shinyGasses.R

In gholtgrieve/gassyPants: Functions Useful for Working With Gasses Dissolved in Water

# Fist try at R shiny script

library(shiny)
library(gassyPants)

ui <- fluidPage(

  titlePanel("Coupled O2 and CO2 diel metabolism 'toy' model"),

  # Sidebar layout with input and output definitions ----
  sidebarLayout(
    # Sidebar panel for inputs and outputs----
    sidebarPanel(
      # Input: Sliders
      sliderInput(inputId = "alphaPI",
                  label = "Slope of P-I curve (alpha PI; umol/m2/hr/uE)",
                  min = 0.1, max = 10, value = 1),
      sliderInput(inputId = "Rstd",
                  label = "Ecosystem respiration to a standard temperature (Rstd; mol/m2/day)",
                  min = 0.1, max = 10, value = 1),
      sliderInput(inputId = "kstd",
                  label = "Gas transfer velocity for CO2 at a standard temperature  (kstd; m/hr)",
                  min = 0.01, max = 10, value = 0.15),
      numericInput(inputId = "depth",
                   label = "Average stream depth (m)",
                   min = 0, max = 100, value = 0.5),
      numericInput(inputId = "TAlk",
                   label = "Total alkalinity (umol/L)",
                   min = 0, max = 10000, value = 1000),
      numericInput(inputId = "TCO2_init",
                   label = "Inital dissolved inorganic carbon (DIC; umol/L)",
                   min = 0, max = 10000, value = 1200),
      numericInput(inputId = "pCO2_init",
                   label = "Inital partial pressure of dissolved CO2 (pCO2; uatm)",
                   min = 0, max = 10000, value = 2000),
      h3(HTML("24 hr GPP:  "),textOutput(outputId = "GPP")),
      h3(HTML("24 hr ER:  "),textOutput(outputId = "ER")),
      h3(HTML("24 hr G:  "),textOutput(outputId = "G"))
    ),
    # Main panel for displaying outputs ----
    mainPanel(
      # Output: Time series plot of dissolved O2 and pCO2 ----
      plotOutput(outputId = "timeSeriesPlot_O2_CO2"),
      plotOutput(outputId = "timeSeriesPlot_pH_DIC")

    )
  )
)

# Define server logic required to time seroes plot of model output ----
server <- function(input, output) {

  # Background physical data from Fishtrap Cr.
  # Not editable by users
  x.lt <- as.POSIXlt(FishtrapCr$dateTime)
  temperature <- FishtrapCr$Temp_C
  PAR <- FishtrapCr$PAR_uE
  localHour <- x.lt$hour + x.lt$min/60 + x.lt$sec/3600
  DOY <- x.lt$yday
  lat <- 48.93861111
  long <- -122.47861111
  tz <- -8
  masl <- 1
  salinity <- 0

  # Static variable inputs (single value) from user interface
  depth <- input$depth
  TAlk <- input$TAlk
  TCO2_init <- input$TCO2_init      # Units of umol/L
  pCO2_init <- input$pCO2_init     # Units of uatm

  # Dynamic variable inputs (sliders) from user interface
  alphaPI_hr <- input$alphaPI    # Units are umol/m2/hr/uE
  Rstd_day <- input$Rstd        # Units are mol/m2/day
  kstd_hr <- input$kstd      # Units are m/hr

  modelResults <- main(temperature = temperature, localHour = localHour, DOY = DOY,
                       PAR = PAR, TALk = TAlk, TCO2_init = TCO2_init, pCO2_init = pCO2_init,
                       PCO2_air = 410, alphaPI_hr = alphaPI_hr, Rstd_day = Rstd_day,
                       kstd_hr = kstd_hr, referenceT = 20, lat = lat, long = long,
                       depth = depth, salinity = 0, masl=1)

  # 2. Output is two plots and numberic values for 24 hr GPP, ER, and G
  output$timeSeriesPlot_O2_CO2 <- renderPlot({
    plotO2_CO2()
  })
  output$timeSeriesPlot_pH_DIC <- renderPlot({
    plotpH_DIC()
  })
  #Add numeric outputs
  output$GPP <- renderText(modelResults$GPP)
  output$ER <- renderText(modelResults$ER)
  output$G <- renderText(modelResults$G)
}

shinyApp(ui = ui, server = server)