## ----initKnitr, echo=FALSE, results="asis"-------------------------------
library(knitr)
#output: rmarkdown::tufte_handout
# output:
# rmdformats::html_clean:
# fig_width: 6
# fig_height: 6
# highlight: pygments
## Global options
options(max.print="75")
opts_chunk$set(fig.path="out/",
echo =TRUE,
eval=TRUE,
cache=TRUE,
cache.path="cache/",
prompt=FALSE,
tidy=FALSE,
comment=NA,
message=FALSE,
warning=FALSE,
fig.margin=TRUE,
fig.height=6,
fig.width=4)
opts_knit$set(width=75)
## ----,fig.caption="Simulated stock"--------------------------------------
library(plyr)
library(biodyn)
bd=sim()
bd=window(bd,end=49)
## ----, fig,caption="Simulated CPUE series",fig.height=2------------------
cpue=(stock(bd)[,-dims(bd)$year]+stock(bd)[,-1])/2
cpue=rlnorm(1,log(cpue),.2)
ggplot(cpue)+geom_point(aes(year,data))
## ----, fig.cap="Fitted compared to actual time series"-------------------
#set parameters
setParams(bd) =cpue
setControl(bd)=params(bd)
control(bd)[3:4,"phase"]=-1
## ----, fig.cap="Fitted compared to actual time series"-------------------
#fit
bdHat=fit(bd,cpue)
plot(biodyns("Estimate"=bdHat,"Actual"=bd))+
theme(legend.position="bottom")
## ----, fig.cap="Jack knife error bars"-----------------------------------
bdJK=fit(bdHat,jackknife(cpue))
## ----, fig.cap="Jack knife error bars"-----------------------------------
plotJack(bdHat,bdJK)
## ------------------------------------------------------------------------
#FLQuant
library(ggplotFL)
true=stock(bd )[,49]
hat =stock(bdHat)[,49]
jack=stock(bdJK )[,49]
n =dims(jack)$iter
mn =apply(jack, 1:5, mean)
rsdl=sweep(jack,1:5,mn,"-")
ss =apply(rsdl^2,1:5,sum)
bias =(n-1)*(hat-mn)
biasCorrected=n*hat-(n-1)*mn
se =sqrt(((n-1)/n)*ss)
## ------------------------------------------------------------------------
# FLPar
true=refpts(bd )
hat =refpts(bdHat)
jack=refpts(bdJK )
n =dims(jack)$iter
mn =apply(jack, seq(length(dim(jack))-1), mean)
rsdl=sweep(jack, seq(length(dim(jack))-1), mn,"-")
ss =apply(rsdl^2,seq(length(dim(jack))-1),sum)
bias =(n-1)*(hat-mn)
biasCorrected=n*hat-(n-1)*mn
se =sqrt(((n-1)/n)*ss)
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