Last updated on 2020-03-07 11:48:16 CET.
| Flavor | Version | Tinstall | Tcheck | Ttotal | Status | Flags |
|---|---|---|---|---|---|---|
| r-devel-linux-x86_64-debian-clang | 0.13.0 | 103.04 | 67.89 | 170.93 | ERROR | |
| r-devel-linux-x86_64-debian-gcc | 0.13.0 | 73.64 | 51.96 | 125.60 | ERROR | |
| r-devel-linux-x86_64-fedora-clang | 0.13.0 | 244.96 | ERROR | |||
| r-devel-linux-x86_64-fedora-gcc | 0.13.0 | 219.16 | ERROR | |||
| r-devel-windows-ix86+x86_64 | 0.13.0 | 264.00 | 456.00 | 720.00 | OK | |
| r-devel-windows-ix86+x86_64-gcc8 | 0.13.0 | 230.00 | 380.00 | 610.00 | OK | |
| r-patched-linux-x86_64 | 0.13.0 | 82.63 | 292.68 | 375.31 | OK | |
| r-patched-solaris-x86 | 0.13.0 | 799.40 | OK | |||
| r-release-linux-x86_64 | 0.13.0 | 83.18 | 298.13 | 381.31 | OK | |
| r-release-windows-ix86+x86_64 | 0.13.0 | 191.00 | 330.00 | 521.00 | OK | |
| r-release-osx-x86_64 | 0.13.0 | NOTE | ||||
| r-oldrel-windows-ix86+x86_64 | 0.13.0 | 169.00 | 360.00 | 529.00 | OK | |
| r-oldrel-osx-x86_64 | 0.13.0 | OK |
Version: 0.13.0
Check: examples
Result: ERROR
Running examples in 'GERGM-Ex.R' failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_network
> ### Title: Plots of value-edged networks.
> ### Aliases: plot_network
>
> ### ** Examples
>
> set.seed(12345)
> sociomatrix <- matrix(rnorm(400,0,20),20,20)
> colnames(sociomatrix) <- rownames(sociomatrix) <- letters[1:20]
> plot_network(sociomatrix)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
GERGM
--- call from context ---
plot_network(sociomatrix)
--- call from argument ---
if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") {
stop("You must provide the network as a numeric matrix.")
}
--- R stacktrace ---
where 1: plot_network(sociomatrix)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (sociomatrix, threshold = 0.5, save_pdf = FALSE, pdf_name = "Test.pdf",
output_directory = "./", comparison_network = NULL, comparison_names = NULL,
seed = NULL, white_background = FALSE, show_legend = TRUE,
title = "", identical_node_positions = FALSE)
{
if (!is.null(seed)) {
set.seed(seed)
}
par(mar = c(1, 0, 1, 0))
if (class(sociomatrix) != "matrix" & class(sociomatrix) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(sociomatrix) != ncol(sociomatrix)) {
stop("You must provide a square matrix.")
}
if (white_background) {
negcolors <- colorRampPalette(c("red", "white"))
poscolors <- colorRampPalette(c("white", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
else {
negcolors <- colorRampPalette(c("red", "black"))
poscolors <- colorRampPalette(c("black", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
COMPARISON <- FALSE
if (!is.null(comparison_network)) {
if (is.null(comparison_names)) {
comparison_names <- c("", "")
}
else {
if (length(comparison_names) != 2) {
stop("You must provide a comparison_names object as a vector containing two strings.")
}
}
if (class(comparison_network) != "matrix" & class(comparison_network) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(comparison_network) != ncol(comparison_network)) {
stop("You must provide a square matrix.")
}
if (nrow(comparison_network) != nrow(sociomatrix)) {
stop("You must provide two matrices with the same dimensions.")
}
COMPARISON <- TRUE
diag(comparison_network) <- 0
temp <- temp2 <- matrix(comparison_network[, ], nrow(comparison_network),
ncol(comparison_network))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net3 <- igraph::graph.adjacency(temp, mode = "directed",
weighted = TRUE, diag = FALSE)
layout_c <- igraph::layout_with_fr(net3, weights = igraph::E(net3)$weight)
net4 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist_c <- igraph::get.edgelist(net4)
weights_c <- igraph::E(net4)$weight
ordering <- order(abs(weights_c), decreasing = F)
edgelist_c <- edgelist_c[ordering, ]
weights_c <- weights_c[ordering]
}
diag(sociomatrix) <- 0
temp <- temp2 <- matrix(sociomatrix[, ], nrow(sociomatrix),
ncol(sociomatrix))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net <- igraph::graph.adjacency(temp, mode = "directed", weighted = TRUE,
diag = FALSE)
layout <- igraph::layout_with_fr(net, weights = igraph::E(net)$weight)
net2 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist <- igraph::get.edgelist(net2)
weights <- igraph::E(net2)$weight
ordering <- order(abs(weights), decreasing = F)
edgelist <- edgelist[ordering, ]
weights <- weights[ordering]
negbreaks <- seq(-max(abs(weights)), 0, length.out = 26)
posbreaks <- seq(0, max(abs(weights)), length.out = 26)
widbreaks <- seq(0, max(abs(weights)), length.out = 50)
widths <- seq(0, 5, length.out = 50)
if (COMPARISON) {
negbreaks <- seq(-max(abs(c(weights, weights_c))), 0,
length.out = 26)
posbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 26)
widbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 50)
widths <- seq(0, 5, length.out = 50)
}
if (COMPARISON) {
if (identical_node_positions) {
layout_c <- layout
}
else {
layout_c <- vegan::procrustes(layout, layout_c, scale = F)$Yrot
}
}
if (save_pdf) {
cur_directory <- getwd()
setwd(output_directory)
if (COMPARISON) {
pdf(file = pdf_name, width = 24, height = 12)
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
else {
pdf(file = pdf_name, width = 12, height = 12)
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
setwd(cur_directory)
}
else {
if (COMPARISON) {
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
print(max_bin)
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
}
else {
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
}
}
par(bg = "white")
}
<bytecode: 0x48b3fc0>
<environment: namespace:GERGM>
--- function search by body ---
Function plot_network in namespace GERGM has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") { :
the condition has length > 1
Calls: plot_network
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.13.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building 'getting_started.Rmd' using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
GERGM
--- call from context ---
plot_network(lending_2005)
--- call from argument ---
if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") {
stop("You must provide the network as a numeric matrix.")
