Multi asset portfolio optimization R - r

I am new to Portfolio Optimization in R. When I add more than 25 assets (each asset has about 25 observations) to my portfolio, optimize.portfolio does not find any solutions. When I run this program with 25 assets or less, it works properly and plots the efficient frontier. Any help on this is much appreciated.
library(data.table)
library(readxl)
library(PerformanceAnalytics)
library(PortfolioAnalytics)
library(ROI)
library(foreach)
library(DEoptim)
library(iterators)
library(fGarch)
library(Rglpk)
library(quadprog)
library(ROI.plugin.glpk)
library(ROI.plugin.quadprog)
library(ROI.plugin.symphony)
library(pso)
library(GenSA)
library(corpcor)
library(testthat)
library(nloptr)
library(MASS)
library(robustbase)
library(ggplot2)
setwd("~/R")
#BRING IN DATA
returns.data <- read_excel("portfolio_sample_4asset.xlsx", sheet = "portfolio")
returns.data <- data.frame(returns.data)
row.names(returns.data) <- (returns.data$year)
returns.data$year <- NULL
meanReturns <- colMeans(returns.data)
#GENERATE COVARIANCE AND CORRELATION TABLES
cov.pop <- function(x,y=NULL) {
cov(x,y)*(NROW(x)-1)/NROW(x)
}
covMat <- cov.pop(returns.data)
corMat <- cor(returns.data)
#SPECIFY PORTFOLIO OBJECT
port <- portfolio.spec(assets = colnames(returns.data))
#CONSTRAINTS
port <- add.constraint(port,type="weight_sum",min=0.99, max=1.01)
#rportfolios <- random_portfolios(port, permutations = 500, rp_method = "sample", eliminate = TRUE)
#OPTIMIZATION SETUP
minreturnLimit <- min(colMeans(returns.data))
maxreturnLimit <- max(colMeans(returns.data))
minret <- minreturnLimit
maxret <- maxreturnLimit
vec <- seq(minret, maxret, length.out = 100)
eff.frontier <- data.frame(Risk = rep(NA, length(vec)), Return = rep(NA, length(vec)))
frontier.weights <- mat.or.vec(nr = length(vec), nc = ncol(returns.data))
colnames(frontier.weights) <- colnames(returns.data)
#GENERATE EFFICIENT FRONTIER
#In add.constraint...the type is return, as in, it is targeting a specific return specified by vec
#Subsequently, it looks for the portfolio that minimizes StdDev for that return constraint...this is the objective
for(i in 1:length(vec)){
eff.port <- add.constraint(port, type = "return", name = "mean", return_target = vec[i])
eff.port <- add.objective(eff.port, type = "risk", name = "var")
# eff.port <- add.objective(eff.port, type = "weight_concentration", name = "HHI",
# conc_aversion = 0.001)
eff.port <- optimize.portfolio(returns.data, eff.port, optimize_method = "ROI")
eff.frontier$Risk[i] <- sqrt(t(eff.port$weights) %*% covMat %*% eff.port$weights)
eff.frontier$Return[i] <- eff.port$weights %*% meanReturns
eff.frontier$Sharperatio[i] <- eff.port$Return[i] / eff.port$Risk[i]
frontier.weights[i,] = eff.port$weights
print(paste(round(i/length(vec) * 100, 0), "% done..."))
}
#PLOT EFFICIENT FRONTIER
ggplot(eff.frontier, aes(x=eff.frontier$Risk, y=eff.frontier$Return)) + geom_point(shape = 18, color = "limegreen", size = 2) + ggtitle("Portfolio Optimization") + labs(x="Risk",y="Return")
eff.frontier$Sharpe <- eff.frontier$Return / eff.frontier$Risk

I figured out why my optimization wasn't working - my dataset contained a rank-deficient matrix which could not be solved (more columns than rows).

Related

How can I use try catch for nls function in R

I am doing a regression for a Quadric Linear function. I got two option is to use either nlsLM and nls2. However, for some dataset, the use of nlsLM casing some problem such as: singular gradient matrix at initial parameter estimates or they ran in to an infinitie loop. I want to use the try catch to deal with this issue. Can anyone help me out? Thanks everyone in advance.
