一些分析表明，您的大部分时间都花在了[<-.data.frame。
因此，缩放问题来自Ops.data.frame 和[<-.dataframe 的工作方式以及[<-.data.frame 的复制方式以及[[<- 命名列表的复制方式。
Ops.data.frame中的相关代码（附我的cmets）
# cn is the names of your data.frame
for (j in seq_along(cn)) {
left <- if (!lscalar)
e1[[j]]
else e1
right <- if (!rscalar)
e2[[j]]
else e2
value[[j]] <- eval(f)
}
# sometimes return a data.frame
if (.Generic %in% c("+", "-", "*", "/", "%%", "%/%")) {
names(value) <- cn
data.frame(value, row.names = rn, check.names = FALSE,
check.rows = FALSE)
} # sometimes return a matrix
else matrix(unlist(value, recursive = FALSE, use.names = FALSE),
nrow = nr, dimnames = list(rn, cn))
当您使用Ops.data.frame 时，它将在for 循环中循环使用您的列，每次使用[[<- 替换。
这意味着随着列数的增加，所需的时间将会增加（因为它是一个 data.frame 被命名为 list 会有一些保护性的内部复制） - 因此它将随着列数线性扩展
# for example only this part will scale with the number of columns
f.df.1 <- function( df , x = 0.5 ){
df <- df - x
return( df )
}
microbenchmark(f.df.1(df1),f.df.1(df2),f.df.1(df3), times = 10L)
# Unit: milliseconds
# expr min lq median uq max neval
# f.df.1(df1) 96.739646 97.143298 98.36253 172.937100 175.539239 10
# f.df.1(df2) 11.697373 11.955173 12.12206 12.304543 281.055865 10
# f.df.1(df3) 3.114089 3.149682 3.41174 3.575835 3.640467 10
当i 是与x 相同维度的逻辑矩阵时，[<-.data.frame 具有类似的列循环
if(is.logical(i) && is.matrix(i) && all(dim(i) == dim(x))) {
nreplace <- sum(i, na.rm=TRUE)
if(!nreplace) return(x) # nothing to replace
## allow replication of length(value) > 1 in 1.8.0
N <- length(value)
if(N > 1L && N < nreplace && (nreplace %% N) == 0L)
value <- rep(value, length.out = nreplace)
if(N > 1L && (length(value) != nreplace))
stop("'value' is the wrong length")
n <- 0L
nv <- nrow(x)
for(v in seq_len(dim(i)[2L])) {
thisvar <- i[, v, drop = TRUE]
nv <- sum(thisvar, na.rm = TRUE)
if(nv) {
if(is.matrix(x[[v]]))
x[[v]][thisvar, ] <- if(N > 1L) value[n+seq_len(nv)] else value
else
x[[v]][thisvar] <- if(N > 1L) value[n+seq_len(nv)] else value
}
n <- n+nv
}
return(x)
f.df.2 <- function( df , x = 0.5 ){
df[df < 0 ] <- 0
return( df )
}
microbenchmark(f.df.2(df1), f.df.2(df2), f.df.2(df3), times = 10L)
# Unit: milliseconds
# expr min lq median uq max neval
# f.df.2(df1) 20.500873 20.575801 20.699469 20.993723 84.825607 10
# f.df.2(df2) 3.143228 3.149111 3.173265 3.353779 3.409068 10
# f.df.2(df3) 1.581727 1.634463 1.707337 1.876240 1.887746 10
[<-data.frame（和<-）也会复制
如何改进。您可以使用 data.table 包中的 lapply 或 set
library(data.table)
sdf <- function(df, x = 0.5){
# explicit copy so there are no changes to original
dd <- copy(df)
for(j in names(df)){
set(dd, j= j, value = dd[[j]] - 0.5)
# this is slow when (necessarily) done repeatedly perhaps this
# could come out of the loop and into a `lapply` or `vapply` statment
whi <- which(dd[[j]] < 0 )
if(length(whi)){
set(dd, j= j, i = whi, value = 0.0)
}
}
return(dd)
}
microbenchmark(sdf(df1), sdf(df2), sdf(df3), times = 10L)
# Unit: milliseconds
# expr min lq median uq max neval
# sdf(df1) 87.471560 88.323686 89.880685 92.659141 153.218536 10
# sdf(df2) 6.235951 6.531192 6.630981 6.786801 7.230825 10
# sdf(df3) 2.631641 2.729612 2.775762 2.884807 2.970556 10
# a base R approach using lapply
ldf <- function(df, x = 0.5){
as.data.frame(lapply(df, function(xx,x){ xxx <- xx-x;replace(xxx, xxx<0,0)}, x=x))
}
# pretty good. Does well with large data.frames
microbenchmark(ldf(df1), ldf(df2), ldf(df3), times = 10L)
# Unit: milliseconds
# expr min lq median uq max neval
# ldf(df1) 84.380144 84.659572 85.987488 159.928249 161.720599 10
# ldf(df2) 11.507918 11.793418 11.948194 12.175975 86.186517 10
# ldf(df3) 4.237206 4.368717 4.449018 4.627336 5.081222 10
# they all produce the same
dd <- sdf(df1)
ddf1 <- f.df(df1)
ldf1 <- ldf(df1)
identical(dd,ddf1)
## [1] TRUE
identical(ddf1, ldf1)
## [1] TRUE
# sdf and ldf comparable with lots of columns
# see benchmarking below.
microbenchmark(sdf(df1), ldf(df1), f.df(df1), times = 10L)
# Unit: milliseconds
# expr min lq median uq max neval
# sdf(df1) 85.75355 86.47659 86.76647 87.88829 172.0589 10
# ldf(df1) 84.73023 85.27622 85.61528 172.02897 356.4318 10
# f.df(df1) 3689.83135 3730.20084 3768.44067 3905.69565 3949.3532 10
# sdf ~ twice as fast with smaller data.frames
microbenchmark(sdf(df2), ldf(df2), f.df(df2), times = 10L)
# Unit: milliseconds
# expr min lq median uq max neval
# sdf(df2) 6.46860 6.557955 6.603772 6.927785 7.019567 10
# ldf(df2) 12.26376 12.551905 12.576802 12.667775 12.982594 10
# f.df(df2) 268.42042 273.800762 278.435929 346.112355 503.551387 10
microbenchmark(sdf(df3), ldf(df3), f.df(df3), times = 10L)
# Unit: milliseconds
# expr min lq median uq max neval
# sdf(df3) 2.538830 2.911310 3.020998 3.120961 74.980466 10
# ldf(df3) 4.698771 5.202121 5.272721 5.407351 5.424124 10
# f.df(df3) 17.819254 18.039089 18.158069 19.692038 90.620645 10
# copying of larger objects is slower, repeated calls to which are slow.
microbenchmark(copy(df1), copy(df2), copy(df3), times = 10L)
# Unit: microseconds
# expr min lq median uq max neval
# copy(df1) 369.926 407.218 480.5710 527.229 618.698 10
# copy(df2) 165.402 224.626 279.5445 296.215 519.773 10
# copy(df3) 150.148 180.625 214.9140 276.035 467.972 10