##########################################################################
# Shiny user interface ###################################################
##########################################################################
shinyUI(navbarPage(
title = 'RC SURPLUS',
tabPanel("About",
navbarPage('About',
tabPanel( 'Introduction', fluidRow(helpText( help$Introduction )) ),
tabPanel( 'Model',
fluidRow(
withMathJax(''),
helpText( help$Model1 ),
helpText( help$Model2 ),
helpText( help$Model3 ),
helpText( help$Model4 ),
helpText( help$Model5 ),
helpText( help$Model6 )
)),
tabPanel( 'UI', fluidRow(helpText( help$UI )) ),
tabPanel( 'Fitting', fluidRow(helpText( help$Fitting )) )
)
),
tabPanel("Input",
navbarPage('Input',
tabPanel('Data',
fluidPage(
sidebarLayout(
sidebarPanel(
checkboxInput("do_catch", "Plot catch", TRUE),
checkboxInput("do_effort", "Plot effort", FALSE),
checkboxInput("do_cpue", "Plot cpue", FALSE),
checkboxInput("one_row", "Plot in one row", TRUE)
),
mainPanel(
plotOutput("plot_data")
)
)
)
)
)
),
tabPanel('Model',
fluidPage(
br(),
fluidRow(
column(4,
h4("Model(s) to fit (multi-choice)"),
selectizeInput("spm", "",choices =
c('Pella-Tomlinson', 'Schaefer', 'Fox', 'Alternative'),
multiple=TRUE),
h4("Bounds of uniform priors"),
sliderInput("Kprior", "Catchability: \\(K\\) and \\(e^\\rho\\)",
min = myglobal$priorK[1],
max = myglobal$priorK[2],
value = c(myglobal$priorK[1],myglobal$priorK[2]),
step = 100 ),
sliderInput("rprior", "Growth rate: \\(r\\)",
min = myglobal$priorr[1],
max = myglobal$priorr[2],
value = c(myglobal$priorr[1],myglobal$priorr[2]),
step = 0.01 ),
sliderInput("PHIprior", "Elasticity: \\(\\phi\\)",
min = myglobal$priorPHI[1],
max = myglobal$priorPHI[2],
value = c(myglobal$priorPHI[1],myglobal$priorPHI[2]),
step = 0.01 ),
sliderInput("qprior", "Log-catchability: \\(\\log (q)\\) and \\(\\chi\\)",
min = myglobal$priorq[1],
max = myglobal$priorq[2],
value = c(myglobal$priorq[1],myglobal$priorq[2]),
step = 0.01 ),
sliderInput("sprior", "Model log-variance: \\(\\log (\\sigma)\\)",
min = myglobal$priors[1],
max = myglobal$priors[2],
value = c(myglobal$priors[1],myglobal$priors[2]),
step = 0.01 )
),
column(4,
h4("MCMC settings"),
sliderInput("MCMCn", "Number of iterations for output:",
min = myglobal$mcmc_n[1],
max = myglobal$mcmc_n[2],
value = myglobal$mcmc_n[1],
step = 100 ),
sliderInput("MCMCb", "Burn-in ratio:",
min = myglobal$mcmc_b[1],
max = myglobal$mcmc_b[2],
value = myglobal$mcmc_b[2],
step = 0.05 ),
sliderInput("MCMCt", "Thinning factor:",
min = myglobal$mcmc_t[1],
max = myglobal$mcmc_t[2],
value = myglobal$mcmc_t[1],
step = 1 ),
sliderInput("MCMCc", "Number of chains:",
min = myglobal$mcmc_c[1],
max = myglobal$mcmc_c[2],
value = myglobal$mcmc_c[1],
step = 1 ),
checkboxInput("overrelax", "Over-relax", FALSE),
p('Total no. MCMC iterations:'),
verbatimTextOutput('model_settings')
),
column(4,
h4("Convergence diagnostics"),
checkboxInput("do_coda", "CODA", FALSE),
h4("Model Status"),
bsAlert(anchorId = "model_inputId"),
bsButton('fit_model',
label = "Fit model(s)",
style = "info",
size="mini"),
verbatimTextOutput('model_status')
)
)
)
),
tabPanel('Output',
navbarPage('Output',
tabPanel('Hyperparameters',
fluidPage(
sidebarLayout(
sidebarPanel(
h4('Plot:'),
selectizeInput("spm_hyper", "",choices = c(
'Pella-Tomlinson',
'Schaefer',
'Fox',
'Alternative'), multiple=TRUE),
checkboxInput("plot_KeRHO", "Carrying capacity: \\(K\\) and/or \\(e^\\rho\\)", FALSE),
checkboxInput("plot_r", "Growth rate: \\(r\\)", FALSE),
checkboxInput("plot_PHI", "Elasticity: \\(\\phi\\)", FALSE),
checkboxInput("plot_qCHI", "Log-catchability: \\(\\log(q)\\) and/or \\(\\chi\\)", FALSE),
checkboxInput("plot_lSIGMA", "Model log-variance: \\(\\log(\\sigma)\\)", FALSE),
checkboxInput("plot_msy", "MSY", FALSE),
checkboxInput("plot_bmsy", "B(MSY)", FALSE),
checkboxInput("plot_fmsy", "F(MSY)", FALSE)
),
mainPanel(
plotOutput("plot_hyperparameters")
)
)
)
),
tabPanel('Fit',
fluidPage(
sidebarLayout(
sidebarPanel(
h4('Observed vs. fitted CPUE:'),
selectizeInput("spm_fit", "",
choices = c('Pella-Tomlinson',
'Schaefer',
'Fox',
'Alternative'),
multiple=TRUE),
sliderInput("years_fit", "Years:",
min = 1965, max = 1988,
value = c(1965,1988), step = 1 ),
checkboxInput("fit_one_row", "Plot in one row", TRUE)
),
mainPanel(
plotOutput("fit_plot")
)
)
)
),
tabPanel('Diagnostics',
fluidPage(
sidebarLayout(
sidebarPanel(
h4('Model:'),
selectizeInput("spm_diag", "",choices = c('Pella-Tomlinson',
'Schaefer',
'Fox',
'Alternative'), multiple=TRUE),
h4('Diagnostic:'),
selectInput("diag", "",choices = c('Summary & Deviance',
'CODA - Gelman',
'CODA - Geweke',
'CODA - Raftery & Lewis'))
),
mainPanel(
verbatimTextOutput("summary_dev")
)
)
)
)
)
)
))
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