}
--- R stacktrace ---
where 1: plot_network(lending_2005)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/GERGM.Rcheck/vign_test/GERGM",
ser_elibs = "/tmp/RtmpxjYXzC/file17c22425b27a.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (sociomatrix, threshold = 0.5, save_pdf = FALSE, pdf_name = "Test.pdf",
output_directory = "./", comparison_network = NULL, comparison_names = NULL,
seed = NULL, white_background = FALSE, show_legend = TRUE,
title = "", identical_node_positions = FALSE)
{
if (!is.null(seed)) {
set.seed(seed)
}
par(mar = c(1, 0, 1, 0))
if (class(sociomatrix) != "matrix" & class(sociomatrix) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(sociomatrix) != ncol(sociomatrix)) {
stop("You must provide a square matrix.")
}
if (white_background) {
negcolors <- colorRampPalette(c("red", "white"))
poscolors <- colorRampPalette(c("white", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
else {
negcolors <- colorRampPalette(c("red", "black"))
poscolors <- colorRampPalette(c("black", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
COMPARISON <- FALSE
if (!is.null(comparison_network)) {
if (is.null(comparison_names)) {
comparison_names <- c("", "")
}
else {
if (length(comparison_names) != 2) {
stop("You must provide a comparison_names object as a vector containing two strings.")
}
}
if (class(comparison_network) != "matrix" & class(comparison_network) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(comparison_network) != ncol(comparison_network)) {
stop("You must provide a square matrix.")
}
if (nrow(comparison_network) != nrow(sociomatrix)) {
stop("You must provide two matrices with the same dimensions.")
}
COMPARISON <- TRUE
diag(comparison_network) <- 0
temp <- temp2 <- matrix(comparison_network[, ], nrow(comparison_network),
ncol(comparison_network))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net3 <- igraph::graph.adjacency(temp, mode = "directed",
weighted = TRUE, diag = FALSE)
layout_c <- igraph::layout_with_fr(net3, weights = igraph::E(net3)$weight)
net4 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist_c <- igraph::get.edgelist(net4)
weights_c <- igraph::E(net4)$weight
ordering <- order(abs(weights_c), decreasing = F)
edgelist_c <- edgelist_c[ordering, ]
weights_c <- weights_c[ordering]
}
diag(sociomatrix) <- 0
temp <- temp2 <- matrix(sociomatrix[, ], nrow(sociomatrix),
ncol(sociomatrix))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net <- igraph::graph.adjacency(temp, mode = "directed", weighted = TRUE,
diag = FALSE)
layout <- igraph::layout_with_fr(net, weights = igraph::E(net)$weight)
net2 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist <- igraph::get.edgelist(net2)
weights <- igraph::E(net2)$weight
ordering <- order(abs(weights), decreasing = F)
edgelist <- edgelist[ordering, ]
weights <- weights[ordering]
negbreaks <- seq(-max(abs(weights)), 0, length.out = 26)
posbreaks <- seq(0, max(abs(weights)), length.out = 26)
widbreaks <- seq(0, max(abs(weights)), length.out = 50)
widths <- seq(0, 5, length.out = 50)
if (COMPARISON) {
negbreaks <- seq(-max(abs(c(weights, weights_c))), 0,
length.out = 26)
posbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 26)
widbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 50)
widths <- seq(0, 5, length.out = 50)
}
if (COMPARISON) {
if (identical_node_positions) {
layout_c <- layout
}
else {
layout_c <- vegan::procrustes(layout, layout_c, scale = F)$Yrot
}
}
if (save_pdf) {
cur_directory <- getwd()
setwd(output_directory)
if (COMPARISON) {
pdf(file = pdf_name, width = 24, height = 12)
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
else {
pdf(file = pdf_name, width = 12, height = 12)
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
setwd(cur_directory)
}
else {
if (COMPARISON) {
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
print(max_bin)
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
}
else {
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
}
}
par(bg = "white")
}
<bytecode: 0x3a0f4c8>
<environment: namespace:GERGM>
--- function search by body ---
Function plot_network in namespace GERGM has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 96-102 (getting_started.Rmd)
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building 'getting_started.Rmd'
SUMMARY: processing the following file failed:
'getting_started.Rmd'
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-clang
Version: 0.13.0
Check: examples
Result: ERROR
Running examples in ‘GERGM-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_network
> ### Title: Plots of value-edged networks.
> ### Aliases: plot_network
>
> ### ** Examples
>
> set.seed(12345)
> sociomatrix <- matrix(rnorm(400,0,20),20,20)
> colnames(sociomatrix) <- rownames(sociomatrix) <- letters[1:20]
> plot_network(sociomatrix)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
GERGM
--- call from context ---
plot_network(sociomatrix)
--- call from argument ---
if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") {
stop("You must provide the network as a numeric matrix.")
}
--- R stacktrace ---
where 1: plot_network(sociomatrix)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (sociomatrix, threshold = 0.5, save_pdf = FALSE, pdf_name = "Test.pdf",
output_directory = "./", comparison_network = NULL, comparison_names = NULL,
seed = NULL, white_background = FALSE, show_legend = TRUE,
title = "", identical_node_positions = FALSE)
{
if (!is.null(seed)) {
set.seed(seed)
}
par(mar = c(1, 0, 1, 0))
if (class(sociomatrix) != "matrix" & class(sociomatrix) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(sociomatrix) != ncol(sociomatrix)) {
stop("You must provide a square matrix.")
