[R] R Package "example" section of .Rd file question (think it's a non-ASCII issue, but not sure...)

[David Winsemius]

On Feb 15, 2012, at 5:30 PM, Yihui Xie wrote:

> Man, the original reply told you to use backticks `` rather than
> double quotes "". They are very different in R; see ?Quotes
>
> And GSE19829-GPL570_eset is really a bad name. I recommend you to  
> rename it.
>
> Regards,
> Yihui
> --
> Yihui Xie <xieyihui at gmail.com>
> Phone: 515-294-2465 Web: http://yihui.name
> Department of Statistics, Iowa State University
> 2215 Snedecor Hall, Ames, IA
>
>
>
> On Wed, Feb 15, 2012 at 4:09 PM, Ben Ganzfried <ben.ganzfried at gmail.com 
> > wrote:
>> Hi Martin,
>>
>> Thanks! You were right.  Quotes seemed to work, except I kept  
>> running into
>> a problem on the following line:
>>
>> time <- "GSE19829-GPL570_eset$days_to_death" / 365

If you use Yihui's advice, you should only back-tick around the  
dataframe name and not around the column name.


>>
>> The error is that R atomic vector operator invalid.

Because you are trying to divide a character value by a number.

-- 
David.

>>  It's actually much
>> easier if I could use quotes rather than re-name-- so is there any  
>> way to
>> put quotes around the columns in "GSE19829-GPL570_eset" such that  
>> it does
>> what i want it to?
>>
>> In the above "time" example, I just want to take the values in the  
>> column
>> and divide by 365, but the quotes are messing it up. Any  
>> clarification
>> would be really greatly appreciated!
>>
>> Thanks!
>>
>> Ben
>>
>>
>>
>> On Wed, Feb 15, 2012 at 4:20 PM, Martin Morgan <mtmorgan at fhcrc.org>  
>> wrote:
>>
>>> On 02/15/2012 12:18 PM, Ben Ganzfried wrote:
>>>
>>>> Hey,
>>>>
>>>> I keep getting the following warning:
>>>>
>>>>  data(GSE19829-GPL570_eset)
>>>>>
>>>> Warning in data(GSE19829 - GPL570_eset) :
>>>>   data set ‘GSE19829 - GPL570_eset’ not found
>>>>
>>>>> ## maybe str(GSE19829-GPL570_eset) ; plot(GSE19829- 
>>>>> GPL570_eset) ...
>>>>>
>>>>
>>> Hi Ben --
>>>
>>> '-' is being parsed as a minus sign;  you could (I think) quote it
>>>
>>>  `GSE19829-GPL570_eset`
>>>
>>> or better come up with a legal name.
>>>
>>> Martin
>>>
>>>
>>>>> if(require(affy)){
>>>>>
>>>> +   summary(GSE19829-GPL570_eset$**vital_status)
>>>> +  }
>>>> Error in summary(GSE19829 - GPL570_eset$vital_status) :
>>>>   object 'GSE19829' not found
>>>> Execution halted
>>>>
>>>> This error does not happen on other of my other .Rd files.  None  
>>>> of the
>>>> other .Rd files have a "-" character in their title.  for  
>>>> example, the
>>>> other files have the following:
>>>>
>>>>> data(GSE1234)
>>>>>
>>>> OR
>>>>
>>>>> data(GSE5678)
>>>>>
>>>>
>>>> I think the issue is the "-" character, but I'm not sure.  Does  
>>>> anyone
>>>> know
>>>> if this is the case?  And if so, how do I fix it?  If not, any  
>>>> other
>>>> suggestions?
>>>>
>>>> Much thanks!
>>>>
>>>> Ben
>>>> tained, reproducible code.

David Winsemius, MD
West Hartford, CT