RQGIS release 0.2.0

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RQGIS release 0.2.0

Jannes
Dear list members,

today we are happy to announce a new version of RQGIS! RQGIS establishes an interface between R and QGIS, i.e. it allows the user to access the more than 1000 QGIS geoalgorithms from within R. The most important news is that you can run again the most recent QGIS releases (>=2.18.2) with RQGIS without having to modify Python source code. This modification became necessary due to a bug introduced in QGIS 2.16 (see https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181).

This release fixes also several bugs which we detected thanks to user feedback. To learn more about these, please refer to https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0.

For more information on RQGIS, how to install it and examples how to use RQGIS, please refer to https://github.com/jannes-m/RQGIS and my https://jannesm.wordpress.com/category/r/.

All the best,

Jannes

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Re: RQGIS release 0.2.0

Ali Santacruz

Awesome work! Thanks a lot!


I've been able to run QGIS and SAGA algorithms without issues. However, I have some problems running GRASS algorithms,

I'm trying to run r.neighbors from GRASS 7, but the resolution, extent and values of the output raster don't match those of the input,


Here is the code:


# Load raster
library(raster)

r1 <- raster("pred_m1_3000_recl5.tif")
r1


class       : RasterLayer
dimensions  : 837, 849, 710613  (nrow, ncol, ncell)
resolution  : 1, 1  (x, y)
extent      : 0, 849, -837, 0  (xmin, xmax, ymin, ymax)
coord. ref. : NA
data source : E:\amsantac\dstl\working\pred\pred_m1_3000_recl5.tif
names       : pred_m1_3000_recl5
values      : 5, 110  (min, max)


# Load RQGIS
library(RQGIS)
my_env <- set_env("C:/OSGeo4W64/")
dir_tmp <- tempdir()


# Set parameters for grass7:r.neighbors
params <- get_args_man(alg = "grass7:r.neighbors", qgis_env = my_env)
params$input  <- r1
params$method  <- 2 # "Mode"
params$output  <- file.path(dir_tmp, "rst_out.tif")

params$GRASS_REGION_PARAMETER <- "0,849,-837,0"    # as xmin, xmax, ymin, ymax
params$GRASS_REGION_CELLSIZE_PARAMETER <- "1.0"

out <- run_qgis(alg = "grass7:r.neighbors", params = params, load_output = params$output, qgis_env = my_env)
out


class       : RasterLayer
dimensions  : 1, 7, 7  (nrow, ncol, ncell)
resolution  : 0.1519435, 1  (x, y)
extent      : 0, 1.063604, 0, 1  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
data source : C:\Users\Guest\AppData\Local\Temp\RtmpwJu31Y\rst_out.tif
names       : rst_out



Note the output only has 1 row, 7 cols (vs. 837 rows, 849 cols in input). The CRS has been set as long-lat, while the CRS is NA in the input,


Also note that the resolution has been changed from 1 to 0.1519,


I wonder if there is an issue on how the params$GRASS_REGION_PARAMETER is defined. I have tried different ways eg., "0,849,-837,0" (as xmin, xmax, ymin, ymax), "0,-837,849,0" (as xmin, ymin, xmax, ymax), extent(r1) (which gives error).


The input image (550 kb) can be downloaded from this link: https://www.dropbox.com/s/do95t48foepw62e/pred_m1_3000_recl5.tif?dl=0



Thanks for your help,


Best regards,


Ali



sessionInfo()


R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] RQGIS_0.2.0.9000     raster_2.5-8         sp_1.2-3             RevoUtilsMath_10.0.0

loaded via a namespace (and not attached):
[1] RevoUtils_10.0.2 rgdal_1.1-10     tools_3.3.2      Rcpp_0.12.7      grid_3.3.2       lattice_0.20-34


________________________________
De: R-sig-Geo <[hidden email]> en nombre de "Jannes M�nchow" <[hidden email]>
Enviado: jueves, 19 de enero de 2017 06:31:34 a. m.
Para: [hidden email]
Asunto: [R-sig-Geo] RQGIS release 0.2.0

Dear list members,

today we are happy to announce a new version of RQGIS! RQGIS establishes an interface between R and QGIS, i.e. it allows the user to access the more than 1000 QGIS geoalgorithms from within R. The most important news is that you can run again the most recent QGIS releases (>=2.18.2) with RQGIS without having to modify Python source code. This modification became necessary due to a bug introduced in QGIS 2.16 (see https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181).

