人们使用什么技巧来管理交互式R会话的可用内存?我使用下面的函数[基于Petr Pikal和David Hinds在2004年发布的r-help列表]来列出(和/或排序)最大的对象，并偶尔rm()其中一些对象。但到目前为止最有效的解决办法是……在64位Linux下运行，有充足的内存。
大家还有什么想分享的妙招吗?请每人寄一份。
# improved list of objects
.ls.objects <- function (pos = 1, pattern, order.by,
decreasing=FALSE, head=FALSE, n=5) {
napply <- function(names, fn) sapply(names, function(x)
fn(get(x, pos = pos)))
names <- ls(pos = pos, pattern = pattern)
obj.class <- napply(names, function(x) as.character(class(x))[1])
obj.mode <- napply(names, mode)
obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
obj.size <- napply(names, object.size)
obj.dim <- t(napply(names, function(x)
as.numeric(dim(x))[1:2]))
vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
obj.dim[vec, 1] <- napply(names, length)[vec]
out <- data.frame(obj.type, obj.size, obj.dim)
names(out) <- c("Type", "Size", "Rows", "Columns")
if (!missing(order.by))
out <- out[order(out[[order.by]], decreasing=decreasing), ]
if (head)
out <- head(out, n)
out
}
# shorthand
lsos <- function(..., n=10) {
.ls.objects(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}
For both speed and memory purposes, when building a large data frame via some complex series of steps, I'll periodically flush it (the in-progress data set being built) to disk, appending to anything that came before, and then restart it. This way the intermediate steps are only working on smallish data frames (which is good as, e.g., rbind slows down considerably with larger objects). The entire data set can be read back in at the end of the process, when all the intermediate objects have been removed.
dfinal <- NULL
first <- TRUE
tempfile <- "dfinal_temp.csv"
for( i in bigloop ) {
if( !i %% 10000 ) {
print( i, "; flushing to disk..." )
write.table( dfinal, file=tempfile, append=!first, col.names=first )
first <- FALSE
dfinal <- NULL # nuke it
}
# ... complex operations here that add data to 'dfinal' data frame
}
print( "Loop done; flushing to disk and re-reading entire data set..." )
write.table( dfinal, file=tempfile, append=TRUE, col.names=FALSE )
dfinal <- read.table( tempfile )
我在推特上看到了这个，觉得德克的功能太棒了!根据JD Long的回答，为了方便用户阅读，我会这样做:
# improved list of objects
.ls.objects <- function (pos = 1, pattern, order.by,
decreasing=FALSE, head=FALSE, n=5) {
napply <- function(names, fn) sapply(names, function(x)
fn(get(x, pos = pos)))
names <- ls(pos = pos, pattern = pattern)
obj.class <- napply(names, function(x) as.character(class(x))[1])
obj.mode <- napply(names, mode)
obj.type <- ifelse(is.na(obj.class), obj.mode, obj.class)
obj.prettysize <- napply(names, function(x) {
format(utils::object.size(x), units = "auto") })
obj.size <- napply(names, object.size)
obj.dim <- t(napply(names, function(x)
as.numeric(dim(x))[1:2]))
vec <- is.na(obj.dim)[, 1] & (obj.type != "function")
obj.dim[vec, 1] <- napply(names, length)[vec]
out <- data.frame(obj.type, obj.size, obj.prettysize, obj.dim)
names(out) <- c("Type", "Size", "PrettySize", "Length/Rows", "Columns")
if (!missing(order.by))
out <- out[order(out[[order.by]], decreasing=decreasing), ]
if (head)
out <- head(out, n)
out
}
# shorthand
lsos <- function(..., n=10) {
.ls.objects(..., order.by="Size", decreasing=TRUE, head=TRUE, n=n)
}
lsos()
结果如下:
Type Size PrettySize Length/Rows Columns
pca.res PCA 790128 771.6 Kb 7 NA
DF data.frame 271040 264.7 Kb 669 50
factor.AgeGender factanal 12888 12.6 Kb 12 NA
dates data.frame 9016 8.8 Kb 669 2
sd. numeric 3808 3.7 Kb 51 NA
napply function 2256 2.2 Kb NA NA
lsos function 1944 1.9 Kb NA NA
load loadings 1768 1.7 Kb 12 2
ind.sup integer 448 448 bytes 102 NA
x character 96 96 bytes 1 NA
注:我补充的主要部分是(再次改编自JD的回答):
obj.prettysize <- napply(names, function(x) {
print(object.size(x), units = "auto") })
