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"pta" <- function (X, scannf = TRUE, nf = 2) {
# 21/08/02 Correction d'un bug suite à message de G. BALENT balent@toulouse.inra.fr
if (!inherits(X, "ktab"))
stop("object 'ktab' expected")
auxinames <- ktab.util.names(X)
sepa <- sepan(X, nf = 4)
blocks <- X$blo
nblo <- length(blocks)
tnames <- tab.names(X)
lw <- X$lw
lwsqrt <- sqrt(X$lw)
nl <- length(lw)
r.n <- row.names(X[[1]])
for (i in 1:nblo) {
r.new <- row.names(X[[i]])
if (any(r.new != r.n))
stop("non equal row.names among array")
}
if (length(unique(blocks)) != 1)
stop("non equal col numbers among array")
unique.col.names <- names(X[[1]])
for (i in 1:nblo) {
c.new <- names(X[[i]])
if (any(c.new != unique.col.names))
stop("non equal col.names among array")
}
indica <- as.factor(rep(1:nblo, blocks))
w <- split(X$cw, indica)
cw <- w[[1]]
for (i in 1:nblo) {
col.w.new <- w[[i]]
if (any(cw != col.w.new))
stop("non equal column weights among array")
}
cwsqrt <- sqrt(cw)
nc <- length(cw)
atp <- list()
for (i in 1:nblo) {
w <- as.matrix(X[[i]]) * lwsqrt
w <- t(t(w) * cwsqrt)
atp[[i]] <- w
}
atp <- matrix(unlist(atp), nl * nc, nblo)
RV <- t(atp) %*% atp
ak <- sqrt(diag(RV))
RV <- sweep(RV, 1, ak, "/")
RV <- sweep(RV, 2, ak, "/")
dimnames(RV) <- list(tnames, tnames)
atp <- list()
inter <- eigen(as.matrix(RV))
if (any(inter$vectors[, 1] < 0))
inter$vectors[, 1] <- -inter$vectors[, 1]
is <- inter$vectors[, (1:min(c(nblo, 4)))]
tabw <- as.vector(is[, 1])
is <- t(t(is) * sqrt(inter$values[1:ncol(is)]))
is <- as.data.frame(is)
row.names(is) <- tnames
names(is) <- paste("IS", 1:ncol(is), sep = "")
atp$RV <- RV
atp$RV.eig <- inter$values
atp$RV.coo <- is
atp$tabw <- tabw
tab <- X[[1]] * tabw[1]
for (i in 2:nblo) {
tab <- tab + X[[i]] * tabw[i]
}
tab <- as.data.frame(tab, row.names = row.names(X))
names(tab) <- unique.col.names
comp <- as.dudi(tab, col.w = cw, row.w = lw, nf = nf, scannf = scannf,
call = match.call(), type = "pta")
atp$rank <- comp$rank
nf <- atp$nf <- comp$nf
atp$tab <- comp$tab
atp$lw <- comp$lw
atp$cw <- comp$cw
atp$eig <- comp$eig
atp$li <- comp$li
atp$co <- comp$co
atp$l1 <- comp$l1
atp$c1 <- comp$c1
w1 <- matrix(0, nblo * 4, nf)
w2 <- matrix(0, nblo * 4, nf)
i1 <- 0
i2 <- 0
for (k in 1:nblo) {
i1 <- i2 + 1
i2 <- i2 + 4
tab1 <- as.matrix(sepa$L1[X$TL[, 1] == levels(X$TL[,1])[k], ])
tab1 <- t(tab1 * lw) %*% as.matrix(comp$l1)
tab2 <- as.matrix(sepa$C1[X$TC[, 1] == levels(X$TC[, 1])[k], ])
tab2 <- (t(tab2) * cw) %*% as.matrix(comp$c1)
for (i in 1:min(nf, 4)) {
if (tab2[i, i] < 0) {
for (j in 1:nf) tab2[i, j] <- -tab2[i, j]
}
if (tab1[i, i] < 0) {
for (j in 1:nf) tab1[i, j] <- -tab1[i, j]
}
}
w1[i1:i2, ] <- tab1
w2[i1:i2, ] <- tab2
}
w1 <- data.frame(w1, row.names = auxinames$tab)
w2 <- data.frame(w2, row.names = auxinames$tab)
names(w2) <- names(w1) <- paste("C", 1:nf, sep = "")
atp$Tcomp <- w1
atp$Tax <- w2
tab <- as.matrix(X[[1]])
w <- as.matrix(comp$c1)
cooli <- t(t(tab) * cw) %*% w
for (k in 2:nblo) {
tab <- as.matrix(X[[k]])
cooliauxi <- t(t(tab) * cw) %*% w
