R stars package netcdf. csv file to create a netCDF file using the R package "ncdf4". Apr 12, 2025 · Write a SpatRaster or SpatRasterDataset to a NetCDF file. The file also have 3 different variables: rn, prec and tair. nc file. To The difference between read_ncdf and read_stars for NetCDF files is that the former uses package RNetCDF to directly read the NetCDF file, where the latter uses the GDAL driver for NetCDF files. To override fixing for subdatasets and The R Stats Package stats-deprecated Deprecated Functions in Package 'stats' step Choose a model by AIC in a Stepwise Algorithm stepfun Step Functions - Creation and Class stl Seasonal Decomposition of Time Series by Loess str. The desired outcomes are ease of exploration of NetCDF contents ease of extracting to georeferenced objects (sf, stars, terra) Jul 18, 2019 · export data cubes as netCDF files, making it easy to process further, e. library (tidyverse) library (stars) # example data ex <- tibble ( NetCDF, GDAL stars provides two functions to read data: read_ncdf and read_stars, where the latter reads through GDAL. However, when trying to handle large NetCDF files it might be more convenient to directly use the ncdf4 package or the Climate Data Operators software and stars objects can be converted into an sf object using st_as_sf. copied from cf-post-staging / r-stars Apr 4, 2025 · The difference between read_ncdf and read_stars for NetCDF files is that the former uses package RNetCDF to directly read the NetCDF file, where the latter uses the GDAL driver for NetCDF files. It is a rapidly deloping package, replacing the old raster package. If nx and ny are missing, they are computed as the ceiling of the ratio of the (x or y) range divided by (dx or dy), unless Details This routine writes data values to a variable in a netCDF file. Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'. The raster and stars packages provide quite different approaches and stars is more general than raster, but is similarly higher-level than tidync. License Apache License if curvilinear is a stars object with longitude and latitude values, its coordinate reference system is typically not that of the latitude and longitude values. As a result, it lacks an intuitive user experience and workflow that R users would be familiar with. Typically the objects have (X, Y, Time) dimensions and, after doing the temporal averages, get an object with dimensions ordered as (Time, X, Y). Here, we’ll look at a couple of “reanalysis” datasets consisting of 4-dimensional cubes of retrospective long-term means of climate data generated by observations and a reanalysis climate model, where the dimensions are longitude by latitude by level by time (and level refers to elevation in the Mar 16, 2021 · I have a NetCDF file with a curvilinear (rotated) grid that contains meteorological data. Most capabilities of 'NetCDF' version 4 are supported. For example, you can read a GeoTIFF file as follows: RNetCDF: R Interface to NetCDF Datasets Description This package provides an interface to Unidata's NetCDF library functions (version 4) and furthermore access to Unidata's UDUNITS (version 2) calendar conversions. The current implementation supports all operations on NetCDF datasets in classic and 64-bit offset file formats, and GSP's guide to netCDF format data and the 'R' package 'ncdf'. Package ncdfCF provides a high-level interface using functions and methods that are familiar to the R The above shows that we have a NetCDF sourced stars proxy derived from the reduced. When using a SpatRasterDataset, the varname, longname, and unit should be set in the object (see examples). July 23, 2025 Title Spatiotemporal Arrays, Raster and Vector Data Cubes Version 0. Once you have a stars object in your environment, you can add layers to your ggplot in the same way you'd work with non-spatial data. The library strongly builds on GDAL, netCDF, and SQLite (the full list of C++ libraries used by gdalcubes is found here). This is especially useful to compute climate indicators spatially aggregated to Network Common Data Form ('netCDF') files are widely used for scientific data. Package ncdf4, the most widely used package to access netCDF Details The following logic is applied to coordinates. ignored var variable name or names (they must be on matching grids) ncsub matrix of start, count columns (see Details) curvilinear length two character named vector with names of variables holding longitude and latitude values for all raster cells. See ncdfgeom for more about this NetCDF-based format for geometry and timeseries. 