You are trying to take the mean of data frames. There is no
"data.frame" method for mean().
Try:
by(hold,Arm,function(x){sapply(x,mean)})
BTW what's the point of "na.rm=TRUE" in your call? There are no missing
values in the data that you present.
In future, please use dput() to present your data; it makes life a lot
easier for respondents.
cheers,
Rolf
--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
On 28/12/15 15:55, John Sorkin wrote:
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
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