I solved it, adding the unique function, inside the ggiNEXT.iNEXT function:
Below are the original command line and the same line altered:
Original command line:
z$lty <- factor(z$method, c("interpolated", "observed", "extrapolated"),
c("interpolation", "interpolation", "extrapolation"))
Changed command line:
z$lty <- factor(z$method, levels=unique(c("interpolated", "observed", "extrapolated"),
c("interpolation", "interpolation", "extrapolation")))
After the change, I could make the graph exactly as the example from https://cran.r-project.org/web/packages/iNEXT/vignettes/Introduction.html
Just for note, I used traceback() to find that the problem was inside ggiNEXT.iNEXT. Then I found the command indicated by the error message, and use the unique function based on a similar problem from this post: ggplot: order of factors with duplicate levels
To run properly and construct the graphs, past all the altered function on R console:
ggiNEXT.iNEXT<-function (x, type = 1, se = TRUE, facet.var = "none", color.var = "site",
grey = FALSE)
{
TYPE <- c(1, 2, 3)
SPLIT <- c("none", "order", "site", "both")
if (is.na(pmatch(type, TYPE)) | pmatch(type, TYPE) == -1)
stop("invalid plot type")
if (is.na(pmatch(facet.var, SPLIT)) | pmatch(facet.var, SPLIT) ==
-1)
stop("invalid facet variable")
if (is.na(pmatch(color.var, SPLIT)) | pmatch(color.var, SPLIT) ==
-1)
stop("invalid color variable")
type <- pmatch(type, 1:3)
facet.var <- match.arg(facet.var, SPLIT)
color.var <- match.arg(color.var, SPLIT)
if (facet.var == "order")
color.var <- "site"
if (facet.var == "site")
color.var <- "order"
options(warn = -1)
z <- fortify(x, type = type)
options(warn = 0)
if (ncol(z) == 7) {
se <- FALSE
}
datatype <- unique(z$datatype)
if (color.var == "none") {
if (levels(factor(z$order)) > 1 & "site" %in% names(z)) {
warning("invalid color.var setting, the iNEXT object consists multiple sites and orders, change setting as both")
color.var <- "both"
z$col <- z$shape <- paste(z$site, z$order, sep = "-")
}
else if ("site" %in% names(z)) {
warning("invalid color.var setting, the iNEXT object consists multiple orders, change setting as order")
color.var <- "site"
z$col <- z$shape <- z$site
}
else if (levels(factor(z$order)) > 1) {
warning("invalid color.var setting, the iNEXT object consists multiple sites, change setting as site")
color.var <- "order"
z$col <- z$shape <- factor(z$order)
}
else {
z$col <- z$shape <- rep(1, nrow(z))
}
}
else if (color.var == "order") {
z$col <- z$shape <- factor(z$order)
}
else if (color.var == "site") {
if (!"site" %in% names(z)) {
warning("invalid color.var setting, the iNEXT object do not consist multiple sites, change setting as order")
z$col <- z$shape <- factor(z$order)
}
z$col <- z$shape <- z$site
}
else if (color.var == "both") {
if (!"site" %in% names(z)) {
warning("invalid color.var setting, the iNEXT object do not consist multiple sites, change setting as order")
z$col <- z$shape <- factor(z$order)
}
z$col <- z$shape <- paste(z$site, z$order, sep = "-")
}
z$lty <- factor(z$method, levels=unique(c("interpolated", "observed", "extrapolated"),
c("interpolation", "interpolation", "extrapolation")))
z$col <- factor(z$col)
data.sub <- z[which(z$method == "observed"), ]
g <- ggplot(z, aes_string(x = "x", y = "y", colour = "col")) +
geom_point(aes_string(shape = "shape"), size = 5, data = data.sub)
g <- g + geom_line(aes_string(linetype = "lty"), lwd = 1.5) +
guides(linetype = guide_legend(title = "Method"), colour = guide_legend(title = "Guides"),
fill = guide_legend(title = "Guides"), shape = guide_legend(title = "Guides")) +
theme(legend.position = "bottom", legend.title = element_blank(),
text = element_text(size = 18))
if (type == 2L) {
g <- g + labs(x = "Number of sampling units", y = "Sample coverage")
if (datatype == "abundance")
g <- g + labs(x = "Number of individuals", y = "Sample coverage")
}
else if (type == 3L) {
g <- g + labs(x = "Sample coverage", y = "Species diversity")
}
else {
g <- g + labs(x = "Number of sampling units", y = "Species diversity")
if (datatype == "abundance")
g <- g + labs(x = "Number of individuals", y = "Species diversity")
}
if (se)
g <- g + geom_ribbon(aes_string(ymin = "y.lwr", ymax = "y.upr",
fill = "factor(col)", colour = "NULL"), alpha = 0.2)
if (facet.var == "order") {
if (length(levels(factor(z$order))) == 1 & type != 2) {
warning("invalid facet.var setting, the iNEXT object do not consist multiple orders.")
}
else {
g <- g + facet_wrap(~order, nrow = 1)
if (color.var == "both") {
g <- g + guides(colour = guide_legend(title = "Guides",
ncol = length(levels(factor(z$order))), byrow = TRUE),
fill = guide_legend(title = "Guides"))
}
}
}
if (facet.var == "site") {
if (!"site" %in% names(z)) {
warning("invalid facet.var setting, the iNEXT object do not consist multiple sites.")
}
else {
g <- g + facet_wrap(~site, nrow = 1)
if (color.var == "both") {
g <- g + guides(colour = guide_legend(title = "Guides",
nrow = length(levels(factor(z$order)))), fill = guide_legend(title = "Guides"))
}
}
}
if (facet.var == "both") {
if (length(levels(factor(z$order))) == 1 | !"site" %in%
names(z)) {
warning("invalid facet.var setting, the iNEXT object do not consist multiple sites or orders.")
}
else {
g <- g + facet_wrap(site ~ order)
if (color.var == "both") {
g <- g + guides(colour = guide_legend(title = "Guides",
nrow = length(levels(factor(z$site))), byrow = TRUE),
fill = guide_legend(title = "Guides"))
}
}
}
if (grey) {
g <- g + theme_bw(base_size = 18) + scale_fill_grey(start = 0,
end = 0.4) + scale_colour_grey(start = 0.2, end = 0.2) +
guides(linetype = guide_legend(title = "Method"),
colour = guide_legend(title = "Guides"), fill = guide_legend(title = "Guides"),
shape = guide_legend(title = "Guides")) + theme(legend.position = "bottom",
legend.title = element_blank())
}
g <- g + theme(legend.box = "vertical")
return(g)
}
