From c7be92dab593dc893524ff992fc0ed5440e03acc Mon Sep 17 00:00:00 2001 From: gisma Date: Fri, 3 Nov 2023 23:35:01 +0100 Subject: [PATCH] update website --- NEWS | 2 +- NEWS.md | 2 +- docs/404.html | 2 +- docs/LICENSE-text.html | 2 +- docs/articles/index.html | 2 +- docs/articles/link2GI1.html | 10 +- docs/articles/link2GI2.html | 33 +- docs/articles/link2GI3.html | 280 ++++++++-------- docs/articles/link2GI4.html | 13 +- docs/articles/link2GI5.html | 4 +- docs/articles/link2GI6.html | 66 ++-- docs/authors.html | 2 +- docs/index.html | 17 +- docs/news/index.html | 12 +- docs/pkgdown.yml | 4 +- docs/reference/add2Path.html | 2 +- docs/reference/findGDAL.html | 2 +- docs/reference/findGRASS.html | 2 +- docs/reference/findOTB.html | 2 +- docs/reference/findSAGA.html | 2 +- docs/reference/getSpatialClass.html | 2 +- docs/reference/gvec2sf.html | 2 +- docs/reference/index.html | 10 +- docs/reference/initProj.html | 2 +- docs/reference/linkAll.html | 2 +- docs/reference/linkGDAL.html | 2 +- docs/reference/linkGRASS.html | 2 +- docs/reference/linkGRASS7.html | 2 +- docs/reference/linkOTB.html | 2 +- docs/reference/linkSAGA.html | 2 +- docs/reference/makGlobalVar.html | 2 +- docs/reference/manuallyBuild.html | 2 +- docs/reference/paramGRASSw.html | 2 +- docs/reference/paramGRASSx.html | 2 +- docs/reference/parseOTBAlgorithms.html | 2 +- docs/reference/parseOTBFunction.html | 2 +- docs/reference/runOTB.html | 12 +- docs/reference/searchGDALW.html | 2 +- docs/reference/searchGDALX.html | 2 +- docs/reference/searchGRASSW.html | 2 +- docs/reference/searchGRASSX.html | 2 +- docs/reference/searchOTBW.html | 2 +- docs/reference/searchOTBX.html | 2 +- docs/reference/searchSAGAW.html | 2 +- docs/reference/searchSAGAX.html | 2 +- docs/reference/setenvGDAL.html | 2 +- docs/reference/setenvGRASSw.html | 2 +- docs/reference/setenvOTB.html | 2 +- docs/reference/sf2gvec.html | 2 +- vignettes/link2GI1.R | 2 +- vignettes/link2GI1.Rmd | 4 +- vignettes/link2GI1.html | 192 +++++++---- vignettes/link2GI1.md | 6 +- vignettes/link2GI6.R | 2 +- vignettes/link2GI6.Rmd | 2 +- vignettes/link2GI6.html | 421 ++++++++++--------------- vignettes/link2GI6.md | 4 +- 57 files changed, 591 insertions(+), 579 deletions(-) diff --git a/NEWS b/NEWS index e22d6f2..656b8af 100644 --- a/NEWS +++ b/NEWS @@ -1,6 +1,6 @@ ## link2GI 0.5-3 bugfixes: -* issue #59 +* issue #59 #58 * fix rgrass7 dependencies ## link2GI 0.5-2 diff --git a/NEWS.md b/NEWS.md index 97f495b..c4b3565 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,6 +1,6 @@ ## link2GI 0.5-3 bugfixes: -* issue #59 +* issue #59 , #58 * fix rgrass7 dependencies ## link2GI 0.5-2 diff --git a/docs/404.html b/docs/404.html index acca824..b0526d5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -32,7 +32,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index 61af18d..b890a77 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/articles/index.html b/docs/articles/index.html index 1a85455..198bb71 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/articles/link2GI1.html b/docs/articles/link2GI1.html index 3c92815..285dc23 100644 --- a/docs/articles/link2GI1.html +++ b/docs/articles/link2GI1.html @@ -33,7 +33,7 @@ link2GI - 0.5-2 + 0.5-3 @@ -97,7 +97,7 @@

Link GI to R

Chris Reudenbach

-

2023-01-27

+

2023-11-03

Source: vignettes/link2GI1.Rmd @@ -140,10 +140,10 @@

Why link2GI now?

The spatial analysis itself is often supported by wrapper packages that integrate external libraries, command line tools or a mixture of -both in an R-like syntax rgeos, geosphere, Distance, maptools, igraph or spatstat.

+both in an R-like syntax geosphere, Distance, igraph or spatstat.

A comprehensive introduction to the spatial R-biotope and its -backgrounds is excellently treated in Geocomputation with R wich -is highly recommend as a reference textbook.

+backgrounds is excellently treated in Geocomputation with R wich is highly +recommend as a reference textbook.

Despite all this capabilities of spatial analysis and data handling in the world of R, it can be stated (at least from a non-R point of view), that there is still a enormous gap between R and the diff --git a/docs/articles/link2GI2.html b/docs/articles/link2GI2.html index c4be33e..df7ba60 100644 --- a/docs/articles/link2GI2.html +++ b/docs/articles/link2GI2.html @@ -33,7 +33,7 @@ link2GI - 0.5-2 + 0.5-3 @@ -97,7 +97,7 @@

link2GI Basic Examples

Chris Reudenbach

-

2023-01-27

+

2023-11-03

Source: vignettes/link2GI2.Rmd @@ -300,15 +300,15 @@
Typical for specified search

If you already did a full search and kow your installation fo example using the command findGRASS you can use the result directly for linking.

-
findGRASS()
-     instDir version installation_type
-1 /opt/grass   7.8.1           grass78
-
-# now linking it 
-linkGRASS(nc,c("/opt/grass","7.8.15","grass78")) 
-
-# corresponding linkage running windows
-linkGRASS(nc,c("C:/Program Files/GRASS GIS7.0.5","GRASS GIS 7.0.5","NSIS"))
+
findGRASS()
+     instDir version installation_type
+1 /opt/grass   7.8.1           grass78
+
+# now linking it 
+linkGRASS(nc,c("/opt/grass","7.8.15","grass78")) 
+
+# corresponding linkage running windows
+linkGRASS(nc,c("C:/Program Files/GRASS GIS7.0.5","GRASS GIS 7.0.5","NSIS"))
Manual choosing the version @@ -391,17 +391,14 @@

A typical usecase for t example will give you an idea how to use it.

 require(link2GI)
-require(terra)
+require(terra)
 require(listviewer)
 
 otblink<-link2GI::linkOTB()
  projRootDir<-tempdir()
  
-data('rgb', package = 'link2GI')  
-terra::plotRGB(rgb)
-r<-terra::writeRaster(rgb, 
-              filename=file.path(projRootDir,"test.tif"),
-              format="GTiff", overwrite=TRUE)
+fn <- system.file("ex/elev.tif", package = "terra")
+
 ## for the example we use the edge detection, 
 algoKeyword<- "EdgeExtraction"
 
@@ -412,7 +409,7 @@ 
A typical usecase for t
 listviewer::jsonedit(cmd$help)
 
 ## define the mandantory arguments all other will be default
-cmd$input  <- file.path(projRootDir,"test.tif")
+cmd$input  <- fn
 cmd$filter <- "touzi"
 cmd$channel <- 2
 cmd$out <- file.path(projRootDir,paste0("out",cmd$filter,".tif"))
diff --git a/docs/articles/link2GI3.html b/docs/articles/link2GI3.html
index e4f31f1..1133abf 100644
--- a/docs/articles/link2GI3.html
+++ b/docs/articles/link2GI3.html
@@ -1,8 +1,24 @@
 
-linkGRASS real world data usecase • link2GI
+
+
+
+
+
+linkGRASS real world data usecase • link2GI
+
+
+
+
+
+
+
+
+
+
+
     