Here is the full code:
# Packages needed for estimaton of Ideal trajectory - nonlinear regression
#-------------------------------------------------------------------------------
library("minpack.lm")
library("nlstools")
library("nlsMicrobio")
library("stats")
library("tseries") #runs test for auto correlation
#Use NLS2
library(proto)
library(nls2)
################################################################
# Set working directory
setwd("C:/Users/Kevin Le/PycharmProjects/Pig Data Black Box - Copy")
#load dataset
load("Data/JRPData_TTC.Rdata") #load dataset created in MissingData.step
ID <- 5470
#Create a new dataframe which will store Data after ITC estimation
#Dataframe contains ITC parameters
ITC.param.pos2 <- data.frame(ANIMAL_ID=factor(),
X0=double(),
Y1=double(),
Y2=double(),
Ylast=double(),
a=double(),
b=double(),
c=double(),
d=double(),
stringsAsFactors=FALSE)
#Dataframe contains data points on the ITC
Data.remain <- data.frame(ANIMAL_ID=character(),
Age=double(),
obs.CFI=double(),
tt=double(),
ttt=double(),
stringsAsFactors=FALSE)
#===============================================================
# For loop for automatically estimating ITC of all pigs
#===============================================================
IDC <- seq_along(ID) # 17, 23, 52, 57, 116
for (idc in IDC){
# idc = 1
i <- ID[idc]
Data <- No.NA.Data.1[No.NA.Data.1$ANIMAL_ID == i,]
idc1 <- unique(as.numeric(Data$idc.1))
####### Create data frame of x (Age) and y (CFI) ########
x <- as.numeric(Data$Age.plot)
Y <- as.numeric(Data$CFI.plot)
Z <- as.numeric(Data$DFI.plot)
Data.xy <- as.data.frame(cbind(x,Y))
#Initial parameteres for parameter estimation
X0.0 <- x[1]
Xlast <- x[length(x)]
##################################################################
# 1. reparametrization CFI at X0 = 0
#function used for reparametrization in MAPLE
# solve({
# 0=a+b*X_0+c*X_0**2,
# DFIs=b+2*c*Xs,CFIs=a+b*Xs+c*Xs**2},
# {a,b,c});
# a = -X0*(2*CFIs*Xs-CFIs*X0-Xs^2*DFIs+Xs*DFIs*X0)/(Xs^2-2*X0*Xs+X0^2)
# b = (-Xs^2*DFIs+DFIs*X0^2+2*CFIs*Xs)/(Xs^2-2*X0*Xs+X0^2)
# c = -(CFIs-Xs*DFIs+X0*DFIs)/(Xs^2-2*X0*Xs+X0^2)
# 2. with the source of the function abcd and pred
##################################################################
#Provide set of initial parameters
Xs.1 <- round(seq(X0.0 + 1, Xlast - 1, len = 30), digits = 0)
X0.1 <- rep(X0.0, length(Xs.1))
DFIs.1 <- NULL
CFIs.1 <- NULL
for(A in seq_along(Xs.1)){
DFIs2 <- Data[Data$Age.plot == Xs.1[A],]$DFI.plot
CFIs2 <- Data[Data$Age.plot == Xs.1[A],]$CFI.plot
DFIs.1 <- c(DFIs.1, DFIs2)
CFIs.1 <- c(CFIs.1, CFIs2)
}
st1 <- data.frame(cbind(X0.1, Xs.1, DFIs.1, CFIs.1))
names(st1) <- c("X0","Xs", "DFIs","CFIs")
#RUN NLS2 to find optimal initial parameters
st2 <- nls2(Y ~ nls.func.2(X0, Xs, DFIs, CFIs),
Data.xy,
start = st1,
# weights = weight,
# trace = T,
algorithm = "brute-force")
par_init <- coef(st2); par_init
#--------------------------------------------
# Create empty lists to store data after loop
#--------------------------------------------
par <- list()
AC.res <- list()
AC.pvalue <- NULL
data2 <- list()
data3 <- list()
param <- data.frame(rbind(par_init))
par.abcd <- data.frame(rbind(abcd.2(as.vector(par_init))))
param.2 <- data.frame(X0=double(),
Xs=double(),
DFIs=double(),
CFIs=double(),
a=double(),
b=double(),
c=double(),
stringsAsFactors=FALSE)
j <- 2
AC_pvalue <- 0
AC.pvalue[1] <- AC_pvalue
datapointsleft <- as.numeric(dim(Data)[1])
dpl <- datapointsleft #vector of all dataponitsleft at each step
#-------------------------------------------------------------------------------
