[R] Odp: error : unused argument(s) when boxplot

[Petr PIKAL]

Hi

It is good to cc posts to help list also as others could have their 
insights and also other users can learn from it.

"Pauline Haleux (JIC)" <pauline.haleux at bbsrc.ac.uk> napsal dne 16.02.2010 
18:04:18:

> I tried 
> 
> growth<-sample(60:80, 20, replace=T)
> sugar<-sample(letters[1:3], replace=T)
> DF<-data.frame(growth=growth, sugar=sugar)
> boxplot(growth~sugar, ylab="growth", xlab="sugar", data=DF)
> 
> and got 
> 
> > growth<-sample(60:80, 20, replace=T)
> > sugar<-sample(letters[1:3], replace=T)
> > DF<-data.frame(growth=growth, sugar=sugar)
> Error in data.frame(growth = growth, sugar = sugar) : 
>   arguments imply differing number of rows: 20, 3

Sorry, I forgot 20 here
sugar<-sample(letters[1:3],20 ,replace=T)

After that correction it shall work
If not, something is wrong with your installation, if yes something is 
wrong with your data or working environment.

Regards
Petr


> 
> I checked with ls and I have no other sugar or growth in my environment. 
I 
> think I will just try to reinstall R. I tried debug (bxp) and got 
> 
> > bxp(sugar~growth, data=Dataset)
> debugging in: bxp(sugar ~ growth, data = Dataset)
> debug: {
>     pars <- c(list(...), pars)
>     pars <- pars[unique(names(pars))]
>     bplt <- function(x, wid, stats, out, conf, notch, xlog, i) {
>         ok <- TRUE
>         if (!any(is.na(stats))) {
>             xP <- if (xlog) 
>                 function(x, w) x * exp(w)
>             else function(x, w) x + w
>             wid <- wid/2
>             if (notch) {
>                 ok <- stats[2L] <= conf[1L] && conf[2L] <= stats[4L]
>                 xx <- xP(x, wid * c(-1, 1, 1, notch.frac, 1, 
>                   1, -1, -1, -notch.frac, -1))
>                 yy <- c(stats[c(2, 2)], conf[1L], stats[3L], 
>                   conf[2L], stats[c(4, 4)], conf[2L], stats[3L], 
>                   conf[1L])
>             }
>             else {
>                 xx <- xP(x, wid * c(-1, 1, 1, -1))
>                 yy <- stats[c(2, 2, 4, 4)]
>             }
>             if (!notch) 
>                 notch.frac <- 1
>             wntch <- notch.frac * wid
>             xypolygon(xx, yy, lty = "blank", col = boxfill[i])
>             xysegments(xP(x, -wntch), stats[3L], xP(x, +wntch), 
>                 stats[3L], lty = medlty[i], lwd = medlwd[i], 
>                 col = medcol[i], lend = 1)
>             xypoints(x, stats[3L], pch = medpch[i], cex = medcex[i], 
>                 col = medcol[i], bg = medbg[i])
>             xysegments(rep.int(x, 2), stats[c(1, 5)], rep.int(x, 
>                 2), stats[c(2, 4)], lty = whisklty[i], lwd = 
whisklwd[i], 
>                 col = whiskcol[i])
>             xysegments(rep.int(xP(x, -wid * staplewex[i]), 2), 
>                 stats[c(1, 5)], rep.int(xP(x, +wid * staplewex[i]), 
>                   2), stats[c(1, 5)], lty = staplelty[i], lwd = 
staplelwd[i], 
>                 col = staplecol[i])
>             xypolygon(xx, yy, lty = boxlty[i], lwd = boxlwd[i], 
>                 border = boxcol[i])
>             if ((nout <- length(out))) {
>                 xysegments(rep(x - wid * outwex, nout), out, 
>                   rep(x + wid * outwex, nout), out, lty = outlty[i], 
>                   lwd = outlwd[i], col = outcol[i])
>                 xypoints(rep.int(x, nout), out, pch = outpch[i], 
>                   lwd = outlwd[i], cex = outcex[i], col = outcol[i], 
>                   bg = outbg[i])
>             }
>             if (any(inf <- !is.finite(out))) {
>                 warning(sprintf(ngettext(length(unique(out[inf])), 
>                   "Outlier (%s) in boxplot %d is not drawn", 
>                   "Outliers (%s) in boxplot %d are not drawn"), 
