Re: [R] zoo:rollapply by multiple grouping factors

From: Mark Novak <mnovak1_at_ucsc.edu>
Date: Mon, 04 Apr 2011 12:40:25 -0700

Thank you very much Gabor! It looks like that's gonna work wonderfully. I didn't even know 'ave' existed.

For others out there: I only needed to add a comma: dat[,c("Site", "Plot", "Sp")]

Small follow up Q: Is there any reason to use 'aggregate' vs. 'ave' in general?

-mark

On 4/3/11 3:27 PM, Gabor Grothendieck wrote:
> Try ave:
>
> dat$cv<- ave(dat$Count, dat[c("Site", "Plot", "Sp")], FUN =
> function(x) rollapply(zoo(x), 2, cv, na.pad = TRUE, align = "right"))

> On Sun, Apr 3, 2011 at 11:58 AM, Mark Novak<mnovak1@ucsc.edu> wrote:
>> # Hi there,
>> # I am trying to apply a function over a moving-window for a large number of
>> multivariate time-series that are grouped in a nested set of factors. I
>> have spent a few days searching for solutions with no luck, so any
>> suggestions are much appreciated.
>>
>> # The data I have are for the abundance dynamics of multiple species
>> observed in multiple fixed plots at multiple sites. (I total I have 7
>> sites, ~3-5 plots/site, ~150 species/plot, for 60 time-steps each.) So my
>> data look something like this:
>>
>> dat<-data.frame(Site=rep(1), Plot=rep(c(rep(1,8),rep(2,8),rep(3,8)),1),
>> Time=rep(c(1,1,2,2,3,3,4,4)), Sp=rep(1:2), Count=sample(24))
>> dat
>>
>> # Let the function I want to apply over a right-aligned window of w=2 time
>> steps be:
>> cv<-function(x){sd(x)/mean(x)}
>> w<-2
>>
>> # The final output I want would look something like this:
>> Out<-data.frame(dat,CV=round(c(NA,NA,runif(6,0,1),c(NA,NA,runif(6,0,1))),2))
>>
>> # I could reshape and apply zoo:rollapply() to a given plot at a given site,
>> and reshape again as follows:
>> library(zoo)
>> a<-subset(dat,Site==1&Plot==1)
>> b<-reshape(a[-c(1,2)],v.names='Count',idvar='Time',timevar='Sp',direction='wide')
>> d<-zoo(b[,-1],b[,1])
>> d
>> out<-rollapply(d, w, cv, na.pad=T, align='right')
>> out
>>
>> # I would thereby have to loop through all my sites and plots which,
>> although it deals with all species at once, still seems exceedingly
>> inefficient.
>>
>> # So the question is, how do I use something like aggregate.zoo or tapply or
>> even lapply to apply rollapply on each species' time series.
>>
>> # The closest I've come is the following two approaches:
>>
>> # First let:
>> datx<-list(Site=dat$Site,Plot=dat$Plot,Sp=dat$Sp)
>> daty<-dat$Count
>>
>> # Method 1.
>> out1<-tapply(seq(along=daty),datx,function(i,x=daty){ rollapply(zoo(x[i]),
>> w, cv, na.pad=T, align='right') })
>> out1
>> out1[,,1]
>>
>> # Which "works" in that it gives me the right answers, but in a format from
>> which I can't figure out how to get back into the format I want.
>>
>> # Method 2.
>> fun<-function(x){y<-zoo(x);coredata(rollapply(y, w,
>> cv,na.pad=T,align='right'))}
>> out2<-aggregate(daty,by=datx,fun)
>> out2
>>
>> # Which superficially "works" better, but again only in a format I can't
>> figure out how to use because the output seems to be a mix of data.frame and
>> lists.
>> out2[1,4]
>> out2[1,5]
>> is.data.frame(out2)
>> is.list(out2)
>>
>> # The situation is made more problematic by the fact that the time point of
>> first survey can differ between plots (e.g., site1-plot3 may only start at
>> time-point 3). As in...
>> dat2<-dat
>> dat2<-dat2[-which(dat2$Plot==3& dat2$Time<3),]
>> dat2
>>
>> # I must therefore ensure that I'm keeping track of the true time associated
>> with each value, not just the order of their occurences. This information
>> is (seemingly) lost by both methods.
>> datx<-list(Site=dat2$Site,Plot=dat2$Plot,Sp=dat2$Sp)
>> daty<-dat2$Count
>>
>> # Method 1.
>> out3<-tapply(seq(along=daty),datx,function(i,x=daty){ rollapply(zoo(x[i]),
>> w, cv, na.pad=T, align='right') })
>> out3
>> out3[1,3,1]
>> time(out3[1,3,1])
>>
>> # Method 2
>> out4<-aggregate(daty,by=datx,fun)
>> out4
>> time(out4[3,4])
>>
>>
>> # Am I going about this all wrong? Is there a different package to try?
>> Any thoughts and suggestions are much appreciated!
>>
>> # R 2.12.2 GUI 1.36 Leopard build 32-bit (5691); zoo 1.6-4
>>
>> # Thanks!
>> # -mark
>>
>



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