[R] Fwd: as.list

Wed Oct 27 22:19:09 CEST 2010

On Oct 27, 2010, at 4:02 PM, Sibylle Stöckli wrote:

> Dear Ivan,
>
> Thanks a lot. I managed to create a list (KANE.LIST) out of my data  
> set (KANE).
>
> There is still the problem within the barplot function (non-numeric  
> argument). There are no NA values and just the variable names are  
> non-numeric...

Except the whole object is a list and barplot expects a vector or  
matrix. This works subject to the varying definitions of what "works"  
might mean and the narrow ylim limits that you are placing on the data.

barplot(as.matrix(KANE[, 5:9]), ylim=c(-20,20), col=as.numeric(KANE 
$diversity))

>
> Thanks
> Sibylle
>
> > PA<-read.table("Biotree_partitioning.txt", header=TRUE)
> > KANE<-PA[PA$site=="KA"&PA$part=="NE",]
> > KANE.LISTs<-subset(KANE, select=c(5:9))
> > KANE.LIST<-as.list(KANE.LISTs)
> > names(KANE.LIST)<-colnames(KANE)[-c(1:4)]
> > for(i in colnames(KANE)[-c(1:4)]){
> + 	KANE.LIST[[i]]
> + 	}
> >
> > barplot(KANE.LIST, ylim=c(-20,20), col=as.numeric(KANE$diversity))
> Error in -0.01 * height : non-numeric argument to binary operator
> >
> > KANE.LIST
> $H5
> [1] -5.33 -1.17  3.17 -1.83 -1.17  2.50  5.33 -3.78 -8.69  0.33  
> -2.83 -4.08
>
> $H8
> [1] -19.58  -7.33   6.17  -3.83   8.17  21.33  16.67  -9.22 -23.94    
> 2.56 -15.00 -15.92
>
> $S5
> [1] -2.75 12.17 16.17  5.00  5.50  7.33 10.56 14.00  4.11  7.33   
> 9.75  8.67
>
> $S8
> [1] -11.96   2.50   3.00  -4.83  -9.33   3.17   6.00   4.33  -7.08   
> -4.56   4.08 -12.08
>
> $C8
> [1] -0.23 -0.07  0.09  0.03  0.09  0.22  0.13 -0.07 -0.22  0.01  
> -0.19 -0.15
>
> > KANE
>   site part plot diversity    H5     H8    S5     S8    C8
> 1    KA   NE    3         2 -5.33 -19.58 -2.75 -11.96 -0.23
> 2    KA   NE    6         2 -1.17  -7.33 12.17   2.50 -0.07
> 3    KA   NE    7         2  3.17   6.17 16.17   3.00  0.09
> 4    KA   NE   10         2 -1.83  -3.83  5.00  -4.83  0.03
> 5    KA   NE   12         2 -1.17   8.17  5.50  -9.33  0.09
> 6    KA   NE   16         2  2.50  21.33  7.33   3.17  0.22
> 7    KA   NE    4         3  5.33  16.67 10.56   6.00  0.13
> 8    KA   NE    5         3 -3.78  -9.22 14.00   4.33 -0.07
> 9    KA   NE    9         3 -8.69 -23.94  4.11  -7.08 -0.22
> 10   KA   NE   15         3  0.33   2.56  7.33  -4.56  0.01
> 11   KA   NE    2         4 -2.83 -15.00  9.75   4.08 -0.19
> 12   KA   NE    8         4 -4.08 -15.92  8.67 -12.08 -0.15
>
> On 27.10.2010, at 15:26, Ivan Calandra wrote:
>
>> Hi Sibylle,
>>
>> I was about to send you an email, but I'll modify it thanks to your  
>> second!
>>
>> Is PA what you expect? Does it contain the data you want?
>> You should provide some sample data.
>> If the importation worked, try to copy/paste the output of  
>> dput(PA), which we can then copy/paste in our console. That  
>> function is great to share R objects. If your dataset is too big,  
>> try dput(head(PA)), which outputs only the first line of it.
>>
>> Regarding the selection, I think you're doing it wrong. which()  
>> returns a logical vector, which is probably not what you're looking  
>> for.
>> Maybe:
>> KANE <- PA[PA$Site=="KA" & PA$part=="NE", ]  ## the last comma is  
>> important to select all the columns for the rows you've chosen
>> Read ?"[" or ?subset to understand more
>>
>> The barplot() might work better then.
>>
>> HTH,
>> Ivan
>>
>> Le 10/27/2010 15:09, "Sibylle Stöckli" a écrit :
>>> -------- Original-Nachricht --------
>>> Datum: Wed, 27 Oct 2010 15:03:48 +0200
>>> Von: "Sibylle Stöckli"<sibylle.stoeckli at gmx.ch>
>>> An: Rhelp<r-help at r-project.org>
>>> Betreff: as.list
>>>
>>> Dear R-users
>>>
>>> sorry, here Rcode included (attachment has been removed)
>>>
>>> I would like to read a txt file as list, to select rows and  
>>> columns, and to create barplots.
>>>
>>> (1) selection of parameter site and part: ok
>>> (2) read txt file as list: problem with (1) as there are NA's (the  
>>> lines not selected)
>>>
>>> (3) barplot: 5 different groups of bars (the selected columns  
>>> H5,H8, S5,S8, C8). In each group 4 different bars (parameter  
>>> diversity)
>>> -->  error in -0.01*height: non-numeric argument to binary operator
>>>
>>> PROBLEM
>>> As (2) gives NULL, I think that there is a mistake in my r-script  
>>> with the vector/list function.
>>>
>>> Thanks
>>> Sibylle
>>>
>>> R-Code
>>>
>>> PA<-read.table("Biotree_partitioning.txt", header=TRUE)
>>> KANE<-which((PA$site=="KA")&(PA$part=="NE"))
>>> KANE.LIST<-vector("list", dim(PA[KANE,])[2]-4)
>>> KANE.LIST
>>>
>>> barplot(KANE.LIST, col=as.numeric(PA$diveristy))
>>>
>>>
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> 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.
>>
>> -- 
>> Ivan CALANDRA
>> PhD Student
>> University of Hamburg
>> Biozentrum Grindel und Zoologisches Museum
>> Abt. Säugetiere
>> Martin-Luther-King-Platz 3
>> D-20146 Hamburg, GERMANY
>> +49(0)40 42838 6231
>> ivan.calandra at uni-hamburg.de
>>
>> **********
>> http://www.for771.uni-bonn.de
>> http://webapp5.rrz.uni-hamburg.de/mammals/eng/mitarbeiter.php
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> 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.
>
> ______________________________________________
> R-help at r-project.org mailing list
> 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.

David Winsemius, MD
West Hartford, CT