[https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181>

GitHub - jannes-m/RQGIS: RQGIS - integrating R with QGIS<https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181>
github.com
RQGIS - integrating R with QGIS ... Now that we have a spatial object, we can move on to using RQGIS. First of all, we need to specify all the paths necessary to run ...




This release fixes also several bugs which we detected thanks to user feedback. To learn more about these, please refer to https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0.

[https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0>

jannes-m/RQGIS<https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0>
github.com
RQGIS - integrating R with QGIS




For more information on RQGIS, how to install it and examples how to use RQGIS, please refer to https://github.com/jannes-m/RQGIS and my https://jannesm.wordpress.com/category/r/.

Posts about R on jannesm<https://jannesm.wordpress.com/category/r/>
jannesm.wordpress.com
Posts about R written by jannesm



[https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://github.com/jannes-m/RQGIS>

GitHub - jannes-m/RQGIS: RQGIS - integrating R with QGIS<https://github.com/jannes-m/RQGIS>
github.com
RQGIS - integrating R with QGIS ... Now that we have a spatial object, we can move on to using RQGIS. First of all, we need to specify all the paths necessary to run ...




All the best,

Jannes

_______________________________________________
R-sig-Geo mailing list
[hidden email]
https://stat.ethz.ch/mailman/listinfo/r-sig-geo

R-sig-Geo Info Page - ETH Zurich<https://stat.ethz.ch/mailman/listinfo/r-sig-geo>
stat.ethz.ch
R-sig-Geo -- R Special Interest Group on using Geographical data and Mapping About R-sig-Geo




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Re: RQGIS release 0.2.0

Patrick Schratz
Dear Ali,

a general note: Please write a new mail if you have a specific problem with
a package instead of replying to the last mail related to the package.

Regarding your issue: I think this error relates to your file and its
missing projection and extent information.

I just tried the code using the RQGIS "dem" dataset and everything worked
fine. Also, I´m not sure if "GRASS_REGION_PARAMETER" and
"GRASS_REGION_CELLSIZE_PARAMETER" need to be set at all or you should
better go with the defaults.

If you want to quickly check the algorithm help you can use
`open_help("grass7:r.neighbors")`.

*library(RQGIS)*
*library(raster)*
*r2 <- data("dem")*

*my_env <- set_env()*

*params <- get_args_man(alg = "grass7:r.neighbors", qgis_env = my_env)*
*params$input  <- dem*
*params$method  <- 2 # "Mode"*
*params$output  <- file.path(tempdir(), "rst_out.tif")*

*out <- run_qgis(alg = "grass7:r.neighbors", params = params, *
*                load_output = params$output, qgis_env = my_env)*
*out*

------

macOS, QGIS 2.18.2, GRASS 7.0

You may also want to post such issues at the Github repository
<https://github.com/jannes-m/RQGIS/issues> or at Stackoverflow/GISexchange
using the tag 'rqgis' in the future.
Issues like this which feature large code blocks and are related to a
specific R package can be much better addressed there than by mail.

Best, Patrick





2017-01-21 15:51 GMT+01:00 Ali Santacruz <[hidden email]>:

