├── .dockerignore ├── .gitattributes ├── .github ├── ISSUE_TEMPLATE.md ├── ISSUE_TEMPLATE │ ├── Bug_report.md │ ├── Doc_changes.md │ └── Feature_request.md ├── PULL_REQUEST_TEMPLATE.md ├── labeler.yml ├── settings.yml └── workflows │ ├── book.yml │ ├── check.yml │ ├── ci-weekly.yml │ ├── ci.yml │ ├── docker-build-image.yml │ ├── docker-stack-sipnet.yml │ ├── docker.yml │ ├── download-met-data.yml │ ├── integration-test.yml │ ├── pkgdown.yml │ ├── prlabeler.yml │ ├── render-quarto.yml │ ├── sipnet.yml │ ├── stale.yml │ ├── styler-actions.yml │ └── test.yml ├── .gitignore ├── .prettierignore ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── DEBUGING.md ├── DEV-INTRO.md ├── LICENSE ├── Makefile ├── Makefile.depends ├── README.md ├── apps └── api │ ├── Dockerfile │ ├── R │ ├── auth.R │ ├── available-models.R │ ├── entrypoint.R │ ├── formats.R │ ├── general.R │ ├── get.file.R │ ├── inputs.R │ ├── ma.R │ ├── models.R │ ├── pfts.R │ ├── posteriors.R │ ├── runs.R │ ├── sites.R │ ├── submit.workflow.R │ └── workflows.R │ ├── README.md │ ├── pecanapi-spec.yml │ ├── test_pecanapi.sh │ └── tests │ ├── alltests.R │ ├── test.auth.R │ ├── test.formats.R │ ├── test.inputs.R │ ├── test.models.R │ ├── test.pfts.R │ ├── test.ping.R │ ├── test.runs.R │ ├── test.sites.R │ ├── test.status.R │ ├── test.workflows.R │ ├── test_workflows │ ├── api.sipnet.json │ └── api.sipnet.xml │ └── testthat.R ├── base ├── all │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── datasets.R │ │ ├── pecan_version.R │ │ └── version.R │ ├── README.md │ ├── data-raw │ │ ├── record_previous_releases.R │ │ └── record_versions.R │ ├── data │ │ ├── pecan_releases.R │ │ ├── pecan_releases.csv │ │ ├── pecan_version_history.R │ │ └── pecan_version_history.csv │ ├── inst │ │ └── CITATION │ ├── man │ │ ├── pecan_releases.Rd │ │ ├── pecan_version.Rd │ │ └── pecan_version_history.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── test-pecan_version.R │ │ └── test.workflow.R ├── db │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── PEcAn.DB-package.R │ │ ├── assign.treatments.R │ │ ├── check.lists.R │ │ ├── check_missing_files.R │ │ ├── clone_pft.R │ │ ├── convert_input.R │ │ ├── covariate.functions.R │ │ ├── db_merge_into.R │ │ ├── dbfiles.R │ │ ├── derive.trait.R │ │ ├── derive.traits.R │ │ ├── fetch.stats2se.R │ │ ├── get.trait.data.R │ │ ├── get.trait.data.pft.R │ │ ├── get_machine_info.R │ │ ├── get_postgres_envvars.R │ │ ├── input.name.check.R │ │ ├── insert.format.vars.R │ │ ├── insert_table.R │ │ ├── met_inputs.R │ │ ├── pft.add.spp.R │ │ ├── query.data.R │ │ ├── query.dplyr.R │ │ ├── query.file.path.R │ │ ├── query.format.vars.R │ │ ├── query.pft.R │ │ ├── query.prior.R │ │ ├── query.site.R │ │ ├── query.trait.data.R │ │ ├── query.traits.R │ │ ├── query.yields.R │ │ ├── query_pfts.R │ │ ├── search_references.R │ │ ├── stamp.R │ │ ├── symmetric_setdiff.R │ │ ├── take.samples.R │ │ ├── try2sqlite.R │ │ ├── update_ensemble_writes.R │ │ ├── utils_db.R │ │ └── version.R │ ├── README.md │ ├── inst │ │ ├── PFT_builder │ │ │ └── PFT_builder.R │ │ ├── bety_mstmip_lookup.csv │ │ ├── import-ForestGEO │ │ │ ├── ForestGEO_spp_website.csv │ │ │ └── import_species_list.R │ │ └── import-try │ │ │ ├── .gitignore │ │ │ ├── 01_try_sqlite.R │ │ │ ├── 02_citations.R │ │ │ ├── 91.global.subset.R │ │ │ ├── 92.data.specific.subset.R │ │ │ ├── 93.create.try.sites.R │ │ │ ├── 94.match.species.R │ │ │ ├── 95.citations.R │ │ │ ├── 96.load.data.R │ │ │ ├── README.md │ │ │ ├── bety_connect.R │ │ │ ├── common.R │ │ │ ├── config.R │ │ │ ├── helpers.species.R │ │ │ └── misc │ │ │ └── add.self.sql │ ├── man │ │ ├── PEcAn.DB-package.Rd │ │ ├── append.covariate.Rd │ │ ├── arrhenius.scaling.traits.Rd │ │ ├── assign.treatments.Rd │ │ ├── bety2pecan.Rd │ │ ├── betyConnect.Rd │ │ ├── check.lists.Rd │ │ ├── check_missing_files.Rd │ │ ├── clone_pft.Rd │ │ ├── convert_input.Rd │ │ ├── db.close.Rd │ │ ├── db.exists.Rd │ │ ├── db.getShowQueries.Rd │ │ ├── db.open.Rd │ │ ├── db.print.connections.Rd │ │ ├── db.query.Rd │ │ ├── db.showQueries.Rd │ │ ├── dbHostInfo.Rd │ │ ├── db_merge_into.Rd │ │ ├── dbfile.check.Rd │ │ ├── dbfile.file.Rd │ │ ├── dbfile.input.check.Rd │ │ ├── dbfile.input.insert.Rd │ │ ├── dbfile.insert.Rd │ │ ├── dbfile.move.Rd │ │ ├── dbfile.posterior.check.Rd │ │ ├── dbfile.posterior.insert.Rd │ │ ├── default_hostname.Rd │ │ ├── derive.trait.Rd │ │ ├── derive.traits.Rd │ │ ├── dplyr.count.Rd │ │ ├── fancy_scientific.Rd │ │ ├── fetch.stats2se.Rd │ │ ├── filter_sunleaf_traits.Rd │ │ ├── get.id.Rd │ │ ├── get.trait.data.Rd │ │ ├── get.trait.data.pft.Rd │ │ ├── get_machine_host.Rd │ │ ├── get_machine_info.Rd │ │ ├── get_postgres_envvars.Rd │ │ ├── get_run_ids.Rd │ │ ├── get_users.Rd │ │ ├── get_var_names.Rd │ │ ├── get_workflow_ids.Rd │ │ ├── insert.format.vars.Rd │ │ ├── insert_table.Rd │ │ ├── load_data_single_run.Rd │ │ ├── match_colnames.Rd │ │ ├── match_dbcols.Rd │ │ ├── met_inputs.Rd │ │ ├── ncdays2date.Rd │ │ ├── pft.add.spp.Rd │ │ ├── query.covariates.Rd │ │ ├── query.data.Rd │ │ ├── query.file.path.Rd │ │ ├── query.format.vars.Rd │ │ ├── query.pft_cultivars.Rd │ │ ├── query.pft_species.Rd │ │ ├── query.priors.Rd │ │ ├── query.site.Rd │ │ ├── query.trait.data.Rd │ │ ├── query.traits.Rd │ │ ├── query.yields.Rd │ │ ├── query_pfts.Rd │ │ ├── query_priors.Rd │ │ ├── reexports.Rd │ │ ├── runs.Rd │ │ ├── search_reference_single.Rd │ │ ├── search_references.Rd │ │ ├── stamp_started.Rd │ │ ├── symmetric_setdiff.Rd │ │ ├── take.samples.Rd │ │ ├── try2sqlite.Rd │ │ ├── update_ensemble_writes.Rd │ │ ├── var_names_all.Rd │ │ ├── workflow.Rd │ │ └── workflows.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── helper-db-setup.R │ │ │ ├── test-get.trait.data.pft.R │ │ │ ├── test-query.pft.R │ │ │ ├── test-query.traits.R │ │ │ ├── test.assign.treatments.R │ │ │ ├── test.check.lists.R │ │ │ ├── test.check.missing.files.R │ │ │ ├── test.contents_sanity.R │ │ │ ├── test.convert_input.R │ │ │ ├── test.covariate.functions.R │ │ │ ├── test.db.utils.R │ │ │ ├── test.dbfiles.R │ │ │ ├── test.derive.traits.R │ │ │ ├── test.insert.R │ │ │ ├── test.met_inputs.R │ │ │ ├── test.query.base.R │ │ │ ├── test.query.data.R │ │ │ ├── test.query.dplyr.R │ │ │ ├── test.query.file.path.R │ │ │ ├── test.query.priors.R │ │ │ ├── test.query.site.R │ │ │ ├── test.query.yields.R │ │ │ ├── test.query_pfts.R │ │ │ ├── test.stamp.R │ │ │ ├── test.symmetric-setdiff.R │ │ │ ├── test.take.samples.R │ │ │ └── test.utils_db.R │ └── vignettes │ │ ├── betydb_access.Rmd │ │ └── create_sites.geometry.Rmd ├── logger │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── logger.R │ │ ├── logifnot.R │ │ ├── print2string.R │ │ └── version.R │ ├── README.md │ ├── cran-comments.md │ ├── man │ │ ├── logger.debug.Rd │ │ ├── logger.error.Rd │ │ ├── logger.getLevel.Rd │ │ ├── logger.info.Rd │ │ ├── logger.message.Rd │ │ ├── logger.setLevel.Rd │ │ ├── logger.setOutputFile.Rd │ │ ├── logger.setQuitOnSevere.Rd │ │ ├── logger.setUseConsole.Rd │ │ ├── logger.setWidth.Rd │ │ ├── logger.severe.Rd │ │ ├── logger.warn.Rd │ │ ├── print2string.Rd │ │ └── severeifnot.Rd │ └── tests │ │ └── testthat │ │ ├── test.logger.R │ │ ├── test.logifnot.R │ │ └── test.print2string.R ├── qaqc │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── cull_database_entries.R │ │ ├── find_formats_without_inputs.R │ │ ├── find_inputs_without_formats.R │ │ ├── get_table_column_names.R │ │ ├── taylor.plot.R │ │ ├── version.R │ │ └── write_out_table.R │ ├── README.Rmd │ ├── README.md │ ├── inst │ │ └── extdata │ │ │ ├── data.csv │ │ │ ├── ebifarm │ │ │ ├── ed2in-template-pavi │ │ │ ├── fast │ │ │ │ ├── misi.xml │ │ │ │ └── pavi.xml │ │ │ ├── post │ │ │ │ └── pavi.xml │ │ │ └── prior │ │ │ │ └── pavi.xml │ │ │ ├── extdata.R │ │ │ └── testdata1.csv │ ├── man │ │ ├── cull_database_entries.Rd │ │ ├── find_formats_without_inputs.Rd │ │ ├── find_inputs_without_formats.Rd │ │ ├── get_table_column_names.Rd │ │ ├── new.taylor.Rd │ │ └── write_out_table.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── _snaps │ │ │ └── taylorplot │ │ │ │ └── taylor-diagram.svg │ │ │ ├── test-taylorplot.R │ │ │ ├── test.cull_database_entries.R │ │ │ ├── test.find_formats_without_inputs.R │ │ │ ├── test.find_inputs_without_formats.R │ │ │ ├── test.get_table_column_names.R │ │ │ └── test.write_out_table.R │ └── vignettes │ │ ├── Pre-release-database-cleanup.Rmd │ │ ├── function_relationships.Rmd │ │ └── module_output.Rmd ├── remote │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── check_model_run.R │ │ ├── check_qsub_status.R │ │ ├── fqdn.R │ │ ├── is.localhost.R │ │ ├── kill.tunnel.R │ │ ├── merge_job_files.R │ │ ├── open.tunnel.R │ │ ├── qsub_get_jobid.R │ │ ├── qsub_parallel.R │ │ ├── rabbitmq.R │ │ ├── remote.copy.from.R │ │ ├── remote.copy.to.R │ │ ├── remote.execute.R.R │ │ ├── remote.execute.cmd.R │ │ ├── setup_modellauncher.R │ │ ├── start_qsub.R │ │ ├── start_rabbitmq.R │ │ ├── start_serial.R │ │ ├── test_remote.R │ │ └── version.R │ ├── README.md │ ├── man │ │ ├── check_model_run.Rd │ │ ├── fqdn.Rd │ │ ├── is.localhost.Rd │ │ ├── kill.tunnel.Rd │ │ ├── merge_job_files.Rd │ │ ├── open_tunnel.Rd │ │ ├── qsub_get_jobid.Rd │ │ ├── qsub_parallel.Rd │ │ ├── qsub_run_finished.Rd │ │ ├── rabbitmq_create_queue.Rd │ │ ├── rabbitmq_get_message.Rd │ │ ├── rabbitmq_parse_uri.Rd │ │ ├── rabbitmq_post_message.Rd │ │ ├── rabbitmq_send_message.Rd │ │ ├── remote.copy.from.Rd │ │ ├── remote.copy.to.Rd │ │ ├── remote.execute.R.Rd │ │ ├── remote.execute.cmd.Rd │ │ ├── setup_modellauncher.Rd │ │ ├── start_qsub.Rd │ │ ├── start_rabbitmq.Rd │ │ ├── start_serial.Rd │ │ └── test_remote.Rd │ └── tests │ │ ├── testthat.R │ │ └── testthat │ │ ├── test-fqdn.R │ │ ├── test.check_model_run.R │ │ ├── test.check_qsub.R │ │ ├── test.kill.tunnel.R │ │ ├── test.localhost.R │ │ ├── test.qsub_get_jobid.R │ │ ├── test.rabbitmq.R │ │ ├── test.remote.R │ │ ├── test.remote.copy.from.R │ │ ├── test.remote.copy.to.R │ │ ├── test.remote.execute.R.R │ │ ├── test.remote.execute.cmd.R │ │ ├── test.start_qsub.R │ │ ├── test.start_rabbitmq.R │ │ └── test.start_serial.R ├── settings │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── MultiSettings.R │ │ ├── SafeList.R │ │ ├── Settings.R │ │ ├── addSecrets.R │ │ ├── check.all.settings.R │ │ ├── clean.settings.R │ │ ├── createMultisiteMultiSettings.r │ │ ├── fix.deprecated.settings.R │ │ ├── get_args.R │ │ ├── inst │ │ │ └── tests │ │ │ │ └── test.xml │ │ ├── known_bety_migrations.R │ │ ├── listToXml.R │ │ ├── loadPath_sitePFT.R │ │ ├── papply.R │ │ ├── pft_site_linker.R │ │ ├── prepare.settings.R │ │ ├── read.settings.R │ │ ├── setEnsemblePaths.R │ │ ├── site_pft_link_settings.R │ │ ├── update.settings.R │ │ ├── version.R │ │ └── write.settings.R │ ├── README.md │ ├── examples │ │ ├── examples.MultiSite.MultiSettings.r │ │ └── examples.papply.R │ ├── man │ │ ├── MultiSettings.Rd │ │ ├── SafeList.Rd │ │ ├── Settings.Rd │ │ ├── addSecrets.Rd │ │ ├── build_pathset.Rd │ │ ├── cash-.SafeList.Rd │ │ ├── check.bety.version.Rd │ │ ├── check.database.Rd │ │ ├── check.database.settings.Rd │ │ ├── check.ensemble.settings.Rd │ │ ├── check.inputs.Rd │ │ ├── check.model.settings.Rd │ │ ├── check.run.settings.Rd │ │ ├── check.settings.Rd │ │ ├── check.workflow.settings.Rd │ │ ├── clean.settings.Rd │ │ ├── createMultiSiteSettings.Rd │ │ ├── createSitegroupMultiSettings.Rd │ │ ├── expandMultiSettings.Rd │ │ ├── fix.deprecated.settings.Rd │ │ ├── getRunSettings.Rd │ │ ├── get_args.Rd │ │ ├── listToXml.Rd │ │ ├── listToXml.default.Rd │ │ ├── loadPath.sitePFT.Rd │ │ ├── papply.Rd │ │ ├── prepare.settings.Rd │ │ ├── printAll.Rd │ │ ├── read.settings.Rd │ │ ├── setDates.Rd │ │ ├── setEnsemblePaths.Rd │ │ ├── setOutDir.Rd │ │ ├── settingNames.Rd │ │ ├── site.pft.link.settings.Rd │ │ ├── site.pft.linkage.Rd │ │ ├── update.settings.Rd │ │ └── write.settings.