 
     

@@ -17,12 +33,13 @@
       
       
         link2GI
-        0.5-2
+        0.5-3
       
     

 
     
-
-

+ + + + + + + - - - - - - -
+

linkGRASS real world data usecase

Chris Reudenbach

-

2023-01-27

+

2023-11-03

Source: vignettes/link2GI3.Rmd @@ -87,8 +106,9 @@

2023-01-27

-
-

Real world example

+
+

Real world example +

A typical example is the usage of an already existing project database in GRASS. GRASS organizes all data in an internal file structure that is known as gisdbase folder, a mapset @@ -96,15 +116,17 @@

Real world example

is stored inside this structure and the organisation is performed by GRASS. So a typical task could be to work on data sets that are already stored in an existing GRASS structure

-
-

Creating a GRASS project

+
+

Creating a GRASS project +

-
-

Download Zensus Data

+
+

Download Zensus Data +

First of all we need some real world data. In this this case the gridded German 2011 micro zensus data. Download the data:

-
# (https://www.zensus2011.de/EN/Service/Contact/contact_node.html)
-wget https://www.zensus2011.de/SharedDocs/Downloads/DE/Pressemitteilung/DemografischeGrunddaten/csv_Bevoelkerung_100m_Gitter.zip?__blob=publicationFile&v=3
+
# (https://www.zensus2011.de/EN/Service/Contact/contact_node.html)
+wget https://www.zensus2011.de/SharedDocs/Downloads/DE/Pressemitteilung/DemografischeGrunddaten/csv_Bevoelkerung_100m_Gitter.zip?__blob=publicationFile&v=3

of Germany. It has some nice aspects:

  • It is provided in a typical authority format
    • @@ -114,61 +136,66 @@

    Download Zensus Data

    We also have to download the meta data description file from the above website for informations about projection and data concepts and so on.

    -
     # we need some additional packages
- require(link2GI)
- require(curl)
-
-# first of all we create  a project folder structure 
-  link2GI::initProj(projRootDir = paste0(tempdir(),"/link2GI_examples"), 
-                    projFolders =  c("run/"),
-                    path_prefix = "path_",
-                    global = TRUE)
-
-# set runtime directory
-  setwd(path_run)
-
-# get some typical authority generated data 
-  url<-"https://www.zensus2011.de/SharedDocs/Downloads/DE/Pressemitteilung/DemografischeGrunddaten/csv_Bevoelkerung_100m_Gitter.zip;jsessionid=294313DDBB57914D6636DE373897A3F2.2_cid389?__blob=publicationFile&v=3"
- res <- curl::curl_download(url, paste0(path_run,"testdata.zip"))
-
-# unzip it
- unzip(res,files = grep(".csv", unzip(res,list = TRUE)$Name,value = TRUE),
-       junkpaths = TRUE, overwrite = TRUE)
-fn <- list.files(pattern = "[.]csv$", path = getwd(), full.names = TRUE)
    -
    -

    Preprocessing of the data

    +
    + # we need some additional packages
+ require(link2GI)
+ require(curl)
+
+# first of all we create  a project folder structure 
+  link2GI::initProj(projRootDir = paste0(tempdir(),"/link2GI_examples"), 
+                    projFolders =  c("run/"),
+                    path_prefix = "path_",
+                    global = TRUE)
+
+# set runtime directory
+  setwd(path_run)
+
+# get some typical authority generated data 
+  url<-"https://www.zensus2011.de/SharedDocs/Downloads/DE/Pressemitteilung/DemografischeGrunddaten/csv_Bevoelkerung_100m_Gitter.zip;jsessionid=294313DDBB57914D6636DE373897A3F2.2_cid389?__blob=publicationFile&v=3"
+ res <- curl::curl_download(url, paste0(path_run,"testdata.zip"))
+
+# unzip it
+ unzip(res,files = grep(".csv", unzip(res,list = TRUE)$Name,value = TRUE),
+       junkpaths = TRUE, overwrite = TRUE)
+fn <- list.files(pattern = "[.]csv$", path = getwd(), full.names = TRUE)
    +
    +

    Preprocessing of the data +

    After downloading the data we will use it for some demonstration stuff. If you have a look the data is nothing than x,y,z with assuming some projection information.

    -
    # fast read with data.table 
- xyz <- data.table::fread(paste0(path_run,"/Zensus_Bevoelkerung_100m-Gitter.csv"))
-
- head(xyz)
    +
    +# fast read with data.table 
+ xyz <- data.table::fread(paste0(path_run,"/Zensus_Bevoelkerung_100m-Gitter.csv"))
+
+ head(xyz)

    We can easy rasterize this data as it is intentionally gridded data.that means we have in at a grid size of 100 by 100 meters a value.

    -
     require(RColorBrewer)
- require(terra)
- require(mapview)
-
-
-# clean dataframe
- xyz <- xyz[,-1]
-
-# rasterize it according to the projection 
-  r <- terra::rast(xyz, type="xyz")
- terra::crs(r) <- 3035
-
-# map it
- p <- colorRampPalette(brewer.pal(8, "Reds"))
- # aet resolution to 1 sqkm
- mapview::mapviewOptions(mapview.maxpixels = r@ncols*r@nrows/10)
- mapview::mapview(r, col.regions = p, 
-                  at = c(-1,10,25,50,100,500,1000,2500), 
-                  legend = TRUE)
    +
    + require(RColorBrewer)
+ require(terra)
+ require(mapview)
+
+
+# clean dataframe
+ xyz <- xyz[,-1]
+
+# rasterize it according to the projection 
+  r <- terra::rast(xyz, type="xyz")
+ terra::crs(r) <- 3035
+
+# map it
+ p <- colorRampPalette(brewer.pal(8, "Reds"))
+ # aet resolution to 1 sqkm
+ mapview::mapviewOptions(mapview.maxpixels = r@ncols*r@nrows/10)
+ mapview::mapview(r, col.regions = p, 
+                  at = c(-1,10,25,50,100,500,1000,2500), 
+                  legend = TRUE)
    -
    -

    Setup GRASS Project

    +
    +

    Setup GRASS Project +

    So far nothing new. Now we create a new but permanent GRASS gisbase using the spatial parameters from the raster object. As you know the linkGRASS function performs a full @@ -178,60 +205,63 @@

    Setup GRASS Project

    Due to the fact that the gisdbase_exist is by default set to FALSE it will create a new structure according to the R object.

    -
    require(link2GI)
-# initialize GRASS and set up a permanent structure  
-link2GI::linkGRASS(x = r, 
-                    gisdbase = paste0(tempdir(),"/link2GI_examples"),
-                    location = "microzensus2011")
    +
    +require(link2GI)
+# initialize GRASS and set up a permanent structure  
+link2GI::linkGRASS(x = r, 
+                    gisdbase = paste0(tempdir(),"/link2GI_examples"),
+                    location = "microzensus2011")

    Finally we can now import the data to the GRASS gisdbase using the rgass package functionality.

    First we must convert the raster/terra object to a GeoTIFF file. Any GDAL format is possible but GeoTIFF is very common and stable.

