Nothing
ITPaovbspline <-
function(formula,order=2,nknots=dim(model.response(model.frame(formula)))[2],B=10000,method='residuals'){
fisher_cf_L <- function(L){ #fisher on rows of the matrix L
return(-2*rowSums(log(L)))
}
fisher_cf <- function(lambda){ #fisher on vector lambda
return(-2*sum(log(lambda)))
}
pval.correct <- function(pval.matrix){
matrice_pval_2_2x <- cbind(pval.matrix,pval.matrix)
p <- dim(pval.matrix)[2]
matrice_pval_2_2x <- matrice_pval_2_2x[,(2*p):1]
corrected.pval <- numeric(p)
for(var in 1:p){
pval_var <- matrice_pval_2_2x[p,var]
inizio <- var
fine <- var
for(riga in (p-1):1){
fine <- fine + 1
pval_cono <- matrice_pval_2_2x[riga,inizio:fine]
pval_var <- max(pval_var,pval_cono)
}
corrected.pval[var] <- pval_var
}
corrected.pval <- corrected.pval[p:1]
return(corrected.pval)
}
stat_lm_glob <- function(anova){
result <- summary.lm(anova)$f[1]
return(result)
}
stat_aov_part <- function(anova){
result <- summary(anova)[[1]][,4]
result <- result[-length(result)]
return(result)
}
extract.residuals = function(anova){
return(anova$residuals)
}
extract.fitted = function(anova){
return(anova$fitted)
}
extract.pval <- function(anova){
result <- summary(anova)[[1]][,5]
result <- result[-length(result)]
return(result)
}
variables = all.vars(formula)
y.name = variables[1]
#data.all = model.frame(formula)
cl <- match.call()
design.matrix = model.matrix(formula)
mf = model.frame(formula)
data = model.response(mf)
dummynames.all <- colnames(design.matrix)[-1]
#var.names = variables[-1]
#nvar = length(var.names)
n <- dim(data)[1]
J <- dim(data)[2]
print('First step: basis expansion')
#splines coefficients:
eval <- data
bspl.basis <- create.bspline.basis(c(1,J),norder=order,breaks=seq(1,J,length.out=nknots))
ascissa <- seq(1,J,1)
data.fd <- Data2fd(t(data),ascissa,bspl.basis)
coeff <- t(data.fd$coef)
p <- dim(coeff)[2]
#functional data
npt <- 1000
ascissa.2 <- seq(1,J,length.out=npt)
bspl.eval.smooth <- eval.basis(ascissa.2,bspl.basis)
data.eval <- t(bspl.eval.smooth %*% t(coeff))
print('Second step: joint univariate tests')
#univariate permutations
formula.const <- deparse(formula[[3]],width.cutoff = 500L) #extracting the part after ~ on formula. this will not work if the formula is longer than 500 char
coeffnames <- paste('coeff[,',as.character(1:p),']',sep='')
formula.coeff <- paste(coeffnames,'~',formula.const)
formula.coeff <- sapply(formula.coeff,as.formula)
formula.temp = coeff ~ design.matrix
mf.temp = cbind(model.frame(formula.temp),as.data.frame(design.matrix[,-1]))
aovcoeff1 <- aov(formula.coeff[[1]],data=mf.temp)
var.names <- rownames(summary(aovcoeff1)[[1]])
df.vars <- summary(aovcoeff1)[[1]][,1]
df.residuals <- df.vars[length(df.vars)]
var.names <- var.names[-length(var.names)]
nvar = length(var.names)
for(ii in 1:nvar){
var.names[ii] <- gsub(' ' , '',var.names[ii])
}
index.vars <- cbind(c(2,(cumsum(df.vars)+2)[-length(df.vars)]),cumsum(df.vars)+1)
regr0 = lm.fit(design.matrix,coeff)
#pval_parametric <- sapply(aov0,extract.pval)
MS0 <- matrix(nrow=nvar+1,ncol=p)
for(var in 1:(nvar+1)){
MS0[var,] <- colSums(rbind(regr0$effects[index.vars[var,1]:index.vars[var,2],]^2))/df.vars[var]
}
# test statistic:
T0_part <- MS0[1:nvar,] / matrix(MS0[nvar+1,],nrow=nvar,ncol=p,byrow=TRUE)
Sigma <- chol2inv(regr0$qr$qr)
resvar <- colSums(regr0$residuals^2)/regr0$df.residual
if(nvar >1){
T0_glob <- colSums((regr0$fitted - matrix(colMeans(regr0$fitted),nrow=n,ncol=p,byrow=TRUE))^2)/ ((nvar)*resvar)
}else if(nvar==1){ #only one factor -> the permutation of the residuals is equivalent to the one of responses
method <- 'responses'
T0_glob <- colSums((regr0$fitted - matrix(colMeans(regr0$fitted),nrow=n,ncol=p,byrow=TRUE))^2)/ ((nvar)*resvar)
