4 Pre-Calculate Growth

Purpose: Precalculate growth to look-up growth rates based on weight, temperature, and ration.

Source dependencies

4.1 Set-up

Set parameters for O. mykiss

Code

spp <- "stealhead"
numFish <- 500 #number of fish in a network per scenario
Constants <- fncReadConstants()
st.wt <- 100 #starting weight
ration.lo <- 0.02
ration.hi <- ration.lo + 0.05
pred.en.dens <- 5900 #predator energy density
oxy <- 13560 #oxygen consumed
pff <- 0.1 #percent indigestible prey
prey.en.dens <- 3500 # see Railsback and Rose 1999, Beauchamp et al. 2007

Set up arrays. Very big to allow much wider range of and more accurate values of rations and weights

Code

waterTemps <- cbind("pid" = seq(1, length(seq(0.1, 25, 0.1))),"WT" = seq(0.1, 25, 0.1))
rations <- seq(0.001, 0.4, 0.001)
weights <- seq(0.25, 1500, 0.25)
wt.growth <- array(NA, dim = c(nrow(waterTemps), length(rations), length(weights))) #dim = c(250 WTs, 400 rations, 6000 weights)
p.values <- respiration <- consumption <- wastes <- cmax <- pvals_derived <- wt.growth

4.2 Calculate growth

Loop through arrays to record growth for each case

Code

for(w in 1:dim(wt.growth)[3]){
  ww <- weights[w]
  for(r in 1:dim(wt.growth)[2]){
    rr <- rations[r]
    Input<- fncGetBioEParms("stealhead", pred.en.dens, prey.en.dens, oxy, pff,
                            waterTemps, 
                            startweights = rep(ww, nrow(waterTemps)), 
                            pvals = rep(1, nrow(waterTemps)),
                            ration = rep(rr, nrow(waterTemps)))
    
    
    Results <- BioE(Input, Constants) #run BioE code given input and constants
    wt.growth[,r,w] <- c(Results$Gg_WinBioE) # growth in g/g/d...growth standardized by fish weight
    # p.values[,r,w] <- c(Results$pp) # these are always constant, by definition
    consumption[,r,w] <- c(Results$Consumption)
    wastes[,r,w] <- c(Results$Egestion + Results$Excretion + Results$S.resp)
    respiration[,r,w] <- c(Results$Respiration)
    cmax[,r,w] <- c(Results$Consumption_max)
    pvals_derived[,r,w] <- c(Results$Pvalue)

    ## In Joules instead of grams:
    # wt.growth[,r,w] <- c(Results$Growth_j)
    # consumption[,r,w] <- c(Results$Consumption_j)
    # wastes[,r,w] <- c(Results$Egestion_j + Results$Excretion_j + Results$Sj.resp)
    # respiration[,r,w] <- c(Results$Respiration_j)
  }
  if (w %% 100 == 0) print(w)
}

Save outputs. Only ‘wt.growth’ is needed for simulations. The others are merely for plotting below.

Code

save("wt.growth", file = "data/wt.growth.array.RData")
save("respiration", file = "data/respiration.array.RData")
save("wastes", file = "data/wastes.array.RData")
save("consumption", file = "data/consumption.array.RData")
save("pvals_derived", file = "data/pvalsderived.array.RData")
save("cmax", file = "data/cmax.array.RData")

Load back in to plot

Code

load("data/wt.growth.array.RData")
load("data/consumption.array.RData")
load("data/wastes.array.RData")
load("data/respiration.array.RData")
load("data/pvalsderived.array.RData")
load("data/cmax.array.RData")
# fncGetBioEParms("stealhead", pred.en.dens, prey.en.dens, oxy, pff,
#                             waterTemps,
#                             startweights = rep(ww, nrow(waterTemps)),
#                             pvals = rep(1, nrow(waterTemps)),
#                             ration = rep(rr, nrow(waterTemps)))

4.3 Plot output

4.3.1 Growth rate

Note that because of the range of values we used for ration, growth of small fish (<5g) is constrained even at the highest rations (max ration < allometric C_max). So it only appears as if max growth increases with size for fish between 0.5 a 5g.

