Package: ccrtm 0.4.1

ccrtm: Coupled Chain Radiative Transfer Models

A set of radiative transfer models to quantitatively describe the absorption, reflectance and transmission of solar energy in vegetation, and model remotely sensed spectral signatures of vegetation at distinct spatial scales (leaf,canopy and stand). The main principle behind ccrtm is that many radiative transfer models can form a coupled chain, basically models that feed into each other in a linked chain (from leaf, to canopy, to stand, to atmosphere). It allows the simulation of spectral datasets in the solar spectrum (400-2500nm) using leaf models as PROSPECT5, 5b, and D which can be coupled with canopy models as 'FLIM', 'SAIL','SAIL2' and 'INFORM' for top of canopy reflectance, and with atmospheric models such as 'SKYL'and 'SMAC' for calculation of top of the atmosphere reflectance. All models can run in forward mode, and a selection are invertable (backward simulations) if provided with spectral data. Jacquemoud et al 2008 provides a comprehensive overview of these and other models <doi:10.1016/j.rse.2008.01.026>.

Authors:Marco D. Visser [aut, cre]

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ccrtm.pdf |ccrtm.html
ccrtm/json (API)

# Install 'ccrtm' in R:
install.packages('ccrtm', repos = c('https://marcodvisser.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/marcodvisser/ccrtm/issues

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:
  • data_prospect5 - Refractive index and specific absorption coefficients for PROSPECT 5
  • data_prospectd - Refractive index and specific absorption coefficients for PROSPECT D
  • soil - Soil reflectance
  • solar - Direct and diffuse light

On CRAN:

3.81 score 13 stars 1 scripts 207 downloads 14 exports 34 dependencies

Last updated 1 years agofrom:1ce276fa46. Checks:OK: 1 WARNING: 8. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 08 2024
R-4.5-win-x86_64WARNINGOct 08 2024
R-4.5-linux-x86_64WARNINGOct 08 2024
R-4.4-win-x86_64WARNINGOct 08 2024
R-4.4-mac-x86_64WARNINGOct 08 2024
R-4.4-mac-aarch64WARNINGOct 08 2024
R-4.3-win-x86_64WARNINGOct 08 2024
R-4.3-mac-x86_64WARNINGOct 08 2024
R-4.3-mac-aarch64WARNINGOct 08 2024

Exports:bRTMcambellcdcumflimfoursailfoursail2foursail2bfRTMgetDefaultsKLdlidfprospect5prospectdskyl

Dependencies:briocallrclicrayondescdiffobjdigestevaluateexpintfansifsgluejsonlitelifecyclemagrittrpillarpkgbuildpkgconfigpkgloadpracmapraiseprocessxpsR6Rcpprematch2rlangrprojroottestthattibbleutf8vctrswaldowithr

Readme and manuals

Help Manual

Help pageTopics
Backward implementation (inversion) of coupled Radiative Transfer Models.bRTM
Leaf inclination distribution function Ellipsoidal distribution functioncambell
ccrtm: Coupled Chain Radiative Transfer Models.ccrtm
Leaf inclination distribution function cummulative lagden function from Wout Verhoef's dissertation Extended here for any anglecdcum
Function to check and return parameterscheckPars
refractive index and specific absorption coefficients for PROSPECT 5data_prospect5
refractive index and specific absorption coefficients for PROSPECT Ddata_prospectd
d = stand density (d) cd = crown diameter (cd) h = mean crown height (h) lai = leaf area index (lai) alpha = light extinction coefficient (alpha) tts = Solar zenith angle (tts) tto = Observer zenith angle (tto) psi = Sun-sensor azimuth angle (psi)defaults.flim
eigen decomposition for PROSPECT5eigenRb
eigen decomposition for PROSPECTDeigenRd
Forest Light Interaction Model (FLIM)flim
Optimized R implementation of foursail (4SAIL)foursail
R implementation of the foursail2 model with 2 canopy layers.foursail2
R implementation of the foursail2 model with 2 canopy layers.foursail2b
Forward implementation of coupled Radiative Transfer Models.fRTM
S3- methods for Generate defaults settings and parameters for all supported models. See ?ccrtm for details.getDefaults
invert a requested RTM (internal function)invertRTM
Kullback-Lieber divergence function D(spec1 || spec2) = sum(spec1 * log(spec1 / spec2))KLd
Leaf inclination distribution function models s3 method for calling leaf models.lidf
Bayesian fitted weight matrix for PROSPECT5model5
Bayesian fitted weight matrix for PROSPECTDmodeld
fitted weight matrix for PROSPECT5nn5b
fitted weight matrix for PROSPECTDnnd
Plot RTM return spectra vs. wavelengthplot.rtm.spectra
fitted PLSR for PROSPECT5plsr5
fitted PLSR for PROSPECTDplsrd
RTM inversionprint.rtm.inversion
RTM generic print functionprint.rtm.spectra
PROSPECT model version 5 and 5Bprospect5
PROSPECT model version Dprospectd
R implementation of foursail (pure R)r_foursail
run a requested RTM (internal function)runRTM
The SAIL BDRF functionsail_BDRF
Sky light modelskyl
soil reflectancesoil
direct and diffuse lightsolar
RTM inversion summarysummary.rtm.inversion