[R] ERROR need finite 'ylim' values

[Peter Ehlers]

Giuseppe,

See comments below.

On 2010-06-13 10:24, David Winsemius wrote:
>
>
> Giuseppe wrote:
>>
>> Hello:
>> I use R with MAC
>> I have a simple data table, numeric and text columns, named dt. The table
>> is imported through read.csv from a csv file. Row numbers are
>> automatically assigned, header is set to TRUE. there are 599 rows and
>> several columns.
>>
>> I am trying to plot using the stripchart command: one numeric variable
>> (say dt$fnatg) vs a text column (say dt$pat). dt$pat contains one of 3
>> values: "pos", "neg", ""
>>
>> So I issue the following command:
>>
>>> stripchart (dt$fnatg~dt$pat)
>>
>> and works well. it works well also with several options and nuances:
>>
>>> stripchart (dt$fnatg ~ dt$pat, method ="jitter", jitter = 0.3, vertical
> =TRUE,log="y", pch=1, ylab="Thyroglobulin (ng/mL)",xlab="Surgical
> Pathology")
>>
>> Now I want my graph to exclude values for which dt$pat == ""
>>
>> I tried:
>>
>>> stripchart (dt$fnatg ~ dt$pat, method ="jitter", subset (dt,
> dt$pat!=""),jitter = 0.3, vertical =TRUE,log="y", pch=1, ylab="Thyroglobulin
> (ng/mL)",xlab="Surgical Pathology")
>>
>> there is no effect: the plot contains the same values as before
>>
>> the I tried first subsetting the table:
>>
>>> patonly<-(dt, dt$pat!="") which works well in creating a new table
> excluding the unwanted rows. I have noticed that the new table keeps the
> same row numbers assigned in the previous table. So row numbers now go 1 to
> 599 but with some intervals (for example there is no row 475 etc.).
>>
>> then I use:
>>
>>> stripchart (patonly$fnatg ~ patonly$pat, method ="jitter", jitter = 0.3,
> vertical =TRUE,log="y", pch=1, ylab="Thyroglobulin (ng/mL)",xlab="Surgical
> Pathology")
>>
>> and I get the following error:
>>
>> Error in plot.window(...) : need finite 'ylim' values
>> In addition: Warning messages:
>> 1: In min(x) : no non-missing arguments to min; returning Inf
>> 2: In max(x) : no non-missing arguments to max; returning -Inf
>> 3: In min(x) : no non-missing arguments to min; returning Inf
>> 4: In max(x) : no non-missing arguments to max; returning -Inf
>>
>> I f I try the same command but I use another text variable (for example
>> patonly$gr) in the same table to split the plot, it now works:
>>
>>> stripchart (patonly$fnatg ~ patonly$gr, method ="jitter", jitter = 0.3,
> vertical =TRUE,log="y", pch=1, ylab="Thyroglobulin (ng/mL)",xlab="Surgical
> Pathology")
>>
>>
>> My question is two fold:
>> Why does not the subset command work within the stripchart command?
>>
>> Why the subsetted table cannot be used in the stripchart command, when the
>> plotting variable is the same previously used in the subsetting process?
>>
>>
>
> You appear to have adopted a strategy of using positional matching. Naming
> your arguments will often result in more informative error messages.
> Looking at the help page for stripchart, it appears that there is no
> "subset" parameter to set in any of its methods and only the formula method
> has a data argument. It should work with:
>
> stripchart(formula1 , data=subset(dta, subset=criteria),   ....<rest of
> arguments preferably named>   )
>
> Your other option might be to use the with() function:
>
> with( subset(patonly, pat!=""),  stripchart(fnatg ~ gr,  ...<named
> arguments>) )
>
>
> HTH. and if it doesn't, then submit a reproducible data example to work
> with.

Actually, Giuseppe appears to have stumbled upon a bug in the
stripchart() function.

First, here's a fix:
After your command

   patonly<-(dt, dt$pat!="")

which I assume is meant to be

   patonly <- subset(dt, dt$pat!="")

and which can be written as

   patonly <- subset(dt, pat!="")

you should issue this:

   patonly$pat <- factor(patonly$pat)

which will remove the empty level; stripchart() should
work well after that (and do use the data= argument
rather than dt$...).

Alternatively, you could change your "text" variables
(which I assume are factors) to character values (or
re-import your data with stringsAsFactors = FALSE).


Now for the bug in stripchart():
If the *first* group of the grouping variable is
empty, then stripchart() has a problem determining
the range of data values (x-values for horizontal
charts, y-values otherwise). I can replicate your
problem withe OrchardSprays dataset:

# this works:
stripchart(decrease ~ treatment, data = OrchardSprays,
            subset = treatment != "B")

# this doesn't
stripchart(decrease ~ treatment, data = OrchardSprays,
            subset = treatment != "A")

I'll be submitting a bug report (and I think the fix
is easy).

   -Peter Ehlers