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── data │ │ ├── testinput.pecan2.bu.edu.xml │ │ ├── testinput.xml │ │ ├── testinputcleanup.xml │ │ ├── testsettings-comment.xml │ │ └── testsettings.xml │ │ ├── helper-get.test.settings.R │ │ ├── test.MultiSettings.class.R │ │ ├── test.Safelist.class.R │ │ ├── test.Settings.class.R │ │ ├── test.addSecrets.R │ │ ├── test.check.all.settings.R │ │ ├── test.check.bety.version.R │ │ ├── test.clean.settings.R │ │ ├── test.createMultisiteMultiSettings.R │ │ ├── test.fix.deprecated.settings.R │ │ ├── test.get_args.R │ │ ├── test.listToXml.R │ │ ├── test.loadPath_sitePFT.R │ │ ├── test.papply.R │ │ ├── test.pft_site_linker.R │ │ ├── test.read.settings.R │ │ ├── test.setEnsemblePaths.R │ │ ├── test.site_pft_link_settings.R │ │ └── test.write.settings.R ├── utils │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── Defunct.R │ │ ├── cf2date.R │ │ ├── clear.scratch.R │ │ ├── combine_model_netcdf.R │ │ ├── datasets.R │ │ ├── days_in_year.R │ │ ├── distn.stats.R │ │ ├── download.url.R │ │ ├── full.path.R │ │ ├── get.ensemble.inputs.R │ │ ├── help.R │ │ ├── listToArgString.R │ │ ├── load_local.R │ │ ├── mail.R │ │ ├── match_file.R │ │ ├── mcmc.list2init.R │ │ ├── n_leap_day.R │ │ ├── nc_write_varfiles.R │ │ ├── need_packages.R │ │ ├── r2bugs.distributions.R │ │ ├── read.output.R │ │ ├── read_web_config.R │ │ ├── remove.config.R │ │ ├── seconds_in_year.R │ │ ├── status.R │ │ ├── timezone_hour.R │ │ ├── to_nc.R │ │ ├── transformstats.R │ │ ├── ud_convert.R │ │ ├── unit_is_parseable.R │ │ ├── units_are_equivalent.R │ │ ├── utils.R │ │ ├── version.R │ │ └── write.config.utils.R │ ├── README.md │ ├── data │ │ ├── standard_vars.R │ │ ├── standard_vars.csv │ │ └── trait.dictionary.csv │ ├── inst │ │ ├── LBNL_remote_test.R │ │ ├── clear.scratch.sh │ │ └── test-data │ │ │ └── CRUNCEP.2000.nc │ ├── man │ │ ├── PEcAn.Rd │ │ ├── PEcAn.utils-defunct.Rd │ │ ├── arrhenius.scaling.Rd │ │ ├── as.sequence.Rd │ │ ├── bibtexify.Rd │ │ ├── bugs.rdist.Rd │ │ ├── capitalize.Rd │ │ ├── cf2datetime.Rd │ │ ├── clear.scratch.Rd │ │ ├── convert.expr.Rd │ │ ├── datetime2cf.Rd │ │ ├── datetime2doy.Rd │ │ ├── days_in_year.Rd │ │ ├── distn.stats.Rd │ │ ├── distn.table.stats.Rd │ │ ├── download.url.Rd │ │ ├── download_file.Rd │ │ ├── extract_nc_sda.Rd │ │ ├── full.path.Rd │ │ ├── get.ensemble.inputs.Rd │ │ ├── get.parameter.stat.Rd │ │ ├── get.quantiles.Rd │ │ ├── get.run.id.Rd │ │ ├── get.sa.sample.list.Rd │ │ ├── get.sa.samples.Rd │ │ ├── get.stats.mcmc.Rd │ │ ├── left.pad.zeros.Rd │ │ ├── listToArgString.Rd │ │ ├── load.modelpkg.Rd │ │ ├── load_local.Rd │ │ ├── match_file.Rd │ │ ├── mcmc.list2init.Rd │ │ ├── met2model.exists.Rd │ │ ├── misc.are.convertible.Rd │ │ ├── misc.convert.Rd │ │ ├── mstmipvar.Rd │ │ ├── n_leap_day.Rd │ │ ├── nc_merge_all_sites_by_year.Rd │ │ ├── nc_merge_single_site.Rd │ │ ├── nc_write_varfiles.Rd │ │ ├── need_packages.Rd │ │ ├── newxtable.Rd │ │ ├── paste.stats.Rd │ │ ├── pdf.stats.Rd │ │ ├── r2bugs.distributions.Rd │ │ ├── read.output.Rd │ │ ├── read_web_config.Rd │ │ ├── retry.func.Rd │ │ ├── robustly.Rd │ │ ├── rsync.Rd │ │ ├── seconds_in_year.Rd │ │ ├── sendmail.Rd │ │ ├── ssh.Rd │ │ ├── standard_vars.Rd │ │ ├── status.Rd │ │ ├── summarize.result.Rd │ │ ├── tabnum.Rd │ │ ├── temp.settings.Rd │ │ ├── timezone_hour.Rd │ │ ├── to_ncdim.Rd │ │ ├── to_ncvar.Rd │ │ ├── trait.lookup.Rd │ │ ├── transformstats.Rd │ │ ├── tryl.Rd │ │ ├── ud_convert.Rd │ │ ├── unit_is_parseable.Rd │ │ ├── units_are_equivalent.Rd │ │ ├── vecpaste.Rd │ │ ├── zero.bounded.density.Rd │ │ └── zero.truncate.Rd │ ├── scripts │ │ ├── metutils.R │ │ └── time.constants.R │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── data │ │ ├── config.example.php │ │ ├── ensemble_fixtures │ │ │ ├── ENS-00001-e968e9c8f8574cb2 │ │ │ │ ├── 2019.nc │ │ │ │ └── 2020.nc │ │ │ ├── ENS-00001-ebb783e86d2ac6fb │ │ │ │ ├── 2019.nc │ │ │ │ └── 2020.nc │ │ │ ├── ENS-00002-e968e9c8f8574cb2 │ │ │ │ ├── 2019.nc │ │ │ │ └── 2020.nc │ │ │ ├── ENS-00002-ebb783e86d2ac6fb │ │ │ │ ├── 2019.nc │ │ │ │ └── 2020.nc │ │ │ └── make_ensemble_fixtures.sh │ │ ├── post.distns.RData │ │ └── prior.distns.RData │ │ ├── helper.R │ │ ├── test-combine_model_netcdf.R │ │ ├── test-nc_write_varfiles.R │ │ ├── test-read.output.R │ │ ├── test-status.R │ │ ├── test-ud_convert.R │ │ ├── test-unit_is_parseable.R │ │ ├── test.cf2date.R │ │ ├── test.clear.scratch.R │ │ ├── test.days_in_year.R │ │ ├── test.distn.stats.R │ │ ├── test.download.url.R │ │ ├── test.get.ensemble.inputs.R │ │ ├── test.listToArgString.R │ │ ├── test.load_local.R │ │ ├── test.n_leap_day.R │ │ ├── test.need_packages.R │ │ ├── test.r2bugs.distributions.R │ │ ├── test.read_web_config.R │ │ ├── test.seconds_in_year.R │ │ ├── test.sendmail.R │ │ ├── test.timezone_hour.R │ │ ├── test.trait.dictionary.R │ │ ├── test.units_are_equivalent.R │ │ └── test.utils.R ├── visualization │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── add_icon.R │ │ ├── ciEnvelope.R │ │ ├── map.output.R │ │ ├── plot_netcdf.R │ │ ├── plots.R │ │ ├── version.R │ │ └── visually.weighted.watercolor.plots.R │ ├── README.md │ ├── inst │ │ ├── extdata │ │ │ └── miscanthusyield.csv │ │ └── favicon.png │ ├── man │ │ ├── add_icon.Rd │ │ ├── ciEnvelope.Rd │ │ ├── data.fetch.Rd │ │ ├── dhist.Rd │ │ ├── iqr.Rd │ │ ├── map.output.Rd │ │ ├── plot_data.Rd │ │ ├── plot_netcdf.Rd │ │ ├── theme_border.Rd │ │ └── vwReg.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── data │ │ │ └── urbana_subdaily_test.nc │ │ │ ├── test.add_icon.R │ │ │ ├── test.plot_data.R │ │ │ ├── test.plot_netcdf.R │ │ │ └── test.viz.R │ └── vignettes │ │ └── usmap.Rmd └── workflow │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ ├── create_execute_test_xml.R │ ├── do_conversions.R │ ├── run.write.configs.R │ ├── runModule.get.trait.data.R │ ├── runModule.run.write.configs.R │ ├── start_model_runs.R │ └── version.R │ ├── README.md │ ├── inst │ ├── batch_run.R │ ├── default_tests.csv │ └── permutation_tests.R │ ├── man │ ├── create_execute_test_xml.Rd │ ├── do_conversions.Rd │ ├── model_specific_tags.Rd │ ├── run.write.configs.Rd │ ├── runModule.get.trait.data.Rd │ ├── runModule.run.write.configs.Rd │ └── start_model_runs.Rd │ └── tests │ ├── Rcheck_reference.log │ ├── testthat.R │ └── testthat │ ├── test-runModule.get.trait.data.R │ ├── test.do_conversions.R │ └── test.start_model_runs.R ├── book_source ├── .gitignore ├── 01_introduction │ ├── 00_introduction.Rmd │ ├── 01_project_overview.Rmd │ ├── 02_code_of_conduct.Rmd │ └── 03_how_to_use_book.Rmd ├── 02_demos_tutorials_workflows │ ├── 00_tutorials_demos_workflows.Rmd │ ├── 01_install_pecan.Rmd │ ├── 02_user_demos │ │ ├── 01_introductions_user.Rmd │ │ ├── 02_Demo_Basic_Run │ │ ├── 03_Demo_Uncertainty_Analysis │ │ ├── 04_other_vignettes │ │ │ ├── 00_other_vignettes.Rmd │ │ │ ├── 01_model-data_comparison.Rmd │ │ │ ├── 02_data_assimilation_concepts.Rmd │ │ │ ├── 03_parameter_data_assimilation.Rmd │ │ │ ├── 04_state-variable_data_assimilation.Rmd │ │ │ └── 05_pecan_sensitivity_vs_observation.Rmd │ │ └── 05_advanced_user_guide │ │ │ ├── 00_advanced_user_guide.Rmd │ │ │ ├── 93_workflow_curl.Rmd │ │ │ └── images │ │ │ ├── Input_ID_name.png │ │ │ ├── data-ingest │ │ │ ├── D1Ingest-1.gif │ │ │ ├── D1Ingest-9_sm.gif │ │ │ ├── DateTime.gif │ │ │ ├── Format-vars1.gif │ │ │ ├── Local_loader_sm.gif │ │ │ ├── Selectize_Input_sm.gif │ │ │ ├── local_browse.gif │ │ │ └── new_format_record.gif │ │ │ ├── example_data.png │ │ │ ├── format_record_1.png │ │ │ └── format_record_2.png │ ├── 03_web_workflow.Rmd │ ├── 04_more_web_interface │ │ ├── 00_intermediate_users_guide.Rmd │ │ ├── 01_additional_web_config.Rmd │ │ └── 02_hidden_analyses.Rmd │ └── 05_developer_workflows │ │ ├── 00_developer_guide.Rmd │ │ ├── 01_update_pecan_code.Rmd │ │ ├── 02_git │ │ ├── 00_git.Rmd │ │ ├── 01_using-git.Rmd │ │ └── 02_Github-issues.Rmd │ │ ├── 03_coding_practices │ │ ├── 00_coding_practices.Rmd │ │ ├── 01-coding-style.Rmd │ │ ├── 02-logging.Rmd │ │ ├── 03-package-data.Rmd │ │ └── 04-roxygen.Rmd │ │ ├── 04-testing.Rmd │ │ ├── 05-compile-pecan.Rmd │ │ └── 06-directory-structure.Rmd ├── 03_topical_pages │ ├── 00_topicalpages.Rmd │ ├── 02_pecan_standards.Rmd │ ├── 03_pecan_xml.Rmd │ ├── 04_R_workflow.Rmd │ ├── 05_models │ │ ├── 00_model_index.Rmd │ │ ├── 99_template.Rmd │ │ ├── biocro.Rmd │ │ ├── clm.Rmd │ │ ├── dalec.Rmd │ │ ├── ed.Rmd │ │ ├── gday.Rmd │ │ ├── ldndc.Rmd │ │ ├── linkages.Rmd │ │ ├── lpj-guess.Rmd │ │ ├── maespa.Rmd │ │ ├── preles.Rmd │ │ ├── sipnet.Rmd │ │ └── stics.Rmd │ ├── 06_data │ │ ├── 01_meteorology.Rmd │ │ └── 02_GFDL.Rmd │ ├── 07_remote_access │ │ └── 01_pecan_api.Rmd │ ├── 08_Database-Synchronization.Rmd │ ├── 09_standalone_tools.Rmd │ ├── 10_shiny │ │ └── shiny.Rmd │ ├── 11_adding_to_pecan.Rmd │ ├── 11_images │ │ ├── bety_main_page.png │ │ ├── bety_modeltype_1.png │ │ ├── bety_modeltype_2.png │ │ ├── bety_new_model.png │ │ ├── bety_pft_1.png │ │ ├── bety_pft_2.png │ │ ├── bety_pft_3.png │ │ ├── bety_priors_1.png │ │ ├── bety_priors_2.png │ │ ├── bety_priors_3.png │ │ ├── bety_priors_4.png │ │ ├── bety_priors_5.png │ │ ├── remotemodule.png │ │ └── var_record.png │ ├── 12_troubleshooting-pecan.Rmd │ ├── 14_backup.Rmd │ ├── 92_workflow_modules.Rmd │ ├── 93_installation │ │ ├── 00_installation_index.Rmd │ │ ├── 01_setup │ │ │ ├── PEcAn-in-the-Cloud.Rmd │ │ │ ├── shiny.Rmd │ │ │ └── thredds.Rmd │ │ └── 03_install_OS │ │ │ ├── 00_install_OS.Rmd │ │ │ ├── 01_Installing-PEcAn-Ubuntu.Rmd │ │ │ ├── 02_Installing-PEcAn-CentOS.Rmd │ │ │ ├── 04_Installing-PEcAn-OSX.Rmd │ │ │ ├── 05_install_BETY.Rmd │ │ │ ├── 06_install_models │ │ │ ├── 00_install_models.Rmd │ │ │ ├── install_BIOCRO.Rmd │ │ │ ├── install_CLM4.5.Rmd │ │ │ ├── install_DALEC.Rmd │ │ │ ├── install_ED2.Rmd │ │ │ ├── install_FATES.Rmd │ │ │ ├── install_GDAY.Rmd │ │ │ ├── install_JULES.Rmd │ │ │ ├── install_LINKAGES.Rmd │ │ │ ├── install_LPJGUESS.Rmd │ │ │ ├── install_MAESPA.Rmd │ │ │ └── install_SIPNET.Rmd │ │ │ └── 07_Installing-PEcAn-Data.Rmd │ ├── 94_docker │ │ ├── 00_docker_index.Rmd │ │ ├── 01_introduction.Rmd │ │ ├── 02_quickstart.Rmd │ │ ├── 03_architecture.Rmd │ │ ├── 04_models.Rmd │ │ ├── 05_building_images.Rmd │ │ ├── 06_troubleshooting.Rmd │ │ ├── 07_migrate.Rmd │ │ ├── 08_pecan_api.Rmd │ │ ├── 09_rabbitmq.Rmd │ │ └── pecan-docker.png │ ├── 95_remote_execution.Rmd │ └── 99_DART_state_data_assimilation.Rmd ├── 04_appendix │ ├── 00_appendix.Rmd │ ├── 01_faq.Rmd │ ├── 03_courses_taught.Rmd │ ├── 04-package-dependencies.Rmd │ ├── 05-testthat.Rmd │ ├── 06_devtools.Rmd │ └── 07_singularity.Rmd ├── 06_reference │ └── 02_models │ │ └── sibcasa.Rmd ├── Makefile ├── _bookdown.yml ├── _output.yml ├── check_bkd_pkg.R ├── figures │ ├── PEcAn_Components.jpeg │ ├── PecanLogo.png │ ├── env-file.PNG │ ├── pic1.jpg │ ├── pic1v2.png │ ├── pic2.jpg │ ├── pic3.jpg │ └── run_output_plot.png └── index.Rmd ├── contrib ├── DART │ ├── DART │ │ └── Kodiak │ │ │ ├── mkmf │ │ │ └── mkmf.template │ │ │ ├── models │ │ │ └── ED2 │ │ │ │ ├── ED2IN │ │ │ │ ├── input.nml │ │ │ │ ├── model_mod.f90 │ │ │ │ ├── model_mod.nml │ │ │ │ ├── shell_scripts │ │ │ │ ├── advance_model.csh │ │ │ │ └── run_filter.csh │ │ │ │ ├── utils │ │ │ │ ├── F2R.f90 │ │ │ │ ├── R2F.f90 │ │ │ │ ├── README │ │ │ │ ├── adjValue.R │ │ │ │ ├── createInput.R │ │ │ │ ├── createTransit.R │ │ │ │ ├── end_file.txt │ │ │ │ ├── file_name.txt │ │ │ │ ├── mkmf_trans_time │ │ │ │ ├── path_names_trans_time │ │ │ │ ├── readValue.R │ │ │ │ ├── sim_year │ │ │ │ ├── temp_ic │ │ │ │ └── trans_time.f90 │ │ │ │ └── work │ │ │ │ ├── .cppdefs │ │ │ │ ├── 4Rdata.dat │ │ │ │ ├── ED2IN │ │ │ │ ├── F2R │ │ │ │ ├── Makefile │ │ │ │ ├── ObsDiagAtts.m │ │ │ │ ├── R2F │ │ │ │ ├── RAW_STATE_VARIABLE_anl_times.dat │ │ │ │ ├── RAW_STATE_VARIABLE_ges_times.dat │ │ │ │ ├── R_ED2IN │ │ │ │ ├── S_ED2IN │ │ │ │ ├── T_ED2IN │ │ │ │ ├── adjValue.R │ │ │ │ ├── advance_model.csh │ │ │ │ ├── build.log │ │ │ │ ├── can_I_create_a_file.txt │ │ │ │ ├── createInput.R │ │ │ │ ├── createTransit.R │ │ │ │ ├── creation.csh │ │ │ │ ├── ed_2.1-opt │ │ │ │ ├── end_date │ │ │ │ ├── end_file.txt │ │ │ │ ├── f_ics │ │ │ │ ├── filter.sh │ │ │ │ ├── filter_ics │ │ │ │ ├── filter_ics_back │ │ │ │ ├── filter_restart │ │ │ │ ├── input.dat │ │ │ │ ├── input.nml │ │ │ │ ├── int.out │ │ │ │ ├── mfilter.csh │ │ │ │ ├── mkmf_create_fixed_network_seq │ │ │ │ ├── mkmf_create_obs_sequence │ │ │ │ ├── mkmf_filter │ │ │ │ ├── mkmf_integrate_model │ │ │ │ ├── mkmf_obs_diag │ │ │ │ ├── mkmf_obs_sequence_tool │ │ │ │ ├── mkmf_perfect_model_obs │ │ │ │ ├── mkmf_preprocess │ │ │ │ ├── mkmf_restart_file_tool │ │ │ │ ├── mkmf_wakeup_filter │ │ │ │ ├── obs_seq.final │ │ │ │ ├── obs_seq.in │ │ │ │ ├── obs_seq.out │ │ │ │ ├── output.log │ │ │ │ ├── output_file.dat │ │ │ │ ├── path_names_create_fixed_network_seq │ │ │ │ ├── path_names_create_obs_sequence │ │ │ │ ├── path_names_filter │ │ │ │ ├── path_names_integrate_model │ │ │ │ ├── path_names_obs_diag │ │ │ │ ├── path_names_obs_sequence_tool │ │ │ │ ├── path_names_perfect_model_obs │ │ │ │ ├── path_names_preprocess │ │ │ │ ├── path_names_restart_file_tool │ │ │ │ ├── path_names_wakeup_filter │ │ │ │ ├── qs.sh │ │ │ │ ├── quickbuild.csh │ │ │ │ ├── readValue.R │ │ │ │ ├── set_def.out │ │ │ │ ├── set_det.out │ │ │ │ ├── sim_year │ │ │ │ ├── using_mpi_for_filter │ │ │ │ ├── using_mpi_for_wakeup_filter │ │ │ │ └── year.dat │ │ │ ├── obs_def │ │ │ └── obs_def_phen_mod.f90 │ │ │ └── obs_kind │ │ │ └── DEFAULT_obs_kind_mod.F90 │ ├── ED2 │ │ ├── build │ │ │ └── bin │ │ │ │ └── include.mk.opt │ │ ├── run │ │ │ └── ED2IN │ │ └── src │ │ │ ├── dynamics │ │ │ ├── phenology_aux.f90 │ │ │ └── phenology_driv.f90 │ │ │ ├── init │ │ │ ├── ed_params.f90 │ │ │ └── phenology_startup.f90 │ │ │ ├── io │ │ │ └── ed_init_full_history.F90 │ │ │ ├── memory │ │ │ └── ed_state_vars.f90 │ │ │ └── utils │ │ │ └── allometry.f90 │ ├── LICENSE │ ├── R │ │ ├── ObsSeq.R │ │ ├── adjValue.R │ │ ├── createInput.R │ │ ├── date2month.R │ │ └── filter_ics.R │ └── fluxnet │ │ └── willow │ │ ├── WCr.NACP.lat45.5lon-90.5.css │ │ ├── WCr.NACP.lat45.5lon-90.5.pss │ │ ├── WCr.NACP.lat45.5lon-90.5.site │ │ └── phenology.lat45.5lon-90.5.txt ├── README.md ├── browndog │ ├── PEcAn#DALEC_convert.R │ ├── PEcAn#ED2_convert.R │ ├── PEcAn#LINKAGES_convert.R │ ├── PEcAn#Sipnet_convert.R │ ├── PEcAn#Site_convert.R │ ├── PEcAn.R │ ├── README.md │ └── example.xml └── modellauncher │ ├── Makefile │ └── modellauncher.c ├── docker-compose.dev.yml ├── docker-compose.https.yml ├── docker-compose.prod.yml ├── docker-compose.vm.yaml ├── docker-compose.yml ├── docker.sh ├── docker ├── add-data.sh ├── base │ ├── Dockerfile │ └── rstudio.sh ├── data │ ├── Dockerfile │ ├── add-data.sh │ └── add.util.sh ├── depends │ ├── Dockerfile │ ├── pecan.depends.R │ ├── pecan_deps_from_github.txt │ └── pecan_package_dependencies.csv ├── docker-compose.example.yml ├── docs │ ├── Dockerfile │ └── index.html ├── env.example ├── executor │ ├── Dockerfile │ ├── executor.py │ └── sender.py ├── models │ ├── Dockerfile │ └── model.py ├── monitor │ ├── Dockerfile │ ├── bootstrap-table.min.css │ ├── bootstrap-table.min.js │ ├── bootstrap.min.css │ ├── bootstrap.min.js │ ├── fa-solid-900.woff2 │ ├── favicon.jpg │ ├── fontawesome.min.css │ ├── index.html │ ├── jquery-3.3.1.min.js │ ├── monitor.py │ ├── popper.min.js │ ├── requirements.txt │ ├── solid.min.css │ └── sticky-footer-navbar.css ├── rstudio-nginx │ ├── Dockerfile │ └── nginx.conf └── web │ ├── Dockerfile │ └── config.docker.php ├── documentation ├── NACP_protocol.pdf ├── README.md ├── dietze2013oic.pdf ├── dietze2014qat.pdf ├── index_vm.html ├── lebauer2013ffb.pdf ├── tutorials │ ├── 01_Demo_Basic_Run │ │ ├── Demo01.Rmd │ │ └── extfiles │ │ │ ├── execstatus.jpg │ │ │ ├── mapmodel.png │ │ │ ├── runspec.png │ │ │ ├── startpecan.jpg │ │ │ └── workflowshiny.png │ ├── 02_Demo_Uncertainty_Analysis │ │ └── Demo02.Rmd │ ├── AnalyzeOutput │ │ └── modelVSdata.Rmd │ ├── Demo_02_Uncertainty_Analysis │ │ ├── pecan.xml │ │ ├── pft │ │ │ └── temperate.coniferous │ │ │ │ └── prior.distns.Rdata │ │ └── uncertainty.qmd │ ├── Demo_1_Basic_Run │ │ ├── download_sipnet.R │ │ ├── pecan.xml │ │ ├── pft │ │ │ └── temperate.coniferous │ │ │ │ └── prior.distns.Rdata │ │ └── run_pecan.qmd │ ├── ICOS_Drought2018 │ │ ├── ICOS_Drought2018_Vignette.Rmd │ │ └── extfiles │ │ │ └── ICOS_Drought2018_Sites.csv │ ├── MCMC │ │ └── MCMC_Concepts.Rmd │ ├── Makefile │ ├── ParameterAssimilation │ │ └── PDA.Rmd │ ├── README.md │ ├── StateAssimilation │ │ └── TreeRingSDA.Rmd │ ├── buildfiles │ ├── deploy.sh │ ├── multisite-workflow │ │ └── multisite-workflow-example.qmd │ └── sensitivity │ │ └── PEcAn_sensitivity_tutorial_v1.0.Rmd └── wang2013pys.pdf ├── index.html ├── models ├── basgra │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── Dockerfile │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── read_restart.BASGRA.R │ │ ├── run_BASGRA.R │ │ ├── version.R │ │ ├── write.config.BASGRA.R │ │ └── write_restart.BASGRA.R │ ├── README.md │ ├── inst │ │ ├── BASGRA_params.csv │ │ ├── last_vals_basgra.Rdata │ │ ├── register.BASGRA.xml │ │ └── template.job │ ├── man │ │ ├── read_restart.BASGRA.Rd │ │ ├── run_BASGRA.Rd │ │ ├── write.config.BASGRA.Rd │ │ └── write_restart.BASGRA.Rd │ ├── model_info.json │ ├── src │ │ ├── BASGRA.f90 │ │ ├── Makevars │ │ ├── environment.f90 │ │ ├── init.c │ │ ├── parameters_plant.f90 │ │ ├── parameters_site.f90 │ │ ├── plant.f90 │ │ ├── resources.f90 │ │ ├── set_params.f90 │ │ ├── soil.f90 │ │ └── yasso.f90 │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── ic_with_yasso_pools.nc │ │ ├── ic_with_yasso_pools_and_met.nc │ │ ├── test.met.2019.nc │ │ ├── test.run_BASGRA.R │ │ └── test.write.config.R ├── biocro │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── Dockerfile │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── call_biocro.R │ │ ├── close_nc_if_open.R │ │ ├── get_biocro_defaults.R │ │ ├── met2model.BIOCRO.R │ │ ├── model2netcdf.BIOCRO.R │ │ ├── read.biocro.config.R │ │ ├── run.biocro.R │ │ ├── version.R │ │ └── write.configs.BIOCRO.R │ ├── README.md │ ├── inst │ │ ├── biocluster_job.sh │ │ ├── biocro.Rscript │ │ ├── extdata │ │ │ ├── c4grass.xml │ │ │ ├── co2.csv │ │ │ ├── defaults │ │ │ │ ├── miscanthus.xml │ │ │ │ ├── miscanthus_default.xml │ │ │ │ ├── panicum.xml │ │ │ │ ├── populus.xml │ │ │ │ ├── saccharum.xml │ │ │ │ ├── salix.RData │ │ │ │ ├── salix.xml │ │ │ │ ├── saof.xml │ │ │ │ ├── setaria.xml │ │ │ │ └── sorghum.xml │ │ │ ├── misp.xml │ │ │ └── pecan.biocro.xml │ │ ├── pointbiocro.Rscript │ │ ├── regionalbiocro.Rscript │ │ ├── regionalbiocro_met_uncertainty.Rscript │ │ ├── register.BIOCRO.xml │ │ ├── salix_benchmarks.Rmd │ │ └── workflow.R │ ├── man │ │ ├── cf2biocro.Rd │ │ ├── convert.samples.BIOCRO.Rd │ │ ├── get_biocro_defaults.Rd │ │ ├── met2model.BIOCRO.Rd │ │ ├── model2netcdf.BIOCRO.Rd │ │ ├── read.biocro.config.Rd │ │ ├── remove.config.BIOCRO.Rd │ │ ├── run.biocro.Rd │ │ └── write.config.BIOCRO.Rd │ ├── model_info.json │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── data │ │ │ ├── README.txt │ │ │ ├── US-Bo1.2004.csv │ │ │ ├── US-Bo1.2004.nc │ │ │ ├── misp.xml │ │ │ ├── pecan.biocro.xml │ │ │ ├── pecan.xml │ │ │ ├── result.RData │ │ │ ├── saof.xml │ │ │ ├── species.csv │ │ │ ├── urbana_subdaily_test.nc │ │ │ └── weather.csv │ │ │ ├── helper.R │ │ │ ├── test-call_biocro.R │ │ │ ├── test-run.biocro.R │ │ │ ├── test.cf2biocro.R │ │ │ ├── test.met2model.R │ │ │ ├── test.model2netcdf.BIOCRO.R │ │ │ └── test.write.configs.BIOCRO.R │ └── vignettes │ │ ├── C4grass_sa_vd.Rmd │ │ └── sa.output.Rdata ├── cable │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── R │ │ ├── met2model.CABLE.R │ │ ├── model2netcdf.CABLE.R │ │ ├── read_restart.CABLE.R │ │ ├── write.config.CABLE.R │ │ └── write_restart.CABLE.R │ ├── README.md │ ├── inst │ │ ├── cable.nml │ │ └── template.job │ ├── man │ │ ├── met2model.CABLE.Rd │ │ ├── model2netcdf.CABLE.Rd │ │ ├── read_restart.CABLE.Rd │ │ ├── write.config.CABLE.Rd │ │ └── write_restart.CABLE.Rd │ └── tests │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ └── test.met2model.R ├── clm45 │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.CLM45.R │ │ ├── model2netcdf.CLM45.R │ │ ├── version.R │ │ └── write.configs.CLM45.R │ ├── README.md │ ├── inst │ │ ├── register.CLM45.xml │ │ └── template.job │ ├── man │ │ ├── met2model.CLM45.Rd │ │ ├── model2netcdf.CLM45.Rd │ │ └── write.config.CLM45.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── test.dummy.R │ │ └── test.met2model.R ├── dalec │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.DALEC.R │ │ ├── model2netcdf.DALEC.R │ │ ├── version.R │ │ └── write.configs.dalec.R │ ├── README.md │ ├── inst │ │ ├── DALEC_priors.R │ │ ├── README.Rmd │ │ ├── dalec_drivers.OREGON.no_obs.dat │ │ ├── dalec_gortt_opts.txt │ │ ├── default_param.dalec │ │ └── register.DALEC.xml │ ├── man │ │ ├── met2model.DALEC.Rd │ │ ├── model2netcdf.DALEC.Rd │ │ └── write.config.DALEC.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ └── testthat │ │ ├── test.dummy.R │ │ └── test.met2model.R ├── dvmdostem │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── globals.R │ │ ├── model2netcdf.dvmdostem.R │ │ ├── pecan2dvmdostem_variable_mapping.R │ │ ├── version.R │ │ └── write.config.dvmdostem.R │ ├── README.md │ ├── inst │ │ ├── README.md │ │ ├── config.js.template │ │ ├── job.sh.template │ │ ├── output_spec.csv │ │ ├── output_spec_pecan0.csv │ │ ├── output_spec_pecan1.csv │ │ └── pecan.dvmdostem.xml │ ├── man │ │ ├── adjust.runmask.dvmdostem.Rd │ │ ├── convert.samples.dvmdostem.Rd │ │ ├── enforce.runmask.cmt.vegmap.harmony.Rd │ │ ├── model2netcdf.dvmdostem.Rd │ │ ├── requested_vars_string2list.Rd │ │ ├── setup.outputs.dvmdostem.Rd │ │ ├── vmap_reverse.Rd │ │ ├── write.config.dvmdostem.Rd │ │ └── write.data2pecan.file.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ ├── test-model2netcdf.dvmdostem.R │ │ └── test.met2model.R ├── ed │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── Dockerfile │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── SAS.ED2.R │ │ ├── SDA.helpers.ED2.R │ │ ├── check_ed2in.R │ │ ├── check_ed_metheader.R │ │ ├── check_veg.R │ │ ├── create_veg.R │ │ ├── data.R │ │ ├── download_edi.R │ │ ├── ed_varlookup.R │ │ ├── example_veg.R │ │ ├── get_ed2in_dates.R │ │ ├── get_met_dates.R │ │ ├── met2model.ED2.R │ │ ├── model2netcdf.ED2.R │ │ ├── modify_ed2in.R │ │ ├── other.helpers.ED2.R │ │ ├── parse.history.R │ │ ├── read_ed2in.R │ │ ├── read_ed_metheader.R │ │ ├── read_ed_veg.R │ │ ├── read_restart.ED2.R │ │ ├── run_ed_singularity.R │ │ ├── sysdata.rda │ │ ├── veg2model.ED2.R │ │ ├── version.R │ │ ├── write.configs.ed.R │ │ ├── write_ed2in.R │ │ ├── write_ed_metheader.R │ │ ├── write_ed_veg.R │ │ ├── write_restart.ED2.R │ │ └── zz.imports.R │ ├── README.md │ ├── data-raw │ │ ├── history.csv │ │ ├── history.r46.csv │ │ ├── history.r81.csv │ │ ├── history.r82.csv │ │ ├── history.r85.csv │ │ ├── history.rgit.csv │ │ ├── include.mk.opt │ │ ├── pftmapping-csv.R │ │ ├── pftmapping.csv │ │ ├── soil.csv │ │ └── sysdata.R │ ├── data │ │ └── pftmapping.rda │ ├── inst │ │ ├── ED2IN.r2.2.0 │ │ ├── ED2IN.r2.2.0.github │ │ ├── ED2IN.r46 │ │ ├── ED2IN.r81 │ │ ├── ED2IN.r82 │ │ ├── ED2IN.r85 │ │ ├── ED2IN.rTess │ │ ├── ED2IN.rgit │ │ ├── ED2IN.rgit.no_storage.resp.scheme │ │ ├── ED2IN.rgit_istfer │ │ ├── ED2IN.rgit_rykelly │ │ ├── batch.jobs.lowp.sh │ │ ├── batch.jobs.sh │ │ ├── example_xml │ │ │ └── ed-ensemble.xml │ │ ├── pecan.ed2.diag.plots.R │ │ ├── pecan.ed2.diagnostics.R │ │ ├── plot.hdf5.R │ │ ├── register.ED2.xml │ │ ├── rewrite.config.R │ │ ├── run-template.ED.old │ │ ├── run.template.ED │ │ ├── run.template.ED2 │ │ ├── template.job │ │ ├── test.read.restart.R │ │ ├── test.timeutils.R │ │ ├── test.write.restart.ED2.R │ │ └── timeutils.R │ ├── man │ │ ├── SAS.ED2.Rd │ │ ├── SAS.ED2.param.Args.Rd │ │ ├── between.Rd │ │ ├── check_css.Rd │ │ ├── check_ed2in.Rd │ │ ├── check_ed_metfile.Rd │ │ ├── check_ed_metheader.Rd │ │ ├── convert.samples.ED.Rd │ │ ├── create_css.Rd │ │ ├── create_ed_veg.Rd │ │ ├── dates_in_month.Rd │ │ ├── download_edi.Rd │ │ ├── ed.var.Rd │ │ ├── ed2in2time.Rd │ │ ├── example_css.Rd │ │ ├── extract_pfts.Rd │ │ ├── get_configxml.ED2.Rd │ │ ├── get_ed2in_dates.Rd │ │ ├── get_latlon.Rd │ │ ├── get_met_dates.Rd │ │ ├── get_restartfile.ED2.Rd │ │ ├── is.ed2in.Rd │ │ ├── list.files.nodir.Rd │ │ ├── met2model.ED2.Rd │ │ ├── met_flag_description.Rd │ │ ├── met_variable_description.Rd │ │ ├── model2netcdf.ED2.Rd │ │ ├── modify_df.Rd │ │ ├── modify_ed2in.Rd │ │ ├── parse.history.Rd │ │ ├── patch_cohort_index.Rd │ │ ├── pftmapping.Rd │ │ ├── prepare_ed_veg_filename.Rd │ │ ├── print.ed2in.Rd │ │ ├── put_E_values.Rd │ │ ├── put_T_values.Rd │ │ ├── read_E_files.Rd │ │ ├── read_S_files.Rd │ │ ├── read_T_files.Rd │ │ ├── read_css.Rd │ │ ├── read_ed2in.Rd │ │ ├── read_ed_metheader.Rd │ │ ├── read_ed_veg.Rd │ │ ├── read_restart.ED2.Rd │ │ ├── remove.config.ED2.Rd │ │ ├── run_ed_singularity.Rd │ │ ├── tags2char.Rd │ │ ├── translate_vars_ed.Rd │ │ ├── veg2model.ED2.Rd │ │ ├── write.config.ED2.Rd │ │ ├── write.config.jobsh.ED2.Rd │ │ ├── write.config.xml.ED2.Rd │ │ ├── write_css.Rd │ │ ├── write_ed2in.Rd │ │ ├── write_ed_metheader.Rd │ │ ├── write_ed_veg.Rd │ │ ├── write_restart.ED2.Rd │ │ └── zz.imports.Rd │ ├── model_info.json │ ├── scripts │ │ ├── README │ │ ├── get.model.output.ed.R │ │ ├── read.output.ed.R │ │ ├── running_ed_from_R.Rmd │ │ ├── write.configs.rscript.R │ │ └── zero_storage_resp.R │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── test_ed_integration.R │ │ ├── testthat.R │ │ └── testthat │ │ ├── data │ │ ├── outdir.zip │ │ └── pecan_checked.xml │ │ ├── test-extract_pfts.R │ │ ├── test-put_ET_files.R │ │ ├── test-read_ET_files.R │ │ ├── test-read_S_files.R │ │ ├── test.met2model.R │ │ ├── test.model2netcdf.ED2.R │ │ ├── test.no_storage_resp.R │ │ └── test.write.configs.ed.R ├── fates │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.FATES.R │ │ ├── model2netcdf.FATES.R │ │ ├── recurse.create.R │ │ ├── version.R │ │ └── write.configs.FATES.R │ ├── README.md │ ├── inst │ │ ├── case.clm2.h0.2004-01-01-00000.nc │ │ ├── clm5_params.c171117.nc │ │ ├── clm_params_ed.c160808.nc │ │ ├── create_1x1_ref_case_old.sh │ │ ├── create_CLM5-FATES_1x1br_refrun.sh │ │ ├── datm.streams.txt.PEcAn_met.template │ │ ├── datm_atm_in.template │ │ ├── datm_in │ │ ├── domain.lnd.1x1pt-brazil_navy.090715.nc │ │ ├── fates_params_2troppftclones.c171018_sps.nc │ │ ├── model2netcdf_test.R │ │ ├── register.FATES.xml │ │ ├── surfdata_1x1_brazil_16pfts_Irrig_CMIP6_simyr2000_c171214.nc │ │ ├── surfdata_ref.nc │ │ ├── template.job │ │ └── template.job.createclone │ ├── man │ │ ├── met2model.FATES.Rd │ │ ├── model2netcdf.FATES.Rd │ │ ├── recurse.create.Rd │ │ └── write.config.FATES.