    -
    require(link2GI)
-require(raster)
-require(rgrass)
-
-# write it to geotiff
-  terra::writeRaster(r, paste0(path_run,"/Zensus_Bevoelkerung_100m-Gitter.tif"), 
-       x               overwrite = TRUE)
-
-# import raster to GRASS
-rgrass::execGRASS('r.external',
-                   flags=c('o',"overwrite","quiet"),
-                   input=paste0(path_run,"/Zensus_Bevoelkerung_100m-Gitter.tif"),
-                   output="Zensus_Bevoelkerung_100m_Gitter",
-                   band=1)
-
-# check imported data set
-rgrass::execGRASS('r.info',
-                   map = "Zensus_Bevoelkerung_100m_Gitter")
    +
    require(link2GI)
+require(raster)
+require(rgrass)
+
+# write it to geotiff
+  terra::writeRaster(r, paste0(path_run,"/Zensus_Bevoelkerung_100m-Gitter.tif"), 
+       x               overwrite = TRUE)
+
+# import raster to GRASS
+rgrass::execGRASS('r.external',
+                   flags=c('o',"overwrite","quiet"),
+                   input=paste0(path_run,"/Zensus_Bevoelkerung_100m-Gitter.tif"),
+                   output="Zensus_Bevoelkerung_100m_Gitter",
+                   band=1)
+
+# check imported data set
+rgrass::execGRASS('r.info',
+                   map = "Zensus_Bevoelkerung_100m_Gitter")

    Let’s do now the same import as a vector data set. First we create a sf object. Please note this will take quite a while.

    -
     xyz_sf = st_as_sf(xyz,
-                    coords = c("x_mp_100m", "y_mp_100m"),
-                    crs = 3035,
-                    agr = "constant")
-
-#map points
- sf::plot_sf(xyz_sf)
    +
    + xyz_sf = st_as_sf(xyz,
+                    coords = c("x_mp_100m", "y_mp_100m"),
+                    crs = 3035,
+                    agr = "constant")
+
+#map points
+ sf::plot_sf(xyz_sf)

    The GRASS gisdbase already exists. So we pass linkGRASS the argument gisdbase_exist=TRUE and import the xyz data as generic GRASS vector points.

    -
     require(sf)
- require(sp)
- require(link2GI)
- 
-  sf2gvec(x =  xyz_sf,
-           obj_name = "Zensus_Bevoelkerung_100m_",
-           gisdbase = paste0(tempdir(),"/link2GI_examples"),
-           location = "microzensus2011",
-           gisdbase_exist = TRUE
-          
-           )
- 
-# check imported data set
-rgrass::execGRASS('v.info', map = "Zensus_Bevoelkerung_100m_")
    +
    + require(sf)
+ require(sp)
+ require(link2GI)
+ 
+  sf2gvec(x =  xyz_sf,
+           obj_name = "Zensus_Bevoelkerung_100m_",
+           gisdbase = paste0(tempdir(),"/link2GI_examples"),
+           location = "microzensus2011",
+           gisdbase_exist = TRUE
+          
+           )
+ 
+# check imported data set
+rgrass::execGRASS('v.info', map = "Zensus_Bevoelkerung_100m_")
    @@ -241,25 +271,29 @@

    Setup GRASS Project

    -
+
-

Developed by Chris Reudenbach.

+

+

Developed by Chris Reudenbach.

-

Site built with pkgdown 2.0.7.

+

+

Site built with pkgdown 2.0.7.

-
+ +
- + + diff --git a/docs/articles/link2GI4.html b/docs/articles/link2GI4.html index 79e9613..02a21ff 100644 --- a/docs/articles/link2GI4.html +++ b/docs/articles/link2GI4.html @@ -33,7 +33,7 @@ link2GI - 0.5-2 + 0.5-3
@@ -97,7 +97,7 @@

OTB Wrapper

Chris Reudenbach

-

2023-01-27

+

2023-11-03

Source: vignettes/link2GI4.Rmd @@ -144,11 +144,8 @@

A typical usecase for t otblink<-link2GI::linkOTB() projRootDir<-tempdir() -data('rgb', package = 'link2GI') -terra::plotRGB(rgb) -r<-terra::writeRaster(rgb, - filename=file.path(projRootDir,"test.tif"), - format="GTiff", overwrite=TRUE) +fn <- system.file("ex/elev.tif", package = "terra") + ## for the example we use the edge detection, algoKeyword<- "EdgeExtraction" @@ -159,7 +156,7 @@

A typical usecase for t listviewer::jsonedit(cmd$help) ## define the mandantory arguments all other will be default -cmd$input <- file.path(projRootDir,"test.tif") +cmd$input <- fn cmd$filter <- "touzi" cmd$channel <- 2 cmd$out <- file.path(projRootDir,paste0("out",cmd$filter,".tif")) diff --git a/docs/articles/link2GI5.html b/docs/articles/link2GI5.html index b1c2bfe..7cdf043 100644 --- a/docs/articles/link2GI5.html +++ b/docs/articles/link2GI5.html @@ -33,7 +33,7 @@ link2GI - 0.5-2 + 0.5-3

@@ -97,7 +97,7 @@

GEOSTAT 2018 Examples

Chris Reudenbach

-

2023-01-27

+

2023-11-03

Source: vignettes/link2GI5.Rmd diff --git a/docs/articles/link2GI6.html b/docs/articles/link2GI6.html index db2152d..15f41f1 100644 --- a/docs/articles/link2GI6.html +++ b/docs/articles/link2GI6.html @@ -33,7 +33,7 @@ link2GI - 0.5-2 + 0.5-3
@@ -98,7 +98,7 @@

Installation guide for link2GI related

Chris Reudenbach

-

2023-01-27

+

2023-11-03

Source: vignettes/link2GI6.Rmd @@ -184,7 +184,7 @@

QGIS, GRASS and SAGAOSGeo4W-executable.

If you additionally want to use the LiDAR processing -tools (LAStools), please follow the steps found here.

+tools (LAStools), please follow the steps found here.

Orfeo Toolbox @@ -219,36 +219,36 @@

Ubuntu GRASS packages you may have installed before from other repositories:

-
sudo apt-get --purge remove qgis
-sudo apt autoremove --purge-remove 
-sudo apt autoremove
-sudo apt-get update
+
sudo apt-get --purge remove qgis
+sudo apt autoremove --purge-remove 
+sudo apt autoremove
+sudo apt-get update

Next add the correct repository to /etc/apt/sources.list. Here, we use the current long-term release (3.10):

QGIS 3.10.x for Ubuntu 20.04

-
# install necessary tools
-sudo apt install gnupg software-properties-common
-
-#add the required keys
-wget -qO - https://qgis.org/downloads/qgis-2020.gpg.key | sudo gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/qgis-archive.gpg --import
-
-# verify the key 
-gpg --fingerprint 51F523511C7028C3
-
-# add the repository
-# if there are problems 
-sudo add-apt-repository "deb https://qgis.org/debian lsb_release -c -s main"
-
-# if there are problems use the hard-wired "focal" release
-sudo add-apt-repository "deb https://qgis.org/debian focal main"
-
+
# install necessary tools
+sudo apt install gnupg software-properties-common
+
+#add the required keys
+wget -qO - https://qgis.org/downloads/qgis-2020.gpg.key | sudo gpg --no-default-keyring --keyring gnupg-ring:/etc/apt/trusted.gpg.d/qgis-archive.gpg --import
+
+# verify the key 
+gpg --fingerprint 51F523511C7028C3
+
+# add the repository
+# if there are problems 
+sudo add-apt-repository "deb https://qgis.org/debian lsb_release -c -s main"
+
+# if there are problems use the hard-wired "focal" release
+sudo add-apt-repository "deb https://qgis.org/debian focal main"
+

After that, we can install QGIS and GRASS saga and Orfeo Toolbox as follows:

-
# install qgis grass otb saga
-
-sudo apt update
-sudo apt install qgis python-qgis qgis-plugin-grass grass saga otb-bin
+
# install qgis grass otb saga
+
+sudo apt update
+sudo apt install qgis python-qgis qgis-plugin-grass grass saga otb-bin

If you would like to use another SAGA version, you need to compile it yourself (see here). Please note, however, that QGIS currently only supports the SAGA LTR @@ -264,7 +264,7 @@

Fedora

You can install current stable QGIS, SAGA and GRASS GIS versions via the standard software package manager:

-
sudo dnf install qgis-python qgis qgis-grass saga grass-gui grass-libs
+
sudo dnf install qgis-python qgis qgis-grass saga grass-gui grass-libs
@@ -275,9 +275,9 @@

SAGA

There is no binary install of SAGA for macOS. We recommend to use the bottle installation from homebrew:

-
# brew tap osgeo4mac
-brew install saga-gis-lts
-brew link saga-gis-lts --force
+
# brew tap osgeo4mac
+brew install saga-gis-lts
+brew link saga-gis-lts --force

If you do not link SAGA with force, QGIS will not be able to detect SAGA.

