Software

hypervolume: n-dimensional geometry

hypervolume is an R package that estimates n-dimensional hypervolumes from observed data. It can calculate shapes and volumes, perform set operations (intersection, union, etc.), detect holes, estimate probability density functions, project to geographic maps for species distribution modeling, and report functional diversity statistics. Supported geometries include kernel density estimation (hyperbox and Gaussian kernels), one-class support vector machine, and convex polytope (hulls). CRAN download. Github repository. Frequently asked questions.

comclim: Community climate analysis of ecological disequilibrium

comclim detects environmental mismatch and filtering in communities by integrating compositional data, climate niches, observed climate, and regional pools in a null modeling framework. CRAN download - Github repository

venation: image analysis of leaf venation networks

venation is a set of MATLAB programs that use traced skeletons of leaf venation networks to extract several summary statistics describing the geometry and topology of the network (e.g. vein density, loopiness, areole elongation index). Other programs allow rapid estimation of vascular bundle radius. The programs can work on user-defined regions of interest and variable resolutions in either a single image or batch processing mode. Github repository.

timeordered: time ordered network analysis

timeordered is an R package that constructs time-ordered networks in which the links between nodes can change over time. It can also perform spreading analyses, project networks to time-aggregated networks, and report summary statistics over time. Website - CRAN download - Github repository

leafarea: Leaf area estimation from scanned images

leafarea estimates projected leaf area from scanned images of leaves. A variety of options are available to specify image resolution, reduce image noise, and fill holes in images. Images can be processed one at a time or in batches. Versions are available for ImageJ and for MATLAB (more feature-rich). Github repository.

herbivory: image analysis of herbivorized leaves

herbivory is a MATLAB program that allows delineation of leaf boundaries by a user to infer herbivory rates. Several damage types can also be scored. Github repository

thermal_analysis: Thermal image calibration and registration

thermal_analysis is a set of MATLAB programs that can radiometrically calibrate raw FLIR infrared image data based on external measurements of relative humidity, sky temperature, object distance, etc. The programs also allow for keypoint-based automatic registration of multiple frames and extraction of time series summary statistics. Github repository.

flir_thermal_control: data logging for FLIR cameras

flir_thermal_control is a set of Python scripts and shell scripts for a Linux host (e.g. Raspberry Pi) that allow a FLIR camera to be controlled via a Gigabit ethernet interface. The code allows for automatic frame grabbing and recalibration at evenly spaced time intervals, for either linear temperature or for radiometric data. Github repository

Cavendish: n-body gravitation

Cavendish is a Mac OS X program that simulates gravitational interactions and collisions between many objects of variable sizes and masses. A 3-dimensional version and a 2-dimensional educational version are available. Full program. Education version of program.

Structure: protein visualization screensaver

Structure is a Mac OS X screensaver that visualizes protein geometry based on PDB files. Website

SophoKeys: Polytonic Greek input

SophoKeys provides an input method to type polytonic Greek on a Mac. It supports Beta Code as well as several other methods. Website.