14-200x200

Ecological niche modelling workflow (v5) run 16 Aug 2017 09:19:16 UTC L.tolaiSVM5fold


Name:

Workflow: Ecological niche modelling workflow

Category: Ecological Niche Modelling

Status: Finished

Created at: 16 Aug 2017 09:19:24 UTC

Started at: 16 Aug 2017 09:19:26 UTC

Finished at: 16 Aug 2017 10:14:34 UTC

Outputs

Results (18)

answer help (text/plain)

no

area_statistics help ((list of depth 1))

  1. (text/plain)

    <AreaStatistics xmlns="http://openmodeller.cria.org.br/xml/2.0" CellsPredicted="276125" PredictionThreshold="0.5" TotalCells="2769053" />

create_final_model_log help (text/plain)

[Info] Creating model
[Warn] SvmAlgorithm: No absence points available.
[Warn] SvmAlgorithm: Number of pseudo absences will be 13 (same number of presences).
[Info] SvmAlgorithm: Generating pseudo-absences.
[Info] Finished creating model  
[Info] Calculating ROC curve
[Info] Generating 10000 background points

external_auc_list help ((list of depth 1))

  1. (text/plain)

    0.9922499999999999653610416

  2. (text/plain)

    0.9849833333333334328685282

  3. (text/plain)

    0.9990499999999999936051154

  4. (text/plain)

    0.9989500000000000046185278

  5. (text/plain)

    0.969849999999999989874766

external_omission_list ((list of depth 1))

  1. (text/plain)

    0

  2. (text/plain)

    33.33333333333332859638176

  3. (text/plain)

    0

  4. (text/plain)

    0

  5. (text/plain)

    50

internal_test_model_log help (text/plain)

[Info] Calculating ROC curve
[Info] Generating 10000 background points
[Warn] No absence points - commission error won't be calculated
[Info] 
Model statistics
[Info] Accuracy:           100.00%
[Info] Omission error:       0.00% (0/13)
[Info] AUC:                  0.99

internal_test_model_statistics help (text/plain)

<Statistics xmlns="http://openmodeller.cria.org.br/xml/2.0">
<ConfusionMatrix Accuracy="100" CommissionError="-100" FalseNegatives="0" FalsePositives="0" OmissionError="0" Threshold="0.5" TrueNegatives="0" TruePositives="13" />
<RocCurve Auc="0.9919807692307691660005275" NumBackgroundPoints="10000" Points="0 0 0 0 0.0001000000000000000047921736 0.3076923076923077093880465 0.007400000000000000327515792 0.8461538461538461453059767 0.02500000000000000138777878 0.8461538461538461453059767 0.05279999999999999971134201 1 0.07480000000000000537347944 1 0.08980000000000000481836793 1 0.1063999999999999945821116 1 0.1208999999999999935829109 1 0.136699999999999988187227 1 0.1504999999999999948929741 1 0.1705000000000000126565425 1 0.2011999999999999899635839 1 0.3306999999999999939603867 1 1 1" /></Statistics>

mean_auc help (text/plain)

0.9890166666666668

mean_omission (text/plain)

16.666666666666664

projection_url help ((list of depth 1))

  1. (text/plain)

project_model_output_log help ((list of depth 1))

  1. (text/plain)

    [Info] Running serial projection version
    [Info] Projecting model
    [Info] Finished projecting model
    
    

serialized_final_model help (text/plain)

