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

On Apr 16, 2016, at 2:03 AM, Akhilesh Singh <

akhileshsingh.igkv at gmail.com> wrote:

Dear All,

I have got your core message, that it is my responsibility to determine

whether any particular function in my version of R satisfies the language
requirements at the time of your use. Jim Albert and Maria Rizzo must have
used their code, which was permitted in the R-code of their time (2012).

Therefore, I have now modified my R-code, as per R-3..2.4 version,

according to my requirement as follows, which is working for my 'brain'
data set, whose output is reproduced below for your information please:

by(brain[,-1], INDICES=list(Gender=brain$Gender), FUN=function(x,

na.rm=FALSE) sapply(x, mean, na.rm=na.rm), na.rm=TRUE)

Gender: Female
      FSIQ        VIQ        PIQ     Weight     Height  MRI_Count
   111.900    109.450    110.450    137.200     65.765 862654.600

--------------------------------------------------------------------------------------------------

Gender: Male
        FSIQ          VIQ          PIQ       Weight       Height

MRI_Count

   115.00000    115.25000    111.60000    166.44444     71.43158

954855.40000

Yes. that is certainly a workable alternative, although I thought the
question of "how to to it" had been effectively answered with the
suggestion from Adrian Dusa to use colMeans. It, too, has an `na.rm=TRUE`
option

I was only responding to your plaintive complaint that the current version
of R had a "bug" because it was not behaving as promised by an introductory
text with a three year-old publishing date.

--
David.

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 2:24 PM, David Winsemius <dwinsemius at comcast.net>

wrote:

On Apr 15, 2016, at 1:16 AM, Akhilesh Singh <

akhileshsingh.igkv at gmail.com> wrote:

Dear All,

Thanks for your help. However, I would like to draw your attention to

the

following:

Actually, I was replicating the Example 2.3, using the dataset
"brainsize.txt" given in Section 2.3.3 ("Summarize by group") at page

55,

of a famous book "R by Example" written by "Jim Albert and Maria Rizzo"
published in Springers (2012) in a Use R! Series. The output of the

by()

function printed in the book is being reproduced below for information

to

all:

by(data=brain[, -1], INDICES=brain$Gender, FUN=mean, na.rm=TRUE)

brain$Gender: Female
FSIQ VIQ PIQ Weight Height MRI_Count
111.900 109.450 110.450 137.200 65.765 862654.600
------------------------------------------------------------
brain$Gender: Male
FSIQ  VIQ    PIQ       Weight    Height   MRI_Count
115.00000 115.25000 111.60000 166.44444 71.43158 954855.40000


I do not know how could the writers of the book have produced the above
results by by() function.

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:

methods(mean)

 [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

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--
Adrian Dusa
University of Bucharest
Romanian Social Data Archive
Soseaua Panduri nr.90
050663 Bucharest sector 5
Romania

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