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Food.web.R
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##' .. content for \description{} (no empty lines) ..
##'
##' .. content for \details{} ..
##' @title Function on shiny R to plot the trophic level of the fucntional groups
##' @param diet.file Diet output file from atlantis
##' @param grp.file Group file. Atlantis input file (.cvs)
##' @param quiet help to debug the function
##' @return
##' @author Demiurgo
food.web <- function(diet.file, grp.file, quiet = TRUE){
txtHelp <- "<h2>Summary</h2>"
txtHelp <- paste(txtHelp, "<p>This bit of code help to visualize the food web change during the simulation output from <b>Atlantis</b> run. </p>")
txtHelp <- paste(txtHelp, "<p>It calculate the trophic position of each functional group at each time step</p>")
## Libraries
if(!quiet) cat('\n\n # - - - - - - - #')
if(!quiet) cat('\n # - Step 1 - #')
if(!quiet) cat('\n # - - - - - - - #')
if(!quiet) cat('\n\n Loading libraries')
if (!require('shiny', quietly = TRUE)) {
stop('The package shiny was not installed')
}
if (!require('ncdf4', quietly = TRUE)) {
stop('The package ncdf4 was not installed')
}
if (!require('plotrix', quietly = TRUE)) {
stop('The package plotrix was not installed')
}
if (!require('reshape', quietly = TRUE)) {
stop('The package reshape was not installed')
}
if (!require('tidyverse', quietly = TRUE)) {
stop('The package tidyverse was not installed')
}
if (!require('stringr', quietly = TRUE)) {
stop('The package stringr was not installed')
}
if (!require('data.table', quietly = TRUE)) {
stop('The package data.table was not installed')
}
if (!require('RColorBrewer', quietly = TRUE)) {
stop('The package RColorBrewer was not installed')
}
if(!quiet) cat(' ...Done!')
## Reading files
if(!quiet) cat('\n Reading files')
dat <- data.frame(fread(diet.file, header = TRUE, sep = ' ', showProgress = FALSE))
time.stp <- round(range(dat$Time), 0)
grp.dat <- read.csv(grp.file)
stk <- unique(dat$Stock)
if(any(names(grp.dat) == 'isPredator')){
names(grp.dat)[which(names(grp.dat) == 'isPredator')] <- 'IsPredator'
warning('You should change the name of the column \'isPredator\' for \'IsPredator\' on your group csv file')
}
code.fg <- grp.dat$Code[grp.dat$IsPredator > 0]
if(!quiet) cat(' ...Done!')
if(!quiet) cat('\n\n # - - - - - - - #')
if(!quiet) cat('\n # - Step 2 - #')
if(!quiet) cat('\n # - - - - - - - #')
if(!quiet) cat('\n Processing and plotting')
shinyApp(
ui <- navbarPage('Atlantis Food Web Tool',
tabPanel('Food Web',
fluidRow(
column(2,
wellPanel(
tags$h3('Functional Group'),
selectInput('foc.fg', 'Functional Group', as.character(code.fg)),
numericInput("m.stg", "Max. Throphic Connections:", min = 1, max = 10, value = 4, step = 1),
numericInput("min", "Min proportion :", min = 0.001, max = 1, value = 0.01, step = 0.001),
numericInput("time", "Time Step :", min = time.stp[1], max = time.stp[2], value = 1, step = 1),
selectInput('stock', 'Stock', stk))
),
column(10,
plotOutput('plot1', width = "100%", height = "800px"),
tableOutput('table')
)
)
),
## -- Exit --
tabPanel(
actionButton("exitButton", "Exit")
)
),
function(input, output, session) {
time.prey <- reactive({
time.prey <- dat[dat$Time == input$time & dat$Stock == input$stock, c(2, 6 : ncol(dat))]
})
## Original Recruitment
t.prey <- reactive({
t.prey <- NULL
foc <- input$foc.fg
stg <- 1
while(stg <= input$m.stg){
for(fg in foc){
## this approach remove not common prey but keeps the proportion
diet <- colSums(time.prey()[time.prey()$Predator == fg, 2 : ncol(time.prey())])
diet <- diet[diet > 0] / sum(diet, na.rm = TRUE)
if(length(diet) == 0) next
diet <- diet[diet >= input$min]
n.prey <- names(diet)
m.prey <- data.frame(Pred = fg, Prey = n.prey, value = diet, Stage = stg)
t.prey <- rbind(t.prey, m.prey)
}
focp <- foc
foc <- as.character(unique(t.prey$Prey[t.prey$Stage == stg]))
