try/tryCatch
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 at fixef[1]
a[ii,2]=lm1 at 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 at 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 at 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 at fixef[1]
a[ii,2]=lm1 at 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 at fixef[1]
a[ii,2]=lm1 at 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 at gmail.com
cell: +49 -0176-87786557
T?bingen, Germany, 72070
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Lisa Wang email: wang.lisay at gmail.com cell: +49 -0176-87786557 T?bingen, Germany, 72070