Updated readme

README.Rmd

@@ -25,5 +25,112 @@ These are the steps to run the projection code:\
 2. Within spm.dat specify the location of the assessment input file 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 -->
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  fig.path = "man/figures/README-",
+  out.width = "100%"
+)
+```
+
+# 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: 2024-02-28T22:42Z
+last_built: 2024-02-28T22:47Z