R devel - Jun 2005 - boxplot by factor (Package base version 2.1.1) (PR#7976)

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

Locale:
en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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