Re: [R] try/tryCatch
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
[R] try/tryCatch
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.
Re: [R] try/tryCatch
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.
[[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.
Re: [R] 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@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
__
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.
[R] try / tryCatch for download.file( ) within a for loop when URL does not exist
I am trying to download a bunch of files from a server, for which I am
using download.file( ) within a for loop. The script is working fine
except until download.file hits a URL which has no file, at which
point it exits. I want to change this behavior to simple log the
failure and maintain state within the for loop and iterate to next. I
read about try / tryCatch but am having trouble understanding what/how
it does. Thanks.
#begin script
date - as.POSIXlt(as.Date(2007-10-15, %Y-%m-%d))
for (i in 1:difftime(as.POSIXlt(as.Date(2007-10-15,
%Y-%m-%d)),2007-10-01))
{
if (date$wday != 0 date$wday != 6) {
datestr - as.character(date, %d%m%y) #make date character string
ddmmyy
url -
paste(http://www.bseindia.com/bhavcopy/eq,datestr,_csv.zip,sep=;)
file - paste(C:/,datestr,_csv.zip,sep=)
#options(show.error.messages = FALSE)
#options(warn = -1)
try(download.file(url, destfile = file, quiet = TRUE, mode = wb),
finally = cat(OK:,url,\n))
date - as.POSIXlt(as.Date(date - 86400))
} else {date - as.POSIXlt(as.Date(date - 86400))}
}
# end script
Thanks,
Vishal Belsare
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] try / tryCatch for download.file( ) within a for loop when URL does not exist
Jim,
Thanks. Actually I just got it working a few minutes ago with:
tryCatch({download.file(url, destfile = file, quiet = FALSE, mode =
wb)}, silent = FALSE, condition = function(err) { } )
but I like your suggestion better. I'll attempt to log the list of
url's downloaded ok and those which encountered an error. Thanks!
Vishal
On 10/17/07, jim holtman [EMAIL PROTECTED] wrote:
I think this is closer to what you want. You can determine what you
want to do; this one just goes to the next iteration:
date - as.POSIXlt(as.Date(2007-10-15, %Y-%m-%d))
for (i in 1:difftime(as.POSIXlt(as.Date(2007-10-15,
%Y-%m-%d)),2007-10-01))
{
if (date$wday != 0 date$wday != 6) {
datestr - as.character(date, %d%m%y) #make date character
string ddmmyy
url -
paste(http://www.bseindia.com/bhavcopy/eq,datestr,_csv.zip,sep=;)
file - paste(C:/,datestr,_csv.zip,sep=)
#options(show.error.messages = FALSE)
#options(warn = -1)
err - try(download.file(url, destfile = file, quiet = TRUE,
mode = wb))
if (class(err) == try-error) next # skip this iteration on error
date - as.POSIXlt(as.Date(date - 86400))
} else {date - as.POSIXlt(as.Date(date - 86400))}
}
On 10/16/07, Vishal Belsare [EMAIL PROTECTED] wrote:
I am trying to download a bunch of files from a server, for which I am
using download.file( ) within a for loop. The script is working fine
except until download.file hits a URL which has no file, at which
point it exits. I want to change this behavior to simple log the
failure and maintain state within the for loop and iterate to next. I
read about try / tryCatch but am having trouble understanding what/how
it does. Thanks.
#begin script
date - as.POSIXlt(as.Date(2007-10-15, %Y-%m-%d))
for (i in 1:difftime(as.POSIXlt(as.Date(2007-10-15,
%Y-%m-%d)),2007-10-01))
{
if (date$wday != 0 date$wday != 6) {
datestr - as.character(date, %d%m%y) #make date character string
ddmmyy
url -
paste(http://www.bseindia.com/bhavcopy/eq,datestr,_csv.zip,sep=;)
file - paste(C:/,datestr,_csv.zip,sep=)
#options(show.error.messages = FALSE)
#options(warn = -1)
try(download.file(url, destfile = file, quiet = TRUE, mode = wb),
finally = cat(OK:,url,\n))
date - as.POSIXlt(as.Date(date - 86400))
} else {date - as.POSIXlt(as.Date(date - 86400))}
}
# end script
Thanks,
Vishal Belsare
__
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
Cincinnati, OH
+1 513 646 9390
What is the problem you are trying to solve?
__
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.