1 Reading, restructuring and writing netCDF files in R The examples provided here include *reading a netCDF file using the ncdf4 package (netCDF4) *reshaping a netCDF “brick” of data into a data frame *reshaping a data frame into an array or “brick” *writing a netCDF file using the ncdf4 package jamster July 13, 2020, 6:03pm 3 Write a SpatRaster or SpatRasterDataset to a NetCDF file. The st_as_stars method for sf Jun 8, 2021 · I'm new to the package stars for R and am trying to do basic spatial operations with curvilinear data. NetCDF, GDAL stars provides two functions to read data: read_ncdf and read_stars, where the latter reads through GDAL. (In the future, both will be integrated in read_stars. merge or split stars object S3 Ops Group Generic Functions for stars objects plot stars object, with subplots for each level of first non-spatial dimension Principle components of stars object Predict values, given a model object, for a stars or stars_proxy object print stars or dimensions object Read NetCDF into stars object Apparently the bilinear extraction in st_extract from the stars package causes problems on a mac with the M1 chip. With this information Mar 26, 2018 · How to open and work with NetCDF data in R. 6-8 Description Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'. 4. The file included metadata which could be used to puzzle out a crs for the xy-indexed Mar 9, 2019 · Related: GDAL and reprojecting a NetCDF file Following above, I would like to reproject a NetCDF ( NOAA GOES-16 file ) using R stars package. Nov 23, 2017 · It shows how stars combines bands and/or subdatasets of GDAL datasets (data cubes) into R arrays with well-referenced space and time dimensions, how it deals with affine (rotated) grids, and how it interfaces to packages dplyr, sf and raster. Within stars is the geom_stars function that allows for rasters to play nice with ggplot2. We’ll start with some basics using datasets included with the stars installation. . Mar 24, 2021 · I'm performing temporal aggregations on netcdf rasters using the stars package in R. If the stars object has only an x/y raster but multiple attributes, these are merged first, then put in a SpatRaster. An R package to explore easy access to NetCDF data sources modeled after the super convenient xarray. Documented in read_ncdf st_as_stars. It is also easy to create new netCDF July 23, 2025 Title Spatiotemporal Arrays, Raster and Vector Data Cubes Version 0. These are both lower-level tools than tidync - they are interfaces to the underlying NetCDF library, and tidync uses both to read information and data. With this information Apr 26, 2020 · Recently, I was working with some netCDF files with raster time-series data in a conic projection. I have been following the suggestions in the package to add the dimension and the variables to the netCDF file. dendrogram General Tree Structures StructTS Fit Structural Time Series summary. Apr 25, 2018 · This writes the NetCDF file, but it only seems to have one month (I'm not sure which), instead of the 12 months of the year when I examine it using panoply. Arguments . However, the new `stars` package is a promising approach to integrate NetCDF files with existing spatial packages for R, i. I will try to make up for the If the stars object has more than three dimensions, all dimensions higher than the third will be collapsed into the third dimensions. R package stars was written to support raster and vector data cubes (Chapter 6), supporting raster layers, raster stacks and feature time series as special cases. 6-8) Spatiotemporal Arrays, Raster and Vector Data Cubes Description Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'. This easy-to-follow guide will navigate you through the NetCDF, GDAL stars provides two functions to read data: read_ncdf and read_stars, where the latter reads through GDAL. 4 days ago · Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. <p>The function materializes a data cube as a temporary netCDF file and loads the file with the stars package. The file should have either been created with nc_create, or opened with nc_open called with parameter write=TRUE. An R st_as_stars of stars packageFor the bbox method: if pretty is TRUE, raster cells may extend the coordinate range of . Library-level access in R is provided through packages 'RNetCDF' and 'ncdf4'. 7. sf first appeared on CRAN in 2016, stars in 2018. An artificial example shows the creation of an origin-destination matrix by travel mode and time. </p> Apr 4, 2025 · The R package 'ncdf4' allows reading from, writing to, and creation of netCDF files, either netCDF version 3 or (optionally) netCDF version 4. The functions support many different kinds of geospatial procedures applied to raster data, like regridding and interpolation, hillslope shading calculations Apr 4, 2025 · Details For the ncdfgeom method: objects are point-timeseries with optional line or polygon geometry for each timeseries specified with the sf_geometry parameter. aov Summarize an Analysis of Variance Oct 15, 2025 · The netCDF data file format from Unidata is a platform-independent, binary file that also contains metadata describing the contents and format of the data in the file. This is the first time I work with NetCDF so I am unsure what I am doing wrong. ncdf4 — Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files. Low-level access The RNetCDF package is developed and maintained by the same team that developed and maintains the netcdf library. Optional conversions of time units are enabled by 'UDUNITS' version 2, also from Unidata. If you choose to create version 4 output files, be aware that older netcdf software might only be able to read version 3 files. 