>
> Awesome work! Thanks a lot!
>
>
> I've been able to run QGIS and SAGA algorithms without issues. However, I
> have some problems running GRASS algorithms,
>
> I'm trying to run r.neighbors from GRASS 7, but the resolution, extent and
> values of the output raster don't match those of the input,
>
>
> Here is the code:
>
>
> # Load raster
> library(raster)
>
> r1 <- raster("pred_m1_3000_recl5.tif")
> r1
>
>
> class       : RasterLayer
> dimensions  : 837, 849, 710613  (nrow, ncol, ncell)
> resolution  : 1, 1  (x, y)
> extent      : 0, 849, -837, 0  (xmin, xmax, ymin, ymax)
> coord. ref. : NA
> data source : E:\amsantac\dstl\working\pred\pred_m1_3000_recl5.tif
> names       : pred_m1_3000_recl5
> values      : 5, 110  (min, max)
>
>
> # Load RQGIS
> library(RQGIS)
> my_env <- set_env("C:/OSGeo4W64/")
> dir_tmp <- tempdir()
>
>
> # Set parameters for grass7:r.neighbors
> params <- get_args_man(alg = "grass7:r.neighbors", qgis_env = my_env)
> params$input  <- r1
> params$method  <- 2 # "Mode"
> params$output  <- file.path(dir_tmp, "rst_out.tif")
>
> params$GRASS_REGION_PARAMETER <- "0,849,-837,0"    # as xmin, xmax, ymin,
> ymax
> params$GRASS_REGION_CELLSIZE_PARAMETER <- "1.0"
>
> out <- run_qgis(alg = "grass7:r.neighbors", params = params, load_output =
> params$output, qgis_env = my_env)
> out
>
>
> class       : RasterLayer
> dimensions  : 1, 7, 7  (nrow, ncol, ncell)
> resolution  : 0.1519435, 1  (x, y)
> extent      : 0, 1.063604, 0, 1  (xmin, xmax, ymin, ymax)
> coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84
> +towgs84=0,0,0
> data source : C:\Users\Guest\AppData\Local\Temp\RtmpwJu31Y\rst_out.tif
> names       : rst_out
>
>
>
> Note the output only has 1 row, 7 cols (vs. 837 rows, 849 cols in input).
> The CRS has been set as long-lat, while the CRS is NA in the input,
>
>
> Also note that the resolution has been changed from 1 to 0.1519,
>
>
> I wonder if there is an issue on how the params$GRASS_REGION_PARAMETER is
> defined. I have tried different ways eg., "0,849,-837,0" (as xmin, xmax,
> ymin, ymax), "0,-837,849,0" (as xmin, ymin, xmax, ymax), extent(r1) (which
> gives error).
>
>
> The input image (550 kb) can be downloaded from this link:
> https://www.dropbox.com/s/do95t48foepw62e/pred_m1_3000_recl5.tif?dl=0
>
>
>
> Thanks for your help,
>
>
> Best regards,
>
>
> Ali
>
>
>
> sessionInfo()
>
>
> R version 3.3.2 (2016-10-31)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
> Running under: Windows >= 8 x64 (build 9200)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
> States.1252    LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C                           LC_TIME=English_United
> States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RQGIS_0.2.0.9000     raster_2.5-8         sp_1.2-3
>  RevoUtilsMath_10.0.0
>
> loaded via a namespace (and not attached):
> [1] RevoUtils_10.0.2 rgdal_1.1-10     tools_3.3.2      Rcpp_0.12.7
> grid_3.3.2       lattice_0.20-34
>
>
> ________________________________
> De: R-sig-Geo <[hidden email]> en nombre de "Jannes
> Münchow" <[hidden email]>
> Enviado: jueves, 19 de enero de 2017 06:31:34 a. m.
> Para: [hidden email]
> Asunto: [R-sig-Geo] RQGIS release 0.2.0
>
> Dear list members,
>
> today we are happy to announce a new version of RQGIS! RQGIS establishes
> an interface between R and QGIS, i.e. it allows the user to access the more
> than 1000 QGIS geoalgorithms from within R. The most important news is that
> you can run again the most recent QGIS releases (>=2.18.2) with RQGIS
> without having to modify Python source code. This modification became
> necessary due to a bug introduced in QGIS 2.16 (see
> https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181).
>
> [https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://
> github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181>
>
> GitHub - jannes-m/RQGIS: RQGIS - integrating R with QGIS<
> https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181>
> github.com
> RQGIS - integrating R with QGIS ... Now that we have a spatial object, we
> can move on to using RQGIS. First of all, we need to specify all the paths
> necessary to run ...
>
>
>
>
> This release fixes also several bugs which we detected thanks to user
> feedback. To learn more about these, please refer to
> https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0.
>
> [https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://
> github.com/jannes-m/RQGIS/releases/tag/v0.2.0>
>
> jannes-m/RQGIS<https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0>
> github.com
> RQGIS - integrating R with QGIS
>
>
>
>
> For more information on RQGIS, how to install it and examples how to use
> RQGIS, please refer to https://github.com/jannes-m/RQGIS and my
> https://jannesm.wordpress.com/category/r/.
>
> Posts about R on jannesm<https://jannesm.wordpress.com/category/r/>
> jannesm.wordpress.com
> Posts about R written by jannesm
>
>
>
> [https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://
> github.com/jannes-m/RQGIS>
>
> GitHub - jannes-m/RQGIS: RQGIS - integrating R with QGIS<
> https://github.com/jannes-m/RQGIS>
> github.com
> RQGIS - integrating R with QGIS ... Now that we have a spatial object, we
> can move on to using RQGIS. First of all, we need to specify all the paths
> necessary to run ...
>
>
>
>
> All the best,
>
> Jannes
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>
> R-sig-Geo Info Page - ETH Zurich<https://stat.ethz.ch/
> mailman/listinfo/r-sig-geo>
> stat.ethz.ch
> R-sig-Geo -- R Special Interest Group on using Geographical data and
> Mapping About R-sig-Geo
>
>
>
>
>         [[alternative HTML version deleted]]
>
>
> _______________________________________________
> R-sig-Geo mailing list
> [hidden email]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo
>

