wff.formula {fuzzyforest} | R Documentation |
WGCNA based fuzzy forest algorithm
Description
Implements formula interface for wff
.
Usage
## S3 method for class 'formula'
wff(formula, data = NULL, ...)
Arguments
formula |
Formula object. |
data |
data used in the analysis. |
... |
Additional arguments |
Value
An object of type fuzzy_forest
. This
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.
Note
See 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_features
and 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.
See Also
wff
,
print.fuzzy_forest
,
predict.fuzzy_forest
,
modplot
Examples
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)