Plot growth rate by temperature for fish of varying masses, variable ration sizes.

Code

par(mfrow = c(2, 3), las = 1)
ylb <- "Growth rate (g/g/d)"
for(fish.mass in c(1, 10, 100, 250, 500, 1500)){
  plot(waterTemps[,"WT"], wt.growth[, 400, fish.mass], type='l', ylab = ylb, xlab = "Water temperature (C)", 
       col = 4, ylim = c(-0.06, 0.1), main = paste0("fish weight = ", fish.mass," g")) #max ration
  for(i in seq(1, length(rations), by = 50)){ lines(waterTemps[,"WT"], wt.growth[,i, fish.mass], col = "gray70")}
  abline(h = 0, lty = 2)
  lines(waterTemps[,"WT"], wt.growth[, 1, fish.mass], col = 2, lwd = 1.5) # min ration
  lines(waterTemps[,"WT"], wt.growth[, 400, fish.mass], col = 4, lwd = 1.5) # max ration
}

Plot growth potential by weight under different temperatures (panels) and ration sizes (line color: red = high, blue = low).

Code

par(mfrow = c(2, 3), las = 1)
speccols <- hcl.colors(9, "Temps")
ratiseq <- seq(1, length(rations), by = 49)
tempseq <- seq(1, length(waterTemps[,"WT"]), by = 45)

for (i in 1:length(tempseq)) { 
  plot(wt.growth[tempseq[i],1,] ~ weights, type = "n", ylim = c(-0.06, 0.1), xlim = c(0,50),
       ylab = "Growth rate (g/g/d)", xlab = "Weight (g)", 
       main = paste0("temp = ", waterTemps[tempseq[i], "WT"]," C"))
  
  for (r in 1:length(ratiseq)) {
    lines(wt.growth[tempseq[i],ratiseq[r],] ~ weights, col = speccols[r])
    # print(range(wt.growth[i,ratiseq[r],]))
  }
  abline(v = 100, lty = 2)
  }

Plot optimal growth temperature and maximum growth rate by fish size: blue = maximum ration, grey = (nearly) minimum ration

Code

# dim(wt.growth)[3]
opttemptib <- tibble(weight = weights, 
                     opttemp_ratlo = NA, opttemp_rathi = NA, 
                     growth_ggd_ratlo = NA, growth_ggd_rathi = NA)

for (i in 1:dim(wt.growth)[3]) {
  opttemptib$opttemp_ratlo[i] <- waterTemps[which.max(wt.growth[,10,i]),2]
  opttemptib$opttemp_rathi[i] <- waterTemps[which.max(wt.growth[,400,i]),2]
  opttemptib$growth_ggd_ratlo[i] <- wt.growth[which.max(wt.growth[,10,i]),10,i]
  opttemptib$growth_ggd_rathi[i] <- wt.growth[which.max(wt.growth[,400,i]),151,i]
}

opttemptib %>% ggplot() +
  geom_line(aes(x = weight, y = opttemp_ratlo), color = 2) +
  geom_line(aes(x = weight, y = opttemp_rathi), color = 4) +
  theme_bw() + xlab("Fish weight (g)") + ylab("Optimal temperature for growth (C)")

Code

opttemptib %>% ggplot() +
  geom_line(aes(x = weight, y = growth_ggd_ratlo), color = 2) +
  geom_line(aes(x = weight, y = growth_ggd_rathi), color = 4) +
  theme_bw() + xlab("Fish weight (g)") + ylab("Maximum growth rate (g/g/d)")

Compare raw growth (g/g/d) to g/g/d derived from J/g/d (as in Fullerton)

