Nothing
###############################################################################
## computation of k-step construction in case x is a matrix
###############################################################################
.onestep.loc.matrix <- function(x, initial.est, A, b, sd){
u <- A*(x-initial.est)/sd^2
ind <- b/abs(u) <= 1
IC <- rowMeans(u*(ind*b/abs(u) + !ind), na.rm = TRUE)
return(initial.est + IC)
}
.kstep.loc.matrix <- function(x, initial.est, A, b, sd, k){
est <- initial.est
for(i in 1:k){
est <- .onestep.loc.matrix(x = x, initial.est = est, A = A, b = b, sd = sd)
}
return(est)
}
.onestep.sc.matrix <- function(x, initial.est, A, a, b, mean){
v <- A*(((x-mean)/initial.est)^2-1)/initial.est - a
ind <- b/abs(v) <= 1
IC <- rowMeans(v*(ind*b/abs(v) + !ind), na.rm = TRUE)
return(initial.est + IC)
}
.kstep.sc.matrix <- function(x, initial.est, A, a, b, mean, k){
est <- .onestep.sc.matrix(x = x, initial.est = initial.est, A = A, a = a, b = b, mean = mean)
if(k > 1){
for(i in 2:k){
A <- est^2*A/initial.est^2
a <- est*a/initial.est
b <- est*b/initial.est
initial.est <- est
est <- .onestep.sc.matrix(x = x, initial.est = est, A = A, a = a, b = b, mean = mean)
}
}
A <- est^2*A/initial.est^2
a <- est*a/initial.est
b <- est*b/initial.est
return(list(est = est, A = A, a = a, b = b))
}
.onestep.locsc.matrix <- function(x, initial.est, A1, A2, a, b){
mean <- initial.est[,1]
sd <- initial.est[,2]
u <- A1*(x-mean)/sd^2
v <- A2*(((x-mean)/sd)^2-1)/sd - a
ind <- b/sqrt(u^2 + v^2) <= 1
IC1 <- rowMeans(u*(ind*b/sqrt(u^2 + v^2) + !ind), na.rm = TRUE)
IC2 <- rowMeans(v*(ind*b/sqrt(u^2 + v^2) + !ind), na.rm = TRUE)
IC <- cbind(IC1, IC2)
return(initial.est + IC)
}
.kstep.locsc.matrix <- function(x, initial.est, A1, A2, a, b, mean, k){
est <- .onestep.locsc.matrix(x = x, initial.est = initial.est, A1 = A1, A2 = A2, a = a, b = b)
if(k > 1){
for(i in 2:k){
A1 <- est[,2]^2*A1/initial.est[,2]^2
A2 <- est[,2]^2*A2/initial.est[,2]^2
a <- est[,2]*a/initial.est[,2]
b <- est[,2]*b/initial.est[,2]
initial.est <- est
est <- .onestep.locsc.matrix(x = x, initial.est = est, A1 = A1, A2 = A2, a = a, b = b)
}
}
A1 <- est[,2]^2*A1/initial.est[,2]^2
A2 <- est[,2]^2*A2/initial.est[,2]^2
a <- est[,2]*a/initial.est[,2]
b <- est[,2]*b/initial.est[,2]
return(list(est = est, A1 = A1, A2 = A2, a = a, b = b))
}
###############################################################################
## Evaluate roblox on rows of a matrix
###############################################################################
rowRoblox <- function(x, mean, sd, eps, eps.lower, eps.upper, initial.est,
k = 1L, fsCor = TRUE, mad0 = 1e-4, na.rm = TRUE){
es.call <- match.call()
if(missing(x))
stop("'x' is missing with no default")
if(is.data.frame(x))
x <- data.matrix(x)
else
x <- as.matrix(x)
if(!is.matrix(x))
stop("'x' has to be a matrix resp. convertable to a matrix by 'as.matrix'
or 'data.matrix'")
completecases <- complete.cases(x)
if(na.rm) x <- na.omit(x)
if(ncol(x) <= 2){
if(missing(mean) && missing(sd)){
warning("Sample size <= 2! => Median and MAD are used for estimation.")
