Short of working on a machine with more RAM, how can I work with large lists in R, for example put them on disk and then work on sections of it?
Here's some code to generate the type of lists I'm using
n = 50; i = 100
WORD <- vector(mode = "integer", length = n)
for (i in 1:n){
WORD[i] <- paste(sample(c(rep(0:9,each=5),LETTERS,letters),5,replace=TRUE),collapse='')
}
dat <- data.frame(WORD = WORD,
COUNTS = sample(1:50, n, replace = TRUE))
dat_list <- lapply(1:i, function(i) dat)
In my actual use case each data frame in the list is unique, unlike the quick example here. I'm aiming for n = 4000 and i = 100,000
This is one example of what I want to do with this list of dataframes:
FUNC <- function(x) {rep(x$WORD, times = x$COUNTS)}
la <- lapply(dat_list, FUNC)
With my actual use case this runs for a few hours, fills up the RAM and most of the swap and then RStudio freezes and shows a message with a bomb on it (RStudio was forced to terminate due to an error in the R session).
I see that bigmemory is limited to matrices and ff doesn't seem to handle lists. What are the other options? If sqldf or a related out-of-memory method possible here, how might I get started? I can't get enough out of the documentation to make any progress and would be grateful for any pointers. Note that instructions to "buy more RAM" will be ignored! This is for a package that I'm hoping will be suitable for average desktop computers (ie. undergrad computer labs).
UPDATE Followining up on the helpful comments from SimonO101 and Ari, here's some benchmarking comparing dataframes and data.tables, loops and lapply, and with and without gc
# self-contained speed test of untable
n = 50; i = 100
WORD <- vector(mode = "integer", length = n)
for (i in 1:n){
WORD[i] <- paste(sample(c(rep(0:9,each=5),LETTERS,letters),5,replace=TRUE),collapse='')
}
# as data table
library(data.table)
dat_dt <- data.table(WORD = WORD, COUNTS = sample(1:50, n, replace = TRUE))
dat_list_dt <- lapply(1:i, function(i) dat_dt)
# as data frame
dat_df <- data.frame(WORD = WORD, COUNTS = sample(1:50, n, replace = TRUE))
dat_list_df <- lapply(1:i, function(i) dat_df)
# increase object size
y <- 10
dt <- c(rep(dat_list_dt, y))
df <- c(rep(dat_list_df, y))
# untable
untable <- function(x) rep(x$WORD, times = x$COUNTS)
# preallocate objects for loop to fill
df1 <- vector("list", length = length(df))
dt1 <- vector("list", length = length(dt))
df3 <- vector("list", length = length(df))
dt3 <- vector("list", length = length(dt))
# functions for lapply
df_untable_gc <- function(x) { untable(df[[x]]); if (x%%10) invisible(gc()) }
dt_untable_gc <- function(x) { untable(dt[[x]]); if (x%%10) invisible(gc()) }
# speedtests
library(microbenchmark)
microbenchmark(
for(i in 1:length(df)) { df1[[i]] <- untable(df[[i]]); if (i%%10) invisible(gc()) },
for(i in 1:length(dt)) { dt1[[i]] <- untable(dt[[i]]); if (i%%10) invisible(gc()) },
df2 <- lapply(1:length(df), function(i) df_untable_gc(i)),
dt2 <- lapply(1:length(dt), function(i) dt_untable_gc(i)),
for(i in 1:length(df)) { df3[[i]] <- untable(df[[i]])},
for(i in 1:length(dt)) { dt3[[i]] <- untable(dt[[i]])},
df4 <- lapply(1:length(df), function(i) untable(df[[i]]) ),
dt4 <- lapply(1:length(dt), function(i) untable(dt[[i]]) ),
times = 10)
And here are the results, without explicit garbage collection, data.table is much faster and lapply slightly faster than a loop. With explicit garbage collection (as I think SimonO101 might be suggesting) they are all much the same speed - a lot slower! I know that using gc is a bit controversial and probably not helpful in this case, but I'll give it a shot with my actual use-case and see if it makes any difference. Of course I don't have any data on memory use for any of these functions, which is really my main concern. Seems that there is no function for memory benchmarking equivalent to the timing functions (for windows, anyway).
Unit: milliseconds
expr
for (i in 1:length(df)) { df1[[i]] <- untable(df[[i]]) if (i%%10) invisible(gc()) }
for (i in 1:length(dt)) { dt1[[i]] <- untable(dt[[i]]) if (i%%10) invisible(gc()) }
df2 <- lapply(1:length(df), function(i) df_untable_gc(i))
dt2 <- lapply(1:length(dt), function(i) dt_untable_gc(i))
for (i in 1:length(df)) { df3[[i]] <- untable(df[[i]]) }
for (i in 1:length(dt)) { dt3[[i]] <- untable(dt[[i]]) }
df4 <- lapply(1:length(df), function(i) untable(df[[i]]))
dt4 <- lapply(1:length(dt), function(i) untable(dt[[i]]))
min lq median uq max neval
37436.433962 37955.714144 38663.120340 39142.350799 39651.88118 10
37354.456809 38493.268121 38636.424561 38914.726388 39111.20439 10
36959.630896 37924.878498 38314.428435 38636.894810 39537.31465 10
36917.765453 37735.186358 38106.134494 38563.217919 38751.71627 10
28.200943 29.221901 30.205502 31.616041 34.32218 10
10.230519 10.418947 10.665668 12.194847 14.58611 10
26.058039 27.103217 27.560739 28.189448 30.62751 10
8.835168 8.904956 9.214692 9.485018 12.93788 10