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── test.dummy.R │ │ └── test.met2model.R ├── gday │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.GDAY.R │ │ ├── model2netcdf.GDAY.R │ │ ├── version.R │ │ └── write.config.GDAY.R │ ├── README.md │ ├── inst │ │ ├── base_start.cfg │ │ ├── generate_forcing_data.py │ │ ├── register.GDAY.xml │ │ ├── run_simulations.py │ │ └── template.job │ ├── man │ │ ├── met2model.GDAY.Rd │ │ ├── model2netcdf.GDAY.Rd │ │ └── write.config.GDAY.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ └── test.met2model.R ├── jules │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── model2netcdf.JULES.R │ │ ├── version.R │ │ └── write.config.JULES.R │ ├── README.md │ ├── inst │ │ ├── register.JULES.xml │ │ ├── template.job │ │ └── template_nml_4.2 │ │ │ ├── ancillaries.nml │ │ │ ├── crop_params.nml │ │ │ ├── drive.nml │ │ │ ├── fire.nml │ │ │ ├── imogen.nml │ │ │ ├── initial_conditions.dat │ │ │ ├── initial_conditions.nml │ │ │ ├── jules_hydrology.nml │ │ │ ├── jules_radiation.nml │ │ │ ├── jules_rivers.nml │ │ │ ├── jules_snow.nml │ │ │ ├── jules_soil.nml │ │ │ ├── jules_surface.nml │ │ │ ├── jules_surface_types.nml │ │ │ ├── jules_vegetation.nml │ │ │ ├── model_grid.nml │ │ │ ├── nveg_params.nml │ │ │ ├── output.nml │ │ │ ├── pft_params.nml │ │ │ ├── prescribed_data.nml │ │ │ ├── tile_fractions.dat │ │ │ ├── timesteps.nml │ │ │ ├── triffid_params.nml │ │ │ └── urban.nml │ ├── man │ │ ├── detect.timestep.Rd │ │ ├── model2netcdf.JULES.Rd │ │ └── write.config.JULES.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ └── test.met2model.R ├── ldndc │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.LDNDC.R │ │ ├── model2netcdf.LDNDC.R │ │ ├── version.R │ │ └── write.config.LDNDC.R │ ├── README.md │ ├── inst │ │ ├── events_template.xml │ │ ├── project.ldndc │ │ ├── register.LDNDC.xml │ │ ├── setup_template.xml │ │ ├── site_template.xml │ │ ├── siteparameters_template.xml │ │ ├── speciesparameter_template.xml │ │ └── template.job │ ├── man │ │ ├── met2model.LDNDC.Rd │ │ ├── model2netcdf.LDNDC.Rd │ │ └── write.config.LDNDC.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ └── test.met2model.R ├── linkages │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.LINKAGES.R │ │ ├── model2netcdf.LINKAGES.R │ │ ├── read_restart.LINKAGES.R │ │ ├── sample.IC.LINKAGES.R │ │ ├── spinup.LINKAGES.R │ │ ├── split_inputs.LINKAGES.R │ │ ├── version.R │ │ ├── write.config.LINKAGES.R │ │ └── write_restart.LINKAGES.R │ ├── README.md │ ├── inst │ │ ├── LINKAGES.lyford.SDA.R │ │ ├── LINKAGES_tree_choices.csv │ │ ├── MIP_workflow_addn.R │ │ ├── SPP.DAT │ │ ├── clat.csv │ │ ├── fdat.csv │ │ ├── output.visualization.LINKAGES.R │ │ ├── pecan_PBL.xml │ │ ├── pecan_PDL.xml │ │ ├── pecan_PHA.xml │ │ ├── pecan_PHO.xml │ │ ├── pecan_PMB.xml │ │ ├── pecan_PUN.xml │ │ ├── register.LINKAGES.xml │ │ ├── remove_files.R │ │ ├── setup_da.R │ │ ├── spp_matrix.csv │ │ ├── switch.csv │ │ ├── switch.mat.Rdata │ │ ├── template.job │ │ └── texture.csv │ ├── man │ │ ├── met2model.LINKAGES.Rd │ │ ├── model2netcdf.LINKAGES.Rd │ │ ├── read_restart.LINKAGES.Rd │ │ ├── split_inputs.LINKAGES.Rd │ │ ├── write.config.LINKAGES.Rd │ │ └── write_restart.LINKAGES.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ └── test.met2model.LINKAGES.R ├── lpjguess │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── RcppExports.R │ │ ├── adjust.biomass.LPJGUESS.R │ │ ├── adjust.density.LPJGUESS.R │ │ ├── allocation.LPJGUESS.R │ │ ├── allometry.LPJGUESS.R │ │ ├── calculateGridcellVariablePerPFT.LPJGUESS.R │ │ ├── met2model.LPJGUESS.R │ │ ├── model2netcdf.LPJGUESS.R │ │ ├── readStateBinary.LPJGUESS.R │ │ ├── read_restart.LPJGUESS.R │ │ ├── read_state.R │ │ ├── split_inputs.LPJGUESS.R │ │ ├── update.state.LPJGUESS.R │ │ ├── version.R │ │ ├── write.config.LPJGUESS.R │ │ ├── write_restart.LPJGUESS.R │ │ └── write_state.R │ ├── README.md │ ├── data │ │ └── co2.1850.2020.csv │ ├── inst │ │ ├── gridind.txt │ │ ├── guess.PalEON.cpp │ │ ├── guess.PalEON.h │ │ ├── lpjguess_params.Rdata │ │ ├── parameters.PalEON.h │ │ ├── pecan.ins │ │ ├── pecan.ins.orig │ │ ├── register.LPJGUESS.xml │ │ ├── template.ins │ │ └── template.job │ ├── man │ │ ├── AbvGrndWood.Rd │ │ ├── TotalCarbon.Rd │ │ ├── adjust.biomass.LPJGUESS.Rd │ │ ├── adjust.density.LPJGUESS.Rd │ │ ├── allometry.Rd │ │ ├── calculateGridcellVariablePerPFT.Rd │ │ ├── extract_from_state_by_key.Rd │ │ ├── find_closing.Rd │ │ ├── find_stream_size.Rd │ │ ├── find_stream_type.Rd │ │ ├── find_stream_var.Rd │ │ ├── met2model.LPJGUESS.Rd │ │ ├── model2netcdf.LPJGUESS.Rd │ │ ├── pecan2lpjguess.Rd │ │ ├── readStateBinary.Rd │ │ ├── read_binary_LPJGUESS.Rd │ │ ├── read_restart.LPJGUESS.Rd │ │ ├── read_state.Rd │ │ ├── serialize_starts_ends.Rd │ │ ├── split_inputs.LPJGUESS.Rd │ │ ├── update_state_LPJGUESS.Rd │ │ ├── write.config.LPJGUESS.Rd │ │ ├── write.insfile.LPJGUESS.Rd │ │ ├── write_binary_LPJGUESS.Rd │ │ └── write_restart.LPJGUESS.Rd │ ├── src │ │ ├── RcppExports.cpp │ │ └── allocation.LPJGUESS.cpp │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ └── test.met2model.R ├── maat │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.MAAT.R │ │ ├── model2netcdf.MAAT.R │ │ ├── version.R │ │ └── write.config.MAAT.R │ ├── README.md │ ├── inst │ │ ├── generate_maat_met_drivers_ngee.R │ │ ├── generate_maat_met_drivers_ngee_pa-bar.R │ │ ├── leaf_user_met.xml │ │ ├── out.csv │ │ ├── pecan.maat.xml │ │ └── register.MAAT.xml │ ├── man │ │ ├── convert.samples.MAAT.Rd │ │ ├── met2model.MAAT.Rd │ │ ├── model2netcdf.MAAT.Rd │ │ └── write.config.MAAT.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── README.txt │ │ │ ├── test.met2model.R │ │ │ └── test.model2netcdf.MAAT.R │ └── vignettes │ │ ├── create_amerifluxLBL_drivers_for_maat.Rmd │ │ ├── graphics │ │ └── example_assimilation_rate.png │ │ └── running_maat_in_pecan.Rmd ├── maespa │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── Dockerfile │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.MAESPA.R │ │ ├── model2netcdf.MAESPA.R │ │ ├── version.R │ │ └── write.config.MAESPA.R │ ├── README.md │ ├── inst │ │ ├── confile.dat │ │ ├── met.dat │ │ ├── phy.dat │ │ ├── register.MAESPA.xml │ │ ├── str.dat │ │ ├── template.job │ │ ├── trees.dat │ │ └── watpars.dat │ ├── man │ │ ├── met2model.MAESPA.Rd │ │ ├── model2netcdf.MAESPA.Rd │ │ └── write.config.MAESPA.Rd │ ├── model_info.json │ ├── namelist.patch │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ └── test.met2model.R ├── preles │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── runPRELES.jobsh.R │ │ ├── version.R │ │ └── write.config.PRELES.R │ ├── README.md │ ├── inst │ │ └── register.PRELES.xml │ ├── man │ │ ├── runPRELES.jobsh.Rd │ │ └── write.config.PRELES.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── README.txt │ │ ├── test.met2model.R │ │ └── test.runPRELES.jobsh.R ├── sibcasa │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── datasets.R │ │ ├── met2model.SIBCASA.R │ │ ├── model2netcdf.SIBCASA.R │ │ ├── read_restart.SIBCASA.R │ │ ├── version.R │ │ ├── write.config.SIBCASA.R │ │ └── write_restart.SIBCASA.R │ ├── README.md │ ├── data │ │ ├── sibcasa_output_vars.R │ │ └── sibcasa_output_vars.csv │ ├── inst │ │ ├── namel_sibdrv │ │ └── template.job │ ├── man │ │ ├── met2model.SIBCASA.Rd │ │ ├── model2netcdf.SIBCASA.Rd │ │ ├── read_restart.SIBCASA.Rd │ │ ├── sibcasa_output_vars.Rd │ │ ├── write.config.SIBCASA.Rd │ │ └── write_restart.SIBCASA.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ └── test-configs.R ├── sipnet │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── Dockerfile │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.SIPNET.R │ │ ├── model2netcdf.SIPNET.R │ │ ├── read_restart.SIPNET.R │ │ ├── sample.IC.SIPNET.R │ │ ├── split_inputs.SIPNET.R │ │ ├── veg2model.SIPNET.R │ │ ├── version.R │ │ ├── write.configs.SIPNET.R │ │ ├── write.events.SIPNET.R │ │ └── write_restart.SIPNET.R │ ├── README.md │ ├── inst │ │ ├── SIPNET.lyford.SDA.R │ │ ├── niwot.clim │ │ ├── register.SIPNET.xml │ │ ├── sipnet.in │ │ ├── sipnet.out │ │ ├── template.job │ │ ├── template.param │ │ ├── template.param-spatial │ │ └── template.param.pecanbak │ ├── man │ │ ├── mergeNC.Rd │ │ ├── met2model.SIPNET.Rd │ │ ├── model2netcdf.SIPNET.Rd │ │ ├── read_restart.SIPNET.Rd │ │ ├── remove.config.SIPNET.Rd │ │ ├── sample.IC.SIPNET.Rd │ │ ├── split_inputs.SIPNET.Rd │ │ ├── veg2model.SIPNET.Rd │ │ ├── write.config.SIPNET.Rd │ │ ├── write.events.SIPNET.Rd │ │ └── write_restart.SIPNET.Rd │ ├── model_info.json │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── test-write.config.SIPNET.R │ │ ├── test-write.events.SIPNET.R │ │ └── test.met2model.R ├── stics │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── met2model.STICS.R │ │ ├── model2netcdf.STICS.R │ │ ├── version.R │ │ └── write.config.STICS.R │ ├── README.md │ ├── inst │ │ ├── crop_plt.xml │ │ ├── param.sol │ │ ├── param_gen.xml │ │ ├── param_newform.xml │ │ ├── pecan_ini.xml │ │ ├── pecan_sta.xml │ │ ├── pecan_tec.xml │ │ ├── preferences.xml │ │ ├── prof.mod │ │ ├── rap.mod │ │ ├── register.STICS.xml │ │ ├── sols.xml │ │ ├── template.job │ │ ├── template.usm │ │ ├── usms.xml │ │ └── var.mod │ ├── man │ │ ├── met2model.STICS.Rd │ │ ├── model2netcdf.STICS.Rd │ │ ├── pecan2stics.Rd │ │ └── write.config.STICS.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ └── test.met2model.R └── template │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── Dockerfile │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ ├── met2model.MODEL.R │ ├── model2netcdf.MODEL.R │ ├── read_restart.ModelName.R │ ├── version.R │ ├── write.config.MODEL.R │ └── write_restart.ModelName.R │ ├── README.md │ ├── inst │ ├── template.job │ └── template_geo.job │ ├── man │ ├── met2model.MODEL.Rd │ ├── model2netcdf.MODEL.Rd │ ├── read_restart.ModelName.Rd │ ├── write.config.MODEL.Rd │ └── write_restart.ModelName.Rd │ ├── model_info.json │ └── tests │ ├── Rcheck_reference.log │ ├── testthat.R │ └── testthat │ ├── README.txt │ └── test.met2model.R ├── modules ├── allometry │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── AllomAve.R │ │ ├── allom.BayesFit.R │ │ ├── allom.predict.R │ │ ├── query.allom.data.R │ │ ├── read.allom.data.R │ │ └── version.R │ ├── README.md │ ├── data │ │ ├── Jenkins2004_Table9.csv │ │ ├── Table3_GTR-NE-319.v2.csv │ │ └── allom.components.RData │ ├── inst │ │ ├── AllomDriver.R │ │ ├── JenkinsPFTs.R │ │ ├── manuscript │ │ │ └── Allom.Rmd │ │ └── workflow.allometry.R │ ├── man │ │ ├── AllomAve.Rd │ │ ├── AllomUnitCoef.Rd │ │ ├── allom.BayesFit.Rd │ │ ├── allom.predict.Rd │ │ ├── load.allom.Rd │ │ ├── nu.Rd │ │ ├── query.allom.data.Rd │ │ └── read.allom.data.