Package: PEcAnRTM 1.7.3.9000

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_1.7.3.9000.tar.gz

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PEcAnRTM.pdf |PEcAnRTM.html✨
PEcAnRTM/json (API)
NEWS

# 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

Datasets:

On CRAN:

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

9.65 score 203 stars 132 scripts 45 exports 277 dependencies

Last updated 2 days agofrom:cab30e89b4. Checks:OK: 1 WARNING: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 20 2024
R-4.5-linux-x86_64	WARNING	Nov 20 2024
R-4.4-mac-x86_64	WARNING	Nov 20 2024
R-4.4-mac-aarch64	WARNING	Nov 20 2024
R-4.3-mac-x86_64	WARNING	Nov 20 2024
R-4.3-mac-aarch64	WARNING	Nov 20 2024

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 admisc alabama amerifluxr ape arrow askpass assertthat base64enc BayesianTools bigleaf bit bit64 bitops blob boot bridgesampling Brobdingnag bslib ca cachem callr CDM cellranger class classInt cli clipr clue cluster coda codetools colorspace commonmark cpp11 crayon crosstalk crul curl data.table DBI dbplyr deldir dendextend DEoptimR DHARMa diagram digest doParallel downloader dplR dplyr duckdb duckdbfs e1071 egg ellipse emulator evaluate expm fansi farver fastmap fauxpas fBasics fontawesome foreach fs furrr future future.apply gap gap.datasets gclus generics geonames getopt ggplot2 ggrepel globals glue gmm gridExtra gss gtable HDInterval heatmaply highr hms htmltools htmlwidgets httpcode httpuv httr IDPmisc igraph isoband iterators jquerylib jsonlite KernSmooth kknn knitr labeling later lattice lava lazyeval lifecycle listenv lme4 lmtest lqmm lubridate magrittr MASS Matrix MatrixModels matrixStats mcmc MCMCpack memoise mgcv mime minqa mlegp modeest msm munsell mvtnorm ncdf4 neonstore neonUtilities nleqslv nlme nloptr nneo numDeriv openssl optparse parallelly pbapply pbv PEcAn.assim.batch PEcAn.benchmark PEcAn.data.atmosphere PEcAn.data.land PEcAn.DB PEcAn.emulator PEcAn.logger PEcAn.MA PEcAn.priors PEcAn.remote PEcAn.settings PEcAn.uncertainty PEcAn.utils PEcAn.visualization PEcAn.workflow permute pillar pkgconfig plotly plyr png polyclip polycor 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 RCurl Rdpack readr readxl REddyProc registry rematch reshape2 rjags rjson rlang rmarkdown rmutil rngWELL robustbase rpart runjags s2 sandwich sass scales seriation sf shape shiny signal SimilarityMeasures sirt solartime sourcetools sp spacefillr SparseGrid SparseM spatial spatstat.data spatstat.geom spatstat.univar spatstat.utils SQUAREM stable stabledist statip storr stringi stringr suntools survival swfscMisc sys TAM terra thor tibble tidyr tidyselect timechange timeDate timeSeries tinytex tmvtnorm traits triebeard TruncatedNormal truncnorm TSP tzdb units urltools utf8 vctrs vegan viridis viridisLite vroom webshot whisker withr wk xfun XML xtable xts yaml zip zoo

The PEcAn RTM package

Alexey Shiklomanov

Rendered frompecanrtm.vignette.Rmdusingknitr::rmarkdownon Nov 20 2024.

Last update: 2024-09-06
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