multigraph <-
function (net, layout = c("circ", "force", "stress", "conc",
"rand"), scope, directed = TRUE, loops, signed, valued, values,
lbs, showLbs, att, lbat, showAtts, main = NULL, cex.main,
col.main, font.main, coord, collRecip, undRecip, seed = NULL,
maxiter = 100, clu, cex, cex2, pch, lwd, lty, vcol, vcol0,
col, ecol, bwd, bwd2, pos, bg, bg2, asp, drp, add, swp, swp2,
alpha = c(1, 1, 1, 1), rot, mirrorX, mirrorY, mirrorD, mirrorL,
mirrorV, mirrorH, scl, hds, vedist, mar, ffamily, fstyle,
fsize, fsize2, fcol, fcol2, lclu, sel, new, mai, lscl, rm.isol,
...)
{
cnet <- attr(net, "class")
flgmlvl <- FALSE
flgcn2 <- FALSE
flgpf <- FALSE
if (isTRUE("Rel.System" %in% cnet) == TRUE) {
net <- net$Ties
}
else if (isTRUE("Multilevel" %in% cnet) == TRUE) {
mlvl <- net
if (isTRUE("bpn" %in% cnet) == TRUE) {
flgmlvl <- TRUE
ifelse(missing(pch) == TRUE, pch <- c(rep(1, length(mlvl$lbs$dm)),
rep(0, length(mlvl$lbs$cdm))), NA)
}
else if (isTRUE("cn2" %in% cnet) == TRUE) {
flgcn2 <- TRUE
}
else {
NA
}
net <- mlvl$mlnet
}
else if (isTRUE("pathfinder" %in% cnet) == TRUE) {
flgpf <- TRUE
maxw <- net$max
net <- net$Q
}
else if (isTRUE(tolower(cnet) == "dataset") == TRUE || isTRUE(tolower(cnet) ==
"data.set") == TRUE) {
if (is.array(net$net) == TRUE) {
att <- net$net[, , which(net$atnet[[1]] == 1)]
net <- net$net[, , which(net$atnet[[1]] == 0)]
}
else if (is.data.frame(net$net) == TRUE) {
net <- multiplex::edgel(net$net, header = TRUE, sep = ",")
}
else {
NA
}
}
else {
NA
}
if (isTRUE(is.data.frame(net) == TRUE) == FALSE) {
if (isTRUE(is.list(net) == TRUE) == TRUE && isTRUE(cnet ==
"Signed") == FALSE) {
net <- multiplex::transf(net, type = "toarray", lb2lb = TRUE)
}
else if (isTRUE(is.vector(net) == TRUE) == TRUE) {
ifelse(missing(add) == FALSE && isTRUE(is.vector(add) ==
TRUE) == TRUE, net <- multiplex::transf(net,
type = "toarray", lb2lb = TRUE, lbs = sort(unique(multiplex::dhc(c(net,
add))))), net <- multiplex::trnf(net, tolist = FALSE,
lb2lb = TRUE))
}
else if (isTRUE(is.null(net) == TRUE) == TRUE && (missing(add) ==
FALSE && isTRUE(is.vector(add) == TRUE) == TRUE)) {
net <- matrix(0L, nrow = length(add), ncol = length(add),
dimnames = list(add, add))
}
else {
NA
}
}
else {
net <- as.matrix(net)
}
if (isTRUE(cnet == "Signed") == FALSE) {
ifelse(is.array(net) == TRUE || is.matrix(net) == TRUE,
NA, stop("\"net\" should be matrix or array."))
}
ifelse(isTRUE(dim(net)[3] == 1) == TRUE, net <- net[, , 1],
NA)
ifelse(missing(undRecip) == FALSE && isTRUE(undRecip == TRUE) ==
TRUE, undRecip <- TRUE, undRecip <- FALSE)
ifelse(missing(valued) == FALSE && isTRUE(valued == TRUE) ==
TRUE, valued <- TRUE, valued <- FALSE)
ifelse(missing(values) == FALSE && isTRUE(values == TRUE) ==
TRUE, values <- TRUE, values <- FALSE)
ifelse(missing(loops) == FALSE && isTRUE(loops == TRUE) ==
TRUE, loops <- TRUE, loops <- FALSE)
ifelse(missing(mirrorH) == FALSE && isTRUE(mirrorH == TRUE) ==
TRUE, mirrorY <- TRUE, NA)
ifelse(missing(mirrorV) == FALSE && isTRUE(mirrorV == TRUE) ==
TRUE, mirrorX <- TRUE, NA)
if (missing(scope) == FALSE && isTRUE(any(attr(scope, "names") ==
"directed") == TRUE) == TRUE) {
if (isTRUE(scope[[which(attr(scope, "names") == "directed")]] ==
FALSE) == TRUE) {
ifelse(missing(collRecip) == FALSE && isTRUE(collRecip ==
TRUE) == FALSE, collRecip <- FALSE, collRecip <- TRUE)
}
else if (isTRUE(scope[[which(attr(scope, "names") ==
"directed")]] == TRUE) == TRUE) {
ifelse(missing(collRecip) == FALSE && isTRUE(collRecip ==
TRUE) == TRUE, collRecip <- TRUE, collRecip <- FALSE)
}
}
else {
if (isTRUE(directed == FALSE) == TRUE || isTRUE(undRecip ==
TRUE) == TRUE) {
ifelse(missing(collRecip) == FALSE && isTRUE(collRecip ==
TRUE) == FALSE, collRecip <- FALSE, collRecip <- TRUE)
}
else if (isTRUE(directed == TRUE) == TRUE) {
ifelse(missing(collRecip) == FALSE && isTRUE(collRecip ==
TRUE) == TRUE, collRecip <- TRUE, collRecip <- FALSE)
}
}
if ((missing(showLbs) == FALSE && isTRUE(showLbs == TRUE) ==
TRUE) || (missing(lbs) == FALSE)) {
showLbs <- TRUE
}
else if (missing(showLbs) == FALSE && isTRUE(showLbs == FALSE) ==
TRUE) {
showLbs <- FALSE
}
else {
ifelse(is.null(dimnames(net)[[1]]) == FALSE, showLbs <- TRUE,
showLbs <- FALSE)
}
ifelse(missing(showAtts) == FALSE && isTRUE(showAtts == FALSE) ==
TRUE, showAtts <- FALSE, showAtts <- TRUE)
ifelse(missing(swp) == FALSE && isTRUE(swp == TRUE) == TRUE,
swp <- TRUE, swp <- FALSE)
ifelse(missing(swp2) == FALSE && isTRUE(swp2 == TRUE) ==
TRUE, swp2 <- TRUE, swp2 <- FALSE)
ifelse(isTRUE(directed == FALSE) == TRUE, directed <- FALSE,
NA)
if (missing(scope) == FALSE) {
if (isTRUE(is.list(scope) == TRUE) == FALSE)
stop("\"scope\" should be a list or a vector of lists.")
for (k in seq_len(length(scope))) {
if (is.factor(scope[[k]]) == TRUE) {
warning("Factor vectors should be outside \"scope\" since levels are ignored.")