}else if(nvar==0){
method = 'responses' # model with only intercept -> the permutation of the residuals is equivalent to the one of responses
T0_glob = numeric(p)
}
#calculate residuals
if(method=='residuals'){
#n residuals for each coefficient of basis expansion (1:p)
#and for each partial test + global test (nvar+1)
#saved in array of dim (nvar+1,n,p)
design.matrix.names2 = design.matrix
var.names2 = var.names
if(length(grep('factor',formula.const))>0){
index.factor = grep('factor',var.names)
replace.names = paste('group',(1:length(index.factor)),sep='')
var.names2[index.factor] = replace.names
colnames(design.matrix.names2) = var.names2
}
residui = array(dim=c(nvar,n,p))
fitted_part = array(dim=c(nvar,n,p)) # fitted values of the reduced model (different for each test)
formula.coeff_part = vector('list',nvar)
regr0_part = vector('list',nvar)
dummy.interaz <- grep(':',dummynames.all)
#coeff.perm_part = array(dim=c(nvar+1,n,p))
for(ii in 1:(nvar)){ #no test on intercept
var.ii = var.names2[ii]
variables.reduced = var.names2[-which(var.names2==var.ii)] #removing the current variable to test
if(length(grep(':',var.ii))>0){ # testing interaction
#print('interaz')
var12 <- strsplit(var.ii,':')
var1 <- var12[[1]][1]
var2 <- var12[[1]][2]
dummy.test1 <- grep(var1,dummynames.all)
dummy.test2 <- grep(var2,dummynames.all)
dummy.test <- intersect(dummy.test1,dummy.test2)
dummynames.reduced <- dummynames.all[-dummy.test]
}else{
#print('nointeraz')
dummy.test <- grep(var.ii,dummynames.all)
dummy.test <- setdiff(dummy.test,dummy.interaz)
dummynames.reduced <- dummynames.all[-dummy.test]
}
if(nvar>1){
formula.temp = paste(dummynames.reduced,collapse=' + ')
}else{
formula.temp = '1' #removing the only variable -> reduced model only has intercept term
}
formula.temp2 = coeff ~ design.matrix.names2
mf.temp2 = cbind(model.frame(formula.temp2)[-((p+1):(p+nvar+1))],as.data.frame(design.matrix.names2[,-1]))
formula.coeff.temp <- paste(coeffnames,'~',formula.temp)
formula.coeff_part[[ii]] <- sapply(formula.coeff.temp,as.formula)
regr0_part[[ii]] = lapply(formula.coeff_part[[ii]],lm,data=mf.temp2)
residui[ii,,] = simplify2array(lapply(regr0_part[[ii]],extract.residuals))
fitted_part[ii,,] = simplify2array(lapply(regr0_part[[ii]],extract.fitted))
}
}
T_glob <- matrix(ncol=p,nrow=B)
T_part = array(dim=c(B,nvar,p))
for (perm in 1:B){
# the F test is the same for both methods
if(nvar >0){
permutazioni <- sample(n)
coeff_perm <- coeff[permutazioni,]
}else{ # testing intercept -> permute signs
signs <- rbinom(n,1,0.5)*2 - 1
coeff_perm <- coeff*signs
}
regr_perm = lm.fit(design.matrix,coeff_perm)
Sigma <- chol2inv(regr_perm$qr$qr)
resvar <- colSums(regr_perm$residuals^2)/regr0$df.residual
if(nvar > 0)
T_glob[perm,] <- colSums((regr_perm$fitted - matrix(colMeans(regr_perm$fitted),nrow=n,ncol=p,byrow=TRUE))^2)/ ((nvar)*resvar)
# partial tests: differ depending on the method
if(method=='responses'){
MSperm <- matrix(nrow=nvar+1,ncol=p)
for(var in 1:(nvar+1)){
MSperm[var,] <- colSums(rbind(regr_perm$effects[index.vars[var,1]:index.vars[var,2],]^2))/df.vars[var]
}
# test statistic:
T_part[perm,,] <- MSperm[1:nvar,] / matrix(MSperm[nvar+1,],nrow=nvar,ncol=p,byrow=TRUE)
}else if(method=='residuals'){
residui_perm = residui[,permutazioni,]
aov_perm_part = vector('list',nvar)
for(ii in 1:(nvar)){
coeff_perm = fitted_part[ii,,] + residui_perm[ii,,]
regr_perm = lm.fit(design.matrix,coeff_perm)
MSperm <- matrix(nrow=nvar+1,ncol=p)
for(var in 1:(nvar+1)){
MSperm[var,] <- colSums(rbind(regr_perm$effects[index.vars[var,1]:index.vars[var,2],]^2))/df.vars[var]
}
