Re: [R-sig-Geo] Guidance/ resources needed for geospatial analysis of floods

[GilbertoCamara]

Dear Saeed 

Please take a look at the CRAN Task View on Spatial Data Analysis:
https://cran.r-project.org/web/views/Spatial.html

Best
Gilberto

Prof Dr Gilberto Camara
Senior Researcher
National Institute for Space Research (INPE), Brazil
https://gilbertocamara.org/
=




> On 27 Mar 2023, at 13:50, Khan, Saeed Akhtar  
> wrote:
> 
> Dear colleagues,
> 
> I want to perform a basic geospatial analysis of flood events (magnitude, 
> extent, etc.) on the rasters data. Can you please suggest some good resources 
> on geospatial analysis and how to do it in R?
> 
> Best wishes,
> Saeed
> 
> 
> Saeed A. Khan
> PhD Candidate
> Institute of Geography, Universit�t Bayreuth
> Universit�tsstra�e 30, 95447 Bayreuth, Germany
> Tel.: +49 921 55-2054  E-Mail: 
> saeed.k...@uni-bayreuth.de
> 
> Personal website | 
> GoogleScholar | 
> ResearchGate | 
> Twitter
> Recent research article: 
> https://doi.org/10.1007/s11629-021-7297-y
> 
> 
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> 
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Re: [R-sig-Geo] Raster Data Management Advice

[GilbertoCamara]

Dear Edzer and Alexander

STAC is rapidly expanding to become a “de facto” standard. STAC is being 
adopted by relevant cloud data providers of Earth observation data, such as 
Microsoft Planetary Computing and Earth on AWS. Its use is gradually replacing 
the OCG catalogue specification.

The “rstac” package is able to access STAC endpoints. For examples on how to 
use the “rstac” package directly, there is a nice tutorial by Marius Appel 
(author of the “gdalcubes” package) that shows how to combine “rstac” with 
“gdalcubes”. It’s available at https://youtu.be/Xlg__2PeTXM?t=3693

For R examples of access to large cloud computing collections using STAC under 
the hood, please take a look at the following chapter of the “sits” package 
documentation: 
https://e-sensing.github.io/sitsbook/earth-observation-data-cubes.html

Hope this helps.

Best
Gilberto

Prof Dr Gilberto Camara
Senior Researcher
National Institute for Space Research (INPE), Brazil
https://gilbertocamara.org/
=




> On 7 Oct 2022, at 16:13, Edzer Pebesma  wrote:
> 
> STAC is clearly the future of catalogues for spatial data, but not everyone 
> has gotten there yet. Searching or browsing available STACs is helped by stac 
> index, https://stacindex.org/
> 
> On 07/10/2022 18:43, Zivan Karaman wrote:
>> Hi,
>> Perhaps STAC  could help you?
>> Best,
>> Zivan
>> On Fri, Oct 7, 2022 at 6:35 PM Alexander Ilich  wrote:
>>> 
>>> Hi, I was wondering if anyone has some advice on how to organize raster
>>> data so that it is easily queryable by various attributes (e.g. find me all
>>> the rasters of data type bathymetry, collected by this organization with
>>> 10m resolution or finer ). Currently we have data on a server organized
>>> often by when/where it was collected but that can make it difficult to find
>>> specific rasters that meet a certain criteria. I've created a table as a
>>> csv file on github  where
>>> each row is a raster and it has various column attributes describing it
>>> (e.g. who collected it, what sonar was used, resolution, coordinate system,
>>> etc) and a path to the filename as a temporary solution, but I think some
>>> type of spatial database that would allow for querying and then reading
>>> into R as terra objects, as well as into QGIS and ArcGIS as layers for
>>> visualization would be optimal as multiple project members use these data.
>>> Tools I've come across that seem potentially useful include PostGIS and
>>> Geopackage, but I'm not entirely sure how to properly set them up or if
>>> they'd suit my needs. Any advice would be greatly appreciated.
>>> 
>>> Thanks,
>>> Alex
>>> 
>>> [[alternative HTML version deleted]]
>>> 
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> 
> -- 
> Edzer Pebesma
> Institute for Geoinformatics
> Heisenbergstrasse 2, 48151 Muenster, Germany
> Phone: +49 251 8333081
> 
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Re: [R-sig-Geo] Satellite Image analysis-TRMM Data

[GilbertoCamara]

Dear Sownal

If you are interested in satellite image time series analysis, please take a 
look at the “sits” package, available on CRAN. Documentation is available at 

https://e-sensing.github.io/sitsbook/index.html

Best
Gilberto

Prof Dr Gilberto Camara
Senior Researcher
National Institute for Space Research (INPE), Brazil
https://gilbertocamara.org/
=




> On 28 Aug 2022, at 04:59, sownal chand  wrote:
> 
> Hello Sir/Madam,
> 
> I was looking for some information on satellite data analysis using R. If
> someone can provide me with a link or some materials for reading it
> would be great.
> 
> Thanking you in advance
> sownalc
> 
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Re: [R-sig-Geo] rgdal retirement

[GilbertoCamara]

Dear Roger 

I would like to offer you a strong praise and recognition from our team at 
INPE, Brasil, for your strong contributions to the R-spatial community. Rgdal 
is perhaps the most tangible direct outcome from your efforts, but your 
influence goes much beyond the support for developing R packages.

You have made a decisive contribution to the whole R-spatial community, by your 
strong community for building bridges between us. I remember vividly your visit 
to Brazil in 2002, where you showed us the benefits of joining the R community. 
It took some time, but now we are firmly on board. 

Your example and your leadership are encouraging proofs that there’s hope to 
build a better and more cooperative planet.

