R/UAStools::plotshpcreate: Create Multi-Polygon Shapefiles for Extraction of Research Plot Scale Agriculture Remote Sensing Data

Abstract

Agricultural researchers are embracing remote sensing tools to phenotype and monitor agriculture crops. Specifically, large quantities of data are now being collected on small plot research studies using Unoccupied Aerial Systems (UAS, aka drones), ground systems, or other technologies but data processing and analysis lags behind. One major contributor to current data processing bottlenecks has been the lack of publicly available software tools tailored towards remote sensing of small plots and usability for researchers inexperienced in remote sensing. To address these needs we created plot shapefile maker (R/UAS::plotshpcreate): an open source R function which rapidly creates ESRI polygon shapefiles to the desired dimensions of individual agriculture research plots areas of interest and associates plot specific information. Plotshpcreate was developed to utilize inputs containing experimental design, field orientation, and plot dimensions for easily creating a multi-polygon shapefile of an entire small plot experiment. Output shapefiles are based on the user inputs geolocation of the research field ensuring accurate overlay of polygons often without manual user adjustment. The output shapefile is useful in GIS software to extract plot level data tracing back to the unique IDs of the experimental plots. Plotshpcreate is available on GitHub (https://github.com/andersst91/UAStools).

Keywords: GIS; agricultural; open source software; shapefiles; small plot.

Figure 1

(A) Executable lines necessary to load UAStools into the R environment. (B) Example of common data structure used as the input file for plotshpcreate. (C) Demonstrates the localization of an “A” point in reference to the first plot polygon of respective experimental design matrix (front, left corner of the fist plot if reading a book from bottom to top, left to right). (D) Visual representation of A-B line. (E) Diagram demonstrating the plot (black) and buffer (red) polygon spacing input parameter. Portions of this figure were adopted from Anderson et al. (2019).

Figure 2

(A) Polygons Created for each individual row of a six row plot. (B) Single polygons created for each plot merging the adjacent rows of each plot. (C) Sub-setting out the middle two rows (purple) of a six row plot (red). (D) Sub-Setting out the middle two rows and merging them to a single polygon (purple) of a six row plot (red). (E) Staggering individual row plot polygons to adjust for staggered planting. (F) Staggering merged two row plot polygons to adjust for staggered planting.

Figure 3

Illustration demonstrating how to properly implement the “stagger” argument of plotshpcreate if (A) border plots are incorporated withing the input file design matrix or (B) border plots are not incorporated withing the input file design matrix.