ccrtm: Coupled Chain Radiative Transfer Models.

Description

A collection of radiative transfer models that can form a coupled chain to model radiative transfer across multiple spatial scales from leaf to canopy to stand.

Details

Currently implemented models:

• [1] = PROSPECT 5, 5B and D

• [2] = FOURSAIL, and FOURSAIL2

• [3] = FLIM

Currently being tested or to be implemented models

• [1] = LIBERTY, PROCOSINE

• [2] = INFORM

Author(s)

Marco D. Visser

Kullback-Lieber divergence function D(spec1 || spec2) = sum(spec1 * log(spec1 / spec2))

Description

Kullback-Lieber divergence function D(spec1 || spec2) = sum(spec1 * log(spec1 / spec2))

Usage

KLd(spec1, spec2)

Arguments

Value

the KL divergence between the vector inputs

Generates an invertable model for backward implementation of Radiative Transfer Models

Description

Generates an invertable model for backward implementation of Radiative Transfer Models

Usage

bRTM(fm = rho ~ prospect5, data = NULL, pars = NULL, fixed = NULL,
  wl = 400:2500)

Arguments

Leaf inclination distribution function Ellipsoidal distribution function

Description

Leaf inclination distribution function Ellipsoidal distribution function

Usage

cambell(ala, tx1, tx2)

Arguments

Value

angle fraction value

Leaf inclination distribution function cummulative lagden function from Wout Verhoef's dissertation Extended here for any angle

Description

Leaf inclination distribution function cummulative lagden function from Wout Verhoef's dissertation Extended here for any angle

Usage

cdcum(a, b, theta)

Arguments

Value

angle fraction value

refractive index and specific absorption coefficient for PROSPECT 5

Description

see http://teledetection.ipgp.jussieu.fr/prosail/ for more details on the data.

Usage

data(prospect5)

details

*********************************************************************** data_prospect5 (february, 25th 2008) The dataset contains the following labels (columns): ***********************************************************************

• [1] = wavelength (nm)

• [2] = refractive index of leaf material ( or the ratio of the velocity of light in a vacuum to its velocity in "leaf medium").

• [3] = specific absorption coefficient of chlorophyll (a+b) (cm2.microg-1)

• [4] = specific absorption coefficient of carotenoids (cm2.microg-1)

• [5] = specific absorption coefficient of brown pigments (arbitrary units)

• [6] = specific absorption coefficient of water (cm-1)

• [7] = specific absorption coefficient of dry matter (g.cm-1)

• [8] = direct light

• [9] = diffuse light

• [10] = dry soil

• [11] = wet soil

references

Feret et al. (2008), PROSPECT-4 and 5: Advances in the Leaf Optical Properties Model Separating Photosynthetic Pigments, Remote Sensing of Environment

refractive index and specific absorption coefficient for PROSPECT D

Description

see http://teledetection.ipgp.jussieu.fr/prosail/ for more details on the data.

Usage

data(prospectd)

details

*********************************************************************** data_prospect5 (february, 25th 2008) The dataset contains the following labels (columns): ***********************************************************************

• [1] = wavelength (nm)

• [2] = refractive index of leaf material ( or the ratio of the velocity of light in a vacuum to its velocity in "leaf medium").

• [3] = specific absorption coefficient of chlorophyll (a+b) (cm2.microg-1)

• [4] = specific absorption coefficient of carotenoids (cm2.microg-1)

• [5] = specific absorption coefficient of brown pigments (arbitrary units)

• [6] = specific absorption coefficient of water (cm-1)

• [7] = specific absorption coefficient of dry matter (g.cm-1)

• [8] = direct light

• [9] = diffuse light

• [10] = dry soil

• [11] = wet soil

references

Feret et al. (2008), PROSPECT-4 and 5: Advances in the Leaf Optical Properties Model Separating Photosynthetic Pigments, Remote Sensing of Environment

Forward implementation of coupled Radiative Transfer Models.

Description

Forward implementation of coupled Radiative Transfer Models.