All the best
Gilberto
===
Prof Dr Gilberto Camara
Senior Researcher
National Institute for Space Research (INPE), Brazil
https://gilbertocamara.org/
==


>>> On Sun, Sep 19, 2021 at 9:35 AM Jean-Luc Dupouey <
>> jean-luc.dupo...@inrae.fr>
>>> wrote:
>>> 
 Dear Roger Bivand,
 
 I read your message about the rgdal retirement. It was a nice package
 and an important step in the development of R-spatial.
 
 I looked for alternatives for the functions I was using, but I didn't
 find them all. Those I am missing:
 
 . ogrInfo
 . ogrFIDs
 . make_EPSG
 
 Do you know of any (more or less) equivalent functions in the packages
 you mentioned that have taken over from rgdal?
 
 Thanks in advance,
 
 Jean-Luc Dupouey
 
 --
 INRAE
 UMR Silva
 F-54280 Champenoux
 France
 
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>>> 
>>> 
>>> 
>> 
>> --
>> Roger Bivand
>> Emeritus Professor
>> Department of Economics, Norwegian School of Economics,
>> Postboks 3490 Ytre Sandviken, 5045 Bergen, Norway.
>> e-mail: roger.biv...@nhh.no
>> https://orcid.org/-0003-2392-6140
>> https://scholar.google.no/citations?user=AWeghB0J=en
>> 
> 
> 
> -- 
> Michael Sumner
> Software and Database Engineer
> Australian Antarctic Division
> Hobart, Australia
> e-mail: mdsum...@gmail.com
> 
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[R-sig-Geo] Reporting an issue with rgdal in macOS BigSur

[GilbertoCamara]

Dear R-SIG-GEO and Roger

I am developing an R package (https://github.com/e-sensing/sits 
) to analyse satellite image time series 
(SITS) which is heavily dependent on “rgdal”. 

I would like to report an issue with rgdal in the new macOS BigSur. While I 
agree with Roger that it is not wise to install a new OS until it is stable, I 
hope the information below will be useful. 

For starters, let me praise Roger, Edzer and all those involved in “rgdal”. I 
did some debugging on the source code and was humbled by the effort involved in 
making the code an operational software many of us rely on. Chapeau bas!

That said, please allow me to report on three issues: 

1. Installation 

I have installed GDAL-3.2.0 using Homebrew on BigSur; it works fine. When 
installing the binary version of rgdal-1.5-18 (SVN revision 1082) from CRAN, 
recently released by Simon Urbanek, “rgdal" reports that is is using 
GDAL-3.1.1, which is not installed. The actual message is:
"Loaded GDAL runtime: GDAL 3.1.1, released 2020/06/22”.  

When installing from source, rgdal recognises GDAL-3.2.0, if the Homebrew 
libraries are on the path. The message changes to:
"Loaded GDAL runtime: GDAL 3.2.0, released 2020/10/26."

It is odd that the binary version would report using a runtime that is not 
there.

2. Errors in /vsis3 file access 

In earlier versions of macOS, rgdal had no problems with accessing files in AWS 
with commands such as:

> s3_file <- "/vsis3/sentinel-s2-l2a/tiles/20/L/KP/2018/8/17/0/R20m/B02.jp2”
> rgdal::GDALinfo(s3_file)

In BigSur, it produces an error. Debugging the rgdal code, I found the error to 
arise from line 723 of the “gdal-bindings.cpp” file. This is one of the places 
where rgdal calls the GDAL function “GDALOpenEx”, as follows:

  GDALDataset *pDataset = (GDALDataset *) GDALOpenEx(fn, RWFlag,
papszAllowedDrivers, papszOpenOptions, NULL);

The function call returns a NULL pointer. Since calling gdalinfo externally or 
using gdalUtils::gdalinfo works, it seems there is a problem with the return 
parameters which are provided to rgdal by GDAL. 

To reproduce the issue, one needs AWS credentials. If Roger and/or Edzer wish 
to have a go at this issue, I can provide a temporary credential for doing so. 

3. Errors in TIFF Decoding 

Running devtools::check() produces a strange error on TIFF decoding on a very 
small file. The error is odd:

"TIFFReadDirectory: Warning, Unknown field with tag 42112 (0xa480) encountered."

The call stack is as follows:

   1: .Call("RGDAL_OpenDataset", .normalize_if_path(filename, mustWork = NA),   
  TRUE, silent, allowedDrivers, options, PACKAGE = "rgdal")
   2: .local(.Object, ...)
   3: initialize(value, ...)
   4: initialize(value, ...)
   5: new("GDALReadOnlyDataset", filename, silent = silent, allowedDrivers = 
allowedDrivers, options = options)
   6: GDAL.open(fname, silent = silent, allowedDrivers = allowedDrivers, 
options = options)
   7: rgdal::GDALinfo(file, silent = FALSE)

The error appears to be in the same place as the one reported above. However, 
it is hard to reproduce, because when running on the console, rgdal works.

> ndvi_file <- c(system.file("extdata/raster/mod13q1/sinop-ndvi-2014.tif", 
> package = "sits”))
> rgdal::GDALinfo(ndvi_file, silent = FALSE)

However, given that the place on the “rgdal” code where the error occurs is the 
same, it might be worthwhile to look into the RGDAL-GDAL interface in more 
detail. 

I know it’s my responsibility to have moved to macOS BigSur too soon. Thus, I 
do not expect that you address the issue. That said, any help would be much 
appreciated.

Best regards
Gilberto
===
Prof Dr Gilberto Camara
Secretariat Director
GEO - Group on Earth Observations
7 bis, Avenue de La Paix
CH-1211 Geneva - Switzerland
Tel: +41227308480
Web: www.earthobservations.org 




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