[R] Simple 'frequency' function?
Dan Bolser
dmb at mrc-dunn.cam.ac.uk
Sat Jul 10 01:19:36 CEST 2004
On Fri, 9 Jul 2004, Marc Schwartz wrote:
>On Fri, 2004-07-09 at 10:43, Dan Bolser wrote:
>> On Fri, 9 Jul 2004, Uwe Ligges wrote:
>>
>> >Dan Bolser wrote:
>> >
>> >> Hi, I have designed the following function to extract count frequencies
>> >> from an array of integers. For example...
>> >>
>> >> # Tipical array
>> >> x <- cbind(1,1,1,1,1,2,2,2,2,3,3,3,3,4,5,6,7,22)
>> >>
>> >> # Define the frequency function
>> >> frequency <-
>> >> function(x){
>> >> max <- max(x)
>> >> j <- c()
>> >> for(i in 1:max){
>> >> j[i] <- length(x[x==i])
>> >> }
>> >> return(j)
>> >> }
>> >>
>> >> fre <- frequency(x)
>> >> plot(fre)
>> >>
>> >> How can I ...
>> >>
>> >> 1) Make this a general function so my array could be of the form
>> >>
>> >> # eats!
>> >> x <- cbind( "egg","egg","egg","egg","ham","ham","ham","ham","chicken" )
>> >>
>> >> fre <- frequency(x)
>> >> plot(fre)
>> >>
>> >> 2) Make frequency return an object which I can call plot on (allowing the
>> >> prob=TRUE option).
>> >
>> >
>> >See ?table:
>> >
>> > table(x)
>> > plot(table(x))
>> > plot(table(x) / sum(table(x)))
>> >
>>
>> Sorry, why does
>>
>> plot(table(x),log='y')
>>
>> fail?
>>
>> I am looking at count/frequency distributions which are linear on log/log
>> scales.
>
>
>Presumably you are getting the following:
>
>> x <- cbind( "egg","egg","egg","egg","ham",
> "ham","ham","ham","chicken" )
>> plot(table(x),log='y')
>Error in plot.window(xlim, ylim, log, asp, ...) :
> Infinite axis extents [GEPretty(0,inf,5)]
>In addition: Warning message:
>Nonfinite axis limits [GScale(-inf,0.60206,2, .); log=1]
>
>The problem here is that the range for the default y axis is being set
>to limits that cannot be used on a log scale.
>
>If you review the code for plot.table(), which is the method that will
>be used here, you see the function definition as follows:
>
>> graphics:::plot.table
>function (x, type = "h", ylim = c(0, max(x)), lwd = 2, xlab = NULL,
> ylab = NULL, frame.plot = is.num, ...)
>
>Note that the default ylim is set to have a min value of 0, which of
>course you cannot have on a log scale.
>
>Thus, instead, use the following:
>
>plot(table(x), log = "y", ylim = range(table(x)))
>
>or otherwise explicitly define the y axis range, such that the min value
>is >0.
>
>Note also that the default plot type here is 'h', which will result in a
>histogram type of plot using vertical lines. If you want a scatterplot
>type of graphic, use:
>
>plot(table(x), log = "y", ylim = range(table(x)), type = "p")
>
Thanks for the exceedingly clear answer. In general I have difficulty
inspecting the 'internals' of a function, but you have given me some
clues as how to do this in the future.
Cheers,
Dan.
>HTH,
>
>Marc Schwartz
>
>
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