        [[alternative HTML version deleted]]

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Re: RQGIS release 0.2.0

Ali Santacruz

Dear Patrick,


Thank you very much for your reply.


You're right. It must be an issue with my file. After your email, I tried the example with the dem dataset and it worked well,


Thanks for the other suggestions. I'll keep them in mind,


Best regards,


Ali


________________________________
De: Patrick Schratz <[hidden email]>
Enviado: s�bado, 21 de enero de 2017 12:16:10 p. m.
Para: Ali Santacruz
Cc: Jannes M�nchow; [hidden email]
Asunto: Re: [R-sig-Geo] RQGIS release 0.2.0

Dear Ali,

a general note: Please write a new mail if you have a specific problem with a package instead of replying to the last mail related to the package.

Regarding your issue: I think this error relates to your file and its missing projection and extent information.

I just tried the code using the RQGIS "dem" dataset and everything worked fine. Also, I�m not sure if "GRASS_REGION_PARAMETER" and "GRASS_REGION_CELLSIZE_PARAMETER" need to be set at all or you should better go with the defaults.

If you want to quickly check the algorithm help you can use `open_help("grass7:r.neighbors")`.

library(RQGIS)
library(raster)
r2 <- data("dem")

my_env <- set_env()

params <- get_args_man(alg = "grass7:r.neighbors", qgis_env = my_env)
params$input  <- dem
params$method  <- 2 # "Mode"
params$output  <- file.path(tempdir(), "rst_out.tif")

out <- run_qgis(alg = "grass7:r.neighbors", params = params,
                load_output = params$output, qgis_env = my_env)
out

------

macOS, QGIS 2.18.2, GRASS 7.0

You may also want to post such issues at the Github repository<https://github.com/jannes-m/RQGIS/issues> or at Stackoverflow/GISexchange using the tag 'rqgis' in the future.
Issues like this which feature large code blocks and are related to a specific R package can be much better addressed there than by mail.

Best, Patrick





2017-01-21 15:51 GMT+01:00 Ali Santacruz <[hidden email]<mailto:[hidden email]>>:

[[elided Hotmail spam]]


I've been able to run QGIS and SAGA algorithms without issues. However, I have some problems running GRASS algorithms,

I'm trying to run r.neighbors from GRASS 7, but the resolution, extent and values of the output raster don't match those of the input,


Here is the code:


# Load raster
library(raster)

r1 <- raster("pred_m1_3000_recl5.tif")
r1


class       : RasterLayer
dimensions  : 837, 849, 710613  (nrow, ncol, ncell)
resolution  : 1, 1  (x, y)
extent      : 0, 849, -837, 0  (xmin, xmax, ymin, ymax)
coord. ref. : NA
data source : E:\amsantac\dstl\working\pred\pred_m1_3000_recl5.tif
names       : pred_m1_3000_recl5
values      : 5, 110  (min, max)


