[R] Histogram with two groups on the same graph (not on separate panels)

Wed, 14 Jul 2010 23:32:45 -0700 

I have been trying to produce a histogram that has two groups (male and female 
snakes) on the same graph (either superimposed or each frequency bar appears 
side by side). I found a couple of functions for superimposed histogram written 
by other people.
The below is the codes I used for my data containing a column of svl (body 
size; 
snout-vent length) and another column of sex (male or female). My data 
structure 
is shown at the bottom of my email message.
My question:  When I ran the codes below (modified from: 
http://onertipaday.blogspot.com/2007/04/how-to-superimpose-histograms.html), I 
got an error message, “Error in hist.default(X[[1L]], ...) : 'x' must be 
numeric”. Could anyone help me figure out the problem, please? Do you know 
alternative codes or a function that produce a histogram containing two groups, 
with each frequency bar appearing side by side, as shown in 
http://home.medewerker.uva.nl/g.dutilh/bestanden/multiple%20group%20histogram.png
 ?
 
gb <- read.csv(file = "D:\\data 
12.24.06\\AllMamushiCorrected5.8.10_7.12.10.csv", header=TRUE, 
strip.white=TRUE, 
na.strings="")
attach(gb)
 
superhist2pdf <- function(x, filename = "super_histograms.pdf",
dev = "pdf", title = "Superimposed Histograms", nbreaks ="Sturges") {
junk = NULL
grouping = NULL
for(i in 1:length(x)) {
junk = c(junk,x[[i]])
grouping <- c(grouping, rep(i,length(x[[i]]))) }
grouping <- factor(grouping)
n.gr <- length(table(grouping))
xr <- range(junk)
histL <- tapply(junk, grouping, hist, breaks=nbreaks, plot = FALSE)
maxC <- max(sapply(lapply(histL, "[[", "counts"), max))
if(dev == "pdf") { pdf(filename, version = "1.4") } else{}
if((TC <- transparent.cols <- .Device %in% c("pdf", "png"))) {
cols <- hcl(h = seq(30, by=360 / n.gr, length = n.gr), l = 65, alpha = 0.5) }
else {
h.den <- c(10, 15, 20)
h.ang <- c(45, 15, -30) }
if(TC) {
plot(histL[[1]], xlim = xr, ylim= c(0, maxC), col = cols[1], xlab = "x", main = 
title) }
else { plot(histL[[1]], xlim = xr, ylim= c(0, maxC), density = h.den[1], angle 
= 
h.ang[1], xlab = "x") }
if(!transparent.cols) {
for(j in 2:n.gr) plot(histL[[j]], add = TRUE, density = h.den[j], angle = 
h.ang[j]) } else {
for(j in 2:n.gr) plot(histL[[j]], add = TRUE, col = cols[j]) }
invisible()
if( dev == "pdf") {
dev.off() }
}

female <- subset(gb, sex=="f", select=svl)
male <- subset(gb, sex=="m", select=svl)
l1 = list(female, male)
superhist2pdf(l1, nbreaks="Sturges")
 
Error in hist.default(X[[1L]], ...) : 'x' must be numeric
 

FYI: The object ‘female’ and ‘male’ looks like:
> female
     svl
1   51.5
2   52.5
3   52.5
4   58.5
<edited>
277   NA
278   NA
279 55.4
280 57.5 
 
> male
     svl
5   41.8
14  49.5
17  49.0
20  53.0
<edited>
231 47.6
235   NA
238 50.3
241 50.5
243 62.8
244 59.0
 
