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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

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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