Read .tar.gz file in R - r

I have compressed file like cat.txt.tar.gz, I just need to load into R and process as follows
zip <-("cat.txt.tar.gz")
data <- read.delim(file=(untar(zip,"cat.txt")),sep="\t")
but "data" is empty while running the code.Is there any way to read a file from .tar.gz

Are you sure your file is named correctly?
Usually compressed files are named cat.tar.gz, excluding the .txt.
Second, try the following code:
tarfile <- "cat.txt.tar.gz" # Or "cat.tar.gz" if that is right
data <- read.delim(file = untar(tarfile,compressed="gzip"),sep="\t")
If this doesn't work, you might need to extract the file first, and then read the extracted file.

To read in a particular csv or txt within a gz archive without having to UNZIP it first one can use library(archive) :
library(archive)
library(readr)
read_csv(archive_read("cat.txt.tar.gz", file = 1), col_types = cols(), sep="\t")
should work.

Related

Read files with a specific a extension from a folder in R

I want to read files with extension .output with the function read.table.
I used pattern=".output" but its'not correct.
Any suggestions?
As an example, heres how you could read in files with the extension ".output" and create a list of tables
list.filenames <- list.files(pattern="\\.output$")
trialsdata <- lapply(list.filenames,read.table,sep="\t")
or if you just want to read them one at a time manually just include the extention in the filename argument.
read.table("ACF.output",sep=...)
So finally because i didn't found a solution(something is going wrong with my path) i made a text file including all the .output files with ls *.output > data.txt.
After that using :
files = read.table("./data.txt")
i am making a data.frame including all my files and using
files[] <- lapply(files, as.character)
Finally with test = read.table(files[i,],header=F,row.names=1)
we could read every file which is stored in i (i = no of line).

Read latest SPSS file from directory

I am trying to read the latest SPSS file from the directory which has several SPSS files. I want to read only the newest file from a list of 3 files which changes with time. Currently, I have manually entered the filename (SPSS-1568207835.sav for ex.) which works absolutely fine, but I want to make this dynamic and automatically fetch the latest file. Any help would be greatly appreciated.
setwd('/file/path/for/this/file/SPSS')
library(expss)
expss_output_viewer()
mydata = read_spss("SPSS-1568207835.sav",reencode = TRUE)
w <- data.frame(mydata)
args <- commandArgs(TRUE)
This should return a character string for the filename of the .sav file modified most recently
# get all .sav files
all_sav <- list.files(pattern ='\\.sav$')
# use file.info to get the index of the file most recently modified
all_sav[with(file.info(all_sav), which.max(mtime))]

How do I zip a csv file and write that zipped file to a folder using R

I have an R script which generates a csv file of nearly 80000 KB after calculations. I want to write this csv file to folder say D:/My_Work/Output with file name result.zip as a zipped file. Please suggest is there any function or any way that i could achieve this.
Use the zip function:
zip(*path to zip*,*path to csv*)
edit: Unfortunately you cannot go from data.frame straight to zipped csv. You need to explicitly make the csv, but it wouldn't be hard to write a wrapper that deletes the csv so that you never know its there like so:
zipped.csv <- function(df, zippedfile) {
# init temp csv
temp <- tempfile(fileext=".csv")
# write temp csv
write.csv(df, file=temp)
# zip temp csv
zip(zippedfile,temp)
# delete temp csv
unlink(temp)
}
If you want just save some space on the disk then it is more convenient to use *.gz compression.
write.csv(iris, gzfile("iris.csv.gz"), row.names = FALSE)
iris2 = read.csv("iris.csv.gz")

Dynamically converting a list of Excel files to csv files in R

I currently have a folder containing all Excel (.xlsx) files, and using R I would like to automatically convert all of these files to CSV files using the "openxlsx" package (or some variation). I currently have the following code to convert one of the files and place it in the same folder:convert("team_order\\team_1.xlsx", "team_order\\team_1.csv")
I would like to automate the process so it does it to all the files in the folder, and also removes the current xlsx files, so only the csv files remain. Thanks!
You can try this using rio, since it seems like that's what you're already using:
library("rio")
xls <- dir(pattern = "xlsx")
created <- mapply(convert, xls, gsub("xlsx", "csv", xls))
unlink(xls) # delete xlsx files
library(readxl)
# Create a vector of Excel files to read
files.to.read = list.files(pattern="xlsx")
# Read each file and write it to csv
lapply(files.to.read, function(f) {
df = read_excel(f, sheet=1)
write.csv(df, gsub("xlsx", "csv", f), row.names=FALSE)
})
You can remove the files with the command below. However, this is dangerous to run automatically right after the previous code. If the previous code fails for some reason, the code below will still delete your Excel files.
lapply(files.to.read, file.remove)
You could wrap it in a try/catch block to be safe.