break
}
}
rm(k)
scope <- list(scope)
ifelse(is.null(scope[[1]]) == TRUE, scope <- scope[2:length(scope)],
NA)
if (isTRUE(length(scope) > 1L) == TRUE && isTRUE(names(scope[1]) ==
"coord") == TRUE) {
scope <- scope[rev(seq_len(length(scope)))]
flgrev <- TRUE
}
else {
flgrev <- FALSE
}
tmp <- scope[[1]]
if (isTRUE(length(scope) > 1L) == TRUE && isTRUE(length(scope[[1]]) >
1L) == TRUE) {
for (k in 2:length(scope)) {
tmp[length(tmp) + 1L] <- as.list(scope[k])
names(tmp)[length(tmp)] <- attr(scope[k], "names")
}
rm(k)
}
else if (isTRUE(length(scope) > 1L) == TRUE) {
names(tmp) <- attr(scope[1], "names")
for (k in 2:length(scope)) {
if (is.list(scope[[k]]) == TRUE && is.data.frame(scope[[k]]) ==
FALSE) {
for (j in seq_len(length(scope[[k]]))) {
tmp[length(tmp) + 1L] <- as.list(scope[[k]][j])
names(tmp)[length(tmp)] <- attr(scope[[k]][j],
"names")
}
rm(j)
}
else if (is.data.frame(scope[[k]]) == FALSE) {
tmp[length(tmp) + 1L] <- as.list(scope[k])
names(tmp)[length(tmp)] <- attr(scope[k], "names")
}
else if (is.data.frame(scope[[k]]) == TRUE) {
tmp[length(tmp) + 1L] <- as.vector(scope[k])
names(tmp)[length(tmp)] <- attr(scope[k], "names")
}
else {
NA
}
}
rm(k)
}
else {
tmp <- scope[[1]]
}
ifelse(isTRUE(flgrev == TRUE) == TRUE, scope <- tmp[rev(seq_len(length(tmp)))],
scope <- tmp)
for (i in seq_len(length(scope))) {
if (isTRUE(names(scope)[i] %in% c("seed", "main")) ==
TRUE) {
tmpi <- as.vector(scope[[i]])
assign(names(scope)[i], get("tmpi"))
}
else {
if (is.null((scope[[i]])) == FALSE) {
tmpi <- as.vector(scope[[i]])
ifelse(isTRUE(names(scope)[i] != "") == TRUE,
assign(names(scope)[i], get("tmpi")), NA)
}
}
}
rm(i)
}
else {
NA
}
ifelse(missing(asp) == TRUE, asp <- 1, NA)
ifelse(missing(lwd) == TRUE, lwd <- 1, NA)
if (isTRUE(flgmlvl == TRUE) == TRUE) {
ifelse(missing(pch) == FALSE && isTRUE(length(pch) ==
2) == TRUE, pch <- c(rep(pch[1], length(mlvl$lbs$dm)),
rep(pch[2], length(mlvl$lbs$cdm))), NA)
ifelse(missing(ecol) == FALSE && isTRUE(length(ecol) ==
2) == TRUE, ecol <- c(rep(ecol[1], length(which(mlvl$modes ==
"1M"))), rep(ecol[2], length(which(mlvl$modes ==
"2M")))), NA)
}
else {
ifelse(missing(pch) == TRUE, pch <- 21, NA)
}
ifelse(missing(fcol) == TRUE, fcol <- 1, NA)
ifelse(missing(bwd) == TRUE, bwd <- 1, NA)
ifelse(isTRUE(bwd < 0L) == TRUE, bwd <- 0, NA)
if (missing(bg) == TRUE) {
bg <- graphics::par()$bg
flgbg <- FALSE
}
else {
obg <- graphics::par()$bg
flgbg <- TRUE
}
ifelse(missing(cex.main) == TRUE, cex.main <- graphics::par()$cex.main,
NA)
ifelse(missing(col.main) == TRUE, col.main <- graphics::par()$col.main,
NA)
ifelse(missing(font.main) == TRUE, font.main <- graphics::par()$font.main,
NA)
if (missing(rot) == FALSE) {
ifelse(isTRUE(rot == -90L) == TRUE, rot <- -89.99 * -1,
rot <- rot[1] * -1)
}
else {
NA
}
if (isTRUE(length(alpha) < 2L) == TRUE) {
alfa <- 1L
alpha <- rep(alpha, 4L)
}
else {
alfa <- alpha[2]
}
if (isTRUE(length(alpha) < 3L) == TRUE)
alpha <- append(alpha, c(0.1, 0.5))
if (!(missing(hds)) && missing(scl) == TRUE) {
if (isTRUE(hds > 1L) == TRUE) {
hds <- (hds/1.5)
}
else if (isTRUE(hds < 1L) == TRUE) {
hds <- (hds/(hds + 0.15))
}
else if (isTRUE(hds == 0L) == TRUE) {
hds <- 0.01
}
}
else {
ifelse(missing(scl) == TRUE, hds <- 1L, hds <- 1L * scl)
}
ifelse(isTRUE(dim(net)[1] > 8) == TRUE || isTRUE(valued ==
TRUE) == TRUE || isTRUE(flgmlvl == TRUE) == TRUE, hds <- hds *
0.75, NA)
ifelse(missing(signed) == FALSE && isTRUE(signed == TRUE) ==
TRUE, signed <- TRUE, signed <- FALSE)
if (isTRUE(signed == TRUE) == TRUE || isTRUE(cnet == "Signed") ==
TRUE) {
if (isTRUE(cnet == "Signed") == TRUE) {
if (any(net$val %in% c(-1, 0, 1)) == TRUE) {
net <- multiplex::zbind(multiplex::dichot(net$s,
c = 1L), 1 - multiplex::dichot(net$s, c = 0))
}
else {
nets <- multiplex::zbnd(net$s, net$s)
net <- array(NA, dim = c(dim(nets)[1], dim(nets)[2],
2), dimnames = list(dimnames(net$s)[[1]], dimnames(net$s)[[1]]))
net <- replace(net, nets == "o", 0L)
net <- replace(net, nets == "a", 1L)
net[, , 1] <- replace(net[, , 1], nets[, , 1] ==
"p", 1L)
net[, , 1] <- replace(net[, , 1], nets[, , 1] ==
"n", 0L)
net[, , 2] <- replace(net[, , 2], nets[, , 2] ==
"n", 1L)
net[, , 2] <- replace(net[, , 2], nets[, , 2] ==
"p", 0L)
rm(nets)
}
}
else {
ifelse(isTRUE(is.na(dim(net)[3]) == TRUE) == TRUE,
NA, net <- net[, , seq_len(2)])
}
}
else {
net <- replace(net, net == Inf, 0L)
}
if (isTRUE(valued == TRUE) == TRUE && missing(lscl) == FALSE) {
ifelse(isTRUE(lscl > 1L) == TRUE || isTRUE(lscl < 0) ==
TRUE, lscl <- 1, NA)
if (isTRUE(max(net) == max(diag(net))) == TRUE) {
net[which(net == max(net))] <- max(net) * lscl
}
else {
invisible(NA)
}
}
ifelse(missing(rm.isol) == FALSE && isTRUE(rm.isol == TRUE) ==
TRUE, rm.isol <- TRUE, rm.isol <- FALSE)
if (isTRUE(rm.isol == TRUE) == TRUE && isTRUE(dim(net)[1] >
1L) == TRUE) {
inc <- multiplex::rel.sys(net)$incl
if (missing(clu) == FALSE && is.vector(clu) == TRUE) {
clu <- clu[which(dimnames(net)[[1]] %in% inc)]
}
else {
clu <- rep(1, dim(net)[1])
}
ifelse(missing(lbs) == FALSE, lbs <- lbs[inc], NA)
ifelse(missing(lclu) == TRUE, lclu <- seq(0, length(unique(clu))),
NA)
net <- multiplex::rm.isol(net)
}
else {
invisible(NA)
}
if (missing(lbs) == TRUE) {
ifelse(is.null(dimnames(net)[[1]]) == TRUE, lbs <- as.character(seq_len(dim(net)[1])),
lbs <- dimnames(net)[[1]])
}
else if (missing(lbs) == FALSE) {
if (identical(lbs, make.unique(lbs)) == FALSE) {
message("Make unique \"lbs\" because of duplicated entry(ies).")
lbs <- make.unique(lbs)
}
else {
NA
}
if (isTRUE(length(lbs) == dim(net)[1]) == TRUE || is.null(dimnames(net)[[1]]) ==
TRUE) {
dimnames(net)[[1]] <- dimnames(net)[[2]] <- lbs
}
else {
message("Length of \"lbs\" not equal to number of nodes in \"net\".")
dimnames(net)[[1]] <- dimnames(net)[[2]] <- lbs[seq_len(dim(net)[1])]
}
}
else {
NA
}
n <- dim(net)[1]
ifelse(isTRUE(is.na(dim(net)[3]) == TRUE) == TRUE, z <- 1L,
z <- dim(net)[3])
ifelse(isTRUE(swp == TRUE) == TRUE && isTRUE(z > 1L) == TRUE,
net <- net[, , rev(seq_len(z))], NA)
if (missing(att) == FALSE && is.array(att) == TRUE) {
if (isTRUE(n != dim(att)[1]) == TRUE) {
message("Dimensions in \"net\" and \"att\" differ; no attributes are shown.")
