[R] Fwd: as.list

Wed Oct 27 22:02:37 CEST 2010

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...

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.