Report template

Author

Meg Oshima and Nicholas Ducharme-Barth with JB 

library(r4ss)
library(dplyr)
library(stringr)
library(magrittr)
library(ggplot2)

main_dir <- this.path::this.proj()

report1 <- SS_output(dir = file.path(main_dir, "stock-synthesis-models", params$model1_dir), verbose=FALSE, printstats=FALSE)
new_steep1 <- report1$parameters %>% 
             filter(str_detect(Label, "SR_BH_steep")) %>% ## Need to change this to match the parameter name in control file
             pull(Value)

report2 <- SS_output(dir = file.path(main_dir, "stock-synthesis-models", params$model2_dir), verbose=FALSE, printstats=FALSE)
new_steep2 <- report2$parameters %>% 
             filter(str_detect(Label, "SR_BH_steep")) %>% ## Need to change this to match the parameter name in control file
             pull(Value)

Model modifications description

I changed the steepness to 0.5 and 0.7.

Plot of SSB for Steepness = 0.5

Here is a plot showing the timeseries of SSB for the modified model with steepness=0.5.

Code 
ssb_summary <- report1$timeseries %>% 
               select(Yr, SpawnBio) %>%
               mutate(model_name = params$model1_dir)

ssb_summary %>%
    ggplot() +
    geom_line(aes(x = Yr, y = SpawnBio)) + 
    xlab("Year") + 
    ylab("Spawning Biomass") +
    theme(panel.background = element_rect(fill = "white", color = "black", linetype = "solid"),
                panel.grid.major = element_line(color = 'gray70',linetype = "dotted"), 
                panel.grid.minor = element_line(color = 'gray70',linetype = "dotted"),
                strip.background =element_rect(fill="white"),
                legend.key = element_rect(fill = "white"))

Plot of SSB for Steepness = 0.7

Here is a plot showing the timeseries of SSB for the modified model with steepness=0.7.

Code 
ssb_summary <- report2$timeseries %>% 
               select(Yr, SpawnBio) %>%
               mutate(model_name = params$model2_dir)

ssb_summary %>%
    ggplot() +
    geom_line(aes(x = Yr, y = SpawnBio)) + 
    xlab("Year") + 
    ylab("Spawning Biomass") +
    theme(panel.background = element_rect(fill = "white", color = "black", linetype = "solid"),
                panel.grid.major = element_line(color = 'gray70',linetype = "dotted"), 
                panel.grid.minor = element_line(color = 'gray70',linetype = "dotted"),
                strip.background =element_rect(fill="white"),
                legend.key = element_rect(fill = "white"))

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