Sarah, I have 669 sites and each site has 7 years of data, so if I'm thinking correctly then there should be 4683 possible combinations of site x year. For each year though I need 3 sampling periods so that there is something like the following:
site 1 year1 sample 1 site 1 year1 sample 2 site 1 year1 sample 3 site 2 year1 sample 1 site 2 year1 sample 2 site 2 year1 sample 3..... site 669 year7 sample 1 site 669 year7 sample 2 site 669 year7 sample 3. I have my max memory allocation set to the amount of RAM (8GB) on my laptop, but it still 'times out' due to memory problems. On Tue, Mar 10, 2015 at 2:50 PM, Sarah Goslee <sarah.gos...@gmail.com> wrote: > You said your data only had 14000 rows, which really isn't many. > > How many possible combinations do you have, and how many do you need to > add? > > On Tue, Mar 10, 2015 at 4:35 PM, Curtis Burkhalter > <curtisburkhal...@gmail.com> wrote: > > Sarah, > > > > This strategy works great for this small dataset, but when I attempt your > > method with my data set I reach the maximum allowable memory allocation > and > > the operation just stalls and then stops completely before it is > finished. > > Do you know of a way around this? > > > > Thanks > > > > On Tue, Mar 10, 2015 at 2:04 PM, Sarah Goslee <sarah.gos...@gmail.com> > > wrote: > >> > >> Hi, > >> > >> I didn't work through your code, because it looked overly complicated. > >> Here's a more general approach that does what you appear to want: > >> > >> # use dput() to provide reproducible data please! > >> comAn <- structure(list(animals = c("bird", "bird", "bird", "bird", > >> "bird", > >> "bird", "dog", "dog", "dog", "dog", "dog", "dog", "cat", "cat", > >> "cat", "cat"), animalYears = c(1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, > >> 1L, 2L, 2L, 2L, 1L, 1L, 1L, 2L), animalMass = c(29L, 48L, 36L, > >> 20L, 34L, 34L, 21L, 28L, 25L, 35L, 18L, 11L, 46L, 33L, 48L, 21L > >> )), .Names = c("animals", "animalYears", "animalMass"), class = > >> "data.frame", row.names = c("1", > >> "2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13", > >> "14", "15", "16")) > >> > >> > >> # add reps to comAn > >> # assumes comAn is already sorted on animals, animalYears > >> comAn$reps <- unlist(sapply(rle(do.call("paste", > >> comAn[,1:2]))$lengths, seq_len)) > >> > >> # create full set of combinations > >> outgrid <- expand.grid(animals=unique(comAn$animals), > >> animalYears=unique(comAn$animalYears), reps=unique(comAn$reps), > >> stringsAsFactors=FALSE) > >> > >> # combine with comAn > >> comAn.full <- merge(outgrid, comAn, all.x=TRUE) > >> > >> > comAn.full > >> animals animalYears reps animalMass > >> 1 bird 1 1 29 > >> 2 bird 1 2 48 > >> 3 bird 1 3 36 > >> 4 bird 2 1 20 > >> 5 bird 2 2 34 > >> 6 bird 2 3 34 > >> 7 cat 1 1 46 > >> 8 cat 1 2 33 > >> 9 cat 1 3 48 > >> 10 cat 2 1 21 > >> 11 cat 2 2 NA > >> 12 cat 2 3 NA > >> 13 dog 1 1 21 > >> 14 dog 1 2 28 > >> 15 dog 1 3 25 > >> 16 dog 2 1 35 > >> 17 dog 2 2 18 > >> 18 dog 2 3 11 > >> > > >> > >> On Tue, Mar 10, 2015 at 3:43 PM, Curtis Burkhalter > >> <curtisburkhal...@gmail.com> wrote: > >> > Hey everyone, > >> > > >> > I've written a function that adds NAs to a dataframe where data is > >> > missing > >> > and it seems to work great if I only need to run it once, but if I run > >> > it > >> > two times in a row I run into problems. I've created a workable > example > >> > to > >> > explain what I mean and why I would do this. > >> > > >> > In my dataframe there are areas where I need to add two rows of NAs > (b/c > >> > I > >> > need to have 3 animal x year combos and for cat in year 2 I only have > >> > one) > >> > so I thought that I'd just run my code twice using the function in the > >> > code > >> > below. Everything works great when I run it the first time, but when I > >> > run > >> > it again it says that the value returned to the list 'x' is of length > 0. > >> > I > >> > don't understand why the function works the first time around and adds > >> > an > >> > NA to the 'animalMass' column, but won't do it again. I've used > >> > (print(str(dataframe)) to see if there is a change in