What is predict value of GBM model in R? and why NaN residual?
Well, I have a GBM model for nematode density with some predictor variables (SI = Spectral Index).
However, my model showed "NaN" residual with poisson distribution, and when I used predicted(gbm.fit) or gbm.fit$fit showed continuous values, but I have discrete values.
What should I use, predicted(gbm.fit) or gbm.fit$fit? What does gbm.fit$fit give me?
Can anyone help me with a problem?
This is the gbm algorithm used:
gbm.fit <- gbm(
formula = juv ~ NDRE + WI + GRAY + RSVI + VDVI,
distribution = "poisson",
data = data_base,
n.trees = 5000,
interaction.depth = 15,
bag.fraction = 3,
shrinkage = 0.01,
cv.folds = 5,
n.cores = NULL, # will use all cores by default
verbose = FALSE
)
Then I do:
sqrt(min(gbm.fit$fit))
Which produces this error:
Warning in sqrt(min(gbm.fit$cv.error)) : NaNs produced
[1] NaN
measure = read_xlsx("quantification.xlsx")
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