Package 'fasterElasticNet'

Fitting ElasticNet in a fast way.

Description

FasterElasticNet uses some math algorithm such as cholesky decomposition and forward solve etc. to reduce the amount of computation. We also use Rcpp with Armadillo to improve our algorithm by speeding up almost 5 times compared by the R version.

Details

To use fasterElasticNet, dataset x(mxn) and y(mx1) should be put into the function to fit the model. Then, a completely trace of lambda1 and lambda2 can be computed if no lambda1 and lambda2 were input by using ElasticNet. Using cv.choosemodel with the number of folds will returns a best model with smallest MSE after cross-validation. Using output to print the output and predict function will return the prediction based on a new dataset.

Author(s)

Jingyi Ma

Maintainer: Linyu Zuo <[email protected]>

References

BRADLEY, EFRON, TREVOR, HASTIE, IAIN, JOHNSTONE, AND, ROBERT, TIBSHIRANI. LEAST ANGLE REGRESSION[J]. The Annals of Statistics, 2004, 32(2): 407-499

See Also

https://github.com/CUFESAM/Elastic-Net

Examples

#Use R built-in datasets mtcars for a model fitting
  x <- mtcars[,-1]
  y <- mtcars[, 1]

  #fit model
  model <- ElasticNetCV(x,y)

  #fit a elastic net with lambda2 = 1
  model$Elasticnet_(lambda2 = 1)

  #choose model using cv
  model$cv.choosemodel(k = 31)    #Leave-one-out cross validation
  model$output()				  #See the output

  #predict
  pre <- mtcars[1:3,-1]
  model$predict(pre)

---

A fast way fitting elastic net using RcppArmadillo

Description

Elastic net is a regularization and variable selection method which linearly combines the L1 penalty of the lasso and L2 penalty of ridge methods. Based on this method, elastic- net is designed to return the trace of finding the best linear regression model. Compared with the existed R version of ElasticNet, our version speeds up the algorithm by using Cholesky decomposition, Givens rotation and RcppArmadillo.

Usage

elasticnet(XTX, XTY, lam2, lam1 = -1)

Arguments

XTX	The product of the transpose of independent variable X and itself.
XTY	The product of the transpose of independent variable X and response variable Y
lam1	Penalty of L1-norm. No L1 penalty when lam1 = -1
lam2	Penalty of L2-norm, a hyper-paramater

Details

When only lambda2 is given, elasticnet will return the trace of variable selection with lambda1 decreasing from lambda1_0 to zero. lambda1_0 is a value for lambda1 when there is only one predictor (the one most correlated with the response variable) in the model.

If lambda1 and lambda2 are both given, it will also return a trace. But in this case, the trace will stop when lambda1 and lambda2 reach the given ones.

To speed up the algorithm, we use some calculational tricks:

In the consideration of the low efficiency of R dealing with high-dimensional matrix, we use lower triangular matrices during the iteration of the algorithm to avoid massive matrix calculations. When adding one predictor into the model, we update XTX by recalcuting the lower triangular matrix in the Cholesky decomposition of it. While re- moving one predictor from the model, we update the lower triangular matrix with the help of Givens rotations.

Furthermore, due to the low efficiency of R dealing with loops, we rewrite the entire algorithm with RcppArmadillo, a C++ linear algebra library.

Value

A list will be returned. When only lambda2 is given, the returned list contains the trace of lambda1 (relamb) and the corresponding coefficients of the predictors (reb). If both lambda1 and lambda2 are given, the corresponding coefficients of the predictors will be returned.

Examples

#Use R built-in datasets mtcars for a model fitting
    x <- as.matrix(mtcars[,-1])
    y <- as.matrix(mtcars[, 1])

    XTX <- t(x) %*% x
    XTY <- t(x) %*% y

    #Prints the output of elastic net model with lambda2 = 0
    res <- elasticnet(XTX,XTY,lam2 = 0)

---

Cross validation

Description

Computes k-fold cross-validation for elastic net.

Usage

ElasticNetCV(x, y)

Arguments

x	A data.frame or matrix of predictors
y	A vector of response variables

Details

This function reads data into its environment and returns a list of three outcomes. To perform elastic net or cross-validation of elastic net, use the corresponding element of the returned list. See examples below. The penalty of L1-norm and L2-norm is denoted by lambda1 and lambda2 respectively.

Value

cv.choosemodel

Given the parameter k folds and lambda2 (optional), cv.choosemodel performs cross-validation to select the opti- mal lambda1 and computes the corresponding coefficient of each variable. If lambda2 is NULL, cv.choosemodel selects the optimal lambda2 from a sequence going from 0 to 1 in steps of 0.1 and the corresponding optimal lambda1, then it returns the coefficient of each variable.

