predict_sdm.md
In caretSDM: Build Species Distribution Modeling using 'caret'

predict_sdm

Code
  p
Output
              caretSDM           
  ...............................
  Class                         : input_sdm
  --------  Occurrences  --------
  Species Names                 : Araucaria angustifolia 
  Number of presences           : 420 
  Pseudoabsence methods         :
      Method to obtain PAs      : random 
      Number of PA sets         : 3 
      Number of PAs in each set : 420 
  --------  Predictors  ---------
  Number of Predictors          : 2 
  Predictors Names              : bio1, bio12 
  ---------  Scenarios  ---------
  Number of Scenarios           : 1 
  Scenarios Names               : current 
  -----------  Models  ----------
  Algorithms Names              : naive_bayes kknn 
  Variables Names               : bio1 bio12 
  Model Validation              :
      Method                    : cv 
      Number                    : 2 
      Metrics                   :
  $`Araucaria angustifolia`
           algo       ROC      Sens       Spec      ROCSD
  1        kknn 0.6025314 0.9865079 0.03333333 0.14949089
  2 naive_bayes 0.8488211 0.9706349 0.43055556 0.06122881

  --------  Predictions  --------
  Ensembles                     :
      Scenarios                 : current 
      Methods                   : mean_occ_prob wmean_AUC committee_avg 
  Thresholds                    :
      Method                    : threshold 
      Criteria                  : 0.5

Code
  p$predictions
Output
           caretSDM        
  .........................
  Class             : Predictions
  Ensembles         :
           Methods  : mean_occ_prob wmean_AUC committee_avg 
  Thresholds        :
           Method   : threshold 
           Criteria : 0.5 
           Metrics  :
  $`Araucaria angustifolia`
              algo       ROC      Sens       Spec      ROCSD      SensSD
  m1.2        kknn 0.5214286 0.9761905 0.06666667 0.03030458 0.033671751
  m2.2        kknn 0.6622768 0.9952381 0.00000000 0.23622838 0.006734350
  m3.2        kknn 0.6238889 0.9880952 0.03333333 0.18193970 0.003367175
  m1.1 naive_bayes 0.8760020 0.9714286 0.42083333 0.05907989 0.026937401
  m2.1 naive_bayes 0.8547569 0.9738095 0.45208333 0.02506441 0.016835876
  m3.1 naive_bayes 0.8157044 0.9666667 0.41875000 0.09954212 0.090913729
           SpecSD
  m1.2 0.09428090
  m2.2 0.00000000
  m3.2 0.04714045
  m1.1 0.15026019
  m2.1 0.15026019
  m3.1 0.07954951

predict_sdm - th 0

Code
  p
Output
              caretSDM           
  ...............................
  Class                         : input_sdm
  --------  Occurrences  --------
  Species Names                 : Araucaria angustifolia 
  Number of presences           : 420 
  Pseudoabsence methods         :
      Method to obtain PAs      : random 
      Number of PA sets         : 3 
      Number of PAs in each set : 420 
  --------  Predictors  ---------
  Number of Predictors          : 2 
  Predictors Names              : bio1, bio12 
  ---------  Scenarios  ---------
  Number of Scenarios           : 1 
  Scenarios Names               : current 
  -----------  Models  ----------
  Algorithms Names              : naive_bayes kknn 
  Variables Names               : bio1 bio12 
  Model Validation              :
      Method                    : cv 
      Number                    : 2 
      Metrics                   :
  $`Araucaria angustifolia`
           algo       ROC      Sens       Spec      ROCSD
  1        kknn 0.6025314 0.9865079 0.03333333 0.14949089
  2 naive_bayes 0.8488211 0.9706349 0.43055556 0.06122881

  --------  Predictions  --------
  Ensembles                     :
      Scenarios                 : current 
      Methods                   : mean_occ_prob wmean_AUC committee_avg 
  Thresholds                    :
      Method                    : threshold 
      Criteria                  : 0

