vcr.svm.train {classmap} | R Documentation |
Prepare for visualization of a support vector machine classification on training data.
Description
Produces output for the purpose of constructing graphical displays such as the classmap
. The user first needs to run a support vector machine classification on the data by e1071::svm
, with the option probability = TRUE
. This classification can be with two or more classes. The output of e1071::svm
is then an argument to vcr.svm.train
. As e1071::svm
does not output the data itself, it needs to be given as well, in the arguments X
and y
.
Usage
vcr.svm.train(X, y, svfit, ortho = FALSE)
Arguments
X |
matrix of data coordinates, as used in |
y |
factor with the given (observed) class labels. It is crucial that X and y are exactly the same as in the call to |
svfit |
an object returned by |
ortho |
If |
Value
A list with components:
yint |
number of the given class of each case. Can contain |
y |
given class label of each case. Can contain |
levels |
levels of the response |
predint |
predicted class number of each case. Always exists. |
pred |
predicted label of each case. |
altint |
number of the alternative class. Among the classes different from the given class, it is the one with the highest posterior probability. Is |
altlab |
label of the alternative class. Is |
PAC |
probability of the alternative class. Is |
figparams |
parameters used in |
fig |
distance of each case |
farness |
farness of each case from its given class. Is |
ofarness |
for each case |
svfit |
as it was input, will be useful for new data. |
X |
the matrix of data coordinates from the arguments. This is useful for classifying new data. |
Author(s)
Raymaekers J., Rousseeuw P.J.
References
Raymaekers J., Rousseeuw P.J., Hubert M. (2021). Class maps for visualizing classification results. Technometrics, appeared online. doi: 10.1080/00401706.2021.1927849(link to open access pdf)
See Also
vcr.knn.newdata
, classmap
, silplot
, stackedplot
, e1071::svm
Examples
library(e1071)
set.seed(1); X <- matrix(rnorm(200 * 2), ncol = 2)
X[1:100, ] <- X[1:100, ] + 2
X[101:150, ] <- X[101:150, ] - 2
y <- as.factor(c(rep("blue", 150), rep("red", 50)))
cols <- c("deepskyblue3", "red")
plot(X, col = cols[as.numeric(y)], pch = 19)
# We now fit an SVM with radial basis kernel to the data:
set.seed(1) # to make the result of svm() reproducible.
svmfit <- svm(y~., data = data.frame(X = X, y = y),
scale = FALSE, kernel = "radial", cost = 10,
gamma = 1, probability = TRUE)
plot(svmfit$decision.values, col = cols[as.numeric(y)]); abline(h = 0)
# so the decision values separate the classes reasonably well.
plot(svmfit, data = data.frame(X = X, y = y), X.2~X.1, col = cols)
# The boundary is far from linear (but in feature space it is).
vcr.train <- vcr.svm.train(X, y, svfit = svmfit)
confmat.vcr(vcr.train)
stackedplot(vcr.train, classCols = cols)
classmap(vcr.train, "blue", classCols = cols)
classmap(vcr.train, "red", classCols = cols)
# For more examples, we refer to the vignette:
## Not run:
vignette("Support_vector_machine_examples")
## End(Not run)