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10-appendix.Rmd
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10-appendix.Rmd
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`r if(knitr:::is_latex_output()) '\\Appendices'`
`r if(!knitr:::is_latex_output()) '# (APPENDIX) Appendix {-}'`
# COMPUTING ENVIRONMENT {#app:a}
This document aims to be transparent and reproducible.
All data and code to reproduce the analysis in the report, and generate it, is available in [this Zenodo hosted](https://doi.org/10.5281/zenodo.13328248) [GitHub repository](https://github.com/Pacific-salmon-assess/FR-PK-ResDoc/tree/v1.0?tab=readme-ov-file)
The document describing model diagnostics and some additional figures can be found within the repository at `Supplement-model-check.html`.
To reproduce this report, clone the repository from GitHub, make sure you have the required software installed, run `fit-sr-stan.R` to fit the models, then `index.Rmd` to create the document.
Look at documentation on the `README` on the main page of the repository for more details.
R packages (and dependencies therein) necessary to recreate this analysis are:
```{r env}
suppressWarnings({suppressMessages({
library(here)
library(tidyverse)
library(rosettafish)
library(csasdown)
library(kableExtra)
library(rstan)
library(gsl)
library(cowplot)
library(scales)
})})
pkgs <- sort(c("here", "tidyverse", "rosettafish", "csasdown", "kableExtra", "rstan", "gsl", "cowplot", "scales"))
pkg_table <- devtools::session_info()$packages %>%
dplyr::filter(package %in% pkgs) %>%
dplyr::select(package, loadedversion, date) %>%
dplyr::rename(Package = package, Version = loadedversion, Date = date)
rownames(pkg_table) <- NULL
csasdown::csas_table(pkg_table)
```