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对于每个级别的因素，我需要提取除当前数据之外的所有 data.frame 子集的聚合值。例如，有几个受试者在几天内执行反应时间任务，我需要计算所有受试者和所有天的平均反应时间，但不包括计算平均值的受试者。目前，我这样做：

 library(lme4)
 ddply(sleepstudy, .(Subject, Days), summarise, 
       avg_rt = mean(sleepstudy[sleepstudy$Subject != Subject &
                   sleepstudy$Days == Days,"Reaction"]), .progress="text")

它适用于小型数据集，但对于大型数据集可能会非常慢。有没有办法更快地做到这一点？

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2 回答 2

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#create big dataset
n <- 1e4
set.seed(1)
sleepstudy <- data.frame(Reaction=rnorm(n),Subject=1:4,Days=sort(rep((1:(n/4)),4)))


library(plyr)
system.time(
  res <- ddply(sleepstudy, .(Subject, Days), summarise, 
               avg_rt = mean(sleepstudy[sleepstudy$Subject != Subject &
                 sleepstudy$Days == Days,"Reaction"]))
)
#User      System      elapsed 
#6.532       0.013       6.556  

#use data.table for big datasets
library(data.table)

dt<- as.data.table(sleepstudy)
system.time(
 {dt[,avg_rt:=mean(Reaction),by=Days];
  dt[,n:=.N,by=Days];
  dt[,avg_rt:=(avg_rt*n-Reaction)/(n-1)]}
)
#User      System      elapsed 
#0.005       0.001       0.005 


#test if results are equal
dt2 <- as.data.table(res)
setkey(dt2,Subject,Days)
setkey(dt,Subject,Days)
all.equal(dt[,avg_rt],dt2[,avg_rt])
#[1] TRUE

对于非常大的数据集，速度增益应该更加明显。我只是无法与更大的数据集进行比较，因为ddply它太慢了。

于 2012-09-30T12:12:08.213 回答
0

lapply使用and可能更快aggregate：

do.call("rbind", (lapply(unique(sleepstudy$Subject),
                         function(x)
                           cbind(Subject = x,
                                 aggregate(Reaction ~ Days,
                                           subset(sleepstudy, Subject != x),
                                           mean)))))

更新：

我比较了这两个命令，system.time看起来原来的速度较慢。

library(lme4)
library(plyr)

system.time(
ddply(sleepstudy, .(Subject, Days), summarise, 
      avg_rt = mean(sleepstudy[sleepstudy$Subject != Subject &
                    sleepstudy$Days == Days,"Reaction"]))
)

   # user  system elapsed 
   # 0.17    0.00    0.22 

system.time(
do.call("rbind", (lapply(unique(sleepstudy$Subject),
                         function(x) 
                           cbind(Subject = x,
                                 aggregate(Reaction ~ Days,
                                           subset(sleepstudy, Subject != x),
                                           mean)))))
)


   # user  system elapsed 
   # 0.12    0.00    0.12
于 2012-09-30T09:58:00.650 回答