R help - Aug 2010 - try-error within for loop

Dear all,

I run a loop wrapped in try(), and for each of the rows where
"try-error" is true I want to fill that row with NA (at the moment it
is
omitted). So I would expect to get a dataframe with 1000 rows some of
which would be empty, but instead I get a dataframe  with 995 rows. In
this case missing 5 rows were omitted.
Any suggestions?

Thanks,
Olga

----------------

result<-list()
for(i in 1:1000)try({
hclass<-mydata2$tclass[mydata2$tspecies%in%com[[i]][[5]][[1]]]
horder<-mydata2$torder[mydata2$tspecies%in%com[[i]][[5]][[1]]]
hfamily<-mydata2$tfamily[mydata2$tspecies%in%com[[i]][[5]][[1]]]
hgenus<-mydata2$tgenus[mydata2$tspecies%in%com[[i]][[5]][[1]]]
hspecies<-mydata2$tspecies[mydata2$tspecies%in%com[[i]][[5]][[1]]]
hier<-cbind(hspecies,hgenus,hfamily,horder,hclass)
s<-nrow(hier) 
s<-ifelse(s>1000,s/10,s) 
taxa<-taxa2dist(hier[sample(s,replace=F),])
abd<-t(cbind(c(1:s),rep(1,s)))
taxdiv<-taxondiveO(abd,taxa)
if(class(result)=="try-error") result[[i]] <- NA  
else result[[i]] <-taxdiv #it doesnt work
result[[i]]<-as.data.frame(result[[i]])[1,]},silent=T)
taxind<-do.call(rbind,result)

taxind[1:5,]
number        D    Dstar   Lambda    Dplus    SDplus
1     589 94.72456 94.93875 142.4468 94.88140  55885.15
2     428 80.38656 80.63660 328.7728 80.90432  34627.05
3     282 88.03613 88.45139 332.8963 88.53554  24967.02
4    1320 80.43822 80.51943 328.1416 80.63355 106436.29
5    1077 80.43121 80.53073 287.2267 80.62954  86838.01

and instead I want to see NA where appropriate

taxind[1:5,]
number        D    Dstar   Lambda    Dplus    SDplus
1     589 94.72456 94.93875 142.4468 94.88140  55885.15
2     428 80.38656 80.63660 328.7728 80.90432  34627.05
3     282 88.03613 88.45139 332.8963 88.53554  24967.02
4     NA NA NA NA NA NA
5    1077 80.43121 80.53073 287.2267 80.62954  86838.01

Assigning the value directly to result[i] would give a null to result. Like
that:

result[[i]]<-taxondiveO(abd,taxa)
result[[i]]<-as.data.frame(result[[i]])[1,]

In fact your code's result should have null elements in it. You lost your
nulls through do.call process.

I can't find a way to assign the value of error into a object. So, try()
inside loop should work. Like

for (....) {
if (class(try(...,silent=T))=="try-error") result[[i]] <- NA
...
}



-----
A R learner.
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Wu Gong wrote:
> So, try() inside loop should work. Like 
> 
> for (....) { 
> if (class(try(...,silent=T))=="try-error") result[[i]] <- NA 
> ... 
> } 
Thanks a lot, it worked for me!

Cheers
Olga