25 degree grid, global daily sea surface temperature product is found here; the subset from 1981 You should use the R-Package netcdf, it has much more possibilities to taylor your resulting data fields. It is built on the RNetCDF package which, like package ncdf4, provides a basic interface to the netcdf library, but which lacks an intuitive user interface. The routines and the documentation follow the NetCDF and UDUNITS C interface, so the corresponding manuals can be consulted for more detailed information. Reading datasets from multiple files Model data are often spread across many files. Contribute to ornldaac/netCDF_data_in_R development by creating an account on GitHub. An interface to the 'NetCDF' file formats designed by Unidata for efficient storage of array-oriented scientific data and descriptions. To hold the GIS compatibility, use the Lon/Lat attribute schema beside the time attribute (Spatial temporal advises ). x character vector with name (s) of file (s) or data source (s) to be read, or a function that returns such a vector sub character, integer or logical; name, index or indicator of sub-dataset (s) to be read passed on to st_as_stars if curvilinear was set options character; opening options driver character; driver to use for opening file. com Arguments . Jul 13, 2020 · 1. ) For reading NetCDF files, package RNetCDF is used, for reading through GDAL, package sf provides the binary linking to GDAL. #'#' The following logic is applied to coordinates. In Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. The above shows that we have a NetCDF sourced stars proxy derived from the reduced. The st_as_stars method for sf processNC is an R package for processing and analysing NetCDF files in R. 1 Reading raster data You can use read_stars() to read a raster data file. Here is a reproducible example of what I'm doing. This R interface is closely based on the C API of the NetCDF4 library, and it includes calendar conversions from the Unidata UDUNITS2 library. `stars` attempts to figure out appropriate curvilinear An interface to the NetCDF file format designed by Unidata for efficient storage of array-oriented scientific data and descriptions. Package 'ncdfCF' is built on top of 'RNetCDF' and makes the data and its attributes available as a set of R6 classes that are informed by the Climate and Forecasting Metadata Conventions. If in addition to nx and ny, dx and dy are also missing, these are set to a single value computed as sqrt (diff (xlim)*diff (ylim)/n). The nc_request object contains the information needed to make requests for data according to the dimensions of the NetCDF data source. Details For the ncdfgeom method: objects are point-timeseries with optional line or polygon geometry for each timeseries specified with the sf_geometry parameter. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. `sf`. As an example, we will use a Sentinel 5P dataset available from package starsdata; this package R package with some netcdf tools. If xy is not specified and the first two dimensions in dims are both numeric, then it is set to these two dimensions. stars (version 0. See full list on github. x NetCDF file or source as a character vector or an nc_proxy object. ncdfgeom #' Read NetCDF into stars object#'#' Read data from a file (or source) using the NetCDF library directly. NetCDF files can easily be loaded into R using the rast() function from the terra package in R or formerly also using the raster() function from the raster package. Mar 7, 2022 · I'm trying to crop a netcdf file with a polygon with stars package from daily netcdf data. Aug 26, 2019 · NetCDF time aggregation using R stars package Ask Question Asked 6 years, 2 months ago Modified 5 years, 10 months ago Apr 4, 2025 · NetCDF data sources are available via more and less granular files and/or OPeNDAP endpoints. Rather than describing the curvature parametrically, the typical (HDF5 or NetCDF) files in which they are found have two raster layers with the longitudes and latitudes for every corresponding pixel of remaining layers. The difference between read_ncdf and read_stars for NetCDF files is that the former uses package RNetCDF to directly read the NetCDF file, where the latter uses the GDAL driver for NetCDF files. There is nothing obviously wrong with the netcdf file, as other packages like tidync can plot the data. License Apache License Nov 5, 2019 · There are various other packages for NetCDF in R, the main ones being RNetCDF and ncdf4. I want to read the file using terra, but I get unexpected res Jul 22, 2020 · In R, there are deviations calculating the mean in function 'zonal. g. Sep 13, 2022 · What is Zarr? Aggregating