showAtts <- FALSE
}
}
if (missing(drp) == FALSE && is.numeric(drp) == TRUE) {
netdrp <- replace(net, net <= drp, 0)
netd <- multiplex::dichot(netdrp, c = 1L)
}
else {
ifelse(isTRUE(sum(net) == 0) == TRUE, netd <- net, netd <- multiplex::dichot(net,
c = min(net[net > 0])))
netdrp <- net
}
if (isTRUE(directed == FALSE) == TRUE && isTRUE(collRecip ==
TRUE) == TRUE && isTRUE(valued == TRUE) == TRUE) {
if (isTRUE(z == 1L) == TRUE) {
netdrp <- netdrp + t(netdrp)
}
else {
for (i in seq_len(z)) {
netdrp[, , i] <- netdrp[, , i] + t(netdrp[, ,
i])
}
rm(i)
}
}
else {
NA
}
if (isTRUE(directed == FALSE) == TRUE && (isTRUE(collRecip ==
TRUE) == TRUE && isTRUE(undRecip == TRUE) == FALSE) ||
isTRUE(directed == FALSE) == TRUE && isTRUE(undRecip ==
TRUE) == TRUE) {
if (isTRUE(z == 1L) == TRUE) {
nt <- netd + t(netd)
rcp <- multiplex::dichot(nt, c = 2L)
rcp[lower.tri(rcp, diag = TRUE)] <- 0L
}
else {
nt <- array(0L, dim = c(n, n, z))
dimnames(nt)[[1]] <- dimnames(nt)[[2]] <- lbs
dimnames(nt)[[3]] <- dimnames(net)[[3]]
for (i in seq_len(z)) {
nt[, , i] <- netd[, , i] + t(netd[, , i])
}
rm(i)
rcp <- multiplex::dichot(nt, c = 2L)
for (i in seq_len(z)) {
rcp[, , i][lower.tri(rcp[, , i], diag = TRUE)] <- 0L
}
rm(i)
}
ucnet <- netd - rcp
}
else {
ucnet <- netd
}
if (isTRUE(collRecip == TRUE) == TRUE) {
bd <- multiplex::bundles(ucnet, loops = loops, lb2lb = FALSE,
collapse = FALSE)
ifelse(isTRUE(directed == TRUE) == FALSE, NA, bd$recp <- multiplex::bundles(netd,
loops = loops, lb2lb = FALSE, collapse = FALSE)$recp)
}
else {
bd <- multiplex::bundles(netd, loops = loops, lb2lb = FALSE,
collapse = FALSE)
}
ifelse(isTRUE(z == 1L) == TRUE, r <- 1L, r <- length(bd[[1]]))
ifelse(isTRUE(sum(net) == 0) == TRUE && isTRUE(loops == TRUE) ==
TRUE, bd$loop <- character(0), NA)
bds <- multiplex::summaryBundles(bd, byties = TRUE)
if (missing(ecol) == TRUE) {
ifelse(isTRUE(signed == TRUE) == TRUE, ecol <- rep(1,
2), ecol <- grDevices::gray.colors(r, start = 0.1,
end = 0.5))
}
else {
ifelse(isTRUE(ecol == 0) == TRUE, ecol <- "transparent",
NA)
}
if (isTRUE(valued == TRUE) == TRUE) {
ifelse(missing(lty) == TRUE, lty <- rep(1, r), lty <- rep(lty,
r))
}
else if (isTRUE(signed == TRUE) == TRUE) {
ifelse(missing(lty) == TRUE, lty <- c(1, 3), NA)
}
else {
ifelse(missing(lty) == TRUE, lty <- seq_len(r), NA)
}
if (isTRUE(z == 1L) == TRUE) {
Lt <- lty[1]
vecol <- ecol[1]
}
else {
ifelse(isTRUE(length(ecol) == 1L) == TRUE, vecol <- rep(ecol,
z), vecol <- rep(ecol, z)[seq_len(z)])
ifelse(isTRUE(length(lty) == 1L) == TRUE, Lt <- seq_len(r),
Lt <- rep(lty, r)[seq_len(r)])
if (isTRUE(length(lty) == length(Lt)) == FALSE) {
Ltc <- seq_along(vecol)
}
else {
if (isTRUE(seq(lty) == lty) == TRUE) {
Ltc <- Lt
}
else {
ifelse(isTRUE(swp == TRUE) == TRUE && isTRUE(valued ==
TRUE) == FALSE, Ltc <- rev(seq_len(r)), Ltc <- seq_len(r))
}
}
}
vltz <- Lt
if (missing(clu) == FALSE) {
if (is.vector(as.vector(clu)) == FALSE) {
if (is.factor(clu) == TRUE) {
tmpclu <- clu
for (i in seq_len(nlevels(factor(clu)))) {
levels(clu) <- c(levels(clu), i)
clu[which(levels(factor(tmpclu))[i] == clu)] <- i
}
rm(i)
clu <- methods::as(as.vector(clu), "numeric")
}
else if (is.character(clu) == TRUE) {
tmpclu <- clu
clu[which(clu == clu[1])] <- 1
for (i in seq_len(nlevels(factor(tmpclu)) - 1L)) {
clu[which(clu == clu[which((clu %in% tmpclu) ==
TRUE)[(i - 0)]])] <- (i + 1L)
}
rm(i)
clu[which((clu %in% tmpclu) == TRUE)] <- nlevels(factor(tmpclu))
clu <- methods::as(as.vector(clu), "numeric")
rm(tmpclu)
}
}
else {
if (is.list(clu) == TRUE) {
uact <- unique(clu[[1]])
uevt <- unique(clu[[2]])
if (is.character(uact) == TRUE || is.factor(uact) ==
TRUE) {
tmp <- as.vector(uact)
for (i in seq_len(nlevels(factor(uact)))) {
tmp[which(levels(factor(uact))[i] == tmp)] <- i
}
rm(i)
uact <- as.numeric(tmp)
rm(tmp)
ifelse(is.character(clu[[1]]) == TRUE, clu[[1]] <- factor(clu[[1]]),
NA)
if (is.factor(clu[[1]]) == TRUE) {
for (i in seq_len(nlevels(factor(clu[[1]])))) {
levels(clu[[1]])[levels(clu[[1]]) == levels(factor(clu[[1]]))[i]] <- uact[i]
}
rm(i)
clu[[1]] <- as.numeric(as.vector(clu[[1]]))
}
}
if (is.character(uevt) == TRUE || is.factor(uevt) ==
TRUE) {
tmp <- as.vector(uevt)
for (i in seq_len(nlevels(factor(uevt)))) {
tmp[which(levels(factor(uevt))[i] == tmp)] <- i
}
rm(i)
uevt <- as.numeric(tmp)
rm(tmp)
if (is.factor(clu[[2]]) == TRUE) {
for (i in seq_len(nlevels(factor(clu[[2]])))) {
levels(clu[[2]])[levels(clu[[2]]) == levels(factor(clu[[2]]))[i]] <- uevt[i]
}
rm(i)
clu[[2]] <- as.numeric(as.vector(clu[[2]]))
}
}
if (any(clu[[2]] %in% clu[[1]]) == TRUE) {
k <- 0L
tmp2 <- clu[[2]]
while (any(tmp2 %in% clu[[1]]) == TRUE) {
tmp2 <- replace(tmp2, which(tmp2 == min(tmp2)),
(max(clu[[1]]) + k))
k <- k + 1L
}
clu[[2]] <- tmp2
rm(tmp2)
}
clu <- as.vector(unlist(clu))
}
else {
NA
}
}
if (missing(lclu) == FALSE && is.vector(lclu) == TRUE) {
nclu <- length(lclu)
}
else {
nclu <- nlevels(factor(clu))
}
}
else {
nclu <- 1L
}
flgcx <- FALSE
if (missing(cex) == TRUE && isTRUE(loops == FALSE) == TRUE) {
if (isTRUE(length(bds) == 0) == TRUE) {
cex <- 1L
}
else {
cex <- length(bds[[1]])/2L
if (isTRUE(length(bds) > 1L) == TRUE) {
for (i in 2:length(bds)) ifelse(isTRUE(cex <
