Package 'agghoo'

Title: Aggregated Hold-Out Cross Validation
Description: The 'agghoo' procedure is an alternative to usual cross-validation. Instead of choosing the best model trained on V subsamples, it determines a winner model for each subsample, and then aggregates the V outputs. For the details, see "Aggregated hold-out" by Guillaume Maillard, Sylvain Arlot, Matthieu Lerasle (2021) <arXiv:1909.04890> published in Journal of Machine Learning Research 22(20):1--55.
Authors: Sylvain Arlot [ctb], Benjamin Auder [aut, cre, cph], Melina Gallopin [ctb], Matthieu Lerasle [ctb], Guillaume Maillard [ctb]
Maintainer: Benjamin Auder <[email protected]>
License: MIT + file LICENSE
Version: 0.1-0
Built: 2024-11-20 06:44:29 UTC
Source: CRAN

Help Index

agghoo

Description

Run the (core) agghoo procedure. Arguments specify the list of models, their parameters and the cross-validation settings, among others.

Usage

agghoo(data, target, task = NULL, gmodel = NULL, params = NULL, loss = NULL)

Arguments

data

Data frame or matrix containing the data in lines.
target

The target values to predict. Generally a vector, but possibly a matrix in the case of "soft classification".
task

"classification" or "regression". Default: regression if target is numerical, classification otherwise.
gmodel

A "generic model", which is a function returning a predict function (taking X as only argument) from the tuple (dataHO, targetHO, param), where 'HO' stands for 'Hold-Out', referring to cross-validation. Cross-validation is run on an array of 'param's. See params argument. Default: see R6::Model.
params

A list of parameters. Often, one list cell is just a numerical value, but in general it could be of any type. Default: see R6::Model.
loss

A function assessing the error of a prediction. Arguments are y1 and y2 (comparing a prediction to known values). loss(y1, y2) –> real number (error). Default: see R6::AgghooCV.

Value

An R6::AgghooCV object o. Then, call o$fit() and finally o$predict(newData)

References

Guillaume Maillard, Sylvain Arlot, Matthieu Lerasle. "Aggregated hold-out". Journal of Machine Learning Research 22(20):1–55, 2021.

See Also

Function compareTo

Examples

# Basic usage:

# Regression:
a_reg <- agghoo(iris[,-c(2,5)], iris[,2])
a_reg$fit()
pr <- a_reg$predict(iris[,-c(2,5)] + rnorm(450, sd=0.1))
# Classification
a_cla <- agghoo(iris[,-5], iris[,5])
a_cla$fit()
pc <- a_cla$predict(iris[,-5] + rnorm(600, sd=0.1))


# Advanced usage:
data(iris)
library(mlbench)
data(PimaIndiansDiabetes)

# Run only agghoo on iris dataset (split into train/test, etc).
# Default parameters: see ?agghoo and ?AgghooCV
compareTo(iris[,-5], iris[,5], agghoo_run)

# Run both agghoo and standard CV, specifiying some parameters.
compareTo(iris[,-5], iris[,5], list(agghoo_run, standardCV_run), gmodel="tree")
compareTo(iris[,-5], iris[,5], list(agghoo_run, standardCV_run),
          gmodel="knn", params=c(3, 7, 13, 17, 23, 31),
          CV = list(type="vfold", V=5, shuffle=TRUE))

# Run both agghoo and standard CV, averaging errors over N=10 runs
# (possible for a single method but wouldn't make much sense...).
nc <- 1 #for CRAN
compareMulti(PimaIndiansDiabetes[,-9], PimaIndiansDiabetes[,9],
             list(agghoo_run, standardCV_run), N=10, gmodel="tree", nc=nc)

# Compare several values of V
compareRange(PimaIndiansDiabetes[,-9], PimaIndiansDiabetes[,9],
             list(agghoo_run, standardCV_run), N=10, V_range=c(10, 20, 30), nc=nc)

# For example to use average of squared differences.
# Default is "mean(abs(y1 - y2))".
loss2 <- function(y1, y2) mean((y1 - y2)^2)

# In regression on artificial datasets (TODO: real data?)
data <- mlbench.twonorm(300, 3)$x
target <- rowSums(data)
compareMulti(data, target, list(agghoo_run, standardCV_run), nc=nc,
             N=10, gmodel="ppr", params=c(1, 3, 5, 7, 9), loss=loss2,
             CV = list(type="MC", V=12, test_size=0.3))

compareMulti(data, target, list(agghoo_run, standardCV_run), nc=nc,
             N=10, floss=loss2, CV = list(type="vfold", V=10, shuffle=FALSE))

# Random tests to check that method doesn't fail in 1D case
M <- matrix(rnorm(200), ncol=2)
compareTo(as.matrix(M[,-2]), M[,2], list(agghoo_run, standardCV_run), gmodel="knn")
compareTo(as.matrix(M[,-2]), M[,2], list(agghoo_run, standardCV_run), gmodel="ppr")

agghoo_run

Description

Run and eval the agghoo procedure.

Usage

agghoo_run(dataTrain, dataTest, targetTrain, targetTest, floss, verbose, ...)

Arguments

dataTrain

Train dataset
dataTest

Test dataset
targetTrain

Train targets
targetTest

Test targets
floss

Loss function to compute error on test dataset
verbose

Show some execution trace
...

List defining the model (gmodel) and its parameters (params)

R6 class with agghoo functions fit() and predict().