cooli <- rbind(cooli, cooliauxi)
}
cooli <- data.frame(cooli, row.names = auxinames$row)
atp$Tli <- cooli
tab <- as.matrix(X[[1]])
w <- as.matrix(comp$l1) * lw
cooco <- t(tab) %*% w
for (k in 2:nblo) {
tab <- as.matrix(X[[k]])
coocoauxi <- t(tab) %*% w
cooco <- rbind(cooco, coocoauxi)
}
cooco <- data.frame(cooco, row.names = auxinames$col)
atp$Tco <- cooco
normcompro <- sum(atp$eig)
indica <- as.factor(rep(1:nblo, sepa$rank))
w <- split(sepa$Eig, indica)
normtab <- unlist(lapply(w, sum))
covv <- rep(0, nblo)
w1 <- atp$tab * lwsqrt
w1 <- t(t(w1) * cwsqrt)
for (k in 1:nblo) {
wk <- X[[k]] * lwsqrt
wk <- t(t(wk) * cwsqrt)
covv[k] <- sum(w1 * wk)
}
atp$cos2 <- covv/sqrt(normcompro)/sqrt(normtab)
atp$TL <- X$TL
atp$TC <- X$TC
atp$T4 <- X$T4
atp$blo <- X$blo
atp$tab.names <- tnames
atp$call <- match.call()
class(atp) <- c("pta", "dudi")
if (!inherits (X,"kcoinertia")) return(atp)
# Modifs pour prendre en compte STATICO
# on a affaire a une pta de type STATICO
# nblo nombre de tableau
blocks <- X$supblo
nblo <- length(blocks)
w <- NULL
for (i in 1:nblo) w <- c(w, 1:blocks[i])
w <- cbind.data.frame(factor(rep(1:nblo, blocks)), factor(w))
names(w) <- c("T", "I")
atp$supTI <- w
supTInames <- as.data.frame(matrix(unlist(strsplit(auxinames$Trow, "[.]")), ncol=2, byrow=T))
levels(atp$supTI$T) <- atp$tab.names
levels(atp$supTI$I) <- supTInames[,2]
# atp$supTI <- auxinames$Trow
# atp$supTI <- as.data.frame(matrix(unlist(strsplit(auxinames$Trow, "[.]")), ncol=2, byrow=T))
# names(atp$supTI) <- c("T", "I")
lw <- X$suplw
lw <- split(lw, factor(rep(1:length(blocks),blocks)))
lw <- lapply(lw, function(x) x/sum(x))
lw <- unlist(lw)
# les lignes d'origine en supplémentaires X
w <- X$supX%*%as.matrix(atp$l1*atp$lw)
# Correction des row names - JT 7 - Jan 2014
w <- data.frame(w, row.names = auxinames$Trow)
w <- scalewt(w, lw, center = FALSE, scale = TRUE)
w <- as.data.frame(w)
names(w) <- gsub("RS","sco",names(atp$l1))
atp$supIX <- w
# les lignes d'origine en supplémentaires Y
w <- X$supY%*%as.matrix(atp$c1*atp$cw)
# Correction des row names - JT - 7 Jan 2014
w <- data.frame(w, row.names = auxinames$Trow)
w <- scalewt(w, lw, center = FALSE, scale = TRUE)
w <- as.data.frame(w)
names(w) <- gsub("RS","sco",names(atp$l1))
atp$supIY <- w
return(atp)
}
"plot.pta" <- function (x, xax = 1, yax = 2, option = 1:4, ...) {
if (!inherits(x, "pta"))
stop("Object of type 'pta' expected")
nf <- x$nf
if (xax > nf)
stop("Non convenient xax")
if (yax > nf)
stop("Non convenient yax")
def.par <- par(no.readonly = TRUE)
on.exit(par(def.par))
mfrow <- n2mfrow(length(option))
par(mfrow = mfrow)
for (j in option) {
if (j == 1) {
coolig <- x$RV.coo[, c(1, 2)]
s.corcircle(coolig, label = x$tab.names,
cgrid = 0, sub = "Interstructure", csub = 1.5,
possub = "topleft", fullcircle = TRUE)
l0 <- length(x$RV.eig)
add.scatter.eig(x$RV.eig, l0, 1, 2, posi = "bottomleft",
ratio = 1/4)
}
if (j == 2) {
coolig <- x$li[, c(xax, yax)]
s.label(coolig, sub = "Compromise", csub = 1.5,
possub = "topleft", )