<SerializedModel xmlns="http://openmodeller.cria.org.br/xml/2.0">
<Sampler>
<Environment NumLayers="8">
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<Map Id="/layers/en/terrestrial/climate/global/worldclim/present/bioclim/10arc-minutes/754f52e2-04da-11e1-be50-0800200c9a66" IsCategorical="0" Max="4024" Min="0" />
<Map Id="/layers/en/terrestrial/climate/global/worldclim/present/bioclim/10arc-minutes/754f52e3-04da-11e1-be50-0800200c9a66" IsCategorical="0" Max="3999" Min="0" />
<Map Id="/layers/en/terrestrial/climate/global/worldclim/present/bioclim/10arc-minutes/bf441530-04d9-11e1-be50-0800200c9a66" IsCategorical="0" Max="211" Min="9" />
<Map Id="/layers/en/terrestrial/climate/global/worldclim/present/bioclim/10arc-minutes/cbea74a0-04d9-11e1-be50-0800200c9a66" IsCategorical="0" Max="95" Min="8" />
<Map Id="/layers/en/terrestrial/climate/global/worldclim/present/bioclim/10arc-minutes/f6e877b1-04d9-11e1-be50-0800200c9a66" IsCategorical="0" Max="375" Min="-251" />
<Map Id="/layers/en/terrestrial/climate/global/worldclim/present/bioclim/10arc-minutes/f6e877b2-04d9-11e1-be50-0800200c9a66" IsCategorical="0" Max="364" Min="-450" />
<Map Id="/layers/en/terrestrial/topography/global/worldclim/altitude/10arc-minutes/ede38a71-16cb-11e1-be50-0800200c9a66" IsCategorical="0" Max="6241" Min="-353" />
<Mask Id="wcs&gt;http://biostif.at.biovel.eu/geoserver/ows?&gt;biovel_temp:lepus_tolai_2MAX_20170803_131216_936" /></Environment>
<Presence Count="13" Label="Lepus tolai">
<CoordinateSystem>GEOGCS["WGS84", DATUM["WGS84", SPHEROID["WGS84", 6378137.0, 298.257223563]], PRIMEM["Greenwich", 0.0], UNIT["degree", 0.017453292519943295], AXIS["Longitude",EAST], AXIS["Latitude",NORTH]]</CoordinateSystem>
<Point Id="154" Sample="76 85 221 87 33 145 230 -8" X="52.681" Y="36.659" />
<Point Id="155" Sample="18 18 105 116 36 86 277 5" X="54.709" Y="37.44" />
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<Point Id="157" Sample="45 45 142 99 34 142 262 -28" X="53.72" Y="36.879" />
<Point Id="158" Sample="0 0 52 143 34 99 277 175" X="62.983" Y="39.336" />
<Point Id="159" Sample="22 22 97 110 34 84 274 -12" X="54.368" Y="37.369" />
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<Point Id="166" Sample="47 47 145 102 35 141 262 120" X="53.983" Y="36.783" /></Presence></Sampler>
<Algorithm Id="SVM" Version="0.5">
<Parameters>
<Parameter Id="C" Value="1" />
<Parameter Id="Coef0" Value="0" />
<Parameter Id="Degree" Value="3" />
<Parameter Id="Gamma" Value="0" />
<Parameter Id="KernelType" Value="2" />
<Parameter Id="Nu" Value="0.5" />
<Parameter Id="NumberOfPseudoAbsences" Value="0" />
<Parameter Id="ProbabilisticOutput" Value="1" />
<Parameter Id="SvmType" Value="0" /></Parameters>
<Normalization Class="MeanVarianceNormalizer" Mean="44.46153846153845989874753 104.7692307692307736033399 117.9230769230769197974951 107.8461538461538395949901 34.84615384615384670041749 131.0384615384615472066798 151.6923076923076791899803 455.1923076923076791899803" StdDev="35.79299458746727680136246 103.3496231990451690307964 94.35376964464029470036621 23.50777285527883719851161 12.2725459712068136752805 57.98653689899460061951686 163.2077863904217451818113 997.2747272133499336632667" />
<Model>
<Svm C="1" Coef0="0" Degree="3" Gamma="0.125" KernelType="2" Labels="-1 1" NrSv="8 5" NumLayers="8" ProbA="-2.704072743002277956492208" ProbB="-0.4431068193201365690292448" Probabilistic="1" Rho="-0.7461561792918429691923166" Type="0">
<Vectors Total="13">
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<Statistics>
<ConfusionMatrix Accuracy="100" CommissionError="-100" FalseNegatives="0" FalsePositives="0" OmissionError="0" Threshold="0.5" TrueNegatives="0" TruePositives="13" />
<RocCurve Auc="0.9911230769230769954702964" NumBackgroundPoints="10000" Points="0 0 0 0 0.0002999999999999999737189393 0.3076923076923077093880465 0.008899999999999999925059946 0.8461538461538461453059767 0.02740000000000000074384943 0.8461538461538461453059767 0.05519999999999999906741266 1 0.07760000000000000230926389 1 0.09039999999999999424904473 1 0.1072000000000000036193271 1 0.1228000000000000063726802 1 0.1391999999999999904076731 1 0.1516000000000000125233157 1 0.1703000000000000069277917 1 0.1981999999999999872990486 1 0.3247999999999999776179038 1 1 1" /></Statistics></SerializedModel>

xval_create_model_log help ((list of depth 1))

  1. (text/plain)

