I would assume that if the code were as follows that the error could the
caught and the loop continued:

metatrials<-function(mydata){

a<-matrix(data=NA, nrow=dim(mydata)[3], ncol=5)
colnames(a)=c("sens", "spec", "corr", "sens_se", "spec_se")

for(ii in 1:dim(mydata)[3]){
    tmp<-mydata[,,ii]
    tmp1<-as.data.frame(tmp)
    names(tmp1)=c("persons", "d1", "tp", "fn", "fp", "fn", "detect", "d0",
"outcome")
    lm1<-try(lmer(outcome~0+d1+d0+(0+d1+d0 | persons), family=binomial,
data=tmp1, nAGQ=3))

    if (!inherits(lm1, 'try-error')){
        a[ii,1]=lm1@fixef[1]
        a[ii,2]=lm1@fixef[2]
        a[ii,3]=vcov(lm1)[1,2]/prod(sqrt(diag(vcov(lm1))))
        a[ii,4:5]=sqrt(diag(vcov(lm1)))
    }
    }
    return(a)
}


On Mon, Mar 18, 2013 at 11:38 AM, lisa <wang.lisay@gmail.com> wrote:

> here is the error:
>
> > aa<-metatrialstry(beta_5_50)
>
> Error in asMethod(object) : matrix is not symmetric [1,2]
>
>
>
> metatrials, the function that i am attempting to convert with
> try/tryCatch, gives me back a matrix with as many rows are there are
> simulations  (z) in the aray with dim(x,y,z). with the data i attached, x
> is 500(number of patients), y is 9 (these are covariates), and z is 500.
>
>
> metatrials<-function(mydata){
>
> a<-matrix(data=NA, nrow=dim(mydata)[3], ncol=5)
> colnames(a)=c("sens", "spec", "corr", "sens_se", "spec_se")
>
> for(ii in 1:dim(mydata)[3]){
>     tmp<-mydata[,,ii]
>     tmp1<-as.data.frame(tmp)
>     names(tmp1)=c("persons", "d1", "tp", "fn", "fp", "fn", "detect", "d0",
> "outcome")
>     lm1<-lmer(outcome~0+d1+d0+(0+d1+d0 | persons), family=binomial,
> data=tmp1, nAGQ=3)
>     a[ii,1]=lm1@fixef[1]
>     a[ii,2]=lm1@fixef[2]
>     a[ii,3]=vcov(lm1)[1,2]/prod(sqrt(diag(vcov(lm1))))
>     a[ii,4:5]=sqrt(diag(vcov(lm1)))
>
>     }
>     return(a)
> }
>
>
> ######################
>
>
> what i want is for the function to go on to the next data set in the array
> and simply return an NA for that line in the metatrials results. so
> basically, just keep going.
>
>
> thanks so much for your help!
>
>
> -Lisa
>
>
> On Mon, Mar 18, 2013 at 4:24 PM, jim holtman <jholtman@gmail.com> wrote:
>
>> It would help if you told us what type of error you are getting and to
>> also provide sample data so that we could run it to see what happens.  I
>> use 'try' a lot to catch errors and have not had any problems with it.
>>
>> On Mon, Mar 18, 2013 at 6:11 AM, lisa <wang.lisay@gmail.com> wrote:
>>
>>> Hi All,
>>>
>>> I have tried every fix on my try or tryCatch that I have found on the
>>> internet, but so far have not been able to get my R code to continue with
>>> the "for loop" after the lmer model results in an error.
>>>
>>> Here is two attemps of my code, the input is a 3D array file, but really
>>> any function would do....
>>>
>>> metatrialstry<-function(mydata){
>>>
>>> a<-matrix(data=NA, nrow=dim(mydata)[3], ncol=5)
>>> #colnames(a)=c("sens", "spec", "corr", "sens_se", "spec_se",
>>> "counter")#colnames(a)=c("sens", "spec", "corr", "sens_se", "spec_se")
>>> k=1
>>> for(ii in 1:dim(mydata)[3]){
>>>     tmp<-mydata[,,ii]
>>>     tmp1<-as.data.frame(tmp)
>>>     names(tmp1)=c("persons", "d1", "tp", "fn", "fp", "fn", "detect",
>>> "d0",
>>> "outcome")
>>>     lm1<-try(lmer(outcome~0+d1+d0+(0+d1+d0 | persons), family=binomial,
>>> data=tmp1, nAGQ=3), silent=T)
>>>     if(class(lm1)[1]!='try-error'){
>>>         a[ii,1]=lm1@fixef[1]
>>>         a[ii,2]=lm1@fixef[2]
>>>         a[ii,3]=vcov(lm1)[1,2]/prod(sqrt(diag(vcov(lm1))))
>>>         a[ii,4:5]=sqrt(diag(vcov(lm1)))
>>>         }
>>>     }
>>>     #k=k+1
>>>     #a[ii,6]=k
>>>
>>>     return(a)
>>> }
>>>
>>> #########################################
>>> ######### try / try catch ###############
>>> #########################################
>>>
>>>
>>>
>>> metatrialstry<-function(mydata){
>>>
>>> a<-matrix(data=NA, nrow=dim(mydata)[3], ncol=5)
>>> #colnames(a)=c("sens", "spec", "corr", "sens_se", "spec_se", "counter")
>>> colnames(a)=c("sens", "spec", "corr", "sens_se", "spec_se")
>>> #a[,6]=rep(0, length(a[,6]))
>>> for(ii in 1:dim(mydata)[3]){
>>>     tmp<-mydata[,,ii]
>>>     tmp1<-as.data.frame(tmp)
>>>     names(tmp1)=c("persons", "d1", "tp", "fn", "fp", "fn", "detect",
>>> "d0",
>>> "outcome")
>>>     lm1<-tryCatch(lmer(outcome~0+d1+d0+(0+d1+d0 | persons),
>>> family=binomial, data=tmp1, nAGQ=3), error=function(e) e)
>>>     a[ii,1]=lm1@fixef[1]
>>>     a[ii,2]=lm1@fixef[2]
>>>     a[ii,3]=vcov(lm1)[1,2]/prod(sqrt(diag(vcov(lm1))))
>>>     a[ii,4:5]=sqrt(diag(vcov(lm1)))
>>>     }
>>>     return(a)
>>> }
>>>
>>>
>>> Any guidance would be greatly appreciated...
>>>
>>> thanks!
>>> Lisa
>>>
>>> --
>>> Lisa Wang
>>> email: wang.lisay@gmail.com
>>> cell: +49 -0176-87786557
>>> Tübingen, Germany, 72070
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>>
>>> ______________________________________________
>>> R-help@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.
>>>
>>>
>>
>>
>> --
>> Jim Holtman
>> Data Munger Guru
>>
>> What is the problem that you are trying to solve?
>> Tell me what you want to do, not how you want to do it.
>
>
>
>
> --
> Lisa Wang
> email: wang.lisay@gmail.com
> cell: +49 -0176-87786557
> Tübingen, Germany, 72070
>
>
>


-- 
Jim Holtman
Data Munger Guru

What is the problem that you are trying to solve?
Tell me what you want to do, not how you want to do it.

	[[alternative HTML version deleted]]