add.scatter.eig(x$eig, x$nf, xax, yax, posi = "bottomleft",
ratio = 1/4)
}
if (j == 3) {
cooco <- x$co[, c(xax, yax)]
s.arrow(cooco, sub = "Compromise", csub = 1.5,
possub = "topleft")
}
if (j == 4) {
plot(x$tabw, x$cos2, xlab = "Tables weights",
ylab = "Cos 2")
scatterutil.grid(0)
title(main = "Typological value")
par(xpd = TRUE)
scatterutil.eti(x$tabw, x$cos2, label = x$tab.names,
clabel = 1)
}
}
}
"print.pta" <- function (x, ...) {
cat("Partial Triadic Analysis\n")
cat("class:")
cat(class(x), "\n")
cat("table number:", length(x$blo), "\n")
cat("row number:", length(x$lw), " column number:", length(x$cw),
"\n")
cat("\n **** Interstructure ****\n")
cat("\neigen values: ")
l0 <- length(x$RV.eig)
cat(signif(x$RV.eig, 4)[1:(min(5, l0))])
if (l0 > 5)
cat(" ...\n")
else cat("\n")
cat(" $RV matrix ", nrow(x$RV), " ", ncol(x$RV), " RV coefficients\n")
cat(" $RV.eig vector ", length(x$RV.eig), " eigenvalues\n")
cat(" $RV.coo data.frame ", nrow(x$RV.coo), " ", ncol(x$RV.coo),
" array scores\n")
cat(" $tab.names vector ", length(x$tab.names), " array names\n")
cat("\n **** Compromise ****\n")
cat("\neigen values: ")
l0 <- length(x$eig)
cat(signif(x$eig, 4)[1:(min(5, l0))])
if (l0 > 5)
cat(" ...\n")
else cat("\n")
cat("\n $nf:", x$nf, "axis-components saved")
cat("\n $rank: ")
cat(x$rank, "\n\n")
sumry <- array("", c(5, 4), list(rep("", 5), c("vector",
"length", "mode", "content")))
sumry[1, ] <- c("$tabw", length(x$tabw), mode(x$tabw), "array weights")
sumry[2, ] <- c("$cw", length(x$cw), mode(x$cw), "column weights")
sumry[3, ] <- c("$lw", length(x$lw), mode(x$lw), "row weights")
sumry[4, ] <- c("$eig", length(x$eig), mode(x$eig), "eigen values")
sumry[5, ] <- c("$cos2", length(x$cos2), mode(x$cos2), "cosine^2 between compromise and arrays")
print(sumry, quote = FALSE)
cat("\n")
sumry <- array("", c(5, 4), list(rep("", 5), c("data.frame",
"nrow", "ncol", "content")))
sumry[1, ] <- c("$tab", nrow(x$tab), ncol(x$tab), "modified array")
sumry[2, ] <- c("$li", nrow(x$li), ncol(x$li), "row coordinates")
sumry[3, ] <- c("$l1", nrow(x$l1), ncol(x$l1), "row normed scores")
sumry[4, ] <- c("$co", nrow(x$co), ncol(x$co), "column coordinates")
sumry[5, ] <- c("$c1", nrow(x$c1), ncol(x$c1), "column normed scores")
print(sumry, quote = FALSE)
cat("\n **** Intrastructure ****\n\n")
sumry <- array("", c(7, 4), list(rep("", 7), c("data.frame",
"nrow", "ncol", "content")))
sumry[1, ] <- c("$Tli", nrow(x$Tli), ncol(x$Tli), "row coordinates (each table)")
sumry[2, ] <- c("$Tco", nrow(x$Tco), ncol(x$Tco), "col coordinates (each table)")
sumry[3, ] <- c("$Tcomp", nrow(x$Tcomp), ncol(x$Tcomp), "principal components (each table)")
sumry[4, ] <- c("$Tax", nrow(x$Tax), ncol(x$Tax), "principal axis (each table)")
sumry[5, ] <- c("$TL", nrow(x$TL), ncol(x$TL), "factors for Tli")
sumry[6, ] <- c("$TC", nrow(x$TC), ncol(x$TC), "factors for Tco")
sumry[7, ] <- c("$T4", nrow(x$T4), ncol(x$T4), "factors for Tax Tcomp")
print(sumry, quote = FALSE)
cat("\n")
}
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