}
if (white_background) {
negcolors <- colorRampPalette(c("red", "white"))
poscolors <- colorRampPalette(c("white", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
else {
negcolors <- colorRampPalette(c("red", "black"))
poscolors <- colorRampPalette(c("black", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
COMPARISON <- FALSE
if (!is.null(comparison_network)) {
if (is.null(comparison_names)) {
comparison_names <- c("", "")
}
else {
if (length(comparison_names) != 2) {
stop("You must provide a comparison_names object as a vector containing two strings.")
}
}
if (class(comparison_network) != "matrix" & class(comparison_network) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(comparison_network) != ncol(comparison_network)) {
stop("You must provide a square matrix.")
}
if (nrow(comparison_network) != nrow(sociomatrix)) {
stop("You must provide two matrices with the same dimensions.")
}
COMPARISON <- TRUE
diag(comparison_network) <- 0
temp <- temp2 <- matrix(comparison_network[, ], nrow(comparison_network),
ncol(comparison_network))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net3 <- igraph::graph.adjacency(temp, mode = "directed",
weighted = TRUE, diag = FALSE)
layout_c <- igraph::layout_with_fr(net3, weights = igraph::E(net3)$weight)
net4 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist_c <- igraph::get.edgelist(net4)
weights_c <- igraph::E(net4)$weight
ordering <- order(abs(weights_c), decreasing = F)
edgelist_c <- edgelist_c[ordering, ]
weights_c <- weights_c[ordering]
}
diag(sociomatrix) <- 0
temp <- temp2 <- matrix(sociomatrix[, ], nrow(sociomatrix),
ncol(sociomatrix))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net <- igraph::graph.adjacency(temp, mode = "directed", weighted = TRUE,
diag = FALSE)
layout <- igraph::layout_with_fr(net, weights = igraph::E(net)$weight)
net2 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist <- igraph::get.edgelist(net2)
weights <- igraph::E(net2)$weight
ordering <- order(abs(weights), decreasing = F)
edgelist <- edgelist[ordering, ]
weights <- weights[ordering]
negbreaks <- seq(-max(abs(weights)), 0, length.out = 26)
posbreaks <- seq(0, max(abs(weights)), length.out = 26)
widbreaks <- seq(0, max(abs(weights)), length.out = 50)
widths <- seq(0, 5, length.out = 50)
if (COMPARISON) {
negbreaks <- seq(-max(abs(c(weights, weights_c))), 0,
length.out = 26)
posbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 26)
widbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 50)
widths <- seq(0, 5, length.out = 50)
}
if (COMPARISON) {
if (identical_node_positions) {
layout_c <- layout
}
else {
layout_c <- vegan::procrustes(layout, layout_c, scale = F)$Yrot
}
}
if (save_pdf) {
cur_directory <- getwd()
setwd(output_directory)
if (COMPARISON) {
pdf(file = pdf_name, width = 24, height = 12)
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
else {
pdf(file = pdf_name, width = 12, height = 12)
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
setwd(cur_directory)
}
else {
if (COMPARISON) {
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
print(max_bin)
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
}
else {
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
}
}
par(bg = "white")
}
<bytecode: 0x5565aee0e850>
<environment: namespace:GERGM>
--- function search by body ---
Function plot_network in namespace GERGM has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") { :
the condition has length > 1
Calls: plot_network
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.13.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
...
--- re-building ‘getting_started.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
GERGM
--- call from context ---
plot_network(lending_2005)
--- call from argument ---
if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") {
stop("You must provide the network as a numeric matrix.")
}
--- R stacktrace ---
where 1: plot_network(lending_2005)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GERGM.Rcheck/vign_test/GERGM",
ser_elibs = "/home/hornik/tmp/scratch/Rtmpq29Hvt/file12813e5609d8.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (sociomatrix, threshold = 0.5, save_pdf = FALSE, pdf_name = "Test.pdf",
output_directory = "./", comparison_network = NULL, comparison_names = NULL,
seed = NULL, white_background = FALSE, show_legend = TRUE,
title = "", identical_node_positions = FALSE)
{
if (!is.null(seed)) {
set.seed(seed)
}
par(mar = c(1, 0, 1, 0))
if (class(sociomatrix) != "matrix" & class(sociomatrix) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(sociomatrix) != ncol(sociomatrix)) {
stop("You must provide a square matrix.")
}
if (white_background) {
negcolors <- colorRampPalette(c("red", "white"))
poscolors <- colorRampPalette(c("white", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
else {
negcolors <- colorRampPalette(c("red", "black"))
poscolors <- colorRampPalette(c("black", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
COMPARISON <- FALSE
if (!is.null(comparison_network)) {
if (is.null(comparison_names)) {
comparison_names <- c("", "")
}
else {
if (length(comparison_names) != 2) {
stop("You must provide a comparison_names object as a vector containing two strings.")
}
}
if (class(comparison_network) != "matrix" & class(comparison_network) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(comparison_network) != ncol(comparison_network)) {
stop("You must provide a square matrix.")
}
if (nrow(comparison_network) != nrow(sociomatrix)) {
stop("You must provide two matrices with the same dimensions.")