if(TRUE){#(require(Biobase))
mean <- rowMedians(x, na.rm = TRUE)
sd <- rowMedians(abs(x-mean), na.rm = TRUE)/qnorm(0.75)
}else{
warning("You can speed up the computations by installing Bioconductor package 'Biobase'!")
mean <- apply(x, 1, median, na.rm = TRUE)
sd <- apply(abs(x-mean), 1, median, na.rm = TRUE)/qnorm(0.75)
}
robEst <- cbind(mean, sd)
colnames(robEst) <- c("mean", "sd")
Info.matrix <- matrix(c("rowRoblox",
paste("median and MAD")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("ALEstimate", name = "Median and MAD",
completecases = completecases,
estimate.call = es.call, estimate = robEst,
samplesize = ncol(x), asvar = NULL,
asbias = NULL, pIC = NULL, Infos = Info.matrix))
}
if(missing(mean)){
warning("Sample size <= 2! => Median is used for estimation.")
if(TRUE){#(require(Biobase))
mean <- rowMedians(x, na.rm = TRUE)
}else{
warning("You can speed up the computations by installing Bioconductor package 'Biobase'!")
mean <- apply(x, 1, median, na.rm = TRUE)
}
robEst <- matrix(mean)
colnames(robEst) <- "mean"
Info.matrix <- matrix(c("rowRoblox",
paste("median")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("ALEstimate", name = "Median",
completecases = completecases,
estimate.call = es.call, estimate = robEst,
samplesize = ncol(x), asvar = NULL,
asbias = NULL, pIC = NULL, Infos = Info.matrix))
}
if(missing(sd)){
warning("Sample size <= 2! => MAD is used for estimation.")
if(!is.numeric(mean) || (length(mean) != 1 && length(mean) != nrow(x)))
stop("'mean' has wrong dimension")
if(TRUE){#(require(Biobase))
sd <- rowMedians(abs(x-mean), na.rm = TRUE)/qnorm(0.75)
}else{
warning("You can speed up the computations by installing Bioconductor package 'Biobase'!")
sd <- apply(abs(x-mean), 1, median, na.rm = TRUE)/qnorm(0.75)
}
robEst <- matrix(sd)
colnames(robEst) <- "sd"
Info.matrix <- matrix(c("rowRoblox",
paste("MAD")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("ALEstimate", name = "MAD",
completecases = completecases,
estimate.call = es.call, estimate = robEst,
samplesize = ncol(x), asvar = NULL,
asbias = NULL, pIC = NULL, Infos = Info.matrix))
}
}
if(missing(eps) && missing(eps.lower) && missing(eps.upper)){
eps.lower <- 0
eps.upper <- 0.5
}
if(missing(eps)){
if(!missing(eps.lower) && missing(eps.upper))
eps.upper <- 0.5
if(missing(eps.lower) && !missing(eps.upper))
eps.lower <- 0
if(length(eps.lower) != 1 || length(eps.upper) != 1)
stop("'eps.lower' and 'eps.upper' have to be of length 1")
if(!is.numeric(eps.lower) || !is.numeric(eps.upper) || eps.lower >= eps.upper)
stop("'eps.lower' < 'eps.upper' is not fulfilled")
if((eps.lower < 0) || (eps.upper > 0.5))
stop("'eps.lower' and 'eps.upper' have to be in [0, 0.5]")
}else{
if(length(eps) != 1)
stop("'eps' has to be of length 1")
if((eps < 0) || (eps > 0.5))
stop("'eps' has to be in (0, 0.5]")
if(eps == 0){
if(missing(mean) && missing(sd)){
warning("eps = 0! => Mean and sd are used for estimation.")
mean <- rowMeans(x, na.rm = TRUE)
n <- rowSums(!is.na(x))
n[n < 1] <- NA
sd <- rowSums((x - mean)^2, na.rm = TRUE)/n
robEst <- cbind(mean, sd)
colnames(robEst) <- c("mean", "sd")
Info.matrix <- matrix(c("rowRoblox",
paste("mean and sd")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("ALEstimate", name = "Mean and sd",
completecases = completecases,
estimate.call = es.call, estimate = robEst,
samplesize = n, asvar = NULL,
asbias = NULL, pIC = NULL, Infos = Info.matrix))
}
if(missing(mean)){
warning("eps = 0! => Mean is used for estimation.")
