library(fda)

library(fda.usc)

data(aemet,package = "fda.usc")

names(aemet)

write.matrix(aemet, "aemet.csv")

tt = aemet$temp$argvals #start with 0.5 to 364.5

temp = as.data.frame(aemet$temp$data,row.names=F)

range.tt = aemet$temp$rangeval#0 to 365

inv.temp = data.frame(t(aemet$temp$data)) # 365 x 73 matrix

names(inv.temp) = aemet$df$name # Oviedo is the 10th column of inv.temp

temp_k7 = create.fourier.basis(rangeval = range(tt),nbasis = 7)

#temp_k8 = create.fourier.basis(rangeval = range(tt),nbasis = 8)

phimat = eval.basis(tt,basisobj=temp_k7)

#phimat1 = eval.basis(tt,basisobj=temp_k8)

phi.frame = data.frame(cbind(phimat,tt))

plot(phi.frame)

#install.packages(melt)

#library(melt)

#melt.phi = melt(data=phi.frame,id.vars="tt")

ovibasis5 = create.fourier.basis(rangeval = range(tt),nbasis = 5)

ovibasis50 = create.fourier.basis(rangeval = range(tt),nbasis = 50)

ovibasis121 = create.fourier.basis(rangeval = range(tt),nbasis = 121)

ovifourier5.fd = smooth.basis(argvals = tt, y = inv.temp[,10],fdParobj = ovibasis5)$fd

ovifourier51.fd = smooth.basis(argvals = tt, y = inv.temp[,10],fdParobj = ovibasis50)$fd

ovifourier121.fd = smooth.basis(argvals = tt, y = inv.temp[,10],fdParobj = ovibasis121)$fd

ovi5 = eval.fd(tt,ovifourier5.fd)

ovi51 = eval.fd(tt,ovifourier51.fd)

ovi121 = eval.fd(tt,ovifourier121.fd)

oviedo =
setNames(data.frame(inv.temp[,10],ovi5,ovi51,ovi121),c("Oviedo","Fourier5","Fourier51","Fourier1
21"))

#plot(inv.temp[,10],ovi5,ovi51,ovi121, xlab="time", ylab="temp")

library(ggplot2)

plot(inv.temp[,10],xlab="time(days)",ylab="temp",pch=16,cex=0.5, main="temperature oviedo")

#lines(inv.temp[,10], col = "red")

lines(smooth.spline(tt,inv.temp[,10]),col="blue",lwd=2)

lines(tt,ovi5,col="red",lwd=2)

lines(tt,ovi51,col="green",lwd=2)

lines(tt,ovi121,col="cornflowerblue",lwd=2)

legend("topleft", # Add legend to line plot

col = c("blue","red", "green", "cornflowerblue"),

lty = 1,

lwd = 2,

c("Smoothing", "ovi5", "ovi51", "ovi121"))

#plot(Minutes, Temperature, type = "l", # Regular X-Y plot in R

main = "Body Temperature of Beavers Over Time")

lines(lowess_values, col = "red")

lines(lowess(Minutes, Temperature, f = 0.1), col = "green") # Add lowess values with different
normalization

lines(lowess(Minutes, Temperature, f = 5), col = "cornflowerblue")

legend("topleft", # Add legend to line plot

col = c("blue","red", "green", "cornflowerblue"),

lty = 1,

lwd = 2,

c("Smoothing", "ovi5", "ovi51", "ovi121"))

maks<-365

for(i in c(1:365)){

ovibasis(i=i)= create.fourier.basis(rangeval = range(tt),nbasis = i)

ovifourier(i).fd = smooth.basis(argvals = tt, y = inv.temp[,10],fdParobj = ovibasis(i))$fd

ovi(i) = eval.fd(tt,ovifourier(i).fd)

** Examples

library(fda.usc)

# Create a minimal Fourier basis for annual data

# using 3 basis functions

yearbasis3 <- create.fourier.basis(c(0,365),

axes=list("axesIntervals") )

# plot the basis

plot(yearbasis3)
# Identify the months with letters

plot(yearbasis3, axes=list('axesIntervals', labels=monthLetters))

# The same labels as part of the basis object

yearbasis3. <- create.fourier.basis(c(0,365),

axes=list("axesIntervals", labels=monthLetters) )

plot(yearbasis3.)