Usage

fRTM(fm = rho + tau ~ prospect5 + foursail, pars = NULL,
  wl = 400:2500)

Arguments

Value

spectra matrix with reflectance (and transmission, depending on the formula inputs). See seperate model helpfiles for details.

Examples

## setup graphics for plots 
oldpar<-par()
par(mfrow=c(3,2))

## get reflectance for a leaf 
ref <- fRTM(rho~prospect5)
plot(ref,main="Prospect 5")
     
## get reflectance and transmission for a leaf 
reftrans <- fRTM(rho+tau~prospect5)
plot(reftrans,main="Prospect 5")
     
## get reflectance for a single layered canopy 
ref <- fRTM(rho~prospect5+foursail)
plot(ref,main="Prospect 5 + 4SAIL")

## get reflectance for a 2 layered canopy with two leaf types 
ref <- fRTM(rho~prospectd+prospect5+foursail2)
plot(ref,main="Prospect D + Prospect 5  + 4SAIL2")

## edit the parameters: sparse vegatation LAI 
parlist<- list(prospect5=NULL,prospectd=NULL,foursail2=c(LAI=0.05))

## update reflectance
ref <- fRTM(rho~prospect5+prospectd+foursail2,parlist)
plot(ref,main="LAI=0.05")

## change leaf area index to dense vegetation
parlist$foursail2["LAI"]<-8.5

## update reflectance
ref <- fRTM(rho~prospect5+prospectd+foursail2,parlist)
plot(ref,main="LAI=8.5")

par(oldpar)   

Forest Light Interaction Model (FLIM)

Description

The FLIM model was first described by Rosema et al (1992). In FLIM forests are assumed a discontinous mix of tree crowns and gaps. Reflectance is modelled in terms of the probabilty to observe either a gap (background) or a tree crown. Both gaps and crowns may be shaded.

Usage

flim(Rc, Rg, To = NULL, Ts = NULL, params, area = 10000)

Arguments

Details

Confounded parameters pairs cannot be inversely estimated, one of the pairs should be set to 1.

Value

a list with reflectance, and the fractions of shaded and sunexplosed crowns, shaded and sun exposed open space.

References

Rosema, A., Verhoef, W., Noorbergen, H., Borgesius, J.J. (1992). A new forest light interaction model in support of forest monitoring. Remote Sens. Environ. 42, 23-41.

Optimized R implementation of foursail (4SAIL)

Description

The foursail (or 4SAIL) radiative transfer model is commonly used to simulate bidirectional reflectance distribution functions within vegetation canopies. Foursail (4SAIL) refers to "Scattering by Arbitrary Inclined Leaves" in a 4-stream model. The four-streams represents the scattering and absorption of upward, downward and two directional radiative fluxes with four linear differential equations in a 1-D canopy. The model was initially developed by Verhoef (1984), who extended work by Suits (1971) 4-steam model.

Usage

foursail(rho, tau, bgr, param)

Arguments

Value

spectra matrixwith 4 reflectance factors and canopy transmission for wavelengths 400 to 2500nm:

• [1] = bi-hemispherical reflectance (rddt). White-sky albedo: the reflectance of the canopy under diffuse illumination. The BRDF integrated over all viewing and illumination directions.

• [2] = hemispherical directional reflectance (rsdt). Black-sky albedo: reflectance of a surface under direct light without a diffuse component. It is the integral of the BRDF over all viewing directions.

• [3] = directional hemispherical reflectance (rdot). Diffuse reflectance in the vieweing direction.

• [4] = bi-directional reflectance (rsot). The ratio of reflected radiance in the viewing direction to the incoming radiant flux in the solar direction.

• [5] = Canopy transmission of diffuse light through the canopy (taud).

• [6] = transmission of direct light through the canopy (taus).

References

Suits, G.H., 1971. The calculation of the directional reflectance of a vegetative canopy. Remote Sens. Environ. 2, 117-125.

Verhoef, W. (1984). Light scattering by leaf layers with application to canopy reflectance modeling: The SAIL model. Remote Sens. Environ. 16, 125-141.

