run_qgis: Interface to QGIS commands
In jannes-m/RQGIS3: Integrating R with QGIS3

Description Usage Arguments Details Value Note Author(s) Examples

run_qgis() calls QGIS algorithms from within R while passing the corresponding function arguments.

1 2	run_qgis(alg = NULL, ..., params = NULL, load_output = FALSE, show_output_paths = TRUE, NA_flag = -99999, qgis_env = set_env())

`alg`	Name of the GIS function to be used (see `find_algorithms()`).
`...`	Triple dots can be used to specify QGIS geoalgorithm arguments as R named arguments. For more details, please refer to `pass_args()`.
`params`	Parameter-argument list for a specific geoalgorithm. Please note that you can either specify R named arguments directly via the triple dots (see above) or via a parameter-argument list. However, you may not mix the two methods. See the example section, `pass_args()` and `get_args_man()` for more details.
`load_output`	If `TRUE`, all QGIS output files (`sf::sf()`-object in the case of vector data and `raster::raster()`-object in the case of a raster) specified by the user (i.e. the user has to indicate output files) will be loaded into R. A list will be returned if there is more than one output file (e.g., `grass7:r.slope.aspect`). See the example section for more details.
`show_output_paths`	Logical. QGIS computes all possible output files for a given geoalgorithm, and saves them to a temporary location in case the user has not specified explicitly another output location. Setting `show_output` to `TRUE` (the default) will print all output paths to the console after the successful geoprocessing.
`NA_flag`	Value used for NAs when exporting raster objects through `pass_args()` and `save_spatial_objects()` (default: -99999).
`qgis_env`	Environment containing all the paths to run the QGIS API. For more information, refer to `set_env()`.

This workhorse function calls the QGIS Python API, and specifically processing.runalg().

The function prints a list (named according to the output parameters) containing the paths to the files created by QGIS. If not otherwise specified, the function saves the QGIS generated output files to a temporary folder (created by QGIS). Optionally, function parameter load_output loads spatial QGIS output (vector and raster data) into R.

Please note that one can also pass spatial R objects as input parameters where suitable (e.g., input layer, input raster). Supported formats are sp::SpatialPointsDataFrame()-, sp::SpatialLinesDataFrame()-, sp::SpatialPolygonsDataFrame()-, sf::sf()- (of class sf, sfc as well as sfg), and raster::raster()-objects. See the example section for more details.

GRASS users do not have to specify manually the GRASS region extent (function argument GRASS_REGION_PARAMETER). If "None" (the QGIS default), run_qgis() (see pass_args() for more details) will automatically determine the region extent based on the user-specified input layers. If you do want to specify it yourself, please do it in accordance with the QGIS documentation, i.e., use a character string and separate the coordinates with a comma: "xmin, xmax, ymin, ymax".

Jannes Muenchow, Victor Olaya, QGIS core team

## Not run: 
# calculate the slope of a DEM
# load dem - a raster object
data(dem, package = "RQGIS3")
# find out the name of a GRASS function with which to calculate the slope
find_algorithms(search_term = "grass7.*slope")
# find out how to use the function
alg = "grass7:r.slope.aspect"
get_usage(alg)
# 1. run QGIS using R named arguments, and load the QGIS output back into R
slope = run_qgis(alg, elevation = dem, slope = "slope.asc",
                  load_output = TRUE)
# 2. doing the same with a parameter-argument list
params = list(elevation = dem, slope = "slope.asc")
slope = run_qgis(alg, params = params, load_output = TRUE)
# 3. calculate the slope, the aspect and the pcurvature.
terrain = run_qgis(alg, elevation = dem, slope = "slope.asc",
                    aspect = "aspect.asc", pcurvature = "pcurv.asc",
                    load_output = TRUE)
# the three output rasters are returned in a list of length 3
terrain

## End(Not run)