fda.usc: classif.ML – R documentation

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classif.ML

Functional classification using ML algotithms

Description

Computes functional classification using functional (and non functional) explanatory variables by rpart, nnet, svm or random forest model

Usage

classif.nnet(formula, data, basis.x = NULL, weights = "equal", size, ...)

classif.rpart(
  formula,
  data,
  basis.x = NULL,
  weights = "equal",
  type = "1vsall",
  ...
)

classif.svm(
  formula,
  data,
  basis.x = NULL,
  weights = "equal",
  type = "1vsall",
  ...
)

classif.ksvm(formula, data, basis.x = NULL, weights = "equal", ...)

classif.randomForest(
  formula,
  data,
  basis.x = NULL,
  weights = "equal",
  type = "1vsall",
  ...
)

classif.lda(
  formula,
  data,
  basis.x = NULL,
  weights = "equal",
  type = "1vsall",
  ...
)

classif.qda(
  formula,
  data,
  basis.x = NULL,
  weights = "equal",
  type = "1vsall",
  ...
)

classif.naiveBayes(formula, data, basis.x = NULL, laplace = 0, ...)

Arguments

`formula`	an object of class `formula` (or one that can be coerced to that class): a symbolic description of the model to be fitted. The details of model specification are given under `Details`.
`data`	List that containing the variables in the model.
`basis.x`	List of basis for functional explanatory data estimation.
`weights`	Weights: if `character` string `='equal'` same weights for each observation (by default) and `='inverse'` for inverse-probability of weighting. if `numeric` vector of length `n`, Weight values of each observation.
`size`	number of units in the hidden layer. Can be zero if there are skip-layer units.
`...`	Further arguments passed to or from other methods.
`type`	If type is`"1vsall"` (by default) a maximum probability scheme is applied: requires G binary classifiers. If type is `"majority"` (only for multicalss classification G > 2) a voting scheme is applied: requires G (G - 1) / 2 binary classifiers.
`laplace`	value used for Laplace smoothing (additive smoothing). Defaults to 0 (no Laplace smoothing).

Details

The first item in the data list is called "df" and is a data frame with the response and non functional explanatory variables, as glm.

Functional covariates of class fdata or fd are introduced in the following items in the data list.
basis.x is a list of basis for represent each functional covariate. The b object can be created by the function: create.pc.basis, pca.fd create.pc.basis, create.fdata.basis o create.basis.
basis.b is a list of basis for represent each functional beta parameter. If basis.x is a list of functional principal components basis (see create.pc.basis or pca.fd) the argument basis.b is ignored.

Value

Return classif object plus:

formula formula.
data List that containing the variables in the model.
group Factor of length n
group.est Estimated vector groups
prob.classification Probability of correct classification by group.
prob.group Matrix of predicted class probabilities. For each functional point shows the probability of each possible group membership.
max.prob Highest probability of correct classification.
type Type of classification scheme: 1 vs all or majority voting.
fit list of binary classification fitted models.

Note

Wrapper versions for multivariate and functional classification:

classif.lda,classif.qda: uses lda and qda functions and requires MASS package.
classif.nnet: uses nnet function and requires nnet package.
classif.rpart: uses nnet function and requires rpart package.
classif.svm,classif.naiveBayes: uses svm and naiveBayes functions and requires e1071 package.
classif.ksvm: uses weighted.ksvm function and requires personalized package.
classif.randomForest: uses randomForest function and requires randomForest package.

Author(s)

Febrero-Bande, M. and Oviedo de la Fuente, M.

References

Ramsay, James O., and Silverman, Bernard W. (2006), Functional Data Analysis, 2nd ed., Springer, New York.

McCullagh and Nelder (1989), Generalized Linear Models 2nd ed. Chapman and Hall.

Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics with S, New York: Springer. Regression for R. R News 1(2):20-25

Examples

## Not run: 
data(phoneme)
mlearn<-phoneme[["learn"]]
glearn<-phoneme[["classlearn"]]
mtest<-phoneme[["test"]]
gtest<-phoneme[["classtest"]]
dataf<-data.frame(glearn)
dat=list("df"=dataf,"x"=mlearn)
a1<-classif.rpart(glearn~x,data=dat)
summary(a1)
newdat<-list("x"=mtest)
p1<-predict(a1,newdat,type="class")
table(gtest,p1)
sum(p1==gtest)/250

## End(Not run)

fda.usc

Functional Data Analysis and Utilities for Statistical Computing

v2.0.2

GPL-2

Authors

Manuel Febrero Bande [aut], Manuel Oviedo de la Fuente [aut, cre], Pedro Galeano [ctb], Alicia Nieto [ctb], Eduardo Garcia-Portugues [ctb]

Initial release

2020-02-17