Code
  p$predictions
Output
           caretSDM        
  .........................
  Class             : Predictions
  Ensembles         :
           Methods  : mean_occ_prob wmean_AUC committee_avg 
  Thresholds        :
           Method   : threshold 
           Criteria : 0 
           Metrics  :
  $`Araucaria angustifolia`
              algo       ROC      Sens       Spec      ROCSD      SensSD
  m1.2        kknn 0.5214286 0.9761905 0.06666667 0.03030458 0.033671751
  m2.2        kknn 0.6622768 0.9952381 0.00000000 0.23622838 0.006734350
  m3.2        kknn 0.6238889 0.9880952 0.03333333 0.18193970 0.003367175
  m1.1 naive_bayes 0.8760020 0.9714286 0.42083333 0.05907989 0.026937401
  m2.1 naive_bayes 0.8547569 0.9738095 0.45208333 0.02506441 0.016835876
  m3.1 naive_bayes 0.8157044 0.9666667 0.41875000 0.09954212 0.090913729
           SpecSD
  m1.2 0.09428090
  m2.2 0.00000000
  m3.2 0.04714045
  m1.1 0.15026019
  m2.1 0.15026019
  m3.1 0.07954951

predict_sdm - th function

Code
  p
Output
              caretSDM           
  ...............................
  Class                         : input_sdm
  --------  Occurrences  --------
  Species Names                 : Araucaria angustifolia 
  Number of presences           : 420 
  Pseudoabsence methods         :
      Method to obtain PAs      : random 
      Number of PA sets         : 3 
      Number of PAs in each set : 420 
  --------  Predictors  ---------
  Number of Predictors          : 2 
  Predictors Names              : bio1, bio12 
  ---------  Scenarios  ---------
  Number of Scenarios           : 1 
  Scenarios Names               : current 
  -----------  Models  ----------
  Algorithms Names              : naive_bayes kknn 
  Variables Names               : bio1 bio12 
  Model Validation              :
      Method                    : cv 
      Number                    : 2 
      Metrics                   :
  $`Araucaria angustifolia`
           algo       ROC      Sens       Spec      ROCSD
  1        kknn 0.6025314 0.9865079 0.03333333 0.14949089
  2 naive_bayes 0.8488211 0.9706349 0.43055556 0.06122881

  --------  Predictions  --------
  Ensembles                     :
      Scenarios                 : current 
      Methods                   : mean_occ_prob wmean_AUC committee_avg 
  Thresholds                    :
      Method                    : function (x, ...)  UseMethod("mean") 
      Criteria                  : function (x, ...)  UseMethod("mean")

Code
  p$predictions
Output
           caretSDM        
  .........................
  Class             : Predictions
  Ensembles         :
           Methods  : mean_occ_prob wmean_AUC committee_avg 
  Thresholds        :
           Method   : function (x, ...)  UseMethod("mean") 
           Criteria : function (x, ...)  UseMethod("mean") 
           Metrics  :
  $`Araucaria angustifolia`
              algo       ROC      Sens      Spec      ROCSD     SensSD     SpecSD
  m1.1 naive_bayes 0.8760020 0.9714286 0.4208333 0.05907989 0.02693740 0.15026019
  m2.1 naive_bayes 0.8547569 0.9738095 0.4520833 0.02506441 0.01683588 0.15026019
  m3.1 naive_bayes 0.8157044 0.9666667 0.4187500 0.09954212 0.09091373 0.07954951

