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.li...@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 <jholt...@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.li...@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.li...@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.li...@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]]
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and provide commented, minimal, self-contained, reproducible code.