Alternatively, you can compile SAGA from source from the SAGA @@ -288,8 +288,8 @@

SAGA

GRASS

You can install GRASS6 and GRASS7 via homebrew:

-
# brew tap osgeo4mac
-brew install grass6 grass7
+
# brew tap osgeo4mac
+brew install grass6 grass7

The binary GRASS installation can be found here. However, we recommend to use the homebrew approach.

When installing GRASS7 independently of QGIS via diff --git a/docs/authors.html b/docs/authors.html index b2c9422..7167c97 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3

diff --git a/docs/index.html b/docs/index.html index e529592..afb84b6 100644 --- a/docs/index.html +++ b/docs/index.html @@ -33,7 +33,7 @@ link2GI - 0.5-2 + 0.5-3 @@ -96,7 +96,8 @@

link2GI

-

License

+ +

Package website: release

link2GI provide some functions which make it a bit easier to connect straightforward the common open source GI software packages to the R-biotop. It supports both the use of wrapper packages and the direct API-use via system calls. It focuses on Linux and WindowsX operating systems but nevertheless it should also work with OSX.

If you have several versions installed or if you want to use the full power of the GI software it will be a nice and helpful tool to deal with some strange behaviours and requirements. Especially helpful is the support of OTB, the GDAL-Python functions and a simple support to use any SAGA version via the CLI. Hopefully RSAGA and Rsagacmd will join forces in one package in the future. Anyway the brand new release 1.2.0 of RSAGA as well as the current Rsagacmd will work with the environment settings as provided by linkSAGA.

@@ -123,17 +124,15 @@

Updated OTB wrapper ## link to OTB require(link2GI) -require(terra) +require(terra) require(listviewer) otblink<-link2GI::linkOTB() projRootDir<-tempdir() -data('rgb', package = 'link2GI') -terra::plotRGB(rgb) -r<-terra::writeRaster(rgb, - filename=file.path(projRootDir,"test.tif"), - format="GTiff", overwrite=TRUE) +fn <- system.file("ex/elev.tif", package = "terra") + + ## for the example we use the edge detection, algoKeyword<- "EdgeExtraction" @@ -144,7 +143,7 @@

Updated OTB wrapperlistviewer::jsonedit(cmd$help) ## define the mandantory arguments all other will be default -cmd$input <- file.path(projRootDir,"test.tif") +cmd$input <- fn cmd$filter <- "touzi" cmd$channel <- 2 cmd$out <- file.path(projRootDir,paste0("out",cmd$filter,".tif")) diff --git a/docs/news/index.html b/docs/news/index.html index d2cf25e..5b532c2 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3

@@ -73,14 +73,20 @@

Changelog

-

link2GI 0.5-1

+

link2GI 0.5-32023-10-30

+

bugfixes: * issue #59 , #58 * fix rgrass7 dependencies

-

link2GI 0.5-2

+

link2GI 0.5-22023-01-27

new feature: * add return of vector data in OTB calls

bugfixes: * issue #58 * minor fixes in runOTB

bugfixes: * prelim fix of issue #57 * fix of issue #56 * minor fixes

new feature: * integration of stars and terra raster objects for linking GRASS * update of documentation

+
+
+

link2GI 0.5-1

+

bugfixes: * prelim fix of issue #57 * fix of issue #56 * minor fixes

+

new feature: * integration of stars and terra raster objects for linking GRASS * update of documentation

link2GI 0.5-02022-08-29

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index d53979b..c74ac19 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -1,4 +1,4 @@ -pandoc: 2.19.2 +pandoc: 3.1.1 pkgdown: 2.0.7 pkgdown_sha: ~ articles: @@ -8,7 +8,7 @@ articles: link2GI4: link2GI4.html link2GI5: link2GI5.html link2GI6: link2GI6.html -last_built: 2023-01-27T17:39Z +last_built: 2023-11-03T22:33Z urls: reference: https://r-spatial.github.io/link2GI/reference article: https://r-spatial.github.io/link2GI/articles diff --git a/docs/reference/add2Path.html b/docs/reference/add2Path.html index 60f3679..e957302 100644 --- a/docs/reference/add2Path.html +++ b/docs/reference/add2Path.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3
diff --git a/docs/reference/findGDAL.html b/docs/reference/findGDAL.html index 20a21c2..b300291 100644 --- a/docs/reference/findGDAL.html +++ b/docs/reference/findGDAL.html @@ -20,7 +20,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/findGRASS.html b/docs/reference/findGRASS.html index 8593389..20d818b 100644 --- a/docs/reference/findGRASS.html +++ b/docs/reference/findGRASS.html @@ -20,7 +20,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/findOTB.html b/docs/reference/findOTB.html index 46830ad..3d690f2 100644 --- a/docs/reference/findOTB.html +++ b/docs/reference/findOTB.html @@ -20,7 +20,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/findSAGA.html b/docs/reference/findSAGA.html index 41cb89c..80bfe21 100644 --- a/docs/reference/findSAGA.html +++ b/docs/reference/findSAGA.html @@ -20,7 +20,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/getSpatialClass.html b/docs/reference/getSpatialClass.html index 1e89233..b0eb360 100644 --- a/docs/reference/getSpatialClass.html +++ b/docs/reference/getSpatialClass.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/gvec2sf.html b/docs/reference/gvec2sf.html index 02716a2..5930afc 100644 --- a/docs/reference/gvec2sf.html +++ b/docs/reference/gvec2sf.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/index.html b/docs/reference/index.html index f0e50e9..cca8bd8 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 @@ -99,10 +99,6 @@

All functions initProj()

Defines and creates folders and variables

- -

link2GI

- -

Bridges to the GI-World

linkAll()

@@ -143,10 +139,6 @@

All functions parseOTBFunction()

Get OTB function argument list

- -

rgb

- -

RGB ortho-image from an arbitrary Marburg Open Forest (MOF) plot

runOTB()