global precipitation time series to countries 50m natural Earth country boundaries simple aggregation CMIP6 data Reading sub-arrays or strided arrays Using the classic GDAL raster API Software versions [view raw Rmd] Summary: Zarr files are the new cloud native NetCDF, and are here to stay. Contribute to odrans/nctools development by creating an account on GitHub. Tim and Doug talked after lunch) to use this format as much as possible when creating or manipulating data sets. I am using netCDF climate data. , precision) of the values written to the file is determined when the variable is created; in particular, it does not matter what type you pass to this function to be written. The problem was the data file did not include latitude/longitude data for the pixels or a coordinate reference system (crs). The st_as_stars method for sf This chapter introduces R packages sf and stars. Development of both packages Apr 7, 2020 · I am trying to work with cordex climatic data (curvelinear and rotated data) in the stars package, and I am having a lot of issues, so decided to simply reproduce online example, and I fail reading Jul 9, 2022 · R Language Collective r netcdf r-stars Share Improve this question Follow this question to receive notifications Feb 1, 2023 · Unfortunately it seems as though there might be something wrong with the netcdf4 files ESA provided, as I'm running into odd errors while working with them in the 'stars' package in R. GSP made an executive decision earlier this year (i. More information is available in R API documentation and usage examples. netCDF is a common, self-describing, portable binary format for geophysical data. It has a number of options, depending on whether pixels represent the point value at the pixel center, or small square polygons with a single value. Does anybody found the problem and/or has a workaround? Jan 7, 2022 · Use the ncdf4 package for reading NetCDF files - it lets you get the variables and dimensions and then you have control. NetCDF is an abstraction How to open and work with NetCDF data in R by Alison Boyer Last updated about 8 years ago Comments (–) Share Hide Toolbars RNetCDF provides an R interface to the NetCDF file format designed by Unidata for efficient storage of array-oriented scientific data and descriptions. e. I have tried both with the ncdf4 and raster packages. sf provides a table format for simple features, where feature geometries are stored in a list-column. License Apache License RNetCDF - Interface to NetCDF Datasets for R RNetCDF provides an R interface to the NetCDF file format designed by Unidata for efficient storage of array-oriented scientific data and descriptions. Read data from a file (or source) using the NetCDF library directly. However, I have been unsuccessful at the first step; The R package 'ncdf4' allows reading from, writing to, and creation of netCDF files, either netCDF version 3 or (optionally) netCDF version 4. Some of the spatial packages seem to make assumptions about NetCDFs that aren't true. Jul 7, 2022 · R terra not reading attributes from NetCDF file Ask Question Asked 3 years, 3 months ago Modified 3 years, 1 month ago This R package presents helper functions to compute zonal statistics using NetCDF and sf objects for climate studies. This blog post will explore how they can be read in R using the GDAL October 11, 2025 Title Spatiotemporal Arrays, Raster and Vector Data Cubes Version 0. Zonal statistics is a Geographic Information System (GIS) method to compute a summary statistic (like mean, standard deviation, or sum) of a spatially contiguous indicator for a given boundary. x on all sides. Access to the data uses standard R subsetting We would like to show you a description here but the site won’t allow us. Mar 10, 2015 · 2 I am trying to use the data on my own . Curvilinear grids Curvilinear grids are grids whose grid lines are not straight. ``` {r, echo = T, eval = F} devtools::install_github ('r-spatial/stars') ``` To load the data, `stars` makes use of its generic `read_stars` function which allows reading raster/array data. 2 The terra package The terra package is large library of functions and methods for dealing with raster data sets, including many geospatial formats, including netCDF. If the data has two or more dimensions and the first two are regular they are nominated as the 'raster' for plotting Summary: Zarr files are the new cloud native NetCDF, and are here to stay. The normal stars dimension(s) are available and a nc_request object is also available. 