}
COMPARISON <- TRUE
diag(comparison_network) <- 0
temp <- temp2 <- matrix(comparison_network[, ], nrow(comparison_network),
ncol(comparison_network))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net3 <- igraph::graph.adjacency(temp, mode = "directed",
weighted = TRUE, diag = FALSE)
layout_c <- igraph::layout_with_fr(net3, weights = igraph::E(net3)$weight)
net4 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist_c <- igraph::get.edgelist(net4)
weights_c <- igraph::E(net4)$weight
ordering <- order(abs(weights_c), decreasing = F)
edgelist_c <- edgelist_c[ordering, ]
weights_c <- weights_c[ordering]
}
diag(sociomatrix) <- 0
temp <- temp2 <- matrix(sociomatrix[, ], nrow(sociomatrix),
ncol(sociomatrix))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net <- igraph::graph.adjacency(temp, mode = "directed", weighted = TRUE,
diag = FALSE)
layout <- igraph::layout_with_fr(net, weights = igraph::E(net)$weight)
net2 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist <- igraph::get.edgelist(net2)
weights <- igraph::E(net2)$weight
ordering <- order(abs(weights), decreasing = F)
edgelist <- edgelist[ordering, ]
weights <- weights[ordering]
negbreaks <- seq(-max(abs(weights)), 0, length.out = 26)
posbreaks <- seq(0, max(abs(weights)), length.out = 26)
widbreaks <- seq(0, max(abs(weights)), length.out = 50)
widths <- seq(0, 5, length.out = 50)
if (COMPARISON) {
negbreaks <- seq(-max(abs(c(weights, weights_c))), 0,
length.out = 26)
posbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 26)
widbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 50)
widths <- seq(0, 5, length.out = 50)
}
if (COMPARISON) {
if (identical_node_positions) {
layout_c <- layout
}
else {
layout_c <- vegan::procrustes(layout, layout_c, scale = F)$Yrot
}
}
if (save_pdf) {
cur_directory <- getwd()
setwd(output_directory)
if (COMPARISON) {
pdf(file = pdf_name, width = 24, height = 12)
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
else {
pdf(file = pdf_name, width = 12, height = 12)
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
setwd(cur_directory)
}
else {
if (COMPARISON) {
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
print(max_bin)
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
}
else {
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
}
}
par(bg = "white")
}
<bytecode: 0x55ba7925ee08>
<environment: namespace:GERGM>
--- function search by body ---
Function plot_network in namespace GERGM has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 96-102 (getting_started.Rmd)
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘getting_started.Rmd’
SUMMARY: processing the following file failed:
‘getting_started.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-debian-gcc
Version: 0.13.0
Check: installed package size
Result: NOTE
installed size is 6.1Mb
sub-directories of 1Mb or more:
libs 4.9Mb
Flavors: r-devel-linux-x86_64-fedora-clang, r-release-osx-x86_64
Version: 0.13.0
Check: examples
Result: ERROR
Running examples in ‘GERGM-Ex.R’ failed
The error most likely occurred in:
> ### Name: plot_network
> ### Title: Plots of value-edged networks.
> ### Aliases: plot_network
>
> ### ** Examples
>
> set.seed(12345)
> sociomatrix <- matrix(rnorm(400,0,20),20,20)
> colnames(sociomatrix) <- rownames(sociomatrix) <- letters[1:20]
> plot_network(sociomatrix)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
GERGM
--- call from context ---
plot_network(sociomatrix)
--- call from argument ---
if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") {
stop("You must provide the network as a numeric matrix.")
}
--- R stacktrace ---
where 1: plot_network(sociomatrix)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (sociomatrix, threshold = 0.5, save_pdf = FALSE, pdf_name = "Test.pdf",
output_directory = "./", comparison_network = NULL, comparison_names = NULL,
seed = NULL, white_background = FALSE, show_legend = TRUE,
title = "", identical_node_positions = FALSE)
{
if (!is.null(seed)) {
set.seed(seed)
}
par(mar = c(1, 0, 1, 0))
if (class(sociomatrix) != "matrix" & class(sociomatrix) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(sociomatrix) != ncol(sociomatrix)) {
stop("You must provide a square matrix.")
}
if (white_background) {
negcolors <- colorRampPalette(c("red", "white"))
poscolors <- colorRampPalette(c("white", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
else {
negcolors <- colorRampPalette(c("red", "black"))
poscolors <- colorRampPalette(c("black", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
COMPARISON <- FALSE
if (!is.null(comparison_network)) {
if (is.null(comparison_names)) {
comparison_names <- c("", "")
}
else {
if (length(comparison_names) != 2) {
stop("You must provide a comparison_names object as a vector containing two strings.")
}
}
if (class(comparison_network) != "matrix" & class(comparison_network) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(comparison_network) != ncol(comparison_network)) {
stop("You must provide a square matrix.")
}
if (nrow(comparison_network) != nrow(sociomatrix)) {
stop("You must provide two matrices with the same dimensions.")
