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Maxent Model For Anaphalis - Javanica - SCH - Bip

This document analyzes a Maxent model for predicting the habitat of Anaphalis javanica. It includes analysis of omission/commission rates, response curves showing the effect of each environmental variable, and the relative contribution of each variable to the model. Pictures show the model predictions across the study area and locations of presence/test points.

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abel mahendra
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23 views10 pages

Maxent Model For Anaphalis - Javanica - SCH - Bip

This document analyzes a Maxent model for predicting the habitat of Anaphalis javanica. It includes analysis of omission/commission rates, response curves showing the effect of each environmental variable, and the relative contribution of each variable to the model. Pictures show the model predictions across the study area and locations of presence/test points.

Uploaded by

abel mahendra
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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4/18/24, 11:04 AM Maxent model for Anaphalis_javanica_Sch.Bip.

Maxent model for Anaphalis_javanica_Sch.Bip.


This page contains some analysis of the Maxent model for Anaphalis_javanica_Sch.Bip., created Thu Apr 18
10:16:05 ICT 2024 using Maxent version 3.4.4. 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
0.936 rather than 1; in practice the test AUC may exceed this bound.

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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 Cloglog Fractional Training


Description
threshold threshold predicted area omission rate
1.000 0.002 Fixed cumulative value 1 0.768 0.000
5.000 0.004 Fixed cumulative value 5 0.387 0.000
10.000 0.009 Fixed cumulative value 10 0.145 0.091
6.008 0.005 Minimum training presence 0.325 0.000
18.219 0.058 10 percentile training presence 0.032 0.091
Equal training sensitivity and
12.166 0.014 0.091 0.091
specificity
Maximum training sensitivity plus
18.219 0.058 0.032 0.091
specificity
Balance training omission, predicted
6.008 0.005 0.325 0.000
area and threshold value
Equate entropy of thresholded and
19.225 0.066 0.028 0.136
original distributions

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Pictures of the model


This is a representation of the Maxent model for Anaphalis_javanica_Sch.Bip.. 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.

Click here to interactively explore this prediction using the Explain tool. If clicking from your browser does not
succeed in starting the tool, try running the script in D:\Diaz\Maxent\Fenologi Lingkungan\Hasil
Maxent\Anaphalis_javanica_Sch.Bip._explain.bat directly. This tool requires the environmental grids to be small
enough that they all fit in memory.

Response curves

These curves show how each environmental variable affects the Maxent prediction. The curves show how the
predicted probability of presence 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.

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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.

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4/18/24, 11:04 AM Maxent model for Anaphalis_javanica_Sch.Bip.

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Analysis of variable contributions

The following table gives estimates of relative contributions of the environmental variables to the Maxent
model. To determine the first 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. For the second estimate, for each environmental variable in turn, the values of that
variable on training presence and background data are randomly permuted. The model is reevaluated on the
permuted data, and the resulting drop in training AUC is shown in the table, normalized to percentages. As with
the variable jackknife, variable contributions should be interpreted with caution when the predictor variables are
correlated.

Variable Percent contribution Permutation importance


Bio_5 56.9 3.1
Elevation 22.3 14.2
Bio_10 6.2 0
SRAD_04 2.7 0
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Bio_11 2.3 0.2


SRAD_07 1.9 8.8
Bio_6 1.5 0
SRAD_05 1.3 25.3
Bio_1 1.2 0
Bio_15 0.9 0
Bio_2 0.7 15
Bio_8 0.5 0
SRAD_11 0.5 10.2
Bio_16 0.3 14.1
Bio_18 0.3 0
SRAD_10 0.1 0
SRAD_01 0.1 0
SRAD_06 0.1 6.6
Bio_14 0 2
Bio_4 0 0
Bio_19 0 0.5
SRAD_12 0 0
SRAD_09 0 0
SRAD_08 0 0
SRAD_03 0 0
SRAD_02 0 0
Bio_9 0 0
Bio_7 0 0
Bio_3 0 0
Bio_17 0 0
Bio_13 0 0
Bio_12 0 0

The following picture shows the results of the jackknife test of variable importance. The environmental variable
with highest gain when used in isolation is Elevation, which therefore appears to have the most useful
information by itself. The environmental variable that decreases the gain the most when it is omitted is
SRAD_05, which therefore appears to have the most information that isn't present in the other variables.

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Raw data outputs and control parameters


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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 3.583, training AUC is 0.972, unregularized training gain is 4.128.
Algorithm terminated after 500 iterations (14 seconds).

The follow settings were used during the run:


22 presence records used for training.
10022 points used to determine the Maxent distribution (background points and presence points).
Environmental layers used (all continuous): Bio_1 Bio_10 Bio_11 Bio_12 Bio_13 Bio_14 Bio_15 Bio_16
Bio_17 Bio_18 Bio_19 Bio_2 Bio_3 Bio_4 Bio_5 Bio_6 Bio_7 Bio_8 Bio_9 Elevation SRAD_01 SRAD_02
SRAD_03 SRAD_04 SRAD_05 SRAD_06 SRAD_07 SRAD_08 SRAD_09 SRAD_10 SRAD_11 SRAD_12
Regularization values: linear/quadratic/product: 0.404, categorical: 0.250, threshold: 1.780, hinge: 0.500
Feature types used: hinge linear quadratic
responsecurves: true
jackknife: true
outputdirectory: D:\Diaz\Maxent\Fenologi Lingkungan\Hasil Maxent
samplesfile: D:\Diaz\Maxent\Fenologi Lingkungan\Koordinat\Koordinat Anaphalis javanica Sch.Bip.csv
environmentallayers: D:\Diaz\Maxent\Fenologi Lingkungan\Ascii
Command line used:

Command line to repeat this species model: java density.MaxEnt nowarnings noprefixes -E "" -E
Anaphalis_javanica_Sch.Bip. responsecurves jackknife "outputdirectory=D:\Diaz\Maxent\Fenologi
Lingkungan\Hasil Maxent" "samplesfile=D:\Diaz\Maxent\Fenologi Lingkungan\Koordinat\Koordinat Anaphalis
javanica Sch.Bip.csv" "environmentallayers=D:\Diaz\Maxent\Fenologi Lingkungan\Ascii"

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