# test statistic:
T_part[perm,ii,] <- (MSperm[1:nvar,] / matrix(MSperm[nvar+1,],nrow=nvar,ncol=p,byrow=TRUE))[ii,]
}
}
}
pval_glob <- numeric(p)
pval_part = matrix(nrow=nvar,ncol=p)
for(i in 1:p){
pval_glob[i] <- sum(T_glob[,i]>=T0_glob[i])/B
pval_part[,i] = colSums(T_part[,,i]>=matrix(T0_part[,i],nrow=B,ncol=nvar,byrow=TRUE))/B
}
#combination
print('Third step: interval-wise combination and correction')
q <- numeric(B)
L_glob <- matrix(nrow=B,ncol=p)
for(j in 1:p){
ordine <- sort.int(T_glob[,j],index.return=T)$ix
q[ordine] <- (B:1)/(B)
L_glob[,j] <- q
}
L_part <- array(dim=c(B,nvar,p))
for(j in 1:p){
for(i in 1:(nvar)){
ordine <- sort.int(T_part[,i,j],index.return=T)$ix
q[ordine] <- (B:1)/(B)
L_part[,i,j] <- q
}
}
#asymmetric combination matrix:
matrice_pval_asymm_glob <- matrix(nrow=p,ncol=p)
matrice_pval_asymm_glob[p,] <- pval_glob[1:p]
pval_2x_glob <- c(pval_glob,pval_glob)
L_2x_glob <- cbind(L_glob,L_glob)
matrice_pval_asymm_part <- array(dim=c(nvar,p,p))
pval_2x_part <- cbind(pval_part,pval_part)
L_2x_part = array(dim=c(B,nvar,p*2))
for(ii in 1:(nvar)){
matrice_pval_asymm_part[ii,p,] <- pval_part[ii,1:p]
L_2x_part[,ii,] <- cbind(L_part[,ii,],L_part[,ii,])
}
for(i in (p-1):1){
for(j in 1:p){
inf <- j
sup <- (p-i)+j
T0_temp <- fisher_cf(pval_2x_glob[inf:sup])
T_temp <- fisher_cf_L(L_2x_glob[,inf:sup])
pval_temp <- sum(T_temp>=T0_temp)/B
matrice_pval_asymm_glob[i,j] <- pval_temp
for(ii in 1:(nvar )){
T0_temp <- fisher_cf(pval_2x_part[ii,inf:sup])
T_temp <- fisher_cf_L(L_2x_part[,ii,inf:sup])
pval_temp <- sum(T_temp>=T0_temp)/B
matrice_pval_asymm_part[ii,i,j] <- pval_temp
}
}
print(paste('creating the p-value matrix: end of row ',as.character(p-i+1),' out of ',as.character(p),sep=''))
}
#symmetric combination matrix
matrice_pval_symm_glob <- matrix(nrow=p,ncol=4*p)
matrice_pval_symm_part <- array(dim=c(nvar,p,4*p))
for(i in 0:(p-1)){
for(j in 1:(2*p)){
matrice_pval_symm_glob[p-i,j+i+p] <- matrice_pval_asymm_glob[p-i,(j+1)%/%2]
if(j+i>2*p-i){
matrice_pval_symm_glob[p-i,j+i-p] <- matrice_pval_asymm_glob[p-i,(j+1)%/%2]
}
for(ii in 1:(nvar)){
matrice_pval_symm_part[ii,p-i,j+i+p] <- matrice_pval_asymm_part[ii,p-i,(j+1)%/%2]
if(j+i>2*p-i){
matrice_pval_symm_part[ii,p-i,j+i-p] <- matrice_pval_asymm_part[ii,p-i,(j+1)%/%2]
}
}
}
}
corrected.pval_glob <- pval.correct(matrice_pval_asymm_glob)
corrected.pval_part = matrix(nrow=nvar,ncol=p)
for(ii in 1:(nvar)){
corrected.pval_part[ii,] = pval.correct(matrice_pval_asymm_part[ii,,])
}
coeff.regr = regr0$coeff
coeff.t <- t(bspl.eval.smooth %*% t(coeff.regr))
fitted.regr = regr0$fitted.values
fitted.t <- t(bspl.eval.smooth %*% t(fitted.regr))
rownames(corrected.pval_part) = var.names
rownames(coeff.t) = colnames(design.matrix)
rownames(coeff.regr) = colnames(design.matrix)
rownames(pval_part) = var.names
residuals.t = data.eval - fitted.t
ybar.t = colMeans(data.eval)
R2.t = colSums((fitted.t - matrix(data=ybar.t,nrow=n,ncol=npt,byrow=TRUE))^2)/colSums((data.eval - matrix(data=ybar.t,nrow=n,ncol=npt,byrow=TRUE))^2)
print('Interval Testing Procedure completed')
ITPresult <- list(call=cl,design.matrix=design.matrix,basis='B-spline',coeff=coeff,coeff.regr=coeff.regr,
pval.F=pval_glob,pval.matrix.F=matrice_pval_asymm_glob,corrected.pval.F=corrected.pval_glob,
pval.factors=pval_part,pval.matrix.factors=matrice_pval_asymm_part,corrected.pval.factors=corrected.pval_part,
data.eval=data.eval,coeff.regr.eval=coeff.t,fitted.eval=fitted.t,residuals.eval=residuals.t,
R2.eval=R2.t,
heatmap.matrix.F=matrice_pval_symm_glob,
heatmap.matrix.factors=matrice_pval_symm_part
#pval_parametric=pval_parametric
)
class(ITPresult) = 'ITPaov'
return(ITPresult)
}
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