# Start the procedure of Non Linear Regression
#-------------------------------------------------------------------------------
while ((AC_pvalue<=0.05) && datapointsleft >= 20){
weight <- 1/Y^2
# ---------------- NON linear reg applied to log(Y) ---------------------------------
st2 <- nls2(Y ~ nls.func.2(X0, Xs, DFIs, CFIs),
Data.xy,
start = st1,
weights = weight,
trace = F,
algorithm = "brute-force")
par_init <- coef(st2)
par_init
# st1 <- st1[!(st1$Xs == par_init[2]),]
nls.CFI <- nlsLM(Y ~ nls.func.2(X0, Xs, DFIs, CFIs),
Data.xy,
control = list(tol = 1e-2, printEval = TRUE, maxiter = 1024),
start = list(X0 = par_init[1], Xs = par_init[2],
DFIs = par_init[3], CFIs = par_init[4]),
weights = weight,
algorithm = "port",
lower = c(-10000,X0.0+1, -10000, -10000),
upper = c(10000, Xlast-1, 10000, 10000),
trace = F)
# nls.CFI <- nls2(Y ~ nls.func.2(X0, Xs, DFIs, CFIs),
# Data.xy,
# start = list(X0 = par_init[1], Xs = par_init[2],
# DFIs = par_init[3], CFIs = par_init[4]),
# weights = weight,
# control = nls.control(warnOnly = TRUE),
# trace = T,
# algorithm = "port",
# lower = c(-100000000,X0.0+1, -1000000000, -1000000000),
# upper = c(1000000000, Xlast-1, 1000000000, 1000000000))
# nls.CFI <- nlsLM(Y ~ nls.func.2(X0, Xs, DFIs, CFIs),
# Data.xy,
# control = nls.control(warnOnly = TRUE),
# start = list(X0 = par_init[1], Xs = par_init[2],
# DFIs = par_init[3], CFIs = par_init[4]),
# weights = weight,
# algorithm = "port",
# lower = c(-1000000000,X0.0+1, -1000000000, -1000000000),
# upper = c(1000000000, Xlast-1, 1000000000, 1000000000),
# trace = F)
#--------RESULTS analysis GOODNESS of fit
#estimate params
par[[j]] <- coef(nls.CFI)
par.abcd[j,] <- abcd.2(as.vector(coef(nls.CFI) )) #calculation of a, b, c and d
param[j,] <- par[[j]]
param.2[j-1,] <- cbind(param[j,], par.abcd[j,])
#summary
# summ = overview((nls.CFI)) #summary
#residuals
res1 <- nlsResiduals(nls.CFI) #residuals
res2 <- nlsResiduals(nls.CFI)$resi1
res <- res2[, 2]
AC.res <- test.nlsResiduals(res1)
AC.pvalue[j] <- AC.res$p.value
#---------Check for negative residuals----------
#Add filtration step order to data
Step <- rep(j - 1, length(x))
#create a new dataset with predicted CFI included
Data.new <- data.frame(cbind(x, Z, Y, pred.func.2(par[[j]],x)[[1]], res, Step))
names(Data.new) <- c("Age", "Observed_DFI","Observed_CFI", "Predicted_CFI", "Residual", "Step")
# plot(Data.new$Age, Data.new$Predicted_CFI, type = "l", col = "black",lwd = 2,
# ylim = c(0, max(Data.new$Predicted_CFI, Data.new$Observed_CFI)))
# lines(Data.new$Age, Data.new$Observed_CFI, type = "p", cex = 1.5)
#
#remove negative res
Data.pos <- Data.new[!Data.new$Residual<0,]
# lines(Data.pos$Age, Data.pos$Predicted_CFI, type = "l", col = j-1, lwd = 2)
# lines(Data.pos$Age, Data.pos$Observed_CFI, type = "p", col = j, cex = 1.5)
#restart
#Criteria to stop the loop when the estimated parameters are equal to initial parameters
# Crite <- sum(param.2[dim(param.2)[1],c(1:4)] == par_init)
datapointsleft <- as.numeric(dim(Data.pos)[1])
par_init <- par[[j]]
AC_pvalue <- AC.pvalue[j]
j <- j+1
x <- Data.pos$Age
Y <- Data.pos$Observed_CFI
Z <- Data.pos$Observed_DFI
Data.xy <- as.data.frame(cbind(x,Y))
dpl <- c(dpl, datapointsleft)
dpl
#Create again the grid
X0.0 <- x[1]
Xlast <- x[length(x)]
#Xs
if(par_init[2] -15 <= X0.0){
Xs.1 <- round(seq(X0.0 + 5, Xlast - 5, len = 30), digits = 0)
} else if(par_init[2] + 5 >= Xlast){
Xs.1 <- round(seq(par_init[2]-10, par_init[2]-1, len = 6), digits = 0)
} else{
Xs.1 <- round(seq(par_init[2]-5, par_init[2] + 5, len = 6), digits = 0)