robEst <- matrix(rowMeans(x, na.rm = TRUE))
colnames(robEst) <- "mean"
Info.matrix <- matrix(c("rowRoblox",
paste("mean")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("ALEstimate", name = "Mean",
completecases = completecases,
estimate.call = es.call, estimate = robEst,
samplesize = length(x), asvar = NULL,
asbias = NULL, pIC = NULL, Infos = Info.matrix))
}
if(missing(sd)){
warning("eps = 0! => sd is used for estimation.")
if(!is.numeric(mean) || (length(mean) != 1 && length(mean) != nrow(x)))
stop("'mean' has wrong dimension")
n <- rowSums(!is.na(x))
n[n < 1] <- NA
robEst <- matrix(rowSums((x - mean)^2, na.rm = TRUE)/n)
colnames(robEst) <- "sd"
Info.matrix <- matrix(c("rowRoblox",
paste("sd")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("ALEstimate", name = "sd",
completecases = completecases,
estimate.call = es.call, estimate = robEst,
samplesize = n, asvar = NULL,
asbias = NULL, pIC = NULL, Infos = Info.matrix))
}
}
}
if(k < 1){
stop("'k' has to be some positive integer value")
}
if(length(k) != 1){
stop("'k' has to be of length 1")
}
k <- as.integer(k)
if(missing(mean) && missing(sd)){
if(missing(initial.est)){
if(TRUE){#(require(Biobase))
mean <- rowMedians(x, na.rm = TRUE)
sd <- rowMedians(abs(x-mean), na.rm = TRUE)/qnorm(0.75)
}else{
warning("You can speed up the computations by installing Bioconductor package 'Biobase'!")
mean <- apply(x, 1, median, na.rm = TRUE)
sd <- apply(abs(x-mean), 1, median, na.rm = TRUE)/qnorm(0.75)
}
if(any(sd == 0)){
stop("'mad(x, na.rm = TRUE) = 0' for some samples => cannot compute a valid initial estimate.
To avoid division by zero 'mad0' is used. You could also specify
a valid scale estimate via 'initial.est'. Note that you have to provide
a location and scale estimate.")
sd[sd == 0] <- mad0
}
mean.sd <- cbind(mean=mean,sd=sd)
}else{
if(nrow(initial.est) != nrow(x) || ncol(initial.est) != 2)
stop("'initial.est' has wrong dimension")
mean <- initial.est[,1]
sd <- initial.est[,2]
if(any(sd <= 0))
stop("initial estimate for scale <= 0 which is no valid scale estimate")
mean.sd <- initial.est
}
if(!missing(eps)){
r <- sqrt(ncol(x))*eps
if(fsCor) r <- finiteSampleCorrection(r = r, n = ncol(x), model = "locsc")
if(r > 10){
b <- sd*1.618128043
const <- 1.263094656
A2 <- b^2*(1+r^2)/(1+const)
A1 <- const*A2
a <- -0.6277527697*A2/sd
mse <- A1 + A2
}else{
A1 <- sd^2*.getA1.locsc(r)
A2 <- sd^2*.getA2.locsc(r)
a <- sd*.geta.locsc(r)
b <- sd*.getb.locsc(r)
mse <- A1 + A2
}
robEst <- .kstep.locsc.matrix(x = x, initial.est = cbind(mean, sd),
A1 = A1, A2 = A2, a = a, b = b, k = k)
colnames(robEst$est) <- c("mean", "sd")
Info.matrix <- matrix(c("roblox",
paste("optimally robust estimates for contamination 'eps' =", round(eps, 3),
"and 'asMSE'")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("kStepEstimate", name = "Optimally robust estimate",
completecases = completecases,
estimate.call = es.call, estimate = robEst$est,
samplesize = ncol(x), steps = k,
pIC = NULL, Infos = Info.matrix,
start = mean.sd, startval = mean.sd, ustartval = mean.sd))
