From 05b66c97319f297b3af7cc89507535711b18a384 Mon Sep 17 00:00:00 2001 From: MOshima-PIFSC Date: Thu, 15 Feb 2024 15:43:16 -1000 Subject: [PATCH] update readme.md --- README.md | 35 ++++++++++++++++------------------- 1 file changed, 16 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index 94490d6..22da06e 100644 --- a/README.md +++ b/README.md @@ -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 @@ -63,8 +62,8 @@ 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 -. +[issue](https://github.com/PIFSCstockassessments/ss3diags/issues) or +email Meg at . ## Reference @@ -72,14 +71,12 @@ 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, +#> . #> #> A BibTeX entry for LaTeX users is #>