Code

par(mfrow = c(2, 3), las = 1)
for(fish.mass in c(1, 10, 100, 250, 500, 1500)){
  plot(wt.growth.raw[, 151, fish.mass] ~ wt.growth[, 151, fish.mass], type='l', ylab = "Raw g/g/d", xlab = "g/g/d calculated from J/g/d\n(Fullerton method)", 
       col = 4, ylim = c(-0.03, 0.08), main = paste0("fish weight = ", fish.mass," g")) #max ration
  for(i in seq(2, length(rations)-1, by = 10)){ lines(wt.growth.raw[,i, fish.mass] ~ wt.growth[,i, fish.mass], col = "gray70")}
  abline(h = 0, lty = 2)
  abline(v = 0, lty = 2)
  lines(wt.growth.raw[, 1, fish.mass] ~ wt.growth[, 1, fish.mass], col = 2, lwd = 1.5) # min ration
  lines(wt.growth.raw[, 151, fish.mass] ~ wt.growth[, 151, fish.mass], col = 4, lwd = 1.5) # max ration
}

Show raw growth

Code

par(mfrow = c(2, 3), las = 1)
ylb <- "Growth rate (g/g/d)"
for(fish.mass in c(1, 10, 100, 250, 500, 1500)){
  plot(waterTemps[,"WT"], wt.growth.raw[, 151, fish.mass], type='l', ylab = ylb, xlab = "Water temperature (C)", 
       col = 4, ylim = c(-0.025, 0.08), main = paste0("fish weight = ", fish.mass," g")) #max ration
  for(i in seq(2, length(rations)-1, by = 10)){ lines(waterTemps[,"WT"], wt.growth.raw[,i, fish.mass], col = "gray70")}
  abline(h = 0, lty = 2)
  lines(waterTemps[,"WT"], wt.growth.raw[, 1, fish.mass], col = 2, lwd = 1.5) # min ration
  lines(waterTemps[,"WT"], wt.growth.raw[, 151, fish.mass], col = 4, lwd = 1.5) # max ration
}

4.3.2 Consumption

Consumption:

Code

par(mfrow = c(2, 3), las = 1)
for(fish.mass in c(1, 10, 100, 250, 500, 1500)){
  plot(waterTemps[,"WT"], consumption[, 151, fish.mass], type='l', ylab = "Consumption (g/g/d)", xlab = "Water temperature (C)", 
       col = 4, ylim = c(0, 0.17), main = paste0("fish weight = ", fish.mass," g")) #max ration
  for(i in seq(2, length(rations)-1, by = 10)){ lines(waterTemps[,"WT"], consumption[,i, fish.mass], col = "gray70")}
  abline(h = 0, lty = 2)
  lines(waterTemps[,"WT"], consumption[, 1, fish.mass], col = 2, lwd = 1.5) # min ration
  lines(waterTemps[,"WT"], consumption[, 151, fish.mass], col = 4, lwd = 1.5) # max ration
  abline(h = 0.17, lty = 2)
}

P-values: proportion of maximum consumption

Code

par(mfrow = c(2, 3), las = 1)
for(fish.mass in c(1, 10, 100, 250, 500, 1500)){
  plot(waterTemps[,"WT"], pvals_derived[, 151, fish.mass], type='l', ylab = "P-value", xlab = "Water temperature (C)", 
       col = 4, ylim = c(0, 1), main = paste0("fish weight = ", fish.mass," g")) #max ration
  for(i in seq(2, length(rations)-1, by = 10)){ lines(waterTemps[,"WT"], pvals_derived[,i, fish.mass], col = "gray70")}
  abline(h = 0, lty = 2)
  abline(h = 1, lty = 2)
  lines(waterTemps[,"WT"], pvals_derived[, 1, fish.mass], col = 2, lwd = 1.5) # min ration
  lines(waterTemps[,"WT"], pvals_derived[, 151, fish.mass], col = 4, lwd = 1.5) # max ration
}

Same as above, but only show lines for ration size = 0.1g, the value we set for patch-level daily food availability (see Habitat.qmd)

Code

focal_ration <- 0.1
par(mfrow = c(2, 3), las = 1)
for(fish.mass in c(1, 10, 100, 250, 500, 1500)){
  plot(waterTemps[,"WT"], pvals_derived[, which.min(abs(rations - focal_ration)), fish.mass], 
       type='l', ylab = "P-value", xlab = "Water temperature (C)", 
       ylim = c(0, 1), main = paste0("fish weight = ", fish.mass," g"))
}

