Maxent model for Podarcis_muralis


This page contains some analysis of the Maxent model for Podarcis_muralis, created Fri Dec 03 15:15:41 CET 2010 using Maxent version 3.2.19. If you would like to do further analyses, the raw data used here is linked to at the end of this page.


Analysis of omission/commission

The following picture shows the omission rate and predicted area as a function of the cumulative threshold. The omission rate is is calculated both on the training presence records, and (if test data are used) on the test records. The omission rate should be close to the predicted omission, because of the definition of the cumulative threshold.


The next picture is the receiver operating characteristic (ROC) curve for the same data. Note that the specificity is defined using predicted area, rather than true commission (see the paper by Phillips, Anderson and Schapire cited on the help page for discussion of what this means). This implies that the maximum achievable AUC is less than 1. If test data is drawn from the Maxent distribution itself, then the maximum possible test AUC would be 0.913 rather than 1; in practice the test AUC may exceed this bound.



Some common thresholds and corresponding omission rates are as follows. If test data are available, binomial probabilities are calculated exactly if the number of test samples is at most 25, otherwise using a normal approximation to the binomial. These are 1-sided p-values for the null hypothesis that test points are predicted no better than by a random prediction with the same fractional predicted area. The "Balance" threshold minimizes 6 * training omission rate + .04 * cumulative threshold + 1.6 * fractional predicted area.

Cumulative thresholdLogistic thresholdDescriptionFractional predicted areaTraining omission rate
1.0000.014Fixed cumulative value 10.6150.000
5.0000.050Fixed cumulative value 50.3840.000
10.0000.093Fixed cumulative value 100.2610.000
20.0280.157Minimum training presence0.1530.000
22.8450.17910 percentile training presence0.1290.100
22.8450.179Equal training sensitivity and specificity0.1290.100
20.0280.157Maximum training sensitivity plus specificity0.1530.000
7.1450.063Balance training omission, predicted area and threshold value0.3280.000
18.7740.150Equate entropy of thresholded and non-thresholded distributions0.1640.000

This is a representation of the Maxent model for Podarcis_muralis. Warmer colors show areas with better predicted conditions. White dots show the presence locations used for training, while violet dots show test locations. Click on the image for a full-size version.




Response curves


These curves show how each environmental variable affects the Maxent prediction. The curves show how the logistic prediction changes as each environmental variable is varied, keeping all other environmental variables at their average sample value. Click on a response curve to see a larger version. Note that the curves can be hard to interpret if you have strongly correlated variables, as the model may depend on the correlations in ways that are not evident in the curves. In other words, the curves show the marginal effect of changing exactly one variable, whereas the model may take advantage of sets of variables changing together.



In contrast to the above marginal response curves, each of the following curves represents a different model, namely, a Maxent model created using only the corresponding variable. These plots reflect the dependence of predicted suitability both on the selected variable and on dependencies induced by correlations between the selected variable and other variables. They may be easier to interpret if there are strong correlations between variables.




Analysis of variable contributions


The following table gives a heuristic estimate of relative contributions of the environmental variables to the Maxent model. To determine the estimate, in each iteration of the training algorithm, the increase in regularized gain is added to the contribution of the corresponding variable, or subtracted from it if the change to the absolute value of lambda is negative. As with the jackknife, variable contributions should be interpreted with caution when the predictor variables are correlated.

VariablePercent contribution
dusaf50.5
idro39.1
strade10.4
urbano0




Raw data outputs and control parameters


The data used in the above analysis is contained in the next links. Please see the Help button for more information on these.
The model applied to the training environmental layers
The coefficients of the model
The omission and predicted area for varying cumulative and raw thresholds
The prediction strength at the training and (optionally) test presence sites
Results for all species modeled in the same Maxent run, with summary statistics and (optionally) jackknife results


Regularized training gain is 1.806, training AUC is 0.960, unregularized training gain is 2.350.
Algorithm converged after 120 iterations (1 seconds).

The follow parameters and settings were used during the run:
10 presence records used for training.
7580 points used to determine the Maxent distribution (background points and presence points).
Environmental layers used: dusaf(categorical) idro strade urbano
Command line:
Feature types used: Linear Quadratic
Regularization multiplier is 1.0
Regularization values: linear/quadratic/product: 0.800 categorical: 0.500
Species file is G:\Voghera\specie.csv
Environmental variables from G:\Voghera\Maxent
Output directory is G:\Voghera\Risultati
Output format is Logistic
Output file type is .asc
Maximum iterations is 500
Convergence threshold is 1.0E-5
Random test percentage is 0
Make pictures selected
Create response curves selected