R/openApp.R

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

#'@title Open Shiny app to experiment with toy model
#'@description This way of viewing the app is a backup. First try visiting https://vlahm.shinyapps.io/CO2_O2_toy_model/.
#'@return None
#'@author Mike Vlah
#'@export
#'@examples
#' openApp()
#'

openApp = function(){

    library(shiny)

    ui = fluidPage(
        # titlePanel("Coupled O2 and CO2 diel metabolism 'toy' model"),
        titlePanel(HTML(paste("<h4 style='color:#663399'>Coupled O2 and CO2 diel",
            "metabolism 'toy' model</h3>")), windowTitle='CO2-O2 Toy Model'),

        sidebarLayout(
            sidebarPanel(

                # Input: Sliders
                fluidRow(
                    column(4,
                        p(strong('Slope of P-I curve'), '(alpha; umol/m2/hr/uE)',
                            style='font-size:75%')
                        # HTML(paste0("<p style='font-size:75%'>Slope of P-I ",
                        #     "curve<br>(alpha PI; umol/m2/hr/uE)</p>"))
                    ),
                    column(8,
                        sliderInput(inputId='alphaPI', label=NULL,
                            min=0.1, max=10, value=1)
                    )
                ),
                fluidRow(
                    column(4,
                        p(strong('ER to std temp'),
                            '(Rstd; mol/m2/day)', style='font-size:75%')
                    ),
                    column(8,
                        sliderInput(inputId='Rstd', label=NULL,
                            min=0.1, max=10, value=1)
                    )
                ),
                fluidRow(
                    column(4,
                        p(strong('k of CO2 at std temp'),
                            '(kstd; m/hr)', style='font-size:75%')
                    ),
                    column(8,
                        sliderInput(inputId='kstd', label=NULL,
                            min=0.01, max=10, value=0.15)
                    )
                ),
                fluidRow(
                    column(6,
                        p(strong('Avg stream depth'), '(m)', style='font-size:75%'),
                        numericInput(inputId='depth', label=NULL,
                            min=0, max=100, value=0.5),
                        p(strong('Tot alkalinity'), '(umol/L)',
                            style='font-size:75%'),
                        numericInput(inputId='TAlk', label=NULL,
                            min=0, max=10000, value=1000),
                        p(strong('Initial [DIC]'), '(umol/L)',
                            style='font-size:75%'),
                        numericInput(inputId='TCO2_init', label=NULL,
                            min=0, max=10000, value=1200)
                    ),
                    column(6,
                        p(strong('Init pCO2 aq'), '(uatm)',
                            style='font-size:75%'),
                        numericInput(inputId='pCO2_init', label=NULL,
                            min=0, max=10000, value=2000),
                        p(strong('pCO2 air'), '(uatm)', style='font-size:75%'),
                        numericInput(inputId='pCO2_air', label=NULL,
                            min=0, max=10000, value=410),
                        p(strong('Init [O2]'), '(umol/L)', style='font-size:75%'),
                        numericInput(inputId='O2_init', label=NULL,
                            min=0, max=10000, value=280)
                    )
                ),
                fluidRow(
                    column(6, align='center',
                        p(strong('Extend to 4 days'), style='font-size:75%'),
                        checkboxInput('extend4days', label=NULL)
                    ),
                    column(6, align='left',
                        p(strong('Select dataset'), style='font-size:75%'),
                        radioButtons('chooseCreek', label=NULL,
                            choiceNames=list(p('Fish Trap Creek', style='font-size:75%'),
                                p('FLBS Stream', style='font-size:75%')),
                            choiceValues=list('fishTrapCreek', 'FLBS'))
                    )
                )
            ),
            mainPanel(

