[R] problem applying the same function twice
Curtis Burkhalter
curtisburkhalter at gmail.com
Tue Mar 10 21:35:21 CET 2015
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.goslee at 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
> <curtisburkhalter at 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/
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