biomod2 (version 3.5.1)

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

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)

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

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

Author

Damien Georges

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.

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)