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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
```
# FIMS-software
<!-- badges: start -->
<!-- badges: end -->
The goal of FIMS software platform project is to compare statistical computing environments for use in the [FIMS](https://www.fisheries.noaa.gov/national/population-assessments/fisheries-integrated-modeling-system) intiative. This is ongoing research. For more details, see the [Working Document](https://andrea-havron-noaa.github.io/FIMS-software/docs/FIMS-software-exploratory-analysis.html)
## Resources
* [Julia GitHub](https://github.com/JuliaLang/julia)
* [Stan User's Guide](https://mc-stan.org/docs/2_19/stan-users-guide/)
* [Stan GitHub](https://github.com/stan-dev/stan)
* [cmdstan GitHub](https://github.com/stan-dev/stan)
* [TMB Documentation](https://kaskr.github.io/adcomp/_book/Introduction.html)
* [TMB GitHub](https://github.com/kaskr/adcomp)
## FIMS Software Organization
The FIMS software platform project is organized as follows:
```{r, toc, echo = FALSE, warning = FALSE}
library(pander)
library(kableExtra)
df <- data.frame(Directory = c("data",'docs','R','results','src','\\\ \\\ src/julia', '\\\ \\\ src/Rcpp', '\\\ \\\ src/stan', '\\\ \\\ src/tmb'),
Description = c("data simulation script, simulated data files, and initial values files",
"working documents detailing project and results",
"* model_setup.R: code used to setup TMB and Stan models
\\\n * modular_demo.R: code runs modular example of passing C++ code to different platforms
\\\n * run_models.R: runs different platforms for benchmark study excluding julia
\\\n * utils.R: base functions for R code",
"results files from benchmark study",
"source files for project",
"* stateSpace.jl: julia file that specifies and run gompertz and logistic models",
"* Common.hpp:
\\\n * likelihoods.hpp: likelihood definitions
\\\n * logisticGrowth.cpp: TMB model specification
\\\n * model.hpp: C++ model definitions",
"* gompertz.stan: gompertz model
\\\n * logistic.stan: logistic growth model",
"* sptail_poisson.cpp: spatially explicit Poisson model
\\\n * stateSpace.cpp: gompertz and logistic growth model"))
pander(df, keep.line.breaks = TRUE, style = 'grid', justify = 'left')
#kbl(df)
```
## Modular TMB Examples
Incorporating TMB functions in a modular C++ framework
[logisticGrowth](https://andrea-havron-noaa.github.io/FIMS-software/docs/logisticGrowth.html)
[ar1xar1](https://andrea-havron-noaa.github.io/FIMS-software/docs/ar1xar1.html)