>                   paste(unique(out[inf]), collapse = ", "), x), 
>                   domain = NA)
>             }
>         }
>         return(ok)
>     }
>     if (!is.list(z) || 0L == (n <- length(z$n))) 
>         stop("invalid first argument")
>     if (is.null(at)) 
>         at <- 1L:n
>     else if (length(at) != n) 
>         stop("'at' must have same length as 'z$n', i.e. ", n)
>     if (is.null(z$out)) 
>         z$out <- numeric()
>     if (is.null(z$group) || !outline) 
>         z$group <- integer()
>     if (is.null(pars$ylim)) 
>         ylim <- range(z$stats[is.finite(z$stats)], if (outline) z$out
> [is.finite(z$out)], 
>             if (notch) z$conf[is.finite(z$conf)])
>     else {
>         ylim <- pars$ylim
>         pars$ylim <- NULL
>     }
>     if (is.null(pars$xlim)) 
>         xlim <- c(0.5, n + 0.5)
>     else {
>         xlim <- pars$xlim
>         pars$xlim <- NULL
>     }
>     if (length(border) == 0L) 
>         border <- par("fg")
>     if (!add) {
>         plot.new()
>         if (horizontal) 
>             plot.window(ylim = xlim, xlim = ylim, log = log, 
>                 xaxs = pars$yaxs)
>         else plot.window(xlim = xlim, ylim = ylim, log = log, 
>             yaxs = pars$yaxs)
>     }
>     xlog <- (par("ylog") && horizontal) || (par("xlog") && !horizontal)
>     pcycle <- function(p, def1, def2 = NULL) rep(if (length(p)) p else 
if 
> (length(def1)) def1 else def2, 
>         length.out = n)
>     p <- function(sym) pars[[sym, exact = TRUE]]
>     boxlty <- pcycle(pars$boxlty, p("lty"), par("lty"))
>     boxlwd <- pcycle(pars$boxlwd, p("lwd"), par("lwd"))
>     boxcol <- pcycle(pars$boxcol, border)
>     boxfill <- pcycle(pars$boxfill, par("bg"))
>     boxwex <- pcycle(pars$boxwex, 0.8 * {
>         if (n <= 1) 
>             1
>         else stats::quantile(diff(sort(if (xlog) 
>             log(at)
>         else at)), 0.1)
>     })
>     medlty <- pcycle(pars$medlty, p("lty"), par("lty"))
>     medlwd <- pcycle(pars$medlwd, 3 * p("lwd"), 3 * par("lwd"))
>     medpch <- pcycle(pars$medpch, NA_integer_)
>     medcex <- pcycle(pars$medcex, p("cex"), par("cex"))
>     medcol <- pcycle(pars$medcol, border)
>     medbg <- pcycle(pars$medbg, p("bg"), par("bg"))
>     whisklty <- pcycle(pars$whisklty, p("lty"), "dashed")
>     whisklwd <- pcycle(pars$whisklwd, p("lwd"), par("lwd"))
>     whiskcol <- pcycle(pars$whiskcol, border)
>     staplelty <- pcycle(pars$staplelty, p("lty"), par("lty"))
>     staplelwd <- pcycle(pars$staplelwd, p("lwd"), par("lwd"))
>     staplecol <- pcycle(pars$staplecol, border)
>     staplewex <- pcycle(pars$staplewex, 0.5)
>     outlty <- pcycle(pars$outlty, "blank")
>     outlwd <- pcycle(pars$outlwd, p("lwd"), par("lwd"))
>     outpch <- pcycle(pars$outpch, p("pch"), par("pch"))
>     outcex <- pcycle(pars$outcex, p("cex"), par("cex"))
>     outcol <- pcycle(pars$outcol, border)
>     outbg <- pcycle(pars$outbg, p("bg"), par("bg"))
>     outwex <- pcycle(pars$outwex, 0.5)
>     width <- if (!is.null(width)) {
>         if (length(width) != n | any(is.na(width)) | any(width <= 
>             0)) 
>             stop("invalid boxplot widths")
>         boxwex * width/max(width)
>     }
>     else if (varwidth) 
>         boxwex * sqrt(z$n/max(z$n))
>     else if (n == 1) 
>         0.5 * boxwex
>     else rep.int(boxwex, n)
>     if (horizontal) {
>         xypoints <- function(x, y, ...) points(y, x, ...)
>         xypolygon <- function(x, y, ...) polygon(y, x, ...)
>         xysegments <- function(x0, y0, x1, y1, ...) segments(y0, 
>             x0, y1, x1, ...)
>     }
>     else {
>         xypoints <- points
>         xypolygon <- polygon
>         xysegments <- segments
>     }
>     ok <- TRUE
>     for (i in 1L:n) ok <- ok & bplt(at[i], wid = width[i], stats = 
z$stats[, 