4.3.3 Energy budget

Create multi-panel energy budget plots for different sized fish: Consumption = metabolism + wastes + growth

Scope for growth is thus the difference between Consumption and (metabolism + wastes), i.e., the space between the green and red lines:

Code

# png("growth.banana.png", 8, 6, "in", res = 300)
par(mfrow = c(2,3), las = 1)
ylb <- "Rates (g/g/d)"
for(fish.mass in c(1, 10, 100, 250, 500, 1500)){
  plot(waterTemps[,"WT"], consumption[,151, fish.mass], type='l', ylab = ylb, xlab="Water temperature (C)",
       col = 4, ylim = c(-0.02, 0.18), main = paste0("fish weight =", fish.mass," g")) #max ration
  lines(waterTemps[,"WT"], wastes[,151, fish.mass], col = 3) #min ration
  lines(waterTemps[,"WT"], respiration[,151, fish.mass], col = 2) #min ration
  abline(h = 0, lty = 2)
  if(fish.mass == 1) legend("topleft", legend = c("C-Max", "Wastes", "Respiration"), lty = 1, col = c(4, 3 , 2), bty = 'n')
}

Code

# dev.off()

Create single panel plot of ‘growth banana’: shaded region is the scope for growth

Code

par(mfrow = c(1,1), las = 1)
ylb <- "Rates (g/g/d)"
fish.mass <- 500
plot(waterTemps[,"WT"], consumption[,151, fish.mass], type = 'l', ylab = ylb, xlab = "Water temperature (C)",
     ylim = c(-0.02, 0.1), main = paste0("fish weight =", fish.mass," g"), col = 4, lwd = 2) #max ration
polygon(c(waterTemps[, "WT"], rev(waterTemps[, "WT"])), c(wastes[, 151, fish.mass], rev(respiration[, 151, fish.mass])),
        border = NA, col = "grey")
lines(waterTemps[,"WT"], wastes[,151, fish.mass], col = 3, lwd = 2) #min ration
lines(waterTemps[,"WT"], respiration[,151, fish.mass], col = 2, lwd = 2) #min ration

