[R] by gives no results, gives warning that data are non-numeric, but the data appears to be numeric.

John Sorkin jsorkin at grecc.umaryland.edu
Mon Dec 28 03:55:44 CET 2015 

When I run by, I get an error message and no results. Any help in understanding what is wrong would be appreciated.
 
Error message:
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

 
Results:
Arm: MUFA
[1] NA
----------------------------------------------------------------------------------------------------------------------- 
Arm: PUFA
[1] NA

Code:
by(hold,Arm,mean,na.rm=TRUE)

I don't understand why I am getting the error message, and why I am not getting any results. I don't believe my data are non-numeric. 

BY str works fine and confirms that the data are numeric
> by(hold,Arm,str)
'data.frame':	23 obs. of  3 variables:
 $ Wtscr: num  97.2 103.9 58.2 130.9 135 ...
 $ Wt0  : num  96.2 106.1 56.7 127.4 133.1 ...
 $ Wt6  : num  93.8 101.7 55.5 127.6 130.9 ...
'data.frame':	16 obs. of  3 variables:
 $ Wtscr: num  120.2 104.6 100.1 74.8 112.6 ...
 $ Wt0  : num  117.2 105.3 99.5 75.7 110.7 ...
 $ Wt6  : num  114.6 104.8 84.5 77.7 107.4 ...
 Here is a listing of my data:
> hold
   Wtscr   Wt0    Wt6
1  120.2 117.2 114.60
2  104.6 105.3 104.80
3   97.2  96.2  93.80
4  103.9 106.1 101.70
5   58.2  56.7  55.50
6  130.9 127.4 127.60
7  135.0 133.1 130.90
8  100.1  99.5  84.50
9  130.3 115.3 115.80
10 150.5 148.7 133.40
11  74.8  75.7  77.70
12 112.6 110.7 107.40
13  90.0  91.0  83.40
14 139.1 138.5 126.70
15  99.1  96.4  95.70
16 108.3 107.5 109.30
17  75.1  72.9  72.20
18  97.5 102.1  98.50
19 202.2  90.1  90.60
20  91.7  89.4  93.40
21 102.1 102.2 100.80
22 116.9 118.9 118.00
23  94.6  95.3  90.30
24 122.2 117.0 117.00
25 105.6 103.3 103.60
26  96.9  96.8  98.80
27 102.9 100.3  89.00
28 115.8 118.5 117.30
29  95.7  96.2  95.40
30  88.2  86.9  88.30
31 108.7 108.8 108.80
32  89.2  88.6  81.20
33  86.8  86.5  82.70
34 135.5 130.1 125.40
35 112.5 113.9 111.45
36 111.0 105.3 109.50
37 103.4 100.5  95.50
38 117.6 117.4 101.40
39 116.7 118.5 101.80

The INDEX is clearly a factor: 
> Arm
 [1] PUFA PUFA MUFA MUFA MUFA MUFA MUFA PUFA MUFA MUFA PUFA PUFA PUFA MUFA MUFA PUFA PUFA PUFA MUFA MUFA MUFA MUFA MUFA PUFA MUFA MUFA PUFA MUFA PUFA MUFA PUFA
[32] MUFA MUFA MUFA MUFA MUFA PUFA PUFA PUFA
Levels: MUFA PUFA

The data and the index have the same length:
> cbind(hold,Arm)
   Wtscr   Wt0    Wt6  Arm
1  120.2 117.2 114.60 PUFA
2  104.6 105.3 104.80 PUFA
3   97.2  96.2  93.80 MUFA
4  103.9 106.1 101.70 MUFA
5   58.2  56.7  55.50 MUFA
6  130.9 127.4 127.60 MUFA
7  135.0 133.1 130.90 MUFA
8  100.1  99.5  84.50 PUFA
9  130.3 115.3 115.80 MUFA
10 150.5 148.7 133.40 MUFA
11  74.8  75.7  77.70 PUFA
12 112.6 110.7 107.40 PUFA
13  90.0  91.0  83.40 PUFA
14 139.1 138.5 126.70 MUFA
15  99.1  96.4  95.70 MUFA
16 108.3 107.5 109.30 PUFA
17  75.1  72.9  72.20 PUFA
18  97.5 102.1  98.50 PUFA
19 202.2  90.1  90.60 MUFA
20  91.7  89.4  93.40 MUFA
21 102.1 102.2 100.80 MUFA
22 116.9 118.9 118.00 MUFA
23  94.6  95.3  90.30 MUFA
24 122.2 117.0 117.00 PUFA
25 105.6 103.3 103.60 MUFA
26  96.9  96.8  98.80 MUFA
27 102.9 100.3  89.00 PUFA
28 115.8 118.5 117.30 MUFA
29  95.7  96.2  95.40 PUFA
30  88.2  86.9  88.30 MUFA
31 108.7 108.8 108.80 PUFA
32  89.2  88.6  81.20 MUFA
33  86.8  86.5  82.70 MUFA
34 135.5 130.1 125.40 MUFA
35 112.5 113.9 111.45 MUFA
36 111.0 105.3 109.50 MUFA
37 103.4 100.5  95.50 PUFA
38 117.6 117.4 101.40 PUFA
39 116.7 118.5 101.80 PUFA