Examples

## lower-level implementation example
## see ?fRTM for the typical mode of simulation
## e.g. fRTM(rho~prospectd+foursail) 

## 1) get parameters
params<-getDefaults(rho~prospectd+foursail) 
## getDefaults("foursail") will also work
bestpars<-params$foursail$best
## ensure the vector is named
names(bestpars) <- rownames(params$foursail)

## 2) get leaf reflectance and transmission 
rt<-fRTM(rho+tau~prospectd)

## 3) get soil reflectance to model background reflectance
data(soil)

## a linear mixture soil model 
bgRef<- bestpars["psoil"]*soil[,"drySoil"] + (1-bestpars["psoil"])*soil[,"wetSoil"]

## 4) run 4SAIL
foursail(rt[,"rho"],rt[,"tau"],bgRef,bestpars)

R implementation of the foursail2 model with 2 canopy layers.

Description

The foursail2 model is a two layer implementation of the foursail model described in Verhoef and Bach (2007). Layers are assumed identical in particle inclination and hotspot, but may differ in the relative density and types of particles (see foursail2b for a layer specific inclination angle). In comparison to foursail, the background (soil), can now be non-Lambertain, having it own 4-stream BDRF (not implemented here but may be input by the user). There are two types of particles, generalized to primary and secondary (originally termed "green" and "brown" particles). The realtive abundance of the secondary particle in the top canopy is regulated by the dissociation paramerter.The model 4SAIL2 combines with prospect, libery or procosine for the reflectance and transmittance of the particles, and with the the foursail or Hapke elements for the background reflectance. If run alone, these require direct inputs which could be measured leaf reflectance.

Usage

foursail2(rhoA, tauA, rhoB = NULL, tauB = NULL, bgr, rsobgr = NULL,
  rdobgr = NULL, rsdbgr = NULL, rddbgr = NULL, param)

Arguments

Value

spectra matrixwith 4 reflectance factors and canopy transmission for wavelengths 400 to 2500nm:

• [1] = bi-hemispherical reflectance (rddt). White-sky albedo: the reflectance of the canopy under diffuse illumination. The BRDF integrated over all viewing and illumination directions. Diffuse reflectance for diffuse incidence.

• [2] = hemispherical directional reflectance (rsdt). Black-sky albedpo: reflectance of a surface under direct light without a diffuse component. It is the integral of the BRDF over all viewing directions. Diffuse reflectance for direct solar incidence.

• [3] = directional hemispherical reflectance (rdot). Diffuse reflectance in the vieweing direction.

• [4] = bi-directional reflectance (rsot). The ratio of reflected radiance in the viewing direction to the incoming radiant flux in the solar direction.

References

Verhoef, W., Bach, H. (2007). Coupled soil-leaf-canopy and atmosphere radiative transfer modeling to simulate hyperspectral multi-angular surface reflectance and TOA radiance data. Remote Sens. Environ. 109, 166-182.

Examples

## see ?foursail for lower-level implementations
fRTM(rho~prospect5+foursail2)

R implementation of the foursail2 model with 2 canopy layers.

Description

The foursail2b model is a two layer implementation of the foursail model described in Zhang et al (2005). Layers are assumed identical in hotspot, but may differ in the relative density, inclination and types of particles. In comparison to foursail, the background (soil), can now be non-Lambertain, having it own 4-stream BDRF. There are two types of particles, generalized to primary and secondary (originally termed "green" and "brown" particles). The realtive abundance of the secondary particle in the top canopy is regulated by the dissociation paramerter.The model 4SAIL2 combines with prospect, libery or procosine for the reflectance and transmittance of the particles, and with the the foursail or Hapke elements for the background reflectance. If run alone, these require direct inputs which could be measured leaf reflectance.

Usage

foursail2b(rhoA, tauA, rhoB = NULL, tauB = NULL, bgr, rsobgr = NULL,
  rdobgr = NULL, rsdbgr = NULL, rddbgr = NULL, param)

Arguments

Value

spectra matrixwith 4 reflectance factors and canopy transmission for wavelengths 400 to 2500nm:

• [1] = bi-hemispherical reflectance (rddt). White-sky albedo: the reflectance of the canopy under diffuse illumination. The BRDF integrated over all viewing and illumination directions. Diffuse reflectance for diffuse incidence.

