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Expand Up @@ -34,85 +34,17 @@ remotes::install_github("r-spatial/link2GI",ref = "master")
## Third Party software
To utilize the power of the open source GI tools from within `R` you need to install them first. As a first promising opportunity to do fulfill most of the requirements you may install `QGIS, GRASS`, `SAGA-GIS` and `Orfeo-toolbox`. For further Information have a look at the [Installation guide for link2GI related Software](https://r-spatial.github.io/link2GI/articles/link2GI7.html).

# Documentation
# New Feature



## OTB wrapper

the OTB wrapper is updated for a more convenient usage. Please have a look at the use case below. For further Information have a look at the article [OTB Wrapper](https://r-spatial.github.io/link2GI/articles/link2GI4.html).

```r

## link to OTB
require(link2GI)
require(terra)

otblink<-link2GI::linkOTB()
projRootDir<-tempdir()

fn <- system.file("ex/elev.tif", package = "terra")


## for the example we use the edge detection,
algoKeyword<- "EdgeExtraction"

## extract the command list for the choosen algorithm
cmd<-parseOTBFunction(algo = algoKeyword, gili = otblink)


## define the mandantory arguments all other will be default
cmd$help = NULL
cmd$input_in <- fn
cmd$filter <- "touzi"
cmd$channel <- 1
cmd$out <- file.path(projRootDir,paste0("out",cmd$filter,".tif"))

## run algorithm
retStack<-runOTB(cmd,gili = otblink)

## plot filter raster on the green channel
plot(retStack)
```
## `initProj` for reproducible projects
`initProj` sets up a reproducible project environment complete with a defined folder structure, an RStudio project, initial scripts and setup templates, and optionally `git` repositories and `renv` environment. Most important parameters are the project root folder and subfolders for data documentation and scripts. It supports automatic loading and if possible installation of required libraries, a default setup option to simplify project initialisation. The function creates a skeleton of the main control script `main.R`, manages variable configurations through the `src/functions/000_settings.R script` and maintains easy access to paths through the `envrmt` list variable, facilitating an light weighted efficient and reproducible project management and data handling.For further Information have a look at the article [Reproducible Projects](https://r-spatial.github.io/link2GI/articles/link2GI5.html).

```r
require(link2GI)

initProj(root_folder = tempdir(), standard_setup = "baseSpatial", newsession = TRUE)

```

In addition you may use the `File -> New Project -> New directory -> New Wizard ` dialogue choosing the ***Create Project structure with link2GI*** template to create a new project via the Rstudio menu.
When using RStudio, a new project can be created by simply selecting the ***Create Project Structure (link2GI)*** template from the ***File -> New Project -> New Directory -> New Project Wizard *** dialogue.

![](https://raw.githubusercontent.com/r-spatial/link2GI/master/figures/usegui.gif)


## Further examples


### Usecases presented on the GEOSTAT August 2018



During the GEOSTAT 2018 (see https://opengeohub.org) in Prague some more complex usescases have been presented.

#### Slides and materials
- [Presentation slides](https://gisma.github.io/link2gi2018/link2gi2018.html#1)
- [Github Repository](https://github.com/gisma/link2gi2018)

#### Basic usage of SAGA and OTB calls
- [SAGA & OTB basic usecase](https://github.com/gisma/link2gi2018/blob/master/R/usecases/saga-otb/useCaseSAGA-OTB.R)

#### Wrapping GRASS
- Wrapping a [GRASS GIS example](https://neteler.gitlab.io/grass-gis-analysis/02_grass-gis_ecad_analysis/) of Markus Neteler as presented on GEOSTAT 2018
- [Analysing the ECA&D climatic data - reloaded](https://github.com/gisma/link2gi2018/blob/master/R/usecases/grass/useCaseGRASS-Neteler2018.R)

#### GRASS based cost analysis
- Performing a GRASS based cost analysis on a huge cost raster
- [Beetle spread over high asia](https://github.com/gisma/link2gi2018/blob/master/R/usecases/cost-analysis/useCaseBeetle.R)

#### API/CLI mixed approach
- Deriving a [Canopy Height Model from UAV derived point clouds](https://github.com/gisma/link2gi2018/blob/master/R/usecases/uav-pc/useCaseCHM.R) a mixed API approach

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