}
COMPARISON <- TRUE
diag(comparison_network) <- 0
temp <- temp2 <- matrix(comparison_network[, ], nrow(comparison_network),
ncol(comparison_network))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net3 <- igraph::graph.adjacency(temp, mode = "directed",
weighted = TRUE, diag = FALSE)
layout_c <- igraph::layout_with_fr(net3, weights = igraph::E(net3)$weight)
net4 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist_c <- igraph::get.edgelist(net4)
weights_c <- igraph::E(net4)$weight
ordering <- order(abs(weights_c), decreasing = F)
edgelist_c <- edgelist_c[ordering, ]
weights_c <- weights_c[ordering]
}
diag(sociomatrix) <- 0
temp <- temp2 <- matrix(sociomatrix[, ], nrow(sociomatrix),
ncol(sociomatrix))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net <- igraph::graph.adjacency(temp, mode = "directed", weighted = TRUE,
diag = FALSE)
layout <- igraph::layout_with_fr(net, weights = igraph::E(net)$weight)
net2 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist <- igraph::get.edgelist(net2)
weights <- igraph::E(net2)$weight
ordering <- order(abs(weights), decreasing = F)
edgelist <- edgelist[ordering, ]
weights <- weights[ordering]
negbreaks <- seq(-max(abs(weights)), 0, length.out = 26)
posbreaks <- seq(0, max(abs(weights)), length.out = 26)
widbreaks <- seq(0, max(abs(weights)), length.out = 50)
widths <- seq(0, 5, length.out = 50)
if (COMPARISON) {
negbreaks <- seq(-max(abs(c(weights, weights_c))), 0,
length.out = 26)
posbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 26)
widbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 50)
widths <- seq(0, 5, length.out = 50)
}
if (COMPARISON) {
if (identical_node_positions) {
layout_c <- layout
}
else {
layout_c <- vegan::procrustes(layout, layout_c, scale = F)$Yrot
}
}
if (save_pdf) {
cur_directory <- getwd()
setwd(output_directory)
if (COMPARISON) {
pdf(file = pdf_name, width = 24, height = 12)
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
else {
pdf(file = pdf_name, width = 12, height = 12)
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
setwd(cur_directory)
}
else {
if (COMPARISON) {
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
print(max_bin)
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
}
else {
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
}
}
par(bg = "white")
}
<bytecode: 0x2d3f460>
<environment: namespace:GERGM>
--- function search by body ---
Function plot_network in namespace GERGM has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") { :
the condition has length > 1
Calls: plot_network
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.13.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘getting_started.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
GERGM
--- call from context ---
plot_network(lending_2005)
--- call from argument ---
if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") {
stop("You must provide the network as a numeric matrix.")
}
--- R stacktrace ---
where 1: plot_network(lending_2005)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-clang/GERGM.Rcheck/vign_test/GERGM",
ser_elibs = "/tmp/RtmpGswe8a/file414367521feb.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (sociomatrix, threshold = 0.5, save_pdf = FALSE, pdf_name = "Test.pdf",
output_directory = "./", comparison_network = NULL, comparison_names = NULL,
seed = NULL, white_background = FALSE, show_legend = TRUE,
title = "", identical_node_positions = FALSE)
{
if (!is.null(seed)) {
set.seed(seed)
}
par(mar = c(1, 0, 1, 0))
if (class(sociomatrix) != "matrix" & class(sociomatrix) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(sociomatrix) != ncol(sociomatrix)) {
stop("You must provide a square matrix.")
}
if (white_background) {
negcolors <- colorRampPalette(c("red", "white"))
poscolors <- colorRampPalette(c("white", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
else {
negcolors <- colorRampPalette(c("red", "black"))
poscolors <- colorRampPalette(c("black", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
COMPARISON <- FALSE
if (!is.null(comparison_network)) {
if (is.null(comparison_names)) {
comparison_names <- c("", "")
}
else {
if (length(comparison_names) != 2) {
stop("You must provide a comparison_names object as a vector containing two strings.")
}
}
if (class(comparison_network) != "matrix" & class(comparison_network) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(comparison_network) != ncol(comparison_network)) {
stop("You must provide a square matrix.")
}
if (nrow(comparison_network) != nrow(sociomatrix)) {
stop("You must provide two matrices with the same dimensions.")
}
COMPARISON <- TRUE
diag(comparison_network) <- 0
temp <- temp2 <- matrix(comparison_network[, ], nrow(comparison_network),
ncol(comparison_network))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net3 <- igraph::graph.adjacency(temp, mode = "directed",
weighted = TRUE, diag = FALSE)
layout_c <- igraph::layout_with_fr(net3, weights = igraph::E(net3)$weight)
net4 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist_c <- igraph::get.edgelist(net4)
weights_c <- igraph::E(net4)$weight
ordering <- order(abs(weights_c), decreasing = F)
edgelist_c <- edgelist_c[ordering, ]
weights_c <- weights_c[ordering]
}
diag(sociomatrix) <- 0
temp <- temp2 <- matrix(sociomatrix[, ], nrow(sociomatrix),
ncol(sociomatrix))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net <- igraph::graph.adjacency(temp, mode = "directed", weighted = TRUE,
diag = FALSE)
layout <- igraph::layout_with_fr(net, weights = igraph::E(net)$weight)
net2 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist <- igraph::get.edgelist(net2)
weights <- igraph::E(net2)$weight
ordering <- order(abs(weights), decreasing = F)
edgelist <- edgelist[ordering, ]
weights <- weights[ordering]
negbreaks <- seq(-max(abs(weights)), 0, length.out = 26)
posbreaks <- seq(0, max(abs(weights)), length.out = 26)
widbreaks <- seq(0, max(abs(weights)), length.out = 50)
widths <- seq(0, 5, length.out = 50)
if (COMPARISON) {
negbreaks <- seq(-max(abs(c(weights, weights_c))), 0,
length.out = 26)
posbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 26)
widbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 50)
widths <- seq(0, 5, length.out = 50)
}
if (COMPARISON) {
if (identical_node_positions) {
layout_c <- layout
}
else {
layout_c <- vegan::procrustes(layout, layout_c, scale = F)$Yrot
}
}
if (save_pdf) {
cur_directory <- getwd()
setwd(output_directory)
if (COMPARISON) {
pdf(file = pdf_name, width = 24, height = 12)
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
else {
pdf(file = pdf_name, width = 12, height = 12)
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
setwd(cur_directory)
}
else {
if (COMPARISON) {
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
print(max_bin)
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
}
else {
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
}
}
par(bg = "white")
}
<bytecode: 0x4679d30>
<environment: namespace:GERGM>
--- function search by body ---
Function plot_network in namespace GERGM has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 96-102 (getting_started.Rmd)
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘getting_started.Rmd’
SUMMARY: processing the following file failed:
‘getting_started.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-clang
Version: 0.13.0
Check: examples
Result: ERROR
Running examples in ‘GERGM-Ex.R’ failed
The error most likely occurred in:
> ### Name: plot_network
> ### Title: Plots of value-edged networks.
