flatten record based list/object into dataframe - r

Question

Edit: this question is outdated. The jsonlite package flattens automatically.
I am dealing with online datastreams that have record-based encoding, usually in JSON. The structure of the object (i.e. the names in the JSON) are known from the API documentation, however, values are mostly optional and not present in every record. Lists can contain new lists, and the structure is sometimes quite deep. Here is a quite simple example of some GPS data: http://pastebin.com/raw.php?i=yz6z9t25. Note that in the lower rows, the "l" object is missing due to no GPS signal.
I am looking for an elegant way to flatten these objects into a dataframe. I am currently using something like this:
library(RJSONIO)
library(plyr)
obj <- fromJSON("http://pastebin.com/raw.php?i=yz6z9t25", simplifyWithNames=FALSE, simplify=FALSE)
flatdata <- lapply(obj$data, as.data.frame);
mydf <- rbind.fill(flatdata)
This does the job, however it is slow and a bit error prone. A problem with this approach is that I am not using my knowledge about the structure (object names) in the data; instead it is inferred from the data. This leads to problems when a certain property happens to be absent in every record. In this case, it will not appear in the dataframe at all, instead of a column with NA values. This can lead to issues downstream. For example, I need to process the location timestamp:
mydf$l.t <- structure(mydf$l.t/1000, class="POSIXct")
However, this will result in an error in case of a dataset in which the l$t object isn't there. Furthermore both the as.data.frame and rbind.fill make things quite slow. The example dataset is a relatively small one. Any suggestions for better implementation? A robust solution would always yield a dataframe with the same columns in the same order, and where only the number of rows varies.
Edit: below a dataset with more meta data. It is larger in size and nested more deeply:
obj <- fromJSON("http://www.stat.ucla.edu/~jeroen/files/output.json", simplifyWithNames=FALSE, simplify=FALSE)

Answer 1

Here's a solution that lets you take advantage of your prior knowledge of data field names and classes. Also, by avoiding repeated calls to as.data.frame and the single call to plyr's rbind.fill() (both time-intensive) it runs about 60 times faster on your example data.
cols <- c("id", "ls", "ts", "l.lo","l.tz", "l.t", "l.ac", "l.la", "l.pr", "m")
numcols <- c("l.lo", "l.t", "l.ac", "l.la")
## Flatten each top-level list element, converting it to a character vector.
x <- lapply(obj$data, unlist)
## Extract fields that might be present in each record (returning NA if absent).
y <- sapply(x, function(X) X[cols])
## Convert to a data.frame with columns of desired classes.
z <- as.data.frame(t(y), stringsAsFactors=FALSE)
z[numcols] <- lapply(numcols, function(X) as.numeric(as.character(z[[X]])))
Edit: To confirm that my approach gives results identical to those in the original question, I ran the following test. (Notice that in both cases I set stringsAsFactors=FALSE to avoid meaningless differences in orderings of the factor levels.)
flatdata <- lapply(obj$data, as.data.frame, stringsAsFactors=FALSE)
mydf <- rbind.fill(flatdata)
identical(z, mydf)
# [1] TRUE
Further Edit:
Just for the record, here's an alternate version of the above that in addition automatically:
finds names of all data fields
determines their class/type
coerces the columns of the final data.frame to the correct class
.
dat <- obj$data
## Find the names and classes of all fields
fields <- unlist(lapply(xx, function(X) rapply(X, class, how="unlist")))
fields <- fields[unique(names(fields))]
cols <- names(fields)
## Flatten each top-level list element, converting it to a character vector.
x <- lapply(dat, unlist)
## Extract fields that might be present in each record (returning NA if absent).
y <- sapply(x, function(X) X[cols])
## Convert to a data.frame with columns of desired classes.
z <- as.data.frame(t(y), stringsAsFactors=FALSE)
## Coerce columns of z (all currently character) back to their original type
z[] <- lapply(seq_along(fields), function(i) as(z[[cols[i]]], fields[i]))

Answer 2

Here's an attempt that tries to make no assumptions about the types of the data. It's a bit slower than #JoshOBrien's, but faster than the OP's original solution.
Joshua <- function(x) {
un <- lapply(x, unlist, recursive=FALSE)
ns <- unique(unlist(lapply(un, names)))
un <- lapply(un, function(x) {
y <- as.list(x)[ns]
names(y) <- ns
lapply(y, function(z) if(is.null(z)) NA else z)})
s <- lapply(ns, function(x) sapply(un, "[[", x))
names(s) <- ns
data.frame(s, stringsAsFactors=FALSE)
}
Josh <- function(x) {
cols <- c("id", "ls", "ts", "l.lo","l.tz", "l.t", "l.ac", "l.la", "l.pr", "m")
numcols <- c("l.lo", "l.t", "l.ac", "l.la")
## Flatten each top-level list element, converting it to a character vector.
x <- lapply(obj$data, unlist)
## Extract fields that might be present in each record (returning NA if absent).
y <- sapply(x, function(X) X[cols])
## Convert to a data.frame with columns of desired classes.
z <- as.data.frame(t(y))
z[numcols] <- lapply(numcols, function(X) as.numeric(as.character(z[[X]])))
z
}
Jeroen <- function(x) {
flatdata <- lapply(x, as.data.frame)
rbind.fill(flatdata)
}
library(rbenchmark)
benchmark(Josh=Josh(obj$data), Joshua=Joshua(obj$data),
Jeroen=Jeroen(obj$data), replications=5, order="relative")
# test replications elapsed relative user.self sys.self user.child sys.child
# 1 Josh 5 0.24 1.000000 0.24 0 NA NA
# 2 Joshua 5 0.31 1.291667 0.32 0 NA NA
# 3 Jeroen 5 12.97 54.041667 12.87 0 NA NA

Answer 3

Just for clarity, I am adding a combination of Josh and Joshua's solution which is the best I have come up with so far.
flatlist <- function(mylist){
lapply(rapply(mylist, enquote, how="unlist"), eval)
}
records2df <- function(recordlist, columns) {
if(length(recordlist)==0 && !missing(columns)){
return(as.data.frame(matrix(ncol=length(columns), nrow=0, dimnames=list(NULL,columns))))
}
un <- lapply(recordlist, flatlist)
if(!missing(columns)){
ns <- columns;
} else {
ns <- unique(unlist(lapply(un, names)))
}
un <- lapply(un, function(x) {
y <- as.list(x)[ns]
names(y) <- ns
lapply(y, function(z) if(is.null(z)) NA else z)})
s <- lapply(ns, function(x) sapply(un, "[[", x))
names(s) <- ns
data.frame(s, stringsAsFactors=FALSE)
}
The function is reasonably fast. I still think it should be able to speed this up though:
obj <- fromJSON("http://www.stat.ucla.edu/~jeroen/files/output.json", simplifyWithNames=FALSE, simplify=FALSE)
flatdata <- records2df(obj$data)
It also allows you to 'force' certain columns, although it doesn't result in too much of a speedup:
flatdata <- records2df(obj$data, columns=c("m", "doesnotexist"))