## we need a class like "list of estimates" to set asvar and asbias consistently ...
# return(new("kStepEstimate", name = "Optimally robust estimate",
# estimate = robEst$est, samplesize = ncol(x), asvar = NULL,
# asbias = r*robEst$b, steps = k, pIC = NULL, Infos = Info.matrix))
}else{
sqrtn <- sqrt(ncol(x))
rlo <- sqrtn*eps.lower
rup <- sqrtn*eps.upper
if(rlo > 10){
r <- (rlo + rup)/2
}else{
r <- uniroot(.getlsInterval, lower = rlo+1e-8, upper = rup,
tol = .Machine$double.eps^0.25, rlo = rlo, rup = rup)$root
}
if(fsCor) r <- finiteSampleCorrection(r = r, n = ncol(x), model = "locsc")
if(r > 10){
b <- sd*1.618128043
const <- 1.263094656
A2 <- b^2*(1+r^2)/(1+const)
A1 <- const*A2
a <- -0.6277527697*A2/sd
mse <- A1 + A2
}else{
A1 <- sd^2*.getA1.locsc(r)
A2 <- sd^2*.getA2.locsc(r)
a <- sd*.geta.locsc(r)
b <- sd*.getb.locsc(r)
mse <- A1 + A2
}
if(rlo == 0){
ineff <- (A1 + A2 - b^2*r^2)/(1.5*sd^2)
}else{
if(rlo > 10){
ineff <- 1
}else{
A1lo <- sd^2*.getA1.locsc(rlo)
A2lo <- sd^2*.getA2.locsc(rlo)
ineff <- (A1 + A2 - b^2*(r^2 - rlo^2))/(A1lo + A2lo)
}
}
robEst <- .kstep.locsc.matrix(x = x, initial.est = cbind(mean, sd),
A1 = A1, A2 = A2, a = a, b = b, k = k)
colnames(robEst$est) <- c("mean", "sd")
Info.matrix <- matrix(c(rep("roblox", 3),
paste("radius-minimax estimates for contamination interval [",
round(eps.lower, 3), ", ", round(eps.upper, 3), "]", sep = ""),
paste("least favorable contamination: ", round(r/sqrtn, 3), sep = ""),
paste("maximum MSE-inefficiency: ", round(ineff[1], 3), sep = "")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("kStepEstimate", name = "Optimally robust estimate",
completecases = completecases,
estimate.call = es.call, estimate = robEst$est, #
samplesize = ncol(x), steps = k,
pIC = NULL, Infos = Info.matrix,
start = mean.sd, startval = mean.sd, ustartval = mean.sd))
## we need a class like "list of estimates" to set asvar and asbias consistently ...
# return(new("kStepEstimate", name = "Optimally robust estimate",
# estimate = robEst$est, samplesize = ncol(x), asvar = NULL,
# asbias = r*robEst$b, steps = k, pIC = NULL, Infos = Info.matrix))
}
}else{
if(missing(mean)){
if(any(sd <= 0))
stop("'sd' has to be positive")
if(!is.numeric(sd) || (length(sd) != 1 && length(sd) != nrow(x)))
stop("'sd' has wrong dimension")
if(missing(initial.est)){
if(TRUE){#(require(Biobase))
mean <- rowMedians(x, na.rm = TRUE)
}else{
warning("You can speed up the computations by installing Bioconductor package 'Biobase'!")
mean <- apply(x, 1, median, na.rm = TRUE)
}
}else{
if(!is.numeric(initial.est) || length(initial.est) != nrow(x))
stop("'initial.est' has wrong dimension")
mean <- initial.est
}
if(length(sd) == 1)
sd <- rep(sd, length(mean))
mean.sd <- cbind(mean=mean,sd=sd)
if(!missing(eps)){
r <- sqrt(ncol(x))*eps
if(fsCor) r <- finiteSampleCorrection(r = r, n = ncol(x), model = "loc")
if(r > 10){
b <- sd*sqrt(pi/2)
A <- b^2*(1+r^2)
}else{
A <- sd^2*.getA.loc(r)
b <- sd*.getb.loc(r)
}
robEst <- as.matrix(.kstep.loc.matrix(x = x, initial.est = mean, A = A, b = b, sd = sd, k = k))
colnames(robEst) <- "mean"
Info.matrix <- matrix(c("roblox",
paste("optimally robust estimates for contamination 'eps' =", round(eps, 3),
"and 'asMSE'")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("kStepEstimate", name = "Optimally robust estimate",
completecases = completecases,
estimate.call = es.call, estimate = robEst,
samplesize = ncol(x), steps = k,
pIC = NULL, Infos = Info.matrix,
start = mean.sd[,1,drop=F], startval = mean.sd[,1,drop=F], ustartval = mean.sd))
