Introduction to GIS scripting

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# Introduction to GIS scripting
## R for GIS

INBO workshop, 9/11 May 2017

Stijn Van Hoey

https://github.com/stijnvanhoey/course_gis_scripting

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# Setup

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* Go to [https://github.com/stijnvanhoey/course_gis_scripting](https://github.com/stijnvanhoey/course_gis_scripting)

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![:scale 80%](./img/download_course.png)]

* Clone or **download** (a ZIP folder) the course material on your computer

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* In `Rstudio` start a new project (`File` > `New Project...`) inside the `notebooks` folder (option `existing Directory`)

![:scale 100%](./img/RStudio_1.png)

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* In `Rstudio` start a new project (`File` > `New Project...`) inside the `notebooks` folder (option `existing Directory`)

![:scale 100%](./img/RStudio_2.png)

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![:scale 80%](https://i.ytimg.com/vi/PlaYMh-u-2w/maxresdefault.jpg)

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# Recap

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* `Packages` provide new objects (classes) and methods

```R
library('ggplot2')
library('sp')
library('raster')
```

* `methods/functions` act on `objects` to do something -> `()`

```R
sum(my_vector)
t(my_df) # transpose data.frame
```

* These objects have `characteristics/attributes`

```R
attributes(my_df)
```

* These objects can be `sliced` -> `[]`

```R
my_vector[1:10]
my_df[1:10, "occurrenceID"]
```

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### Help on a specific `function`

```R
?function_name
```

### Looking for `something`?

```R
??searchterm
```

### Be lazy. Use `TAB`!

![:scale 25%](./img/tabbutton.jpg)

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## Intermezzo!

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ask for help

![:scale 60%](./img/postit.jpg)

list your never-to-forget commands

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![:scale 100%](./img/issuetracker.png)

<div class="alert alert-danger">
Report bugs, typo's, suggestions... as issues: <a href="https://github.com/stijnvanhoey/course_gis_scripting/issues/new">New issue</a>
</div>

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# R session planning

* Introduction to the ecosystem
* Handson vector handling
* Handson raster handling

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# R GIS ecosystem

#### ## Minimal subset of [Spatial Data packages](https://cran.r-project.org/web/views/Spatial.html)
 
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![:scale 10%](./img/gdal_logo.png)

[GDAL (Geospatial Data Abstraction Library)](http://www.gdal.org/) is the 
open source Swiss Army knife for raster and vector geospatial data formats.

Traditionally `GDAL` used to design the raster part of the library, and `OGR` the vector part for Simple Features. Starting with GDAL 2.0, both sides have been more integrated.

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## GDAL functions: CMD

Available on the command line... with [documentation](http://gdal.org/1.11/gdalwarp.html)...

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![:scale 70%](./img/ogr2ogr_cmd.png)
]

This [online cheat-sheet](https://github.com/dwtkns/gdal-cheat-sheet) is a great resource!

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## GDAL functions: R

* Import the GDAL library and use it within a script

```R
library(rgdal)
gdal_rasterize(...

```

* Write an R function to call a specific GDAL command with `system`

```R
# No library(rgdal) (!)
system(paste('gdalinfo', filename))
```

* Use the `gdal_cmd_builder` to call a specific GDAL command (package `gdalUtils`)

```R
gdal_cmd_builder('gdalinfo', parameter_variables,...)
```

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# Vector data in R

[`07-gis-r-vectors.Rmd`](notebooks/07-gis-r-vectors.html)

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# Raster data in R

[`08-gis-r-rasters.Rmd`](notebooks/08-gis-r-rasters.html)

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# ArcPy and R

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[Installation instructions](https://github.com/R-ArcGIS/r-bridge-install) (follow the [`README.md`](https://github.com/R-ArcGIS/r-bridge-install/blob/master/README.md))

![](./img/connect_r_arcgis.png)

[Tutorials](https://r-arcgis.github.io/assets/arcgisbinding-vignette.html) and [examples](https://github.com/R-ArcGIS/r-sample-tools/tree/master/scripts)
]
 
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# ArcPy and R

Interaction with the R data types:

* `arc.data2sp`

* `arc.sp2data`

* `arc.shape2sp`

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# QGis scripts in R

QGis provides its own set of functionalities in the `processing` library. This can be accessed: access QGIS functionalities from R ([RQGIS](https://github.com/jannes-m/RQGIS)) *vs* run R functions in QGIS

[`Demo` of the latter](http://amsantac.co/blog/en/2015/10/31/qgis-r.html)

Check the information [here](https://docs.qgis.org/2.14/en/docs/training_manual/processing/r_intro.html) to write your own QGIS scripts.

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The number 1 resource: [CRAN Task View: Analysis of Spatial Data](https://cran.r-project.org/web/views/Spatial.html)

* [Great overview course](http://rspatial.org)
* [Blog of the spatial tasgroup](http://r-spatial.org/)
* [Cheat-sheet](http://www.maths.lancs.ac.uk/~rowlings/Teaching/UseR2012/cheatsheet.html)
* ...

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![:scale 100%](./img/rutils.png)

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![:scale 100%](./img/rutils_func.PNG)

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![:scale 100%](./img/r_tutorials.png)

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## Good luck!

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