• [2] = hemispherical directional reflectance (rsdt). Black-sky albedpo: reflectance of a surface under direct light without a diffuse component. It is the integral of the BRDF over all viewing directions. Diffuse reflectance for direct solar incidence.

• [3] = directional hemispherical reflectance (rdot). Diffuse reflectance in the vieweing direction.

• [4] = bi-directional reflectance (rsot). The ratio of reflected radiance in the viewing direction to the incoming radiant flux in the solar direction.

References

Zhang, Q., Xiao, X., Braswell, B., Linder, E., Baret, F., Moore, B. (2005). Estimating light absorption by chlorophyll, leaf and canopy in a deciduous broadleaf forest using MODIS data and a radiative transfer model. Remote Sens. Environ. 99, 357-371.

Examples

## see ?foursail for lower-level implementations
fRTM(rho~prospectd+foursail2b)

S3- methods for Generate defaults settings and parameters for all supported models.

Description

S3- methods for Generate defaults settings and parameters for all supported models.

Usage

getDefaults(model = NULL, ...)

Arguments

Value

a data.frame with default model parameters

Leaf inclination distribution models s3 method for calling leaf models

Description

Leaf inclination distribution models s3 method for calling leaf models

Usage

lidf(pars)

Arguments

Value

a vector of proportions for each leaf angle calculated from each leaf inclination model

Plot RTM return spectra vs. wavelength

Description

Plot RTM return spectra vs. wavelength

Usage

## S3 method for class 'rtm.spectra'
plot(x, ...)

Arguments

Value

plots to the device a ccrtm standard spectra plot based on the function call returned from fRTM.

Plot RTM return spectra vs. wavelength

Description

Plot RTM return spectra vs. wavelength

Usage

## S3 method for class 'rtm.spectra'
print(x, ...)

Arguments

Value

prints the standard information from a simulated ccrtm spectra plot

PROSPECT model version 5 and 5B

Description

The PROSPECT5(b) leaf reflectance model. The model was implemented based on Jacquemoud and Ustin (2019), and is further described in detail in Feret et al (2008). PROSPECT models use the plate models developed in Allen (1969) and Stokes (1862). Set Cbrown to 0 for prospect version 5.

Usage

prospect5(param)

Arguments

Value

spectra matrix with leaf reflectance and transmission for wavelengths 400 to 2500nm:

• [1] = leaf reflectance (rho)

• [2] = leaf transmission (tau)

References

Jacquemoud, S., and Ustin, S. (2019). Leaf optical properties. Cambridge University Press.

Feret, J.B., Francois, C., Asner, G.P., Gitelson, A.A., Martin, R.E., Bidel, L.P.R., Ustin, S.L., le Maire, G., Jacquemoud, S. (2008), PROSPECT-4 and 5: Advances in the leaf optical properties model separating photosynthetic pigments. Remote Sens. Environ. 112, 3030-3043.

Allen W.A., Gausman H.W., Richardson A.J., Thomas J.R. (1969), Interaction of isotropic ligth with a compact plant leaf, Journal of the Optical Society of American, 59:1376-1379.

Stokes G.G. (1862), On the intensity of the light reflected from or transmitted through a pile of plates, Proceedings of the Royal Society of London, 11:545-556.

PROSPECT model version D

Description

The PROSPECTD leaf reflectance model. The model was implemented based on Jacquemoud and Ustin (2019), and is further described in detail in Feret et al (2017). PROSPECT models use the plate models developed in Allen (1969) and Stokes (1862).

Usage

prospectd(param)

Arguments

Value

spectra matrix with leaf reflectance and transmission for wavelengths 400 to 2500nm:

• [1] = leaf reflectance (rho)

• [2] = leaf transmission (tau)

References

Jacquemoud, S., and Ustin, S. (2019). Leaf optical properties. Cambridge University Press.

Feret, J.B., Gitelson, A.A., Noble, S.D., Jacquemoud, S. (2017). PROSPECT-D: Towards modeling leaf optical properties through a complete lifecycle. Remote Sens. Environ. 193, 204-215.