(length(bds[[i]])/2L)) == TRUE, cex <- (length(bds[[i]])/2L),
NA)
}
cex <- ceiling(cex)
}
}
else if (missing(cex) == TRUE) {
cex <- 1L
}
if (isTRUE(length(cex) == 1L) == TRUE) {
cex <- rep(cex, n)
}
else {
if (is.vector(cex) == FALSE)
stop("'cex' must be a vector")
cex[which(is.na(cex))] <- 0
cex <- cex[seq_len(n)]
flgcx <- TRUE
}
if (isTRUE(flgcx == TRUE) == TRUE && isTRUE(max(cex) > 10L) ==
TRUE) {
if (isTRUE(mean(cex) > 20L) == TRUE) {
cex <- (((cex - min(cex))/(max(cex) - min(cex))) *
10L)
}
else {
cex <- (cex/(norm(as.matrix(cex), type = "M"))) *
10L
}
ifelse(isTRUE(min(cex) == 0) == TRUE, cex <- cex + 1L +
(2L/n), NA)
}
else if (isTRUE(flgcx == FALSE) == TRUE && isTRUE(valued ==
TRUE) == TRUE) {
ifelse(isTRUE(max(cex) >= 21L) == TRUE, cex <- 20L, NA)
}
else {
NA
}
if (missing(fsize) == TRUE) {
ifelse(isTRUE(max(cex) < 2) == TRUE, fsize <- cex * 0.66,
fsize <- cex * 0.25)
}
else {
fsize <- fsize/10L
}
ifelse(isTRUE(valued == FALSE) == TRUE && isTRUE(bwd > 1L) ==
TRUE, bwd <- 1L, NA)
ifelse(isTRUE(max(cex) < 2) == TRUE, NA, bwd <- bwd * 0.75)
if (isTRUE(length(pch) == 1L) == TRUE) {
pch <- rep(pch, n)
}
else if (isTRUE(length(pch) == nclu) == TRUE) {
if (identical(pch, clu) == FALSE) {
tmppch <- rep(0, n)
for (i in seq_len(nclu)) {
tmppch[which(clu == (levels(factor(clu))[i]))] <- pch[i]
}
rm(i)
pch <- tmppch
rm(tmppch)
}
}
else if (isTRUE(length(pch) != n) == TRUE) {
pch <- rep(pch[1], n)
}
if (missing(vcol) == TRUE) {
if (missing(col) == TRUE) {
vcol <- grDevices::gray.colors(nclu)
}
else {
vcol <- col
}
}
if (isTRUE(length(vcol) == 1L) == TRUE) {
vcol <- rep(vcol, n)
}
else if (isTRUE(length(vcol) != n) == TRUE & isTRUE(nclu ==
1) == TRUE) {
vcol <- rep(vcol[1], n)
}
else if ((isTRUE(length(vcol) == nclu) == TRUE) && (isTRUE(nclu <
length(vcol)) == TRUE || identical(vcol, clu) == FALSE ||
missing(lclu) == FALSE)) {
tmpvcol <- rep(0, n)
if (missing(lclu) == FALSE) {
if (isTRUE(min(lclu) == 0L) == TRUE) {
lclu[which(lclu == 0L)] <- max(lclu) + 1L
lclu <- sort(lclu)
clu[which(clu == 0L)] <- max(lclu)
}
for (i in seq_len(nclu)) {
tmpvcol[which(clu == lclu[i])] <- vcol[i]
}
rm(i)
}
else {
for (i in seq_len(nclu)) {
tmpvcol[which(clu == (levels(factor(clu))[i]))] <- vcol[i]
}
rm(i)
}
vcol <- tmpvcol
rm(tmpvcol)
}
vcol[which(is.na(vcol))] <- graphics::par()$bg
vcol[which(vcol == 0)] <- graphics::par()$bg
if (isTRUE(any(pch %in% 21:25)) == TRUE) {
if (missing(vcol0) == TRUE || isTRUE(vcol0 == 0) == TRUE) {
vcol0 <- vcol
}
else {
ifelse(missing(vcol0) == TRUE, NA, vcol0[which(is.na(vcol0))] <- 1)
}
if (isTRUE(length(vcol0) == 1L) == TRUE) {
vcol0 <- rep(vcol0, n)
}
else if (isTRUE(length(vcol0) == nclu) == TRUE) {
if (identical(vcol0, clu) == FALSE) {
tmpvcol0 <- rep(0, n)
for (i in seq_len(nclu)) {
tmpvcol0[which(clu == (levels(factor(clu))[i]))] <- vcol0[i]
}
rm(i)
vcol0 <- tmpvcol0
rm(tmpvcol0)
}
}
else if (isTRUE(length(vcol0) != n) == TRUE | isTRUE(nclu ==
1) == TRUE) {
vcol0 <- rep(vcol0[1], n)
}
}
else {
vcol0 <- vcol
}
if (isTRUE(n > 100) == TRUE) {
ffds <- n/10L
}
else if (isTRUE(n > 20) == TRUE) {
ffds <- n/100L
}
else if (isTRUE(n == 2) == TRUE) {
ffds <- -5
}
else {
ffds <- 0
}
ifelse(isTRUE(directed == TRUE) == TRUE, fds <- 120L - (n *
ffds), fds <- 145L - (n * ffds))
if (isTRUE(flgcx == TRUE) == TRUE || (isTRUE(flgcx == FALSE) ==
TRUE && isTRUE(cex > 5) == TRUE)) {
fds <- fds - 10L
}
else if (isTRUE(flgcx == FALSE) == TRUE) {
NA
}
ifelse(missing(scl) == TRUE, scl <- rep(1, 2), NA)
ifelse(isTRUE(length(scl) == 1) == TRUE, scl <- rep(scl,
2), scl <- scl[1:2])
if (isTRUE(max(scl) < 1) == TRUE) {
fds <- fds - (1/(mean(scl)/30L))
}
else if (isTRUE(max(scl) > 1) == TRUE) {
fds <- fds + (mean(scl) * 20L)
}
else {
NA
}
if (missing(vedist) == TRUE) {
vedist <- 0
}
else if (isTRUE(vedist > 10L) == TRUE) {
vedist <- 10L
}
else if (isTRUE(vedist < (-10L)) == TRUE) {
vedist <- -10L
}
else {
NA
}
fds <- fds - (vedist * 10L)
ifelse(isTRUE(fds < 1) == TRUE, fds <- (n - vedist), NA)
if (missing(coord) == FALSE) {
if (isTRUE(nrow(coord) == n) == FALSE)
stop("Length of \"coord\" does not match network order.")
flgcrd <- TRUE
crd <- coord
}
else if (missing(coord) == TRUE) {
flgcrd <- FALSE
switch(match.arg(layout), force = {
ifelse(isTRUE(n < 2L) == TRUE, crd <- data.frame(X = sin(2L *
pi * ((0:(n - 1L))/n)), Y = cos(2L * pi * ((0:(n -
1L))/n))), crd <- frcd(netd, seed = seed, maxiter = maxiter))
}, stress = {
ifelse(isTRUE(n < 2L) == TRUE, crd <- data.frame(X = sin(2L *
pi * ((0:(n - 1L))/n)), Y = cos(2L * pi * ((0:(n -
1L))/n))), crd <- stsm(netd, seed = seed, maxiter = maxiter,
...))
ifelse(isTRUE(flgcx == TRUE) == TRUE, fds <- fds -
15L, NA)
}, circ = {
crd <- data.frame(X = sin(2L * pi * ((0:(n - 1L))/n)),
Y = cos(2L * pi * ((0:(n - 1L))/n)))
ifelse(isTRUE(flgcx == TRUE) == TRUE, fds <- fds -
10L, NA)
}, conc = {
if (missing(lbs) == FALSE && is.null(dimnames(netd)[[1]]) ==
TRUE) {
if (identical(lbs, make.unique(lbs)) == FALSE) {
message("Make unique \"lbs\" because of duplicated entry(ies).")
dimnames(netd)[[1]] <- dimnames(netd)[[2]] <- make.unique(lbs)
} else {
dimnames(netd)[[1]] <- dimnames(netd)[[2]] <- lbs
}
}
crd <- conc(netd, ...)