# Load RQGIS
library(RQGIS)
my_env <- set_env("C:/OSGeo4W64/")
dir_tmp <- tempdir()


# Set parameters for grass7:r.neighbors
params <- get_args_man(alg = "grass7:r.neighbors", qgis_env = my_env)
params$input  <- r1
params$method  <- 2 # "Mode"
params$output  <- file.path(dir_tmp, "rst_out.tif")

params$GRASS_REGION_PARAMETER <- "0,849,-837,0"    # as xmin, xmax, ymin, ymax
params$GRASS_REGION_CELLSIZE_PARAMETER <- "1.0"

out <- run_qgis(alg = "grass7:r.neighbors", params = params, load_output = params$output, qgis_env = my_env)
out


class       : RasterLayer
dimensions  : 1, 7, 7  (nrow, ncol, ncell)
resolution  : 0.1519435, 1  (x, y)
extent      : 0, 1.063604, 0, 1  (xmin, xmax, ymin, ymax)
coord. ref. : +proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0
data source : C:\Users\Guest\AppData\Local\Temp\RtmpwJu31Y\rst_out.tif
names       : rst_out



Note the output only has 1 row, 7 cols (vs. 837 rows, 849 cols in input). The CRS has been set as long-lat, while the CRS is NA in the input,


Also note that the resolution has been changed from 1 to 0.1519,


I wonder if there is an issue on how the params$GRASS_REGION_PARAMETER is defined. I have tried different ways eg., "0,849,-837,0" (as xmin, xmax, ymin, ymax), "0,-837,849,0" (as xmin, ymin, xmax, ymax), extent(r1) (which gives error).


The input image (550 kb) can be downloaded from this link: https://www.dropbox.com/s/do95t48foepw62e/pred_m1_3000_recl5.tif?dl=0



Thanks for your help,


Best regards,


Ali



sessionInfo()


R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)


locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] RQGIS_0.2.0.9000     raster_2.5-8         sp_1.2-3             RevoUtilsMath_10.0.0

loaded via a namespace (and not attached):
[1] RevoUtils_10.0.2 rgdal_1.1-10     tools_3.3.2      Rcpp_0.12.7      grid_3.3.2       lattice_0.20-34


________________________________
De: R-sig-Geo <[hidden email]<mailto:[hidden email]>> en nombre de "Jannes M�nchow" <[hidden email]<mailto:[hidden email]>>
Enviado: jueves, 19 de enero de 2017 06:31:34 a. m.
Para: [hidden email]<mailto:[hidden email]>
Asunto: [R-sig-Geo] RQGIS release 0.2.0

Dear list members,

today we are happy to announce a new version of RQGIS! RQGIS establishes an interface between R and QGIS, i.e. it allows the user to access the more than 1000 QGIS geoalgorithms from within R. The most important news is that you can run again the most recent QGIS releases (>=2.18.2) with RQGIS without having to modify Python source code. This modification became necessary due to a bug introduced in QGIS 2.16 (see https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181).

[https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181>

GitHub - jannes-m/RQGIS: RQGIS - integrating R with QGIS<https://github.com/jannes-m/RQGIS#rqgis-modifications-v-216-2181>
github.com<http://github.com>
RQGIS - integrating R with QGIS ... Now that we have a spatial object, we can move on to using RQGIS. First of all, we need to specify all the paths necessary to run ...




This release fixes also several bugs which we detected thanks to user feedback. To learn more about these, please refer to https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0.

[https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0>

jannes-m/RQGIS<https://github.com/jannes-m/RQGIS/releases/tag/v0.2.0>
github.com<http://github.com>
RQGIS - integrating R with QGIS




For more information on RQGIS, how to install it and examples how to use RQGIS, please refer to https://github.com/jannes-m/RQGIS and my https://jannesm.wordpress.com/category/r/.

Posts about R on jannesm<https://jannesm.wordpress.com/category/r/>
jannesm.wordpress.com<http://jannesm.wordpress.com>
Posts about R written by jannesm



[https://avatars0.githubusercontent.com/u/9986952?v=3&s=400]<https://github.com/jannes-m/RQGIS>

GitHub - jannes-m/RQGIS: RQGIS - integrating R with QGIS<https://github.com/jannes-m/RQGIS>
github.com<http://github.com>
RQGIS - integrating R with QGIS ... Now that we have a spatial object, we can move on to using RQGIS. First of all, we need to specify all the paths necessary to run ...




All the best,

Jannes

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