R/plot_selectivities.R

In SPRFMO/jjmr: Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model

#' Plot selectivities by age, year, fleet, and model
#'
#' @param sels selectivity data frame generated by \code{get_selectivities}
#' @param fleet fleets to plot: "fsh" (fishery), "ind" (survey), or "all" (both)
#'
#' @return a ggplot2 plot object
#' @export
#'
#' @examples
#'
#' \dontrun{
#'
#' oldnewMods <- combineModels(mod0.00,mod_prev)
#'selectivities <- get_selectivities(oldnewMods)
#'plot_selectivities(selectivities)
#'
#' }
#'
plot_selectivities <-
  function(sels,
           fleet = "fsh",
           alpha = 0.4,
           scale = 4,
           size = 0.5,
           years = "all") {
    if (fleet == "all") {
      fleet <- unique(sels$fleet_type)
    }
    if (all(years == "all")){
      years <- unique(sels$year)
    }
    
    sels <- sels %>%
      dplyr::filter(fleet_type %in% fleet,
                    year %in% years)
    
    if (nrow(sels) == 0) {
      stop(
        "Specified fleet for plotting not in list of available fleets. Must be one of 'fsh','ind', or 'all'"
      )
    }

    yrs_pretty <- years[(years %% 5) == 0]
    
    tmp <- sels %>%
      ggplot() +
      ggridges::geom_density_ridges(
        aes(
          x = age,
          y = forcats::fct_rev(as.factor(year)),
          height = selectivity,
          group = interaction(model, year),
          fill = model,
          color = model
        ),
        stat = "identity",
        alpha = alpha,
        scale = scale,
        size = size
      ) +
      theme_jjm() +
      ggplot2::scale_x_continuous(name = "Age", guide = ggplot2::guide_axis(check.overlap = TRUE, n.dodge = 2)) +
      ggplot2::scale_y_discrete(name = "Year", breaks=yrs_pretty) +
      ggplot2::scale_color_viridis_d(name = "Model") +
      ggplot2::scale_fill_viridis_d(name = "Model")
    
    if (dplyr::n_distinct(sels$fleet_type) == 1){
      
      out <- tmp + 
        ggplot2::facet_wrap(~fleet_name)
      
    } else {
      out <- tmp + 
        ggplot2::facet_grid(fleet_type ~ fleet_name)
        
    }
    
    return(out)
    
    
  }