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── test_AllomAve.R │ │ │ └── test_coefs.R │ └── vignettes │ │ ├── .gitignore │ │ └── AllomVignette.Rmd ├── assim.batch │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── autoburnin.R │ │ ├── gelman_diag.R │ │ ├── helpers.R │ │ ├── hier.mcmc.R │ │ ├── load.L2Ameriflux.cf.R │ │ ├── minimize.GP.R │ │ ├── pda.bayesian.tools.R │ │ ├── pda.bayestools.helpers.R │ │ ├── pda.define.llik.R │ │ ├── pda.emulator.R │ │ ├── pda.emulator.ms.R │ │ ├── pda.generate.externals.R │ │ ├── pda.get.model.output.R │ │ ├── pda.load.data.R │ │ ├── pda.mcmc.R │ │ ├── pda.mcmc.bs.R │ │ ├── pda.mcmc.recover.R │ │ ├── pda.neff.R │ │ ├── pda.postprocess.R │ │ ├── pda.utils.R │ │ ├── plot.da.R │ │ └── version.R │ ├── README.md │ ├── inst │ │ ├── FATES_BCI_PDA_demo.Rmd │ │ ├── get.da.data.R │ │ ├── get.da.data.growth.R │ │ └── llik.params.csv │ ├── man │ │ ├── assim.batch.Rd │ │ ├── autoburnin.Rd │ │ ├── bounded.Rd │ │ ├── calculate.prior.Rd │ │ ├── correlationPlot.Rd │ │ ├── ddist.Rd │ │ ├── gelman_diag_gelmanPlot.Rd │ │ ├── gelman_diag_mw.Rd │ │ ├── generate_hierpost.Rd │ │ ├── getBurnin.Rd │ │ ├── get_ss.Rd │ │ ├── get_y.Rd │ │ ├── gpeval.Rd │ │ ├── hier.mcmc.Rd │ │ ├── is.accepted.Rd │ │ ├── load.pda.data.Rd │ │ ├── load_pda_history.Rd │ │ ├── makeMCMCList.Rd │ │ ├── mcmc.GP.Rd │ │ ├── minimize.GP.Rd │ │ ├── pda.adjust.jumps.Rd │ │ ├── pda.adjust.jumps.bs.Rd │ │ ├── pda.autocorr.calc.Rd │ │ ├── pda.bayesian.tools.Rd │ │ ├── pda.calc.error.Rd │ │ ├── pda.calc.llik.Rd │ │ ├── pda.calc.llik.par.Rd │ │ ├── pda.create.btprior.Rd │ │ ├── pda.create.ensemble.Rd │ │ ├── pda.define.llik.fn.Rd │ │ ├── pda.define.prior.fn.Rd │ │ ├── pda.emulator.Rd │ │ ├── pda.emulator.ms.Rd │ │ ├── pda.generate.externals.Rd │ │ ├── pda.generate.knots.Rd │ │ ├── pda.generate.sf.Rd │ │ ├── pda.get.model.output.Rd │ │ ├── pda.init.params.Rd │ │ ├── pda.init.run.Rd │ │ ├── pda.load.priors.Rd │ │ ├── pda.mcmc.Rd │ │ ├── pda.mcmc.bs.Rd │ │ ├── pda.mcmc.recover.Rd │ │ ├── pda.neff.calc.Rd │ │ ├── pda.plot.params.Rd │ │ ├── pda.postprocess.Rd │ │ ├── pda.settings.Rd │ │ ├── pda.settings.bt.Rd │ │ ├── pda.sort.params.Rd │ │ ├── prepare_pda_remote.Rd │ │ ├── return.bias.Rd │ │ ├── return_hyperpars.Rd │ │ ├── return_multi_site_objects.Rd │ │ ├── runModule.assim.batch.Rd │ │ ├── sample_MCMC.Rd │ │ ├── sync_pda_remote.Rd │ │ └── write_sf_posterior.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── test.autoburnin.R │ │ │ └── test.bt_prior.R │ └── vignettes │ │ ├── AssimBatchVignette.Rmd │ │ ├── AssimBatchVignette.html │ │ └── MultiSitePDAVignette.Rmd ├── assim.sequential │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── Adjustment.R │ │ ├── Analysis_sda.R │ │ ├── Analysis_sda_block.R │ │ ├── Analysis_sda_multiSite.R │ │ ├── Create_Site_PFT_CSV.R │ │ ├── GEF_Helper.R │ │ ├── Helper.functions.R │ │ ├── Localization.R │ │ ├── Multi_Site_Constructors.R │ │ ├── Nimble_codes.R │ │ ├── Prep_OBS_SDA.R │ │ ├── Remote_helpers.R │ │ ├── SDA_OBS_Assembler.R │ │ ├── SDA_parallel_downscale.R │ │ ├── aggregate.R │ │ ├── assess.params.R │ │ ├── build_X.R │ │ ├── covariates_loader.R │ │ ├── debias_py.R │ │ ├── downscale_function.R │ │ ├── downscale_function_hrly.R │ │ ├── get_ensemble_weights.R │ │ ├── hop_test.R │ │ ├── load_data_paleon_sda.R │ │ ├── matrix_operation.R │ │ ├── metSplit.R │ │ ├── met_filtering_helpers.R │ │ ├── sample.parameters.R │ │ ├── sda.enkf.R │ │ ├── sda.enkf_MultiSite.R │ │ ├── sda.enkf_parallel.R │ │ ├── sda.enkf_refactored.R │ │ ├── sda_bias_correction.R │ │ ├── sda_matchparam.R │ │ ├── sda_plotting.R │ │ ├── sda_weights_site.R │ │ └── version.R │ ├── README.md │ ├── inst │ │ ├── MultiSite-Exs │ │ │ ├── Obs │ │ │ │ ├── LandTrendr_AGB_output-4sites.RData │ │ │ │ ├── LandTrendr_AGB_output31.RData │ │ │ │ ├── LandTrendr_AGB_output50s.RData │ │ │ │ ├── LandTrendr_AGB_output_796-769.RData │ │ │ │ └── example_AGB_output.RData │ │ │ └── SDA │ │ │ │ ├── Bartlett.param │ │ │ │ ├── Create_Multi_settings.R │ │ │ │ ├── Multisite-4sites.R │ │ │ │ ├── Weights.R │ │ │ │ ├── Weights_RDS.R │ │ │ │ ├── Weights_Site.R │ │ │ │ ├── pecan.SDA.4sites.xml │ │ │ │ └── site_pft.csv │ │ ├── NEFI │ │ │ ├── README.html │ │ │ ├── README.md │ │ │ ├── US_Harvard │ │ │ │ ├── download_Harvard.R │ │ │ │ ├── download_Harvard_met.R │ │ │ │ ├── download_soilmoist_harvard.R │ │ │ │ ├── harvard.sh │ │ │ │ └── harvard.xml │ │ │ ├── US_Los │ │ │ │ ├── download_Los.R │ │ │ │ ├── download_Los_met.R │ │ │ │ ├── los.sh │ │ │ │ └── los.xml │ │ │ ├── US_Potato │ │ │ │ ├── download_Potato.R │ │ │ │ ├── potato.sh │ │ │ │ └── potato.xml │ │ │ ├── US_Syv │ │ │ │ ├── download_Syv.R │ │ │ │ ├── download_Syv_met.R │ │ │ │ ├── download_soilmoist_Syv.R │ │ │ │ ├── syv.sh │ │ │ │ └── syv.xml │ │ │ ├── US_WCr │ │ │ │ ├── download_WCr.R │ │ │ │ ├── download_WCr_met.R │ │ │ │ ├── download_soilmoist_WCr.R │ │ │ │ ├── gefs.sipnet.source.xml │ │ │ │ ├── wcr.sh │ │ │ │ └── wcr.xml │ │ │ ├── US_WLEF │ │ │ │ ├── download_WLEF.R │ │ │ │ ├── download_WLEF_met.R │ │ │ │ ├── download_soilmoist_WLEF.R │ │ │ │ ├── wlef.sh │ │ │ │ └── wlef.xml │ │ │ ├── automatic_graphs.sh │ │ │ ├── email.R │ │ │ ├── email_graphs.R │ │ │ ├── forecast.graphs.R │ │ │ ├── generate.gefs.xml.R │ │ │ ├── graph_SDA_fluxtowers.R │ │ │ └── graph_fluxtowers.R │ │ ├── RemoteLauncher │ │ │ ├── Remote_sync.R │ │ │ ├── Run.bash │ │ │ └── SDA_launcher.R │ │ ├── SDA_runner.R │ │ ├── Site_XMLS │ │ │ ├── bart.xml │ │ │ ├── harvard.xml │ │ │ ├── konz.xml │ │ │ ├── los.xml │ │ │ ├── ordway.xml │ │ │ ├── potato.xml │ │ │ ├── santarita.xml │ │ │ ├── syv.xml │ │ │ ├── testingMulti_HF.xml │ │ │ ├── testingMulti_HF_SM.xml │ │ │ ├── wcr.xml │ │ │ └── wlef.xml │ │ ├── WillowCreek │ │ │ ├── Diagram.png │ │ │ ├── NoDataWorkflow.R │ │ │ ├── SDA_Workflow.R │ │ │ ├── Utils.R │ │ │ ├── download_WCr.R │ │ │ ├── download_soilmoist_WCr.R │ │ │ ├── forecast.sh │ │ │ ├── gapfill_WCr.R │ │ │ ├── nodata.xml │ │ │ ├── prep.data.assim.R │ │ │ └── workflow.template.R │ │ ├── alr_test.R │ │ ├── anchor │ │ │ ├── IC_prep_anchorSites.Rmd │ │ │ ├── NA_Site_Selection.Rmd │ │ │ ├── NA_downscale_script.R │ │ │ ├── SDA_NA_runner.R │ │ │ ├── anchorSites_data_prep.Rmd │ │ │ └── update_anchor_sitegroup.Rmd │ │ ├── covariates.R │ │ ├── debias_step.R │ │ ├── ensemble_adj_visualization.R │ │ ├── fluxnet_sandbox │ │ │ ├── ApplyingWeights_sps_v4.R │ │ │ ├── FLUX_plotting_Hamze.R │ │ │ ├── examples │ │ │ │ ├── US-Me2 │ │ │ │ │ ├── US-Me2_SDA_2014_GPP_weekly_comparison_v2.png │ │ │ │ │ ├── US-Me2_SDA_2014_NEE_weekly_comparison_v2.png │ │ │ │ │ ├── US-Me2_raw_SDA_GPP_kgC_m2_s1.png │ │ │ │ │ ├── US-Me2_raw_SDA_NEE_kgC_m2_s1.png │ │ │ │ │ └── timeseries_2000002567.png │ │ │ │ ├── US-Syv │ │ │ │ │ ├── US-Syv_SDA_2002_GPP_weekly_comparison_v2.png │ │ │ │ │ ├── US-Syv_SDA_2002_NEE_weekly_comparison_v2.png │ │ │ │ │ ├── US-Syv_raw_SDA_GPP_kgC_m2_s1.png │ │ │ │ │ ├── US-Syv_raw_SDA_NEE_kgC_m2_s1.png │ │ │ │ │ └── timeseries_2000002575.png │ │ │ │ ├── timeseries_2000002574.png │ │ │ │ ├── timeseries_2000002575.png │ │ │ │ └── timeseries_2000002583.png │ │ │ ├── plot_sda_results_by_site.R │ │ │ └── sda_500_flux_net_site_table.csv │ │ ├── hf_landscape │ │ │ ├── 01_SiteSelection.Rmd │ │ │ ├── 02_SiteConfig.Rmd │ │ │ ├── 03_InitEnsNoSDA.Rmd │ │ │ ├── 04_ForwardOnlyForecast.R │ │ │ ├── 05B_SDA_Workflow_NA.reanalysis.R │ │ │ ├── 05C_SDA_Workflow_NA.forecast.R │ │ │ ├── 05_SDA_Workflow_NA.R │ │ │ ├── 06_cron.Rmd │ │ │ ├── 07_SMAP.R │ │ │ ├── PEcAn2EFI.R │ │ │ └── README.md │ │ ├── metfiltering.exploration.R │ │ ├── paleon_sda.R │ │ ├── python │ │ │ └── pecan_debias │ │ │ │ ├── __init__.py │ │ │ │ └── debias.py │ │ ├── restart_SDAworkflow_scripts │ │ │ ├── SDA_Workflow_LAI.R │ │ │ ├── SDA_Workflow_NA.R │ │ │ └── run_SDAworkflow.sh │ │ ├── sda.particle.R │ │ ├── sda.rewind.R │ │ ├── sda.tobit.simulation.R │ │ ├── sda_backup │ │ │ ├── bmorrison │ │ │ │ ├── Multi_Site_Constructors.R │ │ │ │ ├── Multisite_SDA_Bailey.R │ │ │ │ ├── Multisite_SDA_Bailey_AGB_LAI.R │ │ │ │ ├── Multisite_SDA_Bailey_AGB_LAI_2_sites.R │ │ │ │ ├── Multisite_SDA_Bailey_AGB_LAI_2_sites_with_NA.R │ │ │ │ ├── Multisite_SDA_Bailey_AGB_LAI_7_sites.r │ │ │ │ ├── Multisite_SDA_Bailey_LAI_8_days.R │ │ │ │ ├── Multisite_SDA_Shawn.R │ │ │ │ ├── ecoregion_cluster_analysis.xlsx │ │ │ │ ├── ecoregion_lai_CONUS.R │ │ │ │ ├── ecoregion_lai_agb_trends.R │ │ │ │ ├── extract_500_site_data.R │ │ │ │ ├── extract_50_sitegroup_data.R │ │ │ │ ├── extract_50_sitegroup_data_2.R │ │ │ │ ├── extract_lai_agb_data.R │ │ │ │ ├── extract_lai_agb_data_500.R │ │ │ │ ├── general_sda_setup.R │ │ │ │ ├── general_sda_setup_2.R │ │ │ │ ├── nohuprun.txt │ │ │ │ ├── pft_selection.R │ │ │ │ ├── pft_site_locations.R │ │ │ │ ├── register_site_group.R │ │ │ │ ├── site_selection │ │ │ │ │ └── pick_sda_sites.R │ │ │ │ └── upscaling_sda_output │ │ │ │ │ ├── AGB_2000-2017.jpeg │ │ │ │ │ ├── AGB_rf_model.R │ │ │ │ │ ├── check_site_id_mixup.R │ │ │ │ │ ├── mean_agb_2000-2018.jpeg │ │ │ │ │ ├── pft_site_locations.jpeg │ │ │ │ │ ├── rf_agb_model_2021.Rdata │ │ │ │ │ ├── rf_agb_model_2021_CODE.R │ │ │ │ │ ├── rf_error_sd_model_diagnostics_2021.jpeg │ │ │ │ │ ├── rf_model_comparison_2021.jpeg │ │ │ │ │ ├── rf_model_diagnostics_2021.jpeg │ │ │ │ │ └── sda_500_flux_net_site_table.csv │ │ │ ├── qianyu(cherry) │ │ │ │ └── pecan_HARV_site.xml │ │ │ └── sserbin │ │ │ │ ├── R_scripts_2 │ │ │ │ ├── Multisite-3sites.R │ │ │ │ ├── Multisite-4sites.R │ │ │ │ ├── Multisite_SDA_BNL.R │ │ │ │ ├── Multisite_SDA_BNL_updated.R │ │ │ │ ├── nohuprun.txt │ │ │ │ ├── workflow_doconversions.R │ │ │ │ └── workflow_metprocess.R │ │ │ │ ├── Rscripts │ │ │ │ ├── multi_site_LAI_SDA_BNL.R │ │ │ │ └── single_site_SDA_BNL.R │ │ │ │ ├── nohuprun.txt │ │ │ │ ├── workflow.R │ │ │ │ └── workflow_2.R │ │ ├── variability │ │ │ └── exploratory.Rmd │ │ └── workflow.variance.partitioning.R │ ├── man │ │ ├── Analysis.sda.Rd │ │ ├── Construc_H.Rd │ │ ├── Construct.H.multisite.Rd │ │ ├── Construct.R.Rd │ │ ├── Contruct.Pf.Rd │ │ ├── Create_Site_PFT_CSV.Rd │ │ ├── EnKF.MultiSite.Rd │ │ ├── EnKF.Rd │ │ ├── GEF.MultiSite.Nimble.Rd │ │ ├── GEF.Rd │ │ ├── GrabFillMatrix.Rd │ │ ├── Local.support.Rd │ │ ├── MCMC_Init.Rd │ │ ├── MCMC_block_function.Rd │ │ ├── MCMC_function.Rd │ │ ├── Obs.data.prepare.MultiSite.Rd │ │ ├── Prep_OBS_SDA.Rd │ │ ├── Remote_Sync_launcher.Rd │ │ ├── SDA_OBS_Assembler.Rd │ │ ├── SDA_control.Rd │ │ ├── SDA_downscale.Rd │ │ ├── SDA_downscale_hrly.Rd │ │ ├── SDA_downscale_metrics.Rd │ │ ├── SDA_downscale_preprocess.Rd │ │ ├── SDA_remote_launcher.Rd │ │ ├── adj.ens.Rd │ │ ├── aggregate.Rd │ │ ├── alltocs.Rd │ │ ├── alr.Rd │ │ ├── analysis_sda_block.Rd │ │ ├── assess.params.Rd │ │ ├── block.2.vector.Rd │ │ ├── block_matrix.Rd │ │ ├── build.block.xy.Rd │ │ ├── build_X.Rd │ │ ├── conj_wt_wishart_sampler.Rd │ │ ├── construct_nimble_H.Rd │ │ ├── downscale_main.Rd │ │ ├── downscale_qsub_main.Rd │ │ ├── dwtmnorm.Rd │ │ ├── get_ensemble_weights.Rd │ │ ├── hop_test.Rd │ │ ├── interactive.plotting.sda.Rd │ │ ├── inv.alr.Rd │ │ ├── load_data_paleon_sda.Rd │ │ ├── load_nimble.Rd │ │ ├── matrix_network.Rd │ │ ├── metSplit.Rd │ │ ├── obs_timestep2timepoint.Rd │ │ ├── outlier.detector.boxplot.Rd │ │ ├── parallel_prediction.Rd │ │ ├── parallel_train.Rd │ │ ├── pecan_settings_2_pts.Rd │ │ ├── piecew.poly.local.Rd │ │ ├── prepare_train_dat.Rd │ │ ├── qsub_sda.Rd │ │ ├── qsub_sda_batch.Rd │ │ ├── rescaling_stateVars.Rd │ │ ├── rwtmnorm.Rd │ │ ├── sample.parameters.Rd │ │ ├── sample_met.Rd │ │ ├── sampler_toggle.Rd │ │ ├── sda.enkf.Rd │ │ ├── sda.enkf.multisite.Rd │ │ ├── sda.enkf.original.Rd │ │ ├── sda.enkf_local.Rd │ │ ├── sda_assemble.Rd │ │ ├── sda_bias_correction.Rd │ │ ├── sda_matchparam.Rd │ │ ├── sda_weights_site.Rd │ │ ├── simple.local.Rd │ │ ├── stack_covariates_2_df.Rd │ │ ├── stack_covariates_2_geotiff.Rd │ │ ├── tobit.model.Rd │ │ ├── tobit2space.model.Rd │ │ ├── tobit_model_censored.Rd │ │ └── update_q.