confu_mat_optim: Function to find the cut-off threshold that optimizes the...

In luismurao/nichetoolbox: From getting biodiversity data to evaluating species distribution models in a friendly GUI environment

Description

The function finds out which is the best cut-off threshold that optimizes the confusion matrix based on Kappa or TSS

Usage

confu_mat_optim(sdm_raster, valData, longitude, latitude, pres_aus,
  optim_by = "kappa", th_range = c(0, 1), step = 0.005)

Arguments

valData	A data.frame or a matrix with validation data. The data must contain ongitude, latitude and a column of presences (1) and absences (0).
longitude	Column name of the longitude data
latitude	Column name of the latitude data
pres_aus	Column name of presences and absences. The presences have to represented by 1 and the absences with 0.
optim_by	The optimation should be by kappa (Kappa) metric or by tss (TSS) metric.
th_range	A vector with the minimum and max range of threshold values used in the searching process.
step	A numeric value representing the step size to be used in the searching process.
prediction	SDM predicition raster

Value

Returns a data.frame with the values of: confusion matrix, kappa, tss, prevalence, specificity, sensibility,correct classification rate (correct_class_rate), miss classification rate (miss_cla_rate), positive predictive power (posit_pre_pow), negative predictive power (nega_pre_pow), comission error (comission_error) omission error (omission_error).

luismurao/nichetoolbox documentation built on May 21, 2019, 8:56 a.m.