> ### Aliases: plot_network
>
> ### ** Examples
>
> set.seed(12345)
> sociomatrix <- matrix(rnorm(400,0,20),20,20)
> colnames(sociomatrix) <- rownames(sociomatrix) <- letters[1:20]
> plot_network(sociomatrix)
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
GERGM
--- call from context ---
plot_network(sociomatrix)
--- call from argument ---
if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") {
stop("You must provide the network as a numeric matrix.")
}
--- R stacktrace ---
where 1: plot_network(sociomatrix)
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (sociomatrix, threshold = 0.5, save_pdf = FALSE, pdf_name = "Test.pdf",
output_directory = "./", comparison_network = NULL, comparison_names = NULL,
seed = NULL, white_background = FALSE, show_legend = TRUE,
title = "", identical_node_positions = FALSE)
{
if (!is.null(seed)) {
set.seed(seed)
}
par(mar = c(1, 0, 1, 0))
if (class(sociomatrix) != "matrix" & class(sociomatrix) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(sociomatrix) != ncol(sociomatrix)) {
stop("You must provide a square matrix.")
}
if (white_background) {
negcolors <- colorRampPalette(c("red", "white"))
poscolors <- colorRampPalette(c("white", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
else {
negcolors <- colorRampPalette(c("red", "black"))
poscolors <- colorRampPalette(c("black", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
COMPARISON <- FALSE
if (!is.null(comparison_network)) {
if (is.null(comparison_names)) {
comparison_names <- c("", "")
}
else {
if (length(comparison_names) != 2) {
stop("You must provide a comparison_names object as a vector containing two strings.")
}
}
if (class(comparison_network) != "matrix" & class(comparison_network) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(comparison_network) != ncol(comparison_network)) {
stop("You must provide a square matrix.")
}
if (nrow(comparison_network) != nrow(sociomatrix)) {
stop("You must provide two matrices with the same dimensions.")
}
COMPARISON <- TRUE
diag(comparison_network) <- 0
temp <- temp2 <- matrix(comparison_network[, ], nrow(comparison_network),
ncol(comparison_network))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net3 <- igraph::graph.adjacency(temp, mode = "directed",
weighted = TRUE, diag = FALSE)
layout_c <- igraph::layout_with_fr(net3, weights = igraph::E(net3)$weight)
net4 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist_c <- igraph::get.edgelist(net4)
weights_c <- igraph::E(net4)$weight
ordering <- order(abs(weights_c), decreasing = F)
edgelist_c <- edgelist_c[ordering, ]
weights_c <- weights_c[ordering]
}
diag(sociomatrix) <- 0
temp <- temp2 <- matrix(sociomatrix[, ], nrow(sociomatrix),
ncol(sociomatrix))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net <- igraph::graph.adjacency(temp, mode = "directed", weighted = TRUE,
diag = FALSE)
layout <- igraph::layout_with_fr(net, weights = igraph::E(net)$weight)
net2 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist <- igraph::get.edgelist(net2)
weights <- igraph::E(net2)$weight
ordering <- order(abs(weights), decreasing = F)
edgelist <- edgelist[ordering, ]
weights <- weights[ordering]
negbreaks <- seq(-max(abs(weights)), 0, length.out = 26)
posbreaks <- seq(0, max(abs(weights)), length.out = 26)
widbreaks <- seq(0, max(abs(weights)), length.out = 50)
widths <- seq(0, 5, length.out = 50)
if (COMPARISON) {
negbreaks <- seq(-max(abs(c(weights, weights_c))), 0,
length.out = 26)
posbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 26)
widbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 50)
widths <- seq(0, 5, length.out = 50)
}
if (COMPARISON) {
if (identical_node_positions) {
layout_c <- layout
}
else {
layout_c <- vegan::procrustes(layout, layout_c, scale = F)$Yrot
}
}
if (save_pdf) {
cur_directory <- getwd()
setwd(output_directory)
if (COMPARISON) {
pdf(file = pdf_name, width = 24, height = 12)
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
else {
pdf(file = pdf_name, width = 12, height = 12)
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
setwd(cur_directory)
}
else {
if (COMPARISON) {
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
print(max_bin)
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
}
else {
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
}
}
par(bg = "white")
}
<bytecode: 0x2c9ee28>
<environment: namespace:GERGM>
--- function search by body ---
Function plot_network in namespace GERGM has this body.
----------- END OF FAILURE REPORT --------------
Error in if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") { :
the condition has length > 1
Calls: plot_network
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc
Version: 0.13.0
Check: re-building of vignette outputs
Result: WARN
Error(s) in re-building vignettes:
--- re-building ‘getting_started.Rmd’ using rmarkdown
----------- FAILURE REPORT --------------
--- failure: the condition has length > 1 ---
--- srcref ---
:
--- package (from environment) ---
GERGM
--- call from context ---
plot_network(lending_2005)
--- call from argument ---
if (class(sociomatrix) != "matrix" & class(sociomatrix) != "data.frame") {
stop("You must provide the network as a numeric matrix.")
