[R] dimnames in array

[David Winsemius]

On Aug 8, 2012, at 3:19 AM, aleksandr russell wrote:

> Hello,
>
> I'm working with an array; I'm trying to make it so that an array of
> dim(42,2,2) has names whose length corresponds to that of the array,
> and am hoping someone with experience with this can see what I'm not
> doing correctly:
>
>
>
>
> data11 = array(0,c(41,2,2))
>
> y = lsoda(x0,times,fhn$fn.ode,pars)#This is make.fhn() from colloc
> infer package#

>  y = y[,2:3]
>
> data11<-array(0,c(41,2,2))
>
>
> m8<-cbind(.29,1:41)
>    m9<-as.array(m8,dim=c(41,2))
>
>  data11[,1,] = y+m9
>   data11[,2,] = y+m9

I didn't run that code since your difficulties did not seem to have  
anything to do with the values inside the array but only with the  
dimension labeling.
>
> rownames(data2, do.NULL = FALSE, prefix="row")

What is 'data2'?

> varnames=c("V","R")
> colnames(data6)=c("one","two")

Ditto... what is 'data6'?

> colnames(data10)=colnames(data6)
> dimnames(data11)=list(rownames(data2),varnames,colnames(data10))
> data11a<-as.array(data11,dimnames=dimnames(data11))
> attributes(data11a)
>
> #so this seems to print out the array attributes as they
> should be:

For which object?

> two sets of two columns each, and the first column of
> each set is called 'v' and the second 'r'- no problem#

The data11 object had three dimenstions.

>
> now the analysis from colloc infer(I've put it in below*)
> takes this array but will not complete the analysis, saying
>
> 	"Error in `colnames<-`(`*tmp*`, value = c("V", "R")) :
>  length of 'dimnames' [2] not equal to array extent"

Here's one way to label a 41 x 2 x 2 array:

 > dimnames(data11)<- c(list(X=paste0("X",1:41)), list(Y=paste0("Y", 
1:2)), list(Z=paste0("Z",1:2)) )
 > attributes(data11)
$dim
[1] 41  2  2

$dimnames
$dimnames$X
  [1] "X1"  "X2"  "X3"  "X4"  "X5"  "X6"  "X7"  "X8"  "X9"  "X10"  
"X11" "X12" "X13" "X14" "X15" "X16" "X17" "X18" "X19"
[20] "X20" "X21" "X22" "X23" "X24" "X25" "X26" "X27" "X28" "X29" "X30"  
"X31" "X32" "X33" "X34" "X35" "X36" "X37" "X38"
[39] "X39" "X40" "X41"

$dimnames$Y
[1] "Y1" "Y2"

$dimnames$Z
[1] "Z1" "Z2"
>
> When I type in
>
> 	length(dimnames(data11a)[2])
>
> I get the answer:
>
> 	[1] 1
>
> which seems odd when
>
> 	dimnames(data11a)[2]
>
> gives
>
> 	[[1]]
> 	[1] "V" "R"

It is a one element list whose single element is a 2 element vector.

>
> I would like to ask "How can I get the names of the second dimension
> of the array(data11a) to have length "2" ?
>
> It seems to me that the analysis will run if I can make this array
> have the correct length dimnames
>
> I thank you for your help.
>
> ____________
>
>
> *
>  fd.data11a = data11a
>  DEfd11a = Data2fd(fd.data11a, times, bbasis,
>  fdnames=list(NULL,NULL,varnames))
>
>
> profile11a.obj=LS.setup(pars,DEfd11a 
> $coefs,fhn,basisvals=bbasis,lambda,fd.obj=NULL,
>   
> more 
> =NULL,data=data11a,weights=NULL,times=times,quadrature=NULL,eps=1e-6,
>  posproc=FALSE,poslik=FALSE,discrete=FALSE,names=NULL,sparse=FALSE)
> lik = profile11a.obj$lik
> proc = profile11a.obj$proc
> qwts = rep(1/length(knots),length(knots))
>  qwts = qwts %*% t(lambda)
>  weights = array(1,dim(data11a))
>  likmore = make.id()
>  likmore$weights = weights
>  lik = make.SSElik()
>  lik$more = likmore
>  lik$bvals = eval.basis(times,bbasis)
>  procmore = make.fhn()
>  procmore$weights = qwts
>  procmore$qpts = qpts
>  procmore$names = varnames
>  procmore$parnames = parnames
>  proc = make.SSEproc()
>  proc$more = procmore
>  proc$bvals = list(bvals = eval.basis(procmore$qpts,bbasis,0),
>  dbvals = eval.basis(procmore$qpts,bbasis,1))
> res11a = inneropt(coefs, times=times, data=data11a, lik=lik,  
> proc=proc,
>  pars=spars, in.meth='nlminb', control.in=control.out)


-- 
David Winsemius, MD
Alameda, CA, USA