Bug in by() function which works for some FUN argument and does not work for others

Fri, Apr 15, 2016 1:54 AM

There was in the not-so-distant past a function named `mean.data.frame` which would have "worked" in that instance. That function was removed. I thought you could  find the exact date of that action by searching the NEWS but failed. Reviewing the citations of `mean.data.frame` in the r-help archives I see that users were being warned that its use was deprecated in mid 2012.  It's very possible that the authors of a book in 2012 were using an earlier version of R that had that facility available to them before it was deprecated. With a more than current version of R 3.3.0 and a modest number of loaded packages I see this:

[1] mean,ANY-method          mean,Matrix-method       mean,Raster-method      
 [4] mean,sparseMatrix-method mean,sparseVector-method mean.Date               
 [7] mean.default             mean.difftime            mean.POSIXct            
[10] mean.POSIXlt             mean.yearmon*            mean.yearqtr*           
[13] mean.zoo*

It is your responsibility to determine whether any particular function in your version of R satisfies the language requirements at the time of your use. Jim Albert and Maria Rizzo do not set the standards for what is an evolving piece of software.

David.


> But, when I could not reproduce these results,
> then I thought that probably, this could possibly be due to some missing
> values NA's in Weight and Height variables. Then I tried the above code for
> the "mtcars" dataset for INDICES=mtcars$am. When I found the same results
> here too, then I reported the case in "r-help at R-project.org".
> 
> With best regards,
> 
> Dr. A.K. Singh
> Head, Department of Agril. Statistics
> Indira Gandhi Krishi Vishwavidyalaya, Raipur
> Chhattisgarh, India, PIN-492012
> Mobile: +919752620740
> Email: akhileshsingh.igkv at gmail.com
> 
> On Fri, Apr 15, 2016 at 3:06 AM, Adrian Du?a <dusa.adrian at unibuc.ro> wrote:
> 
>> I think you are not using the best function for what your intentions are.
>> Try:
>> 
>>> by(data=mtcars, INDICES=list(as.factor(mtcars$am)), FUN=colMeans)
>> : 0
>>        mpg         cyl        disp          hp        drat          wt
>>     qsec          vs
>> 17.1473684   6.9473684 290.3789474 160.2631579   3.2863158   3.7688947
>> 18.1831579   0.3684211
>>         am        gear        carb
>>  0.0000000   3.2105263   2.7368421
>> 
>> ---------------------------------------------------------------------------
>> : 1
>>        mpg         cyl        disp          hp        drat          wt
>>     qsec          vs
>> 24.3923077   5.0769231 143.5307692 126.8461538   4.0500000   2.4110000
>> 17.3600000   0.5384615
>>         am        gear        carb
>>  1.0000000   4.3846154   2.9230769
>> 
>> See the difference between colMeans() and mean() in their respective help
>> files.
>> Hth,
>> Adrian
>> 
>> On Thu, Apr 14, 2016 at 11:14 PM, Akhilesh Singh <
>> akhileshsingh.igkv at gmail.com> wrote:
>> 
>>> Dear Sirs,
>>> 
>>> I am Professor at Indira Gandhi Krishi Vishwavidyalaya, Raipur,
>>> Chhattisgarh, India.
>>> 
>>> While taking classes, I found the *by() *function producing following
>>> error
>>> 
>>> when I use FUN=mean or median and some other functions, however,
>>> FUN=summary works.
>>> 
>>> Given below is the output of the example I used on a built-in dataset
>>> "mtcars", along with error message reproduced herewith:
>>> 
>>>> by(data=mtcars, INDICES=list(mtcars$am), FUN=mean)
>>> : 0
>>> [1] NA
>>> ------------------------------------------------------------
>>> : 1
>>> [1] NA
>>> Warning messages:
>>> 1: In mean.default(data[x, , drop = FALSE], ...) :
>>>  argument is not numeric or logical: returning NA
>>> 2: In mean.default(data[x, , drop = FALSE], ...) :
>>>  argument is not numeric or logical: returning NA
>>> 
