Software

This repository provides a workflow to run the Joint Ecosystem Modeling (JEM) tool KiteNest. KiteNest is a spatially explicit model that predicts the daily probability of Everglade snail kite (SNKI; Rostrhamus sociabilis plumbeus) nest-site selection across the southern Everglades (Water Conservation Areas 1, 2, and 3 in addition to Everglades National Park). The repository takes the...

The {ncview} package was developed out of a need to quickly visualize and compare NetCDF data. It was developed primarily to work with NetCDF outputs from the Joint Ecosystem Modeling (JEM) lab’s jemnetcdfio package3. An effort was made to make the methods robust enough to handle gridded NetCDF data from other sources, but the package may require modifications or extensions for some use...

EverSparrow is a spatially explicit Bayesian model of Cape Sable Seaside Sparrow (CSSS; Ammospiza maritima mirabilis) presence that quantifies the relationships between environmental factors and CSSS presence. Using hydrologic variables such as mean 4-year hydroperiod and maximum depth, fire history, and woody vegetation across the range of the CSSS, EverSparrow provides weekly...

The Everglades Vulnerability Analysis (EVA) is a series of connected Bayesian networks that model the landscape-scale response of indicators of Everglades ecosystem health to changes in hydrology, salinity, and temperature on the landscape. The modeling framework currently predicts the probability of vegetation types, wading bird regional nest abundance, freshwater prey fish biomass...

This repository provides a workflow to run the Joint Ecosystem Modeling (JEM) tool EverWaders. The repository takes the published model (D'Acunto et al. 2021) and allows a user to generate hydrometrics and model predictions from daily water depth data derived from the Everglades Depth Estimation Network (EDEN) or the Regional Simulation Model (RSM).

This repository contains code to run the Estuarine Prey Fish Biomass model, using the biomass equation developed by Lorenz (2003). This equation was used for modeling prey fish biomass in Romañach et al. 2011 using Java, and this release implements the model in R to facilitate further model development and collaboration with partners. Some minor changes were made from the Java version to...

This repository contains code to run the Days Since Dry (DSD) model. DSD is defined as the number of days since a cell had less than 5cm of water depth (Trexler et al. 2010). The maximum value of DSD is 1181 days.

This repository contains code to run the Alligator Production Suitability Index (APSI), a Joint Ecosystem Modeling (JEM) hosted model developed by the National Park Service. The model has been refactored in R from Java to facilitate further model development, updates, and collaboration with Everglades partners. The R version has been modified slightly from the original Java version to...

The spread of non-native dreissenid mussels across North America has resulted in significant ecological and economic damage. Management efforts implementing early detection efforts (including watercraft inspections) may help reduce potential spread and new introductions, but optimizing effective deployment of these efforts in a resource-constrained environment is challenging. Raymond et...

The Everglades Forecasting application (EverForecast) is a hydrologic and multi-species management tool. Designed to support natural resource managers, the tool simulates near future water levels across the Florida Everglades and models the likely impacts on the habitats and populations of numerous species. EverForecast is part of the Joint Ecosystem Modeling (JEM) suite of tools. The...

restoration_runs is a library of R-language scripts used to summarize/post-process output of Joint Ecosystem Modeling (JEM; https://jem.gov/) models used in Everglades restoration planning for projects such as the Lake Okeechobee System Operating Manual (LOSOM) and the Western Everglades Restoration Project (WERP). The scripts summarize model output and create graphs and maps for each...

R-language code library to support netCDF I/O. This package was written to ease the process of reading and writing netcdfs in R for the Joint Ecosystem Modeling (JEM; https://jem.gov/) community. NetCDF files created using this package follow the Comprehensive Everglades Restoration Plan (CERP) data standards to facilitate data sharing among scientists in the Everglades area.