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ └── testthat │ │ ├── test_aggregation.R │ │ ├── test_aggregation │ │ ├── ensemble1.tif │ │ ├── ensemble2.tif │ │ ├── ensemble3.tif │ │ └── us_states.rds │ │ └── test_rescaling.R ├── benchmark │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── .gitignore │ │ ├── align_by_first_observation.R │ │ ├── align_data.R │ │ ├── align_data_to_data_pft.R │ │ ├── align_pft.R │ │ ├── bm_settings.R │ │ ├── calc_benchmark.R │ │ ├── calc_metrics.R │ │ ├── check_if_legal_table.R │ │ ├── check_if_list_of_pfts.R │ │ ├── check_if_species_list.R │ │ ├── create_BRR.R │ │ ├── define_benchmark.R │ │ ├── format_wide2long.R │ │ ├── get_species_list_standard.R │ │ ├── load_csv.R │ │ ├── load_data.R │ │ ├── load_netcdf.R │ │ ├── load_rds.R │ │ ├── load_tab.R │ │ ├── match_timestep.R │ │ ├── mean_over_larger_timestep.R │ │ ├── metric_AME.R │ │ ├── metric_Frechet.R │ │ ├── metric_MAE.R │ │ ├── metric_MSE.R │ │ ├── metric_PPMC.R │ │ ├── metric_R2.R │ │ ├── metric_RAE.R │ │ ├── metric_RMSE.R │ │ ├── metric_cor.R │ │ ├── metric_lmDiag_plot.R │ │ ├── metric_residual_plot.R │ │ ├── metric_run.R │ │ ├── metric_scatter_plot.R │ │ ├── metric_timeseries_plot.R │ │ ├── pecan_bench.R │ │ └── version.R │ ├── README.md │ ├── inst │ │ └── scripts │ │ │ ├── benchmark.workflow.FATES_BCI.R │ │ │ ├── benchmark.workflow.R │ │ │ ├── benchmarking.documentation.md │ │ │ ├── bm.1var.1metric.1site.1model.xml │ │ │ ├── bm.1var.1site.1model.xml │ │ │ ├── bm.2var.1site.1model.xml │ │ │ └── bm.2var.2metric.2site.1model.xml │ ├── man │ │ ├── add_workflow_info.Rd │ │ ├── align_by_first_observation.Rd │ │ ├── align_data.Rd │ │ ├── align_data_to_data_pft.Rd │ │ ├── align_pft.Rd │ │ ├── bm_settings2pecan_settings.Rd │ │ ├── calc_benchmark.Rd │ │ ├── calc_metrics.Rd │ │ ├── check_BRR.Rd │ │ ├── check_if_legal_table.Rd │ │ ├── check_if_list_of_pfts.Rd │ │ ├── check_if_species_list.Rd │ │ ├── clean_settings_BRR.Rd │ │ ├── create_BRR.Rd │ │ ├── define_benchmark.Rd │ │ ├── format_wide2long.Rd │ │ ├── get_species_list_standard.Rd │ │ ├── load_csv.Rd │ │ ├── load_data.Rd │ │ ├── load_rds.Rd │ │ ├── load_tab_separated_values.Rd │ │ ├── load_x_netcdf.Rd │ │ ├── match_timestep.Rd │ │ ├── mean_over_larger_timestep.Rd │ │ ├── metric_AME.Rd │ │ ├── metric_Frechet.Rd │ │ ├── metric_MAE.Rd │ │ ├── metric_MSE.Rd │ │ ├── metric_PPMC.Rd │ │ ├── metric_R2.Rd │ │ ├── metric_RAE.Rd │ │ ├── metric_RMSE.Rd │ │ ├── metric_cor.Rd │ │ ├── metric_lmDiag_plot.Rd │ │ ├── metric_residual_plot.Rd │ │ ├── metric_run.Rd │ │ ├── metric_scatter_plot.Rd │ │ ├── metric_timeseries_plot.Rd │ │ └── read_settings_BRR.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ └── test-align_pft.R ├── data.atmosphere │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── Ameriflux_met_ensemble.R │ │ ├── ERA5_download.R │ │ ├── ERA5_met_process.R │ │ ├── GEFS_helper_functions.R │ │ ├── align_met.R │ │ ├── average_ERA5.R │ │ ├── check_met_input.R │ │ ├── closest_xy.R │ │ ├── data.R │ │ ├── debias.met.R │ │ ├── debias_met_regression.R │ │ ├── download.Ameriflux.R │ │ ├── download.AmerifluxLBL.R │ │ ├── download.CRUNCEP_Global.R │ │ ├── download.FACE.R │ │ ├── download.Fluxnet2015.R │ │ ├── download.FluxnetLaThuile.R │ │ ├── download.GFDL.R │ │ ├── download.GLDAS.R │ │ ├── download.Geostreams.R │ │ ├── download.ICOS.R │ │ ├── download.MACA.R │ │ ├── download.MERRA.R │ │ ├── download.MsTMIP_NARR.R │ │ ├── download.NARR.R │ │ ├── download.NARR_site.R │ │ ├── download.NEONmet.R │ │ ├── download.NLDAS.R │ │ ├── download.NOAA_GEFS.R │ │ ├── download.PalEON.R │ │ ├── download.PalEON_ENS.R │ │ ├── download.US_WCr.R │ │ ├── download.US_Wlef.R │ │ ├── download.raw.met.module.R │ │ ├── download_noaa_gefs_efi.R │ │ ├── downscaling_helper_functions.R │ │ ├── extract.nc.R │ │ ├── extract.nc.module.R │ │ ├── extract.success.R │ │ ├── extract_ERA5.R │ │ ├── extract_local_CMIP5.R │ │ ├── extract_local_NLDAS.R │ │ ├── get_cf_variables_table.R │ │ ├── half_hour_downscale.R │ │ ├── lightME.R │ │ ├── load.cfmet.R │ │ ├── merge.met.variable.R │ │ ├── met.process.R │ │ ├── met.process.stage.R │ │ ├── met2CF.ALMA.R │ │ ├── met2CF.Ameriflux.R │ │ ├── met2CF.AmerifluxLBL.R │ │ ├── met2CF.FACE.R │ │ ├── met2CF.Geostreams.R │ │ ├── met2CF.ICOS.R │ │ ├── met2CF.NARR.R │ │ ├── met2CF.csv.R │ │ ├── met2cf.ERA5.R │ │ ├── met2cf.module.R │ │ ├── met2cf.nc.R │ │ ├── met2model.module.R │ │ ├── met_temporal_downscale.Gaussian_ensemble.R │ │ ├── metgapfill.NOAA_GEFS.R │ │ ├── metgapfill.R │ │ ├── metgapfill.module.R │ │ ├── metutils.R │ │ ├── nc_merge.R │ │ ├── noaa_gefs_efi_helper.R │ │ ├── pecan_standard_met_table.R │ │ ├── permute.nc.R │ │ ├── read.register.R │ │ ├── site.lst.R │ │ ├── solar_angle.R │ │ ├── spin.met.R │ │ ├── split_wind.R │ │ ├── tdm_generate_subdaily_models.R │ │ ├── tdm_lm_ensemble_sims.R │ │ ├── tdm_model_train.R │ │ ├── tdm_predict_subdaily_met.R │ │ ├── tdm_save_betas.R │ │ ├── tdm_save_model.R │ │ ├── tdm_subdaily_pred.R │ │ ├── tdm_temporal_downscale_functions.R │ │ ├── temporal.downscaling.R │ │ ├── upscale_met.R │ │ ├── version.R │ │ └── zzz.R │ ├── README.md │ ├── data │ │ ├── FLUXNET.sitemap.R │ │ ├── FLUXNET.sitemap.csv │ │ ├── cruncep_landmask.RData │ │ ├── narr_cruncep_ebifarm.RData │ │ ├── ncep.latlon.RData │ │ └── ncep_landmask.RData │ ├── inst │ │ ├── ERA5 │ │ │ ├── ERA5_NA_download.R │ │ │ └── ERA5_db_register.R │ │ ├── integrationTests │ │ │ ├── test.download.AmerifluxLBL.R │ │ │ ├── test.download.CRUNCEP.R │ │ │ └── test.download.ERA5.R │ │ ├── python │ │ │ └── download_Global_MsTMIP_CRUNCEP.py │ │ ├── registration │ │ │ ├── register.Ameriflux.xml │ │ │ ├── register.AmerifluxLBL.xml │ │ │ ├── register.CFmet.xml │ │ │ ├── register.CRUNCEP.xml │ │ │ ├── register.ERA5.xml │ │ │ ├── register.FACE.xml │ │ │ ├── register.FieldObservatory.xml │ │ │ ├── register.Fluxnet2015.xml │ │ │ ├── register.GFDL.xml │ │ │ ├── register.Geostreams.xml │ │ │ ├── register.ICOS.xml │ │ │ ├── register.MERRA.xml │ │ │ ├── register.NARR.xml │ │ │ ├── register.NEONmet.xml │ │ │ ├── register.NOAA_GEFS.xml │ │ │ ├── register.NOAA_GEFS_downscale.xml │ │ │ ├── register.PalEON.xml │ │ │ └── register.PalEONregional.xml │ │ └── scripts │ │ │ ├── CF.FACE.sh │ │ │ ├── CF.NARR.sh │ │ │ ├── DUKE_FACE_MET.v2.R │ │ │ ├── ExtractNOAAstation.R │ │ │ ├── GetLSHRG.R │ │ │ ├── MetMerge.R │ │ │ ├── NACP2DRIVER.R │ │ │ ├── NARRdriver.R │ │ │ ├── NARRinventory.R │ │ │ ├── ORNL_FACE_MET.v2.R │ │ │ ├── PRISMlapse.R │ │ │ ├── WeathGenPPT.R │ │ │ ├── checkMetHDF.R │ │ │ ├── cruncep │ │ │ ├── README.md │ │ │ ├── cluster_cruncep.sh │ │ │ ├── concatenate.sh │ │ │ ├── gunzipall.sh │ │ │ ├── permute.sh │ │ │ ├── permute_all.sh │ │ │ ├── permutedimensions.sh │ │ │ ├── qconcatenate.sh │ │ │ └── weather.sh │ │ │ ├── download_Global_MsTMIP_CRUNCEP.sh │ │ │ ├── extract2driver.R │ │ │ ├── extract2driver.grid.R │ │ │ ├── flux2lsm.cc │ │ │ ├── flux2lsm.v2.R │ │ │ ├── isimip │ │ │ ├── README.md │ │ │ └── wget-20131121234222.sh │ │ │ ├── lapse.R │ │ │ ├── load.ameriflux.R │ │ │ ├── lsmMerge.R │ │ │ ├── met.workflow.NARR.R │ │ │ ├── met.workflow.R │ │ │ ├── met.workflow.gen.R │ │ │ ├── met.workflow.params.NARR.R │ │ │ ├── met.workflow.params.R │ │ │ ├── met_ensemble_testing.R │ │ │ ├── ncep │ │ │ ├── Globalmet.R │ │ │ ├── README.md │ │ │ ├── concatenate_ncep.sh │ │ │ ├── met2csv.R │ │ │ ├── met2csv.sh │ │ │ ├── ncep.sh │ │ │ ├── qmet2csv.sh │ │ │ └── qsubncep.sh │ │ │ ├── runtest-download.NOAA_GEFS.R │ │ │ ├── runtests-download.NOAA_GEFS.sh │ │ │ ├── timepoint.cc │ │ │ ├── timepoint.h │ │ │ ├── util.cc │ │ │ └── util.h │ ├── man │ │ ├── AirDens.Rd │ │ ├── AmeriFlux_met_ensemble.Rd │ │ ├── Average_ERA5_2_GeoTIFF.Rd │ │ ├── ERA5_met_process.Rd │ │ ├── align.met.Rd │ │ ├── build_cf_variables_table_url.Rd │ │ ├── cfmet.downscale.daily.Rd │ │ ├── cfmet.downscale.subdaily.Rd │ │ ├── cfmet.downscale.time.Rd │ │ ├── check_met_input_file.Rd │ │ ├── check_unit.Rd │ │ ├── closest_xy.Rd │ │ ├── col2ncvar.Rd │ │ ├── cos_solar_zenith_angle.Rd │ │ ├── debias.met.regression.Rd │ │ ├── debias_met.Rd │ │ ├── download.Ameriflux.Rd │ │ ├── download.AmerifluxLBL.Rd │ │ ├── download.CRUNCEP.Rd │ │ ├── download.ERA5_cds.Rd │ │ ├── download.FACE.Rd │ │ ├── download.Fluxnet2015.Rd │ │ ├── download.FluxnetLaThuile.Rd │ │ ├── download.GFDL.Rd │ │ ├── download.GLDAS.Rd │ │ ├── download.Geostreams.Rd │ │ ├── download.ICOS.Rd │ │ ├── download.MACA.Rd │ │ ├── download.MERRA.Rd │ │ ├── download.MsTMIP_NARR.Rd │ │ ├── download.NARR.Rd │ │ ├── download.NARR_site.Rd │ │ ├── download.NEONmet.Rd │ │ ├── download.NLDAS.Rd │ │ ├── download.NOAA_GEFS.Rd │ │ ├── download.PalEON.Rd │ │ ├── download.PalEON_ENS.Rd │ │ ├── download.US_WCr.Rd │ │ ├── download.US_Wlef.Rd │ │ ├── download.raw.met.module.Rd │ │ ├── download_NOAA_GEFS_EFI.Rd │ │ ├── download_grid.Rd │ │ ├── downscale_ShortWave_to_half_hrly.Rd │ │ ├── downscale_ShortWave_to_hrly.Rd │ │ ├── downscale_one_cfmet_day.Rd │ │ ├── downscale_repeat_6hr_to_half_hrly.Rd │ │ ├── downscale_repeat_6hr_to_hrly.Rd │ │ ├── downscale_solar_geom.Rd │ │ ├── downscale_solar_geom_halfhour.Rd │ │ ├── downscale_spline_to_half_hrly.Rd │ │ ├── downscale_spline_to_hrly.Rd │ │ ├── equation_of_time.Rd │ │ ├── exner.Rd │ │ ├── extract.local.CMIP5.Rd │ │ ├── extract.local.NLDAS.Rd │ │ ├── extract.nc.ERA5.Rd │ │ ├── extract.nc.Rd │ │ ├── gen.subdaily.models.Rd │ │ ├── generate_narr_url.Rd │ │ ├── get.lv.Rd │ │ ├── get.ncvector.Rd │ │ ├── get.rh.Rd │ │ ├── get.vpd.Rd │ │ ├── get_NARR_thredds.Rd │ │ ├── get_cf_variables_table.Rd │ │ ├── get_clowderauth.Rd │ │ ├── get_narr_url.Rd │ │ ├── half_hour_downscale.Rd │ │ ├── latlon2lcc.Rd │ │ ├── latlon2narr.Rd │ │ ├── lightME.Rd │ │ ├── lm_ensemble_sims.Rd │ │ ├── load.cfmet.Rd │ │ ├── merge_met_variable.Rd │ │ ├── met.process.Rd │ │ ├── met.process.stage.Rd │ │ ├── met2CF.ALMA.Rd │ │ ├── met2CF.Ameriflux.Rd │ │ ├── met2CF.AmerifluxLBL.Rd │ │ ├── met2CF.ERA5.Rd │ │ ├── met2CF.FACE.Rd │ │ ├── met2CF.Geostreams.Rd │ │ ├── met2CF.ICOS.Rd │ │ ├── met2CF.NARR.Rd │ │ ├── met2CF.PalEON.Rd │ │ ├── met2CF.PalEONregional.Rd │ │ ├── met2CF.csv.Rd │ │ ├── met_temporal_downscale.Gaussian_ensemble.Rd │ │ ├── metgapfill.NOAA_GEFS.Rd │ │ ├── metgapfill.Rd │ │ ├── model.train.Rd │ │ ├── narr_flx_vars.Rd │ │ ├── nc.merge.Rd │ │ ├── noaa_grid_download.Rd │ │ ├── noaa_stage2.Rd │ │ ├── par2ppfd.Rd │ │ ├── pecan_standard_met_table.Rd │ │ ├── permute.nc.Rd │ │ ├── post_process.Rd │ │ ├── predict_subdaily_met.Rd │ │ ├── prepare_narr_year.Rd │ │ ├── process_gridded_noaa_download.Rd │ │ ├── qair2rh.Rd │ │ ├── read.register.Rd │ │ ├── read_narr_var.Rd │ │ ├── rh2qair.Rd │ │ ├── sat_vapor_pressure.Rd │ │ ├── save.betas.Rd │ │ ├── save.model.Rd │ │ ├── site.lst.Rd │ │ ├── site_from_tag.Rd │ │ ├── solarMJ2ppfd.Rd │ │ ├── spin.met.Rd │ │ ├── split_wind.Rd │ │ ├── step_means.Rd │ │ ├── subdaily_pred.Rd │ │ ├── sw2par.Rd │ │ ├── sw2ppfd.Rd │ │ ├── temporal.downscale.functions.Rd │ │ ├── temporal_downscale.Rd │ │ ├── upscale_met.Rd │ │ ├── wide2long.Rd │ │ └── write_noaa_gefs_netcdf.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── test.NARR.R │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── data │ │ │ ├── test.met2CF.csv.csv │ │ │ ├── urbana_daily_test.nc │ │ │ └── urbana_subdaily_test.nc │ │ │ ├── helper.R │ │ │ ├── test-GEFS_helper_functions.R │ │ │ ├── test-download.NOAA_GEFS.R │ │ │ ├── test.cf-downscaling.R │ │ │ ├── test.check_met_file.R │ │ │ ├── test.download.AmerifluxLBL.R │ │ │ ├── test.download.CRUNCEP.R │ │ │ ├── test.download.ERA5_cds.R │ │ │ ├── test.download.GFDLR.R │ │ │ ├── test.download.ICOS.R │ │ │ ├── test.download.MERRA.R │ │ │ ├── test.download.NARR.R │ │ │ ├── test.download.raw.met.module.R │ │ │ ├── test.load.cfmet.R │ │ │ ├── test.met.process.R │ │ │ ├── test.met2CF.ALMA.R │ │ │ ├── test.met2CF.csv.R │ │ │ ├── test.met_temporal_downscale.Gaussian_ensemble.R │ │ │ ├── test.metutils.R │ │ │ └── test.upscale_met.R │ └── vignettes │ │ ├── ameriflux_demo.Rmd │ │ ├── cfmet_downscaling.Rmd │ │ ├── compare_narr_cruncep_met.Rmd │ │ └── tdm_downscaling.Rmd ├── data.land │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── DataONE_doi_download.R │ │ ├── IC_BADM_Utilities.R │ │ ├── IC_SOILGRID_Utilities.R │ │ ├── ISCN_extract.R │ │ ├── InventoryGrowthFusion.R │ │ ├── InventoryGrowthFusionDiagnostics.R │ │ ├── Read_Tuscon.R │ │ ├── Soilgrids_SoilC_prep.R │ │ ├── buildJAGSdata_InventoryRings.R │ │ ├── clip_and_save_raster_file.R │ │ ├── cohort2pool.R │ │ ├── data.R │ │ ├── dataone_download.R │ │ ├── download.SM_CDS.R │ │ ├── download_NEON_soilmoisture.R │ │ ├── ens.veg.module.R │ │ ├── extract.stringCode.R │ │ ├── extract_FIA.R │ │ ├── extract_NEON_veg.R │ │ ├── extract_SM_CDS.R │ │ ├── extract_soil_nc.R │ │ ├── extract_veg.R │ │ ├── fia2ED.R │ │ ├── fuse_plot_treering.R │ │ ├── gSSURGO_Query.R │ │ ├── get.soil.R │ │ ├── get_veg_module.R │ │ ├── gis.functions.R │ │ ├── ic_process.R │ │ ├── land.utils.R │ │ ├── load_veg.R │ │ ├── look_up_fertilizer_components.R │ │ ├── matchInventoryRings.R │ │ ├── match_pft.R │ │ ├── match_species_id.R │ │ ├── parse.MatrixNames.R │ │ ├── partition_roots.R │ │ ├── plot2AGB.R │ │ ├── pool_ic_list2netcdf.R │ │ ├── pool_ic_netcdf2list.R │ │ ├── prepare_pools.R │ │ ├── put_veg_module.R │ │ ├── read.plot.R │ │ ├── read.velmex.R │ │ ├── remote.copy.update.R │ │ ├── sample_ic.R │ │ ├── soil2netcdf.R │ │ ├── soil_params_ensemble.R │ │ ├── soil_process.R │ │ ├── soil_utils.R │ │ ├── soilgrids_soc_extraction.R │ │ ├── soilgrids_texture_extract.R │ │ ├── validate_events.R │ │ ├── version.R │ │ ├── write_ic.R │ │ └── write_veg.R │ ├── README.md │ ├── contrib │ │ ├── FIA │ │ │ ├── README.txt │ │ │ ├── data │ │ │ │ ├── .gitignore │ │ │ │ ├── FIADB_version4.accdb │ │ │ │ └── FIADB_version5_1.accdb │ │ │ ├── fiadb4.mysql │ │ │ ├── fiadb5_1.mysql │ │ │ ├── fiadb5_1.psql │ │ │ ├── fiadb5_1_extra.mysql │ │ │ ├── fiadb5_1_extra.psql │ │ │ ├── html2text.py │ │ │ └── mirror.sh │ │ └── FIA_allometry │ │ │ ├── GlobalWoodDensityDatabase.xls │ │ │ ├── README.Rmd │ │ │ ├── allometry.r │ │ │ ├── biolib10.csv │ │ │ ├── biomass.r │ │ │ ├── sp_eqlib.csv │ │ │ ├── sp_matchup.csv │ │ │ ├── spcodes.csv │ │ │ └── spcodes_auto.csv │ ├── data-raw │ │ ├── BADM.csv │ │ ├── README.md │ │ ├── build_soil_texture_variables.R │ │ ├── create_fertilizer_data.R │ │ ├── load_BADM.R │ │ └── texture.csv │ ├── data │ │ ├── BADM.rda │ │ ├── fertilizer_composition_data.rda │ │ ├── iscn_soc.rda │ │ └── soil_class.rda │ ├── inst │ │ ├── BCI_AGB.R │ │ ├── CanopyCover2NLCD.R │ │ ├── LoadFLUXNETsites.R │ │ ├── LoadPalEONsites.R │ │ ├── Multi_Site_IC_Process_Script.R │ │ ├── StatsModel_FIA.R │ │ ├── diametergrow.R │ │ ├── download_vswc.R │ │ ├── events_fixtures │ │ │ ├── events_site1.json │ │ │ └── events_site1_site2.json │ │ ├── events_schema_v0.1.0.json │ │ ├── extdata │ │ │ ├── eco-region.json │ │ │ └── eco-regionl2.json │ │ ├── generate_events.R │ │ ├── meta2format.EML.R │ │ ├── sitefiles.radius_0.075.lat_29.8848_lon_-83.3542.pss.csv │ │ ├── time_statespace3.doc │ │ └── treecore_StateSpace.R │ ├── man │ │ ├── BADM.Rd │ │ ├── BADM_IC_process.Rd │ │ ├── Clean_Tucson.Rd │ │ ├── EPA_ecoregion_finder.Rd │ │ ├── IC_ISCN_SOC.Rd │ │ ├── InventoryGrowthFusion.Rd │ │ ├── InventoryGrowthFusionDiagnostics.Rd │ │ ├── Read.IC.info.BADM.Rd │ │ ├── Read_Tucson.Rd │ │ ├── Soilgrids_SoilC_prep.Rd │ │ ├── buildJAGSdata_InventoryRings.Rd │ │ ├── clip_and_save_raster_file.Rd │ │ ├── cohort2pool.Rd │ │ ├── dataone_download.Rd │ │ ├── download.SM_CDS.Rd │ │ ├── download_NEON_soilmoist.Rd │ │ ├── download_package_rm.Rd │ │ ├── ens_veg_module.Rd │ │ ├── estimate_dirichlet_parameters.Rd │ │ ├── extract.stringCode.Rd │ │ ├── extract_FIA.Rd │ │ ├── extract_NEON_veg.Rd │ │ ├── extract_SM_CDS.Rd │ │ ├── extract_soil_gssurgo.Rd │ │ ├── extract_soil_nc.Rd │ │ ├── extract_veg.Rd │ │ ├── fertilizer_composition_data.Rd │ │ ├── fia.to.psscss.Rd │ │ ├── format_identifier.Rd │ │ ├── from.Tag.Rd │ │ ├── from.TreeCode.Rd │ │ ├── gSSURGO.Query.Rd │ │ ├── generate_soilgrids_ensemble.Rd │ │ ├── get.attributes.Rd │ │ ├── get.soil.Rd │ │ ├── get_resource_map.Rd │ │ ├── get_veg_module.Rd │ │ ├── ic_process.Rd │ │ ├── id_resolveable.Rd │ │ ├── iscn_soc.Rd │ │ ├── load_veg.Rd │ │ ├── look_up_fertilizer_components.Rd │ │ ├── matchInventoryRings.Rd │ │ ├── match_pft.Rd │ │ ├── match_species_id.Rd │ │ ├── mpot2smoist.Rd │ │ ├── netcdf.writer.BADM.Rd │ │ ├── om2soc.Rd │ │ ├── parse.MatrixNames.Rd │ │ ├── partition_roots.Rd │ │ ├── plot2AGB.Rd │ │ ├── pool_ic_list2netcdf.Rd │ │ ├── pool_ic_netcdf2list.Rd │ │ ├── prepare_pools.Rd │ │ ├── preprocess_soilgrids_data.Rd │ │ ├── put_veg_module.Rd │ │ ├── sample_ic.Rd │ │ ├── sclass.Rd │ │ ├── shp2kml.Rd │ │ ├── soc2ocs.Rd │ │ ├── soil.units.Rd │ │ ├── soil2netcdf.Rd │ │ ├── soil_class.Rd │ │ ├── soil_params.Rd │ │ ├── soil_params_ensemble_soilgrids.Rd │ │ ├── soil_process.Rd │ │ ├── soilgrids_ic_process.Rd │ │ ├── soilgrids_soilC_extract.Rd │ │ ├── soilgrids_texture_extraction.Rd │ │ ├── subset_layer.Rd │ │ ├── to.Tag.Rd │ │ ├── to.TreeCode.Rd │ │ ├── validate_events_json.Rd │ │ ├── write_ic.Rd │ │ └── write_veg.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ ├── dup_species.xml │ │ ├── test-IC_BADM_Utilities.R │ │ ├── test-PFT_consistency.R │ │ ├── test-clip_and_save_raster_file.R │ │ ├── test-extract_soil_nc.R │ │ ├── test-match_species_id.R │ │ ├── test-soil_params.R │ │ ├── test-validate_events_json.R │ │ ├── test.look_up_fertilizer_components.R │ │ └── wrong_pft.xml ├── data.mining │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── README.md │ ├── inst │ │ ├── ModelResidualSpectra.R │ │ ├── NACPspecPost.R │ │ ├── NACPspecPost.v2.R │ │ ├── NACPspectral.Keenan.R │ │ ├── NACPspectral.R │ │ ├── NACPspectral.v2.R │ │ ├── NEON_soils │ │ │ ├── soil_resp_markdown.Rmd │ │ │ └── soilcarbon_validation.Rmd │ │ ├── NullSpectra.R │ │ ├── NullSpectra.v2.R │ │ ├── NullSpectraPost.R │ │ ├── NullSpectraPost.v2.R │ │ ├── ResidSpectra.R │ │ ├── SPECsub.K.sh │ │ ├── SPECsub.sh │ │ ├── SpectralSlice.R │ │ └── bigmv.R │ └── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ └── test.dummy.R ├── data.remote │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── GEDI_AGB_prep.R │ │ ├── LandTrendr.AGB.R │ │ ├── Landtrendr_AGB_prep.R │ │ ├── MODIS_LAI_prep.R │ │ ├── MODIS_LC_prep.R │ │ ├── NASA_DAAC_download.R │ │ ├── NLCD.R │ │ ├── Prep_AGB_IC_from_2010_global.R │ │ ├── SMAP_SMP_prep.R │ │ ├── call_MODIS.R │ │ ├── download.thredds.AVHRR.R │ │ ├── download.thredds.AVHRR.monthAGG.R │ │ ├── download.thredds.R │ │ ├── extract_phenology_MODIS.R │ │ ├── merge_image_tiles.R │ │ ├── regrid.R │ │ ├── remote_process.R │ │ └── version.R │ ├── README.md │ ├── inst │ │ ├── FieldvsSMAP_compare.R │ │ ├── LandIQ_new_shapefile_intake_function.R │ │ ├── Python │ │ │ ├── CCMMF_Irrigation_API.py │ │ │ ├── CCMMF_Irrigation_CalcVis.py │ │ │ ├── CCMMF_Irrigation_DataDownload.py │ │ │ ├── CCMMF_Irrigation_Events.py │ │ │ ├── CCMMF_Irrigation_GEE.py │ │ │ ├── CCMMF_Irrigation_GEEvAPI.py │ │ │ ├── README.txt │ │ │ └── __pycache__ │ │ │ │ ├── CCMMF_Irrigation_CalcVis.cpython-312.pyc │ │ │ │ ├── CCMMF_Irrigation_DataDownload.cpython-312.pyc │ │ │ │ └── CCMMF_Irrigation_Events.cpython-312.pyc │ │ ├── RpTools │ │ │ ├── RpTools │ │ │ │ ├── __init__.py │ │ │ │ ├── appeears2pecan.py │ │ │ │ ├── bands2lai_snap.py │ │ │ │ ├── biophys_xarray.py │ │ │ │ ├── create_geojson.py │ │ │ │ ├── gee2pecan_gedi.py │ │ │ │ ├── gee2pecan_l8.py │ │ │ │ ├── gee2pecan_s2.py │ │ │ │ ├── gee2pecan_smap.py │ │ │ │ ├── gee_utils.py │ │ │ │ ├── get_remote_data.py │ │ │ │ ├── lpdaacdatapool2pecan.py │ │ │ │ ├── merge_files.py │ │ │ │ ├── process_remote_data.py │ │ │ │ └── rp_control.py │ │ │ └── setup.py │ │ ├── SMAPvsModel_Comparison.R │ │ ├── conus_sites.xml │ │ ├── download_SMAP.R │ │ ├── download_SMAP_gee2pecan.R │ │ ├── download_updated.R │ │ ├── extract_modis_data.py │ │ ├── hlsp-scene-explorer.qmd │ │ ├── landiq-file-explorer.qmd │ │ ├── modisWSDL.py │ │ ├── ndti_evi_timeseries_example.R │ │ ├── netCDFvarExtraction.R │ │ ├── registration │ │ │ ├── register.APPEEARS.xml │ │ │ ├── register.GEE.xml │ │ │ └── register.LPDAACDATAPOOL.xml │ │ ├── scripts │ │ │ ├── Bayesian_curve_fitting.R │ │ │ ├── ChEAS_FIA_03142014.R │ │ │ ├── ChEAS_FIA_04042014.R │ │ │ ├── Download_OSU_AGB_data_v5.R │ │ │ ├── Restrict_to_growing_season.R │ │ │ ├── figure_generator.R │ │ │ ├── old │ │ │ │ ├── ChEAS_FIA.R │ │ │ │ ├── ChEAS_FIA_02102014.R │ │ │ │ ├── ChEAS_FIA_03102014.R │ │ │ │ ├── ChEAS_FIA_03112014.R │ │ │ │ ├── ChEAS_FIA_03132014.R │ │ │ │ ├── LMfit_and_disturbance_chronosequence.R │ │ │ │ ├── Park_Falls_Golf.R │ │ │ │ ├── Park_Falls_Runway.R │ │ │ │ ├── ROI_sd.R │ │ │ │ ├── Raster_snapshots.R │ │ │ │ ├── build_params_table.R │ │ │ │ ├── build_polygons.R │ │ │ │ ├── curve_fitting_07282013.R │ │ │ │ ├── curve_fitting_07292013.R │ │ │ │ ├── curve_fitting_07312013.R │ │ │ │ ├── extract_UNDERC_points.R │ │ │ │ ├── extract_WLEF.R │ │ │ │ ├── extract_WLEF_buff7.R │ │ │ │ ├── extract_WLEF_using_ChEAS_FIA.R │ │ │ │ ├── extract_palsar_metadata_function.R │ │ │ │ ├── extract_polygons_function.R │ │ │ │ ├── extract_polygons_function_v05092013.R │ │ │ │ ├── extract_polygons_function_v05282013.R │ │ │ │ ├── extract_polygons_function_v06252013.R │ │ │ │ ├── extract_polygons_function_v06262013.R │ │ │ │ ├── ll.monod.R │ │ │ │ ├── ll.monod_v07292013.R │ │ │ │ └── read_binary.R │ │ │ ├── palsar_extractor.R │ │ │ ├── palsar_plotter.R │ │ │ └── spp_cleanup.R │ │ └── test.geojson │ ├── man │ │ ├── GEDI_AGB_prep.Rd │ │ ├── GEDI_L4A_2_mean_var.Rd │ │ ├── GEDI_L4A_2_mean_var.batch.Rd │ │ ├── GEDI_L4A_Finder.Rd │ │ ├── GEDI_L4A_Finder_batch.Rd │ │ ├── Landtrendr_AGB_prep.Rd │ │ ├── MODIS_LAI_prep.Rd │ │ ├── MODIS_LAI_ts_filter.Rd │ │ ├── MODIS_LC_prep.Rd │ │ ├── NASA_CMR_finder.Rd │ │ ├── NASA_DAAC_URL.Rd │ │ ├── NASA_DAAC_download.Rd │ │ ├── Prep.MODIS.CSV.from.DAAC.Rd │ │ ├── Prep.SMAP.CSV.from.DAAC.Rd │ │ ├── Prep_AGB_IC_from_2010_global.Rd │ │ ├── SMAP_SMP_prep.Rd │ │ ├── call_MODIS.Rd │ │ ├── construct_remotedata_filename.Rd │ │ ├── download.LandTrendr.AGB.Rd │ │ ├── download.NLCD.Rd │ │ ├── download_thredds.Rd │ │ ├── extract.LandTrendr.AGB.Rd │ │ ├── extract_NLCD.Rd │ │ ├── extract_phenology_MODIS.Rd │ │ ├── extract_thredds_nc.Rd │ │ ├── gdal_conversion.Rd │ │ ├── gdal_translate.Rd │ │ ├── get_site_info.Rd │ │ ├── get_subdatasets.Rd │ │ ├── getnetrc.Rd │ │ ├── grid2netcdf.Rd │ │ ├── merge_image_tiles.Rd │ │ ├── read_remote_registry.Rd │ │ ├── regrid.Rd │ │ ├── remote_process.Rd │ │ ├── remotedata_db_check.Rd │ │ ├── remotedata_db_insert.Rd │ │ └── set_stage.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ └── testthat │ │ └── test.dummy.R ├── emulator │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── GaussProcess.R │ │ ├── PEcAn.emulator-package.R │ │ ├── arate.R │ │ ├── calcSpatialCov.R │ │ ├── calcSpatialCov.list.R │ │ ├── calcSpatialCov.matrix.R │ │ ├── distance.R │ │ ├── distance.matrix.R │ │ ├── distance12.matrix.R │ │ ├── gp_mle.R │ │ ├── groupid.R │ │ ├── jump.R │ │ ├── ldinvgamma.R │ │ ├── lhc.R │ │ ├── nderiv.R │ │ ├── p.R │ │ ├── p.jump.R │ │ ├── plot.jump.R │ │ ├── predict.GP.R │ │ ├── predict.density.R │ │ ├── summarize.GP.R │ │ ├── update.jump.R │ │ ├── version.R │ │ └── zzz.R │ ├── README.md │ ├── man │ │ ├── GaussProcess.Rd │ │ ├── PEcAn.emulator-package.Rd │ │ ├── arate.Rd │ │ ├── calcSpatialCov.Rd │ │ ├── calcSpatialCov.list.Rd │ │ ├── calcSpatialCov.matrix.Rd │ │ ├── distance.Rd │ │ ├── distance.martix.Rd │ │ ├── distance12.martix.Rd │ │ ├── gp_mle.Rd │ │ ├── gp_mle2.Rd │ │ ├── groupid.Rd │ │ ├── jump-class.Rd │ │ ├── jump.Rd │ │ ├── ldinvgamma.Rd │ │ ├── lhc.Rd │ │ ├── mvjump-class.Rd │ │ ├── mvjump.Rd │ │ ├── nderiv.Rd │ │ ├── p.Rd │ │ ├── p.jump.Rd │ │ ├── p.mvjump.Rd │ │ ├── plot.jump.Rd │ │ ├── plot.mvjump.Rd │ │ ├── predict.GP.Rd │ │ ├── predict.density.Rd │ │ ├── summarize.GP.Rd │ │ ├── update.jump.Rd │ │ └── update.mvjump.Rd │ └── tests │ │ ├── Rcheck_reference.log │ │ └── testthat │ │ └── test.dummy.R ├── meta.analysis │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── approx.posterior.R │ │ ├── jagify.R │ │ ├── meta.analysis.R │ │ ├── meta.analysis.summary.R │ │ ├── meta.analysis.write.model.R │ │ ├── rename_jags_columns.R │ │ ├── run.meta.analysis.R │ │ ├── single.MA.R │ │ ├── version.R │ │ └── zzz.R │ ├── README.md │ ├── inst │ │ ├── citation_search.py │ │ ├── extdata │ │ │ └── singleMAvignetteinputs.RData │ │ ├── ma.model.template.bug │ │ ├── magic │ │ │ ├── extract_rows_traitID.R │ │ │ ├── get_stats.R │ │ │ ├── initialize_planting.R │ │ │ ├── main.R │ │ │ └── run_program.R │ │ └── mamodel.svg │ ├── man │ │ ├── approx.posterior.Rd │ │ ├── jagify.Rd │ │ ├── p.point.in.prior.Rd │ │ ├── pecan.ma.Rd │ │ ├── pecan.ma.summary.Rd │ │ ├── rename_jags_columns.Rd │ │ ├── run.meta.analysis.Rd │ │ ├── runModule.run.meta.analysis.Rd │ │ ├── single.MA.Rd │ │ ├── transform.nas.Rd │ │ └── write.ma.model.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── data │ │ │ ├── post.distns.RData │ │ │ ├── prior.distns.RData │ │ │ └── trait.mcmc.RData │ │ │ ├── test.approx.posterior.R │ │ │ ├── test.jagify.R │ │ │ └── test.run.meta.analysis.R │ └── vignettes │ │ └── single.MA_demo.Rmd ├── photosynthesis │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── Licor.QC.R │ │ ├── fitA.R │ │ ├── plots.R │ │ └── version.R │ ├── README.md │ ├── code │ │ ├── BB_model.R │ │ ├── C3_photomodel.R │ │ ├── C3_photomodel_XF.R │ │ ├── C4_photomodel.r │ │ ├── FBB_cluster_processing.R │ │ ├── FBB_compare.R │ │ ├── FBB_functions.R │ │ ├── FBB_main.R │ │ ├── FBB_mcmc.R │ │ ├── FBB_multi_chain_analysis.R │ │ ├── FBB_param_corr.R │ │ ├── FBB_setup.R │ │ ├── FBB_summary.R │ │ ├── Sunny.preliminary.code │ │ │ ├── C3_Species.csv │ │ │ ├── C3_photomodel.r │ │ │ └── Documentations.docx │ │ ├── c3covariates.csv │ │ ├── c3photosynthesis.csv │ │ ├── c4covariates.csv │ │ ├── c4photosynthesis.csv │ │ ├── serbin.simple.code │ │ │ ├── Process_LiCor_GE_ACi_Data.R │ │ │ └── photo.processing.functions.R │ │ └── test.fitA.R │ ├── inst │ │ └── extdata │ │ │ ├── cov.csv │ │ │ ├── flux-course-1aci │ │ │ ├── flux-course-1aq │ │ │ ├── flux-course-2aci │ │ │ ├── flux-course-2aq │ │ │ ├── flux-course-3aci │ │ │ ├── flux-course-3aq │ │ │ ├── flux-course-4aci │ │ │ ├── flux-course-4aq │ │ │ ├── flux-course-5aci │ │ │ ├── flux-course-5aq │ │ │ ├── flux-course-6aci │ │ │ └── flux-course-6aq │ ├── man │ │ ├── Licor_QC.Rd │ │ ├── estimate_mode.Rd │ │ ├── fitA.Rd │ │ ├── plot_photo.Rd │ │ └── read_Licor.