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I am trying to predict species presence or absence using randomForest in R (classification). In fact, I am trying to do it for several species, in separate models.

For a couple of the species, the training data are quite unbalanced e.g., 70 observations of species presence, and and 6500 observations of species absence.

This is my code: 

#read in data frame containing observations of species presence/absence and predictor     variables
mydata <- read.csv('mydata.csv')

#fit random forests model
fitmodelA <- randomForest(SPECIESA ~ var1 + var2 + var3 + var4 + var5 +var6 + var7 +   var8 + var9 + var10, data=mydata, mytry=3, ntrees=500, replace=TRUE, importance=TRUE,   keep.forest=TRUE)

#predict to new data
predictmodel <- predict(fitmodelA, newdata, type="prob")

In the output prediction, almost the entire study area is predicted with prob > 0.7. I take this to be predictions of species occurrence? or is it the probability of species absence?

I want to try to balance the data by forcing the model to select equal sample sizes from observations of presence and absence, e.g., adding the argument 

sampsize(70,70)

But I get the error message "Error in if (ncol(x) != ncol(xtest)) stop("x and xtest must have same number of columns")"

What am I doing wrong here?

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you probably want 

sampsize(c(70,70))

You can also play with class weights which influence the gini impurity function for picking splits. Check out this paper

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  • $\begingroup$ Thank you Andrew, your suggestion worked. I have also seen examples that use the term "rep" in the sampsize argument. Any idea of how this works? $\endgroup$
    – sth
    Commented Mar 17, 2014 at 22:26
  • $\begingroup$ rep(70, 2) = [70, 70] which is the same as c(70, 70). Type ?rep to read about the function $\endgroup$
    – Andrew Cassidy
    Commented Mar 17, 2014 at 22:50
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    $\begingroup$ I used the argument sampsize=(c(70,70)) and while I don't get an error message, it doesn't appear to be working, or I don't understand what is going on behind the scenes. The confusion matrix that is output displays the predictions and class error for the full, unbalanced sample size, not the number that I specified. I tried adding the argument strata="mydata$SPECIESA" in order to make sure it knew what variable to sample from, but that does not seem to make a difference. Do you have any idea what could be going wrong? $\endgroup$
    – sth
    Commented Jul 17, 2014 at 22:48
  • $\begingroup$ @sth the outputed confusion matrix should be the full unbalanced sample size. The sampsize argument is used on a "per-tree" basis. I admit that the outputed confusion matrix is particularly confusing. The sampsize argument says for each tree in the forest sample 70 of class 1 and 70 of class 2 (with replacement by default) and then split this data into a training and testing set. So each tree has a training and testing set. Can you elaborate on anything else that is specifically wrong besides the full confusion matrix. I would potentially open a new question so I can post code as well. $\endgroup$
    – Andrew Cassidy
    Commented Jul 19, 2014 at 19:53
  • $\begingroup$ it is the full confusion matrix that confused me! Your explanation makes sense though - thank you very much! $\endgroup$
    – sth
    Commented Jul 21, 2014 at 19:58

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