}
--- R stacktrace ---
where 1: plot_network(lending_2005)
where 2: eval(expr, envir, enclos)
where 3: eval(expr, envir, enclos)
where 4: withVisible(eval(expr, envir, enclos))
where 5: withCallingHandlers(withVisible(eval(expr, envir, enclos)), warning = wHandler,
error = eHandler, message = mHandler)
where 6: handle(ev <- withCallingHandlers(withVisible(eval(expr, envir,
enclos)), warning = wHandler, error = eHandler, message = mHandler))
where 7: timing_fn(handle(ev <- withCallingHandlers(withVisible(eval(expr,
envir, enclos)), warning = wHandler, error = eHandler, message = mHandler)))
where 8: evaluate_call(expr, parsed$src[[i]], envir = envir, enclos = enclos,
debug = debug, last = i == length(out), use_try = stop_on_error !=
2L, keep_warning = keep_warning, keep_message = keep_message,
output_handler = output_handler, include_timing = include_timing)
where 9: evaluate::evaluate(...)
where 10: evaluate(code, envir = env, new_device = FALSE, keep_warning = !isFALSE(options$warning),
keep_message = !isFALSE(options$message), stop_on_error = if (options$error &&
options$include) 0L else 2L, output_handler = knit_handlers(options$render,
options))
where 11: in_dir(input_dir(), evaluate(code, envir = env, new_device = FALSE,
keep_warning = !isFALSE(options$warning), keep_message = !isFALSE(options$message),
stop_on_error = if (options$error && options$include) 0L else 2L,
output_handler = knit_handlers(options$render, options)))
where 12: block_exec(params)
where 13: call_block(x)
where 14: process_group.block(group)
where 15: process_group(group)
where 16: withCallingHandlers(if (tangle) process_tangle(group) else process_group(group),
error = function(e) {
setwd(wd)
cat(res, sep = "\n", file = output %n% "")
message("Quitting from lines ", paste(current_lines(i),
collapse = "-"), " (", knit_concord$get("infile"),
") ")
})
where 17: process_file(text, output)
where 18: knitr::knit(knit_input, knit_output, envir = envir, quiet = quiet)
where 19: rmarkdown::render(file, encoding = encoding, quiet = quiet, envir = globalenv(),
output_dir = getwd(), ...)
where 20: vweave_rmarkdown(...)
where 21: engine$weave(file, quiet = quiet, encoding = enc)
where 22: doTryCatch(return(expr), name, parentenv, handler)
where 23: tryCatchOne(expr, names, parentenv, handlers[[1L]])
where 24: tryCatchList(expr, classes, parentenv, handlers)
where 25: tryCatch({
engine$weave(file, quiet = quiet, encoding = enc)
setwd(startdir)
output <- find_vignette_product(name, by = "weave", engine = engine)
if (!have.makefile && vignette_is_tex(output)) {
texi2pdf(file = output, clean = FALSE, quiet = quiet)
output <- find_vignette_product(name, by = "texi2pdf",
engine = engine)
}
outputs <- c(outputs, output)
}, error = function(e) {
thisOK <<- FALSE
fails <<- c(fails, file)
message(gettextf("Error: processing vignette '%s' failed with diagnostics:\n%s",
file, conditionMessage(e)))
})
where 26: tools:::buildVignettes(dir = "/data/gannet/ripley/R/packages/tests-devel/GERGM.Rcheck/vign_test/GERGM",
ser_elibs = "/tmp/Rtmpu2Oa1d/file2f1c46a23894.rds")
--- value of length: 2 type: logical ---
[1] FALSE TRUE
--- function from context ---
function (sociomatrix, threshold = 0.5, save_pdf = FALSE, pdf_name = "Test.pdf",
output_directory = "./", comparison_network = NULL, comparison_names = NULL,
seed = NULL, white_background = FALSE, show_legend = TRUE,
title = "", identical_node_positions = FALSE)
{
if (!is.null(seed)) {
set.seed(seed)
}
par(mar = c(1, 0, 1, 0))
if (class(sociomatrix) != "matrix" & class(sociomatrix) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(sociomatrix) != ncol(sociomatrix)) {
stop("You must provide a square matrix.")
}
if (white_background) {
negcolors <- colorRampPalette(c("red", "white"))
poscolors <- colorRampPalette(c("white", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
else {
negcolors <- colorRampPalette(c("red", "black"))
poscolors <- colorRampPalette(c("black", "blue"))
negcolors <- negcolors(25)
poscolors <- poscolors(25)
}
COMPARISON <- FALSE
if (!is.null(comparison_network)) {
if (is.null(comparison_names)) {
comparison_names <- c("", "")
}
else {
if (length(comparison_names) != 2) {
stop("You must provide a comparison_names object as a vector containing two strings.")
}
}
if (class(comparison_network) != "matrix" & class(comparison_network) !=
"data.frame") {
stop("You must provide the network as a numeric matrix.")
}
if (nrow(comparison_network) != ncol(comparison_network)) {
stop("You must provide a square matrix.")
}
if (nrow(comparison_network) != nrow(sociomatrix)) {
stop("You must provide two matrices with the same dimensions.")
