Bug in by() function which works for some FUN argument and does not work for others
On 15/04/2016 4:16 AM, Akhilesh Singh 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:
See their errata page http://personal.bgsu.edu/~mrizzo/Rx/Rx-errata.txt. They corrected "mean" to "colMeans". Duncan Murdoch
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$Gender: Male FSIQ VIQ PIQ Weight Height MRI_Count 115.00000 115.25000 111.60000 166.44444 71.43158 954855.40000 I do not know how could the writers of the book have produced the above results by by() function. But, when I could not reproduce these results, then I thought that probably, this could possibly be due to some missing values NA's in Weight and Height variables. Then I tried the above code for the "mtcars" dataset for INDICES=mtcars$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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______________________________________________ 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.