But the by function does not work!
> by(hold,Arm,mean,na.rm=TRUE)
Arm: MUFA
[1] NA
----------------------------------------------------------------------------------------------------------------------- 
Arm: PUFA
[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


Perhaps this is a hint, print does not give two separate group:
> by(hold,Arm,print)
   Wtscr   Wt0    Wt6
3   97.2  96.2  93.80
4  103.9 106.1 101.70
5   58.2  56.7  55.50
6  130.9 127.4 127.60
7  135.0 133.1 130.90
9  130.3 115.3 115.80
10 150.5 148.7 133.40
14 139.1 138.5 126.70
15  99.1  96.4  95.70
19 202.2  90.1  90.60
20  91.7  89.4  93.40
21 102.1 102.2 100.80
22 116.9 118.9 118.00
23  94.6  95.3  90.30
25 105.6 103.3 103.60
26  96.9  96.8  98.80
28 115.8 118.5 117.30
30  88.2  86.9  88.30
32  89.2  88.6  81.20
33  86.8  86.5  82.70
34 135.5 130.1 125.40
35 112.5 113.9 111.45
36 111.0 105.3 109.50
   Wtscr   Wt0   Wt6
1  120.2 117.2 114.6
2  104.6 105.3 104.8
8  100.1  99.5  84.5
11  74.8  75.7  77.7
12 112.6 110.7 107.4
13  90.0  91.0  83.4
16 108.3 107.5 109.3
17  75.1  72.9  72.2
18  97.5 102.1  98.5
24 122.2 117.0 117.0
27 102.9 100.3  89.0
29  95.7  96.2  95.4
31 108.7 108.8 108.8
37 103.4 100.5  95.5
38 117.6 117.4 101.4
39 116.7 118.5 101.8
Arm: MUFA
   Wtscr   Wt0    Wt6
3   97.2  96.2  93.80
4  103.9 106.1 101.70
5   58.2  56.7  55.50
6  130.9 127.4 127.60
7  135.0 133.1 130.90
9  130.3 115.3 115.80
10 150.5 148.7 133.40
14 139.1 138.5 126.70
15  99.1  96.4  95.70
19 202.2  90.1  90.60
20  91.7  89.4  93.40
21 102.1 102.2 100.80
22 116.9 118.9 118.00
23  94.6  95.3  90.30
25 105.6 103.3 103.60
26  96.9  96.8  98.80
28 115.8 118.5 117.30
30  88.2  86.9  88.30
32  89.2  88.6  81.20
33  86.8  86.5  82.70
34 135.5 130.1 125.40
35 112.5 113.9 111.45
36 111.0 105.3 109.50
----------------------------------------------------------------------------------------------------------------------- 
Arm: PUFA
   Wtscr   Wt0   Wt6
1  120.2 117.2 114.6
2  104.6 105.3 104.8
8  100.1  99.5  84.5
11  74.8  75.7  77.7
12 112.6 110.7 107.4
13  90.0  91.0  83.4
16 108.3 107.5 109.3
17  75.1  72.9  72.2
18  97.5 102.1  98.5
24 122.2 117.0 117.0
27 102.9 100.3  89.0
29  95.7  96.2  95.4
31 108.7 108.8 108.8
37 103.4 100.5  95.5
38 117.6 117.4 101.4
39 116.7 118.5 101.8

But summary works as expected, giving two groups of results!
> by(hold,Arm,summary)
Arm: MUFA
     Wtscr             Wt0             Wt6       
 Min.   : 58.20   Min.   : 56.7   Min.   : 55.5  
 1st Qu.: 95.75   1st Qu.: 92.7   1st Qu.: 92.0  
 Median :105.60   Median :103.3   Median :101.7  
 Mean   :112.75   Mean   :106.3   Mean   :104.0  
 3rd Qu.:130.60   3rd Qu.:118.7   3rd Qu.:117.7  
 Max.   :202.20   Max.   :148.7   Max.   :133.4  
----------------------------------------------------------------------------------------------------------------------- 
Arm: PUFA
     Wtscr             Wt0              Wt6        
 Min.   : 74.80   Min.   : 72.90   Min.   : 72.20  
 1st Qu.: 97.05   1st Qu.: 98.67   1st Qu.: 87.88  
 Median :104.00   Median :103.70   Median : 99.95  
 Mean   :103.15   Mean   :102.54   Mean   : 97.58  
 3rd Qu.:113.62   3rd Qu.:112.28   3rd Qu.:107.75  
 Max.   :122.20   Max.   :118.50   Max.   :117.00  

BY also shows that there are no NAs in the data, and the BY works properly.
> by(hold,Arm,is.na)
Arm: MUFA
   Wtscr

John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing) 

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