[Biomod-commits] Evaluation.results interpretations

[Hedvig .n]

Hello fellow Biomodders,


After using Biomod for a while, I'm still confused by the Evaluation.results
file, so here is my own interpretation which I don't know if it's correct. I
hope I don't confuse anyone more now...

Say I'm running models with no pseudoabsences, one repetition run and 80-20
split. Evaluation.results.kappa is a list of data frames $Sp1_full and
$Sp1_full_rep1.

For repetition 1, the first column is the crossvalidation, from comparing
predictions on the 20% evaluation data (from the models calibrated on 80% of
data) to original distribution data. But how are the 'leftover' columns
made? Crossvalidation with the 80%-models applied on 100% of data? Are
Cutoffs made by comparing the predictions from 80%-models on 20% evaluation
data, to the real distribution (in the same 20% of locations)?

For $Sp1_full, the first column is the average of all cross-validations (so
it's the same value in my case). Are the other columns the model calibrated
on 100% of the data, i.e. a 'final model'? Are those Cutoffs made by the
100%-models applied on the entire studyarea? Values for Sensitivity and
Specificity seem to be generally higher than for the repetitions. (The
manual says 'using the model built with all data for calibration' which
confuses me).

Finally, does Biomod make a 'final model' trained on 100% of the data?

Thank you very much,

Hedvig Nenzén


 One of my species as an example:

> Evaluation.results.Kappa

$Sp1_full

Cross.validation indepdt.data total.score Cutoff Sensitivity Specificity

ANN 0.688 none 0.7149572 495.00 89.70370 81.40044

CTA 0.735 none 0.8010009 435.16 94.88889 84.13567

GAM 0.683 none 0.7108026 526.29 90.59259 79.75930

GBM 0.738 none 0.7730225 588.36 93.85185 82.38512

GLM 0.670 none 0.6884088 588.82 87.18519 81.72867

MARS 0.759 none 0.7729465 454.08 93.03704 83.47921

FDA 0.733 none 0.7568880 372.35 92.66667 82.16630

RF 0.745 none 1.0000000 440.00 100.00000 100.00000

SRE 0.545 none 0.5607607 10.00 91.18519 62.69147


 $Sp1_full_rep1

Cross.validation indepdt.data total.score Cutoff Sensitivity Specificity

ANN 0.688 none 0.7166007 486.71 89.92593 81.29103

CTA 0.735 none 0.8030243 407.90 93.77778 85.88621

GAM 0.683 none 0.7103411 546.15 90.22222 80.19694

GBM 0.738 none 0.7740735 572.40 94.66667 81.40044

GLM 0.670 none 0.6887384 589.41 86.96296 82.05689

MARS 0.759 none 0.7715822 502.25 92.51852 84.02626

FDA 0.733 none 0.7554794 355.14 93.03704 81.50985

RF 0.745 none 0.9494617 480.00 98.29630 96.49891

SRE 0.545 none 0.5783646 10.00 90.66667 65.20788
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