├── .gitignore ├── .travis.yml ├── LICENSE ├── Readme.md ├── Rpkg ├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── NEWS.md ├── R │ ├── carbon.R │ ├── coordinates.R │ ├── flatterSIDb.R │ ├── incubationTime.R │ ├── isCumulative.R │ ├── loadEntries.R │ ├── missingFields.R │ ├── nitrogen.R │ ├── onePoolFlux.R │ ├── onepFit.R │ ├── plotEntry.R │ ├── readEntry.R │ ├── sidb.R │ ├── threeppFit.R │ ├── threepsFit.R │ ├── treatmentLevels.R │ ├── treatmentNames.R │ ├── treatmentUnitNames.R │ ├── twopMMFit.R │ ├── twopfFit.R │ ├── twoppFit.R │ └── twopsFit.R ├── README.md ├── Rpkg.Rproj ├── cran-comments.md ├── data │ └── sidb.RData ├── inst │ └── extdata │ │ ├── sidbEntries │ │ ├── Andrews2000SBB │ │ │ ├── initConditions.csv │ │ │ ├── metadata.yaml │ │ │ └── timeSeries.csv │ │ └── Sierra2017BG │ │ │ ├── initConditions.csv │ │ │ ├── metadata.yaml │ │ │ └── timeSeries.csv │ │ └── template_metadata.yaml ├── man │ ├── carbon.Rd │ ├── coordinates.Rd │ ├── flatterSIDb.Rd │ ├── incubationTime.Rd │ ├── isCumulative.Rd │ ├── loadEntries.Rd │ ├── missingFields.Rd │ ├── nitrogen.Rd │ ├── onePoolFlux.Rd │ ├── onepFit.Rd │ ├── plotEntry.Rd │ ├── readEntry.Rd │ ├── sidb.Rd │ ├── threeppFit.Rd │ ├── threepsFit.Rd │ ├── treatmentLevels.Rd │ ├── treatmentNames.Rd │ ├── treatmentUnitNames.Rd │ ├── twopMMFit.Rd │ ├── twopfFit.Rd │ ├── twoppFit.Rd │ └── twopsFit.Rd └── vignettes │ ├── .gitignore │ └── sidbQueryReportPlot.Rmd ├── data ├── Andrews2000SBB │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Arevalo2012 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Barrett2006 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Bracho2016SBB │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Bradford2010 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── BradleyCook2016 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Conant2008 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Craine2010NatGeo │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Crow2018 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Crow2019a │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Crow2019b │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Dalias2001 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Doetterl2015 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Fontaine2007 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Gillabel2010 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Haddix2011 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Hopkins2006 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Karhu2010 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Lavoie2011JGR │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── NeffHooper2002 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Niklinska1999 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Readme.md ├── Reichstein2000 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Rey2008 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Richardson2020 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Salome2010 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Sierra2017BG │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Song2010 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Stewart2008SBB │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Townsend1997 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Wang2010 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Wells2022 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── WicklandNeff2008 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Winkler1996 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── Zhang2007 │ ├── initConditions.csv │ ├── metadata.yaml │ └── timeSeries.csv ├── initConditions.csv ├── studies_list.csv ├── template_metadata.yaml └── template_metadata_workingfile.yaml ├── demo ├── Readme.md ├── Summary.Rmd ├── Summary.html ├── Summary.md ├── Summary.pdf ├── figure │ ├── unnamed-chunk-3-1.png │ ├── unnamed-chunk-7-1.png │ └── unnamed-chunk-8-1.png └── modelFit.Rmd ├── devel ├── Crow2019a_AIC.csv ├── multiFit_example.r └── multiSIdbFit_example.r ├── docs ├── LICENSE.txt ├── README.txt ├── _config.yml ├── _data │ ├── entries │ │ ├── Andrews2000SBB.yaml │ │ ├── Arevalo2012.yaml │ │ ├── Barrett2006.yaml │ │ ├── Bracho2016SBB.yaml │ │ ├── Bradford2010.yaml │ │ ├── BradleyCook2016.yaml │ │ ├── Conant2008.yaml │ │ ├── Craine2010NatGeo.yaml │ │ ├── Crow2019a.yaml │ │ ├── Crow2019b.yaml │ │ ├── Dalias2001.yaml │ │ ├── Doetterl2015.yaml │ │ ├── Fontaine2007.yaml │ │ ├── Gillabel2010.yaml │ │ ├── Haddix2011.yaml │ │ ├── Hopkins2006.yaml │ │ ├── Karhu2010.yaml │ │ ├── Lavoie2011JGR.yaml │ │ ├── NeffHooper2002.yaml │ │ ├── Niklinska1999.yaml │ │ ├── Reichstein2000.yaml │ │ ├── Rey2008.yaml │ │ ├── Salome2010.yaml │ │ ├── Sierra2017BG.yaml │ │ ├── Song2010.yaml │ │ ├── Stewart2008SBB.yaml │ │ ├── Townsend1997.yaml │ │ ├── Wang2010.yaml │ │ ├── WicklandNeff2008.yaml │ │ ├── Winkler1996.yaml │ │ └── Zhang2007.yaml │ └── summary.yml ├── _includes │ ├── banner.html │ ├── footer.html │ ├── head.html │ └── header.html ├── _layouts │ ├── default.html │ ├── landing-page.html │ └── post.html ├── _posts │ └── 2018-08-21-intro.md ├── assets │ ├── incubationTime.png │ ├── map.png │ ├── pic01.jpg │ ├── pic02.jpg │ ├── pic03.jpg │ └── pic04.jpg ├── blog.html ├── contact.html ├── css │ ├── font-awesome.min.css │ ├── ie │ │ ├── backgroundsize.min.htc │ │ ├── html5shiv.js │ │ ├── v8.css │ │ └── v9.css │ ├── images │ │ ├── dark-bl.svg │ │ ├── dark-br.svg │ │ ├── dark-tl.svg │ │ ├── dark-tr.svg │ │ ├── light-bl.svg │ │ ├── light-br.svg │ │ ├── light-tl.svg │ │ ├── light-tr.svg │ │ └── overlay.png │ ├── skel.css │ ├── style-mobile.css │ ├── style-narrow.css │ ├── style-narrower.css │ ├── style-normal.css │ ├── style-noscript.css │ ├── style-wide.css │ └── style.css ├── entries │ └── index.md ├── feed.xml ├── fonts │ ├── FontAwesome.otf │ ├── fontawesome-webfont.eot │ ├── fontawesome-webfont.svg │ ├── fontawesome-webfont.ttf │ └── fontawesome-webfont.woff ├── images │ ├── banner.jpg │ ├── pic01.jpg │ ├── pic02.jpg │ ├── pic03.jpg │ └── pic04.jpg ├── index.html ├── js │ ├── init.js │ ├── jquery.dropotron.min.js │ ├── jquery.min.js │ ├── jquery.scrollgress.min.js │ ├── jquery.scrolly.min.js │ ├── skel-layers.min.js │ └── skel.min.js ├── left-sidebar.html ├── no-sidebar.html ├── references.md └── right-sidebar.html ├── manuscript ├── AllTS-modelFit.Rmd ├── AllTS-modelFit.pdf ├── AllTS_modelFit.R ├── Histograms.R ├── HistogramsAug28_2019.pdf ├── ModFitTS_DataSaving_Func.R ├── ModFitTS_Rmd_Func.R ├── SIDB_mapCode.R ├── Statistics.R ├── modelFit.Rmd ├── modelFit.docx ├── modelsFit.pdf ├── statisticTest.R ├── testModelFit_cumulative.Rmd └── testModelFit_cumulative.pdf ├── out ├── Readme.md └── baseMetadata.csv ├── scripts ├── Readme.md ├── baseMetadata.R ├── docInstall.sh ├── mkReferences.R ├── modelsFit.R ├── multiSidbFit │ └── multiFit.R ├── pkgDocumentation.R ├── queryReportPlot_vignette.R ├── saveBinaryData.R ├── sidb_1.0.0.tar.gz └── websiteReports.R ├── sidb.Rproj └── tests ├── Readme.md ├── data_test.R ├── non_ascii_test.sh ├── pkg_test.sh └── testthat └── test_dataStructure.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/SoilBGC-Datashare/sidb/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: 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