diff --git a/docs/reference/initProj.html b/docs/reference/initProj.html index cd01d9d..ed78102 100644 --- a/docs/reference/initProj.html +++ b/docs/reference/initProj.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/linkAll.html b/docs/reference/linkAll.html index ce419fe..824f9eb 100644 --- a/docs/reference/linkAll.html +++ b/docs/reference/linkAll.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/linkGDAL.html b/docs/reference/linkGDAL.html index 579ec15..c598ece 100644 --- a/docs/reference/linkGDAL.html +++ b/docs/reference/linkGDAL.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/linkGRASS.html b/docs/reference/linkGRASS.html index 0414c08..64cbdd9 100644 --- a/docs/reference/linkGRASS.html +++ b/docs/reference/linkGRASS.html @@ -21,7 +21,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/linkGRASS7.html b/docs/reference/linkGRASS7.html index c446d9f..80102e6 100644 --- a/docs/reference/linkGRASS7.html +++ b/docs/reference/linkGRASS7.html @@ -20,7 +20,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/linkOTB.html b/docs/reference/linkOTB.html index 50687bc..f732306 100644 --- a/docs/reference/linkOTB.html +++ b/docs/reference/linkOTB.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/linkSAGA.html b/docs/reference/linkSAGA.html index 3664254..d70ab0f 100644 --- a/docs/reference/linkSAGA.html +++ b/docs/reference/linkSAGA.html @@ -22,7 +22,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/makGlobalVar.html b/docs/reference/makGlobalVar.html index b949029..c98b760 100644 --- a/docs/reference/makGlobalVar.html +++ b/docs/reference/makGlobalVar.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/manuallyBuild.html b/docs/reference/manuallyBuild.html index d9634a9..b67df49 100644 --- a/docs/reference/manuallyBuild.html +++ b/docs/reference/manuallyBuild.html @@ -19,7 +19,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/paramGRASSw.html b/docs/reference/paramGRASSw.html index 1ca2420..1d59dfe 100644 --- a/docs/reference/paramGRASSw.html +++ b/docs/reference/paramGRASSw.html @@ -18,7 +18,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/paramGRASSx.html b/docs/reference/paramGRASSx.html index b8be5d0..58c6ab7 100644 --- a/docs/reference/paramGRASSx.html +++ b/docs/reference/paramGRASSx.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/parseOTBAlgorithms.html b/docs/reference/parseOTBAlgorithms.html index eb57cf5..41ee030 100644 --- a/docs/reference/parseOTBAlgorithms.html +++ b/docs/reference/parseOTBAlgorithms.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/parseOTBFunction.html b/docs/reference/parseOTBFunction.html index 348919c..6fccdf5 100644 --- a/docs/reference/parseOTBFunction.html +++ b/docs/reference/parseOTBFunction.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/runOTB.html b/docs/reference/runOTB.html index b77307f..251b9f1 100644 --- a/docs/reference/runOTB.html +++ b/docs/reference/runOTB.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 @@ -118,7 +118,7 @@

Details

Examples

if (FALSE) {
 require(link2GI)
-require(terra)
+require(terra)
 require(listviewer)
 
 ## link to OTB
@@ -126,11 +126,7 @@ 
Examples

 
 if (otblink$exist) {
  projRootDir<-tempdir()
- data('rgb', package = 'link2GI')  
- terra::plotRGB(rgb)
- r<-terra::writeRaster(rgb, 
-                        filename=file.path(projRootDir,"test.tif"),
-                        overwrite=TRUE)
+ fn <- system.file("ex/elev.tif", package = "terra")
 
 ## for an image output example we use the Statistic Extraction, 
 algoKeyword<- "LocalStatisticExtraction"
@@ -143,7 +139,7 @@ 
Examples

 listviewer::jsonedit(cmd$help)
 
 ## define the mandatory arguments all other will be default
-cmd$input_in  <- file.path(tempdir(),"test.tif")
+cmd$input_in  <- fn
 cmd$out <- file.path(tempdir(),"test_otb_stat.tif")
 cmd$radius <- 7
 
diff --git a/docs/reference/searchGDALW.html b/docs/reference/searchGDALW.html
index 67f79c4..45ab1ac 100644
--- a/docs/reference/searchGDALW.html
+++ b/docs/reference/searchGDALW.html
@@ -17,7 +17,7 @@
       
       
         link2GI
-        0.5-2
+        0.5-3
diff --git a/docs/reference/searchGDALX.html b/docs/reference/searchGDALX.html index 06783f5..4e2e4c3 100644 --- a/docs/reference/searchGDALX.html +++ b/docs/reference/searchGDALX.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/searchGRASSW.html b/docs/reference/searchGRASSW.html index f3257c2..c7ab390 100644 --- a/docs/reference/searchGRASSW.html +++ b/docs/reference/searchGRASSW.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/searchGRASSX.html b/docs/reference/searchGRASSX.html index 4030b77..7c75f1a 100644 --- a/docs/reference/searchGRASSX.html +++ b/docs/reference/searchGRASSX.html @@ -18,7 +18,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/searchOTBW.html b/docs/reference/searchOTBW.html index d5fa695..8c90fb1 100644 --- a/docs/reference/searchOTBW.html +++ b/docs/reference/searchOTBW.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/searchOTBX.html b/docs/reference/searchOTBX.html index 495a0a8..5e879ab 100644 --- a/docs/reference/searchOTBX.html +++ b/docs/reference/searchOTBX.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/searchSAGAW.html b/docs/reference/searchSAGAW.html index c0b5c4b..20c5684 100644 --- a/docs/reference/searchSAGAW.html +++ b/docs/reference/searchSAGAW.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/searchSAGAX.html b/docs/reference/searchSAGAX.html index 824f668..557aba2 100644 --- a/docs/reference/searchSAGAX.html +++ b/docs/reference/searchSAGAX.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/setenvGDAL.html b/docs/reference/setenvGDAL.html index 7654467..b329fd7 100644 --- a/docs/reference/setenvGDAL.html +++ b/docs/reference/setenvGDAL.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/setenvGRASSw.html b/docs/reference/setenvGRASSw.html index 456f99b..d6bc3a7 100644 --- a/docs/reference/setenvGRASSw.html +++ b/docs/reference/setenvGRASSw.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/setenvOTB.html b/docs/reference/setenvOTB.html index 92f7be3..e31fc51 100644 --- a/docs/reference/setenvOTB.html +++ b/docs/reference/setenvOTB.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/docs/reference/sf2gvec.html b/docs/reference/sf2gvec.html index 490b8d7..c75353b 100644 --- a/docs/reference/sf2gvec.html +++ b/docs/reference/sf2gvec.html @@ -17,7 +17,7 @@ link2GI - 0.5-2 + 0.5-3 diff --git a/vignettes/link2GI1.R b/vignettes/link2GI1.R index daeac3d..d1776e9 100644 --- a/vignettes/link2GI1.R +++ b/vignettes/link2GI1.R @@ -1,4 +1,4 @@ -## ---- eval=FALSE-------------------------------------------------------------- +## ----eval=FALSE--------------------------------------------------------------- # # find all SAGA GIS installations at the default search location # require(link2GI) # diff --git a/vignettes/link2GI1.Rmd b/vignettes/link2GI1.Rmd index 5a44279..f121e57 100644 --- a/vignettes/link2GI1.Rmd +++ b/vignettes/link2GI1.Rmd @@ -35,9 +35,9 @@ This vignette: R has quite a lot of classes for storing and dealing with spatial data. For vector data in the past the [sp](https://CRAN.R-project.org/package=sp) and at present the great [sf](https://CRAN.R-project.org/package=sf) packages are well known and the raster data world is widely covered by the [raster](https://CRAN.R-project.org/package=raster) and currently the [terra](https://CRAN.R-project.org/package=terra) package. For more specific links as needed for manipulating atmospheric modeling packages as [ncdf4](https://CRAN.R-project.org/package=ncdf4) are very helpful. -The spatial analysis itself is often supported by wrapper packages that integrate external libraries, command line tools or a mixture of both in an R-like syntax [rgeos](https://CRAN.R-project.org/package=rgeos), [geosphere](https://CRAN.R-project.org/package=geosphere), [Distance](https://CRAN.R-project.org/package=Distance), [maptools](https://CRAN.R-project.org/package=maptools), [igraph](https://CRAN.R-project.org/package=igraph) or [spatstat](https://CRAN.R-project.org/package=spatstat). +The spatial analysis itself is often supported by wrapper packages that integrate external libraries, command line tools or a mixture of both in an R-like syntax [geosphere](https://CRAN.R-project.org/package=geosphere), [Distance](https://CRAN.R-project.org/package=Distance), [igraph](https://CRAN.R-project.org/package=igraph) or [spatstat](https://CRAN.R-project.org/package=spatstat). -A comprehensive introduction to the spatial R-biotope and its backgrounds is excellently treated in [Geocomputation with R](https://geocompr.robinlovelace.net) wich is highly recommend as a reference textbook. +A comprehensive introduction to the spatial R-biotope and its backgrounds is excellently treated in [Geocomputation with R](https://r.geocompx.org/) wich is highly recommend as a reference textbook. Despite all this capabilities of spatial analysis and data handling in the world of `R`, it can be stated (at least from a non-R point of view), that there is still a enormous gap between R and the mature open source Geographic Information System (GIS) and even more Remote Sensing (RS) software community. `QGIS`, `GRASS GIS` and `SAGA GIS` are providing a comprehensive, growing and mature collection of highly sophisticated algorithms. The provided algorithms are fast, stable and most of them are well proofed. Probably most of the `R` users who are somehow related to the GI community know that there are awesome good wrapper packages for bridging this gap. For [GRASS GIS 7/8](https://grass.osgeo.org/) it is [rgrass](https://CRAN.R-project.org/package=rgrass) and for [SAGA GIS](https://saga-gis.sourceforge.io/) the [RSAGA](https://CRAN.R-project.org/package=RSAGA) package. In addition there is no wrapper for the great `OTB`. It seems to be at least convenient to provide a lightweight wrapping utility for the usage of `OTB` modules from `R`. diff --git a/vignettes/link2GI1.html b/vignettes/link2GI1.html index 7533ca3..76c37da 100644 --- a/vignettes/link2GI1.html +++ b/vignettes/link2GI1.html @@ -1,88 +1,153 @@ - - + + Link GI to R - - - - - - + - - - - -

