README.md

In andrew-edwards/EDMsimulate: Simulating Fish Populations for Empirical Dynamic Modeling

EDMsimulate - an R package for simulating fish populations in the context of Empirical Dynamic Modelling

Simulating populations for some EDM analyses. Under development, and not really designed to be used by others.

report/ contains earlier analyses that have now been included in first manuscript, and code likely better as vignettes in pbsEDM.

We use the R package cmdstanr which uses cmdstan which needs Rtools4.3 (if running R 4.3). Install Rtools. Do library(cmdstanr) and follow the instructions for getting cmdstan and setting it up.

Vignette

The vignette showing examples of the functions is available here, and directly in the package (see below).

To install from GitHub (Carrie and Luke)

I gave you access to push to this repo. So no need to fork on GitHub, just clone the repository onto your computer:

git clone https://github.com/andrew-edwards/EDMsimulate

then in R in the EDMsimulate/ directory:

install(build_vignettes = TRUE)

Then try:

vignette("salmon_sim", package="EDMsimulate")

which should show the vignette in an html browser.

It's hard for me to test a clean build, so let me know if it's working.

To install from GitHub (not Carrie and Luke)

You need the package devtools, so you need to install it once:

install.packages("devtools")

This enables installation directly from the GitHub site:

devtools::install_github("andrew-edwards/EDMsimulate", build_vignettes = TRUE)
library(EDMsimulate)

Also, this packages requires the Larkin package, which is available here:

devtools::install_github("pbs-assess/larkin", build_vignettes = TRUE)
library(larkin)

And several other R packages

library(ggplot2)
library(RcolorBrewer)
library(grid.arrange)
library(dplyr)

andrew-edwards/EDMsimulate documentation built on Oct. 25, 2023, 2:43 p.m.