}, rand = {
set.seed(seed)
crd <- data.frame(X = round(stats::runif(n) * 1L,
5), Y = round(stats::runif(n) * 1L, 5))
})
}
if (missing(rot) == FALSE) {
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(rot))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
cnt <- 1L
ifelse(isTRUE(n == 2) == TRUE && isTRUE(rot == -90) ==
TRUE, rot <- -89.9, NA)
}
else {
cnt <- 0
}
if (isTRUE(flgcrd == FALSE) == TRUE) {
if (match.arg(layout) == "circ" && missing(pos) == TRUE) {
angl <- vector()
length(angl) <- n
for (i in seq_len(n)) {
ifelse((atan2((crd[i, 2] - cnt), (crd[i, 1] -
cnt)) * (180L/pi)) >= 0, angl[i] <- atan2((crd[i,
2] - cnt), (crd[i, 1] - cnt)) * (180L/pi),
angl[i] <- ((atan2((crd[i, 2] - cnt), (crd[i,
1] - cnt)) * (180L/pi))%%180L) + 180L)
}
rm(i)
pos <- vector()
for (i in seq_len(length(angl))) {
if (isTRUE(65 < angl[i]) == TRUE && isTRUE(115 >
angl[i]) == TRUE) {
pos <- append(pos, 3)
}
else if (isTRUE(115 <= angl[i]) == TRUE && isTRUE(245 >=
angl[i]) == TRUE) {
pos <- append(pos, 2)
}
else if (isTRUE(245 < angl[i]) == TRUE && isTRUE(295 >
angl[i]) == TRUE) {
pos <- append(pos, 1)
}
else {
pos <- append(pos, 4)
}
}
rm(i)
}
}
if (missing(pos) == TRUE) {
pos <- 4
}
else {
if (isTRUE(pos < 0L) == TRUE | isTRUE(pos > 4L) == TRUE) {
message("\"pos\" value must be between 0-4; set to 4.")
pos <- 4
}
else {
invisible(NA)
}
}
ifelse(missing(mirrorX) == FALSE && isTRUE(mirrorX == TRUE) ==
TRUE || missing(mirrorV) == FALSE && isTRUE(mirrorV ==
TRUE) == TRUE, crd[, 1] <- crd[, 1] * cos(pi) - crd[,
2] * sin(pi), mirrorX <- FALSE)
ifelse(missing(mirrorY) == FALSE && isTRUE(mirrorY == TRUE) ==
TRUE || missing(mirrorH) == FALSE && isTRUE(mirrorH ==
TRUE) == TRUE, crd[, 2] <- crd[, 2] * cos(pi) - crd[,
1] * sin(pi), mirrorY <- FALSE)
if (match.arg(layout) == "circ" && isTRUE(flgcrd == FALSE) ==
TRUE) {
if (isTRUE(mirrorX == TRUE) == TRUE && isTRUE(length(pos) ==
n) == TRUE) {
pos[which(pos == 2)] <- 0
pos[which(pos == 4)] <- 2
pos[which(pos == 0)] <- 4
}
else if (isTRUE(mirrorY == TRUE) == TRUE && isTRUE(length(pos) ==
n) == TRUE) {
pos[which(pos == 1)] <- 0
pos[which(pos == 3)] <- 1
pos[which(pos == 0)] <- 3
}
else {
NA
}
}
if (missing(mirrorL) == FALSE && isTRUE(mirrorL == TRUE) ==
TRUE) {
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(45))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
crd[, 2] <- crd[, 2] * cos(pi) - crd[, 1] * sin(pi)
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(-45))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
}
else if (missing(mirrorD) == FALSE && isTRUE(mirrorD == TRUE) ==
TRUE) {
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(-45))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
crd[, 2] <- crd[, 2] * cos(pi) - crd[, 1] * sin(pi)
crd[, 1:2] <- xyrt(crd[, 1:2], as.numeric(45))
crd[, 1:2] <- crd[, 1:2] - min(crd[, 1:2])
}
else {
NA
}
if (isTRUE(n > 1) == TRUE) {
rat <- (max(crd[, 1]) - min(crd[, 1]))/(max(crd[, 2]) -
min(crd[, 2]))
crd[, 1] <- (crd[, 1] - min(crd[, 1]))/(max(crd[, 1]) -
min(crd[, 1]))
ifelse(isTRUE(rat > 0) == TRUE, crd[, 2] <- ((crd[, 2] -
min(crd[, 2]))/(max(crd[, 2]) - min(crd[, 2]))) *
(1L/rat), crd[, 2] <- ((crd[, 2] - min(crd[, 2]))/(max(crd[,
2]) - min(crd[, 2]))) * (rat))
}
else {
NA
}
if (isTRUE(flgcrd == TRUE) == TRUE && isTRUE(ncol(crd) >
2) == TRUE) {
lbgml <- tolower(as.vector(crd[, 3]))
lbnet <- tolower(as.vector(lbs))
lbp <- vector()
for (i in seq_len(nrow(crd))) {
lbp <- append(lbp, which(lbnet[i] == lbgml))
}
rm(i)
if (isTRUE(ncol(crd) > 3) == TRUE) {
atgml <- as.vector(crd[, 4])
atgml[which(is.na(atgml))] <- ""
atts <- atgml[lbp]
}
nds <- data.frame(X = as.numeric(as.vector(crd[lbp, 1])),
Y = as.numeric(as.vector(crd[lbp, 2])))
}
else {
nds <- data.frame(X = as.numeric(as.vector(crd[, 1])),
Y = as.numeric(as.vector(crd[, 2])))
}
nds <- ((2L/max(nds * (0.75))) * (nds * 0.75)) * (0.5)
mscl <- mean(scl)
cex <- cex * mscl
fsize <- fsize * mscl
omr <- graphics::par()$mar
omi <- graphics::par()$mai
if (missing(mar) == TRUE) {
mar <- c(0, 0, 0, 0)
}
else {
NA
}
if (missing(mai) == TRUE) {
ifelse(isTRUE(loops == TRUE) == TRUE, mai <- c(0, 0,
0.2, 0), mai <- c(0, 0, 0, 0))
}
else {
NA
}
graphics::par(mar = mar)
ifelse(is.null(main) == TRUE, graphics::par(mai = mai), graphics::par(mai = mai +
c(0, 0, cex.main/10L, 0)))
obg <- graphics::par()$bg
graphics::par(bg = grDevices::adjustcolor(bg, alpha = alpha[3]))
if (isTRUE(loops == TRUE) == TRUE) {
ylim <- c(min(nds[, 2]) - (max(cex)/100L), max(nds[,
2]) + (max(cex)/70L))
xlim <- c(min(nds[, 1]) - (max(cex)/100L), max(nds[,
1]) + (max(cex)/100L))
}
else if (isTRUE(flgcx == TRUE) == TRUE) {
ylim <- c(min(nds[, 2]) - (max(cex)/500L), max(nds[,
2]) + (max(cex)/500L))
xlim <- c(min(nds[, 1]) - (max(cex)/500L), max(nds[,
1]) + (max(cex)/500L))
}
else {
ylim <- c(min(nds[, 2]) - ((cex[1])/200L), max(nds[,
2]) + ((cex[1])/200L))
xlim <- c(min(nds[, 1]) - ((cex[1])/200L), max(nds[,
1]) + ((cex[1])/200L))
}
ifelse(missing(font.main) == FALSE && isTRUE(font.main %in%
names(grDevices::postscriptFonts())) == TRUE, graphics::par(family = font.main),
NA)
ifelse(missing(new) == FALSE && isTRUE(new == TRUE) == TRUE,
par(new = TRUE), NA)
suppressWarnings(graphics::plot(nds, type = "n", axes = FALSE,
xlab = "", ylab = "", ylim = ylim, xlim = xlim, asp = asp,
main = main, cex.main = cex.main, col.main = col.main,
...))