add_input_sdm

Code
  p1
Output
          caretSDM       
  .......................
  Class                 : occurrences
  Species Names         : Araucaria angustifolia Salminus brasiliensis 
  Number of presences   : 420 46 
  ========================================
  Data:
  Simple feature collection with 6 features and 2 fields
  Geometry type: POINT
  Dimension:     XY
  Bounding box:  xmin: -5263273 ymin: -3156734 xmax: -5002956 ymax: -2830253
  Projected CRS: WGS 84 / NSIDC EASE-Grid 2.0 Global
    cell_id               species                  geometry
  1      17 Salminus brasiliensis POINT (-5002956 -3034581)
  2      16 Salminus brasiliensis POINT (-5123570 -3049429)
  3       2 Salminus brasiliensis POINT (-5138591 -2830253)
  4      22 Salminus brasiliensis POINT (-5263273 -3143263)
  5      23 Salminus brasiliensis POINT (-5172118 -3156734)
  6      23 Salminus brasiliensis POINT (-5172118 -3156734)

Code
  p2
Output
            caretSDM         
  ...........................
  Class                     : sdm_area
  Extent                    : -5301744 -3295037 -4601744 -2795037 (xmin, xmax, ymin, ymax)
  CRS                       : WGS 84 / NSIDC EASE- 
  Resolution                : (1e+05, 1e+05) (x, y)
  Number of Predictors      : 2 
  Predictors Names          : bio1, bio12

Code
  p3
Output
            caretSDM         
  ...........................
  Class                     : sdm_area
  Extent                    : -5301744 -3295037 -4601744 -2795037 (xmin, xmax, ymin, ymax)
  CRS                       : WGS 84 / NSIDC EASE- 
  Resolution                : (1e+05, 1e+05) (x, y)
  Number of Predictors      : 2 
  Predictors Names          : bio1, bio12

Code
  p4
Output
           caretSDM        
  .........................
  Class                   : Models
  Algorithms Names        : naive_bayes 
  Variables Names         : bio1 bio12 
  Model Validation        :
           Method          : boot 
           Number          : 1 
           Metrics         :
  $`Salminus brasiliensis`
              algo       ROC        TSS Sensitivity Specificity Pos Pred Value
  m1.1 naive_bayes 0.5666667 0.07222222         0.9       0.222          0.708
  m2.1 naive_bayes 0.6269841 0.44444444         1.0       0.444          0.737
       Neg Pred Value Precision Recall    F1 Prevalence Detection Rate
  m1.1            0.4     0.708    0.9 0.783      0.690          0.621
  m2.1            1.0     0.737    1.0 0.848      0.609          0.609
       Detection Prevalence Balanced Accuracy Accuracy Kappa AccuracyLower
  m1.1                0.897             0.536    0.655 0.082         0.457
  m2.1                0.913             0.722    0.783 0.493         0.563
       AccuracyUpper AccuracyNull AccuracyPValue McnemarPValue Positive Negative
  m1.1         0.821        0.690          0.732         0.343       20        9
  m2.1         0.925        0.609          0.264         0.074       14        9
       True Positive False Positive True Negative False Negative ROCSD TSSSD
  m1.1            18              3             2              8    NA    NA
  m2.1            14              0             4              7    NA    NA
       SensitivitySD SpecificitySD Pos Pred ValueSD Neg Pred ValueSD PrecisionSD
  m1.1            NA            NA               NA               NA          NA
  m2.1            NA            NA               NA               NA          NA
       RecallSD F1SD PrevalenceSD Detection RateSD Detection PrevalenceSD
  m1.1       NA   NA           NA               NA                     NA
  m2.1       NA   NA           NA               NA                     NA
       Balanced AccuracySD AccuracySD KappaSD AccuracyLowerSD AccuracyUpperSD
  m1.1                  NA         NA      NA              NA              NA
  m2.1                  NA         NA      NA              NA              NA
       AccuracyNullSD AccuracyPValueSD McnemarPValueSD PositiveSD NegativeSD
  m1.1             NA               NA              NA         NA         NA
  m2.1             NA               NA              NA         NA         NA
       True PositiveSD False PositiveSD True NegativeSD False NegativeSD
  m1.1              NA               NA              NA               NA
  m2.1              NA               NA              NA               NA