A list of three outcomes will be returned:

Elasticnet	Given lambda1 (optional) and lambda2, Elasticnet_ calculates an elastic net-regularized regression and returns the coefficients of each variable. If lambda1 is NULL, Elasticnet_ prints out the trace of lambda1 and the corresponding coefficient of each variable.
output	Prints the cross-validation outputs, including the minimum MSE, the coefficient of each variable, lambda1 and lambda2.
predict	Reads a data.frame of the testing data set and returns predictions using the trained model.

Examples

#Use R built-in datasets mtcars for a model fitting
  x <- mtcars[,-1]
  y <- mtcars[, 1]

  #fit model
  model <- ElasticNetCV(x,y)

  #fit a elastic net with lambda2 = 1
  model$Elasticnet_(lambda2 = 1)

  #choose model using cv
  model$cv.choosemodel(k = 31)    #Leave-one-out cross validation
  model$output()				  #See the output

  #predict
  pre <- mtcars[1:3,-1]
  model$predict(pre)

---

Housing data from kaggle

Description

A subdata from kaggle "Get start" competition

Usage

data("housing")

Format

A data frame with 10153 observations on the following 140 variables.

floor

for apartments, floor of the building

area_m

Area, sq.m.

green_zone_part

Proportion of area of greenery in the total area

indust_part

Share of industrial zones in area of the total area

preschool_quota

Number of seats in pre-school organizations

preschool_education_centers_raion

Number of pre-school institutions

school_quota

Number of high school seats in area

school_education_centers_raion

Number of high school institutions

school_education_centers_top_20_raion

Number of high schools of the top 20 best schools in Moscow

healthcare_centers_raion

Number of healthcare centers in district

university_top_20_raion

Number of higher education institutions in the top ten ranking of the Federal rank

sport_objects_raion

Number of higher education institutions

additional_education_raion

Number of additional education organizations

culture_objects_top_25_raion

Number of objects of cultural heritage

shopping_centers_raion

Number of malls and shopping centres in district

office_raion

Number of malls and shopping centres in district

build_count_block

Share of block buildings

build_count_wood

Share of wood buildings

build_count_frame

Share of frame buildings

build_count_brick

Share of brick buildings

build_count_monolith

Share of monolith buildings

build_count_panel

Share of panel buildings

build_count_foam

Share of foam buildings

build_count_slag

Share of slag buildings

build_count_before_1920

Share of before_1920 buildings

build_count_1921.1945

Share of 1921-1945 buildings

build_count_1946.1970

Share of 1946-1970 buildings

build_count_1971.1995

Share of 1971-1995 buildings

build_count_after_1995

Share of after_1995 buildings

kindergarten_km

Distance to kindergarten

school_km

Distance to high school

park_km

Distance to park

green_zone_km

Distance to green zone

industrial_km

Distance to industrial zone

water_treatment_km

Distance to water treatment

cemetery_km

Distance to the cemetery

incineration_km

Distance to the incineration

railroad_station_walk_min

Time to the railroad station (walk)

railroad_station_avto_km

Distance to the railroad station (avto)

railroad_station_avto_min

Time to the railroad station (avto)

public_transport_station_min_walk

Time to the public transport station (walk)

water_km

Distance to the water reservoir / river

mkad_km

Distance to MKAD (Moscow Circle Auto Road)

big_road1_km

Distance to Nearest major road

big_road2_km

The distance to next distant major road

railroad_km

Distance to the railway / Moscow Central Ring / open areas Underground

bus_terminal_avto_km

Distance to bus terminal (avto)

