![]() ![]() Rf.stats <- median(summary(model.rf$mse)) Rf.stats <- median(summary(model.rf$rsq)) Model.rf <- randomForest(logZn ~ ffreq x y dist.m elev soil lime,ĭata=meuse, importance=T, na.action=na.omit, mtry=5) Rf.stats <- ame(rep=1:10, rsq=as.numeric(NA), mse=as.numeric(NA)) There is likely substitution.Ĭompute the RF several times and collect statistics. After the first two dist.mĪnd elev (obviously the most important) the others are not VarImpPlot(m.lzn.rf, type=2, main = "Importance: node impurity") VarImpPlot(m.lzn.rf, type=1, main = "Importance: permutation") # lime 12.10099 randomForest::importance(m.lzn.rf, type=2) # IncNodePurity We compare both: randomForest::importance(m.lzn.rf, type=1) # %IncMSE Here we have a regression, so Type 2 is the change in RSS due to the The node impurity is measured by the Gini index. Splitting on the variable, averaged over all trees. “The second measure is the total decrease in node impurities from The differenceīetween the two are then averaged over all trees, and normalized by the Same is done after permuting each predictor variable. Recorded (error rate for classification, MSE for regression). ![]() Tree, the prediction error on the out-of-bag portion of the data is “The first measure is computed from permuting OOB data: For each To 3 to get better trees but still include weak predictors this isĭisplay the cross-validation error rate against the number of By default this is \(\lfloor\rfloor = 1\). Randomly sampled as candidates at each split. The mtry optional argument gives the number of variables # randomForest(formula = logZn ~ ffreq x y dist.m elev soil lime, data = meuse, importance = TRUE, nperm = 3, mtry = 3, na.action = na.omit) # three permutations per tree to estimate importance M.lzn.rf <- randomForest(logZn ~ ffreq x y dist.m elev soil lime, data=meuse, Make a log10-transformed copy of the Zn metal concentration to obtainĪ somewhat balanced distribution of the target variable: meuse$logZn <- log10(meuse$zinc) # 锌įirst build the forest, using the randomForest lime whether agricultural lime was applied to the field.elev elevation above mean sea level (m).dist.m distance from the Meuse river (m).We try to model one of the heavy metals (Zn) from all possibly Sample point dataset: Meuse River heavy metals in soil. Packages used in this section: sp for the sample ![]()
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