  $`Araucaria angustifolia`
              algo       ROC       TSS Sensitivity Specificity Pos Pred Value
  m1.1 naive_bayes 0.8763975 0.4937888       0.994       0.500          0.970
  m2.1 naive_bayes 0.8222934 0.5106838       0.955       0.556          0.974
       Neg Pred Value Precision Recall    F1 Prevalence Detection Rate
  m1.1          0.833     0.970  0.994 0.982      0.942          0.936
  m2.1          0.417     0.974  0.955 0.964      0.945          0.903
       Detection Prevalence Balanced Accuracy Accuracy Kappa AccuracyLower
  m1.1                0.965             0.747    0.965 0.608         0.925
  m2.1                0.933             0.755    0.933 0.441         0.884
       AccuracyUpper AccuracyNull AccuracyPValue McnemarPValue Positive Negative
  m1.1         0.987        0.942          0.326         0.724      161       10
  m2.1         0.966        0.945          0.882         0.773      156        9
       True Positive False Positive True Negative False Negative ROCSD TSSSD
  m1.1           160              3             5              5    NA    NA
  m2.1           149              7             5              5    NA    NA
       SensitivitySD SpecificitySD Pos Pred ValueSD Neg Pred ValueSD PrecisionSD
  m1.1            NA            NA               NA               NA          NA
  m2.1            NA            NA               NA               NA          NA
       RecallSD F1SD PrevalenceSD Detection RateSD Detection PrevalenceSD
  m1.1       NA   NA           NA               NA                     NA
  m2.1       NA   NA           NA               NA                     NA
       Balanced AccuracySD AccuracySD KappaSD AccuracyLowerSD AccuracyUpperSD
  m1.1                  NA         NA      NA              NA              NA
  m2.1                  NA         NA      NA              NA              NA
       AccuracyNullSD AccuracyPValueSD McnemarPValueSD PositiveSD NegativeSD
  m1.1             NA               NA              NA         NA         NA
  m2.1             NA               NA              NA         NA         NA
       True PositiveSD False PositiveSD True NegativeSD False NegativeSD
  m1.1              NA               NA              NA               NA
  m2.1              NA               NA              NA               NA

Code
  p5
Output
           caretSDM        
  .........................
  Class             : Predictions
  Ensembles         :
           Methods  : mean_occ_prob wmean_AUC committee_avg 
  Thresholds        :
           Method   : threshold 
           Criteria : 0.5 0.6 
           Metrics  :
  $`Salminus brasiliensis`
              algo       ROC        TSS Sensitivity Specificity Pos Pred Value
  m1.1 naive_bayes 0.5666667 0.07222222         0.9       0.222          0.708
  m2.1 naive_bayes 0.6269841 0.44444444         1.0       0.444          0.737
       Neg Pred Value Precision Recall    F1 Prevalence Detection Rate
  m1.1            0.4     0.708    0.9 0.783      0.690          0.621
  m2.1            1.0     0.737    1.0 0.848      0.609          0.609
       Detection Prevalence Balanced Accuracy Accuracy Kappa AccuracyLower
  m1.1                0.897             0.536    0.655 0.082         0.457
  m2.1                0.913             0.722    0.783 0.493         0.563
       AccuracyUpper AccuracyNull AccuracyPValue McnemarPValue Positive Negative
  m1.1         0.821        0.690          0.732         0.343       20        9
  m2.1         0.925        0.609          0.264         0.074       14        9
       True Positive False Positive True Negative False Negative ROCSD TSSSD
  m1.1            18              3             2              8    NA    NA
  m2.1            14              0             4              7    NA    NA
       SensitivitySD SpecificitySD Pos Pred ValueSD Neg Pred ValueSD PrecisionSD
  m1.1            NA            NA               NA               NA          NA
  m2.1            NA            NA               NA               NA          NA
       RecallSD F1SD PrevalenceSD Detection RateSD Detection PrevalenceSD
  m1.1       NA   NA           NA               NA                     NA
  m2.1       NA   NA           NA               NA                     NA
       Balanced AccuracySD AccuracySD KappaSD AccuracyLowerSD AccuracyUpperSD
  m1.1                  NA         NA      NA              NA              NA
  m2.1                  NA         NA      NA              NA              NA
       AccuracyNullSD AccuracyPValueSD McnemarPValueSD PositiveSD NegativeSD
  m1.1             NA               NA              NA         NA         NA
  m2.1             NA               NA              NA         NA         NA
       True PositiveSD False PositiveSD True NegativeSD False NegativeSD
  m1.1              NA               NA              NA               NA
  m2.1              NA               NA              NA               NA

