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Joint Ecosystem Modeling (JEM) Restoration Runs R Library

restoration_runs is a library of R-language scripts used to summarize/post-process output of Joint Ecosystem Modeling (JEM; 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 model.

Joint Ecosystem Modeling (JEM) NetCDF R Package

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; 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.


This repository contains the source code and package for the eDNAoccupancy package. This readme file contains the installation instructions for the package. The purpose of the R package is to fit three-level occupancy models. Although designed with eDNA-based observations, the package can be used for any occupancy situation with sampling and sub-sampling.


eDNAoccupancy allows users to specify and fit multi-scale occupancy models with or without covariates, to estimate posterior summaries of occurrence and detection probabilities, and to compare different models using Bayesian model-selection criteria.