVeL

extract_confusion_matrix (1)

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Extracts confusion matrix data from a test result XML.

Created: 2014-10-13 | Last updated: 2014-12-04

extract_roc_points (1)

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Extracts the ROC points from a test result XML.

Created: 2014-10-13 | Last updated: 2014-12-04

Credits: BioVeL

extract_auc (2)

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Extracts the AUC value from a test result XML.

Created: 2014-10-09 | Last updated: 2014-10-13

Credits: BioVeL