  $`Araucaria angustifolia`
              algo       ROC       TSS Sensitivity Specificity Pos Pred Value
  m1.1 naive_bayes 0.8763975 0.4937888       0.994       0.500          0.970
  m2.1 naive_bayes 0.8222934 0.5106838       0.955       0.556          0.974
       Neg Pred Value Precision Recall    F1 Prevalence Detection Rate
  m1.1          0.833     0.970  0.994 0.982      0.942          0.936
  m2.1          0.417     0.974  0.955 0.964      0.945          0.903
       Detection Prevalence Balanced Accuracy Accuracy Kappa AccuracyLower
  m1.1                0.965             0.747    0.965 0.608         0.925
  m2.1                0.933             0.755    0.933 0.441         0.884
       AccuracyUpper AccuracyNull AccuracyPValue McnemarPValue Positive Negative
  m1.1         0.987        0.942          0.326         0.724      161       10
  m2.1         0.966        0.945          0.882         0.773      156        9
       True Positive False Positive True Negative False Negative ROCSD TSSSD
  m1.1           160              3             5              5    NA    NA
  m2.1           149              7             5              5    NA    NA
       SensitivitySD SpecificitySD Pos Pred ValueSD Neg Pred ValueSD PrecisionSD
  m1.1            NA            NA               NA               NA          NA
  m2.1            NA            NA               NA               NA          NA
       RecallSD F1SD PrevalenceSD Detection RateSD Detection PrevalenceSD
  m1.1       NA   NA           NA               NA                     NA
  m2.1       NA   NA           NA               NA                     NA
       Balanced AccuracySD AccuracySD KappaSD AccuracyLowerSD AccuracyUpperSD
  m1.1                  NA         NA      NA              NA              NA
  m2.1                  NA         NA      NA              NA              NA
       AccuracyNullSD AccuracyPValueSD McnemarPValueSD PositiveSD NegativeSD
  m1.1             NA               NA              NA         NA         NA
  m2.1             NA               NA              NA         NA         NA
       True PositiveSD False PositiveSD True NegativeSD False NegativeSD
  m1.1              NA               NA              NA               NA
  m2.1              NA               NA              NA               NA

