Implements formula interface for
data used in the analysis.
An object of type
object is a list containing useful output of fuzzy forests.
In particular it contains a data.frame with list of selected features.
It also includes the random forest fit using the selected features.
ff for additional arguments.
Note that the matrix,
Z, of features that do not go through
the screening step must specified separately from the formula.
test_y are not supported in formula
interface. As in the
randomForest package, for large data sets
the formula interface may be substantially slower.
This work was partially funded by NSF IIS 1251151 and AMFAR 8721SC.
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data(ctg) y <- ctg$NSP X <- ctg[, 2:22] dat <- as.data.frame(cbind(y, X)) WGCNA_params <- WGCNA_control(p = 6, minModuleSize = 1, nThreads = 1) mtry_factor <- 1; min_ntree <- 500; drop_fraction <- .5; ntree_factor <- 1 screen_params <- screen_control(drop_fraction = drop_fraction, keep_fraction = .25, min_ntree = min_ntree, ntree_factor = ntree_factor, mtry_factor = mtry_factor) select_params <- select_control(drop_fraction = drop_fraction, number_selected = 5, min_ntree = min_ntree, ntree_factor = ntree_factor, mtry_factor = mtry_factor) library(WGCNA) wff_fit <- wff(y ~ ., data=dat, WGCNA_params = WGCNA_params, screen_params = screen_params, select_params = select_params, final_ntree = 500) #extract variable importance rankings vims <- wff_fit$feature_list #plot results modplot(wff_fit)
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