                # Output: Time series plot of dissolved O2 and pCO2 ----
                plotOutput(outputId='plotLegend', height='30px', width='auto'),
                plotOutput(outputId='timeSeriesPlot_O2_CO2',
                    height='200px', width='auto'),
                plotOutput(outputId='timeSeriesPlot_pH_DIC',
                    height='250px', width='auto'),
                # fluidRow(
                #     column(12, align='center',
                #         p(strong('24 hour averages (mol/m2/day):'),
                #             style='font-size:75%; color:#663399')
                #     )
                # ),
                fluidRow(
                    column(2, align='left', offset=1,
                        p(strong('24 hour averages (mol/m2/day):'),
                            style='font-size:75%; color:#663399')
                    ),
                    column(2, align='center',
                        div(style='outline:solid #663399',
                            p(strong('GPP'), style='font-size:75%'),
                            htmlOutput(outputId='GPP')
                        )
                    ),
                    column(2, align='center',
                        div(style='outline:solid #663399',
                            p(strong('ER'), style='font-size:75%'),
                            htmlOutput(outputId='ER')
                        )
                    ),
                    column(2, align='center',
                        div(style='outline:solid #663399',
                            p(strong('G O2'),style='font-size:75%'),
                            htmlOutput(outputId='G_O2')
                        )
                    ),
                    column(2, align='center',
                        div(style='outline:solid #663399',
                            p(strong('G CO2'),style='font-size:75%'),
                            htmlOutput(outputId='G_CO2')
                        )
                    )
                )
            )
        )
    )

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

        getModRes = reactive({

            # set background data for selected dataset
            if(input$chooseCreek == 'fishTrapCreek'){
                x.lt = as.POSIXlt(FishtrapCr$dateTime)
                temperature = FishtrapCr$Temp_C
                PAR = FishtrapCr$PAR_uE
                lat = 48.93861111
                long = -122.47861111
                tz = -8
            } else {
                x.lt = as.POSIXlt(RoysCr$dateTime)
                temperature = RoysCr$Temp_C
                PAR = RoysCr$lux
                lat = 47.887404
                long = -114.117811
                tz = -6
            }

            masl = 1
            salinity = 0

            #extend time and temperature time series if box is checked,
            #then determine local hour and DOY
            extnd = input$extend4days
            if(extnd){
                x.lt = as.POSIXlt(seq(x.lt[1], by='10 min', length.out=96 * 6))
                # localHour = seq(localHour[1], by=1/6, length.out=96 * 6)
                temperature = c(temperature, rep(10, 96 * 6 - length(temperature)))
                PAR = c(PAR, rep(mean(PAR, na.rm=TRUE), 96 * 6 - length(PAR)))
            }
            localHour = x.lt$hour + x.lt$min/60 + x.lt$sec/3600
            DOY = x.lt$yday

            # 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
            O2_init = input$O2_init     # Units of umol
            pCO2_air = input$pCO2_air     # 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, pCO2_init=pCO2_init,
                pCO2_air=pCO2_air, alphaPI_hr=alphaPI_hr, Rstd_day=Rstd_day,
                kstd_hr=kstd_hr, referenceT=20, lat=lat, long=long,
                depth=depth, salinity=0, masl=1, O2_init=O2_init)

            return(modelResults)
        })

        # 2. Output is two plots and numberic values for 24 hr GPP, ER, and G
        output$plotLegend = renderPlot({
            plotLegend()
        })
        output$timeSeriesPlot_O2_CO2 = renderPlot({
            modres = getModRes()
            # mm <<- modres
            plotO2_CO2(modres)
        })
        output$timeSeriesPlot_pH_DIC = renderPlot({
            modres = getModRes()
            plotpH_DIC(modres)
        })
        #Add numeric outputs
        output$GPP = renderText({
            modres = getModRes()
            gppout = paste("<p style='color:#663399'>", round(modres$GPP, 3), '</p>')
            return(HTML(gppout))
        })
        output$ER = renderText({
            modres = getModRes()
            erout = paste("<p style='color:#663399'>", round(modres$ER, 3), '</p>')
            return(HTML(erout))
        })
        output$G_O2 = renderText({
            modres = getModRes()
            gO2out = paste("<p style='color:#663399'>",
                round(modres$G_O2_24hr, 3), '</p>')
            return(HTML(gO2out))
        })
        output$G_CO2 = renderText({
            modres = getModRes()
            gCO2out = paste("<p style='color:#663399'>",
                round(modres$G_CO2_24hr, 3), '</p>')
            return(HTML(gCO2out))
        })
    }

shinyApp(ui=ui, server=server, options=list(launch.browser=TRUE))

}