## we need a class like "list of estimates" to set asvar and asbias consistently ...
# return(new("kStepEstimate", name = "Optimally robust estimate",
# estimate = robEst$est, samplesize = ncol(x), asvar = as.matrix(A - r^2*b^2),
# asbias = r*b, steps = k, pIC = NULL, Infos = Info.matrix))
}else{
sqrtn <- sqrt(ncol(x))
rlo <- sqrtn*eps.lower
rup <- sqrtn*eps.upper
if(rlo > 10){
r <- (rlo+rup)/2
}else{
r <- uniroot(.getlInterval, lower = rlo+1e-8, upper = rup,
tol = .Machine$double.eps^0.25, rlo = rlo, rup = rup)$root
}
if(fsCor) r <- finiteSampleCorrection(r = r, n = ncol(x), model = "loc")
if(r > 10){
b <- sd*sqrt(pi/2)
A <- b^2*(1+r^2)
}else{
A <- sd^2*.getA.loc(r)
b <- sd*.getb.loc(r)
}
if(rlo == 0){
ineff <- (A - b^2*r^2)/sd^2
}else{
if(rlo > 10){
ineff <- 1
}else{
Alo <- sd^2*.getA.loc(rlo)
ineff <- (A - b^2*(r^2 - rlo^2))/Alo
}
}
robEst <- as.matrix(.kstep.loc.matrix(x = x, initial.est = mean, A = A, b = b, sd = sd, k = k))
colnames(robEst) <- "mean"
Info.matrix <- matrix(c(rep("roblox", 3),
paste("radius-minimax estimates for contamination interval [",
round(eps.lower, 3), ", ", round(eps.upper, 3), "]", sep = ""),
paste("least favorable contamination: ", round(r/sqrtn, 3), sep = ""),
paste("maximum MSE-inefficiency: ", round(ineff[1], 3), sep = "")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("kStepEstimate", name = "Optimally robust estimate",
completecases = completecases,
estimate.call = es.call, estimate = robEst,
samplesize = ncol(x), steps = k,
pIC = NULL, Infos = Info.matrix,
start = mean.sd[,1,drop=F], startval = mean.sd[,1,drop=F], ustartval = mean.sd))
## we need a class like "list of estimates" to set asvar and asbias consistently ...
# return(new("kStepEstimate", name = "Optimally robust estimate",
# estimate = robEst$est, samplesize = ncol(x), asvar = as.matrix(A - r^2*b^2),
# asbias = r*b, steps = k, pIC = NULL, Infos = Info.matrix))
}
}
if(missing(sd)){
if(!is.numeric(mean) || (length(mean) != 1 && length(mean) != nrow(x)))
stop("'mean' has wrong dimension")
if(missing(initial.est)){
if(TRUE){#(require(Biobase))
sd <- rowMedians(abs(x-mean), na.rm = TRUE)/qnorm(0.75)
}else{
warning("You can speed up the computations by installing Bioconductor package 'Biobase'!")
sd <- apply(abs(x-mean), 1, median, na.rm = TRUE)/qnorm(0.75)
}
if(any(sd == 0)){
stop("'mad(x, na.rm = TRUE) = 0' for some samples => cannot compute a valid initial estimate.
