In duplisea/vbrecruit: Calculate proportion of a cohort recruit each year based on VB growth

knitr::opts_chunk$set(echo = TRUE)

Time of recruitment to different sizes

Based on von Bertalanffy growth parameters given to the function, the CV around length at age and the year of birth, this determines the proporption of a year class's individuals that are at or above a certain specified length in each year. This is plotted as cumulative distribution functions. It assumes normally distributed lengths for an age based on the cv supplied. There are assumptions about mortality inherent in this, namely that mortality is not size based.

It is a broad method that will provide an idea of the year when the majority of individuals in a cohort will reach a certain size.

Install the package

devtools::install_github("duplisea/vbrecruit")
library(vbrecruit)

library(vbrecruit)
library(rfishbase)

Calculate the curves based on Unit 1+2 redfish (Sebastes spp.)

recruit= vbrecruit.f(birth.year=2011, final.year = 2035, Linf = 42, k = 0.086, t0 = -1.57, 
  cv = 0.089, lengths.of.interest=c(22,25,27,30,35))

The top figure shows the Von Bertalanffy growth curve give the parameters supplied. The bottom figure shows the cumlative probability distributions for each size. So if a curve is identified by the number in the circle "25", the way you read this is by seeing what propoportion of a cohort from your specified birth year will be greater than or equal to 25cm in each year. The 50% values are highlighted for each of your lengths of interest. That is, the 50% mark shows when half of your individuals in the cohort will at or above that size.

The growth parameters used for Sebastes here are based on fitting median length at age for the 1980 cohort of Sebastes mentella from the survey data. There are not stock specific growth parameters for all species. In such cases it can be good to use estimates from fishbase. This is easy using hte rfishbase package.

Use rfishbase to get VB parameters for all sorts of species from fishbase

devtools::install_github("ropensci/rfishbase")
library("rfishbase")

Now query fishbase and make some plots for Atlantic cod. This averages over all the VB parameters for cod in fishbase so we call it a generic stock.

fish= "Gadus morhua"
vb.params= matrix(as.numeric(as.matrix(popgrowth(fish,fields=c("TLinfinity","K","to")))),ncol=3)
vb.mean= apply(vb.params,2,mean,na.rm=T)

Make plots for a generic cod stock for say a 2017 year class and length of 25cm (recuit index), 45cm (size at recruitment, 60cm (when they start to get valuable, 80cm (when they are very valuable)

cod= vbrecruit.f(birth.year= 2017, final.year= 2030, Linf= round(vb.mean[1],0), k= round(vb.mean[2],2), t0= round(vb.mean[3],2), 
  cv= 0.1, lengths.of.interest=c(25,45,60,80))
title(fish,outer=T,line=-0.75)

fish= "Trachurus murphyi"
vb.params= matrix(as.numeric(as.matrix(popgrowth(fish,fields=c("TLinfinity","K","to")))),ncol=3)
vb.mean= apply(vb.params,2,mean,na.rm=T)

Make plots for a Chilean mackerel, Trachurus murphyi, stock for say a 2017 year class and lengths of 30cm, 40cm, 50, cm and 60cm.

cod= vbrecruit.f(birth.year= 2017, final.year= 2030, Linf= round(vb.mean[1],0), k= round(vb.mean[2],2), t0= round(vb.mean[3],2), 
  cv= 0.1, lengths.of.interest=c(30, 40, 50, 60))
title(fish,outer=T,line=-0.75)

duplisea/vbrecruit documentation built on Oct. 21, 2020, 6:10 p.m.