[R] getting the by() function to work properly

[chao gai]

Hi Jasper,

For me it seems that you are fooling around with attach() or something.
For one thing, it will not work like this,:
e.g. twodied=x[died==2,]    is the first statement
died is not locally defined, hence it is gotten from somewhere else...
For the second thing, this will throw an error:
by(ss3, sub, f3)
sub is defind (unless attached from some data.frame), it is a statement.
Both these seem to suggest that somewhere there is a version of your dataframe 
attached from which values are being read. 
As a quick fix I made the following:
f3 <- function(x) {
   attach(x)
   twodied <- x[died==2,]
   twosaved=x[saved==2,]
   hit2=x[saved==2 & choice=="+",]
   fa2=x [died==2 & choice=="+",]
   d2=(qnorm(((nrow(hit2))/(nrow(twosaved))))-qnorm((nrow(fa2))/(nrow(twodied))))
   hitrate=((nrow(hit2))/(nrow(twosaved)))
   FArate=((nrow(fa2))/(nrow(twodied)))
   zhit2=qnorm(((nrow(hit2))/(nrow(twosaved))))
   zfa2=qnorm((nrow(fa2))/(nrow(twodied)))
   B2= -.5*(zhit2+zfa2)
   tp2=mean(twosaved$resp)
   ta2=mean(twodied$resp)
   tpsd2=sd(twosaved$resp)
   tasd2=sd(twodied$resp)
   dmj2=((tp2-ta2)/((tasd2+tpsd2)/2))
   detach(x)
   L=list(d2=d2,B2=B2,dmj2=dmj2,tpsd2=tpsd2,tasd2=tasd2,tp2=tp2,ta2=ta2,hitrate=hitrate,FArate=FArate)
   return(L)
}
f3(SS2)

by(SS2, SS2$sub, f3)

It did not throw an error for me.

As a note, could you not use table() or xtabs() for some of these 
calculations? All this nrow() stuff does not look very efficient.

Kees

On Monday 23 October 2006 04:49, Jancik, Jasper F. wrote:
> Hola everyone,
>
> Solving this issue would be a huge time saver for analyzing my thesis data,
> so I'll try to be as concise as possible and hope that someone can give me
> a hand.
>
> I am trying to run a function that I created, which works fine until I try
> to use it with the by function.  That function is listed at the bottom (f3)
> just in case that might be the issue.  Essentially I have compiled a large
> list of data coming from about 30 subjects with 88 trials each and I am
> trying to get that function to apply to each subject without having to
> manually attach each subject's data.  The entire filename is 'ss2' so when
> i run
>
> >ss2f3=f3(ss2)
> >ss2f3
>
> everything is fine.  However when I try to use the by() function:
> >by(ss3, sub, f3)
>
> #sub=subject header in the data
> I get the error message: " Error in var(x, na.rm = na.rm) : missing
> observations in cov/cor " There are no missing observations anywhere in the
> data so I'm really confused as to how this is happening.  My professor
> thought it might have something to do with the variance calculations in the
> function, so when we had it remove bad data the function would run, however
> it did not calculate everything and it erroneously gave the exact same
> calculations for each subject.
>
> I even get the message when I try to manually subset the data e.g.:
> > s2f3=f3(alldata[sub==2,])
>
> "Error in var(x, na.rm = na.rm) : missing observations in cov/cor"
>
> I hope I've provided all the necessary info (the data set is attached just
> in case anyone has the time to make it work), but I'd be glad to give more
> if its needed.  I would really appreciate any suggestions at all.  Thanks
> in advance.
>
>
>
> f3=function(x) {
> +
> +  twodied=x[died==2,];
> +  twosaved=x[saved==2,];
> +  hit2=x[saved==2 & choice=="+",];
> +  fa2=x [died==2 & choice=="+",];
> d2=(qnorm(((nrow(hit2))/(nrow(twosaved))))-qnorm((nrow(fa2))/(nrow(twodied)
>))); +  hitrate=((nrow(hit2))/(nrow(twosaved)));
> FArate=((nrow(fa2))/(nrow(twodied))); + 
> zhit2=qnorm(((nrow(hit2))/(nrow(twosaved))));zfa2=qnorm((nrow(fa2))/(nrow(t
>wodied)));B2= -.5*(zhit2+zfa2); +  tp2=mean(twosaved$resp);
> +  ta2=mean(twodied$resp);
> +  tpsd2=sd(twosaved$resp);
> +  tasd2=sd(twodied$resp);
> +  dmj2=((tp2-ta2)/((tasd2+tpsd2)/2));
> +
> +
> L=list(d2=d2,B2=B2,dmj2=dmj2,tpsd2=tpsd2,tasd2=tasd2,tp2=tp2,ta2=ta2,hitrat
>e=hitrate,FArate=FArate) }
>
>
> Jasper Jancik
> 910.352.7546