ENMevaluate
(Package: ENMeval) :
Tuning and evaluation of ENMs with Maxent
ENMevaluate automatically executes Maxent (Phillips et al. 2006; Phillips and Dudik 2008) across a range of settings, returning a data.frame of evaluation metrics to aid in identifying settings that balance model fit and predictive ability. The function calls Maxent using the maxent function in the dismo package (Hijmans et al. 2011). Users should consult ENMeval-package and help documentation of the dismo package for guidelines on how to run Maxent in R.
● Data Source:
CranContrib
● Keywords:
● Alias: ENMevaluate, tuning
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ENMeval-package
(Package: ENMeval) :
Automated runs and evaluations of ecological niche models
Automatically partitions data into bins for model training and testing, executes ecological niche models (ENMs) across a range of user-defined settings, and calculates evaluation metrics to help achieve a balance between goodness-of-fit and model complexity.
● Data Source:
CranContrib
● Keywords: ENM, SDM, niche
● Alias: ENMeval, ENMeval-package
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make.args
(Package: ENMeval) :
Generate arguments for Maxent
This function generates a list of arguments to pass to Maxent or to use as convenient labels for plotting.
● Data Source:
CranContrib
● Keywords:
● Alias: make.args
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calc.niche.overlap
(Package: ENMeval) :
Calculate Similarity of ENMs in Geographic Space
Compute pairwise "niche overlap" in geographic space for Maxent predictions. The value ranges from 0 (no overlap) to 1 (identical predictions). The function uses the nicheOverlap function of the dismo package (Hijmans et al. 2011).
● Data Source:
CranContrib
● Keywords:
● Alias: calc.niche.overlap
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Objects of this class are generated by a call of ENMevaluate.
● Data Source:
CranContrib
● Keywords: classes
● Alias: ENMevaluation, ENMevaluation-class
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calc.aicc
(Package: ENMeval) :
Calculate AICc from Maxent model prediction
This function calculates AICc for Maxent models based on Warren and Seifert (2011).
● Data Source:
CranContrib
● Keywords:
● Alias: calc.aicc, get.params
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corrected.var
(Package: ENMeval) :
Calculate variance corrected for non-independence of emph{k
This function calculates variance corrected for non-independence of k-fold iterations. See Appendix of Shcheglovitova & Anderson (2013) and other references (Miller 1974; Parr 1985; Shao and Wu 1989) for additional details.
● Data Source:
CranContrib
● Keywords:
● Alias: corrected.var
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eval.plot
(Package: ENMeval) :
Generate Basic Plot for ENMevaluate Output
This function can be used to generate a basic plot of evaluation metrics generated by a call of ENMevaluate.
● Data Source:
CranContrib
● Keywords:
● Alias: eval.plot
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1 images
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enmeval_results
(Package: ENMeval) :
An object of class "ENMevaluation"
An example results file based on a call of ENMevaluate (see example).
● Data Source:
CranContrib
● Keywords:
● Alias: enmeval_results
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1 images
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get.evaluation.bins
(Package: ENMeval) :
Methods to partition data for evaluation
ENMeval provides six methods to partition occurrence and background localities into bins for training and testing (or, evaluation and calibration). Users should carefully consider the objectives of their study and the influence of spatial bias when deciding on a method of data partitioning.
● Data Source:
CranContrib
● Keywords:
● Alias: get.block, get.checkerboard1, get.checkerboard2, get.evaluation.bins, get.jackknife, get.randomkfold, get.user
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