User Tools

Site Tools


wiki:kappar

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

wiki:kappar [2017/12/05 22:53] (current)
Line 1: Line 1:
 +====== ​ Plotting a confusion matrix and calculate kappa statistics ======
  
 +==== generate simulated data ====
 +<code r>
 +library(PresenceAbsence)
 +     ​set.seed(666)
 +     ​N=1000
 +N
 +     ​SIMDATA<​-matrix(0,​N,​3)
 +str(SIMDATA)
 +     ​SIMDATA<​-as.data.frame(SIMDATA)
 +str(SIMDATA)
 +     ​names(SIMDATA)<​-c("​plotID","​Observed","​Predicted"​)
 +     ​SIMDATA$plotID<​-1:​N
 +str(SIMDATA)
 +     ​SIMDATA$Observed<​-rbinom(n=N,​size=1,​prob=.2)
 +str(SIMDATA)
 +     ​SIMDATA$Predicted[SIMDATA$Observed==1]<​-rnorm(n=length(SIMDATA$Observed[SIMDATA$Observed==1]),​mean=.8,​sd=.15)
 +     ​SIMDATA$Predicted[SIMDATA$Observed==0]<​-rnorm(n=length(SIMDATA$Observed[SIMDATA$Observed==0]),​mean=.2,​sd=.15)
 +     ​SIMDATA$Predicted<​-(SIMDATA$Predicted-min(SIMDATA$Predicted))/​(max(SIMDATA$Predicted)-min(SIMDATA$Predicted))
 +
 +     ### plot simulated data
 +     ​hist(SIMDATA$Predicted,​100)
 +     ​hist(SIMDATA$Observed,​100)
 +     ### calculate confusion matrix ###
 +     ​confusion.matrix=cmx(SIMDATA)
 +     ​Kappa(confusion.matrix,​ st.dev = TRUE)
 +
 +data(SIM3DATA)
 +
 +     ​cmx(SIM3DATA)
 +     ​cmx(SIM3DATA,​which.model=2)
 +     ​cmx(SIM3DATA,​which.model=3,​threshold=.2)
 +
 +</​code>​
wiki/kappar.txt ยท Last modified: 2017/12/05 22:53 (external edit)