[Rd] boxplot by factor (Package base version 2.1.1) ( PR#7976)

[Liaw, Andy]

The issue is not with boxplot, but with split.  boxplot.formula() 
calls boxplot(split(split(mf[[response]], mf[-response]), ...), 
but look at what split() returns when there are empty levels in
the factor:

> f <- factor(gl(3, 6), levels=1:5)
> y <- rnorm(f)
> split(y, f)
$"1"
[1] 0.4832124 1.1924811 0.3657797 1.7400198 0.5577356 0.9889520

$"2"
[1] -1.1296642 -0.4808355 -0.2789933  0.1220718  0.1287742 -0.7573801

$"3"
[1]  1.2320902  0.5090700 -1.5508074  2.1373780  1.1681297 -0.7151561

The "culprit" is the following in split.default():

    f <- factor(f)

which drops empty levels in f, if there are any.  BTW, ?split doesn't
mention what it does in such situation.  Perhaps it should?

If this is to be "fixed", I suppose an additional argument, e.g.,
drop=TRUE, can be added, and the corresponding line mentioned
above changed to something like:

    if (drop || !is.factor(f)) f <- factor(f)

Then this additional argument can be pass on from boxplot.formula() to 
split().

Just my $0.02...

Andy

> From: mwtoews at sfu.ca
> 
> I consider this to be an old bug, which also persists in Splus 7. It  
> is unnecessary, and annoying.
> 
> ## Section 1: Consider a simple data frame with three possible  
> factors (in levels)
> 
> d <- data.frame(a=sort(rnorm(10)*10), b=factor(c(rep("A",4), rep("C", 
> 6)), levels=c("A","B","C")))
> tapply(d$a, d$b, mean) # returns three results, which I would expect
> plot(a ~ b, d) # plots only two of three objects, ignoring 
> that there  
> was "C" in the second position
> 
> # if I tried to plot a blank in between the two boxplots:
> plot(a ~ b, d, at=1:3) # nope: error
> plot(a ~ b, d, at=c(1,3)) # nope: out of range (also xlim does  
> nothing for the formula boxplot method)
> 
> # to make this work with the current R/Splus implementation, I have  
> to add a zero:
> d <- rbind(d, data.frame(a=0,b="B")) # which I don't want to do,  
> since there are no "B"
> plot(a ~ b, d) # yuk!
> 
> ## Section 2: Why is this important? Consider another realistic  
> example of [synthetic] daily temperature
> 
> temp <- 5 - 10*cos(1:365*2*pi/365) + rnorm(365)*3
> d1 <- data.frame(year=2005, jday=1:365, date=NA, month=NA, temp) #  
> jday is Julian day [1,365]
> d1$date <- as.Date(paste(d1$year, d1$jday), "%Y %j")
> d1$month <- factor(months(d1$date,TRUE), levels=month.abb)
> plot(temp ~ month, d1) # perfect, in a perfect meteorological world
> 
> d2 <- d1[!d1$month %in% c("Mar","Apr","May","Sep"),] # now let's  
> remove some data
> tapply(d2$temp,d2$month,mean)  # perfect
> plot(temp ~ month, d2) # ugly, not 12 months, etc. (despite 
> having 12  
> levels)
> 
> # again the only cure is to add zeros to the missing months  
> (unnecessary forgery of data)
> d3 <- d2
> for (i in c("Mar","Apr","May","Sep")) {
>      d3 <- rbind(d3,NA)
>      d3$month[nrow(d3)] <- i
>      d3$temp[nrow(d3)] <- 0
> }
> plot(temp ~ month, d3) # still ugly, but at least has 12 months!
> 
> ## Section 3: Solution
> The obvious solution is to leave a blank where a boxplot should go,  
> similar to tapply. This would have 1:n positions, where n is the  
> number of levels of the factor, not the number of factors that have  
> one or more numbers.  The position should also have a label 
> under the  
> tick mark.
> I don't see any reason why the missing data should be completely  
> ignored. Users wishing to not plot the blanks where the data 
> could go  
> can simply type (for back-compatibility):
> 
> d2$month <- factor(d2$month) # from 12 to 8 levels
> 
> Which will produce the same 8-factor plot as above.
> 
> ## Section 4: Conclusion
> I consider this to be a bug in regards to data representation, and  
> this function is not consistant with other functions like `tapply'.   
> Considering that the back-compatibility solution is very simple, and  
> most users would probably prefer a result including all levels (NULL  
> or real values in each), I feel this an appropriate improvement (and  
> easy to fix in the code). At the very least, include an option to  
> honour the factor levels.
> 
> Thanks.
> -mt
> 
> --please do not edit the information below--
> 
> Version:
> platform = powerpc-apple-darwin8.1.0
> arch = powerpc
> os = darwin8.1.0
> system = powerpc, darwin8.1.0
> status = Patched
> major = 2
> minor = 1.1
> year = 2005
> month = 06
> day = 26
> language = R
> 
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