In PaulRegular/surveyTestr: Test Surveys by Simulating Spatially-Correlated Populations

library(plotly)
library(viridis)
knitr::opts_chunk$set(echo = FALSE, fig.height = 7, fig.width = 8, cache = FALSE)

Abundance

Row {.tabset}

Total abundance

plot_trend(sim)

Recruitment

plot_trend(sim, sum_ages = min(sim$ages))

Total mortality

plot_surface(sim, mat = "Z")

Abundance at age

plot_surface(sim, mat = "N")

Abundance at length

plot_surface(sim, mat = "N_at_length", xlab = "Length", zlab = "N")

Distribution { r if(!"sp_N" %in% names(sim)) ".hidden"}

Column {.sidebar}

sliderInput("age", "Age", min = min(sim$ages), max = max(sim$ages), 
            value = 1, step = 1)
sliderInput("year", "Year", min = min(sim$years), max = max(sim$years), 
            value = 1, step = 1)
selectInput("type", "Type", choices = c("heatmap", "contour"), 
            selected = "contour")
selectInput("scale", "Scale", choices = c("natural", "log"), 
            selected = "natural")

Column

Distribution

renderPlotly({
  plot_distribution(sim, ages = input$age, year = input$year, type = input$type,
                    scale = input$scale)
})

Survey { r if(!"setdet" %in% names(sim)) ".hidden"}

Column {.sidebar}

sliderInput("samp_year", "Year", 
            min = min(sim$years), max = max(sim$years), 
            value = 1, step = 1)
sliderInput("samp_sim", "Simulation", 
            min = min(sim$setdet$sim), max = max(sim$setdet$sim), 
            value = 1, step = 1)

Column

Survey sampling

renderPlotly({
  plot_survey(sim, which_year = input$samp_year, which_sim = input$samp_sim)
})

Estimates { r if(!"age_strat_error" %in% names(sim)) ".hidden"}

Column {.sidebar}

selectInput("set_den", "Set density", 
            choices = sort(unique(sim$surveys$set_den)))
selectInput("lengths_cap", "Lengths cap", 
            choices = sort(unique(sim$surveys$lengths_cap)))
selectInput("ages_cap", "Ages cap", 
            choices = sort(unique(sim$surveys$ages_cap)))
selectInput("fan_length", "Length", 
            choices = sim$lengths)
selectInput("fan_age", "Age", 
            choices = sim$ages)

Column {.tabset}

Total abundance

renderPlotly({
  s <- sim$surveys
  i <- s$survey[s$set_den == input$set_den & 
                        s$lengths_cap == max(s$lengths_cap) &
                        s$ages_cap == max(s$ages_cap)]
  plot_total_strat_fan(sim, surveys = i)
})

Abundance at length

renderPlotly({
  s <- sim$surveys
  i <- s$survey[s$set_den == input$set_den & 
                        s$lengths_cap == input$lengths_cap &
                        s$ages_cap == max(s$ages_cap)]
  plot_length_strat_fan(sim, surveys = i, years = sim$years,
                        lengths = input$fan_length, select_by = "length")
})

Abundance at age

renderPlotly({
  s <- sim$surveys
  i <- s$survey[s$set_den == input$set_den & 
                        s$lengths_cap == input$lengths_cap &
                        s$ages_cap == input$ages_cap]
  plot_age_strat_fan(sim, surveys = i, years = sim$years,
                        ages = input$fan_age, select_by = "age")
})

Error { r if(!"surveys" %in% names(sim)) ".hidden"}

Column {.tabset}

Error surface by rule

plot_error_surface(sim, plot_by = "rule")

Error surface by sample size

plot_error_surface(sim, plot_by = "samples")

PaulRegular/surveyTestr documentation built on Sept. 21, 2023, 7:44 p.m.