Allen W.A., Gausman H.W., Richardson A.J., Thomas J.R. (1969), Interaction of isotropic ligth with a compact plant leaf, Journal of the Optical Society of American, 59:1376-1379.

Stokes G.G. (1862), On the intensity of the light reflected from or transmitted through a pile of plates, Proceedings of the Royal Society of London, 11:545-556.

R implementation of foursail (pure R)

Description

The pure R version of foursail is included in the package as an easy way to review the code, and to check more optimized versions against. Model originally developed by Wout Verhoef.

Usage

r_foursail(rho, tau, bgr, param)

Arguments

Value

spectra matrixwith 4 reflectance factors and canopy transmission for wavelengths 400 to 2500nm:

• [1] = bi-hemispherical reflectance (rddt). White-sky albedo: the reflectance of the canopy under diffuse illumination. The BRDF integrated over all viewing and illumination directions.

• [2] = hemispherical directional reflectance (rsdt). Black-sky albedo: reflectance of a surface under direct light without a diffuse component. It is the integral of the BRDF over all viewing directions.

• [3] = directional hemispherical reflectance (rdot). Diffuse reflectance in the vieweing direction.

• [4] = bi-directional reflectance (rsot). The ratio of reflected radiance in the viewing direction to the incoming radiant flux in the solar direction.

• [5] = Canopy transmission of diffuse light through the canopy (taud).

• [6] = transmission of direct light through the canopy (taus).

Author(s)

Marco D. Visser (R implementation)

The SAIL BDRF function

Description

The SAIL BDRF function

Usage

sail_BDRF(w, lai, sumint, tsstoo, rsoil, rdd, tdd, tsd, rsd, tdo, rdo, tss,
  too, rsod)

Arguments

Value

spectra matrixwith 4 reflectance factors and canopy transmission for wavelengths 400 to 2500nm:

• [1] = bi-hemispherical reflectance (rddt). White-sky albedo: the reflectance of the canopy under diffuse illumination. The BRDF integrated over all viewing and illumination directions.

• [2] = hemispherical directional reflectance (rsdt). Black-sky albedo: reflectance of a surface under direct light without a diffuse component. It is the integral of the BRDF over all viewing directions.

• [3] = directional hemispherical reflectance (rdot). Diffuse reflectance in the vieweing direction.

• [4] = bi-directional reflectance (rsot). The ratio of reflected radiance in the viewing direction to the incoming radiant flux in the solar direction.

• [5] = Canopy transmission of diffuse light through the canopy (taud).

• [6] = transmission of direct light through the canopy (taus).

Sky light model

Description

Simple atmospherical model that builds on recommendations from Francois et al. (2002).

Usage

skyl(rddt, rsdt, rdot, rsot, Es, Ed, tts, skyl = NULL)

Arguments

Value

a list with hemispherical and directional reflectance. rt<-fRTM(rho~prospect5+foursail) skyl(rt[,"rddt"],rt[,"rsdt"],rt[,"rdot"],rt[,"rsot"], Es=solar[,1],Ed=solar[,2],tts=45,skyl=NULL)

References

Francois, C., Ottle, C., Olioso, A., Prevot, L., Bruguier, N., Ducros, Y.(2002). Conversion of 400-1100 nm vegetation albedo measurements into total shortwave broadband albedo using a canopy radiative transfer model. Agronomie 22, 611-618.

Examples

data(solar)

soil reflectance

Description

soil reflectance

Usage

data(soil)

details

***********************************************************************

• [1] = wet soil

• [2] = dry soil

references

Feret et al. (2008), PROSPECT-4 and 5: Advances in the Leaf Optical Properties Model Separating Photosynthetic Pigments, Remote Sensing of Environment

direct and diffuse light

Description

direct and diffuse light

Usage

data(solar)

details

***********************************************************************

• [1] = direct light

• [2] = diffuse light

references

Feret et al. (2008), PROSPECT-4 and 5: Advances in the Leaf Optical Properties Model Separating Photosynthetic Pigments, Remote Sensing of Environment