if (isTRUE(showLbs == TRUE) == TRUE || isTRUE(values == TRUE) ==
TRUE) {
ifelse(missing(ffamily) == FALSE && isTRUE(ffamily %in%
names(grDevices::postscriptFonts())) == TRUE, graphics::par(family = ffamily),
NA)
}
tlbs <- vector()
if (isTRUE(length(bds) > 0) == TRUE) {
for (i in seq_len(length(attr(bds, "names")))) {
ifelse(isTRUE(length(multiplex::dhc(attr(bds, "names")[i],
sep = "")) > 4L) == TRUE, tlbs <- append(tlbs,
tolower(paste(multiplex::dhc(attr(bds, "names")[i],
sep = "")[1:4], collapse = ""))), tlbs <- append(tlbs,
tolower(attr(bds, "names"))[i]))
}
rm(i)
}
if (isTRUE(loops == TRUE) == TRUE) {
tlbslp <- tlbs
tlbs <- tlbs[which(tlbs != "loop")]
}
else {
NA
}
if (isTRUE(flgcn2 == TRUE) == TRUE) {
tlbs <- rev(tlbs)
bds <- rev(bds)
bd <- rev(bd)
}
else {
NA
}
ifelse(isTRUE(flgpf == TRUE) == TRUE, fnnetdrp <- maxw, fnnetdrp <- (norm(as.matrix(netdrp),
type = "F")))
if (isTRUE(swp == TRUE) == TRUE) {
Lt <- Lt[rev(seq_len(length(Lt)))]
lwd <- lwd[length(lwd):1]
ifelse(isTRUE(valued == TRUE) == TRUE, vecol <- vecol[rev(seq_len(length(vecol)))],
NA)
alfa <- alfa[rev(seq_len(length(alfa)))]
}
if (isTRUE(loops == TRUE) == TRUE && isTRUE(valued == TRUE) ==
TRUE && isTRUE(max(netdrp) > 10L) == TRUE) {
if (isTRUE(z == 1L) == TRUE) {
diag(netdrp) <- (diag(netdrp)/fnnetdrp) * (15L)
}
else {
for (i in seq_len(z)) {
diag(netdrp[, , i]) <- as.vector((diag(netdrp[,
, i])/fnnetdrp) * (15L))
}
}
}
else {
NA
}
if ((isTRUE(collRecip == TRUE) == TRUE && isTRUE(undRecip ==
TRUE) == FALSE) && isTRUE(valued == TRUE) == FALSE &&
isTRUE(c("recp") %in% attr(bds, "names")) == TRUE) {
trcp <- multiplex::transf(rcp, type = "tolist")
}
else {
NA
}
if (isTRUE(values == TRUE) == TRUE) {
mdp <- data.frame(matrix(nrow = 0L, ncol = 3L))
}
else {
NA
}
if (isTRUE(length(tlbs) > 0) == TRUE) {
for (k in seq_len(length(tlbs))) {
prs <- as.numeric(multiplex::dhc(bds[[k]]))
if (isTRUE(directed == TRUE) == TRUE | isTRUE(collRecip ==
FALSE) == TRUE | (isTRUE(directed == FALSE) ==
TRUE && isTRUE(tlbs[k] %in% c("txch", "mixd",
"full")) == TRUE)) {
pars <- as.matrix(nds[as.numeric(levels(factor(multiplex::dhc(bds[[k]])))),
])
}
else {
pars <- as.matrix(nds[prs, ])
if (isTRUE(tlbs[k] %in% c("mixd", "full")) ==
TRUE && isTRUE(collRecip == TRUE) == TRUE) {
ifelse(isTRUE(prs[1] == prs[length(prs)]) ==
TRUE, pars[c(1:2, 3:nrow(pars)), ] <- pars[c(2:1,
3:nrow(pars)), ], NA)
}
else {
NA
}
}
rbds <- length(bds[[k]])
if (isTRUE(rbds > 0L) == TRUE) {
q <- which(tlbs[k] == attr(bd, "names"))
if (isTRUE(z == 1L) == TRUE) {
vlt <- rep(Lt, rbds)
vecol <- rep(ecol[1], rbds)
tbnd <- as.vector(unlist(bd[q]))
if (isTRUE(length(tbnd) > 0L) == TRUE) {
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vlt <- append(vlt, rep(Lt, q)), NA)
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vltz <- append(vltz, rep(Lt, q)),
NA)
}
vltc <- vlt[1]
}
else {
vlt <- vector()
for (i in seq_along(Lt)) {
tbnd <- as.vector(unlist(bd[[q]][i]))
if (isTRUE(length(tbnd) > 0L) == TRUE) {
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vlt <- append(vlt, rep(Lt[i], length(which(tbnd %in%
bds[[k]])))), NA)
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vltz <- append(vltz, rep(Lt[i],
length(which(tbnd %in% bds[[k]])))),
NA)
}
}
rm(i)
if (isTRUE(length(lty) == 1L) == TRUE) {
vlt1 <- rep(lty, length(vlt))
vltc <- vlt
}
else {
vltc <- vector()
if (isTRUE(Lt == Ltc) == FALSE) {
for (i in seq_along(Ltc)) {
tbnd <- as.vector(unlist(bd[[q]][i]))
if (isTRUE(length(tbnd) > 0L) == TRUE) {
ifelse(isTRUE(any(tbnd %in% bds[[k]])) ==
TRUE, vltc <- append(vltc, rep(Ltc[i],
length(which(tbnd %in% bds[[k]])))),
NA)
}
}
rm(i)
}
else {
if (isTRUE(seq(lty) == lty) == TRUE) {
vltc <- vlt
}
else {
for (i in seq_along(lty)) {
vltc <- append(vltc, replace(vlt[which(vlt ==
lty[i])], vlt[which(vlt == lty[i])] !=
i, i))
}
rm(i)
}
}
}
}
if (isTRUE(flgcx == TRUE) == TRUE) {
if ((isTRUE(directed == TRUE) == TRUE && isTRUE(tlbs[k] %in%
c("asym", "tent", "txch", "mixd")) == TRUE) |
(isTRUE(collRecip == FALSE) == TRUE && isTRUE(tlbs[k] %in%
c("asym", "tent", "txch", "mixd")) == TRUE) |
(isTRUE(directed == TRUE) == FALSE && isTRUE(tlbs[k] %in%
c("txch")) == TRUE)) {
if (isTRUE(multiplex::dhc(bds[[k]][1])[1] >
multiplex::dhc(bds[[k]][1])[2]) == TRUE) {
Prs <- vector()
length(Prs) <- length(prs)
Prs[which(seq_len(length(prs))%%2L == 1L)] <- prs[which(seq_len(length(prs))%%2L ==
0L)]
Prs[which(seq_len(length(prs))%%2L == 0L)] <- prs[which(seq_len(length(prs))%%2L ==
1L)]
cx <- cex[Prs]
}
else {
cx <- cex[prs]
}
}
else {
cx <- cex[prs]
}
ifelse(isTRUE(match.arg(layout) == "rand") ==
TRUE, NA, cx[which(cx == max(cx))] <- max(cx) *
0.85)
}
else {
cx <- cex
}
if (isTRUE(valued == TRUE) == TRUE) {
Lw <- vector()
i <- 1
for (j in seq_len(length(bds[[k]]))) {
qn <- c(prs[i], prs[(i + 1)])
if (isTRUE(directed == FALSE) == TRUE &&
isTRUE(collRecip == TRUE) == TRUE) {
ifelse(isTRUE(z == 1L) == TRUE, Lw <- append(Lw,
netdrp[qn[1], qn[2]]), Lw <- append(Lw,
netdrp[qn[1], qn[2], vltc[j]] + t(netdrp[qn[1],
qn[2], vltc[j]])))
}
else if (isTRUE(directed == TRUE) == TRUE |
isTRUE(collRecip == FALSE) == TRUE) {
ifelse(isTRUE(z == 1L) == TRUE, Lw <- append(Lw,
netdrp[qn[1], qn[2]]), Lw <- append(Lw,
netdrp[qn[1], qn[2], vltc[j]]))
}
i <- i + 2L
}
rm(j)
rm(i)
if (isTRUE(max(netdrp) > 10L) == TRUE) {
lw <- (Lw/fnnetdrp) * (10L * 5L)
}
else {
lw <- Lw
}
}
else {
lw <- rep(lwd[1], rbds)
}
ifelse((isTRUE(swp2 == TRUE) == TRUE && isTRUE(tlbs[k] %in%
c("recp")) == TRUE) && isTRUE(valued == FALSE) ==
TRUE, bds[[k]] <- multiplex::swp(bds[[k]]),
NA)
if (isTRUE(collRecip == TRUE) == TRUE && isTRUE(tlbs[k] %in%
c("recp")) == TRUE) {
bw <- 0L
if (isTRUE(undRecip == TRUE) == TRUE) {
hd <- 0
}
else {
hd <- hds
}
}
else if (isTRUE(collRecip == TRUE) == FALSE &&
isTRUE(tlbs[k] %in% c("recp")) == TRUE) {
ifelse(isTRUE(undRecip == TRUE) == TRUE, hd <- 0L,
hd <- hds)
bw <- bwd
}
else {