}
#
X0.1 <- rep(X0.0, length(Xs.1))
DFIs.1 <- NULL
CFIs.1 <- NULL
for(A in seq_along(Xs.1)){
DFIs2 <- Data[Data$Age.plot == Xs.1[A],]$DFI.plot
CFIs2 <- Data[Data$Age.plot == Xs.1[A],]$CFI.plot
DFIs.1 <- c(DFIs.1, DFIs2)
CFIs.1 <- c(CFIs.1, CFIs2)
}
st1 <- data.frame(cbind(X0.1, Xs.1, DFIs.1, CFIs.1))
if(X0.0 <= par_init[2] && Xlast >=par_init[2]){
st1 <- rbind(st1, par_init)
}
names(st1) <- c("X0","Xs", "DFIs","CFIs")
}
} # end FOR loop
Here is the data file. I have exported my data into the .Rdata for an easier import.: https://drive.google.com/file/d/1GVMarNKWMEyz-noSp1dhzKQNtu2uPS3R/view?usp=sharing
In this file, the set id: 5470 will have this error: singular gradient matrix at initial parameter estimates in this part:
nls.CFI <- nlsLM(Y ~ nls.func.2(X0, Xs, DFIs, CFIs),
Data.xy,
control = list(tol = 1e-2, printEval = TRUE, maxiter = 1024),
start = list(X0 = par_init[1], Xs = par_init[2],
DFIs = par_init[3], CFIs = par_init[4]),
weights = weight,
algorithm = "port",
lower = c(-10000,X0.0+1, -10000, -10000),
upper = c(10000, Xlast-1, 10000, 10000),
trace = F)
The complementary functions (file Function.R):
abcd.2 <- function(P){
X0 <- P[1]
Xs <- P[2]
DFIs <- P[3]
CFIs <- P[4]
a <- -X0*(2*CFIs*Xs-CFIs*X0-Xs^2*DFIs+Xs*DFIs*X0)/(Xs^2-2*X0*Xs+X0^2)
b <- (-Xs^2*DFIs+DFIs*X0^2+2*CFIs*Xs)/(Xs^2-2*X0*Xs+X0^2)
c <- -(CFIs-Xs*DFIs+X0*DFIs)/(Xs^2-2*X0*Xs+X0^2)
pp <- as.vector(c(a, b, c))
return(pp)
}
#--------------------------------------------------------------
# NLS function
#--------------------------------------------------------------
nls.func.2 <- function(X0, Xs, DFIs, CFIs){
pp <- c(X0, Xs, DFIs, CFIs)
#calculation of a, b and c using these new parameters
c <- abcd.2(pp)[3]
b <- abcd.2(pp)[2]
a <- abcd.2(pp)[1]
ind1 <- as.numeric(x < Xs)
return (ind1*(a+b*x+c*x^2)+(1-ind1)*((a+b*(Xs)+c*(Xs)^2)+(b+2*c*(Xs))*(x-(Xs))))
}
#--------------------------------------------------------------
# Fit new parameters to a quadratic-linear function of CFI
#--------------------------------------------------------------
pred.func.2 <- function(pr,age){
#
X0 <- pr[1]
Xs <- pr[2]
DFIs <- pr[3]
CFIs <- pr[4]
#
x <- age
#calculation of a, b and c using these new parameters
c <- abcd.2(pr)[3]
b <- abcd.2(pr)[2]
a <- abcd.2(pr)[1]
#
ind1 <- as.numeric(x < Xs)
#
results <- list()
cfi <- ind1*(a+b*x+c*x^2)+(1-ind1)*((a+b*(Xs)+c*(Xs)^2)+(b+2*c*(Xs))*(x-(Xs))) #CFI
dfi <- ind1*(b+2*c*x) + (1 - ind1)*(b+2*c*(Xs)) #DFI
results[[1]] <- cfi
results[[2]] <- dfi
return (results)
}
#---------------------------------------------------------------------------------------------------------------
# Quadratic-linear function of CFI curve and its 1st derivative (DFI) with original parameters (only a, b and c)
#---------------------------------------------------------------------------------------------------------------
pred.abcd.2 <- function(pr,age){
#
a <- pr[1]
b <- pr[2]
c <- pr[3]
x <- age
#calculation of a, b and c using these new parameters
#
ind1 <- as.numeric(x < Xs)
#
results <- list()
cfi <- ind1*(a+b*x+c*x^2)+(1-ind1)*((a+b*(Xs)+c*(Xs)^2)+(b+2*c*(Xs))*(x-(Xs))) #CFI
dfi <- ind1*(b+2*c*x) + (1 - ind1)*(b+2*c*(Xs)) #DFI
results[[1]] <- cfi
results[[2]] <- dfi
return (results)
}
Updated: I did review my logic from the previous step and found that my data is a bit messed up because of it. I have fixed it. The case where a set f data ran into an infinite loop has no longer exists, but this error is still there however: singular gradient matrix at initial parameter estimates.

