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Add composition plots for diagnostics etc

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#422 0 comentarios 0 reacciones 0 asignados Ver en GitHub

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Evaluación

Dificultad
5/5
Tiempo estimado
Más de una semana
Aptitud para principiantes
15/100
Tipo de issue
Nueva funcionalidad
Claridad
Bastante claro
Estado de actividad
Activo
Stack tecnológico
r
Área
data-visualization

Línea de trabajo

The issue lists seven composition plot types (observed-only distributions, bubble plots, observed-vs-expected distributions, Pearson residuals, sex ratios, mean age or length time series, plus fleet-specific and aggregated variants) but names no stockplotr file, function or test. Start by reading the existing plotting functions in the R package and the r4ss examples linked in the issue, then agree with maintainers on the input data format and which plot to build first. Done means one plot type generates from composition data and has a test.

Escrito por el modelo de indexación a partir del texto del issue.

Descripción

See this conversation for more detail https://github.com/NOAA-FIMS/FIMS/pull/1873 from @iantaylor-NOAA

The categories of composition that r4ss creates for SS3 models include

  • Distribution plots of observations only (I think this is the most intuitive way to look at comps)
  • Bubble plots of observations only (Easier to see patterns of cohort strengths across years)
  • Distribution plots of observations and expected values (intuitive way to look at fit)
  • Pearson residuals (more statistically rigorous way to look at fit, easier to see blocks/stripes of misfit among years or bins)
  • Sex ratios implied by the ratio of female / (female + male) observed and expected comps (helps see trends in lack of fit, especially for bins with smaller proportions that have small residuals)
  • Time series of mean age or length in the observed and expected comps (created as diagnostic for Francis weighting method, but very helpful to summarize trends among years)
  • The set include both fleet-specific plots and plots for all fleets aggregated across years.

Examples of the r4ss plots are at

https://r4ss.github.io/r4ss/BigSkate/_SS_output_CompDat.html (observations only)
https://r4ss.github.io/r4ss/BigSkate/_SS_output_LenComp.html (most of the rest)
https://r4ss.github.io/r4ss/BigSkate/[email protected] (residuals and "Andre plots" for conditional age-at-length data)

Lenguaje dominante
R
Estrellas
20
Forks
9
Merge medio
1 d 5 h
PR fusionados (30 d)
12

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Primeros pasos

  1. Lee el issue completo y luego la guía de contribución del proyecto.
  2. Comenta en el issue que vas a ocuparte — evita que dos personas hagan lo mismo.
  3. Haz un fork del repositorio y trabaja en una rama.
  4. Abre un pull request que haga referencia al número del issue.

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