What is link2GI?

+
+
+
+

Link GI to R

+

Chris Reudenbach

+

2023-10-30

+
+
+

What is link2GI?

The link2GI package provides a small linking tool to simplify the usage of GRASS GIS, SAGA GIS, Orfeo Toolbox (OTB) and GDAL binaries for R users. the focus is to simplify the the accessibility of this software for non operating system specialists or highly experienced GIS geeks. Acutally it is a direct result of numerous graduate courses with R(-GIS) beginners in the hostile world of university computer pools running under extremely restricted Windows systems.

This vignette:

    @@ -90,26 +155,26 @@

    What is link2GI?

  • gives some hands on examples of how to use
  • give some applied examples for more efficient spatial analysis
-

Why link2GI now?

+

Why link2GI now?

R has quite a lot of classes for storing and dealing with spatial data. For vector data in the past the sp and at present the great sf packages are well known and the raster data world is widely covered by the raster and currently the terra package. For more specific links as needed for manipulating atmospheric modeling packages as ncdf4 are very helpful.

-

The spatial analysis itself is often supported by wrapper packages that integrate external libraries, command line tools or a mixture of both in an R-like syntax rgeos, geosphere, Distance, maptools, igraph or spatstat.

-

A comprehensive introduction to the spatial R-biotope and its backgrounds is excellently treated in Geocomputation with R wich is highly recommend as a reference textbook.

+

The spatial analysis itself is often supported by wrapper packages that integrate external libraries, command line tools or a mixture of both in an R-like syntax geosphere, Distance, igraph or spatstat.

+

A comprehensive introduction to the spatial R-biotope and its backgrounds is excellently treated in Geocomputation with R wich is highly recommend as a reference textbook.

Despite all this capabilities of spatial analysis and data handling in the world of R, it can be stated (at least from a non-R point of view), that there is still a enormous gap between R and the mature open source Geographic Information System (GIS) and even more Remote Sensing (RS) software community. QGIS, GRASS GIS and SAGA GIS are providing a comprehensive, growing and mature collection of highly sophisticated algorithms. The provided algorithms are fast, stable and most of them are well proofed. Probably most of the R users who are somehow related to the GI community know that there are awesome good wrapper packages for bridging this gap. For GRASS GIS ⅞ it is rgrass and for SAGA GIS the RSAGA package. In addition there is no wrapper for the great OTB. It seems to be at least convenient to provide a lightweight wrapping utility for the usage of OTB modules from R.

Unfortunately one will run into a lot of technical problems depending on the choosen operating system (OS) or library dependencies or GIS software versions. In case of e.g. RSAGA the main problem has been that the SAGA GIS developers are not only changing the syntax and strategy of the command line interface (CLI) but also within the same release the calls differ from OS to OS. So the maintenance of RSAGA is at least laborious (but thumbs up is running again). Another example is given by GRASS GIS which is well known for a sophisticated setup of the environment and the spatial properties of the database. If you “just” want to use a specific GRASS algorithm from R, you will probablys get lost in setting up all OS-dependencies that are neccessary to set up a correct temporary or permanent GRASS-environment from “outside”. This is not only caused due to the strict spatial and projection requirements of GRASS but much more by challenging OS enviroments especially Windows.

To make it short it is a bit cumbersome to deal with all this stuff if one just want to start e.g. GRASS from the R command line for e.g. a powerful random walk cost analysis (r.walk) call as provided by GRASS.

-

What means linking?

+

What means linking?

Linking means simply to provide all necessary environment settings that satisfy the existing wrapper packages as well as in addition the full access to the the command line (CLI) APIs of the mentioned software tools. link2GI tries to analyze which software is installed to set up an temporary enviroment meeting the above mentioned needs.

-

GRASS GIS

+

GRASS GIS

GRASS GIS has the most challenging requirements. It needs a bunch of environment and path variables as and a correct setup of the geographical data parameters. The linkGRASS function tries to find all installations let you (optionally) choose the one you want to use and generate the necessary variables. As a result you can use both the rgrass package or the command line API of GRASS.

-

SAGA GIS

+

SAGA GIS

SAGA GIS is a far easier to set up. Again the linkSAGA function tries to find all SAGA installations, let you (optionally) choose one and generate the necessary variables. You may also use RSAGA but you have to hand over the result of linkSAGA like RSAGA::rsaga.env(path = saga$sagaPath). For a straightforward usage you may simply use the R system() call to interface R with the saga_cmd API.

-

Orfeo Toolbox (OTB)

+

Orfeo Toolbox (OTB)

The Orfeo Toolbox (OTB) is a very powerful remote sensing toolbox. It is widely used for classification, filtering and machine learning applications. You will find some of the implemented algorithm within different R packages but always much slower or only running on small data chunks. link2GI searches and connects all OTB installations of a given search path and provides the result as a clear list. Due to a missing wrapper package, a list-based OTB module and function parser is also available, which can be piped into the function runOTB for a convenient function call.

-

GDAL

+

GDAL

Notwithstanding that GDAL is perfectly integrated in R in some cases it is beneficial to use system calls and grab the binaries directly. In particular the evolution to GDAL 3.x and optionally various boxed versions of GDAL binaries working together with different Python and proj4/proj6 libs makes it sometimes difficult to grab the correct version of GDAL. link2GI generates a list of all pathes and commands of all GDAL installation in the provided search path. With this list, you can easily use all available API calls of each installation.

-

Usage of the link2GI package - Basic Examples

-

Brute force search usage

+

Usage of the link2GI package - Basic Examples

+

Brute force search usage

Automatic search and find of the installed GIS software binaries is performed by the find functions. Depending of you OS and the number of installed versions you will get a dataframe providing the binary and module folders.