Looping a function in R

I have written a cross validation/grid search style code in R that tries to find an optimal threshold value for a given value of mtry (using the random forest algorithm). I have posted my code below using the Sonar data from the library mlbench However, there seems to be some problems with this code.
library(caret)
library(mlbench)
library(randomForest)
res <- matrix(0, nrow = 10, ncol = 6)
colnames(res) <- c("mtry","Threshhold","Accuracy", "PositivePred", "NegativePred", "F-value")
out <- matrix(0, nrow = 17, ncol = 6)
colnames(out) <- c("mtry","Threshhold","Avg.Accuracy", "Avg.PosPred", "Avg.NegPred", "Avg.F_Value")
rep <- matrix(0, nrow = 10, ncol = 6)
colnames(out) <- c("mtry","Threshhold","Avg_Accuracy", "Avg_PosPred", "Avg_NegPred", "Avg_F_Value")
data(Sonar)
N=Sonar
### creating 10 folds
folds <- cut(seq(1,nrow(N)),breaks=10,labels=FALSE)
for (mtry in 5:14) {
K=mtry-4
for(thresh in seq(1,9,0.5)) {
J = 2*thresh-1
dataset<-N[sample(nrow(N)),] #### mix up the dataset N
for(I in 1:10){
#Segement your data by fold using the which() function
testIndexes <- which(folds==I,arr.ind=TRUE)
N_test <- dataset[testIndexes, ] ### select each fold for test
N_train <- dataset[-testIndexes, ] ### select rest for training
rf = randomForest(Class~., data = N_train, mtry=mtry, ntree=500)
pred = predict(rf, N_test, type="prob")
label = as.factor(ifelse(pred[,2]>=thresh,"M","R"))
confusion = confusionMatrix(N_test$Class, label)
res[I,1]=mtry
res[I,2]=thresh
res[I,3]=confusion$overall[1]
res[I,4]=confusion$byClass[3]
res[I,5]=confusion$byClass[4]
res[I,6]=confusion$byClass[7]
}
print(res)
out[J,1] = mtry
out[J,2] = thresh
out[J,3] = mean(res[,2])
out[J,4] = mean(res[,3])
out[J,5] = mean(res[,4])
out[J,6] = mean(res[,5])
}
print(out)
rep[K,1] = mtry
rep[K,2] = thresh
rep[K,3] = mean(out[,2])
rep[K,4] = mean(out[,3])
rep[K,5] = mean(out[,4])
rep[K,6] = mean(out[,5])
}
print(rep)
Earlier, I wrote a similar code with the "iris" dataset, and I did not seem to have any problems:
library(caret)
library(randomForest)
data(iris)
N <- iris
N$Species = ifelse(N$Species == "setosa", "a", "b")
N$Species = as.factor(N$Species)
res <- matrix(0, nrow = 10, ncol = 5)
colnames(res) <- c("Threshhold","Accuracy", "PositivePred", "NegativePred", "F-value")
out <- matrix(0, nrow = 9, ncol = 5)
colnames(out) <- c("Threshhold","Avg.Accuracy", "Avg.PosPred", "Avg.NegPred", "Avg.F_Value")
### creating 10 folds
folds <- cut(seq(1,nrow(N)),breaks=10,labels=FALSE)
for(J in 1:9) {
thresh = J/10
dataset<-N[sample(nrow(N)),] #### mix up the dataset N
for(I in 1:10){
#Segement your data by fold using the which() function
testIndexes <- which(folds==I,arr.ind=TRUE)
N_test <- dataset[testIndexes, ] ### select each fold for test
N_train <- dataset[-testIndexes, ] ### select rest for training
rf = randomForest(Species~., data = N_train, mtry=3, ntree=10)
pred = predict(rf, N_test, type="prob")
label = as.factor(ifelse(pred[,1]>=thresh,"a","b"))
confusion = confusionMatrix(N_test$Species, label)
res[I,1]=thresh
res[I,2]=confusion$overall[1]
res[I,3]=confusion$byClass[3]
res[I,4]=confusion$byClass[4]
res[I,5]=confusion$byClass[7]
}
print(res)
out[J,1] = thresh
out[J,2] = mean(res[,2])
out[J,3] = mean(res[,3])
out[J,4] = mean(res[,4])
out[J,5] = mean(res[,5])
}
print(out)
Could someone please assist me in debugging the first code?
Thanks
You need to close parenthesis ) in your for loop.
Replace this
for(thresh in seq(1,9,0.5) {
with
for(thresh in seq(1,9,0.5)) {
Update:
Also, it appears that your thresh is always above 1 giving a single value R in the label, as it is never above thresh.
label = as.factor(ifelse(pred[,2]>=thresh,"M","R"))
and that creates a problem in the next statement
confusion = confusionMatrix(N_test$Class, label)
I tested with 0.5, and I get no error.
label = as.factor(ifelse(pred[,2]>=0.5,"M","R"))
If you can define a better thresh - to stay between 0 and 1, you should be fine.