# set up the Fourier basis for the monthly temperature data,

# using 9 basis functions with period 12 months.

monthbasis <- create.fourier.basis(c(0,12), 9, 12.0)

# plot the basis

plot(monthbasis)

# Create a false Fourier basis using 1 basis function.

falseFourierBasis <- create.fourier.basis(nbasis=5)

# plot the basis: constant

plot(falseFourierBasis)

## Not run:

a1<-seq(0,1,by=.01)

a2=rnorm(length(a1),sd=0.2)

f1<-(sin(2*pi*a1))+rnorm(length(a1),sd=0.2)

nc<-50

np<-length(f1)

tt=1:101

S<-S.NW(tt,2)

mdata<-matrix(NA,ncol=np,nrow=50)

for (i in 1:50) mdata[i,]<- (sin(2*pi*a1))+rnorm(length(a1),sd=0.2)

mdata<-fdata(mdata)

nb<-floor(seq(5,29,len=5))

l<-2^(-5:15)

out<-optim.basis(mdata,lambda=l,numbasis=nb,type.basis="fourier")

matplot(t(out$gcv),type="l",main="GCV with fourier basis")

# out1<-optim.basis(mdata,type.CV = CV.S,lambda=l,numbasis=nb)

# out2<-optim.basis(mdata,lambda=l,numbasis=nb)

# variance calculations

y<-mdata

i<-3

z=qnorm(0.025/np)

fdata.est<-out$fdata.est

var.e<-Var.e(mdata,out$S.opt)

var.y<-Var.y(mdata,out$S.opt)

var.y2<-Var.y(mdata,out$S.opt,var.e)

# estimated fdata and point confidence interval

upper.var.e<-out$fdata.est[["data"]][i,]-z*sqrt(diag(var.e))

lower.var.e<-out$fdata.est[["data"]][i,]+z*sqrt(diag(var.e))

dev.new()

plot(y[i,],lwd=1,ylim=c(min(lower.var.e),max(upper.var.e)))

lines(out$fdata.est[["data"]][i,],col=gray(.1),lwd=1)

lines(out$fdata.est[["data"]][i,]+z*sqrt(diag(var.y)),col=gray(0.7),lwd=2)

lines(out$fdata.est[["data"]][i,]-z*sqrt(diag(var.y)),col=gray(0.7),lwd=2)

lines(upper.var.e,col=gray(.3),lwd=2,lty=2)

lines(lower.var.e,col=gray(.3),lwd=2,lty=2)

legend("top",legend=c("Var.y","Var.error"), col = c(gray(0.7),

gray(0.3)),lty=c(1,2))
## End(Not run)

###################################################

### tecator dataset

###################################################

library("fda.usc")

data("tecator")

names(tecator)

absorp <- tecator$absorp.fdata

Fat20 <- ifelse(tecator$y$Fat < 20, 0, 1) * 2 + 2

absorp$names$main <- ""

dev.new( width = 150,height = 110, units = "mm")

par(mfrow = c(1 , 2))

# Figure 1 (left panel)

plot(absorp, col = Fat20)

absorp.d1 <- fdata.deriv(absorp, nderiv = 1)

# Figure 1 (right panel)

plot(absorp.d1, col = Fat20)

###################################################

### convert fdata class to fd class

###################################################

class( absorp.fd <- fdata2fd( absorp, type.basis = "fourier", nbasis = 15) )

class( absorp.fdata <- fdata(absorp.fd) )

###################################################

### phoneme data and smoothing

###################################################

data(phoneme)
learn <- phoneme$learn

l <- c(0 ,2 ^ seq(-2, 9, len = 30))

nb <- seq(7, 31, by = 2)

out0 <- optim.basis(learn, lambda = l, numbasis = nb)

out1 <- optim.np(learn, type.S = S.NW, par.CV = list(criteria = "GCV"))

out2 <- optim.np(learn, type.S = S.LLR, par.CV = list(criteria = "GCV"))

out3 <- optim.np(learn, type.S = S.KNN, h = 3:25, Ker = Ker.unif)