So the most straightforward call to link temporary to GRASS GIS woud be:

# find all SAGA GIS installations at the default search location
@@ -118,9 +183,10 @@ 
Brute force search usage

 grass <- link2GI::linkGRASS()
 grass
- - - +
+
+
+ + - diff --git a/vignettes/link2GI1.md b/vignettes/link2GI1.md index 5ac87e1..5e2277c 100644 --- a/vignettes/link2GI1.md +++ b/vignettes/link2GI1.md @@ -1,7 +1,7 @@ --- author: "Chris Reudenbach" title: "Link GI to R" -date: "2023-01-27" +date: "2023-10-30" editor_options: chunk_output_type: console output: @@ -35,9 +35,9 @@ This vignette: R has quite a lot of classes for storing and dealing with spatial data. For vector data in the past the [sp](https://CRAN.R-project.org/package=sp) and at present the great [sf](https://CRAN.R-project.org/package=sf) packages are well known and the raster data world is widely covered by the [raster](https://CRAN.R-project.org/package=raster) and currently the [terra](https://CRAN.R-project.org/package=terra) package. For more specific links as needed for manipulating atmospheric modeling packages as [ncdf4](https://CRAN.R-project.org/package=ncdf4) are very helpful. -The spatial analysis itself is often supported by wrapper packages that integrate external libraries, command line tools or a mixture of both in an R-like syntax [rgeos](https://CRAN.R-project.org/package=rgeos), [geosphere](https://CRAN.R-project.org/package=geosphere), [Distance](https://CRAN.R-project.org/package=Distance), [maptools](https://CRAN.R-project.org/package=maptools), [igraph](https://CRAN.R-project.org/package=igraph) or [spatstat](https://CRAN.R-project.org/package=spatstat). +The spatial analysis itself is often supported by wrapper packages that integrate external libraries, command line tools or a mixture of both in an R-like syntax [geosphere](https://CRAN.R-project.org/package=geosphere), [Distance](https://CRAN.R-project.org/package=Distance), [igraph](https://CRAN.R-project.org/package=igraph) or [spatstat](https://CRAN.R-project.org/package=spatstat). -A comprehensive introduction to the spatial R-biotope and its backgrounds is excellently treated in [Geocomputation with R](https://geocompr.robinlovelace.net) wich is highly recommend as a reference textbook. +A comprehensive introduction to the spatial R-biotope and its backgrounds is excellently treated in [Geocomputation with R](https://r.geocompx.org/) wich is highly recommend as a reference textbook. Despite all this capabilities of spatial analysis and data handling in the world of `R`, it can be stated (at least from a non-R point of view), that there is still a enormous gap between R and the mature open source Geographic Information System (GIS) and even more Remote Sensing (RS) software community. `QGIS`, `GRASS GIS` and `SAGA GIS` are providing a comprehensive, growing and mature collection of highly sophisticated algorithms. The provided algorithms are fast, stable and most of them are well proofed. Probably most of the `R` users who are somehow related to the GI community know that there are awesome good wrapper packages for bridging this gap. For [GRASS GIS 7/8](https://grass.osgeo.org/) it is [rgrass](https://CRAN.R-project.org/package=rgrass) and for [SAGA GIS](https://saga-gis.sourceforge.io/) the [RSAGA](https://CRAN.R-project.org/package=RSAGA) package. In addition there is no wrapper for the great `OTB`. It seems to be at least convenient to provide a lightweight wrapping utility for the usage of `OTB` modules from `R`. diff --git a/vignettes/link2GI6.R b/vignettes/link2GI6.R index 839dfbe..abb8359 100644 --- a/vignettes/link2GI6.R +++ b/vignettes/link2GI6.R @@ -1,4 +1,4 @@ -## ---- include = FALSE--------------------------------------------------------- +## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( #fig.path = "https://raw.githubusercontent.com/r-spatial/link2GI/master/figures/", fig.align = "center", diff --git a/vignettes/link2GI6.Rmd b/vignettes/link2GI6.Rmd index 3060b3c..e585f92 100644 --- a/vignettes/link2GI6.Rmd +++ b/vignettes/link2GI6.Rmd @@ -89,7 +89,7 @@ Clicking "Next" once more will start the download and installation process which If you wish to to modify, uninstall or update some of the installed components, you might do so later on by running `../OSGeo4W/bin/osgeo4w-setup.exe`. Alternatively, you can download and run again the latest [OSGeo4W-executable](https://trac.osgeo.org/osgeo4w/). -If you additionally want to use the **LiDAR processing tools** (LAStools), please follow the steps found [here](https://rapidlasso.com/2013/09/29/how-to-install-lastools-toolbox-in-qgis/). +If you additionally want to use the **LiDAR processing tools** (LAStools), please follow the steps found [here](https://rapidlasso.de/how-to-install-lastools-toolbox-in-qgis/). ## Orfeo Toolbox diff --git a/vignettes/link2GI6.html b/vignettes/link2GI6.html index f79e788..a0c7c1b 100644 --- a/vignettes/link2GI6.html +++ b/vignettes/link2GI6.html @@ -1,269 +1,216 @@ - - -Vignette info - - - - - - - + + +Installation guide for link2GI related Software + - - - - -

Vignette info

- +
+
+
+

Installation guide for link2GI related Software

+

Chris Reudenbach

+

2023-10-30

+
+
+

Vignette info

The vignette is a slightly adapted version of the installation guide of the archived RQGIS package. Big thanks to Patrick Schratz and Jannis Muenchow.

- -

This vignette guides you through the installation process of QGIS, GRASS- and SAGA-GIS as well as Orfeo Toolbox and GDAL on three different platforms (Windows, Mac, Linux). -Following the instructions should ensure that link2GI will work properly. +

This vignette guides you through the installation process of QGIS, GRASS- and SAGA-GIS as well as Orfeo Toolbox and GDAL on three different platforms (Windows, Mac, Linux). +Following the instructions should ensure that link2GI will work properly. With the exception of SAGA (SAGA is pretty idiosyncratic in questions of interface conformity), we recommend to use the latest stable version of all software packages.

-

Overall, link2GI allows access to more than some thousands of reliable and well known geo-algorithms. However, please note that the number of geo-algorithms you can use linking with link2GI depends on the platform, the system architecture, the selection of installed third-party providers and software package versions.

- -

Windows

- -

QGIS, GRASS and SAGA

- -

There are at least two options to install QGIS on Windows. The first option is the Standalone Installer from the QGIS installer page. -This will install QGIS along with the third-party providers GRASS and SAGA. -However, if you would like to use even more third-party providers (e.g., GDAL, GEOS, Taudem, OTB, PostGIS, etc.), it is strongly recommended to use the OSGeo4W Network installer. -This installer is available on the QGIS installer page as well as on the OSGeo4W-website.

- +

Windows

+

QGIS, GRASS and SAGA

+

There are at least two options to install QGIS on Windows. The first option is the Standalone Installer from the QGIS installer page. +This will install QGIS along with the third-party providers GRASS and SAGA. +However, if you would like to use even more third-party providers (e.g., GDAL, GEOS, Taudem, OTB, PostGIS, etc.), it is strongly recommended to use the OSGeo4W Network installer. +This installer is available on the QGIS installer page as well as on the OSGeo4W-website.

NOTE: Do not install QGIS 2.x

-

To install OSGeo4W, the easiest way is to to use the Express installation:

- -

- +

Sorry for the German dialogues. Nevertheless, it should be easy enough to follow our steps.

-
    -
  1. Select “Express Installation”
    2. -
  2. Next check “QGIS, GRASS and GDAL”
    3. +
  3. Select “Express Installation”
    4. +
  4. Next check “QGIS, GRASS and GDAL”
  5. Start the installation.
-

This installation is more or less equivalent to the standalone QGIS-installation. However, to have the full choice of available geoalgorithms provided by QGIS, we recommend to use the advanced settings of the OSGeo4W Network installer:

-
    -
  1. Run the OSGeo4W setup and choose the advanced installation.
    2. +
  2. Run the OSGeo4W setup and choose the advanced installation.
- -

- -
    +

    +
    1. Subsequently, accept the default settings until you reach the “Select Packages” window.
    - -

    - -
      +

      +
      1. After expanding the command line utilities, we choose several commandline tools such as gdal and python-core (of course, you can select other components as well):
      - -

      - -

      Additionally, we choose the Desktop-GIS GRASS, the Orfeo Toolbox, SAGA, and QGIS (even if not directly supported by link2GI right now). Here, we install both the most recent QGIS 3.x version as well as the long-term release.

      - -
        -
      1. We leave the rest as is, click “Next” and wait for the OSGeo4W-suggestions which we accept.
        2. +

        +

        Additionally, we choose the Desktop-GIS GRASS, the Orfeo Toolbox, SAGA, and QGIS (even if not directly supported by link2GI right now). Here, we install both the most recent QGIS 3.x version as well as the long-term release.