Unable to run foreach in doParallel package

I'm trying to run the following R codes (https://www.r-bloggers.com/general-regression-neural-network-with-r/) to implement a General Regression Neural Network (GRNN) in R. "foreach" function is used (two times) to search for the optimal value of sigma.
pkgs <- c('MASS', 'doParallel', 'foreach', 'grnn')
lapply(pkgs, require, character.only = T)
registerDoParallel(cores = 8)
data(Boston)
# PRE-PROCESSING DATA
X <- Boston[-14]
st.X <- scale(X)
Y <- Boston[14]
boston <- data.frame(st.X, Y)
# SPLIT DATA SAMPLES
set.seed(2013)
rows <- sample(1:nrow(boston), nrow(boston) - 200)
set1 <- boston[rows, ]
set2 <- boston[-rows, ]
# DEFINE A FUNCTION TO SCORE GRNN
pred_grnn <- function(x, nn){
xlst <- split(x, 1:nrow(x))
pred <- foreach(i = xlst, .combine = rbind) %dopar% {
data.frame(pred = guess(nn, as.matrix(i)), i, row.names = NULL)
}
}
# SEARCH FOR THE OPTIMAL VALUE OF SIGMA BY THE VALIDATION SAMPLE
cv <- foreach(s = seq(0.2, 1, 0.05), .combine = rbind) %dopar% {
grnn <- smooth(learn(set1, variable.column = ncol(set1)), sigma = s)
pred <- pred_grnn(set2[, -ncol(set2)], grnn)
test.sse <- sum((set2[, ncol(set2)] - pred$pred)^2)
data.frame(s, sse = test.sse)
}
cat("\n### SSE FROM VALIDATIONS ###\n")
print(cv)
jpeg('grnn_cv.jpeg', width = 800, height = 400, quality = 100)
with(cv, plot(s, sse, type = 'b'))
cat("\n### BEST SIGMA WITH THE LOWEST SSE ###\n")
print(best.s <- cv[cv$sse == min(cv$sse), 1])
# SCORE THE WHOLE DATASET WITH GRNN
final_grnn <- smooth(learn(set1, variable.column = ncol(set1)), sigma = best.s)
pred_all <- pred_grnn(boston[, -ncol(set2)], final_grnn)
jpeg('grnn_fit.jpeg', width = 800, height = 400, quality = 100)
plot(pred_all$pred, boston$medv)
dev.off()
But the following error occurred after the second "foreach" function (I mean, after cv).
Error in { : task 1 failed - "unused argument (sigma = s)"
any help would be appreciated.

Performing t-Test Selection manually

I’m trying to write simulation code, that generates data and runs t-test selection (discarding those predictors whose t-test p-value exceeds 0.05, retaining the rest) on it. The simulation is largely an adaptation of Applied Econometrics with R by Kleiber and Zeileis (2008, pp. 183–189).
When running the code, it usually fails. Yet with certain seeds (e.g. 1534) it produces plausible output. If it does not produce output (e.g. 1911), it fails due to: "Error in x[, ii] : subscript out of bounds", which traces back to na.omit.data.frame(). So, for some reason, the way I attempt to handle the NAs seems to fail, but I'm unable to figure out in how so.
coef <- rep(coef[,3], length.out = pdim+1)
err <- as.vector(rnorm(nobs, sd = sd))
uX <- c(rep(1, times = nobs))
pX <- matrix(scale(rnorm(nobs)), byrow = TRUE, ncol = pdim, nrow = nobs)
X <- cbind(uX, pX)
y <- coef %*% t(X) + err
y <- matrix(y)
tTp <- (summary(lm(y ~ pX)))$coefficients[,4]
tTp <- tTp[2:length(tTp)]
TTT <- matrix(c(tTp, rep(.7, ncol(pX)-length(tTp))))
tX <- matrix(NA, ncol = ncol(pX), nrow = nrow(pX))
for(i in 1:ncol(pX)) {ifelse(TTT[i,] < ALPHA, tX[,i] <- pX[,i], NA)}
tX <- matrix(Filter(function(x)!all(is.na(x)), tX), nrow = nobs)
TTR <- lm(y ~ tX)
The first block is unlikely to the cause of the error. It merely generates the data and works well on its own and with other methods, like PCA, as well. The second block pulls the p-values from the regression output; removes the p-value of the intercept (beta_0); and fills the vector with as many 7s as necessary to have the same length as the number of variables, to ensure the same dimension for matrix calculations. Seven is arbitrary and could be any number larger than 0.05 to not pass the test of the loop. This becomes – I believe – necessary, if R discards predictors due to multicollinearity.
The final block creates an empty matrix of the original dimensions; inserts the original data, if the t-test p-value is lower than 0.05, else retains the NA; while the penultimate line removes all columns containing NAs ((exclusively NA or one NA is the same here) taken from mnel’s answer to Remove columns from dataframe where ALL values are NA); lastly, the modified data is again put in the shape of a linear regression.