###################################################

### plot GCV criteria

###################################################

dev.new(width = 150, height = 110, units = "mm")

par(mfrow = c(1,2))

contour(nb, l, out0$gcv, ylab = "Lambda", xlab = "Number of basis",

main = "GCV criteria by min.basis()")

plot(out1$h, out1$gcv, type = "l", main = "GCV criteria by min.np() ",

xlab = "Bandwidth (h) values",ylab = "GCV criteria", col = 3, lwd = 2)

legend(x = 3, y = 4.3, legend = c("Ker.norm-S.NW", "Ker.norm-S.LLR", "Ker.unif-S.KNN"),

box.col = "white", lwd = c(2, 2, 2), col = c(3, 4, 2),cex = 0.75)

lines(out2$h,out2$gcv, col = 4, lwd = 2)

lines(out3$h,out3$gcv, col = 2, lwd = 2)

###################################################

### smoothing a fdata curve

###################################################

dev.new( width = 150, height = 100, units = "mm")

ind <- 11

nam <- expression( paste("Phoneme curve"[11]) )

plot(learn[ind, ], main = nam, lty = 2, lwd = 2, col = 8)

legend(x = 70, y = 19, legend = c("Curve","Bspline basis",

"Ker.norm-S.NW", "Ker.norm-S.LLR", "Ker.unif-S.KNN"),

lty = c(2, 1, 1, 1, 1), lwd = 2, col = c(8, 1, 3, 4, 2), box.col = "white")

lines(out0$fdata.est[ind, ], col = 1, lty = 1, lwd = 2)

lines(out1$fdata.est[ind, ], col = 3, lty = 1, lwd = 2)

lines(out2$fdata.est[ind, ], col = 4, lty = 1, lwd = 2)

lines(out3$fdata.est[ind, ], col = 2, lty = 1, lwd = 2)

lines(out0$fdata.est[ind, ], col = 1, lty = 1, lwd = 2)

###################################################

### metric and semimetric measures

###################################################

glearn <- phoneme$classlearn

mdist <- metric.lp(learn)

###################################################

### dendogram

###################################################

ind <- c(120:130,220:230)

dev.new()

a <- mdist[ind,ind]

b <- as.dist(a)

c2 <- hclust(b)

c2$labels <- phoneme$classlearn[ind]

dev.new( width = 110, height = 80, units = "mm")

plot(c2, main = "Dendogram", xlab = "Class of each leaf")

###################################################

### figure depth

###################################################

data(poblenou)

nox <- poblenou$nox

working <- poblenou$nox[poblenou$df$day.festive == 0 &

as.integer(poblenou$df$day.week) < 6]

nonworking <- poblenou$nox[poblenou$df$day.festive == 1 |

as.integer(poblenou$df$day.week) > 5]

# Centrality measures (working)

dev.new( width = 180,height = 150, units = "mm")

par( mfrow=c(2, 2) )

plot(func.mean(working), ylim = c(10, 170),

main = "Centrality measures in working days")

legend(x = 11, y = 170, cex = 1, box.col = "white", lty = 1:5,

col = c(1:5), legend = c("mean","trim.mode","trim.RP",

"median.mode","median.RP"))

lines(func.trim.mode(working, trim = 0.15), col = 2, lty = 2)

lines(func.trim.RP(working, trim = 0.15), col = 3, lty = 3)

lines(func.med.mode(working, trim = 0.15), col = 4, lty = 4)

lines(func.med.RP(working, trim = 0.15), col = 5, lty = 5)

# Centrality measures (non-working)

plot(func.mean(nonworking), ylim = c(10,170),

main = "Centrality measures in non-working days")

legend(x = 11, y = 170, cex = 1, box.col = "white",lty = 1:5,

col = c(1:5), legend = c("mean","trim.mode","trim.RP",

"median.mode","median.RP"))

lines(func.trim.mode(nonworking, trim = 0.15),col = 2, lty = 2)

lines(func.trim.RP(nonworking, trim = 0.15),col = 3, lty = 3)

lines(func.med.mode(nonworking, trim = 0.15),col = 4, lty = 4)

lines(func.med.RP(nonworking, trim = 0.15),col = 5, lty = 5)

# Measures of dispersion (working)

plot(func.var(working),

main = "Dispersion measures in working days", ylim = c(100 ,5500))

legend(x = 11, y = 5300,cex = 1, box.col = "white", lty = 1:3, col = 1:3,

legend = c("var", "trimvar.mode", "trimvar.RP"))

lines(func.trimvar.mode(working,trim = 0.15), col = 2, lty = 2)

lines(func.trimvar.RP(working,trim = 0.15), col = 3, lty = 3)

