[R] Error when using anova(lm())

[David Winsemius]

On Oct 8, 2010, at 1:09 PM, Alison Callahan wrote:

> See below.
>
> On Fri, Oct 8, 2010 at 1:01 PM, David Winsemius <dwinsemius at comcast.net 
> > wrote:
>>
>> On Oct 8, 2010, at 12:46 PM, Alison Callahan wrote:
>>
>>> Hello all,
>>>
>>> I am trying to perform an ANOVA on some data in a data frame, but  
>>> when
>>> I try to use lm(), I get the following error:

The question that should have been posed was how did you use lm()?

It could be that the inappropriate use of a factor as a dependent  
variable was the cause. Did you use something like:

lm(island_id ~ refseq_better, data=dfrm)  # ??

Example:
 > dfrm <- data.frame(a=factor(rnorm(10)), b=rnorm(10))
 > lm(a ~ b, data=dfrm)
Error in storage.mode(y) <- "double" :
   invalid to change the storage mode of a factor
In addition: Warning message:
In model.response(mf, "numeric") :
   using type="numeric" with a factor response will be ignored


>>>
>>> Error in storage.mode(y) <- "double" :
>>>  invalid to change the storage mode of a factor
>>> In addition: Warning message:
>>> In model.response(mf, "numeric") :
>>>  using type="numeric" with a factor response will be ignored
>>>
>>> Here is a subset of my data:
>>>
>>>  island_id     refseq_better     total        refseq_proportion
>>> fiveprime   threeprime        island_size
>>>      1a            29                  57          0.508771929824561
>>>   11127     201378               190251
>>>      1c            27                  90               0.3
>>>            6303879    6600994            297115
>>>      1d            33                 115         0.28695652173913
>>>  7001283    7421591            420308
>>>      2b            11                  42          0.261904761904762
>>>  4381375    4520137            138762
>>>      2d            27                  81          0.333333333333333
>>>  5203929    5497271            293342
>>>      3a            44                 141         0.312056737588652
>>>  28792      552044              523252
>>>
>>> When I use sapply(dataframe,mode) to check the modes of the columns,
>>> this is my output:
>>>
>>>      island_id     refseq_better             total
>>>  refseq_proportion
>>>       "numeric"         "numeric"         "numeric"          
>>> "numeric"
>>>       fiveprime        threeprime       island_size
>>>       "numeric"         "numeric"         "numeric"
>>
>> So?
>>
>>> mode(factor(1:10))
>> [1] "numeric"
>>
>> Storage mode is not the right question. "class" is the correct  
>> question.
>> Best would be to try is.factor()
>
> Looking at the error message, the problem does appear to be with
> storage mode ... is this affected by whether the variables are
> factors? Note this part of the error:
>
> Error in storage.mode(y) <- "double" :
> invalid to change the storage mode of a factor
>
>>
>>
>>> How do I need to change the format of my data frame so that I do not
>>> get the above error?
>>
>> Figure out which of your columns are factors and apply the FAQ 7.12
>>
>> --
>> David.
>>>
>>> Thanks!
>>>
>>> Alison Callahan
>>> PhD candidate
>>
>>
>> David Winsemius, MD
>> West Hartford, CT
>>
>>
> Thanks,
>
> Alison

David Winsemius, MD
West Hartford, CT