Does anyone know what causes this behavior or how it would work as intended? I would expect it to either work or not, but not kind of both. Ideally, the former.
A working version of the code is:
set.seed(1534)
Sim_TTS <- function(nobs = c(1000, 15000), pdim = pdims, coef = coef100,
model = c("MLC", "MHC"), ...){
DGP_TTS <- function(nobs = 1000, model = c("MLC", "MHC"), coef = coef100,
sd = 1, pdim = pdims, ALPHA = 0.05)
{
model <- match.arg(model)
if(model == "MLC") {
coef <- rep(coef[,1], length.out = pdim+1)
err <- as.vector(rnorm(nobs, sd = sd))
uX <- c(rep(1, times = nobs))
pX <- matrix(scale(rnorm(nobs)), byrow = TRUE, ncol = pdim, nrow = nobs)
X <- cbind(uX, pX)
y <- coef %*% t(X) + err
y <- matrix(y)
tTp <- (summary(lm(y ~ pX)))$coefficients[,4]
tTp <- tTp[2:length(tTp)]
TTT <- matrix(c(tTp, rep(.7, ncol(pX)-length(tTp))))
tX <- matrix(NA, ncol = ncol(pX), nrow = nrow(pX))
for(i in 1:ncol(pX)) {ifelse(TTT[i,] < ALPHA, tX[,i] <- pX[,i], NA)}
tX <- matrix(Filter(function(x)!all(is.na(x)), tX), nrow = nobs)
TTR <- lm(y ~ tX)
} else {
coef <- rep(coef[,2], length.out = pdim+1)
err <- as.vector(rnorm(nobs, sd = sd))
uX <- c(rep(1, times = nobs))
pX <- matrix(scale(rnorm(nobs)), byrow = TRUE, ncol = pdim, nrow = nobs)
X <- cbind(uX, pX)
y <- coef %*% t(X) + err
y <- matrix(y)
tTp <- (summary(lm(y ~ pX)))$coefficients[,4]
tTp <- tTp[2:length(tTp)]
TTT <- matrix(c(tTp, rep(.7, ncol(pX)-length(tTp))))
tX <- matrix(NA, ncol = ncol(pX), nrow = nrow(pX))
for(i in 1:ncol(pX)) {ifelse(TTT[i,] < ALPHA, tX[,i] <- pX[,i], NA)}
tX <- matrix(Filter(function(x)!all(is.na(x)), tX), nrow = nobs)
TTR <- lm(y ~ tX)
}
return(TTR)
}
PG_TTS <- function(nrep = 1, ...)
{
rsq <- matrix(rep(NA, nrep), ncol = 1)
rsqad <- matrix(rep(NA, nrep), ncol = 1)
pastr <- matrix(rep(NA, nrep), ncol = 1)
vmat <- cbind(rsq, rsqad, pastr)
colnames(vmat) <- c("R sq.", "adj. R sq.", "p*")
for(i in 1:nrep) {
vmat[i,1] <- summary(DGP_TTS(...))$r.squared
vmat[i,2] <- summary(DGP_TTS(...))$adj.r.squared
vmat[i,3] <- length(DGP_TTS(...)$coefficients)-1
}
return(c(mean(vmat[,1]), mean(vmat[,2]), round(mean(vmat[,3]))))
}
SIM_TTS <- function(...)
{
prs <- expand.grid(pdim = pdim, nobs = nobs, model = model)
nprs <- nrow(prs)
pow <- matrix(rep(NA, 3 * nprs), ncol = 3)
for(i in 1:nprs) pow[i,] <- PG_TTS(pdim = prs[i,1],
nobs = prs[i,2], model = as.character(prs[i,3]), ...)
rval <- rbind(prs, prs, prs)
rval$stat <- factor(rep(1:3, c(nprs, nprs, nprs)),
labels = c("R sq.", "adj. R sq.", "p*"))
rval$power <- c(pow[,1], pow[,2], pow[,3])
rval$nobs <- factor(rval$nobs)
return(rval)
}
psim_TTS <- SIM_TTS()
tab_TTS <- xtabs(power ~ pdim + stat + model + nobs, data = psim_TTS)
ftable(tab_TTS, row.vars = c("model", "nobs", "stat"), col.vars = "pdim")}
FO_TTS <- Sim_TTS()
FO_TTS
}
Preceeded by:
pdims <- seq(12, 100, 4)
coefLC12 <- c(0, rep(0.2, 4), rep(0.1, 4), rep(0, 4))/1.3
rtL <- c(0.2, rep(0, 3))/1.3
coefLC100 <- c(coefLC12, rep(rtL, 22))
coefHC12 <- c(0, rep(0.8, 4), rep(0.4, 4), rep(0, 4))/1.1
rtH <- c(0.8, rep(0, 3))/1.1
coefHC100 <- c(coefHC12, rep(rtH, 22))
coef100 <- cbind(coefLC100, coefHC100)
I’m aware that model selection via the significance of individual predictors is not recommended, but that is the whole point – it is meant to be compared to more sophisticated methods.

