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)
}
我非常喜欢Dirk开发的改进的对象函数。不过，大多数时候，一个包含对象名称和大小的更基本的输出对我来说就足够了。这是一个具有类似目标的简单函数。内存使用可以按字母顺序或大小排序，可以限制为一定数量的对象，并且可以按升序或降序排序。此外，我经常处理1GB以上的数据，因此该函数相应地改变单位。
showMemoryUse <- function(sort="size", decreasing=FALSE, limit) {
objectList <- ls(parent.frame())
oneKB <- 1024
oneMB <- 1048576
oneGB <- 1073741824
memoryUse <- sapply(objectList, function(x) as.numeric(object.size(eval(parse(text=x)))))
memListing <- sapply(memoryUse, function(size) {
if (size >= oneGB) return(paste(round(size/oneGB,2), "GB"))
else if (size >= oneMB) return(paste(round(size/oneMB,2), "MB"))
else if (size >= oneKB) return(paste(round(size/oneKB,2), "kB"))
else return(paste(size, "bytes"))
})
memListing <- data.frame(objectName=names(memListing),memorySize=memListing,row.names=NULL)
if (sort=="alphabetical") memListing <- memListing[order(memListing$objectName,decreasing=decreasing),]
else memListing <- memListing[order(memoryUse,decreasing=decreasing),] #will run if sort not specified or "size"
if(!missing(limit)) memListing <- memListing[1:limit,]
print(memListing, row.names=FALSE)
return(invisible(memListing))
}
下面是一些输出示例:
> showMemoryUse(decreasing=TRUE, limit=5)
objectName memorySize
coherData 713.75 MB
spec.pgram_mine 149.63 kB
stoch.reg 145.88 kB
describeBy 82.5 kB
lmBandpass 68.41 kB
我喜欢Dirk的.ls.objects()脚本，但我总是眯着眼睛数大小列中的字符。所以我做了一些丑陋的hack，使它呈现出漂亮的格式大小:
.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.prettysize <- sapply(obj.size, function(r) prettyNum(r, big.mark = ",") )
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", "Rows", "Columns")
if (!missing(order.by))
out <- out[order(out[[order.by]], decreasing=decreasing), ]
out <- out[c("Type", "PrettySize", "Rows", "Columns")]
names(out) <- c("Type", "Size", "Rows", "Columns")
if (head)
out <- head(out, n)
out
}
