R help - Nov 2011 - problem to tunning RandomForest, an unexpected result

Dear Researches,

I am using RF (in regression way) for analize several metrics extract from
image. I am tuning RF setting a loop using different range of mtry, tree
and nodesize using the lower value of MSE-OOB

mtry from 1 to 5
nodesize from1 to 10
tree from 1 to 500

using this paper as refery

Palmer, D. S., O'Boyle, N. M., Glen, R. C., & Mitchell, J. B. O. (2007).
Random Forest Models To Predict Aqueous Solubility. Journal of Chemical
Information and Modeling, 47, 150-158.

my problem is the following using data(airquality) :

the tunning parameters with the lower value is:
> print(result.mtry.df[result.
mtry.df$RMSE == min(result.mtry.df$RMSE),])
*RMSE  = 15.44751
MSE = 238.6257
mtry = 3
nodesize = 5
tree = 35*

the numer of tree is very low, different respect how i can read in several
pubblications

And the second value lower is a tunning parameters with *tree = 1*

print(head(result.mtry.df[with(result.mtry.df, order(MSE)), ]))
          RMSE      MSE mtry nodesize tree
12035 15.44751 238.6257    3        5   35
*18001 15.44861 238.6595    4        7    1
*7018  16.02354 256.7539    2        5   18
20031 16.02536 256.8121    5        1   31
11037 16.02862 256.9165    3        3   37
11612 16.05162 257.6544    3        4  112

i am wondering if i wrong in the setting or there are some aspects i don't
conseder.
thanks for attention and thanks in advance for suggestions and help

Gianni


require(randomForest)
data(airquality)
set.seed(131)
MyOzone <- data.frame(na.omit(airquality))
str(MyOzone)

#all data
My.mtry=c(1,2,3,4,5)
My.nodesize=c(seq(1,10,by=1))
My.tree=c(seq(1,500,by=1))


# {}

result.mtry <- list()
for(i in 1:length(My.mtry)){
    result.nodesize <- list()
    for(m in 1:length(My.nodesize)){
        result.tree <- list()
        for(l in 1:length(My.tree)){
            ozone.rf <- randomForest(MyOzone[,-c(1)],MyOzone[,c(1)],
                mtry=My.mtry[[i]],
                nodesize=My.nodesize[[m]],
                ntree=My.tree[[l]], importance=TRUE)
        result.tree[[l]] <-
data.frame(RMSE=sqrt(ozone.rf$mse[ozone.rf$ntree]),MSE=ozone.rf$mse[ozone.rf$ntree],mtry=My.mtry[[i]],nodesize=My.nodesize[[m]],tree=My.tree[[l]])
        }
        result.tree.df <- do.call(rbind,result.tree)
        result.nodesize[[m]] <- result.tree.df
    }
    result.nodesize.df <- do.call(rbind,result.nodesize)
    result.mtry[[i]] <- result.nodesize.df
}

result.mtry.df <- do.call(rbind,result.mtry)
print(result.mtry.df[result.mtry.df$RMSE == min(result.mtry.df$RMSE),])
       RMSE      MSE mtry nodesize tree
12035 15.44751 238.6257    3        5   35

head(result.mtry.df[with(result.mtry.df, order(RMSE)), ])
       RMSE      MSE mtry nodesize tree
12035 15.44751 238.6257    3        5   35
18001 15.44861 238.6595    4        7    1
7018  16.02354 256.7539    2        5   18
20031 16.02536 256.8121    5        1   31
11037 16.02862 256.9165    3        3   37
11612 16.05162 257.6544    3        4  112

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