class or type > when > >> > the function runs through the original dataframe and there is for > >> > 'animalYears', but I just convert it back before rerunning the > function > >> > for > >> > second time. > >> > > >> > Any thoughts on this would be greatly appreciated b/c my actual data > >> > dataframe I have to input into WinBUGS is 14000x12, so it's not a > >> > trivial > >> > thing to just add in an NA here or there. > >> > > >> >>comAn > >> > animals animalYears animalMass > >> > 1 bird 1 29 > >> > 2 bird 1 48 > >> > 3 bird 1 36 > >> > 4 bird 2 20 > >> > 5 bird 2 34 > >> > 6 bird 2 34 > >> > 7 dog 1 21 > >> > 8 dog 1 28 > >> > 9 dog 1 25 > >> > 10 dog 2 35 > >> > 11 dog 2 18 > >> > 12 dog 2 11 > >> > 13 cat 1 46 > >> > 14 cat 1 33 > >> > 15 cat 1 48 > >> > 16 cat 2 21 > >> > > >> > So every animal has 3 measurements per year, except for the cat in > year > >> > two > >> > which has only 1. I run the code below and get: > >> > > >> > #combs defines the different combinations of > >> > #animals and animalYears > >> > combs<-paste(comAn$animals,comAn$animalYears,sep=':') > >> > #counts defines how long the different combinations are > >> > counts<-ave(1:nrow(comAn),combs,FUN=length) > >> > #missing defines the combs that have length less than one and puts it > in > >> > #the data frame missing > >> > missing<-data.frame(vals=combs[counts<2],count=counts[counts<2]) > >> > > >> > genRows<-function(dat){ > >> > vals<-strsplit(dat[1],':')[[1]] > >> > #not sure why dat[2] is being converted to a string > >> > newRows<-2-as.numeric(dat[2]) > >> > newDf<-data.frame(animals=rep(vals[1],newRows), > >> > animalYears=rep(vals[2],newRows), > >> > animalMass=rep(NA,newRows)) > >> > return(newDf) > >> > } > >> > > >> > > >> > x<-apply(missing,1,genRows) > >> > comAn=rbind(comAn, > >> > do.call(rbind,x)) > >> > > >> >> comAn > >> > animals animalYears animalMass > >> > 1 bird 1 29 > >> > 2 bird 1 48 > >> > 3 bird 1 36 > >> > 4 bird 2 20 > >> > 5 bird 2 34 > >> > 6 bird 2 34 > >> > 7 dog 1 21 > >> > 8 dog 1 28 > >> > 9 dog 1 25 > >> > 10 dog 2 35 > >> > 11 dog 2 18 > >> > 12 dog 2 11 > >> > 13 cat 1 46 > >> > 14 cat 1 33 > >> > 15 cat 1 48 > >> > 16 cat 2 21 > >> > 17 cat 2 <NA> > >> > > >> > So far so good, but then I adjust the code so that it reads (**notice > >> > the > >> > change in the specification in 'missing' to counts<3**): > >> > > >> > #combs defines the different combinations of > >> > #animals and animalYears > >> > combs<-paste(comAn$animals,comAn$animalYears,sep=':') > >> > #counts defines how long the different combinations are > >> > counts<-ave(1:nrow(comAn),combs,FUN=length) > >> > #missing defines the combs that have length less than one and puts it > in > >> > #the data frame missing > >> > missing<-data.frame(vals=combs[counts<3],count=counts[counts<3]) > >> > > >> > genRows<-function(dat){ > >> > vals<-strsplit(dat[1],':')[[1]] > >> > #not sure why dat[2] is being converted to a string > >> > newRows<-2-as.numeric(dat[2]) > >> > newDf<-data.frame(animals=rep(vals[1],newRows), > >> > animalYears=rep(vals[2],newRows), > >> > animalMass=rep(NA,newRows)) > >> > return(newDf) > >> > } > >> > > >> > > >> > x<-apply(missing,1,genRows) > >> > comAn=rbind(comAn, > >> > do.call(rbind,x)) > >> > > >> > The result for 'x' then reads: > >> > > >> >> x > >> > [[1]] > >> > [1] animals animalYears animalMass > >> > <0 rows> (or 0-length row.names) > >> > > >> > Any thoughts on why it might be doing this instead of adding an > >> > additional > >> > row to get the result: > >> > > >> >> comAn > >> > animals animalYears animalMass > >> > 1 bird 1 29 > >> > 2 bird 1 48 > >> > 3 bird 1 36 > >> > 4 bird 2 20 > >> > 5 bird 2 34 > >> > 6 bird 2 34 > >> > 7 dog 1 21 > >> > 8 dog 1 28 > >> > 9 dog 1 25 > >> > 10 dog 2 35 > >> > 11 dog 2 18 > >> > 12 dog 2 11 > >> > 13 cat 1 46 > >> > 14 cat 1 33 > >> > 15 cat 1 48 > >> > 16 cat 2 21 > >> > 17 cat 2 <NA> > >> > 18 cat 2 <NA> > >> > > >> > Thanks > >> > -- > >> > Curtis Burkhalter > > > > > -- Curtis Burkhalter https://sites.google.com/site/curtisburkhalter/ [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.