# Measures of dispersion (non-working)

plot(func.var(nonworking),

main = "Dispersion measures in non-working days", ylim = c(100, 5500))

legend(x = 11, y = 5300, cex = 1, box.col = "white", lty = 1:3, col = 1:3,

legend = c("var", "trimvar.mode", "trimvar.RP"))

lines(func.trimvar.mode(nonworking, trim = 0.15), col = 2, lty = 2)

lines(func.trimvar.RP(nonworking, trim = 0.15), col = 3, lty = 3)

###################################################

### plot funtional bootstrap

###################################################

# This takes a lot

dev.new(width = 150, height = 110, units = "mm")

par(mfrow = c(1, 2))

out.boot1 <- fdata.bootstrap(working, statistic = func.trim.RP, nb = 1000, draw = TRUE)

out.boot2 <- fdata.bootstrap(nonworking,statistic = func.trim.RP ,nb = 1000, draw = TRUE)

###################################################

### functional outlier detection

###################################################

# This take a lot

nox <- poblenou$nox

working <- poblenou$nox[poblenou$df$day.festive == 0 &

as.integer(poblenou$df$day.week) < 6]

nonworking <- poblenou$nox[poblenou$df$day.festive == 1 |

as.integer(poblenou$df$day.week) > 5]
out1 <- outliers.depth.trim(working, dfunc=depth.FM,

nb=1000, smo=0.1, trim=0.06)

out2 <- outliers.depth.trim(nonworking, dfunc=depth.FM,

nb=1000, smo=0.1, trim=0.1)

###################################################

### Figure outlier detection

###################################################

dev.new( width=150, height=110, units="mm")

par(mfrow=c(1, 2))

plot(working, ylim=c(0,400), col="gray", lty=1,

main="NOx - Working days")

lines(working[out1[[1]]], col=2, lty=2, lwd=2)

plot(nonworking, ylim=c(0,400), col="gray", lty=1,

main="NOx - Non working days")

lines(nonworking[out2[[1]]], col=2, lty=2, lwd=2)

###################################################

### functional regression model

###################################################

ind <- 1:165

tt <- absorp[["argvals"]]

# training data

y <- tecator$y$Fat[ind]

X <- absorp[ind, ]

X.d1 <- fdata.deriv(X, nbasis = 19, nderiv = 1)

X.d2 <- fdata.deriv(X, nbasis = 19, nderiv = 2)

###################################################

### fregre.basis
###################################################

rangett <- absorp$rangeval

basis1 <- create.fourier.basis(rangeval = rangett,

nbasis=5)

res.basis1 <- fregre.basis(X.d1, y, basis.x = basis1)

###################################################

### summary.fregre.fd

###################################################

dev.new( width = 160, height = 130,units = "mm")

summary(res.basis1)

###################################################

### fregre.pc

###################################################

res.pc1 <- fregre.pc(X.d1, y, l = 1:6)

###################################################

### fregre.pc.cv

###################################################

res.pc2 <- fregre.pc.cv(X.d2, y, kmax = 7)

res.pc2$pc.opt

res.pc2$MSC

###################################################

### fregre.pls

###################################################

fregre.pls(X.d1, y, l = 1:5)

res.pls1 <- fregre.pls.cv(X.d1, y)$fregre.pls

###################################################
### influence measures

###################################################

# This take a lot

res.infl <- influence.fdata(res.basis1)

# Influence Measure for FPC regression

mat <- cbind(res.infl$DCP, res.infl$DCE, res.infl$DP)

colnames(mat)=c("CPi", "CEi", "Pi")

dev.new( width=140, height = 110, units = "mm")

pairs(mat)

