Updated readme

README.Rmd

@@ -5,9 +5,6 @@ date: "2023-09-15"
 output: github_document
 ---
 
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
 
 ## Standard Projection Model for Alaska Groundfish
 

README.md

@@ -26,3 +26,115 @@ ai_spm.dat
 relative to the folder with spm.exe  
 3. From the command line pointed to the folder with these inputs, type
 “spm”  
+
+<!-- README.md is generated from README.Rmd. Please edit that file -->
+
+# East Bering Sea pollock <img src="man/figures/logo.png" align="right" height=140/>
+
+The R package `spmR` was developed for doing stock projections for
+groundfish at the AFSC. The model was coded using the Autodif (`AD`)
+Model Builder (`ADMB`) software.
+
+## Cloning the repository (optional)
+
+The R package `spmR` lives on a public GitHub repository. The repository
+can be cloned to your computer from the command line or using a user
+interface. From the command line using Linux the repository can be
+cloned using:
+
+``` r
+git clone https://github.com/afsc-assessments/spmR
+```
+
+## Installation
+
+There are several options for installing the `spmR` R package.
+
+### Option 1
+
+The `spmR` package can be installed from within R using:
+
+``` r
+devtools::install_github(repo = "afsc-assessments/spmR", dependencies = TRUE, 
+                         build_vignettes = TRUE, auth_token = "your_PAT")
+```
+
+### Option 2
+
+The GitHub repository can be cloned to your computer and the package
+installed from the command line. From Linux this would involve:
+
+``` r
+git clone https://github.com/afsc-assessments/spmR
+R CMD INSTALL spmR
+```
+
+### Option 3
+
+This time from within R using:
+
+``` r
+devtools::install("spmR")
+```
+
+## Help
+
+Help for all `spmR` functions and data sets can be found on the R help
+pages associated with each function and data set. Help for a specific
+function can be viewed using `?function_name`, for example:
+
+``` r
+?run_model
+?tab_fit
+?plot_sel
+```
+
+Alternatively, to see a list of all available functions and data sets
+use:
+
+``` r
+help(package = "spmR")
+```
+
+## Examples
+
+The package vignettes are a great place to see what `spmR` can do. You
+can view the package vignettes from within R using:
+
+``` r
+browseVignettes(package = "spmR")
+vignette(topic = "spmR", package = "spmR")
+```
+
+## Website
+
+All of the vignettes and the help pages for each function are bundled
+together and published on the website
+<https://afsc-assessments.github.io/spmR/>.
+
+## Developers
+
+Developers will want to do things slightly differently. See the
+`Model development` vignette.
+
+# Acronymns
+
+NOAA: National Oceanic and Atmospheric Administration  
+NMFS: National Marine Fisheries Service  
+AFSC: Alaska Fisheries Science Center  
+REFM: Resource and Ecology and Fisheries Management
+
+# Legal disclaimer
+
+This repository is a software product and is not official communication
+of the National Oceanic and Atmospheric Administration (NOAA), or the
+United States Department of Commerce (DOC). All NOAA GitHub project code
+is provided on an ‘as is’ basis and the user assumes responsibility for
+its use. Any claims against the DOC or DOC bureaus stemming from the use
+of this GitHub project will be governed by all applicable Federal law.
+Any reference to specific commercial products, processes, or services by
+service mark, trademark, manufacturer, or otherwise, does not constitute
+or imply their endorsement, recommendation, or favoring by the DOC. The
+DOC seal and logo, or the seal and logo of a DOC bureau, shall not be
+used in any manner to imply endorsement of any commercial product or
+activity by the DOC or the United States Government.

docs/pkgdown.yml

@@ -4,5 +4,5 @@ pkgdown_sha: ~
 articles:
   00-spm-example: 00-spm-example.html
   01-Background: 01-Background.html
-last_built: 2024-02-28T22:47Z
+last_built: 2024-02-28T22:59Z