--- title: "Pre-Calculate Growth" --- ```{r include=FALSE} library(tidyverse) library(ggpubr) library(egg) ``` **Purpose:** Precalculate growth to look-up growth rates based on weight, temperature, and ration. Source dependencies ```{r include=FALSE} #| cache: false source("Habitat.R") source("Functions.R") ``` ## Set-up Set parameters for *O. mykiss* ```{r} spp <- "stealhead" numFish <- 500 #number of fish in a network per scenario Constants <- fncReadConstants() st.wt <- 100 #starting weight ration.lo <- 0.02 ration.hi <- ration.lo + 0.05 pred.en.dens <- 5900 #predator energy density oxy <- 13560 #oxygen consumed pff <- 0.1 #percent indigestible prey prey.en.dens <- 3500 # see Railsback and Rose 1999, Beauchamp et al. 2007 ``` Set up arrays. Very big to allow much wider range of and more accurate values of rations and weights ```{r} #| cache: false waterTemps <- cbind("pid" = seq(1, length(seq(0.1, 25, 0.1))),"WT" = seq(0.1, 25, 0.1)) rations <- seq(0.001, 0.4, 0.001) weights <- seq(0.25, 1500, 0.25) wt.growth <- array(NA, dim = c(nrow(waterTemps), length(rations), length(weights))) #dim = c(250 WTs, 400 rations, 6000 weights) p.values <- respiration <- consumption <- wastes <- cmax <- pvals_derived <- wt.growth ``` ## Calculate growth Loop through arrays to record growth for each case ```{r eval=FALSE} for(w in 1:dim(wt.growth)[3]){ ww <- weights[w] for(r in 1:dim(wt.growth)[2]){ rr <- rations[r] Input<- fncGetBioEParms("stealhead", pred.en.dens, prey.en.dens, oxy, pff, waterTemps, startweights = rep(ww, nrow(waterTemps)), pvals = rep(1, nrow(waterTemps)), ration = rep(rr, nrow(waterTemps))) Results <- BioE(Input, Constants) #run BioE code given input and constants wt.growth[,r,w] <- c(Results$Gg_WinBioE) # growth in g/g/d...growth standardized by fish weight # p.values[,r,w] <- c(Results$pp) # these are always constant, by definition consumption[,r,w] <- c(Results$Consumption) wastes[,r,w] <- c(Results$Egestion + Results$Excretion + Results$S.resp) respiration[,r,w] <- c(Results$Respiration) cmax[,r,w] <- c(Results$Consumption_max) pvals_derived[,r,w] <- c(Results$Pvalue) ## In Joules instead of grams: # wt.growth[,r,w] <- c(Results$Growth_j) # consumption[,r,w] <- c(Results$Consumption_j) # wastes[,r,w] <- c(Results$Egestion_j + Results$Excretion_j + Results$Sj.resp) # respiration[,r,w] <- c(Results$Respiration_j) } if (w %% 100 == 0) print(w) } ``` Save outputs. Only 'wt.growth' is needed for simulations. The others are merely for plotting below. ```{r eval=FALSE} save("wt.growth", file = "data/wt.growth.array.RData") save("respiration", file = "data/respiration.array.RData") save("wastes", file = "data/wastes.array.RData") save("consumption", file = "data/consumption.array.RData") save("pvals_derived", file = "data/pvalsderived.array.RData") save("cmax", file = "data/cmax.array.RData") ``` Load back in to plot ```{r} load("data/wt.growth.array.RData") load("data/consumption.array.RData") load("data/wastes.array.RData") load("data/respiration.array.RData") load("data/pvalsderived.array.RData") load("data/cmax.array.RData") # fncGetBioEParms("stealhead", pred.en.dens, prey.en.dens, oxy, pff, # waterTemps, # startweights = rep(ww, nrow(waterTemps)), # pvals = rep(1, nrow(waterTemps)), # ration = rep(rr, nrow(waterTemps))) ``` ## Plot output ### Growth rate **Note that because of the range of values we used for ration, growth of small fish (<5g) is constrained even at the highest rations (max ration < allometric C~max~). So it only appears as if max growth increases with size for fish between 0.5 a 5g.