###################################################

### functional beta estimation

###################################################

res.boot1 <- fregre.bootstrap(res.basis1, nb = 1000,

kmax.fix = TRUE, alpha = 0.999)

res.boot2 <- fregre.bootstrap(res.pc1, nb = 1000,

kmax.fix = TRUE, alpha = 0.999)

res.boot3 <- fregre.bootstrap(res.pls1, nb = 1000,

kmax.fix = TRUE, alpha = 0.999)

dev.new( width = 170, height = 130, units = "mm")

par(mfrow=c(1, 3))

yl <- c(-200, 220)

out <- res.boot1$norm.boot > quantile(res.boot1$norm.boot, 0.999)

plot(res.boot1$betas.boot,

col="grey", main = "5 Fourier basis elements", ylim = yl, lty=1, lwd=2)

lines(res.basis1$beta.est, col = 4, lwd = 1, lty = 1)

lines(res.boot1$betas.boot[out], lwd = 2, col = 2, lty = 2)

out <- res.boot2$norm.boot > quantile(res.boot2$norm.boot, 0.999)

plot(res.boot2$betas.boot,

col="grey", main="1st 6 FPC", ylim = yl, lty = 1, lwd = 2)

lines(res.pc1$beta.est,col = 4, lwd = 1, lty = 1)

lines(res.boot2$betas.boot[out], lwd = 2, col = 2, lty = 2)

out <- res.boot3$norm.boot > quantile(res.boot3$norm.boot, 0.999)

plot(res.boot3$betas.boot,

col = "grey", main = "1st 5 FPLS", ylim = yl, lty = 1, lwd = 2)

lines(res.pls1$beta.est, col = 4, lwd = 1, lty = 1)

lines(res.boot3$betas.boot[out], col = 2, lwd=2, lty = 2)

###################################################

### fregre.lm

###################################################

ind <- 1:165

dataf <- as.data.frame(tecator$y[ind, ])

newdataf <- as.data.frame(tecator$y[-ind, ])

ldata=list("df" = dataf, "X" = X, "X.d1" = X.d1, "X.d2" = X.d2)

basis.x <- list("X" = basis1)

basis2 <- create.bspline.basis(rangeval = rangett, nbasis = 5)

basis.b <- list("X" = basis2)

# functional data with basis representation

f2<- Fat ~ Water + X.d2

basis.x1 <- list("X.d1" = basis1)

basis.b1 <- list("X.d1" = basis2)

res.lm2 <- fregre.lm(f2, ldata, basis.x = basis.x1, basis.b = basis.b1)

###################################################

### fregre.np

###################################################

# Functional nonparametric regression

fregre.np(X.d1, y)

###################################################
### fregre.plm

###################################################

# Functional semi-parametric regression

res.plm2 <- fregre.plm(Fat ~ Water + X.d2,ldata)

###################################################

### prediction I

###################################################

newy <- matrix(tecator$y$Fa[-ind], ncol = 1)

newX.d1 <- fdata.deriv(absorp[-ind , ], nbasis = 19,nderiv = 1)

newX.d2 <- fdata.deriv(absorp[-ind, ], nbasis = 19,nderiv = 2)

res.basis2 <- fregre.basis.cv(X.d2, y, type.basis = "bspline")

pred.basis2 <- predict.fregre.fd(res.basis2, newX.d2)

res.np2 <- fregre.np.cv(X.d1, y, metric = semimetric.deriv)

pred.np2 <- predict.fregre.fd(res.np2, newX.d1)

# Functional and nonfunctional covariate

newldata <- list("df" = newdataf, "X.d1" = newX.d1, "X.d2" = newX.d2)

f1 <- Fat ~ Water + X.d1

basis.x1 <- list(X.d1 = basis1)

basis.b1 <- list(X.d1 = basis2)

res.lm1 <- fregre.lm(f1, ldata, basis.x = basis.x1,

basis.b <- basis.b1)

pred.lm1<-predict.fregre.lm(res.lm1, newldata)

res.plm1 <- fregre.plm(f1, ldata)

pred.plm1 <- predict.fregre.plm(res.plm1, newldata)

###################################################

### prediction III

###################################################

pred.basis1 <- predict.fregre.fd(res.basis1, newX.d1)

pred.pc1 <- predict.fregre.fd(res.pc1, newX.d1)

pred.pls1 <- predict.fregre.fd(res.pls1, newX.d1)

res.np1 <- fregre.np.cv(X.d1, y)

pred.np1 <- predict.fregre.fd(res.np1, newX.d1)

res.pls2 <- fregre.pls.cv(X.d2, y, criteria = "CV")$fregre.pls

pred.pls2 <- predict.fregre.fd(res.pls2, newX.d2)

pred.pc2 <- predict.fregre.fd(res.pc2$fregre.pc, newX.d2)

pred.lm2 <- predict.fregre.lm(res.lm2, newldata)

pred.plm2 <- predict.fregre.plm(res.plm2, newldata)

