dis-organization/ncdf4

(fork of CRAN ncdf4 version 1.16)

ncdf4

The goal of ncdf4 is to provide an "Interface to Unidata netCDF (Version 4 or Earlier) Format Data Files".

This fork of the CRAN package ncdf4 is intended to update the Windows build process, and specifically to add support for Thredds.

Alternatives:

• Unidata provides Visual Studio binaries that can be used to put a build together
• pmjherman has this repo

Todo

• check Makevars.win (assume can remove "DHAVE_LIBUDUNITS2" but what about "-DHAVE_DECL_NC_RENAME_GRP=1"?)
• add tests, especially for Thredds (make sure 32-bit Windows limitation is understood)
• roxygenize?

Installation

You can install the released version of ncdf4 from CRAN with:

install.packages("ncdf4")

And the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("mdsumner/ncdf4")

Example

Read from Thredds (will only work in Windows 64-bit, not 32-bit).

u <- "http://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwind3day"
nc <- ncdf4::nc_open(u)
class(nc)
#> [1] "ncdf4"
## note that "ncdf" argument is required to trigger use of ncdf4
r <- raster::raster(u, ncdf = TRUE, varname = "x_wind")
print(r)
#> class       : RasterLayer 
#> band        : 1  (of  3774  bands)
#> dimensions  : 1201, 2881, 3460081  (nrow, ncol, ncell)
#> resolution  : 0.125, 0.125  (x, y)
#> extent      : -0.0625, 360.0625, -75.0625, 75.0625  (xmin, xmax, ymin, ymax)
#> coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 
#> data source : http://coastwatch.pfeg.noaa.gov/erddap/griddap/erdQSwind3day 
#> names       : Zonal.Wind 
#> z-value     : 932644800 
#> zvar        : x_wind 
#> level       : 1

ncdf4's Issues

Issue with nc_open on Windows

Hi @mdsumner , this code fails on Windows

ncdf4::nc_open("https://www.ncei.noaa.gov/thredds/dodsC/ncFC/fc-oisst-daily-avhrr-only-dly/OISST_Daily_AVHRR-only_Feature_Collection_best.ncd")

Error in R_nc4_open: NetCDF: Invalid argument

The same code goes well on linux;

Any idea how to solve that?

Different time dimension reads across ncdf4 vs. xarray & panoply

Hesitant to raise this issue because it felt above my head to diagnose, but here is a synopsis of deeper issue of an original question raised here on stackoverflow.

Original question was how to convert dates of a netcdf file, read into R using ncdf4::nc_open() that had units of "minutes since 1850-01-16T14:06:00"

Through exploring answers to the question we noticed that we could answer the original question of how to convert the dates, but the outputs never aligned with the expected results, which we knew from opening the same file in {xarray} and panoply. With the ultimate solution resulting in multiplying the time dimension by sixty before converting to datetime (which is counterintuitive to the netcdf units) and then correcting the alignment of the day.

I guess the larger question is whether anyone else has encountered this mismatch of time/attributes across packages.

Happy to provide more context if there is an avenue to diagnosing the issue. Also understand if this is an edge case where the juice is not worth the squeeze. Appreciate the work you do.

source that doesn't work

HELP! Does anyone know why this source doesn't work? (rwinlib is at 4.4.1.1)

https://cida.usgs.gov/thredds/dodsC/stageiv_combined

It's in this catalog:

https://cida.usgs.gov/thredds/catalog.html

Combine multiple netcdf files containing multiple variables

Dear Sir,
Please can you advice me how to combine the attached netcdf argo files contaning multiple variables into a single netcdf file gathering all the data?

argo_download (15).tar.gz