Microclimate Sensor Networks: Site Selection and Visualization Program

(please see README.txt for an unformatted version of this readme)

Questions? Please submit an issue here. If you don't have a GitHub account and can't submit issues, then reach out to Dave Klinges at: dklinges9@gmail.com. Responses will be faster for issues than emails, however!

See our paper published in Ecological Informatics for further info:
Klinges, D.H., Lembrechts, J.J., Van de Vondel, S., Greenlee, E.J., Hayles-Cotton, K., Senior, R.A., 2025. A workflow for microclimate sensor networks: Integrating geographic tools, statistics, and local knowledge. Ecological Informatics 91, 103376. https://doi.org/10.1016/j.ecoinf.2025.103376

Instructions

1. Set Parameters

scripts/set_parameters.R

Requires user input of parameters specifying your target landscape, budget, desired environmental drivers, and so on. By default provides sensor selection for a landscape in Madagascar, but can work for anywhere non-polar terrestrial location on Earth. See instructions within this script.

Alternatively, you can set the parameters using our Excel template, found in docs/parameters/parameter_template.xlsx

2. Main Program

scripts/main.R

This file is your home base. Used to run all steps in the program, in their appropriate sequence. Running scripts out of order may cause the data pipeline to be interrupted due to error messages.

3. Inspect Outputs

• CSV of chosen sensor locations, and environmental information corresponding to these locations, is provided in the directory data/chosen_sites/
• CSVs and TIF rasters of landscape environmental variation and bins are provided in the directory data/landscape_data/
• Visualizations of environmental variation in your landscape, locations of bins, and locations of chosen sensor locations are provided in figures/point_selection/.
• TIF rasters of input environmental layers are queried and stored to the directory data/spatial_drivers.
• Additional diagnostics about chosen sensor locations, if necessary, are provided in the directory data/chosen_sites/diagnostics/.

That's it! See below for descriptions of other source files, which should not be modified (unless further customization desired).

Internal files (do not modify)

Source Code

scripts/00_source/functions.R

Source code used internally to support other scripts. Do not modify.

Check Packages

scripts/00_source/check_pkgs.R

Checks that the user has all necessary R packages, whom is prompted to install missing packages, if any. Do not modify.

Check Parameters

scripts/01_parameters/check_parameters.R

Checks all user parameter inputs to confirm they meet the program's standards. Do not modify.

Power Analysis

scripts/02_power_analysis/power_analysis.R

Performs a test of the statistical power of a study design based upon the chosen number of spatial drivers and sample size (i.e. number of sensors). Do not modify.

Get DEM

scripts/03_data_extraction/get_dem.R

Downloads a DEM for a desired spatial extent and desired spatial resolution, and uses this DEM to calculate elevation, slope, and aspect. Do not modify.

Prep Spatial data

scripts/03_data_extraction/prep_spatial.R

Preps spatial data for spatial environmental drivers to be used in point selection and visualization scripts. Do not modify.

Site Selection

scripts/04_site_selection/site_selection.R

Performs selection of sensor sites that adequately represent environmental space across the specified landscape. Do not modify.

Visualize Sites

scripts/05_visualize_sites/visualize_sites.R

Generates maps of chosen sites over environmental layers, and other plots of distribution of environmental space and how it was sampled. Do not modify.