arcgisbinding: Testing the new ArcGIS interface for the R

language
Apr 30, 2016

A couple of months ago, ESRI released a bridge library to connect ArcGIS and R. This library was developed with the purpose of
facilitating management and processing of ArcGIS data for R users, and at the same time making easier for ArcGIS users to
incorporate all the power of R analysis tools into their workflows.

This bridge library sounds quite promising so Ive written a brief tutorial to learn, and also to test, the capabilities of this bridge
between two of the leading players in the fields of GIS and data analysis. Below I describe how to install the required library and how
to create and execute a tool that combines Arc datasets and functionalities from R packages for addressing species distribution
modeling within ArcGIS environment. Lets start!
Install the R ArcGIS Bridge

First, go to https://r-arcgis.github.io/ and enter into r-bridge-install. Click the Download ZIP button to download the repository
content into the r-bridge-install-master.zip file and then unzip it in a local folder.

Start ArcMap (for ArcGIS 10.3.1 or later) as administrator and use the Catalog window to navigate to the folder where the unzipped
file is located. You must see the R Integration Python Toolbox with four scripts in it. Double click the Install R bindings script and
then just click OK to run it. This script downloads and installs the latest version of an R package called arcgisbinding which provides
classes and functions for importing, managing and exporting ArcGIS datasets in R. To check that the R ArcGIS bridge has been
successfully installed, run the R Version and R Installation Details scripts.

If you open R or RStudio you will find that the arcgisbinding package has been installed to your R library. Note that the R ArcGIS
bridge can also be installed using ArcGIS Pro 1.1 (or later).

The video below shows the step-by-step installation of the R ArcGIS bridge:

https://www.youtube.com/watch?v=sZ6o3iKjOuc

Also note that, alternatively, you can download the Windows binary zip file of the arcgisbinding package and install it into R
manually.

Create an R script

We are going to follow the templates in the scripts folder in the r-sample-tools repository to create an script for species distribution
modeling using functionality provided by the arcgisbinding and the dismo R packages. First, we need to load the required packages
and read the input and output parameters:

tool_exec <- function(in_params, out_params)

{
if (!requireNamespace("dismo", quietly = TRUE))
install.packages("dismo")
if (!requireNamespace("raster", quietly = TRUE))
install.packages("raster")
require(dismo)
 require(raster)

occurrence_dataset = in_params[[1]]
continuous_rasters_folder = in_params[[2]]
biome_raster = in_params[[3]]
model = in_params[[4]]

out_raster = out_params[[1]]
out_table = out_params[[2]]
out_shp = out_params[[3]]

Next, we are going to open the input (points) shapefile dataset (e.g., occurrence data of the studied species) using the arc.open
function from the arcgisbinding package, and convert the resulting dataset to an SpatialPointsDataFrame object using arc.select
and arc.data2sp:

d <- arc.open(occurrence_dataset)
occurrence <- arc.data2sp(arc.select(d))

Then well proceed to read the raster files. As arc.open does not open raster datasets yet (up to version 1.0.0.118 of arcgisbinding),
Im following the next work-around for this tutorial: a set of continuous rasters files (e.g., temperature, precipitation) are read from a
folder that contains all of them, while a categorical raster (e.g., biome) is read from a separate file.

# read the continuous raster files from a folder

rfiles1 <- list.files(path = continuous_rasters_folder, full.names = TRUE)
rasters1 <- stack(rfiles1[-grep(".aux", rfiles1)])

# read the categorical raster (biome) from a file

raster2 <- raster(gsub("/", "\\\\", biome_raster))
Next we need to create a RasterStack object with all the continuous and categorical raster layers that are going to be used as predictors
in the model, and then extract the values from the RasterStack at the (point) locations of the species occurrence:

predictors <- stack(rasters1, raster2)

presvals <- as.data.frame(extract(predictors, occurrence))

There are several models that can be implemented for species distribution modeling. For the bioclim model, for example, we can use
the following code:

if(model == "bioclim"){
fitmodel <- bioclim(subset(presvals, select = -c(biome)))
p <- predict(predictors, fitmodel)
}

For the implementation of domain, glm (generalized linear models) and mahal (Mahalanobis) models, see the complete script in
this link. Other modeling methods such as MaxEnt or randomForests can also be easily implemented in this script.

Finally, well use arc.write to export an output table and a shapefile with data resulting from the extract step above. To export the
predicted species distribution raster object, well have to use writeRaster from the raster package:

if (!is.null(out_raster) && out_raster != "NA")

writeRaster(p, out_raster)
if (!is.null(out_table) && out_table != "NA")
arc.write(out_table, presvals)
if (!is.null(out_shp) && out_shp != "NA")
arc.write(out_shp, presvals, coords = coordinates(occurrence), shape_info = arc.shapeinfo(d))
return(out_params)
}
The script above shows the usage of some of the R ArcGIS bridge functions available for loading and managing datasets between R
and ArcGIS, such as arc.open, arc.select, arc.data2sp, arc.shapeinfo and arc.write. For info about additional
functionalities, please refer to the arcgisbinding package documentation.

Create an ArcGIS toolbox

Now lets create a toolbox in ArcGIS for an interactive execution of our script. In the Catalog window, navigate to Toolboxes - My
Toolboxes and right-click My Toolboxes. Go to New, click Toolbox and provide a name for your new toolbox.

