Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/chantelwetzel-noaa/xsss
Data-limited assessment approach based on Stock Synthesis which uses index data
https://github.com/chantelwetzel-noaa/xsss
assessment data-limited stock-synthesis
Last synced: about 2 months ago
JSON representation
Data-limited assessment approach based on Stock Synthesis which uses index data
- Host: GitHub
- URL: https://github.com/chantelwetzel-noaa/xsss
- Owner: chantelwetzel-noaa
- Created: 2014-05-14T14:56:28.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2018-10-19T16:26:59.000Z (about 6 years ago)
- Last Synced: 2024-06-11T17:22:04.863Z (7 months ago)
- Topics: assessment, data-limited, stock-synthesis
- Language: R
- Homepage:
- Size: 1.14 MB
- Stars: 4
- Watchers: 7
- Forks: 1
- Open Issues: 2
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
## Extended Simple Stock Synthesis
Extended Simple Stock Synthesis (XSSS) is an assessment method for application to data-limited stocks. XSSS uses adaptive importance sampling to update parameter priors based upon index data.
*Code available on this website comes with no warranty or guarantee of accuracy.*
## Installation
```S
install.packages(c("devtools", "kableExtra"))
library(devtools)
devtools::install_github("CWetzel/XSSS", build_vignettes = TRUE)
```
Note: devtools may give this message: "*WARNING: Rtools is required to build R packages, but is not currently installed.*" However, Rtools is NOT required for installing xsss via devtools, so ignore the warning.
Once you have installed the xsss package, it can be loaded using:
```S
library(xsss)
```
A vignette is available and can be accessed with
```S
vignette("xsss")
```
## Setting up a model
XSSS is data-limited assessment approach for application when only catches and indices of abundance are available allowing for multiple fishing and survey fleets. XSSS requires four input files used by Stock Synthesis: starter, forecast, data, and control file. Biological relationships (e.g., weight-at-length, fecundity, maturity) and selectivity forms must be defined in the control file. Example model files are located within the "example" folder.
## Running XSSS
The user must define distributions for three parameters: natural mortality, steepness, and relative stock status is a specific year. Example model files and calls to the main function are included in the "example" folder. Please see the vignette for additional information.
## Software requirements
XSSS is written to work with Stock Synthesis version 3.30.11 or later. The latest version of Stock Synthesis and user manual is available on NOAA Vlab. A user account may be created for non-NOAA indivuals by contacting [email protected]. An executable for Stock Synthesis version 3.30.11 is included in the "examples" folder.
## Description of package
Wetzel, C.R., and Punt, A.E. 2015. Evaluating the performance of data-moderate and catch-only assessment methods for U.S. west coast groundfish. Fisheries Research, 171: 170-187. https://www.sciencedirect.com/science/article/pii/S016578361500185X