Error in R-script: error in abs (alpha) non-numeric argument to mathematical function

I am trying to reproduce some results from the book "Financial Risk Modelling and Portfolio Optimisation with R" and I get an error that I can't seem to get my head around.
I get the following error in the COPPosterior function:
error in abs(alpha) : non-numeric argument to mathematical function
Is anyone able to see why I get the error?
The error is from the following script:
library(urca)
library(vars)
library(fMultivar)
## Loading data set and converting to zoo
data(EuStockMarkets)
Assets <- as.zoo(EuStockMarkets)
## Aggregating as month-end series
AssetsM <- aggregate(Assets, as.yearmon, tail, 1)
head(AssetsM)
## Applying unit root tests for sub-sample
AssetsMsub <- window(AssetsM, start = start(AssetsM),
end = "Jun 1996")
## Levels
ADF <- lapply(AssetsMsub, ur.df, type = "drift",
selectlags = "AIC")
ERS <- lapply(AssetsMsub, ur.ers)
## Differences
DADF <- lapply(diff(AssetsMsub), ur.df, selectlags = "AIC")
DERS <- lapply(diff(AssetsMsub), ur.ers)
## VECM
VEC <- ca.jo(AssetsMsub, ecdet = "none", spec = "transitory")
summary(VEC)
## Index of time stamps in back test (extending window)
idx <- index(AssetsM)[-c(1:60)]
ANames <- colnames(AssetsM)
NAssets <- ncol(AssetsM)
## Function for return expectations
f1 <- function(x, ci, percent = TRUE){
data <- window(AssetsM, start = start(AssetsM), end = x)
Lobs <- t(tail(data, 1))
vec <- ca.jo(data, ecdet = "none", spec = "transitory")
m <- vec2var(vec, r = 1)
fcst <- predict(m, n.ahead = 1, ci = ci)
LU <- matrix(unlist(fcst$fcst),
ncol = 4, byrow = TRUE)[, c(2, 3)]
RE <- rep(0, NAssets)
PView <- LU[, 1] > Lobs
NView <- LU[, 2] < Lobs
RE[PView] <- (LU[PView, 1] / Lobs[PView, 1] - 1)
RE[NView] <- (LU[NView, 1] / Lobs[NView, 1] - 1)
names(RE) <- ANames
if(percent) RE <- RE * 100
return(RE)
}
ReturnEst <- lapply(idx, f1, ci = 0.5)
qv <- zoo(matrix(unlist(ReturnEst),
ncol = NAssets, byrow = TRUE), idx)
colnames(qv) <- ANames
tail(qv)
library(BLCOP)
library(fPortfolio)
## Computing returns and EW-benchmark returns
R <- (AssetsM / lag(AssetsM, k = -1) -1.0) * 100
## Prior distribution
## Fitting of skewed Student's t distribution
MSTfit <- mvFit(R, method = "st")
mu <- c(MSTfit#fit[["beta"]])
S <- MSTfit#fit[["Omega"]]
skew <- c(MSTfit#fit[["alpha"]])
df <- MSTfit#fit[["df"]]
CopPrior <- mvdistribution("mvst", dim = NAssets, mu = mu,
Omega = S, alpha = skew, df = df)
## Pick matrix and view distributions for last forecast
RetEstCop <- ReturnEst[[27]]
RetEstCop
PCop <- matrix(0, ncol = NAssets, nrow = 3)
colnames(PCop) <- ANames
PCop[1, ANames[1]] <- 1
PCop[2, ANames[2]] <- 1
PCop[3, ANames[4]] <- 1
Sds <- apply(R, 2, sd)
RetViews <- list(distribution("norm", mean = RetEstCop[1],
sd = Sds[1]),
distribution("norm", mean = RetEstCop[2],
sd = Sds[2]),
distribution("norm", mean = RetEstCop[4],
sd = Sds[4])
)
CopViews <- COPViews(pick = PCop, viewDist = RetViews,
confidences = rep(0.5, 3),
assetNames = ANames)
## Simulation of posterior
NumSim <- 10000
CopPost <- COPPosterior(CopPrior, CopViews,
numSimulations = NumSim)
print(CopPrior)
print(CopViews)
slotNames(CopPost)
look at the structure of MSTfit:
str(MSTfit)
You can see that if you want the estimated alpha value, you need to access it via:
MSTfit#fit$estimated[['alpha']]
rather than
MSTfit#fit[['alpha']]

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