Using R to download zipped data file, extract, and import data

#EZGraphs on Twitter writes:
"Lots of online csvs are zipped. Is there a way to download, unzip the archive, and load the data to a data.frame using R? #Rstats"
I was also trying to do this today, but ended up just downloading the zip file manually.
I tried something like:
fileName <- "http://www.newcl.org/data/zipfiles/a1.zip"
con1 <- unz(fileName, filename="a1.dat", open = "r")
but I feel as if I'm a long way off.
Any thoughts?
Zip archives are actually more a 'filesystem' with content metadata etc. See help(unzip) for details. So to do what you sketch out above you need to
Create a temp. file name (eg tempfile())
Use download.file() to fetch the file into the temp. file
Use unz() to extract the target file from temp. file
Remove the temp file via unlink()
which in code (thanks for basic example, but this is simpler) looks like
temp <- tempfile()
download.file("http://www.newcl.org/data/zipfiles/a1.zip",temp)
data <- read.table(unz(temp, "a1.dat"))
unlink(temp)
Compressed (.z) or gzipped (.gz) or bzip2ed (.bz2) files are just the file and those you can read directly from a connection. So get the data provider to use that instead :)
Just for the record, I tried translating Dirk's answer into code :-P
temp <- tempfile()
download.file("http://www.newcl.org/data/zipfiles/a1.zip",temp)
con <- unz(temp, "a1.dat")
data <- matrix(scan(con),ncol=4,byrow=TRUE)
unlink(temp)
I used CRAN package "downloader" found at http://cran.r-project.org/web/packages/downloader/index.html . Much easier.
download(url, dest="dataset.zip", mode="wb")
unzip ("dataset.zip", exdir = "./")
For Mac (and I assume Linux)...
If the zip archive contains a single file, you can use the bash command funzip, in conjuction with fread from the data.table package:
library(data.table)
dt <- fread("curl http://www.newcl.org/data/zipfiles/a1.zip | funzip")
In cases where the archive contains multiple files, you can use tar instead to extract a specific file to stdout:
dt <- fread("curl http://www.newcl.org/data/zipfiles/a1.zip | tar -xf- --to-stdout *a1.dat")
Here is an example that works for files which cannot be read in with the read.table function. This example reads a .xls file.
url <-"https://www1.toronto.ca/City_Of_Toronto/Information_Technology/Open_Data/Data_Sets/Assets/Files/fire_stns.zip"
temp <- tempfile()
temp2 <- tempfile()
download.file(url, temp)
unzip(zipfile = temp, exdir = temp2)
data <- read_xls(file.path(temp2, "fire station x_y.xls"))
unlink(c(temp, temp2))
To do this using data.table, I found that the following works. Unfortunately, the link does not work anymore, so I used a link for another data set.
library(data.table)
temp <- tempfile()
download.file("https://www.bls.gov/tus/special.requests/atusact_0315.zip", temp)
timeUse <- fread(unzip(temp, files = "atusact_0315.dat"))
rm(temp)
I know this is possible in a single line since you can pass bash scripts to fread, but I am not sure how to download a .zip file, extract, and pass a single file from that to fread.
Using library(archive) one can also read in a particular csv file within the archive, without having to UNZIP it first; read_csv(archive_read("http://www.newcl.org/data/zipfiles/a1.zip", file = 1), col_types = cols())
which I find more convenient & is faster.
It also supports all major archive formats & is quite a bit faster than the base R untar or unz - it supports tar, ZIP, 7-zip, RAR, CAB, gzip, bzip2, compress, lzma, xz & uuencoded files.
To unzip everything one can use archive_extract("http://www.newcl.org/data/zipfiles/a1.zip", dir=XXX)
This works on all platforms & given the superior performance for me would be the preferred option.
Try this code. It works for me:
unzip(zipfile="<directory and filename>",
exdir="<directory where the content will be extracted>")
Example:
unzip(zipfile="./data/Data.zip",exdir="./data")
rio() would be very suitable for this - it uses the file extension of a file name to determine what kind of file it is, so it will work with a large variety of file types. I've also used unzip() to list the file names within the zip file, so its not necessary to specify the file name(s) manually.
library(rio)
# create a temporary directory
td <- tempdir()
# create a temporary file
tf <- tempfile(tmpdir=td, fileext=".zip")
# download file from internet into temporary location
download.file("http://download.companieshouse.gov.uk/BasicCompanyData-part1.zip", tf)
# list zip archive
file_names <- unzip(tf, list=TRUE)
# extract files from zip file
unzip(tf, exdir=td, overwrite=TRUE)
# use when zip file has only one file
data <- import(file.path(td, file_names$Name[1]))
# use when zip file has multiple files
data_multiple <- lapply(file_names$Name, function(x) import(file.path(td, x)))
# delete the files and directories
unlink(td)
I found that the following worked for me. These steps come from BTD's YouTube video, Managing Zipfile's in R:
zip.url <- "url_address.zip"
dir <- getwd()
zip.file <- "file_name.zip"
zip.combine <- as.character(paste(dir, zip.file, sep = "/"))
download.file(zip.url, destfile = zip.combine)
unzip(zip.file)

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