if(all(length(foc) == length(focp), all(foc %in% focp))) break
stg <- stg + 1
}
t.prey$TLprey <- prey.pos(t.prey$Prey, grp.dat)
t.prey <- as.data.frame(t.prey)
})
## assing the value of trophic level for the prey
TL <- reactive({
#browser()
npred <- unique(t.prey()$Pred)
TL <- NULL
for(pred in npred){
pospred <- which(t.prey()$Pred %in% pred)
TL <- c(TL, Tlevel(t.prey()$value[pospred], t.prey()$TLprey[pospred]))
}
pp.prey <- unique(t.prey()$Prey[-which(t.prey()$Prey %in% npred)])
pp.prey <- data.frame(FG = pp.prey, Tlevel = prey.pos(pp.prey, grp.dat))
TL <- data.frame(FG = npred, Tlevel = TL)
TL <- rbind(TL, pp.prey)
## location on the plot
his <- hist(TL$Tlevel, breaks = c(1.5 : 6.5), plot = FALSE)
v.lev <- max(his$counts)
brk <- his$breaks
h.lev <- max(his$mids[his$counts > 0]) + 1 ## getting the top of the plor
TL$v.lev <- v.lev
TL$h.lev <- h.lev
TL$vpos <- NA
for(i in 1 : (length(brk) - 1)){
nfg.ly <- which(TL$Tlevel > brk[i] & TL$Tlevel < brk[i + 1] )
tot.fg <- length(nfg.ly)
vpos <- cumsum(rep(v.lev / tot.fg, tot.fg)) - (v.lev / tot.fg) * 0.5
TL$vpos[nfg.ly] <- vpos
}
TL <- as.data.frame(TL)
})
output$plot1 <- renderPlot({
rad <- 0.25
plot(1, type = "n", xlab = '', ylab = "Trophic-level",
xlim = c(0, unique(TL()$v.lev)), ylim = c(1.5, unique(TL()$h.lev)), axes = FALSE)
axis(2, at = c(1 : unique(TL()$h.lev)), las = 1)
for( i in 1 : nrow(t.prey())){
p.pred <- which(TL()$FG %in% t.prey()$Pred[i])
p.prey <- which(TL()$FG %in% t.prey()$Prey[i])
## Direction of predation
col <- ifelse(TL()$Tlevel[p.pred] < TL()$Tlevel[p.prey], 'forestgreen', 'red1')
y <- c(TL()$Tlevel[p.pred], TL()$Tlevel[p.prey] )
x <- c(TL()$vpos[p.pred], TL()$vpos[p.prey] )
lines(x, y , lty = 1, lwd = (t.prey()$value[i] * 3), col = col)
}
## circles
for( i in 1 : nrow(TL())){
draw.circle(TL()$vpos[i], TL()$Tlevel[i], radius = rad, nv = 1500, border = NULL,
col = ifelse(i == 1, 'steelblue', 'gray91'), lty = 1, lwd = 1)
text(TL()$vpos[i], TL()$Tlevel[i], TL()$FG[i], cex = .8, font = 2, col = ifelse(i == 1, 'white', 1))
}
legend('topright', c('DownTop', 'TopDown'), lty = 1, col = c('forestgreen', 'red1'), lwd = 1.5, bty = 'n')
})
output$table <- renderTable({
table <- with(TL(), data.frame(Functional.group = FG, Trophic.Level = Tlevel))
})
observeEvent(input$exitButton, {
stopApp()
})
}
)
}
## functions
##' .. content for \description{} (no empty lines) ..
##'
##' .. content for \details{} ..
##' @title Assing trophic level of the prey the values are based on Pauly et al 1998 [Diet composition and trophic levels of marine mammals]
##' And Tucket and Rogers 2014 [Examining predator–prey body size, trophic level and body mass across marine and terrestrial mammals]
##' @param FGs Preys
##' @param grp.dat
##' @return
##' @author Demiurgo
prey.pos <- function(FGs, grp.dat){
ctg <- vector('numeric')
for( i in 1 : length(FGs)){
ctg[i] <- which(grp.dat$Code %in% FGs[i], arr.ind = TRUE)
}
typ <- grp.dat$GroupType[ctg]
TL.v <- ifelse(typ == 'FISH', 3.2,
ifelse(typ %in% c('SED_EP_FF', 'PWN', 'REPTILE', 'FISH_INVERT', 'MOB_EP_OTHER', 'SED_EP_OTHER', 'SM_ZOO', 'MED_ZOO', 'LG_ZOO'), 2.5,
ifelse(typ %in% c('CEP'), 3.2,
ifelse(typ %in% c('SHARK', 'BIRD', 'MAMMAL'), 4,
ifelse(typ %in% c('PL_BACT', 'SED_BACT', 'CARRION', 'LAB_DET', 'REF_DET', 'SM_PHY', 'LG_PHY', 'MICROPHYTOBENTHOS', 'DINOFLAG', 'PHYTOBEN', 'SEAGRASS', 'TURF', 'CORAL'), 2, 2)))))
return(TL.v)
}
##' .. content for \description{} (no empty lines) ..
##'
##' .. content for \details{} ..
##' @title Throphic level estimation. Equation based on Pauly et al 1998 [Diet composition and trophic levels of marine mammals]
##' @param DC Diet composition
##' @param TLp Trophic level of the prey
##' @return The trophic level of the predator
##' @author Demiurgo
Tlevel <- function(DC, TLp){
tl <- 1 + (sum(DC * TLp, na.rm = TRUE) / sum(DC, na.rm = TRUE))
return(tl)
}