Nothing
## ----echo=FALSE---------------------------------------------------------------
library(knitr)
opts_chunk$set(tidy = FALSE, dev = "pdf", message = FALSE, fig.align = "center", cache = FALSE)
## -----------------------------------------------------------------------------
library(dtComb)
## ----eval = TRUE, echo=TRUE---------------------------------------------------
data(exampleData1)
head(exampleData1)
## -----------------------------------------------------------------------------
# # train set from the exampleData1
set.seed(2128)
inTrain <- caret::createDataPartition(exampleData1$group, p = 3 / 4, list = FALSE)
trainData <- exampleData1[inTrain, ]
head(trainData)
## -----------------------------------------------------------------------------
# # test set from the exampleData1
set.seed(2128)
testData <- exampleData1[-inTrain, -1]
## -----------------------------------------------------------------------------
markers <- trainData[, -1]
status <- factor(trainData$group, levels = c("not_needed", "needed"))
## ----fig.height=4.8, fig.width=5----------------------------------------------
set.seed(2128)
# linComb Function
fit.lin <- linComb(
markers = markers,
status = status,
event = "needed",
method = "scoring",
resample = "cv",
standardize = "range",
ndigits = 2, direction = "auto",
cutoff.method = "Youden"
)
## ----fig.height=4.8, fig.width=5----------------------------------------------
# nonlinComb Function
set.seed(2128)
fit.nonlin <- nonlinComb(
markers = markers,
status = status,
event = "needed",
method = "lassoreg",
include.interact = "TRUE",
resample = "boot",
direction = "auto",
cutoff.method = "Youden"
)
## ----fig.height=4.8, fig.width=5----------------------------------------------
# mlComb Function
set.seed(2128)
fit.ml <- mlComb(
markers = markers,
status = status,
event = "needed",
method = "knn",
resample = "repeatedcv", nfolds = 10, nrepeats = 5,
preProcess = c("center", "scale"),
direction = "<", cutoff.method = "Youden"
)
## ----fig.height=4.8, fig.width=5----------------------------------------------
# mathComb Function
fit.math <- mathComb(
markers = markers,
status = status,
event = "needed",
method = "distance",
distance = "euclidean",
direction = "<",
cutoff.method = "Youden"
)
## -----------------------------------------------------------------------------
predict(fit.nonlin, testData)
## -----------------------------------------------------------------------------
sessionInfo()
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