What the solution for this ggplot2 error on gigINEXT function:" Error in levels<-..."?

Question

I'm running some examples from iNEXT package on Rstudio and having trouble with the graphical example. To help possible suggestions, below are some initial steps that run without any major problems, followed by the command line that generates the error:

#packages and dependencies

>install.packages("iNEXT")
>install.packages('devtools')
>library(devtools)
>install_github('JohnsonHsieh/iNEXT')
>library(iNEXT)
>library(ggplot2)

#example dataset

>data(spider)

#last line that runs properly before the error

>out <- iNEXT(spider, q=c(0, 1, 2), datatype="abundance", endpoint=500)

#here comes to the problematic line and its error

>ggiNEXT(out, type=1, facet.var="site")

Error in `levels<-`(`*tmp*`, value = if (nl == nL) as.character(labels) else paste0(labels,  : factor level [2] is duplicated

Any idea how to solve this?

Answer 1

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)
}