Package: PEcAn.assim.batch 1.8.0.9000

Istem Fer

PEcAn.assim.batch: PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Authors:Mike Dietze [aut], Istem Fer [aut, cre], Ryan Kelly [aut], University of Illinois, NCSA [cph]

# Install 'PEcAn.assim.batch' in R:

install.packages('PEcAn.assim.batch', 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:

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

57 exports 202 stars 6.35 score 308 dependencies 2 dependents 20 scripts

Last updated 5 hours agofrom:f22a7c4bbc. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 18 2024
R-4.5-win	NOTE	Sep 18 2024
R-4.5-linux	NOTE	Sep 18 2024
R-4.4-win	NOTE	Sep 18 2024
R-4.4-mac	NOTE	Sep 18 2024
R-4.3-win	NOTE	Sep 18 2024
R-4.3-mac	NOTE	Sep 18 2024

Exports:assim.batch autoburnin bounded calculate.prior correlationPlot ddist gelman_diag_gelmanPlot gelman_diag_mw generate_hierpost get_ss get_y getBurnin gpeval hier.mcmc is.accepted load_pda_history load.L2Ameriflux.cf load.pda.data makeMCMCList mcmc.GP minimize.GP pda.adjust.jumps pda.adjust.jumps.bs pda.autocorr.calc pda.bayesian.tools pda.calc.error pda.calc.llik pda.calc.llik.par pda.create.btprior pda.create.ensemble pda.define.llik.fn pda.define.prior.fn pda.emulator pda.emulator.ms pda.generate.externals pda.generate.knots pda.generate.sf pda.get.model.output pda.init.params pda.init.run pda.load.priors pda.mcmc pda.mcmc.bs pda.neff.calc pda.plot.params pda.postprocess pda.settings pda.settings.bt pda.sort.params prepare_pda_remote return_hyperpars return_multi_site_objects return.bias runModule.assim.batch sample_MCMC sync_pda_remote write_sf_posterior

Dependencies:abind admisc alabama amerifluxr ape arrow askpass assertthat backports base64enc BayesianTools bigleaf bit bit64 bitops blob boot bridgesampling Brobdingnag bslib ca cachem callr CDM cellranger checkmate class classInt cli clipr clue cluster coda codetools colorspace commonmark conditionz 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 fastmatch fauxpas fBasics fontawesome foreach foreign Formula fs furrr future future.apply gap gap.datasets gclus generics geonames getopt ggplot2 ggrepel globals glue gmm gridExtra gss gtable HDInterval heatmaply highr Hmisc hms hoardr htmlTable 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 natserv ncdf4 neonstore neonUtilities nleqslv nlme nloptr nneo nnet numDeriv openssl optparse parallelly pbapply pbv 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 phangorn pillar pkgconfig plotly plyr png polyclip polycor prettyunits processx prodlim progress progressr promises proxy ps purrr qap qgam qrng quadprog quantreg R.methodsS3 R.oo R.utils R6 randtoolbox rappdirs raster ratelimitr rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readr readxl REddyProc registry rematch rentrez reshape2 rex ritis rjags rjson rlang rmarkdown rmutil rncl rngWELL robustbase rotl rpart rredlist rstudioapi runjags rvest s2 sandwich sass scales selectr seriation sf shape shiny signal SimilarityMeasures sirt solartime solrium 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 taxize terra thor tibble tidyr tidyselect timechange timeDate timeSeries tinytex tmvtnorm traits triebeard TruncatedNormal truncnorm TSP tzdb units urltools utf8 uuid vctrs vegan viridis viridisLite vroom webshot whisker WikidataQueryServiceR WikidataR WikipediR wikitaxa withr wk worrms xfun XML xml2 xtable xts yaml zip zoo

Multi-site hierarchical calibration vignette

Istem Fer

Rendered fromMultiSitePDAVignette.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2020-01-27
Started: 2020-01-27

PEcAn.assim.batch Vignette

Istem Fer, Ryan Kelly

Rendered fromAssimBatchVignette.Rmdusingknitr::rmarkdownon Sep 18 2024.

Last update: 2022-04-06
Started: 2015-07-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Run Batch PDA	assim.batch
Automatically calculate and apply burnin value	autoburnin
bounded	bounded
calculate.prior	calculate.prior
Flexible function to create correlation density plots	correlationPlot
ddist	ddist
Calculate Gelman Diagnostic using coda::gelman.plot	gelman_diag_gelmanPlot
Calculate Gelman diagnostic on moving window	gelman_diag_mw
Helper function that generates the hierarchical posteriors	generate_hierpost
get_ss	get_ss
get_y	get_y
Calculate burnin value	getBurnin
gpeval	gpeval
Hierarchical MCMC using emulator	hier.mcmc
is.accepted	is.accepted
Helper function that loads history from previous PDA run, but returns only requested objects	load_pda_history
Load Ameriflux L2 Data From NetCDF	load.L2Ameriflux.cf load.pda.data
Make MCMC list from samples list	makeMCMCList
mcmc.GP	mcmc.GP
minimize.GP	minimize.GP
Adjust PDA MCMC jump size	pda.adjust.jumps
Adjust PDA block MCMC jump size	pda.adjust.jumps.bs
autocorrelation correction	pda.autocorr.calc
Paramater Data Assimilation using BayesianTools	pda.bayesian.tools
Calculate sufficient statistics	pda.calc.error
Calculate Likelihoods for PDA	pda.calc.llik
pda.calc.llik.par	pda.calc.llik.par
Create priors for BayesianTools	pda.create.btprior
Create ensemble record for PDA ensemble	pda.create.ensemble
Define PDA Likelihood Functions	pda.define.llik.fn
Define PDA Prior Functions	pda.define.prior.fn
Paramater Data Assimilation using emulator	pda.emulator
Paramater Data Assimilation using emulator on multiple sites in three modes: local, global, hierarchical First draft, not complete yet	pda.emulator.ms
This is a helper function for preparing PDA external objects, but it doesn't cover all the cases yet, use it with care You can use this function just to generate either one of the external.* PDA objects, but note that some args cannot be blank depending on what you aim to generate	pda.generate.externals
Generate Parameter Knots for PDA Emulator	pda.generate.knots
Generate scaling factor knots for PDA Emulator	pda.generate.sf
Get Model Output for PDA	pda.get.model.output
Initialise Parameter Matrix for PDA	pda.init.params
Initialise Model Runs for PDA	pda.init.run
Load Priors for Paramater Data Assimilation	pda.load.priors
Paramater Data Assimilation using MCMC	pda.mcmc
Paramater Data Assimilation using MCMC	pda.mcmc.bs
Clean up a failed PDA run	pda.mcmc.recover
Calculate N_eff	pda.neff.calc
Plot PDA Parameter Diagnostics	pda.plot.params
Postprocessing for PDA Results	pda.postprocess
Set PDA Settings	pda.settings
Apply settings for BayesianTools	pda.settings.bt
Function to sort Hierarchical MCMC samples	pda.sort.params
helper function for submitting remote pda runs	prepare_pda_remote
return_hyperpars	return_hyperpars
This is a helper function partly uses pda.emulator code	return_multi_site_objects
return.bias	return.bias
Run Batch module	runModule.assim.batch
Helper function to sample from previous MCMC chain while proposing new knots	sample_MCMC
helper function for syncing remote pda runs this function resembles remote.copy.from but we don't want to sync everything back	sync_pda_remote
Function to write posterior distributions of the scaling factors	write_sf_posterior