}
COMPARISON <- TRUE
diag(comparison_network) <- 0
temp <- temp2 <- matrix(comparison_network[, ], nrow(comparison_network),
ncol(comparison_network))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net3 <- igraph::graph.adjacency(temp, mode = "directed",
weighted = TRUE, diag = FALSE)
layout_c <- igraph::layout_with_fr(net3, weights = igraph::E(net3)$weight)
net4 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist_c <- igraph::get.edgelist(net4)
weights_c <- igraph::E(net4)$weight
ordering <- order(abs(weights_c), decreasing = F)
edgelist_c <- edgelist_c[ordering, ]
weights_c <- weights_c[ordering]
}
diag(sociomatrix) <- 0
temp <- temp2 <- matrix(sociomatrix[, ], nrow(sociomatrix),
ncol(sociomatrix))
cutoff <- max(abs(temp)) * threshold
temp[which(abs(temp) < cutoff)] <- 0
net <- igraph::graph.adjacency(temp, mode = "directed", weighted = TRUE,
diag = FALSE)
layout <- igraph::layout_with_fr(net, weights = igraph::E(net)$weight)
net2 <- igraph::graph.adjacency(temp2, mode = "directed",
weighted = TRUE, diag = FALSE)
edgelist <- igraph::get.edgelist(net2)
weights <- igraph::E(net2)$weight
ordering <- order(abs(weights), decreasing = F)
edgelist <- edgelist[ordering, ]
weights <- weights[ordering]
negbreaks <- seq(-max(abs(weights)), 0, length.out = 26)
posbreaks <- seq(0, max(abs(weights)), length.out = 26)
widbreaks <- seq(0, max(abs(weights)), length.out = 50)
widths <- seq(0, 5, length.out = 50)
if (COMPARISON) {
negbreaks <- seq(-max(abs(c(weights, weights_c))), 0,
length.out = 26)
posbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 26)
widbreaks <- seq(0, max(abs(c(weights, weights_c))),
length.out = 50)
widths <- seq(0, 5, length.out = 50)
}
if (COMPARISON) {
if (identical_node_positions) {
layout_c <- layout
}
else {
layout_c <- vegan::procrustes(layout, layout_c, scale = F)$Yrot
}
}
if (save_pdf) {
cur_directory <- getwd()
setwd(output_directory)
if (COMPARISON) {
pdf(file = pdf_name, width = 24, height = 12)
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
else {
pdf(file = pdf_name, width = 12, height = 12)
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 2), (max(layout[,
1]) + 2)), ylim = c((min(layout[, 2]) - 2),
(max(layout[, 2]) + 2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
dev.off()
}
setwd(cur_directory)
}
else {
if (COMPARISON) {
if (white_background) {
par(bg = "white", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "black", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
else {
par(bg = "black", oma = c(1, 1, 2, 1) + 0.1,
mar = c(0, 0.5, 1, 0.5) + 0.5, xpd = TRUE,
mfrow = c(1, 2))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[1],
col.main = "white", xlim = c((min(layout[,
1]) - 0.1), (max(layout[, 1]) + 0.1)), ylim = c((min(layout[,
2]) - 1.3), (max(layout[, 2]) + 0.5)))
}
max_bin <- 1
min_bin <- 1
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin) {
max_bin <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin) {
min_bin <- bin
}
}
}
print(max_bin)
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "white", text.col = "black", box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c(negcolors[min_bin -
1], poscolors[max_bin - 1]), horiz = T,
bg = "black", text.col = "white")
}
}
if (white_background) {
plot(layout_c, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "black", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
else {
plot(layout_c, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = comparison_names[2],
col.main = "white", xlim = c((min(layout_c[,
1]) - 0.1), (max(layout_c[, 1]) + 0.1)),
ylim = c((min(layout_c[, 2]) - 1.3), (max(layout_c[,
2]) + 0.5)))
}
max_bin_c <- 1
min_bin_c <- 1
for (i in 1:length(weights_c)) {
cur1 <- layout_c[edgelist_c[i, 1], ]
cur2 <- layout_c[edgelist_c[i, 2], ]
curweight <- weights_c[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
if (bin > max_bin_c) {
max_bin_c <- bin
}
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
if (bin > min_bin_c) {
min_bin_c <- bin
}
}
}
if (white_background) {
text(layout_c, labels = rownames(comparison_network),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout_c, labels = rownames(comparison_network),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(comparison_network),
2), round(max(comparison_network), 2)),
fill = c(negcolors[min_bin_c - 1], poscolors[max_bin_c -
1]), horiz = T, bg = "black", text.col = "white")
}
}
}
else {
if (white_background) {
par(bg = "white", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "white",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
else {
par(bg = "black", oma = c(0.1, 0.1, 0.1, 0.1) +
0.1, mar = c(0, 0, 0, 0), xpd = TRUE, mfrow = c(1,
1))
plot(layout, pch = 20, cex = 1, col = "black",
axes = F, xlab = "", ylab = "", main = title,
xlim = c((min(layout[, 1]) - 0.2), (max(layout[,
1]) + 0.2)), ylim = c((min(layout[, 2]) -
0.2), (max(layout[, 2]) + 0.2)))
}
for (i in 1:length(weights)) {
cur1 <- layout[edgelist[i, 1], ]
cur2 <- layout[edgelist[i, 2], ]
curweight <- weights[i]
nf <- TRUE
counter <- 1
bin <- 1
while (nf) {
if (curweight > 0) {
if (posbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
else {
if (negbreaks[counter] >= curweight) {
bin <- counter
nf <- FALSE
}
}
counter <- counter + 1
}
nf <- TRUE
counter <- 1
wid <- 1
while (nf) {
if (widbreaks[counter] >= abs(curweight)) {
wid <- counter
nf <- FALSE
}
counter <- counter + 1
}
if (curweight > 0) {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = poscolors[bin], lwd = widths[wid])
}
else {
lines(c(cur1[1], cur2[1]), c(cur1[2], cur2[2]),
col = negcolors[bin], lwd = widths[wid])
}
}
if (white_background) {
text(layout, labels = rownames(sociomatrix),
col = "black")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "black", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "white", text.col = "black",
box.col = "white")
}
}
else {
text(layout, labels = rownames(sociomatrix),
col = "white")
if (show_legend) {
legend("bottom", inset = 0, title = "Edge Values",
title.col = "white", legend = c(round(min(sociomatrix),
2), round(max(sociomatrix), 2)), fill = c("red",
"blue"), horiz = T, bg = "black", text.col = "white")
}
}
}
}
par(bg = "white")
}
<bytecode: 0x43e1168>
<environment: namespace:GERGM>
--- function search by body ---
Function plot_network in namespace GERGM has this body.
----------- END OF FAILURE REPORT --------------
Quitting from lines 96-102 (getting_started.Rmd)
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
the condition has length > 1
--- failed re-building ‘getting_started.Rmd’
SUMMARY: processing the following file failed:
‘getting_started.Rmd’
Error: Vignette re-building failed.
Execution halted
Flavor: r-devel-linux-x86_64-fedora-gcc