[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 05:47:57 CET 2015
Rolf,
Thank you!
John
> 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)
> On Dec 27, 2015, at 10:40 PM, Rolf Turner <r.turner at auckland.ac.nz> wrote:
>
>
> 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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