FIMS-software

The goal of FIMS software platform project is to compare statistical computing environments for use in the FIMS intiative. This is ongoing research. For more details, see the Working Document

Resources

• Julia GitHub
• Stan User’s Guide
• Stan GitHub
• cmdstan GitHub
• TMB Documentation
• TMB GitHub

FIMS Software Organization

The FIMS software platform project is organized as follows:

Directory	Description
data	data simulation script, simulated data files, and initial values files
docs	working documents detailing project and results
R	model_setup.R: code used to setup TMB and Stan models modular_demo.R: code runs modular example of passing C++ code to different platforms run_models.R: runs different platforms for benchmark study excluding julia utils.R: base functions for R code
results	results files from benchmark study
src	source files for project
src/julia	stateSpace.jl: julia file that specifies and run gompertz and logistic models
src/Rcpp	Common.hpp: likelihoods.hpp: likelihood definitions logisticGrowth.cpp: TMB model specification model.hpp: C++ model definitions
src/stan	gompertz.stan: gompertz model logistic.stan: logistic growth model
src/tmb	sptail_poisson.cpp: spatially explicit Poisson model stateSpace.cpp: gompertz and logistic growth model

Modular TMB Examples

Incorporating TMB functions in a modular C++ framework

logisticGrowth

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