>>> However, the same by() function works for FUN=summary, given below is the
>>> output:
>>> 
>>>> by(data=mtcars, INDICES=list(mtcars$am), FUN=summary)
>>> : 0
>>>      mpg             cyl             disp             hp
>>> Min.   :10.40   Min.   :4.000   Min.   :120.1   Min.   : 62.0
>>> 1st Qu.:14.95   1st Qu.:6.000   1st Qu.:196.3   1st Qu.:116.5
>>> Median :17.30   Median :8.000   Median :275.8   Median :175.0
>>> Mean   :17.15   Mean   :6.947   Mean   :290.4   Mean   :160.3
>>> 3rd Qu.:19.20   3rd Qu.:8.000   3rd Qu.:360.0   3rd Qu.:192.5
>>> Max.   :24.40   Max.   :8.000   Max.   :472.0   Max.   :245.0
>>>      drat             wt             qsec             vs               am
>>> 
>>> Min.   :2.760   Min.   :2.465   Min.   :15.41   Min.   :0.0000   Min.
>>> :0
>>> 
>>> 1st Qu.:3.070   1st Qu.:3.438   1st Qu.:17.18   1st Qu.:0.0000   1st
>>> Qu.:0
>>> 
>>> Median :3.150   Median :3.520   Median :17.82   Median :0.0000   Median
>>> :0
>>> 
>>> Mean   :3.286   Mean   :3.769   Mean   :18.18   Mean   :0.3684   Mean
>>> :0
>>> 
>>> 3rd Qu.:3.695   3rd Qu.:3.842   3rd Qu.:19.17   3rd Qu.:1.0000   3rd
>>> Qu.:0
>>> 
>>> Max.   :3.920   Max.   :5.424   Max.   :22.90   Max.   :1.0000   Max.
>>> :0
>>> 
>>>      gear            carb
>>> Min.   :3.000   Min.   :1.000
>>> 1st Qu.:3.000   1st Qu.:2.000
>>> Median :3.000   Median :3.000
>>> Mean   :3.211   Mean   :2.737
>>> 3rd Qu.:3.000   3rd Qu.:4.000
>>> Max.   :4.000   Max.   :4.000
>>> ------------------------------------------------------------
>>> : 1
>>>      mpg             cyl             disp             hp             drat
>>> 
>>> Min.   :15.00   Min.   :4.000   Min.   : 71.1   Min.   : 52.0   Min.
>>> :3.54
>>> 1st Qu.:21.00   1st Qu.:4.000   1st Qu.: 79.0   1st Qu.: 66.0   1st
>>> Qu.:3.85
>>> Median :22.80   Median :4.000   Median :120.3   Median :109.0   Median
>>> :4.08
>>> Mean   :24.39   Mean   :5.077   Mean   :143.5   Mean   :126.8   Mean
>>> :4.05
>>> 3rd Qu.:30.40   3rd Qu.:6.000   3rd Qu.:160.0   3rd Qu.:113.0   3rd
>>> Qu.:4.22
>>> Max.   :33.90   Max.   :8.000   Max.   :351.0   Max.   :335.0   Max.
>>> :4.93
>>>       wt             qsec             vs               am         gear
>>> 
>>> Min.   :1.513   Min.   :14.50   Min.   :0.0000   Min.   :1   Min.
>>> :4.000
>>> 
>>> 1st Qu.:1.935   1st Qu.:16.46   1st Qu.:0.0000   1st Qu.:1   1st
>>> Qu.:4.000
>>> 
>>> Median :2.320   Median :17.02   Median :1.0000   Median :1   Median
>>> :4.000
>>> 
>>> Mean   :2.411   Mean   :17.36   Mean   :0.5385   Mean   :1   Mean
>>> :4.385
>>> 
>>> 3rd Qu.:2.780   3rd Qu.:18.61   3rd Qu.:1.0000   3rd Qu.:1   3rd
>>> Qu.:5.000
>>> 
>>> Max.   :3.570   Max.   :19.90   Max.   :1.0000   Max.   :1   Max.
>>> :5.000
>>> 
>>>      carb
>>> Min.   :1.000
>>> 1st Qu.:1.000
>>> Median :2.000
>>> Mean   :2.923
>>> 3rd Qu.:4.000
>>> Max.   :8.000
>>>> 
>>> 
>>> I am using the latest version of *R-3.2.4 on Windows*, however, this error
>>> is being generated in the previous version too,
>>> 
>>> Hope this reporting will get serious attention in debugging.
>>> 
>>> With best regards,
>>> 
>>> Dr. A.K. Singh
>>> Head, Department of Agril. Statistics
>>> Indira Gandhi Krishi Vishwavidyalaya, Raipur
>>> Chhattisgarh, India, PIN-492012
>>> Mobile: +919752620740
>>> Email: akhileshsingh.igkv at gmail.com
>>> 
>>>        [[alternative HTML version deleted]]
>>> 
>>> ______________________________________________
>>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>> 
>> 
>> 
>> 
>> --
>> Adrian Dusa
>> University of Bucharest
>> Romanian Social Data Archive
>> Soseaua Panduri nr.90
>> 050663 Bucharest sector 5
>> Romania
>> 
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

David Winsemius
Alameda, CA, USA

Bug in by() function which works for some FUN argument and does not work for others

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