How can I read and write the following file using R ?
https://www.dropbox.com/s/vlnrlxjs7f977zz/3B42_daily.2012.11.23.7.nc
In other words, I would like to read the "3B42_daily.2012.11.23.7.nc" file and write with the same structure that it is written.
Best regards
Package ncdf have functions to do this. You should also read other Q&A on this site tagged with netcdf and r.
Basically to read a netcdf file:
library(ncdf)
a <- open.ncdf('your/path/to/your/file.nc') #that opens a connection to the file
Then function get.var.ncdf helps you extract the data, variable by variable.
The process to write one is described in this Q&A.
The idea is to create dimensions first using dim.def.ncdf then the variables with var.def.ncdf and finally the file itself using create.ncdf.
Related
I've a lot of .hyper files to work with. Most of the time I work with them using Python (using tableauhyperio lib), but I need to read them in R and I could not find a way to do it. Does anyone know some way to read hyper files in R?
Right now I'm reading the data in python and exporting them as csv to read in R the csv files...
I've been trying to create some graphs with the Shiny for R, I used this finished example, right here :
http://shiny.rstudio.com/gallery/telephones-by-region.html
But there is one problem : data is being scanned from the library file.
I tried to create my own library file with the data.
And there comes another problem : my data is taken from .csv file,
My question is : How can I create package file, that is just a data taken from the .csv file?
Thank you so much for your help
I think that this page can help you
http://r-pkgs.had.co.nz/data.html
I want to export a dataset in the MASS package to SPSS for further investigation. I'm looking for the EuStockMarkets data set in the package.
As described in http://www.statmethods.net/input/exportingdata.html, I did:
library(foreign)
write.foreign(EuStockMarkets, "c:/mydata.txt", "c:/mydata.sps", package="SPSS")
I got a text file but the sps file is not a valid SPSS file. I'm really looking for a way to export the dataset to something that a SPSS can open.
As Thomas has mentioned in the comments, write.foreign doesn't generate native SPSS datafiles (.sav). What it does generate is the data in a comma delimited format (the .txt file) and a basic syntax file for reading that data into SPSS (the .sps file). The EuStockMarkets data object class is multivariate time series (mts) so when it's exported the metadata is lost and the resulting .sps file, lacking variable names, throws an error when you try to run it in SPSS. To get around this you can export it as a data frame instead:
write.foreign(as.data.frame(EuStockMarkets), "c:/mydata.txt", "c:/mydata.sps", package="SPSS")
Now you just need to open mydata.sps as a syntax file (NOT as a datafile) in SPSS and run it to read in the datafile.
Rather than exporting it, use the STATS GET R extension command. It will take a specified data frame from an R workspace/dataset and convert it into a Statistics dataset. You need the R Essentials for Statistics and the extension command, which are available via the SPSS Community site (www.ibm.com/developerworks/spssdevcentral)
I'm not trying to answer a question that has been answered. I just think there is something else to complement for other users looking for this.
On your SPSS window, you just need to find the first line of code and edit it. It should be something like this:
"file-name.txt"
You need to find the folder path where you're keeping your file:
"C:\Users\DELL\Google Drive\Folder-With-Your-File"
Then you just need to add this path to your file's name:
"C:\Users\DELL\Google Drive\Folder-With-Your-File\file-name.txt"
Otherwise SPSS will not recognize the .txt file.
Sorry if I'm repeating some information here, I just wanted to make it easier to understand.
I suppose that EuStockMarkets is a (labelled) data frame.
This should work and even keep the variable and value labels:
require(sjlabelled)
write_spss(EuStockMarkets, "mydata.sav")
Or you try rio:
rio::export(EuStockMarkets, "mydata.sav")
I've got a netCDF data file.The file can be downloaded at:
http://www.nodc.noaa.gov/OC5/WOA09/pr_woa09.html
It's the one called WOA09 netCDF version.
I want to use only climatology data (variable 4) and the first depth range [ , ,1] so I've used the code below so far in R. In now want to have the subset called MyData in RData format.
I want to convert it to RData to be able to play around with it in R. I haven't found anything on the internet about doing this, is it even possible? How?
Thank you so much if you can help! And let me know if I haven't given enough info .
library(ncdf)
MyFile<-open.ncdf("/home/et1211/wspd.mean.nc")
MyFile$var[[4]]->var4
MyData<-get.var.ncdf(MyFile,var4)
MyData<-MyData[,,1]
It's simple. You just save the object from R and use .RData as extension:
save(MyData, file="myNCDFdata.RData")
Or else you can read the ncdf data to an empty workspace, do whatever transformations you need, and then quit R and click ok to save workspace.
I am using R to work with meteorological data. I proceed in two steps:
convert grib to netcdf using the command line function ncl_convert2nc from ncar command language
use package ncdf in R to import the netcdf data.
I still have one problem:
2- For some particular grib files, the conversion with ncar tool does not work. Is there other ways or trick (other than transcription into netcdf) to read grib files in R ?
Problem Answered by Dirk: 1- I would like to do automatic treatment of many files within R. Can I call ncl_convert2nc within R ? (answered by Dirk Eddelbuettel below )
Regarding question 1, the answer is 'Yes' -- see help(system) and the internal=TRUE option if you want to capture results.
rgdal also can do it, but is less flexible and requires more care and detail than ncdf or RNetCDF - and depends of your GDAL/rgdal built including the GRIB driver.
ncl_convert2nc seems to be the best solution. However, if the structure of data is a little bit more complicated I use GrADS to convert GRIB file to ASCII (e.g. .csv) and then it is possible to create NetCDF file using ncdf4 package dedicated for R. GrADS also provides support for re-writing GRIB to NetCDF, but there is limitation to only 1 variable.
As an alternative to calling ncl_convert2nc from R, there are two alternatives I can suggest:
1. CDO conversion
Another quick and easy command line solution is to use cdo to convert to netcdf to read in:
cdo -f nc copy file.grb file.nc
If you want to output a netcdf4 file you specify "-f nc4".
One potential glitch with this approach is if your grib file has more than one time axis (e.g. for multiple seasonal forecasts) which can cause issues with the conversion.
2. ECCODES conversion
Instead eccodes offers a grib converter that is very robust and can handle all cases of multiple time axes which usually cause CDO and NCL based conversions to fail.
The command is called grib_to_netcdf
grib_to_netcdf -o output.nc input_grib.grb
So far, grib_to_netcdf has been able to handle every grib file I have thrown at it without problems.
Another solution is to use the wgrib/wgrib2 software (http://www.cpc.ncep.noaa.gov/products/wesley/wgrib2/) and dump your GRIB-1/GRIB-2 file directly to CSV format, e.g.:
/path/to/your/wgrib2 input_file.grb -csv output_file.csv
Then it may be read directly in R...