To avoid division by zero 'mad0' is used. You could also specify
a valid scale estimate via 'initial.est'.")
sd[sd == 0] <- mad0
}
}else{
if(!is.numeric(initial.est) || length(initial.est) != nrow(x))
stop("'initial.est' has wrong dimension")
if(any(initial.est <= 0))
stop("'initial.est <= 0'; i.e., is no valid scale estimate")
sd <- initial.est
}
mean.sd <- cbind(mean=mean,sd=sd)
if(!missing(eps)){
r <- sqrt(ncol(x))*eps
if(fsCor) r <- finiteSampleCorrection(r = r, n = ncol(x), model = "sc")
if(r > 10){
b <- sd/(4*qnorm(0.75)*dnorm(qnorm(0.75)))
A <- b^2*(1+r^2)
a <- (qnorm(0.75)^2 - 1)/sd*A
}else{
A <- sd^2*.getA.sc(r)
a <- sd*.geta.sc(r)
b <- sd*.getb.sc(r)
}
robEst <- .kstep.sc.matrix(x = x, initial.est = sd, A = A, a = a, b = b, mean = mean, k = k)
robEst$est <- as.matrix(robEst$est)
colnames(robEst$est) <- "sd"
Info.matrix <- matrix(c("roblox",
paste("optimally robust estimates for contamination 'eps' =", round(eps, 3),
"and 'asMSE'")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("kStepEstimate", name = "Optimally robust estimate",
completecases = completecases,
estimate.call = es.call, estimate = robEst$est,
samplesize = ncol(x), steps = k,
pIC = NULL, Infos = Info.matrix,
start = mean.sd[,2,drop=F], startval = mean.sd[,2,drop=F], ustartval = mean.sd))
## we need a class like "list of estimates" to set asvar and asbias consistently ...
# return(new("kStepEstimate", name = "Optimally robust estimate",
# estimate = robEst$est, samplesize = ncol(x), asvar = as.matrix(robEst$A - r^2*robEst$b^2),
# asbias = r*robEst$b, steps = k, pIC = NULL, Infos = Info.matrix))
}else{
sqrtn <- sqrt(ncol(x))
rlo <- sqrtn*eps.lower
rup <- sqrtn*eps.upper
if(rlo > 10){
r <- (rlo+rup)/2
}else{
r <- uniroot(.getsInterval, lower = rlo+1e-8, upper = rup,
tol = .Machine$double.eps^0.25, rlo = rlo, rup = rup)$root
}
if(fsCor) r <- finiteSampleCorrection(r = r, n = ncol(x), model = "sc")
if(r > 10){
b <- sd/(4*qnorm(0.75)*dnorm(qnorm(0.75)))
A <- b^2*(1+r^2)
a <- (qnorm(0.75)^2 - 1)/sd*A
}else{
A <- sd^2*.getA.sc(r)
a <- sd*.geta.sc(r)
b <- sd*.getb.sc(r)
}
if(rlo == 0){
ineff <- (A - b^2*r^2)/(0.5*sd^2)
}else{
if(rlo > 10){
ineff <- 1
}else{
Alo <- sd^2*.getA.sc(rlo)
ineff <- (A - b^2*(r^2 - rlo^2))/Alo
}
}
robEst <- .kstep.sc.matrix(x = x, initial.est = sd, A = A, a = a, b = b, mean = mean, k = k)
robEst$est <- as.matrix(robEst$est)
colnames(robEst$est) <- "sd"
Info.matrix <- matrix(c(rep("roblox", 3),
paste("radius-minimax estimates for contamination interval [",
round(eps.lower, 3), ", ", round(eps.upper, 3), "]", sep = ""),
paste("least favorable contamination: ", round(r/sqrtn, 3), sep = ""),
paste("maximum MSE-inefficiency: ", round(ineff[1], 3), sep = "")),
ncol = 2, dimnames = list(NULL, c("method", "message")))
return(new("kStepEstimate", name = "Optimally robust estimate",
completecases = completecases,
estimate.call = es.call, estimate = robEst$est,
samplesize = ncol(x), steps = k,
pIC = NULL, Infos = Info.matrix,
start = mean.sd[,2,drop=F], startval = mean.sd[,2,drop=F],
ustartval = mean.sd))
## we need a class like "list of estimates" to set asvar and asbias consistently ...
# return(new("kStepEstimate", name = "Optimally robust estimate",
# estimate = robEst$est, samplesize = ncol(x), asvar = as.matrix(robEst$A - r^2*robEst$b^2),
# asbias = r*robEst$b, steps = k, pIC = NULL, Infos = Info.matrix))
}
}
}
}
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