How to extract and read a bzip2ed hdf5 in a zipped file in R? - r

I would like to read a hdf5 file in a zipped file. The issue here is that this hdf5 file is also double zipped as a bzip2ed (.bz2) file.
Please refer to the figure shown below.
The zip file is "g2_BIOPAR_SWI_201012250000_GLOBE_ASCAT_V2_0_0.ZIP".
The target bz2 file is "g2_BIOPAR_SWI_201012250000_GLOBE_ASCAT_V2_0_0.h5.bz2".
Could someone show me some tips or guidances in how to do it?

Give a look at this question:
Extract bz2 file in R
It explains how to read a.bz2 file and I think the last answer is the right one for you,; or just type ?bzfile.
After that for hdf5 files you can give a look at rhdf5 package from Bioncoductor; here is the link:
http://www.bioconductor.org/packages/release/bioc/html/rhdf5.html

Related

R zip multiple files from multiple subfolers into one zip with one folder

I have some files in some folders/subfolders
subfolder1/file1.csv
subfolder2/file2.csv
when using r to zip these files, with the following code
zip::zip("test.zip",files=c("subfolder1/file1.csv","subfolder2/file2.csv"))
It will create a zip file, but the files will be in their subfolders.
How can I create a zip file without the structure of the subfolders? which means that the files will be in the test.zip directly.
Thanks to stefan's comment, I tried some arguments in the zip::zip function and found out the argument to do so:
zip(..., mode="cherry-pick")

use read_sas to read specific file under a zipped file in R

I have a zipped sas file and there are couple sas files inside that. Just want to know if there is a chance that I can use read_sas function to read specific file under that zipped file? Couldn't find anything online about that.
Checked the ?read_sas nothing mentioned about that.
code I used :
# zipped file name: example.zip
# files inside example.zip file are file1.sas7bdat, file2.sas7bdat and targetfilename.sas7bdat
file <- read_sas(example.zip, 'targetfilename.sas7bdat')
outcome: read_sas only read the first file inside that zipped file.
Sorted solution:
read_sas(unz("examp;e.zip", "'targetfilename.sas7bdat'"))
solved:
read_sas(unz("examp;e.zip", "'targetfilename.sas7bdat'"))

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I tried to download a file from LSData, but it brings me to a page full of weird characters. The first few are:
7z¼¯'�DÙ™µUa�����b�������’³_èÚ†à]�&Jgl›Ü)ÉZKŒP7þò|¤ˆëÁëxŠ§u6²ã]’“Àé3lGê7ñ"!èÞ’ïjP³
l½Öv<¹-žøZ¹Æ âäùëOKä#;cÞ Žmï•&?^¢Ø"Á.=ù‚u|õ9žG<އ趽ÈËŒøÂtŠÍÝê/ÂG×à×–R§Ýj×zÛ¥™éwG—ï‘ývíõåò ÂÑ\‡W�ܱò§úßxlø¾Ö¾EºáPnÚR"økv§}6“SLÒ¢ø€m]-Ì«gÐáÅMŠWGU�µOÿDõ™}u¦HŠ_qŠ,/¦lÔ}Áô|,Òäêÿ2l«ª»°úö¡]+€™´í¿¢«|Ãw#êñ:t!
I have no clue what I'm looking at. How can I convert this entire page into a CSV, or in whatever file so I can use it in R?
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Read sheet names from a xlsb file

I've been trying to read xlsb files into R.
I've tried using excel.link and readxlsb packages and they do work for reading the file but i also need to read the sheet names.
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Any suggestion?
Thanks

How to read .hdf file in R?

I have a large number of files in .hdf format. These are sadly not the hdf5 files that I know are readable in R. Is there a way to load and read hdf files in R? Or is there a way to convert .hdf to hdf5? I downloaded the C-based h4toh5 tool, but it is not useful. Are there any other ways to convert? Many thanks.
I wouldn't describe hdf4 as a legacy format #mdsummer. NASA still provides a lot of its data in hdf4.
This is similar to a few posts where people (myself included) haven't been sure whether their .hdf files are hdf4 or hdf5. You can use a program called HDFView which is free to download and really easy to use to find out if you've got hdf4/5 files. Just load a file in and look under "properties".
If you've got hdf4 files then you should check out the gdal_translate from the gdalUtils package. There's some more info here including the code I used for my hdf files:
Reading hdf files into R and converting them to geoTIFF rasters
You can use ncdf4 or rgdal packages as we explain here:
https://hdfeos.org/software/r.php
If you don't like h4toh5, h4tonccf is another tool that you can try:
http://hdfeos.org/software/h4cflib.php

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