bw <- bwd
hd <- hds
}
lw <- lw * mscl
if (isTRUE((collRecip == TRUE) == TRUE && isTRUE(undRecip ==
TRUE) == FALSE) && isTRUE(tlbs[k] %in% c("recp")) ==
FALSE && isTRUE(valued == TRUE) == FALSE &&
isTRUE(c("recp") %in% attr(bds, "names")) ==
TRUE) {
flgcr <- numeric()
sbds <- multiplex::swp(bds[[k]])
if (any(sbds %in% unlist(trcp)) == TRUE) {
for (i in seq_len(z)) {
ifelse(any(sbds %in% trcp[[i]]) == TRUE,
flgcr <- append(flgcr, as.numeric(i)),
NA)
}
rm(i)
}
}
else {
flgcr <- rep(0L, z)
}
pars[, 1] <- pars[, 1] * scl[1]
pars[, 2] <- pars[, 2] * scl[2]
if (isTRUE(z == 1L) == TRUE) {
mbnd(pars, rbds, bds[[k]], vlt, cx * mscl,
lw, vecol, directed, bw, alfa, fds, flgcx,
valued, flgcr, hd, n)
}
else {
ifelse(isTRUE(length(lty) == 1L) == TRUE, mbnd(pars,
rbds, bds[[k]], vlt1, cx * mscl, lw, vecol[vltc],
directed, bw, alfa, fds, flgcx, valued, flgcr,
hd, n), mbnd(pars, rbds, bds[[k]], vlt, cx *
mscl, lw, vecol[vltc], directed, bw, alfa,
fds, flgcx, valued, flgcr, hd, n))
}
if (isTRUE(values == TRUE) == TRUE) {
if (isTRUE(z == 1L) == TRUE) {
ifelse(isTRUE(isSymmetric(net) == TRUE) ==
TRUE, fsym <- 2L, fsym <- 1L)
ifelse(isTRUE(directed == FALSE) == TRUE,
mdp[nrow(mdp) + 1, ] <- c((pars[1, 1] +
pars[2, 1])/2L, (pars[1, 2] + pars[2,
2])/2L, as.numeric(net[as.numeric(multiplex::dhc(bds[[k]])[1]),
as.numeric(multiplex::dhc(bds[[k]])[2])]/fsym +
net[as.numeric(multiplex::dhc(bds[[k]])[2]),
as.numeric(multiplex::dhc(bds[[k]])[1])]/fsym)),
mdp[nrow(mdp) + 1, ] <- c((pars[1, 1] +
pars[2, 1])/2L, (pars[1, 2] + pars[2,
2])/2L, as.numeric(net[as.numeric(multiplex::dhc(bds[[k]])[1]),
as.numeric(multiplex::dhc(bds[[k]])[2])]) +
net[as.numeric(multiplex::dhc(bds[[k]])[2]),
as.numeric(multiplex::dhc(bds[[k]])[1])]))
}
else {
mpnet <- multiplex::mnplx(net, dichot = FALSE,
directed = TRUE)
ifelse(isTRUE(directed == FALSE) == TRUE,
mdp[nrow(mdp) + 1, ] <- c((pars[1, 1] +
pars[2, 1])/2L, (pars[1, 2] + pars[2,
2])/2L, as.numeric(mpnet[as.numeric(multiplex::dhc(bds[[k]])[1]),
as.numeric(multiplex::dhc(bds[[k]])[2])] +
mpnet[as.numeric(multiplex::dhc(bds[[k]])[2]),
as.numeric(multiplex::dhc(bds[[k]])[1])])),
mdp[nrow(mdp) + 1, ] <- c((pars[1, 1] +
pars[2, 1])/2L, (pars[1, 2] + pars[2,
2])/2L, multiplex::mnplx(netdrp, dichot = FALSE,
directed = FALSE)[as.numeric(multiplex::dhc(bds[[k]])[1]),
as.numeric(multiplex::dhc(bds[[k]])[2])]))
}
}
}
else {
NA
}
}
rm(k)
}
else {
ifelse(isTRUE(loops == TRUE) == TRUE && isTRUE(length(lty) ==
1) == TRUE, vlt <- lty, NA)
}
if (isTRUE(loops == TRUE) == TRUE) {
if (isTRUE(swp == TRUE) == TRUE) {
bdlp <- bd$loop[rev(seq_len(length(bd$loop)))]
if (isTRUE(valued == TRUE) == TRUE) {
netdrpl <- netdrp
}
else {
vecol <- vecol[rev(seq_len(length(vecol)))]
netdrpl <- netdrp[, , rev(seq_len(dim(netdrp)[3]))]
}
}
else {
bdlp <- bd$loop
netdrpl <- netdrp
}
dz <- (rng(z) + abs(min(rng(z))))/(10L)
ndss <- nds
ndss[, 1] <- ndss[, 1] * scl[1]
ndss[, 2] <- ndss[, 2] * scl[2]
if (isTRUE(z == 1L) == TRUE) {
lp <- as.vector(which(diag(net) > 0))
if (isTRUE(length(lp) > 0) == TRUE) {
for (i in seq_len(length(lp))) {
if (isTRUE(n == 1L) == TRUE) {
dcx <- (cex[lp[i]]^2) * 0.00025
lpsz <- (cex[lp[i]]^2) * 0.00015
}
else if (isTRUE(n < 3) == TRUE) {
dcx <- (cex[lp[i]] * 0.0075)
lpsz <- (cex[lp[i]] * 0.005) - (dz)
}
else {
dcx <- (cex[lp[i]] * 0.01)
lpsz <- (cex[lp[i]] * 0.0075) - (dz)
}
ifelse(isTRUE(length(lty) == 1) == TRUE, Ltl <- vlt,
Ltl <- Lt)
ifelse(isTRUE(valued == TRUE) == TRUE, hc(ndss[lp[i],
1], ndss[lp[i], 2] + (dcx), lpsz, col = grDevices::adjustcolor(vecol,
alpha = alfa), lty = Ltl, lwd = diag(netdrpl)[lp[i]]),
hc(ndss[lp[i], 1], ndss[lp[i], 2] + (dcx),
lpsz, col = grDevices::adjustcolor(vecol,
alpha = alfa), lty = Ltl, lwd = lwd))
}
rm(i)
}
else {
NA
}
}
else if (isTRUE(z > 1) == TRUE) {
if (missing(bwd2) == TRUE) {
bwd2 <- 1L
}
else if (missing(bwd2) == FALSE) {
if (isTRUE(bwd2 < 1L) == TRUE && isTRUE(bwd2 ==
0) == FALSE) {
bwd2 <- 1L
}
else if (isTRUE(bwd2 > 10L) == TRUE) {
bwd2 <- 10L
}
if (isTRUE(bwd2 == 0) == TRUE) {
dz <- rep(0, z)
}
else {
ifelse(isTRUE(valued == TRUE) == TRUE && isTRUE(max(net) >
1L) == TRUE, dz <- (bwd2 * 1L) * (rng(z) +
abs(min(rng(z))))/(5L), dz <- (bwd2 * 1L) *
(rng(z) + abs(min(rng(z))))/(10L))
}
}
for (k in seq_len(length(bdlp))) {
lp <- as.numeric(unique(multiplex::dhc(bdlp)[k][[1]]))
if (isTRUE(length(lp) > 0) == TRUE) {
for (i in seq_len(length(lp))) {
ifelse(isTRUE(cex[lp[i]] <= 3L) == TRUE |
isTRUE(n < 3) == TRUE, dz <- dz * 0.75,
NA)
if (isTRUE(n == 1L) == TRUE) {
dcx <- (cex[lp[i]]^2) * 0.00025
lpsz <- abs((cex[lp[i]]^2) * 0.00015)
}
else if (isTRUE(n < 3) == TRUE) {
dcx <- cex[lp[i]]/110L
lpsz <- abs((cex[lp[i]] * 0.007) - dz[k])
}
else {
dcx <- cex[lp[i]]/100L
lpsz <- abs((cex[lp[i]] * 0.0075) - dz[k])
}
ifelse(isTRUE(length(lty) == 1) == TRUE,
Ltl <- rep(lty, length(bdlp)), Ltl <- Lt)
ifelse(isTRUE(valued == TRUE) == TRUE, hc(ndss[lp[i],
1], ndss[lp[i], 2] + (dcx), lpsz, col = grDevices::adjustcolor(vecol[k],
alpha = alfa), lty = Ltl[k], lwd = netdrpl[i,
i, k]), hc(ndss[lp[i], 1], ndss[lp[i],
2] + (dcx), lpsz, col = grDevices::adjustcolor(vecol[k],
alpha = alfa), lty = Ltl[k], lwd = (lwd[k] -
k)))
}
rm(i)
}
else {
dz <- append(0, dz)
}
}
rm(k)
}
}
else {
NA
}
if (isTRUE(values == TRUE) == TRUE) {
mdps <- mdp[, 1:2]
mdps[, 1] <- mdps[, 1] * scl[1]
mdps[, 2] <- mdps[, 2] * scl[2]
ifelse(missing(fsize2) == TRUE, fsize2 <- fsize, fsize2 <- fsize2/10L)
ifelse(missing(cex2) == TRUE, cex2 <- fsize2, NA)
ifelse(missing(fcol2) == TRUE, fcol2 <- "#000000", NA)
ifelse(missing(bg2) == TRUE, bg2 <- "transparent", NA)
if (isTRUE(flgbg == TRUE) == TRUE) {
graphics::points(mdps[, 1], mdps[, 2], pch = 16,
cex = fsize2 * 2, col = bg2, bg = bg)
}
else if (isTRUE(flgbg == FALSE) == TRUE) {
graphics::points(mdps[, 1], mdps[, 2], pch = 16,
cex = fsize2 * 2, col = grDevices::adjustcolor(bg2,
alpha = alpha[4]), bg = obg)
}
else {
NA
}
