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update readme.md #103

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35 changes: 16 additions & 19 deletions README.md
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Expand Up @@ -12,26 +12,25 @@ The R package `ss3diags` enables users to apply advanced diagnostics to
evaluate a Stock Synthesis model. Diagnostics include residual analyses,
hindcast cross-validation techniques, and retrospective analyses.
Functions also allow users to reproduce the key model diagnostics plots
that are presented in the paper ‘A Cookbook for Using Model Diagnostics in
Integrated Stock Assessments’.
that are presented in the paper ‘A Cookbook for Using Model Diagnostics
in Integrated Stock Assessments’ [(Carvalho et
al. 2021)](https://www.sciencedirect.com/science/article/pii/S0165783621000874).

The `ss3diags` Github repository provides step-by-step R recipes on how
to:

- [Run jitter
- [Run jitter
analysis](https://pifscstockassessments.github.io/ss3diags/articles/Jitter.html)
- [Conduct retrospective
- [Conduct retrospective
analysis](https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html)
- [Use hindcast
- [Use hindcast
cross-validation](https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html)
- [Do log-likelood profiling for
- [Do log-likelood profiling for
R0](https://pifscstockassessments.github.io/ss3diags/articles/likelihood.html)
- [Run the ASPM
- [Run the ASPM
diagnostic](https://pifscstockassessments.github.io/ss3diags/articles/aspm.html)
- [Evaluate model fit](https://pifscstockassessments.github.io/ss3diags/articles/residuals.html)



- [Evaluate model
fit](https://pifscstockassessments.github.io/ss3diags/articles/residuals.html)

with Stock Synthesis by making use of a comprehensive collection of R
functions available in the R packages
Expand Down Expand Up @@ -63,23 +62,21 @@ visualize the results of those diagnostic tests using the `r4ss` and

If you would like to contribute to `ss3diags` or have suggestions for
diagnostic tests to include in the package, you can submit a new
[issue](https://github.com/PIFSCstockassessments/ss3diags/issues) or contact Meg at
<[email protected]>.
[issue](https://github.com/PIFSCstockassessments/ss3diags/issues) or
email Meg at <[email protected]>.

## Reference

To cite `ss3diags` for a publication you can use

``` r
citation("ss3diags")
#>
#> To cite package 'ss3diags' in publications use:
#>
#> Henning Winker, Felipe Carvalho, Massimiliano Cardinale, Laurence
#> Kell, Megumi Oshima and Eric Fletcher (2023). ss3diags: Stock
#> Synthesis Model Diagnostics for Intergated Stock Assessments. R
#> package version 2.1.1.
#> https://github.com/PIFSCstockassessments/ss3diags
#> Winker H, Carvalho F, Cardinale M, Kell L, Oshima M, Fletcher E
#> (2023). _ss3diags: Stock Synthesis Model Diagnostics for Intergated
#> Stock Assessments_. R package version 2.1.1,
#> <https://github.com/PIFSCstockassessments/ss3diags>.
#>
#> A BibTeX entry for LaTeX users is
#>
Expand Down
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