FYI:  The structure of my dataset, gb looks like:
> str(gb)
'data.frame':   308 obs. of 43 variables:
 $ id           : Factor w/ 290 levels "(023.541.040) G7",..: 241 
244 243 245 
278 193 194 195 196 197 ...
 $ studysite    : Factor w/ 29 levels "Assabu","Astushinai",..: 20 19 19 19 
19 
29 29 29 29 29 ...
 $ studysitecode: int  NA NA NA NA NA 7 7 7 7 7 ...
 $ subsite      : int  NA NA NA NA NA 18 18 18 18 18 ...
 $ sitecond     : int  NA NA NA NA NA 1 1 1 1 1 ...
 $ Habitat      : Factor w/ 6 levels "Beach","On road",..: 5 5 5 5 5 5 5 
5 5 5 
...
 $ Baskingspots : int  1 1 1 1 1 1 1 1 1 1 ...
 $ sex          : Factor w/ 2 levels "f","m": 1 1 1 1 2 1 1 1 1 1 ...
 $ sexcode      : int  NA NA NA 0 1 0 0 0 0 0 ...
 $ svl          : num  51.5 52.5 52.5 58.5 41.8 57.6 59 55.6 62 58.5 
...
 $ tl           : num  8 8 8 10 8.2 9.2 9 8.5 9.5 8.8 ...
 $ bm           : num  142 128 148.3 192.3 70.5 ...
 $ defensiveness: int  NA NA NA NA NA 1 1 1 1 2 ...
 $ ftr          : int  NA NA NA NA NA 5 10 60 18 30 ...
 $ latency      : num  NA NA NA NA NA NA NA NA NA NA ...
 $ dvc          : int  NA NA NA NA NA 25 25 38 28 28 ...
 $ RepCnd       : Factor w/ 4 levels "Male","Nonpregnant",..: 4 4 4 2 1 
2 2 2 2 
2 ...
 $ repcnd       : int  1 1 1 0 2 0 0 0 0 0 ...
 $ repstatus    : int  1 1 1 1 NA 0 0 0 0 0 ...
 $ LS.w_egg     : int  NA NA NA NA NA NA NA NA NA NA ...
 $ estimatedLS  : int  NA NA NA NA NA NA NA NA NA NA ...
 $ lit.size     : int  NA NA NA NA NA NA NA NA NA NA ...
 $ lit.mass     : num  NA NA NA NA NA NA NA NA NA NA ...
 $ post.BM      : num  NA NA NA NA NA NA NA NA NA NA ...
 $ rcm          : num  NA NA NA NA NA NA NA NA NA NA ...
 $ mean.nSVL    : num  NA NA NA NA NA NA NA NA NA NA ...
 $ mean.nBM     : num  NA NA NA NA NA NA NA NA NA NA ...
 $ ta           : num  23 20 20 20 21 20 20 20 20 20 ...
 $ tm           : num  24 29 29 30 20 20.8 20.8 20.8 20.8 20.8 ...
 $ tb           : num  23 29 30 NA 23 30 29.6 30.2 29 27 ...
 $ partdate     : int  NA NA NA NA NA NA NA NA NA NA ...
 $ time         : int  1255 1330 1340 1355 1300 1600 1600 1600 1600 
1600 ...
 $ julian       : int  NA NA NA NA NA 1999186 1999186 1999186 1999186 
1999186 
...
 $ JulianDate   : int  NA NA NA NA NA 186 186 186 186 186 ...
 $ year         : int  1999 1999 1999 1999 1999 1999 1999 1999 1999 
1999 ...
 $ calenderdate : Factor w/ 106 levels "10/11/2002","10/12/2001",..: 18 20 20 
20 
22 49 49 49 49 49 ...
 $ logSVL       : num  NA NA NA NA NA 1.76 1.77 1.75 1.79 1.77 ...
 $ logBM        : num  NA NA NA NA NA 2.26 2.23 2.26 2.28 2.23 ...
 $ bc           : num  NA NA NA NA NA ...
 $ Rsvl         : num  NA NA NA NA NA ...
 $ Rftr         : num  NA NA NA NA NA ...
 $ Rdefense     : num  NA NA NA NA NA 97 97 97 97 212 ...
 $ Rdvc         : num  NA NA NA NA NA ...
 
Thank you so much for your time and help!
Sincerely,
Kiyoshi  Sasaki


      
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