    [Info] Creating model
    [Warn] SvmAlgorithm: No absence points available.
    [Warn] SvmAlgorithm: Number of pseudo absences will be 10 (same number of presences).
    [Info] SvmAlgorithm: Generating pseudo-absences.
    [Info] Finished creating model  
    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    
    

  2. (text/plain)

    [Info] Creating model
    [Warn] SvmAlgorithm: No absence points available.
    [Warn] SvmAlgorithm: Number of pseudo absences will be 10 (same number of presences).
    [Info] SvmAlgorithm: Generating pseudo-absences.
    [Info] Finished creating model  
    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    
    

  3. (text/plain)

    [Info] Creating model
    [Warn] SvmAlgorithm: No absence points available.
    [Warn] SvmAlgorithm: Number of pseudo absences will be 10 (same number of presences).
    [Info] SvmAlgorithm: Generating pseudo-absences.
    [Info] Finished creating model  
    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    
    

  4. (text/plain)

    [Info] Creating model
    [Warn] SvmAlgorithm: No absence points available.
    [Warn] SvmAlgorithm: Number of pseudo absences will be 11 (same number of presences).
    [Info] SvmAlgorithm: Generating pseudo-absences.
    [Info] Finished creating model  
    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    
    

  5. (text/plain)

    [Info] Creating model
    [Warn] SvmAlgorithm: No absence points available.
    [Warn] SvmAlgorithm: Number of pseudo absences will be 11 (same number of presences).
    [Info] SvmAlgorithm: Generating pseudo-absences.
    [Info] Finished creating model  
    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    
    

xval_test_model_log help ((list of depth 1))

  1. (text/plain)

    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    [Warn] No absence points - commission error won't be calculated
    [Info] 
    Model statistics
    [Info] Accuracy:           100.00%
    [Info] Omission error:       0.00% (0/3)
    [Info] AUC:                  0.99
    
    

  2. (text/plain)

    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    [Warn] No absence points - commission error won't be calculated
    [Info] 
    Model statistics
    [Info] Accuracy:            66.67%
    [Info] Omission error:      33.33% (1/3)
    [Info] AUC:                  0.98
    
    

  3. (text/plain)

    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    [Warn] No absence points - commission error won't be calculated
    [Info] 
    Model statistics
    [Info] Accuracy:           100.00%
    [Info] Omission error:       0.00% (0/3)
    [Info] AUC:                  1.00
    
    

  4. (text/plain)

    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    [Warn] No absence points - commission error won't be calculated
    [Info] 
    Model statistics
    [Info] Accuracy:           100.00%
    [Info] Omission error:       0.00% (0/2)
    [Info] AUC:                  1.00
    
    

  5. (text/plain)

    [Info] Calculating ROC curve
    [Info] Generating 10000 background points
    [Warn] No absence points - commission error won't be calculated
    [Info] 
    Model statistics
    [Info] Accuracy:            50.00%
    [Info] Omission error:      50.00% (1/2)
    [Info] AUC:                  0.97
    
    

xval_test_model_statistics help ((list of depth 1))

  1. (text/plain)

    <Statistics xmlns="http://openmodeller.cria.org.br/xml/2.0">
    <ConfusionMatrix Accuracy="100" CommissionError="-100" FalseNegatives="0" FalsePositives="0" OmissionError="0" Threshold="0.5688100000000000378008735" TrueNegatives="0" TruePositives="3" />
    <RocCurve Auc="0.9922499999999999653610416" NumBackgroundPoints="10000" Points="0 0 0 0 0 0 0.002799999999999999971550535 0.6666666666666666296592325 0.01519999999999999996946887 0.6666666666666666296592325 0.02570000000000000062172489 1 0.03590000000000000135447209 1 0.04299999999999999655830862 1 0.05040000000000000035527137 1 0.05770000000000000128785871 1 0.06729999999999999871214129 1 0.07969999999999999307220833 1 0.09529999999999999582556143 1 0.1418999999999999983568699 1 0.6947999999999999731770117 1 1 1" /></Statistics>

  2. (text/plain)

    <Statistics xmlns="http://openmodeller.cria.org.br/xml/2.0">
    <ConfusionMatrix Accuracy="66.66666666666665719276352" CommissionError="-100" FalseNegatives="0" FalsePositives="1" OmissionError="33.33333333333332859638176" Threshold="0.7699899999999999522515282" TrueNegatives="0" TruePositives="2" />
    <RocCurve Auc="0.9849833333333334328685282" NumBackgroundPoints="10000" Points="0 0 0 0 0.001199999999999999894875757 0.6666666666666666296592325 0.01959999999999999936717288 0.6666666666666666296592325 0.03699999999999999816813201 0.6666666666666666296592325 0.05070000000000000200950367 1 0.0627999999999999947153384 1 0.07320000000000000117683641 1 0.08659999999999999642508186 1 0.09729999999999999760191827 1 0.1103999999999999981348253 1 0.1247000000000000052846616 1 0.144400000000000000577316 1 0.1743999999999999994670929 1 0.2805000000000000270894418 1 1 1" /></Statistics>