6-9 Description Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'. R has the capability of reading and writing (and hence analyzing) netCDF files, using the ncdf and ncdf4 packages provided by David Pierce, and through other packages like terr, metR1, and RNetCDF. Learn how to effectively subset climatic variables from `ncdf` files using the `stars` package in R. We'll start with some basics using datasets included with the stars installation. Is it possible to write the NetCDF file and keep as much of the data from the R-grid file as possible? Especially the data for each month! EDIT: New working code: test <- brick('/TavgM_1981 Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Jul 5, 2023 · 3 I am trying to load data from a NetCDF file to r and continue having issues even after following a couple tutorials and SO posts. It shows how stars plots look (now), how subsetting works, and how conversion to Raster and ST (spacetime) objects works. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF Apr 26, 2024 · I have a netcdf file that has the dimensions of lat, lon, time and effect. We see it has four variables and their units are displayed. The R package ncdf4 can read either format. An example of a 0. Version 4 of the netcdf library stores data in HDF5 format files; earlier versions stored data in a custom format. stats' of package 'spatialEco' compared to 'extract' in package 'raster'. , with stars or raster. CMIP6 data is being released as Zarr data on the Google Cloud. I am trying to crop the NetCDF based on a mask shapefile in R, but the rotated grid does not project the da Jul 22, 2019 · Check out the stars package for manipulating spatiotemporal arrays. It provides an interface to the netcdf library that stays very close to the API of the C library. I am able to read the netcdf into r along with a shapefile I w Mar 22, 2018 · Summary Plots of raster data Subsetting Conversions: raster, spacetime Easier set-up Earlier stars blogs [view raw Rmd] Summary This is the second blog on the stars project, an R-Consortium funded project for spatiotemporal tidy arrays with R. The R interface is closely based on the C API of the NetCDF library, and it includes calendar conversions from the Unidata UDUNITS library. Dec 29, 2022 · Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'. If any coordinate axes have regularly spaced coordinate variables they are reduced to the offset/delta form with 'affine = c (0, 0)', otherwise the values of the coordinates are stored and used to define a rectilinear grid. `stars` attempts to figure out appropriate curvilinear Sep 16, 2022 · I'm trying to save properly formatted stars object to netCDF file with no success. I think I have managed to do it and could get this plot with this script library (tidyverse) library (sf) l The ncdfCF package provides an easy to use interface to netCDF resources in R, either in local files or remotely on a THREDDS server. It is also easy to create new netCDF Jul 12, 2024 · Trying to reconstruct a similar structure to the original netcdf file using the ncdf4 package doesn't get me there either (but as with the stars package, it may be due to my lack of familiarity & skills): ## using ncdf4 package, fetch the relevant variables and dimensions and then rebuild a netcdf file: dta <- nc_open(filename) # 2 stars The stars package, like terra and sf can easily read and write netCDF files. NetCDF data sources are available via more and less granular files and/or OPeNDAP endpoints. I was doing some calculations with the data and wished to plot the results as a map. This blog post will explore how they can be read in R using the GDAL “classic” raster API and the (relatively) new GDAL multidimensional array API, and how we can read sub-arrays or strided (subsampled, lower resolution) arrays. It can be particularly useful for those who use spatiotemporal raster data often (like :exclamation: This is a read-only mirror of the CRAN R package repository. It is very unlikely that the raster file you are trying to read is not in one of the supported formats. Note that the data type (i. My best best guess is that there is something related to nc_coord_var function in the ncmeta package, which the read_ncdf function uses, but I'm not really sure, nor am I sure about my course of action here. Apr 4, 2025 · Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'. If any coordinate axes have#' regularly spaced coordinate variables they are reduced to the#' offset/delta form with 'affine = c (0, 0)', otherwise the values of the coordinates#' are stored and Sep 24, 2024 · Before you start In this Chapter, we introduce the stars package (Pebesma 2020) for raster data handling. For both I used a polygon as the zone field and a raster These are both lower-level tools than tidync - they are interfaces to the underlying NetCDF library, and tidync uses both to read information and data. My dataset is composed by 3 columns: longitude, latitude and temperature and it has 2592 rows. This article demonstrates how stars enables discovery, access, and processing of NetCDF data across a wide range of such source-data organization schemes. Technically, the R package is a relatively lightweight wrapper around the gdalcubes C++ library. The R package provides additional functionality, with adaptations of the exactextract algorithm to rasterize polygonal data or resample gridded data. 4pni cn477 k3cq 5orh 57q a2n ngo jnksc 3gcod7ws l1