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ └── testthat │ │ │ └── test.dummy.R │ └── vignettes │ │ ├── .gitignore │ │ └── ResponseCurves.Rmd ├── priors │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── plots.R │ │ ├── priors.R │ │ └── version.R │ ├── README.md │ ├── inst │ │ └── extdata │ │ │ ├── glopnet.csv │ │ │ ├── wullschleger1993updated.csv │ │ │ └── wullschleger_join_usdaplants.csv │ ├── man │ │ ├── create.density.df.Rd │ │ ├── fit.dist.Rd │ │ ├── get.quantiles.from.density.Rd │ │ ├── get.sample.Rd │ │ ├── plot_densities.Rd │ │ ├── plot_posterior.density.Rd │ │ ├── plot_prior.density.Rd │ │ ├── plot_trait.Rd │ │ ├── pr.dens.Rd │ │ ├── pr.samp.Rd │ │ ├── prior.fn.Rd │ │ └── priorfig.Rd │ ├── tests │ │ ├── Rcheck_reference.log │ │ ├── testthat.R │ │ └── testthat │ │ │ └── test.priors.R │ └── vignettes │ │ └── priors_demo.Rmd ├── rtm │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ │ ├── bayestools.R │ │ ├── cbind.spectra.R │ │ ├── check.convergence.R │ │ ├── defparam.R │ │ ├── edr.wrapper.R │ │ ├── fortran.datamodule.R │ │ ├── generate-rsr.R │ │ ├── generate.noise.R │ │ ├── gpm.R │ │ ├── helpers.R │ │ ├── invert.auto.R │ │ ├── invert.custom.R │ │ ├── invert.lsq.R │ │ ├── matplot.spectra.R │ │ ├── neff.R │ │ ├── params2edr.R │ │ ├── plot.spectra.R │ │ ├── print.spectra.R │ │ ├── print_results_summary.R │ │ ├── prior.R │ │ ├── pro2s.R │ │ ├── process-output.R │ │ ├── process.specresponse.R │ │ ├── prosail.R │ │ ├── prospect.R │ │ ├── resample.R │ │ ├── sail.R │ │ ├── select.spectra.R │ │ ├── setup_edr.R │ │ ├── spectra.R │ │ ├── spectral-response.R │ │ ├── str.spectra.R │ │ ├── truncnorm.R │ │ └── version.R │ ├── README.md │ ├── TODO │ ├── data │ │ ├── .gitignore │ │ ├── dataSpec_prospectd.RData │ │ ├── model.list.csv │ │ ├── raw.sensor.data.RData │ │ ├── sensor.rsr.RData │ │ └── testspec.RData │ ├── inst │ │ ├── extdata │ │ │ ├── soil_reflect_par.dat │ │ │ └── wood_reflect_par.dat │ │ └── scripts │ │ │ ├── analyze_results.R │ │ │ ├── benchmark_inversion.R │ │ │ ├── edr_test.R │ │ │ ├── effectivesize.R │ │ │ ├── invert_quadratic.R │ │ │ ├── like_scale_compare.R │ │ │ └── read_dataspec.R │ ├── man │ │ ├── EDR.Rd │ │ ├── EDR.preprocess.history.Rd │ │ ├── burnin.thin.Rd │ │ ├── cbind.spectra.Rd │ │ ├── check.convergence.Rd │ │ ├── default.settings.prospect.Rd │ │ ├── defparam.Rd │ │ ├── dtnorm.Rd │ │ ├── fortran_data_module.Rd │ │ ├── foursail.Rd │ │ ├── generalized_plate_model.Rd │ │ ├── generate.noise.Rd │ │ ├── get.EDR.output.Rd │ │ ├── invert.auto.Rd │ │ ├── invert.custom.Rd │ │ ├── invert.lsq.Rd │ │ ├── invert_bt.Rd │ │ ├── load.from.name.Rd │ │ ├── lognorm.mu.Rd │ │ ├── lognorm.sigma.Rd │ │ ├── matplot.Rd │ │ ├── matplot.default.Rd │ │ ├── matplot.spectra.Rd │ │ ├── neff.Rd │ │ ├── params.prospect4.Rd │ │ ├── params.prospect5.Rd │ │ ├── params.prospect5b.Rd │ │ ├── params.prospectd.Rd │ │ ├── params2edr.Rd │ │ ├── plot.spectra.Rd │ │ ├── print.spectra.Rd │ │ ├── print_results_summary.Rd │ │ ├── prior.defaultvals.prospect.Rd │ │ ├── priorfunc.prospect.Rd │ │ ├── pro2s.Rd │ │ ├── pro4sail.Rd │ │ ├── pro4saild.Rd │ │ ├── prospect.Rd │ │ ├── prospect_bt_prior.Rd │ │ ├── read.rsr.folder.Rd │ │ ├── resample.Rd │ │ ├── rsr.from.fwhm.Rd │ │ ├── rtm_loglike.Rd │ │ ├── rtnorm.Rd │ │ ├── sensor.list.Rd │ │ ├── sensor.proper.Rd │ │ ├── setup_edr.Rd │ │ ├── spectra.Rd │ │ ├── spectral.response.Rd │ │ ├── str.spectra.Rd │ │ ├── sub-.spectra.Rd │ │ ├── sub-sub-.spectra.Rd │ │ ├── sub-subset-.spectra.Rd │ │ ├── summary_mvnorm.Rd │ │ ├── summary_simple.Rd │ │ ├── trim.rsr.Rd │ │ └── wavelengths.Rd │ ├── src │ │ ├── Makevars │ │ └── RTM │ │ │ ├── modules │ │ │ ├── dataSpec │ │ │ │ ├── dataSpec_prospect4.f90 │ │ │ │ ├── dataSpec_prospect5b.f90 │ │ │ │ ├── dataSpec_prospectd.f90 │ │ │ │ ├── dataSpec_refractive.f90 │ │ │ │ ├── dataSpec_soil.f90 │ │ │ │ ├── dataSpec_sun.f90 │ │ │ │ └── dataSpec_wavelength.f90 │ │ │ └── mod_types.f90 │ │ │ ├── pro2s │ │ │ ├── pro42s.f90 │ │ │ ├── pro52s.f90 │ │ │ └── pro5B2s.f90 │ │ │ ├── prosail │ │ │ ├── prosail.main.f90 │ │ │ └── prosaild.main.f90 │ │ │ ├── prospect │ │ │ ├── prospect.4.f90 │ │ │ ├── prospect.5.f90 │ │ │ ├── prospect.5B.f90 │ │ │ ├── prospect.D.f90 │ │ │ ├── prospect.expint.f90 │ │ │ ├── prospect.gpm.f90 │ │ │ └── prospect.tav.f90 │ │ │ ├── sail │ │ │ ├── sail.brdf.f90 │ │ │ ├── sail.hotspot.f90 │ │ │ ├── sail.lidf.f90 │ │ │ ├── sail.refltrans.f90 │ │ │ ├── sail.sail.f90 │ │ │ ├── sail.sensgeom.f90 │ │ │ ├── sail.suits.f90 │ │ │ └── sail.volscatt.f90 │ │ │ └── twostream │ │ │ ├── gamma.functions.f90 │ │ │ ├── meador.f90 │ │ │ ├── mod_biggamma.f90 │ │ │ ├── mod_hapke_soil.f90 │ │ │ └── two.stream.f90 │ ├── tests │ │ ├── .gitignore │ │ ├── Rcheck_reference.log │ │ ├── benchmark_spectra.R │ │ ├── testthat.R │ │ └── testthat │ │ │ ├── .gitignore │ │ │ ├── test.2s.R │ │ │ ├── test.foursail.R │ │ │ ├── test.gpm.R │ │ │ ├── test.invert_bayestools.R │ │ │ ├── test.invert_simple.R │ │ │ ├── test.prospect.R │ │ │ ├── test.resample.R │ │ │ ├── test.sail.R │ │ │ └── test.spectra.R │ └── vignettes │ │ ├── edr.sensitivity.R │ │ ├── invert.edr.R │ │ ├── pecanrtm.vignette.Rmd │ │ └── test.edr.R └── uncertainty │ ├── .Rbuildignore │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── NAMESPACE │ ├── NEWS.md │ ├── R │ ├── compute_sobol_indices.R │ ├── ensemble.R │ ├── flux_uncertainty.R │ ├── generate_joint_ensemble_design.R │ ├── get.analysis.filenames.r │ ├── get.parameter.samples.R │ ├── get.results.R │ ├── plots.R │ ├── run.ensemble.analysis.R │ ├── run.sensitivity.analysis.R │ ├── sensitivity.R │ ├── sensitivity.analysis.R │ ├── variance.R │ └── version.R │ ├── README.md │ ├── data │ ├── output.RData │ └── samples.RData │ ├── inst │ ├── abbreviated_workflow_SIPNET.R │ └── sobol │ │ └── sobol_analysis.R │ ├── man │ ├── compute_sobol_indices.Rd │ ├── ensemble.filename.Rd │ ├── ensemble.ts.Rd │ ├── flux.uncertainty.Rd │ ├── generate_joint_ensemble_design.Rd │ ├── get.change.Rd │ ├── get.coef.var.Rd │ ├── get.elasticity.Rd │ ├── get.ensemble.samples.Rd │ ├── get.gi.phii.Rd │ ├── get.parameter.samples.Rd │ ├── get.results.Rd │ ├── get.sensitivity.Rd │ ├── input.ens.gen.Rd │ ├── kurtosis.Rd │ ├── plot_flux_uncertainty.Rd │ ├── plot_sensitivities.Rd │ ├── plot_sensitivity.Rd │ ├── plot_variance_decomposition.Rd │ ├── read.ameriflux.L2.Rd │ ├── read.ensemble.output.Rd │ ├── read.ensemble.ts.Rd │ ├── read.sa.output.Rd │ ├── run.ensemble.analysis.Rd │ ├── run.sensitivity.analysis.Rd │ ├── runModule.get.results.Rd │ ├── runModule.run.sensitivity.analysis.Rd │ ├── sa.splinefun.Rd │ ├── sd.var.Rd │ ├── sensitivity.analysis.Rd │ ├── sensitivity.filename.Rd │ ├── spline.ensemble.Rd │ ├── spline.truncate.Rd │ ├── variance.stats.Rd │ ├── write.ensemble.configs.Rd │ └── write.sa.configs.Rd │ └── tests │ ├── Rcheck_reference.log │ ├── testthat.R │ └── testthat │ ├── test.plot.sensitivity.R │ ├── test.plot.variance.decomposition.R │ ├── test.sensitivity.analysis.R │ └── test_ensemble.R ├── release.sh ├── scripts ├── .gitignore ├── EFI_metprocess.R ├── EFI_workflow.R ├── HARV_metdownload_efi.R ├── README.md ├── Rfcn.R ├── add.data.sh ├── add.models.sh ├── add.util.sh ├── backup.bety.sh ├── build_pkgdown.R ├── check_with_errors.R ├── cleansettings.R ├── compile.sh ├── confirm_deps.R ├── create-hooks.sh ├── cron.sh ├── dataprep_10_site.csv ├── dataprep_10_sites.csv ├── dependencies.R ├── docker_rebuild.sh ├── efi_data_process.R ├── ensure_version_bump.sh ├── find.string.sh ├── generate_dependencies.R ├── get_orphaned_functions.py ├── install_pecan.sh ├── install_shiny_deps.R ├── ncsa-build.sh ├── quickbuild.R ├── sshkey.sh ├── syncgit.sh ├── thredds.sh ├── time.sh ├── updateVersion.sh ├── workflow.bm.R ├── workflow.pda.R ├── workflow.pda.recover.r ├── workflow.treering.R └── workflow.wcr.assim.R ├── shiny ├── BenchmarkReport │ ├── DESCRIPTION │ ├── LICENSE │ ├── server.R │ └── ui.R ├── Data-Ingest │ ├── DESCRIPTION │ ├── Data_Ingest_Functions.R │ ├── LICENSE │ ├── app.R │ ├── helper.R │ ├── modules │ │ ├── d1_download_module.R │ │ ├── dbFiles_module.R │ │ ├── formats_module.R │ │ ├── inputs_module.R │ │ └── local_upload_module.R │ ├── server_files │ │ ├── create_input_record_svr.R │ │ ├── d1_download_svr.R │ │ ├── dbfiles_record_svr.R │ │ ├── formats_record_svr.R │ │ ├── ingest_workflow_svr.R │ │ ├── input_record_svr.R │ │ └── local_upload_svr.R │ ├── ui_files │ │ ├── create_input_record_ui.R │ │ ├── d1_download_ui.R │ │ ├── dbfiles_record_ui.R │ │ ├── formats_record_ui.R │ │ ├── homepage_ui.R │ │ ├── ingest_workflow_ui.R │ │ ├── input_record_ui.R │ │ ├── local_file_upload_ui.R │ │ └── sidebar_ui.R │ └── ui_utils.R ├── Elicitation │ ├── DESCRIPTION │ ├── LICENSE │ ├── README.md │ ├── prior.RData │ ├── server.R │ └── ui.R ├── ForecastingDashboard │ ├── LICENSE │ ├── WcR_Test.Rmd │ ├── animated_WCr_graphs.R │ └── wcr.graphs.R ├── Pecan.depend │ ├── DESCRIPTION │ ├── LICENSE │ ├── SERVER.R │ ├── UI.R │ ├── global.R │ └── www │ │ └── style.css ├── SDAdashboard │ ├── .gitignore │ ├── LICENSE │ ├── Utilities │ │ ├── Math_Utility.R │ │ ├── l1.json │ │ ├── l2.json │ │ └── uihelp.R │ ├── server.R │ ├── ui.R │ └── www │ │ ├── loader.gif │ │ ├── scripts.js │ │ └── style.css ├── ViewMet │ ├── DESCRIPTION │ ├── LICENSE │ ├── server.R │ └── ui.R ├── dbsync │ ├── DESCRIPTION │ ├── Dockerfile │ ├── LICENSE │ ├── app.R │ ├── geoip.json │ └── save-env-shiny.sh ├── global-sensitivity │ ├── DESCRIPTION │ ├── LICENSE │ ├── README.md │ ├── load_ensemble.R │ ├── plotEnsemble.R │ ├── server.R │ ├── tests │ │ ├── plot.R │ │ └── setup.R │ └── ui.R └── workflowPlot │ ├── .gitignore │ ├── DESCRIPTION │ ├── LICENSE │ ├── README.md │ ├── helper.R │ ├── markdown │ ├── app_documentation.Rmd │ ├── benchmarking_plots.Rmd │ ├── benchmarking_scores.Rmd │ ├── benchmarking_setting.Rmd │ ├── exploratory_plot.Rmd │ ├── setup_page.Rmd │ └── workflowPlot_doc.Rmd │ ├── server.R │ ├── server_files │ ├── benchmarking_server.R │ ├── history_server.R │ ├── model_data_plots_server.R │ ├── model_plots_server.R │ ├── pdf_viewer_server.R │ ├── select_data_server.R │ └── sidebar_server.R │ ├── ui.R │ ├── ui_files │ ├── benchmarking_ScoresPlots_UI.R │ ├── benchmarking_settings_UI.R │ ├── documentation_UI.R │ ├── model_data_plots_UI.R │ ├── model_plots_UI.R │ ├── pdf_viewer_UI.R │ ├── select_data_UI.R │ └── sidebar_UI.R │ ├── ui_utils.R │ ├── workflowPlot_fcns.R │ └── www │ ├── scripts.js │ └── style.css ├── tests ├── .gitignore ├── README.md ├── api.sipnet.xml ├── browndog.ed.xml ├── browndog.sipnet.xml ├── docker-ghaction.sipnet.xml ├── docker.ed2.xml ├── docker.sipnet.xml ├── ebi-forecast.igb.illinois.edu.biocro.xml ├── ebi-forecast.igb.illinois.edu.sipnet.xml ├── fail.ghaction.sipnet_Postgres.xml ├── ghaction.sipnet_PostgreSQL.xml ├── integration.sh ├── interactive-workflow.R ├── met_download_settings │ └── docker.CRUNCEP.xml ├── migration-test-ebi-forecast.xml ├── modellauncher.xml ├── modex.modellauncher.xml ├── pecan.LINKAGES.xml ├── pecan.biocro.xml ├── pecan.dalec.xml ├── pecan.geo.sipnet.xml ├── pecan.testbnl.ed.xml ├── pecan.testbnl.sipnet.xml ├── pecan2.browndog.sipnet.xml ├── pecan2.bu.edu.sipnet.xml ├── pecan2.geo.tests.xml ├── pecan2.tests.xml ├── pecan32.ed.xml ├── pecan32.sipnet.xml ├── pecan64.biocro.xml ├── pecan64.ed.xml ├── pecan64.sipnet.xml ├── test_met_downloads.R └── testpfts.R └── web ├── 01-introduction.php ├── 02-modelsite.php ├── 02a-createsite.php ├── 03-inputs.php ├── 03a-ameriflux.php ├── 03a-fluxnet.php ├── 03a-narr.php ├── 04-remote.php ├── 04-runpecan.php ├── 05-running.php ├── 06-edit.php ├── 07-analysis.php ├── 07-continue.php ├── 08-finished.php ├── checkfailed.php ├── common.php ├── config.example.php ├── curl.php ├── dataset.php ├── delete.php ├── drag.and.drop.upload.php ├── favicon.ico ├── history.php ├── historylist.php ├── hostmodelinfo.php ├── images ├── browndog-small-transparent.gif ├── icon.jpeg ├── pecan_qrcode.png ├── pecan_small.jpg └── poweredby-transparent.gif ├── 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