LBSPR.R
In LBSPR: Length-Based Spawning Potential Ratio

## ---- eval=FALSE--------------------------------------------------------------
#  install.packages("LBSPR")

## ---- eval=FALSE--------------------------------------------------------------
#  install.packages("devtools")
#  devtools::install_github("AdrianHordyk/LBSPR")

## -----------------------------------------------------------------------------
library(LBSPR)

## -----------------------------------------------------------------------------
MyPars <- new("LB_pars")

## -----------------------------------------------------------------------------
slotNames(MyPars)

## ---- eval=FALSE--------------------------------------------------------------
#  class?CLASSNAME
#  
#  class?LB_pars

## -----------------------------------------------------------------------------
MyPars@Linf <- 100 
MyPars@L50 <- 66 
MyPars@L95 <- 70
MyPars@MK <- 1.5 

MyPars@SL50 <- 50 
MyPars@SL95 <- 65
MyPars@SPR <- 0.4
MyPars@BinWidth <- 5

## -----------------------------------------------------------------------------
MySim <- LBSPRsim(MyPars)

## -----------------------------------------------------------------------------
MyPars@BinMax <- 150
MyPars@BinMin <- 0

## -----------------------------------------------------------------------------
MyPars@L_units <- "mm"

## -----------------------------------------------------------------------------
MySim@SPR 

## -----------------------------------------------------------------------------
MySim@FM 

## -----------------------------------------------------------------------------
MyPars@SPR <- numeric() # remove value for SPR 
MyPars@FM <- 1 # set value for FM
MySim <- LBSPRsim(MyPars)
round(MySim@SPR, 2) # SPR at F/M = 1 

## -----------------------------------------------------------------------------
MyPars@MK <- 2.0 
MySim <- LBSPRsim(MyPars)
round(MySim@SPR, 2) # SPR 

MyPars@MK <- 0.5
MySim <- LBSPRsim(MyPars)
round(MySim@SPR, 2) # SPR 

MyPars@Linf <- 120
MySim <- LBSPRsim(MyPars)
round(MySim@SPR, 2) # SPR 

## -----------------------------------------------------------------------------
MyPars@MK <- 1.5 
MyPars@SL50 <- 10
MyPars@SL95 <- 15 
MyPars@FM <- 1 
MySim <- LBSPRsim(MyPars)
round(MySim@SPR, 2) # SPR 

MyPars@SL50 <- 80
MyPars@SL95 <- 85 
MySim <- LBSPRsim(MyPars)
round(MySim@SPR, 2) # SPR 

## -----------------------------------------------------------------------------
MyPars@Linf <- 100 
MyPars@SL50 <- 50
MyPars@SL95 <- 55 
MyPars@FM <- numeric()
MyPars@SPR <- 0.4
MySim <- LBSPRsim(MyPars, Control=list(modtype="absel"))
MySim@FM 

MySim <- LBSPRsim(MyPars, Control=list(modtype="GTG"))
MySim@FM  # lower F/M for the GTG model

## ---- fig.width = 6, fig.height=6---------------------------------------------
plotSim(MySim) 

## ---- fig.width = 6, fig.height=6---------------------------------------------
plotSim(MySim, lf.type="pop")

## ---- fig.width = 4, fig.height=4---------------------------------------------
plotSim(MySim, type="len.freq")

## -----------------------------------------------------------------------------
MyLengths <- new("LB_lengths")
slotNames(MyLengths)

## ---- eval=FALSE--------------------------------------------------------------
#  datdir <- DataDir()

## ---- include=FALSE-----------------------------------------------------------
datdir <- DataDir()
if (datdir == "E:\\GitRepos\\LBSPR/") # during build
  datdir <- "E:/GitRepos/LBSPR/inst"

## -----------------------------------------------------------------------------
list.files(datdir, pattern=".csv")

## -----------------------------------------------------------------------------
MyPars <- new("LB_pars")
MyPars@Species <- "MySpecies"
MyPars@Linf <- 100 
MyPars@L50 <- 66 
MyPars@L95 <- 70
MyPars@MK <- 1.5 
MyPars@L_units <- "mm"

## -----------------------------------------------------------------------------
Len1 <- new("LB_lengths", LB_pars=MyPars, file=paste0(datdir, "/LFreq_MultiYr.csv"), 
            dataType="freq")

## -----------------------------------------------------------------------------
Len2 <- new("LB_lengths", LB_pars=MyPars, file=paste0(datdir, "/LFreq_MultiYrHead.csv"), 
            dataType="freq", header=TRUE)

## -----------------------------------------------------------------------------
Len3 <- new("LB_lengths", LB_pars=MyPars, file=paste0(datdir, "/LRaw_MultiYr.csv"), 
            dataType="raw")

## ---- fig.width=7, fig.height=4-----------------------------------------------
plotSize(Len1)
plotSize(Len2)
plotSize(Len3)

## ---- echo=FALSE, message=FALSE-----------------------------------------------
myFit1 <- LBSPRfit(MyPars, Len1)
myFit2 <- LBSPRfit(MyPars, Len2)

## ---- eval=FALSE--------------------------------------------------------------
#  myFit1 <- LBSPRfit(MyPars, Len1)
#  myFit2 <- LBSPRfit(MyPars, Len2)

## -----------------------------------------------------------------------------
myFit1@Ests

## -----------------------------------------------------------------------------
data.frame(rawSL50=myFit1@SL50, rawSL95=myFit1@SL95, rawFM=myFit1@FM, rawSPR=myFit1@SPR)

## ---- fig.width=7, fig.height=4-----------------------------------------------
plotSize(myFit1)

## ---- fig.width=5, fig.height=5-----------------------------------------------
plotMat(myFit1)

## ---- fig.width=8, fig.height=5-----------------------------------------------
plotEsts(myFit1)

## -----------------------------------------------------------------------------
MyPars <- new("LB_pars", verbose=FALSE)
MyPars@Linf <- 100 
MyPars@L50 <- 66 
MyPars@L95 <- 70
MyPars@MK <- 1.5 
MyPars@SPR <- 0.75 # Target SPR 
MyPars@BinWidth <- 5

## -----------------------------------------------------------------------------
LenDat <- new("LB_lengths", LB_pars=MyPars, file=paste0(datdir, "/LRaw_MultiYr.csv"), 
              dataType="raw", verbose=FALSE)

## ---- fig.width=5, fig.height=5-----------------------------------------------
Mod <- LBSPRfit(MyPars, LenDat, verbose=FALSE)

yr <- 1 # first year of data
MyPars@SL50 <- Mod@SL50[yr]
MyPars@SL95 <- Mod@SL95[yr] 

plotTarg(MyPars, LenDat, yr=yr)

## ---- eval=FALSE--------------------------------------------------------------
#  Shiny("LBSPR")

## ---- eval=FALSE--------------------------------------------------------------
#  Shiny("Sim")