>         i], out = z$out[z$group == i], conf = z$conf[, i], notch = 
notch, 
>         xlog = xlog, i = i)
>     if (!ok) 
>         warning("some notches went outside hinges ('box'): maybe set 
notch=FALSE")
>     axes <- is.null(pars$axes)
>     if (!axes) {
>         axes <- pars$axes
>         pars$axes <- NULL
>     }
>     if (axes) {
>         ax.pars <- pars[names(pars) %in% c("xaxt", "yaxt", "xaxp", 
>             "yaxp", "las", "cex.axis", "col.axis", "format")]
>         if (is.null(show.names)) 
>             show.names <- n > 1
>         if (show.names) 
>             do.call("axis", c(list(side = 1 + horizontal, at = at, 
>                 labels = z$names), ax.pars))
>         do.call("Axis", c(list(x = z$stats, side = 2 - horizontal), 
>             ax.pars))
>     }
>     do.call("title", pars[names(pars) %in% c("main", "cex.main", 
>         "col.main", "sub", "cex.sub", "col.sub", "xlab", "ylab", 
>         "cex.lab", "col.lab")])
>     if (frame.plot) 
>         box()
>     invisible(at)
> }
> Browse[2]> 
> debug: pars <- c(list(...), pars)
> Browse[2]> 
> debug: pars <- pars[unique(names(pars))]
> Browse[2]> 
> debug: bplt <- function(x, wid, stats, out, conf, notch, xlog, i) {
>     ok <- TRUE
>     if (!any(is.na(stats))) {
>         xP <- if (xlog) 
>             function(x, w) x * exp(w)
>         else function(x, w) x + w
>         wid <- wid/2
>         if (notch) {
>             ok <- stats[2L] <= conf[1L] && conf[2L] <= stats[4L]
>             xx <- xP(x, wid * c(-1, 1, 1, notch.frac, 1, 1, -1, 
>                 -1, -notch.frac, -1))
>             yy <- c(stats[c(2, 2)], conf[1L], stats[3L], conf[2L], 
>                 stats[c(4, 4)], conf[2L], stats[3L], conf[1L])
>         }
>         else {
>             xx <- xP(x, wid * c(-1, 1, 1, -1))
>             yy <- stats[c(2, 2, 4, 4)]
>         }
>         if (!notch) 
>             notch.frac <- 1
>         wntch <- notch.frac * wid
>         xypolygon(xx, yy, lty = "blank", col = boxfill[i])
>         xysegments(xP(x, -wntch), stats[3L], xP(x, +wntch), stats[3L], 
>             lty = medlty[i], lwd = medlwd[i], col = medcol[i], 
>             lend = 1)
>         xypoints(x, stats[3L], pch = medpch[i], cex = medcex[i], 
>             col = medcol[i], bg = medbg[i])
>         xysegments(rep.int(x, 2), stats[c(1, 5)], rep.int(x, 
>             2), stats[c(2, 4)], lty = whisklty[i], lwd = whisklwd[i], 
>             col = whiskcol[i])
>         xysegments(rep.int(xP(x, -wid * staplewex[i]), 2), stats[c(1, 
>             5)], rep.int(xP(x, +wid * staplewex[i]), 2), stats[c(1, 
>             5)], lty = staplelty[i], lwd = staplelwd[i], col = 
staplecol[i])
>         xypolygon(xx, yy, lty = boxlty[i], lwd = boxlwd[i], border = 
boxcol[i])
>         if ((nout <- length(out))) {
>             xysegments(rep(x - wid * outwex, nout), out, rep(x + 
>                 wid * outwex, nout), out, lty = outlty[i], lwd = 
outlwd[i], 
>                 col = outcol[i])
>             xypoints(rep.int(x, nout), out, pch = outpch[i], 
>                 lwd = outlwd[i], cex = outcex[i], col = outcol[i], 
>                 bg = outbg[i])
>         }
>         if (any(inf <- !is.finite(out))) {
>             warning(sprintf(ngettext(length(unique(out[inf])), 
>                 "Outlier (%s) in boxplot %d is not drawn", "Outliers 
(%s) in 
> boxplot %d are not drawn"), 
>                 paste(unique(out[inf]), collapse = ", "), x), 
>                 domain = NA)
>         }
>     }
>     return(ok)
> }
> Browse[2]> 
> debug: if (!is.list(z) || 0L == (n <- length(z$n))) stop("invalid first 
argument")
> Browse[2]> 
> debug: stop("invalid first argument")
> Browse[2]> 
> Error in bxp(sugar ~ growth, data = Dataset) : invalid first argument
> 
> Thanks a lot,
> 
> Pauline
>