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32.4. Anexa D: Sintaxa scrípturilor R din QGIS

Contributed by Matteo Ghetta - funded by Scuola Superiore Sant’Anna

Writing R scripts in Processing is a bit tricky because of the special syntax.

A Processing R script starts with defining its Inputs and Outputs, each preceded with double hash characters (##).

Before the inputs, the group to place the algoritm in can be specified. If the group already exists, the algorithm will be added to it, if not, the group will be created. In the example below, the name of the group is My group:

##My Group=group

32.4.1. Intrări

All input data and parameters have to be specified. There are several types of inputs:

• vector: ##Layer = vector

• vector field: ##F = Field Layer (where Layer is the name of an input vector layer the field belongs to)

• raster: ##r = raster

• table: ##t = table

• number: ##Num = number

• string: ##Str = string

• boolean: ##Bol = boolean

• elements in a dropdown menu. The items must be separated with semicolons ;: ##type=selection point;lines;point+lines

32.4.2. Rezultat

Ca și intrările, fiecare ieșire trebuie să fie definită la începutul script-ului:

• vector: ##output= output vector

• raster: ##output= output raster

• table: ##output= output table

• plots: ##output_plots_to_html (##showplots in earlier versions)

• To show R output in the Result Viewer, put > in front of the command whose output you would like to show.

32.4.3. Syntax Summary for QGIS R scripts

A number of input and output parameter types are offered.

32.4.3.1. Input parameter types

Parametru	Exemplu de sintaxă	Obiecte returnate
vector	Layer = vector	sf object (or SpatialDataFrame object, if ##load_vector_using_rgdal is specified)
vector point	Layer = vector point	sf object (or SpatialDataFrame object, if ##load_vector_using_rgdal is specified)
vector line	Layer = vector line	sf object (or SpatialDataFrame object, if ##load_vector_using_rgdal is specified)
vector polygon	Layer = vector polygon	sf object (or SpatialPolygonsDataFrame object, if ##load_vector_using_rgdal is used)
multiple vector	Layer = multiple vector	sf object (or SpatialDataFrame objects if ##load_vector_using_rgdal is specified)
tabelă	Layer = table	dataframe convertit din csv, obiect implicit al funcției read.csv
field	Field = Field Layer	numele câmpului selectat, ex.: "Area"
raster	Layer = raster	Obiect RasterBrick, obiect implicit al pachetului raster
multiple raster	Layer = multiple raster	Obiect RasterBrick, obiect implicit al pachetului raster
number	N = number	numărul întreg sau zecimal ales
string	S = string	textul adăugat în casetă
longstring	LS = longstring	șirul de caractere adăugat în casetă, ar putea fi mai lung decât șirul normal
selection	S = selection first;second;third	șirul cu elementele care vor putea fi selectate din meniul derulant
crs	C = crs	string of the resulting CRS chosen, in the format: "EPSG:4326"
extent	E = extent	Obiectul extindere din pachetul raster, puteți extrage valorile astfel: E@xmin
point	P = point	când faceți clic pe hartă, puteți vedea coordonatele punctului
file	F = file	calea fișierului ales, ex.: „/home/matteo/file.txt”
folder	F = folder	calea directorului ales, ex.: „/home/matteo/Downloads”

A parameter can be OPTIONAL, meaning that it can be ignored.

In order to set an input as optional, you add the string optional before the input, e.g:

##Layer = vector
##Field1 = Field Layer
##Field2 = optional Field Layer

32.4.3.2. Output parameter types

Parametru	Exemplu de sintaxă
vector	Output = output vector
raster	Output = output raster
tabelă	Output = output table
file	Output = output file

Notă

You can save plots as png from the Processing Result Viewer, or you can choose to save the plot directly from the algorithm interface.

32.4.3.3. Corpul scriptului

The script body follows R syntax and the Log panel can help you if there is something wrong with your script.