  3. (text/plain)

    <Statistics xmlns="http://openmodeller.cria.org.br/xml/2.0">
    <ConfusionMatrix Accuracy="100" CommissionError="-100" FalseNegatives="0" FalsePositives="0" OmissionError="0" Threshold="0.8041899999999999604227696" TrueNegatives="0" TruePositives="3" />
    <RocCurve Auc="0.9990499999999999936051154" NumBackgroundPoints="10000" Points="0 0 0 0 0.001899999999999999996183608 1 0.02560000000000000122679644 1 0.03860000000000000236477504 1 0.05070000000000000200950367 1 0.06169999999999999790167848 1 0.07340000000000000690558721 1 0.08269999999999999573674359 1 0.09170000000000000373034936 1 0.1033000000000000029309888 1 0.1165999999999999953148588 1 0.1363999999999999934718886 1 0.1663999999999999923616656 1 0.3588999999999999968025577 1 1 1" /></Statistics>

  4. (text/plain)

    <Statistics xmlns="http://openmodeller.cria.org.br/xml/2.0">
    <ConfusionMatrix Accuracy="100" CommissionError="-100" FalseNegatives="0" FalsePositives="0" OmissionError="0" Threshold="0.7252699999999999702637865" TrueNegatives="0" TruePositives="2" />
    <RocCurve Auc="0.9989500000000000046185278" NumBackgroundPoints="10000" Points="0 0 0 0 0.0004000000000000000191686944 0 0.001699999999999999905284098 1 0.006799999999999999621136393 1 0.01420000000000000081601392 1 0.02500000000000000138777878 1 0.04039999999999999841238107 1 0.05279999999999999971134201 1 0.06079999999999999987787547 1 0.07000000000000000666133815 1 0.08129999999999999726885136 1 0.1044000000000000066835426 1 0.1678000000000000047073456 1 0.5110000000000000097699626 1 1 1" /></Statistics>

  5. (text/plain)

    <Statistics xmlns="http://openmodeller.cria.org.br/xml/2.0">
    <ConfusionMatrix Accuracy="50" CommissionError="-100" FalseNegatives="0" FalsePositives="1" OmissionError="50" Threshold="0.6799300000000000343547413" TrueNegatives="0" TruePositives="1" />
    <RocCurve Auc="0.969849999999999989874766" NumBackgroundPoints="10000" Points="0 0 0 0 0 0 0.001399999999999999985775267 0.5 0.007199999999999999802935413 0.5 0.0156999999999999986788346 0.5 0.03030000000000000054400928 0.5 0.04329999999999999821254093 0.5 0.05539999999999999785726956 0.5 0.06379999999999999560351682 1 0.07689999999999999613642387 1 0.0937999999999999944932938 1 0.1255999999999999894306768 1 0.197399999999999992139621 1 0.6946999999999999841904241 1 1 1" /></Statistics>

xval_threshold ((list of depth 1))

  1. (text/plain)

    0.56881

  2. (text/plain)

    0.76999

  3. (text/plain)

    0.80419

  4. (text/plain)

    0.72527

  5. (text/plain)

    0.67993

Errors/Logs (0)

None

Inputs

Data (2)

input_points help

occurrenceID,Clade,nameComplete,decimalLongitude,decimalLatitude
154,C,Lepus tolai,52.681,36.659 
155,C,Lepus tolai,54.709,37.440 
156,C,Lepus tolai,54.344,37.005
157,C,Lepus tolai,53.720,36.879 
158,C,Lepus tolai,62.983,39.336 
159,C,Lepus tolai,54.368,37.369 
160,C,Lepus tolai,54.323,37.778 
161,C,Lepus tolai,54.091,36.806 
162,C,Lepus tolai,55.936,37.945 
163,C,Lepus tolai,55.100,37.380 
164,C,Lepus tolai,55.039,37.122 
165,C,Lepus tolai,55.175,37.943 
166,C,Lepus tolai,53.983,36.783

use_biostif_layers help

yes

Parameters (0)

None

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BioVeL has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 283359.

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