Then right-click the new toolbox, and go to Add - Script. In the Add Script windows, provide a name and a label, and select the
script we created previously.
In the last Add Script window, we are required to provide the properties of the input and output parameters of our script. In this case,
we have four inputs and three outputs. Enter the Display Name and the Data Type properties of each parameter as shown in the
picture below. Also be sure to define the Direction property of each parameter (i.e., Input or Output) appropriately. When done,
click Finish.
Load the data and run the R ArcGIS tool

For this tutorial we are going to use sample data consisting of a set of eight continuous raster files (i.e., bioclimatic variables from the
WorldClim database, including temperature and precipitation), one categorical raster file (corresponding to terrestrial biomes data
from WWF), and a points shapefile containing occurrence records (presence) of three-toed sloths (Bradypus sp.), a tree-living
mammal species found in South and Central America. This shapefile was generated from data installed with the dismo package. The
goal of this exercise will be to model the spatial distribution of Bradypus sp. using climate and biome data as predictors.

After loading the data in ArcMap, go to the previously created toolbox in the Catalog window, right-click the script and click Open
(or just double-click it). In the open interface, select the occurrence dataset (i.e. the bradypus feature layer), the folder containing the
continuous rasters, and the biome raster file. Then enter the model you want to run and provide the parameters for the output files (i.e.,
the predicted raster, and the table and shapefile outputs). Execute the script by clicking OK. You should find the expected output files
in the paths you defined previously.
Thats it! For more info, see the creation and execution of the R ArcGIS species distribution modeling tool in the video below:

https://www.youtube.com/watch?v=CUIEVk5icR8&feature=youtu.be

Final remarks

The R ArcGIS bridge offers several interesting features that enable the integration between ArcGIS and the R language. First, package
installation can be conducted from the R ArcGIS tool, eliminating additional work for users. A second attractive functionality is the
ability of producing several outputs at once, which improves the efficiency of these tools by allowing the creation of several tables,
graphs and datasets through the same script. Additionally, debugging the script is facilitated by errors being printed and shown in the
typical Arc tools execution window.

Perhaps the main drawback of the R ArcGIS bridge to date is the lack of native support for opening and writing raster datasets through
arc.open and arc.write respectively, although there are work-arounds as the one shown above. This is a much needed feature that I
expect developers at ESRI incorporate in future versions of the arcgisbinding package. On the other hand, creating a graphic
interface for an R script in QGIS is much simpler than in ArcGIS, but Arc toolboxes are not complicated to create and offer a great
flexibility.

To learn more about species distribution modeling and the models implemented in the script, I invite you to read the Species
distribution modeling with R vignette from the dismo package. You can find the complete R script for this post in this link and
download the toolbox and the datasets used in this tutorial from this GitHub repository.

The arcgisbinding package is still in beta release and some issues may be found, so let me know about your experience with the R
ArcGIS bridge if you try this tutorial. Have fun!
You may also be interested in:

* Integrating QGIS and R: A stratified sampling example

COMMENTS

11 comments
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 Kamrul Islam Sujon 4 months ago

Very helpful and instructive. Thank you for your nice work.

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 Ali Mod Kamrul Islam Sujon 4 months ago

So glad you find it helpful. Thank you Kamrul for appreciating my work!!

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Marco Ven Ali 3 months ago

Oh now I got it... thanks!

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Marco Ven 3 months ago

Hi, thanks for the blog post! I installed the R ArcGIS Bridge but when trying to reproduce your code I notice that the first function
(tool_exec) is not complete. There is { opening the function but it stops without the end. What do I miss?

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Ali Mod Marco Ven 3 months ago

Hi Marco. Thanks for commenting on my blog. The complete script can be found in this link: https://gist.github.com/amsant....
It should work well. Please let me know if it doesn't!

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Josiah Parry 4 months ago

This is super awesome! I was really hoping that I could use the dplyr sql queries through the console though. Would I have to create a
whole toolbox for that?

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 Ali Mod Josiah Parry 4 months ago

Thanks a lot for your comment Josiah! You're question is quite interesting. I wonder whether it's possible to use rpy2 to
execute R commands from the Python console in ArcGIS. Please see this link for more on Python interfaces for the R
language: http://stackoverflow.com/quest.... I have never tried it but it would be great to make it work. On the other hand, I am
not sure what you're planning to do exactly but I think a toolbox may not be the most efficient/flexible approach. Alternatively,
you may try working with Python and R using Jupyter notebook as shown here: http://amsantac.co/blog/en/201...

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Fabio 6 months ago

Thank you for the post!

I started looking at integrating R and ArcGIS (http://r-video-tutorial.blogsp... as well and I was wondering, were you able to make the
functions arc.progress_label and arc.progress_pos work?
I tried to use them to allow users to have a feeling of what's happening, but thus far the only real solution is to use print in the R script.

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Ali Mod Fabio 6 months ago

 Hi Fabio. Thanks for stopping by with your comment! I must say I really enjoyed reading your recent posts on the R-ArcGIS
integration.
I found the same issue. Those functions didn't work and that's one of the reasons why I didn't include them in my script. As you
did, I used print, mainly for debugging my code

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scdub Ali 6 months ago

Hi Fabio and Ali,

 There was a bug with the progressor that has been fixed in the 1.0.0.121 version of the binding we released a few days ago.
With it, arc.progress_label should work in ArcMap and in Pro, though as mentioned in the package documentation,
arc.progress_pos has no effect in ArcMap, only in Pro currently.

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Ali Mod scdub 4 months ago

Thank you very much for the update! And thanks also for stopping by my blog. I'll check out the new arcgisbinding version as
soon as I can. Best regards