I am getting this error:
Error in rbind(deparse.level, ...) :
numbers of columns of arguments do not match

I think it is due to columns added to dat2011 in lines 61-66 but not to dat2001.

Can replace with the following:
speclist<-levels(as.factor(offl$SPECIES))

Hey, I am getting the following error when running this line:
sampsum25 <- focal(samprast, w=5, na.rm=TRUE)
Error: is.matrix(w) is not TRUE

The merge command is not pulling the offsets from the s2001 dataframe. I think the indexing needs to change as below:

dat1 <- merge(s2001[,c(1:5,19)],surveydate[,1:3],by=c("SS","PCODE","PKEY"),all.y=TRUE)