Description

Class encapsulating the methods to run to obtain the best predictor from the list of models (see 'Model' class).

Methods

Public methods

Method new()

Create a new AgghooCV object.

Usage
AgghooCV$new(data, target, task, gmodel, loss)
Arguments
data

Matrix or data.frame

target

Vector of targets (generally numeric or factor)

task

"regression" or "classification". Default: classification if target not numeric.

gmodel

Generic model returning a predictive function Default: tree if mixed data, knn/ppr otherwise.

loss

Function assessing the error of a prediction Default: error rate or mean(abs(error)).

Method fit()

Fit an agghoo model.

Usage
AgghooCV$fit(CV = NULL)
Arguments
CV

List describing cross-validation to run. Slots:
- type: 'vfold' or 'MC' for Monte-Carlo (default: MC)
- V: number of runs (default: 10)
- test_size: percentage of data in the test dataset, for MC (irrelevant for V-fold). Default: 0.2.
- shuffle: wether or not to shuffle data before V-fold. Irrelevant for Monte-Carlo; default: TRUE
Default (if NULL): type="MC", V=10, test_size=0.2

Method predict()

Predict an agghoo model (after calling fit())

Usage
AgghooCV$predict(X)
Arguments
X

Matrix or data.frame to predict

Method getParams()

Return the list of V best parameters (after calling fit())

Usage
AgghooCV$getParams()

Method clone()

The objects of this class are cloneable with this method.

Usage
AgghooCV$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

compareMulti

Description

Run compareTo N times in parallel.

Usage

compareMulti(
  data,
  target,
  method_s,
  N = 100,
  nc = NA,
  floss = NULL,
  verbose = TRUE,
  ...
)

Arguments

data

Data matrix or data.frame
target

Target vector (generally)
method_s

Either a single function, or a list (examples: agghoo_run, standardCV_run)
N

Number of calls to method(s)
nc

Number of cores. Set to parallel::detectCores() if undefined. Set it to any value <=1 to say "no parallelism".
floss

Loss function to compute the error on testing dataset.
verbose

TRUE to print task numbers and "Errors:" in the end.
...

arguments passed to method_s function(s)

compareRange

Description

Run compareMulti on several values of the parameter V.

Usage

compareRange(
  data,
  target,
  method_s,
  N = 100,
  nc = NA,
  floss = NULL,
  V_range = c(10, 15, 20),
  ...
)

Arguments

data

Data matrix or data.frame
target

Target vector (generally)
method_s

Either a single function, or a list (examples: agghoo_run, standardCV_run)
N

Number of calls to method(s)
nc

Number of cores. Set to parallel::detectCores() if undefined. Set it to any value <=1 to say "no parallelism".
floss

Loss function to compute the error on testing dataset.
V_range

Values of V to be tested.
...

arguments passed to method_s function(s)

compareTo

Description

Compare a list of learning methods (or run only one), on data/target.

Usage

compareTo(
  data,
  target,
  method_s,
  rseed = -1,
  floss = NULL,
  verbose = TRUE,
  ...
)

Arguments

data

Data matrix or data.frame
target

Target vector (generally)
method_s

Either a single function, or a list (examples: agghoo_run, standardCV_run)
rseed

Seed of the random generator (-1 means "random seed")
floss

Loss function to compute the error on testing dataset.
verbose

TRUE to request methods to be verbose.
...

arguments passed to method_s function(s)

CVvoting_run

Description

Run and eval the voting cross-validation procedure.

Usage

CVvoting_run(dataTrain, dataTest, targetTrain, targetTest, floss, verbose, ...)

Arguments

dataTrain

Train dataset
dataTest

Test dataset
targetTrain

Train targets
targetTest

Test targets
floss

Loss function to compute error on test dataset
verbose

Show some execution trace
...

List defining the model (gmodel) and its parameters (params)

R6 class representing a (generic) model.

Description

"Model" class, containing a (generic) learning function, which from data + target [+ params] returns a prediction function X –> y. Parameters for cross-validation are either provided or estimated. Model family can be chosen among "tree", "ppr" and "knn" for now.

Public fields

nmodels

Number of parameters (= number of [predictive] models)

Methods

Public methods

Method new()

Create a new generic model.

Usage
Model$new(data, target, task, gmodel = NULL, params = NULL)
Arguments
data

Matrix or data.frame

target

Vector of targets (generally numeric or factor)

task

"regression" or "classification"

gmodel

Generic model returning a predictive function; chosen automatically given data and target nature if not provided.

params

List of parameters for cross-validation (each defining a model)

Method get()

Returns the model at index "index", trained on dataHO/targetHO.

Usage
Model$get(dataHO, targetHO, index)
Arguments
dataHO

Matrix or data.frame

targetHO

Vector of targets (generally numeric or factor)

index

Index of the model in 1...nmodels

Method getParam()

Returns the parameter at index "index".

Usage
Model$getParam(index)
Arguments
index

Index of the model in 1...nmodels

Method clone()

The objects of this class are cloneable with this method.

Usage
Model$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

standardCV_run

Description

Run and eval the standard cross-validation procedure.

Usage

standardCV_run(
  dataTrain,
  dataTest,
  targetTrain,
  targetTest,
  floss,
  verbose,
  ...
)

Arguments

dataTrain

Train dataset
dataTest

Test dataset
targetTrain

Train targets
targetTest

Test targets
floss

Loss function to compute error on test dataset
verbose

Show some execution trace
...

List defining the model (gmodel) and its parameters (params)