Find.Optim.Stat: Calculate the best score according to a given evaluation...

In biomod2: Ensemble Platform for Species Distribution Modeling

Description

Find.Optim.Stat is an internal biomod2 function to find the threshold to convert continuous values into binary ones leading to the best score for a given evaluation metric.

Usage

Find.Optim.Stat(Stat='TSS',
                  Fit,
                  Obs,
                  Nb.thresh.test = 100,
                  Fixed.thresh = NULL)

Arguments

Stat	either 'ROC', TSS', 'KAPPA', 'ACCURACY', 'BIAS', 'POD', 'FAR', 'POFD', 'SR', 'CSI', 'ETS', 'HK', 'HSS', 'OR' or 'ORSS'
Fit	vector of fitted values (continuous)
Obs	vector of observed values (binary)
Nb.thresh.test	integer, the numer of thresholds tested over the range of fitted value
Fixed.thresh	integer, if not NULL, the only threshold value tested

Details

Please refer to BIOMOD_Modeling to get more information about this metrics. If you give a Fixed.thresh, no optimisation will be done. Only the score for this threshold will be returned.

Value

A 1 row x 4 column matrix :

• best.iter: the best score obtained for chosen statistic

• cutoff: the associated cut-off used for transform fitted vector into binary

• sensibility: the sensibility with this threshold

• specificity: the specificity with this threshold

Author(s)

Damien Georges

See Also

BIOMOD_Modeling, getStatOptimValue, calculate.stat

Examples

  a <- sample(c(0,1),100, replace=TRUE)
                
  ##' random drawing
  b <- runif(100,min=0,max=1000)
  Find.Optim.Stat(Stat='TSS',
                  Fit=b,
                  Obs=a)
                
  ##' biased drawing
  BiasedDrawing <- function(x, m1=300, sd1=200, m2=700, sd2=200){
    return(ifelse(x<0.5, rnorm(1,m1,sd1), rnorm(1,m2,sd2)))
  }
                
  c <- sapply(a,BiasedDrawing)
                
  Find.Optim.Stat(Stat='TSS',
                  Fit=c,
                  Obs=a,
                  Nb.thresh.test = 100)  
                
                

Example output

Loading required package: sp
Loading required package: raster
Loading required package: parallel
Loading required package: reshape
Loading required package: ggplot2
biomod2 3.3-7 loaded.

Type browseVignettes(package='biomod2') to access directly biomod2 vignettes.
    best.stat cutoff sensitivity specificity
TSS 0.1502463    703    35.71429    79.31034
    best.stat cutoff sensitivity specificity
TSS 0.8489327    470     95.2381    89.65517

biomod2 documentation built on May 2, 2019, 5:08 p.m.