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07. Sensitivity: Direct vs. Indirect Trait Effects

t07-sensitivity.Rmd
library(ToolsRTM)
library(SCOPEinR)

SCOPE couples radiative transfer, energy balance, and photosynthesis – so a trait with no direct radiative-transfer role (Vcmax25, photosynthetic capacity) can still leave a signature in reflectance indirectly, through the leaf temperature the energy balance solves for. This page sweeps one trait at a time and looks at three outputs: reflectance (refl), canopy temperature (Tcave), and photosynthesis (Actot).

path_input <- system.file("input", package = "SCOPEinR")
scope_options <- read.table(file.path(path_input, "setoptions.csv"), header = TRUE, sep = ",")
LUT_default <- read.table(file.path(path_input, "LUT_input.csv"), header = TRUE, sep = ",")

run_scope <- function(row) {
  invisible(capture.output(
    r <- get.SCOPE(LUT = row, options.SCOPE = scope_options, optipar = SCOPEinR::optipar2021.Pro.CX,
                    leaf.model = "fluspect-CX", canopy.model = "fourSAIL",
                    get.outputs = "ALL", get.plots = FALSE)[[1]]
  ))
  r
}
wl_optical <- 400:2400; n <- length(wl_optical)

1. Sweeping Cab (chlorophyll content) 

cab_values <- seq(15, 65, length.out = 6)
res_cab <- lapply(cab_values, function(v) { row_i <- LUT_default[1, ]; row_i$Cab <- v; run_scope(row_i) })

cols <- colorRampPalette(c("gold", "darkgreen"))(length(cab_values))
matplot(wl_optical, sapply(res_cab, function(r) r$data.rad$refl[1:n]), type = "l", lty = 1, col = cols,
        xlab = "Wavelength (nm)", ylab = "Reflectance", main = "TOC reflectance sensitivity to Cab")
legend("topright", paste("Cab =", round(cab_values)), col = cols, lty = 1, cex = 0.7)

Chlorophyll’s own signature (red-edge/visible absorption) dominates – the expected, direct radiative-transfer effect.

2. Sweeping Vcmax25 (photosynthetic capacity)

Vcmax25 has no role in Fluspect/4SAIL’s radiative transfer at all – any reflectance change it causes is entirely indirect, through the energy balance:

vcmax_values <- seq(20, 200, length.out = 6)
res_vcmax <- lapply(vcmax_values, function(v) { row_i <- LUT_default[1, ]; row_i$Vcmax25 <- v; run_scope(row_i) })

Tcave_vals <- sapply(res_vcmax, function(r) r$data.fluxes$Tcave)
Actot_vals <- sapply(res_vcmax, function(r) r$data.fluxes$Actot)

op <- par(mfrow = c(1, 2))
plot(vcmax_values, Tcave_vals, type = "o", pch = 19, col = "#2166AC",
     xlab = "Vcmax25", ylab = "Canopy-average leaf temperature (degC)", main = "Tcave vs Vcmax25")
plot(vcmax_values, Actot_vals, type = "o", pch = 19, col = "#B2182B",
     xlab = "Vcmax25", ylab = "Actot (umol m-2 s-1)", main = "Actot vs Vcmax25")

par(op)
cols2 <- colorRampPalette(c("gold", "darkblue"))(length(vcmax_values))
matplot(wl_optical, sapply(res_vcmax, function(r) r$data.rad$refl[1:n]), type = "l", lty = 1, col = cols2,
        xlab = "Wavelength (nm)", ylab = "Reflectance",
        main = "TOC reflectance sensitivity to Vcmax25 (indirect, via energy balance)")
legend("topright", paste("Vcmax25 =", round(vcmax_values)), col = cols2, lty = 1, cex = 0.7)

Actot responds strongly and directly to Vcmax25, as expected from the Farquhar-type model. The reflectance panel is the real point: any spread there is not Fluspect/4SAIL reacting to Vcmax25 (it has no such input) – it’s the small, indirect effect of a different leaf temperature feeding into the thermal part of the spectrum. Compare its magnitude to the Cab sweep above.

3. Sweeping LAI 

lai_values <- seq(0.5, 6, length.out = 6)
res_lai <- lapply(lai_values, function(v) { row_i <- LUT_default[1, ]; row_i$LAI <- v; run_scope(row_i) })

cols3 <- colorRampPalette(c("gold", "darkred"))(length(lai_values))
matplot(wl_optical, sapply(res_lai, function(r) r$data.rad$refl[1:n]), type = "l", lty = 1, col = cols3,
        xlab = "Wavelength (nm)", ylab = "Reflectance", main = "TOC reflectance sensitivity to LAI")
legend("topright", paste("LAI =", round(lai_values, 1)), col = cols3, lty = 1, cex = 0.7)

NIR reflectance rises with LAI to a plateau (more leaf layers scattering) – see ToolsRTM’s Tutorial 15 for how this same LAI-driven canopy closure also controls how much a soil trait can influence the signal.

Summary

Trait swept Direct RT effect? Where it shows up
Cab Yes – Fluspect input Visible/red-edge reflectance, strong
LAI Yes – 4SAIL input NIR plateau height, strong
Vcmax25 No – biochemistry only Actot strongly; reflectance only indirectly, via leaf temperature

This distinction is exactly what Tutorial 08 tests the practical consequence of: can Vcmax25 actually be retrieved from reflectance the way Cab/LAI can?

What’s next

  • Tutorial 08 – hybrid inversion: retrieving Cab, LAI, and Vcmax25 from reflectance, and seeing which one this sensitivity result predicts will fail.