###################################################

### Table 1, Goodness of fit

###################################################

GOF.predict <- function(model,pred,newy){

if (any(class(model)=="fregre.fd")) {

df <- model$df

r2 <- model$r2

sr2 <- model$sr2

else {

if (any(class(model) == "lm")) {

smr <- summary(model)

df <- smr$df[1]

r2 <- smr$r.squared

sr2 <- sum(model$residuals^2) / (length(model$residuals) - df)

MEP <- ((1 / length(newy)) * sum((newy - pred)^2)) / var(newy)

out <- cbind(round(df, 1), round(r2, 3), round(sr2, 3), round(MEP, 4))

colnames(out) <- c("df", "R-squared", "Sr2", "MEP")

out
}

tabl <- matrix(NA, nrow = 12, ncol = 4)

tabl[1, ] <- GOF.predict(res.basis1, pred.basis1, newy)

tabl[2, ] <- GOF.predict(res.basis2, pred.basis2, newy)

tabl[3, ] <- GOF.predict(res.pc1, pred.pc1, newy)

tabl[4, ] <- GOF.predict(res.pc2$fregre.pc, pred.pc2, newy)

tabl[5, ] <- GOF.predict(res.pls1, pred.pls1, newy)

tabl[6, ] <- GOF.predict(res.pls2, pred.pls2, newy)

tabl[7, ] <- GOF.predict(res.lm1, pred.lm1, newy)

tabl[8, ] <- GOF.predict(res.lm2, pred.lm2, newy)

tabl[9, ] <- GOF.predict(res.np1, pred.np1, newy)

tabl[10, ] <- GOF.predict(res.np2, pred.np2, newy)

tabl[11, ] <- GOF.predict(res.plm1, pred.plm1, newy)

tabl[12, ] <- GOF.predict(res.plm2, pred.plm2,newy)

colnames(tabl) <- c("df", "R-squared", "Sr2", "MEP")

tabl

## Not run:

a1<-seq(0,1,by=.01)

a2=rnorm(length(a1),sd=0.2)

f1<-(sin(2*pi*a1))+rnorm(length(a1),sd=0.2)

nc<-50

np<-length(f1)

tt=1:101

S<-S.NW(tt,2)

mdata<-matrix(NA,ncol=np,nrow=50)

for (i in 1:50) mdata[i,]<- (sin(2*pi*a1))+rnorm(length(a1),sd=0.2)

mdata<-fdata(mdata)

nb<-floor(seq(5,29,len=5))

l<-2^(-5:15)
out<-optim.basis(mdata,lambda=l,numbasis=nb,type.basis="fourier")

matplot(t(out$gcv),type="l",main="GCV with fourier basis")

out1<-optim.basis(mdata,type.CV = CV.S,lambda=l,numbasis=nb)

out2<-optim.basis(mdata,lambda=l,numbasis=nb)

# variance calculations

y<-mdata

i<-3

z=qnorm(0.025/np)

fdata.est<-out$fdata.est

var.e<-Var.e(mdata,out$S.opt)

var.y<-Var.y(mdata,out$S.opt)

var.y2<-Var.y(mdata,out$S.opt,var.e)

# estimated fdata and point confidence interval

upper.var.e<-out$fdata.est[["data"]][i,]-z*sqrt(diag(var.e))

lower.var.e<-out$fdata.est[["data"]][i,]+z*sqrt(diag(var.e))

dev.new()

plot(y[i,],lwd=1,ylim=c(min(lower.var.e),max(upper.var.e)))

lines(out$fdata.est[["data"]][i,],col=gray(.1),lwd=1)

lines(out$fdata.est[["data"]][i,]+z*sqrt(diag(var.y)),col=gray(0.7),lwd=2)

lines(out$fdata.est[["data"]][i,]-z*sqrt(diag(var.y)),col=gray(0.7),lwd=2)

lines(upper.var.e,col=gray(.3),lwd=2,lty=2)

lines(lower.var.e,col=gray(.3),lwd=2,lty=2)

legend("top",legend=c("Var.y","Var.error"), col = c(gray(0.7),

gray(0.3)),lty=c(1,2))

## End(Not run)