Package: PEcAnRTM 1.9.1.9000

Alexey Shiklomanov

PEcAnRTM: PEcAn Functions Used for Radiative Transfer Modeling

Functions for performing forward runs and inversions of radiative transfer models (RTMs). Inversions can be performed using maximum likelihood, or more complex hierarchical Bayesian methods. Underlying numerical analyses are optimized for speed using Fortran code.

Authors:Mike Dietze [aut], Shawn Serbin [aut], Alexey Shiklomanov [aut, cre], University of Illinois, NCSA [cph]

PEcAnRTM_1.9.1.9000.tar.gz

PEcAnRTM_1.9.1.9000.tgz(r-4.6-x86_64)PEcAnRTM_1.9.1.9000.tgz(r-4.6-arm64)PEcAnRTM_1.9.1.9000.tgz(r-4.5-x86_64)PEcAnRTM_1.9.1.9000.tgz(r-4.5-arm64)
PEcAnRTM_1.9.1.9000.tar.gz(r-4.7-arm64)PEcAnRTM_1.9.1.9000.tar.gz(r-4.7-x86_64)PEcAnRTM_1.9.1.9000.tar.gz(r-4.6-arm64)PEcAnRTM_1.9.1.9000.tar.gz(r-4.6-x86_64)
PEcAnRTM_1.9.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
PEcAnRTM/json (API)

# Install 'PEcAnRTM' in R:

install.packages('PEcAnRTM', repos = c('https://pecanproject.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pecanproject/pecan/issues

Uses libs:

jags– Just Another Gibbs Sampler for Bayesian MCMC
c++– GNU Standard C++ Library v3

On CRAN:

radiative-transfer-modeling bayesian-inversion pecan bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation plants glibc jags cpp

9.93 score 237 stars 143 scripts 45 exports 248 dependencies

Last updated from:770075d62a. Checks:11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	WARNING	209
linux-devel-x86_64	WARNING	199
source / vignettes	OK	310
linux-release-arm64	WARNING	238
linux-release-x86_64	WARNING	211
macos-release-arm64	WARNING	94
macos-release-x86_64	WARNING	211
macos-oldrel-arm64	WARNING	107
macos-oldrel-x86_64	WARNING	182
windows-devel	WARNING	136
windows-release	WARNING	141
windows-oldrel	WARNING	108
wasm-release	OK	211

Exports:burnin.thin check.convergence default.settings.prospect defparam dtnorm EDR EDR.preprocess.history fortran_data_module foursail generalized_plate_model generate.noise get.EDR.output invert_bt invert.auto invert.custom invert.lsq is_spectra load.from.name lognorm.mu lognorm.sigma matplot neff params.prospect4 params.prospect5 params.prospect5b params.prospectd params2edr print_results_summary prior.defaultvals.prospect priorfunc.prospect pro2s pro4sail pro4saild prospect prospect_bt_prior resample rtnorm sensor.list sensor.proper setup_edr spectra spectral.response summary_mvnorm summary_simple wavelengths

Dependencies:abind alabama amerifluxr ape arrow askpass assertthat base64enc BayesianTools bigleaf bit bit64 bitops blob boot bridgesampling Brobdingnag bslib ca cachem callr cellranger class classInt cli clipr clue cluster coda codetools colorspace commonmark cpp11 crayon crosstalk curl data.table DBI dbplyr dendextend DEoptimR DHARMa diagram digest doParallel dplyr dtw dtwclust duckdb e1071 egg ellipse emulator evaluate expm farver fastmap flexclust fontawesome foreach fs furrr future future.apply gap gap.datasets gclus generics geonames ggplot2 ggrepel globals glue gmm gridExtra gtable heatmaply here highr hms htmltools htmlwidgets httpuv httr httr2 IDPmisc isoband iterators jquerylib jsonlite KernSmooth knitr labeling later lattice lava lazyeval lifecycle listenv lme4 lmtest lqmm lubridate magrittr MASS Matrix MatrixModels mcmc MCMCpack memoise mgcv mime minqa mlegp modeltools MODISTools msm mvtnorm ncdf4 nleqslv nlme nloptr numbers numDeriv openssl optparse otel parallelly PEcAn.assim.batch PEcAn.benchmark PEcAn.data.atmosphere PEcAn.data.land PEcAn.data.remote PEcAn.DB PEcAn.emulator PEcAn.logger PEcAn.MA PEcAn.priors PEcAn.remote PEcAn.settings PEcAn.uncertainty PEcAn.utils PEcAn.workflow permute pillar pkgconfig plotly plyr png prettyunits processx prodlim progress progressr promises proxy ps purrr qap qgam qrng quantreg R.methodsS3 R.oo R.utils R6 randtoolbox rappdirs raster rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel RcppThread RcppTOML RCurl Rdpack readr readxl REddyProc reformulas registry rematch reshape2 reticulate rjags rjson rlang rmarkdown rngWELL robustbase rprojroot RSpectra s2 S7 sandwich sass scales sensitivity seriation sf shape shiny shinyjs SimilarityMeasures solartime sourcetools sp spacefillr SparseGrid SparseM SQUAREM stringi stringr suntools survival sys terra tibble tidyr tidyselect timechange tinytex tmvtnorm triebeard TruncatedNormal truncnorm TSP tzdb units urltools utf8 vctrs vegan viridis viridisLite vroom webshot withr wk xfun XML xtable xts yaml zoo

