In tcarruth/MERA: Method Evaluation and Risk Assessment

knitr::opts_chunk$set(echo = TRUE)

library('corpcor')
library('DLMtool')
library('dplyr')
library('formattable')
library('kableExtra')
library('knitr')
library('shiny')
library('shinyjs')
library('shinyalert')
library('MSEtool')
library('tinytex')
library('DT')
library('rmarkdown')

source("./R/MSC4vig.R")

tosource<-list.files("../inst/shiny_apps/MERA/Source/Questionnaire/",full.names = T)
for(i in 1:length(tosource))source(tosource[i]) # all fishery, management and data plots
source("./R/global4UG.R") # sources the list objects for the various questions
source("./R/Q_setup.R")
source("../inst/shiny_apps/MERA/Source/AI/AI_results.r")

load("./dat/MSEobj")
MSEobj2<-readRDS("./dat/MSEobj_2.Rdata")
MSClog<-readRDS("./dat/MSClog.mera")
PanelState<-MSClog[[1]]
load("./dat/MSEobj_reb")
#load("./dat/MSEobj_reb2")
MSEobj_reb2<-readRDS("./dat/MSEobj_reb_2.Rdata")
MSEobj_Eval<-MSEobj2
eff_values<-readRDS("./dat/eff_values.rda")
Syear=eff_values$df$x[1]
Lyear=eff_values$df$x[nrow(eff_values$df)]
input<-c(input,list(Syear=Syear,Lyear=Lyear))
dat<-readRDS("./dat/dat.rda")
dat_ind<-readRDS("./dat/dat_ind.rda")
FT<-FeaseLabs(MPs=MSEobj2@MPs) # uses panel state
MPcols<-FT$MPcols  # needed for planning color coding

FigInd<-0
TabInd<-1
SecInd<-0

#for making the question figures

fcol = rgb(0.4,0.8,0.95)#"#0299f"
fcol2 = "dark grey"
icol <- "dodgerblue4"
maxcol="cadetblue"
mincol="dark grey"

Qwidth=5
Qheight=3.5
Qretina=2
Qout.width='300px'
Qout.height='180px'

#for making planning figures

Pwidth=13
Pheight=13
Pretina=2
Pout.width='1000px'
Pout.height='1000px'

nFish<-19    # number of fishery questions
nManage<-7   # number of management questions
nDat<-4      # number of data questions

#library(knitr); library(dplyr)

library(knitr)
rmd.files <- c("Rmds/Introductory/Intro_M.Rmd",
               "Rmds/Menus/Menus_M.Rmd",
               "Rmds/Qs/Qs_M.Rmd",
               "Rmds/Management_Planning/Management_Planning_M.Rmd",
               "Rmds/Management_Performance/Management_Performance_M.Rmd",
               "Rmds/Risk_Assessment/Risk_Assessment_M.Rmd",
               "Rmds/Status_Determination/Status_Determination_M.Rmd",
               "Rmds/Data/Data_M.Rmd",
               "Rmds/Support/Support_M.Rmd",
               "Rmds/Acknowledgements/Acknowledgements_M.Rmd",
               "Rmds/References/References_M.Rmd",
               "Rmds/Appendices/Appendices_M.Rmd")

out <- NULL
for (rmd in rmd.files) {
  out <- c(out, knitr::knit_child(rmd))
}