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) >ss2f3everything 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(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)); + + L=list(d2=d2,B2=B2,dmj2=dmj2,tpsd2=tpsd2,tasd2=tasd2,tp2=tp2,ta2=ta2,hitrate=hitrate,FArate=FArate) } Jasper Jancik 910.352.7546 -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: SS2full.txt Url: https://stat.ethz.ch/pipermail/r-help/attachments/20061022/b9241ad2/attachment.txt
Hi maybe somebody can help you more but in meantime I would recommend to debug your function with debug(f3) and call by(ss3, sub, f3) to see where exactly comes the error from. HTH Petr On 22 Oct 2006 at 22:49, Jancik, Jasper F. wrote: Date sent: Sun, 22 Oct 2006 22:49:23 -0400 From: "Jancik, Jasper F." <jfj4094 at uncw.edu> To: <r-help at stat.math.ethz.ch> Subject: [R] getting the by() function to work properly> 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(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)); > + > + L=list(d2=d2,B2=B2,dmj2=dmj2,tpsd2=tpsd2,tasd2=tasd2,tp2=tp2,ta2=ta2 > + ,hitrate=hitrate,FArate=FArate) } > > > Jasper Jancik > 910.352.7546 > > >Petr Pikal petr.pikal at precheza.cz
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