Extract bz2 file in R

Question

I have bunch of .csv.bz2 files, which i have to download, extract, and read in R. I downloaded the file and want to extract it to current working directory, then read it. unz(filename,filename.csv) but it does not seem to work. How can I do that?

I heard somewhere that bzfiles can be read directly without decompressing. How can I do that?

Pitiable

Answer 1

You can use any of these two commands:

1. read.csv()command: with this command you can directly supply your compressed filename containing csv file.

   read.csv("file.csv.bz2")

2. read.table() command: This command is generic version of read.csv() command. You can set delimiters and others options that read.csv() automatically sets. You don't need to uncompress the file separately. This command does it automatically for you.

   read.csv("file.csv.bz2", header = TRUE, sep = ",", quote = "\"",...)

Revolver

Answer 2

Like this:

readcsvbz2file <- read.csv(bzfile("file.csv.bz2"))

Munniks

bzfile()is not necessary, read.csv() can handle compressed files automatically. So it's just read.csv("file.csv.bz2"). Here is an example (first section "Loading the Data"). – Kalat

bzipfile() is a more general solution because it useful for other formats. Thanks – Quieten

Answer 3

You can make use of the super fast fread which has built-in support for bz2-compressed files

require(data.table)
fread("file.csv.bz2")

Lanham

Answer 4

Basically, you need to type:

library(R.utils)
bunzip2("dataset.csv.bz2", "dataset.csv", remove = FALSE, skip = TRUE)

dataset <- read.csv("dataset.csv")

See documentation here: bunzip2 {R.utils}.

Apothecary

Answer 5

According to read.table description, one can read a compressed file directly.

read.table("file.csv.bz2")

Mexicali