In laurieKell/FLCandy: Candidate methods for FLR

knitr::opts_chunk$set(echo = FALSE)
# getwd()
library(knitr)
opts_chunk$set(cache     =!TRUE, 
               comment   =NA, 
               warning   =FALSE, 
               message   =FALSE, 
               error     =FALSE, 
               echo      =FALSE, 
               eval      =TRUE,
               cache     =TRUE,
               cache.path="cache/rSole/",
               fig.path  ="../outputs/tex/rSole/",
               fig.width =8,
               fig.height=8,
               dev       ="png")
iFig=0
iTab=0

install.packages("devtools")
library(devtools)

install.packages("ggplot2")
install.packages("ggpubr")
install.packages("GGallay")
install.packages("plyr")

devtools::install_github("flr/FLCore")
devtools::install_github("flr/ggplotFL")
devtools::install_github("flr/FLBRP")
devtools::install_github("flr/FLife")

devtools::install_github("henning-winker/FLRef")
devtools::install_github("henning-winker/SPMpriors")

devtools::install_github("ropensci/rfishbase")
devtools::install_github("ricardo-bion/ggradar")

library(ggplot2)

library(FLCore)
library(ggplotFL)
library(FLBRP)
library(FLife)
library(mydas)
library(FLCandy)

library(FLSRTMB)

library(popbio)

library(rfishbase)

library(FishLife)

library(ggpubr)
library(GGally)
library(ggradar)

library(statcomp)

library(plyr)
library(reshape)

library(numDeriv)

theme_set(theme_bw(16))

setwd("~/Desktop/flr/FLCandy/vignettes")

load("data/sol274.rda")

sr=as.FLSR(run,model=bevholtSV)
sr=(sr,s.est=T,s=0.7,s.logitsd=0.3,spr0=spr0Yr(run))

arsehole=nonStationarity(run,sr)

ggplot(subset(arsehole,refpt%in%c("msy","crash")&quant=="harvest"&year>1970))+
  geom_line(aes(year,1-exp(-data),col=refpt))

permutation_entropy(ordinal_pattern_distribution(x=ssb(run),    ndemb=5))  
permutation_entropy(ordinal_pattern_distribution(x=rlnorm(100), ndemb=5))
permutation_entropy(ordinal_pattern_distribution(x=seq(1,100),  ndemb=5))

Figure r iFig=iFig+1; iFig Plot of biological vectors-at-age

load("data/sol274.rda") 

fits=srrTMB(as.FLSRs(run, models=c("bevholt", "ricker", "segreg")), 
  spr0=mean(spr0y(run)), uplim=0.4)

load("data/sol274.rda")  

eqs=FLBRPs(llply(fits, function(x) FLBRP(run,sr=x))) 

ggplot(ldply(eqs,function(x) model.frame(FLQuants(ssb=ssb(x),yield=catch(x)),drop=T)))+
  geom_line(aes(ssb,yield,col=.id))

i=1
fn<-function(x,i) {
  params(eqs[[i]])[]=x
  computeRefpts(eqs[[i]])["msy",c("harvest","ssb","yield"),drop=T]}

jac=jacobian(fn,params(eqs[[i]]),i=i) 

vcov =matrix((jac) %*% vcov(fits[[i]]) %*% t((jac)),
               3,3,
               dimnames=list(params=c("harvest","ssb","yield"),
                             params=c("harvest","ssb","yield")))