        +
          +
        1. We leave the rest as is, click “Next” and wait for the OSGeo4W-suggestions which we accept.
        - -

        - -

        Clicking “Next” once more will start the download and installation process which might take a while.

        - -

        If you wish to to modify, uninstall or update some of the installed components, you might do so later on by running ../OSGeo4W/bin/osgeo4w-setup.exe. +

        +

        Clicking “Next” once more will start the download and installation process which might take a while.

        +

        If you wish to to modify, uninstall or update some of the installed components, you might do so later on by running ../OSGeo4W/bin/osgeo4w-setup.exe. Alternatively, you can download and run again the latest OSGeo4W-executable.

        - -

        If you additionally want to use the LiDAR processing tools (LAStools), please follow the steps found here.

        - -

        Orfeo Toolbox

        - +

        If you additionally want to use the LiDAR processing tools (LAStools), please follow the steps found here.

        +

        Orfeo Toolbox

        Please download the current (at this point OTB-7.2.0-Win64) or appropriate version of the Orfeo Toolbox software. Then follow the advice of the OTB team:

        - -

        “We provide standalone binaries for Windows which do not require administrative privileges. Download the archive below (32 or 64 bits), and extract it somewhere. Double-click on the monteverdi.bat to launch Monteverdi, or mapla.bat for the OTB application browser. Please see the CookBook for detailed installation instructions.”

        - -

        Linux

        - -

        Ubuntu

        - -

        If you install QGIS with the built-in software managers, you will most likely get an outdated QGIS version. -To install more recent QGIS releases, we recommend to follow the installation instructions from the QGIS installers website.

        - +

        “We provide standalone binaries for Windows which do not require administrative privileges. Download the archive below (32 or 64 bits), and extract it somewhere. Double-click on the monteverdi.bat to launch Monteverdi, or mapla.bat for the OTB application browser. Please see the CookBook for detailed installation instructions.”

        +

        Linux

        +

        Ubuntu

        +

        If you install QGIS with the built-in software managers, you will most likely get an outdated QGIS version. +To install more recent QGIS releases, we recommend to follow the installation instructions from the QGIS installers website.

        Here, we just describe exemplarily the QGIS installation procedure under Debian/Ubuntu following the description found here. link2GI should work as well with Linux derivatives other than Ubuntu. However, just Ubuntu , Debian and Manjaro are tested.

        -

        Open a terminal window. First of all, make sure to remove QGIS and GRASS packages you may have installed before from other repositories:

        - - -
        sudo apt-get --purge remove qgis
+
        sudo apt-get --purge remove qgis
 sudo apt autoremove --purge-remove 
 sudo apt autoremove
 sudo apt-get update
 
        
-
 
        Next add the correct repository to /etc/apt/sources.list.
 Here, we use the current long-term release (3.10):
        
-
 
        QGIS 3.10.x for Ubuntu 20.04
        
-
-
        # install necessary tools
+
        # install necessary tools
 sudo apt install gnupg software-properties-common
 
 #add the required keys
@@ -281,79 +228,57 @@ 
        Ubuntu
        
 
 
 
        
-
 
        After that, we can install QGIS and GRASS saga and Orfeo Toolbox as follows:
        
-
-
        # install qgis grass otb saga
+
        # install qgis grass otb saga
 
 sudo apt update
 sudo apt install qgis python-qgis qgis-plugin-grass grass saga otb-bin
 
        
-
-
        If you would like to use another SAGA version, you need to compile it yourself (see here). 
+
        If you would like to use another SAGA version, you need to compile it yourself (see here).
 Please note, however, that QGIS currently only supports the SAGA LTR 2.3.x as far as we know.
        
-
-
        Arch Linux
        
-
-
        You can install various QGIS, SAGA and GRASS versions from the Arch User Repository. 
        
-
-
        Fedora
        
-
+
        Arch Linux
        
+
        You can install various QGIS, SAGA and GRASS versions from the Arch User Repository.
        
+
        Fedora
        
 
        You can install current stable QGIS, SAGA and GRASS GIS versions via the standard software package manager:
        
-
-
        sudo dnf install qgis-python qgis qgis-grass saga grass-gui grass-libs
+
        sudo dnf install qgis-python qgis qgis-grass saga grass-gui grass-libs
 
        
-
-
        Mac OSX
        
-
-
        SAGA
        
-
+
        Mac OSX
        
+
        SAGA
        
 
        There is no binary install of SAGA for macOS.
 We recommend to use the bottle installation from homebrew:
        
-
-
        # brew tap osgeo4mac
+
        # brew tap osgeo4mac
 brew install saga-gis-lts
 brew link saga-gis-lts --force
 
        
-
 
        If you do not link SAGA with force, QGIS will not be able to detect SAGA.
        
-
-
        Alternatively, you can compile SAGA from source from the SAGA website. 
+
        Alternatively, you can compile SAGA from source from the SAGA website.
 However, this is tedious and QGIS2 only supports the SAGA LTS version.
        
-
-
        GRASS
        
-
+
        GRASS
        
 
        You can install GRASS6 and GRASS7 via homebrew:
        
-
-
        # brew tap osgeo4mac
+
        # brew tap osgeo4mac
 brew install grass6 grass7
 
        
-
-
        The binary GRASS installation can be found here. 
+
        The binary GRASS installation can be found here.
 However, we recommend to use the homebrew approach.
        
-
 
        When installing GRASS7 independently of QGIS via homebrew, please make sure to install it before you have installed QGIS.
 Only this way, the path for the QGIS processing plugin will be updated.
 Otherwise, the GRASS installation will work, however, GRASS7Utils.grassPath(), a QGIS function that links to the GRASS installation, gives back a non-existing path such as /Applications/Grass-7.0.app/Contents/MacOS which in turn prevents GRASS algorithms from working from within QGIS.
        
-
-
        QGIS
        
-
+
        QGIS
        
 
        Two options exist installing QGIS on macOS
        
-
 
          
 
        1. Using homebrew (recommended)
          2. 
 
        
-
 
        # brew tap osgeo4mac
 brew install qgis3
 
        
-
-
        Check brew info qgis3 for more available options. 
+
        Check brew info qgis3 for more available options.
 However, if you use them, QGIS will be compiled from source which may take > 30 min (depending on your system).
 Otherwise, pre-built bottles (= binaries) will be used which speeds up the installation process a lot.
        
-
 
        Note: Make sure to install SAGA and GRASS before QGIS so that QGIS finds the correct paths.
        
-
+
+
+
+ + - diff --git a/vignettes/link2GI6.md b/vignettes/link2GI6.md index 5ecf5cc..60ace1e 100644 --- a/vignettes/link2GI6.md +++ b/vignettes/link2GI6.md @@ -1,7 +1,7 @@ --- author: "Chris Reudenbach" title: "Installation guide for link2GI related Software" -date: "2022-10-12" +date: "2023-10-30" editor_options: chunk_output_type: console output: @@ -82,7 +82,7 @@ Clicking "Next" once more will start the download and installation process which If you wish to to modify, uninstall or update some of the installed components, you might do so later on by running `../OSGeo4W/bin/osgeo4w-setup.exe`. Alternatively, you can download and run again the latest [OSGeo4W-executable](https://trac.osgeo.org/osgeo4w/). -If you additionally want to use the **LiDAR processing tools** (LAStools), please follow the steps found [here](https://rapidlasso.com/2013/09/29/how-to-install-lastools-toolbox-in-qgis/). +If you additionally want to use the **LiDAR processing tools** (LAStools), please follow the steps found [here](https://rapidlasso.de/how-to-install-lastools-toolbox-in-qgis/). ## Orfeo Toolbox