# Cascading Pools with Steady Unit Inflow

#### Set drainage time for each pool ### MODEL DESCRIPTION

Demonstration of flows through a cascading series of pools with different “drain rates.” At the top of the cascade is an inflow (rate = 1). Each pool then drains at a rate that’s directly proportional to the volume of the pool.

For each pool, $\frac{dP}{dt} = inflow - \frac{P}{\tau}$ where P is the volume in the pool and $$\tau$$ is the e-folding timescale for the pool to drain downstream.

The program that does the calculation is very simple, and the code that controls this website is surprisingly simple too! It is all written in the programming language R, using a web programming package called shiny. You can read all about it on the “Website Code” tab to the right.

### How this website works (including all the code!)

This website is controlled using the R package “shiny.” There are four important components:

• A script (run.pools.R) that integrates the cascading pools model
• A script (plot.pools.R) that plots the output
• The user interface (ui.R) that controls the sliders and passes inputs to the model
• The “server” (server.R) that responds to user interface events in the web browser

Scroll down or click links in the list above to read all about it!

run.pools.R:

run.pools <- function(time1=3, time2=10, time3=100){

# Create drainage and flow transfer matrix
drain <- c(1./time1, 1./time2, 1./time3)
flow <- matrix(c(-drain,     0,        0,
drain, -drain,    0,
0,       drain, -drain),
byrow=TRUE, nrow=3)

# Inflow into top pool only
inflow <- c(1,0,0)

# Compute steady-state solution
steady <- solve(flow, -inflow)

# Initialize pools & outflows to zeros
nTime <- 2*max(c(time1, time2, time3))
pool <- matrix(replicate(3*nTime, 0.), nrow=nTime)
outflow <- pool

# Run the model forward in time
for (i in 1:(nTime-1)) {
pool[i+1, ] <- pool[i, ] + inflow + flow %*% pool[i, ]
outflow[i+1,] <- drain * pool[i+1, ]
}

# return timeseries of each pool to calling program
return(list(pool=pool, outflow=outflow, steady=steady))

}


plot.pools.R:

plot.pools <- function(pools){

# Set up plot parameters for a 2-panel (landscape) page
orig.par <- par(no.readonly=TRUE)  # Remember changable parameters to reset later
par(mfrow=c(3,2), cex=1.2, mar=c(2,2,2,2))

# Top row shows volume and outflow from top pool
plot(pools$pool[,1], type='l', col='red', lwd=4, main='Top Volume', ylim=c(0,pools$steady), ylab='', xlab='time')
abline(h=pools$steady, col='blue', lty=2, lwd=4) plot(pools$outflow[,1], type='l', col='blue', lwd=4, main='Top outflow',
ylim=c(0,1), ylab='', xlab='time')

# Middle row shows volume and outflow from middle pool
plot(pools$pool[,2], type='l', col='red', lwd=4, main='Middle Volume', ylim=c(0,pools$steady), ylab='', xlab='time')
abline(h=pools$steady, col='blue', lty=2, lwd=4) plot(pools$outflow[,2], type='l', col='blue', lwd=4, main='Middle outflow',
ylim=c(0,1), ylab='', xlab='time')

# Bottom row shows volume and outflow from bottom pool
plot(pools$pool[,3], type='l', col='red', lwd=4, main='Bottom Volume', ylim=c(0,pools$steady), ylab='', xlab='time')
abline(h=pools$steady, col='blue', lty=2, lwd=4) plot(pools$outflow[,3], type='l', col='blue', lwd=4, main='Bottom outflow',
ylim=c(0,1), ylab='', xlab='time')

par(orig.par)

}


#### This is the user interface that actually controls this website

ui.R:

library(shiny)
library(markdown)
library(knitr)

# Define user interface for logistic growth model
shinyUI(pageWithSidebar(

#  Application title
headerPanel("Logistic Growth with Nutrient Limitation"),

# Sidebar on the left with controls for the user to specify atmospheric properties
sidebarPanel(

img(src='growth.jpg'),

h4('Set Models Parameter Below'),

# Set drainage times for each pool
sliderInput("max.growth", "Maximum Growth Rate (percent)",
min = 1, max = 100, value = 10, step= 1),
sliderInput("lifetime", "Average Lifetime (time steps)",
min = 1, max = 50, value = 10, step= 1),
sliderInput("limit", "Nutrient-Limited Maximum Population",
min = 1, max = 1000, value = 100, step=1),
sliderInput("nTime", "Number of time steps",
min = 10, max = 500, value = 100, step=10)
),

# Show a tabset in the main panel of the browser that displays model output
mainPanel(
tabsetPanel(

# First tab shows plots of model output for both control and modified atmosphere
tabPanel("Output",
h4('Population Over Time'),
p('  death <- max.growth / lifetime'),
p('  growth[i+1] <- max.growth * (1 - life[i] / limit)'),
p('  life[i+1] <- life[i] * (1 + growth[i] - death)'),
plotOutput('population.plot')),

# Second tab displays a brief model description
tabPanel("Model Description",
includeHTML('doc/model.description.html')),

# Third tab displays website code
tabPanel("Website code",
includeMarkdown('doc/website.code.md'))
)
)
))


server.R:

library(shiny)

# Source required R scripts
source('logistic.R')

shinyServer(function(input, output) {

#  plot of model output
output$population.plot <- renderPlot( plot(logistic(max.growth=input$max.growth/100, lifetime=input$lifetime, limit=input$limit, nTime=input\$nTime),
type='l', lwd=10, col='darkgreen', ylab='', xlab='time',
cex.lab=2, cex.axis=2)
)
})