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

[Alison Callahan]

Hi again

On Fri, Oct 8, 2010 at 1:13 PM, David Winsemius <dwinsemius at comcast.net> wrote:
>
> 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)  # ??
>
My usage of lm() was as follows:

lmout <- lm(refseq_proportion~fiveprime,data=props_df)

> 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
>
>