FLife package

library(ggplotFL)
library(plyr)
library(reshape)
library(FLBRP)
library(FLife)

Life history parameters

data(wklife)

wklife

                      species             name          area    stock sex
1             Clupea harengus          Herring   Celtic Seas  her-nis   F
2       Pollachius pollachius          Pollack     North Sea pol-nsea   C
3                 Molva molva             Ling        Widely lin-comb   C
4         Sebastes norvegicus        Rose fish      Northern  smn-con   C
5           Mullus surmuletus       Red mullet   Celtic Seas mut-comb   F
6         Scopthalmus maximus           Turbot     North Sea tur-nsea   F
7            Microstomus kitt       Lemon sole     North Sea lem-nsea   C
8  Lepidorhombus whiffiagonis           Megrim     North Sea meg-4a6a   C
9              Ammodytes spp.         Sandeels     North Sea  san-ns4   C
10      Pleuronectes platessa           Plaice   Celtic Seas ple-celt   F
11       Merlangius merlangus          Whiting   Celtic Seas whg-7e-k   F
12   Melanogrammus aeglefinus          Haddock   Celtic Seas had-iris   C
13        Lophius piscatorius White anglerfish   Celtic Seas ang-78ab   C
14        Lophius piscatorius White anglerfish     North Sea ang-ivvi   C
15                   Nephrops        Shellfish Biscay-Iberia nep-2829   F
         a    b  linf     k    t0 lmax  l50 a50
1  0.00480 3.20  33.0 0.606    NA   NA 23.0  NA
2  0.00760 3.07  85.6 0.190    NA   NA 47.1  NA
3  0.00360 3.11 119.0 0.140    NA   NA 74.0 7.2
4  0.01780 2.97  50.2 0.110  0.08   NA 40.3  NA
5  0.00570 3.24  47.5 0.210    NA   NA 16.9  NA
6  0.01490 3.08  66.7 0.320  0.29   NA 34.2 2.2
7  0.01230 2.97  37.0 0.420    NA   NA 27.0  NA
8  0.00220 3.34  54.0 0.120    NA   NA 23.0 3.0
9  0.00490 2.78  24.0 1.000    NA   NA 12.0  NA
10 0.01100 2.96  48.0 0.230    NA   NA 22.9  NA
11 0.01030 2.40  38.0 0.380 -1.01   NA 28.0  NA
12 0.01130 2.96  79.9 0.200 -0.36   NA   NA 2.0
13 0.01980 2.90 105.6 0.180 -0.38  133 73.0  NA
14 0.02970 2.84 106.0 0.180    NA   NA 61.0  NA
15 0.00056 3.03  65.0 0.065    NA   NA 30.0  NA

Figure 1 Pairwise scatter plots of life history parameters.

Equilibrium Dynamics

Create an FLPar

wkpar=as(wklife[,6:13],"FLPar")
attributes(wkpar)[names(wklife)[1:5]]=wklife[,1:5]

Then use life history relationships to estimate missing values

par <- lhPar(wkpar)

and then to derive vectors for processses such as natural mortality

eql=lhEql(par)

sel<-function(x) 
  catch.sel(x)%/%fapex(catch.sel(x))

ggplot(FLQuants(eql,"m","catch.sel"=sel,"mat","catch.wt"))+
  geom_line(aes(age,data,col=attributes(wkpar)$stock[as.numeric(iter)]))+
  facet_wrap(~qname,scale="free")+
  scale_x_continuous(limits=c(0,15))+
  guides(colour=guide_legend(title="Species",title.position="top"))

Figure 2 Vectors of m, selection pattern, maturity and weight-at-age.

and estimate equilibrium dynamics and reference points, e.g. for lemon sole

plot(iter(eql,3))

Figure 3 Equilibrium curves for ling.

Simulation

Create a forward projection, i.e. an FLStock from an equilibrium object

lmsl=as(iter(eql,7),"FLStock")

units(mat(lmsl))="NA"
units(harvest(lmsl))="f"
plot(lmsl)

Figure 4 Simulate a stock with increasing F

References