** Plot growth rate by temperature for fish of varying masses, variable ration sizes. ```{r fig.width=7, fig.height=6} par(mfrow = c(2, 3), las = 1) ylb <- "Growth rate (g/g/d)" for(fish.mass in c(1, 10, 100, 250, 500, 1500)){ plot(waterTemps[,"WT"], wt.growth[, 400, fish.mass], type='l', ylab = ylb, xlab = "Water temperature (C)", col = 4, ylim = c(-0.06, 0.1), main = paste0("fish weight = ", fish.mass," g")) #max ration for(i in seq(1, length(rations), by = 50)){ lines(waterTemps[,"WT"], wt.growth[,i, fish.mass], col = "gray70")} abline(h = 0, lty = 2) lines(waterTemps[,"WT"], wt.growth[, 1, fish.mass], col = 2, lwd = 1.5) # min ration lines(waterTemps[,"WT"], wt.growth[, 400, fish.mass], col = 4, lwd = 1.5) # max ration } ``` Plot growth potential by weight under different temperatures (panels) and ration sizes (line color: red = high, blue = low). ```{r fig.width=7, fig.height=6} par(mfrow = c(2, 3), las = 1) speccols <- hcl.colors(9, "Temps") ratiseq <- seq(1, length(rations), by = 49) tempseq <- seq(1, length(waterTemps[,"WT"]), by = 45) for (i in 1:length(tempseq)) { plot(wt.growth[tempseq[i],1,] ~ weights, type = "n", ylim = c(-0.06, 0.1), xlim = c(0,50), ylab = "Growth rate (g/g/d)", xlab = "Weight (g)", main = paste0("temp = ", waterTemps[tempseq[i], "WT"]," C")) for (r in 1:length(ratiseq)) { lines(wt.growth[tempseq[i],ratiseq[r],] ~ weights, col = speccols[r]) # print(range(wt.growth[i,ratiseq[r],])) } abline(v = 100, lty = 2) } ``` Plot optimal growth temperature and maximum growth rate by fish size: blue = maximum ration, grey = (nearly) minimum ration ```{r} # dim(wt.growth)[3] opttemptib <- tibble(weight = weights, opttemp_ratlo = NA, opttemp_rathi = NA, growth_ggd_ratlo = NA, growth_ggd_rathi = NA) for (i in 1:dim(wt.growth)[3]) { opttemptib$opttemp_ratlo[i] <- waterTemps[which.max(wt.growth[,10,i]),2] opttemptib$opttemp_rathi[i] <- waterTemps[which.max(wt.growth[,400,i]),2] opttemptib$growth_ggd_ratlo[i] <- wt.growth[which.max(wt.growth[,10,i]),10,i] opttemptib$growth_ggd_rathi[i] <- wt.growth[which.max(wt.growth[,400,i]),151,i] } opttemptib %>% ggplot() + geom_line(aes(x = weight, y = opttemp_ratlo), color = 2) + geom_line(aes(x = weight, y = opttemp_rathi), color = 4) + theme_bw() + xlab("Fish weight (g)") + ylab("Optimal temperature for growth (C)") opttemptib %>% ggplot() + geom_line(aes(x = weight, y = growth_ggd_ratlo), color = 2) + geom_line(aes(x = weight, y = growth_ggd_rathi), color = 4) + theme_bw() + xlab("Fish weight (g)") + ylab("Maximum growth rate (g/g/d)") ``` Compare raw growth (g/g/d) to g/g/d derived from J/g/d (as in Fullerton) ```{r fig.width=7, fig.height=6, eval=FALSE} par(mfrow = c(2, 3), las = 1) for(fish.mass in c(1, 10, 100, 250, 500, 1500)){ plot(wt.growth.raw[, 151, fish.mass] ~ wt.growth[, 151, fish.mass], type='l', ylab = "Raw g/g/d", xlab = "g/g/d calculated from J/g/d\n(Fullerton method)", col = 4, ylim = c(-0.03, 0.08), main = paste0("fish weight = ", fish.mass," g")) #max ration for(i in seq(2, length(rations)-1, by = 10)){ lines(wt.growth.raw[,i, fish.mass] ~ wt.growth[,i, fish.mass], col = "gray70")} abline(h = 0, lty = 2) abline(v = 0, lty = 2) lines(wt.growth.raw[, 1, fish.mass] ~ wt.growth[, 1, fish.mass], col = 2, lwd = 1.5) # min ration lines(wt.growth.raw[, 151, fish.mass] ~ wt.growth[, 151, fish.mass], col = 4, lwd = 1.5) # max ration } ``` Show raw growth ```{r fig.width=7, fig.height=6, eval=FALSE} par(mfrow = c(2, 3), las = 1) ylb <- "Growth rate (g/g/d)" for(fish.mass in c(1, 10, 100, 250, 500, 1500)){ plot(waterTemps[,"WT"], wt.growth.raw[, 151, fish.mass], type='l', ylab = ylb, xlab = "Water temperature (C)", col = 4, ylim = c(-0.025, 0.08), main = paste0("fish weight = ", fish.mass," g")) #max ration for(i in seq(2, length(rations)-1, by = 10)){ lines(waterTemps[,"WT"], wt.growth.raw[,i, fish.mass], col = "gray70")} abline(h = 0, lty = 