if (isTRUE(directed == FALSE) == TRUE) {
for (k in seq_along(tlbs)) {
graphics::text(mdps[k, ], labels = mdp[k, 3],
cex = fsize2, col = fcol2)
}
rm(k)
}
else {
for (k in seq_along(tlbs)) {
graphics::text(mdps[k, ], labels = mdp[k, 3],
cex = fsize2, col = fcol2)
}
rm(k)
}
}
if (all(pch %in% 21:25) == TRUE) {
graphics::points(nds[, 1] * scl[1], nds[, 2] * scl[2],
pch = pch, cex = cex, col = grDevices::adjustcolor(vcol0,
alpha = alpha[1]), bg = grDevices::adjustcolor(vcol,
alpha = alpha[1]))
}
else {
graphics::points(nds[, 1] * scl[1], nds[, 2] * scl[2],
pch = pch, cex = cex, col = grDevices::adjustcolor(vcol,
alpha = alpha[1]), bg = grDevices::adjustcolor(vcol,
alpha = alpha[1]))
}
if (isTRUE(showLbs == TRUE) == TRUE) {
ndss <- nds
ndss[, 1] <- ndss[, 1] * scl[1]
ndss[, 2] <- ndss[, 2] * scl[2]
if (missing(sel) == TRUE) {
lbs[which(is.na(lbs))] <- ""
}
else {
ifelse(is.data.frame(sel) == TRUE, sel <- as.vector(unlist(sel,
use.names = FALSE)), NA)
if (any(sel %in% lbs) == FALSE) {
options(warn = 0)
message("Values in \"sel\" are not found in \"net\".")
lbs <- rep("", length(lbs))
}
else {
lbb <- lbs
lbs <- rep("", length(lbs))
vec <- vector()
for (i in seq_len(length(sel))) {
vec <- append(vec, which(lbb %in% sel[i]))
}
rm(i)
suppressWarnings(lbs[vec] <- sel)
}
}
options(warn = -1)
if (isTRUE(length(pos) == 1) == TRUE) {
if (isTRUE(pos == 0) == TRUE) {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, labels = lbs, cex = fsize,
adj = 0.5, col = fcol)
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
adj = 0.5, col = fcol)
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
adj = 0.5, col = fcol)
}
else if (isTRUE(fstyle == "bolditalic") ==
TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))),
cex = fsize, adj = 0.5, col = fcol)
}
}
}
else {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, lbs, cex = fsize, pos = pos,
col = fcol, offset = (cex/4L), adj = c(0.5,
1))
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
pos = pos, col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
pos = pos, col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bolditalic") ==
TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))),
cex = fsize, pos = pos, col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
}
}
}
else if (isTRUE(length(pos) == n) == TRUE) {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, lbs, cex = fsize, pos = pos,
col = fcol[1], offset = (cex/4L), adj = c(0.5,
1))
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
pos = pos, col = fcol[1], offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
pos = pos, col = fcol[1], offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bolditalic") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))), cex = fsize,
pos = pos, col = fcol[1], offset = (cex/4L),
adj = c(0.5, 1))
}
}
}
else {
if (isTRUE(pos[1] == 0) == TRUE) {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, labels = lbs, cex = fsize,
adj = 0.5, col = fcol)
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
adj = 0.5, col = fcol)
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
adj = 0.5, col = fcol)
}
else if (isTRUE(fstyle == "bolditalic") ==
TRUE) {
graphics::text(ndss, labels = as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))),
cex = fsize, adj = 0.5, col = fcol)
}
}
}
else {
if (missing(fstyle) == TRUE || (missing(fstyle) ==
FALSE && isTRUE(fstyle %in% c("italic", "bold",
"bolditalic") == FALSE))) {
graphics::text(ndss, lbs, cex = fsize, pos = pos[1],
col = fcol, offset = (cex/4L), adj = c(0.5,
1))
}
else if (missing(fstyle) == FALSE) {
if (isTRUE(fstyle == "italic") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(italic(.(x))))), cex = fsize,
pos = pos[1], col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bold") == TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bold(.(x))))), cex = fsize,
pos = pos[1], col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(fstyle == "bolditalic") ==
TRUE) {
graphics::text(ndss, as.expression(lapply(lbs,
function(x) bquote(bolditalic(.(x))))),
cex = fsize, pos = pos[1], col = fcol,
offset = (cex/4L), adj = c(0.5, 1))
}
}
}
}
}
if (isTRUE(showAtts == TRUE) == TRUE) {
ndss <- nds
ndss[, 1] <- ndss[, 1] * scl[1]
ndss[, 2] <- ndss[, 2] * scl[2]
if (isTRUE(flgcrd == TRUE) == TRUE && isTRUE(ncol(coord) >
3L) == TRUE) {
NA
}
else {
atts <- rep("", nrow(nds))
if (missing(att) == FALSE) {
if (is.array(att) == TRUE) {
if (is.na(dim(att)[3]) == TRUE | isTRUE(dim(att)[3] ==
1) == TRUE) {
ifelse(missing(lbat) == FALSE, atts[which((att) !=
0)] <- lbat, atts[which((att) != 0)] <- "1")
}
else {
if (missing(lbat) == FALSE) {
atts[which(diag(multiplex::mnplx(netd,
diag.incl = TRUE)) != 0)] <- lbat
}
else {
dimnames(netd)[[3]] <- NULL
neta <- multiplex::zbind(netd, att)
clss <- multiplex::expos(multiplex::rel.sys(neta,
att = (z + 1L):dim(neta)[3]), classes = TRUE)$Classes
attr(clss, "names")[which(attr(clss, "names") ==
"ALL")] <- multiplex::jnt(dimnames(att)[[3]],
sep = "")
ifelse(isTRUE(attr(clss, "names")[1] ==
"NONE") == TRUE, nnone <- 2, nnone <- 1)
for (i in nnone:length(clss)) {
atts[which(lbs %in% clss[[i]])] <- attr(clss,
"names")[i]
}
rm(i)
}
}
}
else if (is.vector(att) == TRUE | is.factor(att) ==
TRUE) {
ifelse(isTRUE(length(att) == n) == TRUE, atts <- as.vector(att),
atts <- rep("", length(lbs)))
}
else {
atts <- rep("", length(lbs))
}
}
else {
NA
}
}
if (isTRUE(flgcx == FALSE) == TRUE) {
graphics::text(ndss, labels = atts, cex = fsize,
pos = pos%%4 + 1L, col = fcol, offset = (cex/4L),
adj = c(0.5, 1))
}
else if (isTRUE(flgcx == TRUE) == TRUE) {
graphics::text(ndss, labels = atts, cex = fsize,
pos = pos%%4 + 1L, col = fcol, offset = (min(cex)/4L),
adj = c(0.5, 1))
}
}
options(warn = 0)
graphics::par(mar = omr)
graphics::par(bg = obg)
graphics::par(lend = 0)
graphics::par(mai = omi)
}
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