oil_chemistry_km

Distance to dirty industries

nuclear_reactor_km

Distance to nuclear reactor

radiation_km

Distance to burial of radioactive waste

power_transmission_line_km

Distance to power transmission line

thermal_power_plant_km

Distance to thermal power plant

ts_km

Distance to power station

big_market_km

Distance to grocery / wholesale markets

market_shop_km

Distance to markets and department stores

fitness_km

Distance to fitness

swim_pool_km

Distance to swimming pool

ice_rink_km

Distance to ice palace

stadium_km

Distance to stadium

basketball_km

Distance to the basketball courts

hospice_morgue_km

Distance to hospice/morgue

detention_facility_km

Distance to detention facility

public_healthcare_km

Distance to public healthcare

university_km

Distance to universities

workplaces_km

Distance to workplaces

shopping_centers_km

Distance to shopping centers

office_km

Distance to business centers/ offices

additional_education_km

Distance to additional education

preschool_km

Distance to preschool education organizations

big_church_km

Distance to large church

church_synagogue_km

Distance to Christian chirches and Synagogues

mosque_km

Distance to mosques

theater_km

Distance to theater

museum_km

Distance to museums

exhibition_km

Distance to exhibition

catering_km

Distance to catering

green_part_500

The share of green zones in 500 meters zone

prom_part_500

The share of industrial zones in 500 meters zone

office_count_500

The number of office space in 500 meters zone

office_sqm_500

The square of office space in 500 meters zone

trc_count_500

The number of shopping malls in 500 meters zone

trc_sqm_500

The square of shopping malls in 500 meters zone

cafe_count_500_na_price

Cafes and restaurant bill N/A in 500 meters zone

cafe_count_500_price_500

Cafes and restaurant bill, average under 500 in 500 meters zone

cafe_count_500_price_1000

Cafes and restaurant bill, average 500-1000 in 500 meters zone

cafe_count_500_price_1500

Cafes and restaurant bill, average 1000-1500 in 500 meters zone

cafe_count_500_price_2500

Cafes and restaurant bill, average 1500-2500 in 500 meters zone

cafe_count_500_price_4000

Cafes and restaurant bill, average 2500-4000 in 500 meters zone

cafe_count_500_price_high

Cafes and restaurant bill, average over 4000 in 500 meters zone

big_church_count_500

The number of big churchs in 500 meters zone

church_count_500

The number of churchs in 500 meters zone

mosque_count_500

The number of mosques in 500 meters zone

leisure_count_500

The number of leisure facilities in 500 meters zone

sport_count_500

The number of sport facilities in 500 meters zone

market_count_500

The number of markets in 500 meters zone

green_part_1000

The share of green zones in 1000 meters zone

prom_part_1000

The share of industrial zones in 1000 meters zone

office_sqm_1000

The square of office space in 1000 meters zone

trc_count_1000

The number of shopping malls in 1000 meters zone

trc_sqm_1000

The square of shopping malls in 1000 meters zone

cafe_count_1000_na_price

Cafes and restaurant bill N/A in 1000 meters zone

cafe_count_1000_price_high

Cafes and restaurant bill, average over 4000 in 1000 meters zone

big_church_count_1000

The number of big churchs in 1000 meters zone

mosque_count_1000

The number of mosques in 1000 meters zone

leisure_count_1000

The number of leisure facilities in 1000 meters zone

sport_count_1000

The number of sport facilities in 1000 meters zone

market_count_1000

The number of markets in 1000 meters zone

green_part_1500

The share of green zones in 1500 meters zone

prom_part_1500

The share of industrial zones in 1500 meters zone

office_sqm_1500

The square of office space in 1500 meters zone

trc_count_1500

The number of shopping malls in 1500 meters zone

trc_sqm_1500

The square of shopping malls in 1500 meters zone

cafe_count_1500_price_high

Cafes and restaurant bill, average over 4000 in 1500 meters zone

mosque_count_1500

The number of mosques in 1500 meters zone

sport_count_1500

The number of sport facilities in 1500 meters zone

market_count_1500

The number of markets in 1500 meters zone

green_part_2000

The share of green zones in 2000 meters zone

prom_part_2000

The share of industrial zones in 2000 meters zone

office_sqm_2000

The square of office space in 2000 meters zone

trc_count_2000

The number of shopping malls in 2000 meters zone

trc_sqm_2000

The square of shopping malls in 2000 meters zone

mosque_count_2000

The number of mosques in 2000 meters zone

sport_count_2000

The number of sport facilities in 2000 meters zone

market_count_2000

The number of markets in 2000 meters zone

green_part_3000

The share of green zones in 3000 meters zone

prom_part_3000

The share of industrial zones in 3000 meters zone

office_sqm_3000

The square of office space in 3000 meters zone

trc_count_3000

The number of shopping malls in 3000 meters zone

trc_sqm_3000

The square of shopping malls in 3000 meters zone

mosque_count_3000

The number of mosques in 3000 meters zone

sport_count_3000

The number of sport facilities in 3000 meters zone

market_count_3000

The number of markets in 3000 meters zone

green_part_5000

The share of green zones in 5000 meters zone

prom_part_5000

The share of industrial zones in 5000 meters zone

trc_count_5000

The number of shopping malls in 5000 meters zone

trc_sqm_5000

The square of shopping malls in 5000 meters zone

mosque_count_5000

The number of mosques in 5000 meters zone

sport_count_5000

The number of sport facilities in 5000 meters zone

market_count_5000

The number of markets in 5000 meters zone

price_doc

I don't know

Source

www.kaggle.com

Examples

data(housing)

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