The PEcAn RTM package

Introduction | Installation | Overview of features | Simulating reflectance | Inversion

Rendered frompecanrtm.vignette.Rmdusingknitr::rmarkdown

Last update: 2025-05-25
Started: 2015-07-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Select spectra	[.spectra
Select spectra by wavelength	[[.spectra
Assign values to spectra by wavelength	[[<-.spectra
Burn-in and thinning of MCMC samples	burnin.thin
Combine spectra by wavelength	cbind.spectra
Check convergence of multiple MCMC chains	check.convergence
Defult inversion settings for PROSPECT 5 models	default.settings.prospect
Get default parameters	defparam
Truncated normal distribution density	dtnorm
ED radiative transfer module (EDR) wrapper function	EDR
Preprocess history file for EDR	EDR.preprocess.history
List to FORTRAN data module	fortran_data_module
SAIL model	foursail
Generalized plate model	generalized_plate_model
Generate autocorrelated spectral noise	generate.noise
Read EDR output	get.EDR.output
Perform Bayesian inversion using BayesianTools package	invert_bt
Inversion with automatic convergence checking	invert.auto
Bayesian inversion of a model	invert.custom
Least squares model inversion	invert.lsq
Load object from an RData file	load.from.name
Functions for default priors Lognormal mean parameters	lognorm.mu
Lognormal sigma parameter	lognorm.sigma
Matplot generic method	matplot
Matplot default method	matplot.default
Plot multiple spectra on same graph	matplot.spectra
Effective sample size	neff
PROSPECT 4 parameters	params.prospect4
PROSPECT 5 parameters	params.prospect5
PROSPECT 5B parameters	params.prospect5b
PROSPECT D parameters	params.prospectd
Convert named parameter vector to EDR-compatible inputs	params2edr
Plot spectra vs. wavelength	plot.spectra
Neatly print inversion results summary	print_results_summary
Print method for spectra S3 class	print.spectra
Default prior parameters for PROSPECT models	prior.defaultvals.prospect
Default PROSPECT 5 prior function	priorfunc.prospect
Coupled PROSPECT-Two-stream model	pro2s
PRO4SAIL model	pro4sail
PRO4SAILD model	pro4saild
PROSPECT (4, 5, or 5B) model	prospect
Quick BayesianTools prior creator for PROSPECT model	prospect_bt_prior
Read and process RSR data from directory	read.rsr.folder
Resample vector, matrix, or spectra	resample resample.default resample.matrix resample.spectra
Generate relative spectral response (RSR) matrix based on FWHM data	rsr.from.fwhm
Generic log-likelihood generator for RTMs	rtm_loglike
Random sampling from one-sided truncated normal distribution	rtnorm
Sensor spectral response functions	sensor.list
Sensor list with proper names	sensor.proper
Setup EDR run	setup_edr
Spectra S3 class	is_spectra spectra
Convolution of spectra to sensor RSR	spectral.response
Structure of 'spectra' object	str.spectra
Multivariate normal fit	summary_mvnorm
Simple summary statistics on MCMC samples	summary_simple
Trim RSR matrix to wavelength limits	trim.rsr
Retrieve wavelengths from spectra object	wavelengths