2) lines(waterTemps[,"WT"], wt.growth.raw[, 1, fish.mass], col = 2, lwd = 1.5) # min ration lines(waterTemps[,"WT"], wt.growth.raw[, 151, fish.mass], col = 4, lwd = 1.5) # max ration } ``` ### Consumption Consumption: ```{r fig.width=7, fig.height=6} par(mfrow = c(2, 3), las = 1) for(fish.mass in c(1, 10, 100, 250, 500, 1500)){ plot(waterTemps[,"WT"], consumption[, 151, fish.mass], type='l', ylab = "Consumption (g/g/d)", xlab = "Water temperature (C)", col = 4, ylim = c(0, 0.17), main = paste0("fish weight = ", fish.mass," g")) #max ration for(i in seq(2, length(rations)-1, by = 10)){ lines(waterTemps[,"WT"], consumption[,i, fish.mass], col = "gray70")} abline(h = 0, lty = 2) lines(waterTemps[,"WT"], consumption[, 1, fish.mass], col = 2, lwd = 1.5) # min ration lines(waterTemps[,"WT"], consumption[, 151, fish.mass], col = 4, lwd = 1.5) # max ration abline(h = 0.17, lty = 2) } ``` P-values: proportion of maximum consumption ```{r fig.width=7, fig.height=6} par(mfrow = c(2, 3), las = 1) for(fish.mass in c(1, 10, 100, 250, 500, 1500)){ plot(waterTemps[,"WT"], pvals_derived[, 151, fish.mass], type='l', ylab = "P-value", xlab = "Water temperature (C)", col = 4, ylim = c(0, 1), main = paste0("fish weight = ", fish.mass," g")) #max ration for(i in seq(2, length(rations)-1, by = 10)){ lines(waterTemps[,"WT"], pvals_derived[,i, fish.mass], col = "gray70")} abline(h = 0, lty = 2) abline(h = 1, lty = 2) lines(waterTemps[,"WT"], pvals_derived[, 1, fish.mass], col = 2, lwd = 1.5) # min ration lines(waterTemps[,"WT"], pvals_derived[, 151, fish.mass], col = 4, lwd = 1.5) # max ration } ``` Same as above, but only show lines for ration size = 0.1g, the value we set for patch-level daily food availability (see `Habitat.qmd`) ```{r fig.width=7, fig.height=6} focal_ration <- 0.1 par(mfrow = c(2, 3), las = 1) for(fish.mass in c(1, 10, 100, 250, 500, 1500)){ plot(waterTemps[,"WT"], pvals_derived[, which.min(abs(rations - focal_ration)), fish.mass], type='l', ylab = "P-value", xlab = "Water temperature (C)", ylim = c(0, 1), main = paste0("fish weight = ", fish.mass," g")) } ``` ### Energy budget Create multi-panel energy budget plots for different sized fish: *Consumption* = *metabolism* + *wastes* + *growth* Scope for growth is thus the difference between *Consumption* and (*metabolism* + *wastes*), i.e., the space between the green and red lines: ```{r fig.width=7, fig.height=6} # png("growth.banana.png", 8, 6, "in", res = 300) par(mfrow = c(2,3), las = 1) ylb <- "Rates (g/g/d)" for(fish.mass in c(1, 10, 100, 250, 500, 1500)){ plot(waterTemps[,"WT"], consumption[,151, fish.mass], type='l', ylab = ylb, xlab="Water temperature (C)", col = 4, ylim = c(-0.02, 0.18), main = paste0("fish weight =", fish.mass," g")) #max ration lines(waterTemps[,"WT"], wastes[,151, fish.mass], col = 3) #min ration lines(waterTemps[,"WT"], respiration[,151, fish.mass], col = 2) #min ration abline(h = 0, lty = 2) if(fish.mass == 1) legend("topleft", legend = c("C-Max", "Wastes", "Respiration"), lty = 1, col = c(4, 3 , 2), bty = 'n') } # dev.off() ``` Create single panel plot of 'growth banana': shaded region is the scope for growth ```{r} par(mfrow = c(1,1), las = 1) ylb <- "Rates (g/g/d)" fish.mass <- 500 plot(waterTemps[,"WT"], consumption[,151, fish.mass], type = 'l', ylab = ylb, xlab = "Water temperature (C)", ylim = c(-0.02, 0.1), main = paste0("fish weight =", fish.mass," g"), col = 4, lwd = 2) #max ration polygon(c(waterTemps[, "WT"], rev(waterTemps[, "WT"])), c(wastes[, 151, fish.mass], rev(respiration[, 151, fish.mass])), border = NA, col = "grey") lines(waterTemps[,"WT"], wastes[,151, fish.mass], col = 3, lwd = 2) #min ration lines(waterTemps[,"WT"], respiration[,151, fish.mass], col = 2, lwd = 2) #min ration ```