Remember that you have to load all additional libraries in the script:

library(sp)

32.4.4. Exemple

32.4.4.1. Exemplu de ieșire vectorială

Let’s take an algorithm from the online collection that creates random points from the extent of an input layer:

##Point pattern analysis=group
##Layer=vector polygon
##Size=number 10
##Output=output vector
library(sp)
spatpoly = as(Layer, "Spatial")
pts=spsample(spatpoly,Size,type="random")
spdf=SpatialPointsDataFrame(pts, as.data.frame(pts))
Output=st_as_sf(spdf)

Explanation (per line in the script):

1. Analiza modelului de puncte reprezintă grupul algoritmului

2. Stratul reprezintă stratul de intrare vectorial

3. Size is a numerical parameter with a default value of 10

4. Ieșire reprezintă stratul vectorial care va fi creat de către algoritm

5. library(sp) loads the sp library

6. spatpoly = as(Layer, "Spatial") translate to an sp object

7. Call the spsample function of the sp library and run it using the input defined above (Layer and Size)

8. Create a SpatialPointsDataFrame object using the SpatialPointsDataFrame function

9. Create the output vector layer using the st_as_sf function

That’s it! Just run the algorithm with a vector layer you have in the QGIS Legend, choose the number of random point. The resulting layer will be added to your map.

32.4.4.2. Exemplu de ieșire raster

The following script will perform basic ordinary kriging to create a raster map of interpolated values from a specified field of the input point vector layer by using the autoKrige function of the automap R package. It will first calculate the kriging model and then create a raster. The raster is created with the raster function of the raster R package:

##Basic statistics=group
##Layer=vector point
##Field=Field Layer
##Output=output raster
##load_vector_using_rgdal
require("automap")
require("sp")
require("raster")
table=as.data.frame(Layer)
coordinates(table)= ~coords.x1+coords.x2
c = Layer[[Field]]
kriging_result = autoKrige(c~1, table)
prediction = raster(kriging_result$krige_output)
Output<-prediction

By using ##load_vector_using_rgdal, the input vector layer will be made available as a SpatialDataFrame objects, so we avoid having to translate it from an sf object.

32.4.4.3. Exemplu de generare a unui tabel

Let’s edit the Summary Statistics algorithm so that the output is a table file (csv).

The script body is the following:

##Basic statistics=group
##Layer=vector
##Field=Field Layer
##Stat=Output table
Summary_statistics<-data.frame(rbind(
    sum(Layer[[Field]]),
    length(Layer[[Field]]),
    length(unique(Layer[[Field]])),
    min(Layer[[Field]]),
    max(Layer[[Field]]),
    max(Layer[[Field]])-min(Layer[[Field]]),
    mean(Layer[[Field]]),
    median(Layer[[Field]]),
    sd(Layer[[Field]])),
  row.names=c("Sum:","Count:","Unique values:","Minimum value:","Maximum value:","Range:","Mean value:","Median value:","Standard deviation:"))
colnames(Summary_statistics)<-c(Field)
Stat<-Summary_statistics

The third line specifies the Vector Field in input and the fourth line tells the algorithm that the output should be a table.

The last line will take the Stat object created in the script and convert it into a csv table.

32.4.4.4. Example with console output

We can use the previous example and instead of creating a table, print the result in the Result Viewer:

##Basic statistics=group
##Layer=vector
##Field=Field Layer
Summary_statistics<-data.frame(rbind(
sum(Layer[[Field]]),
length(Layer[[Field]]),
length(unique(Layer[[Field]])),
min(Layer[[Field]]),
max(Layer[[Field]]),
max(Layer[[Field]])-min(Layer[[Field]]),
mean(Layer[[Field]]),
median(Layer[[Field]]),
sd(Layer[[Field]])),row.names=c("Sum:","Count:","Unique values:","Minimum value:","Maximum value:","Range:","Mean value:","Median value:","Standard deviation:"))
colnames(Summary_statistics)<-c(Field)
>Summary_statistics

The script is exactly the same as the one above except for two edits:

1. no output specified (the fourth line has been removed)

2. the last line begins with >, telling Processing to make the object available through the result viewer

32.4.4.5. Exemplu de grafic

To create plots, you have to use the ##output_plots_to_html parameter as in the following script:

##Basic statistics=group
##Layer=vector
##Field=Field Layer
##output_plots_to_html
####output_plots_to_html
qqnorm(Layer[[Field]])
qqline(Layer[[Field]])

The script uses a field (Field) of a vector layer (Layer) as input, and creates a QQ Plot (to test the normality of the distribution).

The plot is automatically added to the Processing Result Viewer.