Code
  p6
Output
           caretSDM        
  .........................
  Class             : Predictions
  Ensembles         :
           Methods  : mean_occ_prob wmean_AUC committee_avg 
  Thresholds        :
           Method   : threshold 
           Criteria : 0.5 
           Metrics  :
  $`Salminus brasiliensis`
              algo       ROC        TSS Sensitivity Specificity Pos Pred Value
  m1.1 naive_bayes 0.5666667 0.07222222         0.9       0.222          0.708
  m2.1 naive_bayes 0.6269841 0.44444444         1.0       0.444          0.737
       Neg Pred Value Precision Recall    F1 Prevalence Detection Rate
  m1.1            0.4     0.708    0.9 0.783      0.690          0.621
  m2.1            1.0     0.737    1.0 0.848      0.609          0.609
       Detection Prevalence Balanced Accuracy Accuracy Kappa AccuracyLower
  m1.1                0.897             0.536    0.655 0.082         0.457
  m2.1                0.913             0.722    0.783 0.493         0.563
       AccuracyUpper AccuracyNull AccuracyPValue McnemarPValue Positive Negative
  m1.1         0.821        0.690          0.732         0.343       20        9
  m2.1         0.925        0.609          0.264         0.074       14        9
       True Positive False Positive True Negative False Negative ROCSD TSSSD
  m1.1            18              3             2              8    NA    NA
  m2.1            14              0             4              7    NA    NA
       SensitivitySD SpecificitySD Pos Pred ValueSD Neg Pred ValueSD PrecisionSD
  m1.1            NA            NA               NA               NA          NA
  m2.1            NA            NA               NA               NA          NA
       RecallSD F1SD PrevalenceSD Detection RateSD Detection PrevalenceSD
  m1.1       NA   NA           NA               NA                     NA
  m2.1       NA   NA           NA               NA                     NA
       Balanced AccuracySD AccuracySD KappaSD AccuracyLowerSD AccuracyUpperSD
  m1.1                  NA         NA      NA              NA              NA
  m2.1                  NA         NA      NA              NA              NA
       AccuracyNullSD AccuracyPValueSD McnemarPValueSD PositiveSD NegativeSD
  m1.1             NA               NA              NA         NA         NA
  m2.1             NA               NA              NA         NA         NA
       True PositiveSD False PositiveSD True NegativeSD False NegativeSD
  m1.1              NA               NA              NA               NA
  m2.1              NA               NA              NA               NA

Code
  p7
Output
           caretSDM        
  .........................
  Class             : Predictions
  Ensembles         :
           Methods  : mean_occ_prob wmean_AUC committee_avg 
  Thresholds        :
           Method   : threshold 
           Criteria : 0.6 
           Metrics  :
  $`Araucaria angustifolia`
              algo       ROC       TSS Sensitivity Specificity Pos Pred Value
  m1.1 naive_bayes 0.8763975 0.4937888       0.994       0.500          0.970
  m2.1 naive_bayes 0.8222934 0.5106838       0.955       0.556          0.974
       Neg Pred Value Precision Recall    F1 Prevalence Detection Rate
  m1.1          0.833     0.970  0.994 0.982      0.942          0.936
  m2.1          0.417     0.974  0.955 0.964      0.945          0.903
       Detection Prevalence Balanced Accuracy Accuracy Kappa AccuracyLower
  m1.1                0.965             0.747    0.965 0.608         0.925
  m2.1                0.933             0.755    0.933 0.441         0.884
       AccuracyUpper AccuracyNull AccuracyPValue McnemarPValue Positive Negative
  m1.1         0.987        0.942          0.326         0.724      161       10
  m2.1         0.966        0.945          0.882         0.773      156        9
       True Positive False Positive True Negative False Negative ROCSD TSSSD
  m1.1           160              3             5              5    NA    NA
  m2.1           149              7             5              5    NA    NA
       SensitivitySD SpecificitySD Pos Pred ValueSD Neg Pred ValueSD PrecisionSD
  m1.1            NA            NA               NA               NA          NA
  m2.1            NA            NA               NA               NA          NA
       RecallSD F1SD PrevalenceSD Detection RateSD Detection PrevalenceSD
  m1.1       NA   NA           NA               NA                     NA
  m2.1       NA   NA           NA               NA                     NA
       Balanced AccuracySD AccuracySD KappaSD AccuracyLowerSD AccuracyUpperSD
  m1.1                  NA         NA      NA              NA              NA
  m2.1                  NA         NA      NA              NA              NA
       AccuracyNullSD AccuracyPValueSD McnemarPValueSD PositiveSD NegativeSD
  m1.1             NA               NA              NA         NA         NA
  m2.1             NA               NA              NA         NA         NA
       True PositiveSD False PositiveSD True NegativeSD False NegativeSD
  m1.1              NA               NA              NA               NA
  m2.1              NA               NA              NA               NA