John Kathena Jim Ianelli 2024-07-19
The goal of NamibianHake is to setup a package for the Namibian hake assessment.
You can install the development version of NamibianHake from GitHub with:
# install.packages("devtools")
devtools::install_github("jimianelli/NamibianHake")Below are examples which show how models can be run based on the directory location.
library(NamibianHake)
## basic example code
library(here)
library(tidyverse)
library(ggridges)
theme_set(ggthemes::theme_few())
bc <- run_nh("bc")
m1 <- run_nh("m1",runit=FALSE)
m2 <- run_nh("m2",runit=FALSE)
m3 <- run_nh("m3",runit=FALSE)
mods <- rbind(
read_csv(here("mods", "bc", "nh_out.csv")) |> mutate(Model = "Base Case"),
read_csv(here("mods", "m1", "nh_out.csv")) |> mutate(Model = "Model 1"),
read_csv(here("mods", "m2", "nh_out.csv")) |> mutate(Model = "Model 2"),
read_csv(here("mods", "m3", "nh_out.csv")) |> mutate(Model = "Model 3")
)
df <- rbind(
data.frame(SSB = bc$SSB, R = bc$Pred_Rec, Model = "Base Case"),
data.frame(SSB = m1$SSB, R = m1$Pred_Rec, Model = "Model 1"),
data.frame(SSB = m2$SSB, R = m2$Pred_Rec, Model = "Model 2"),
data.frame(SSB = m3$SSB, R = m3$Pred_Rec, Model = "Model 3")
)
p1 <- df %>% ggplot(aes(x = SSB, y = R, color = Model, shape=Model)) +
geom_point() +
geom_line();p1
PlotAgeFit(x=bc, title="Base case",type="fishery",fage=2,lage=7)
PlotAgeFit(x=bc, title="Base case",type="survey1",fage=1,lage=7)
M<- data.frame(Year = 1964:2023,Sel = bc$S[1:60,], Model = "h=0.7, base case")
plot_sel()