Files in ncss-tech/aqp
Algorithms for Quantitative Pedology

.Rbuildignore
.Rinstignore
.gitattributes
.github/.gitignore
.github/workflows/R-CMD-check.yaml
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md R/AAAA.R R/Class-SoilProfileCollection.R R/HzDepthLogicSubset.R R/L1_profiles.R R/PMS2Munsell.R R/SoilProfileCollection-coercion.R R/SoilProfileCollection-integrity.R R/SoilProfileCollection-iterators.R R/SoilProfileCollection-methods.R R/SoilProfileCollection-operators.R R/SoilProfileCollection-setters.R R/SoilProfileCollection-slice-methods.R R/SoilProfileCollection-spatial.R R/accuracy_uncertainty.R R/addBracket.R R/addVolumeFraction.R R/aggregateColor.R R/aggregateSoilDepth.R R/alignTransect.R R/allocate.R R/aqp-package.R R/bootstrapSoilTexture.R R/checkHzDepthLogic.R R/checkSPC.R R/colorContrast.R R/colorContrastPlot.R R/colorQuantiles.R R/combine.R R/compositeSPC.R R/contrastChart.R R/contrastClass.R R/data-documentation.R R/datadots.R R/denormalize.R R/depthOf.R R/depthWeights.R R/dice.R R/duplicate.R R/enforce_df_class.R R/estimateAWC.R R/estimatePSCS.R R/estimateSoilDepth.R R/evalGenHz.R R/evalMissingData.R R/explainPlotSPC.R R/f.noise.R R/factor-level-setters.R R/fillHzGaps.R R/findOverlap-fixOverlap.R R/genSlabLabels.R R/generalize.hz.R R/get.increase.matrix.R R/get.ml.hz.R R/getArgillicBounds.R R/getCambicBounds.R R/getClosestMunsellChip.R R/getLastHorizonID.R R/getSoilDepthClass.R R/getSurfaceHorizonDepth.R R/glom.R R/glomApply.R R/group_by.R R/groupedProfilePlot.R R/guessColumnNames.R R/guessGenHzLevels.R R/harmonize.R R/huePosition.R R/hzBoundary.R R/hzTransitionProbabilities.R R/invertLabelColor.R R/lunique.R R/missingDataGrid.R R/mixMunsell.R R/mollicEpipedon.R R/mostLikelyHzSequence.R R/munsell2rgb.R R/mutate_profile.R R/panel.depth_function.R R/perturb.R R/plotColorMixture.R R/plotMultipleSPC.R R/plotSPC.R R/plot_distance_graph.R R/prepanel.depth_function.R R/previewColors.R R/profile_compare.R R/random_profile.R R/rebuildSPC.R R/repairMissingHzDepths.R R/resample.twotheta.R R/segment.R R/sim.R R/similarMunsellChips.R R/sketch-utils.R R/slab.R R/slicedHSD.R R/soilColorIndices.R R/soilColorSignature.R R/soilPalette.R R/soiltexture.R R/spc2mpspline.R R/spec2Munsell.R R/split.R R/splitLogicErrors.R R/summarize.R R/tauW.R R/texture.R R/textureTriangleSummary.R R/transform.R R/unroll.R R/zzz.R README.md
data/ROSETTA.centroids.rda
data/ca630.rda
data/equivalent_munsell.rda
data/jacobs2000.rda
data/munsell.rda
data/munsell.spectra.rda
data/munsell.spectra.wide.rda
data/pms.munsell.lut.rda
data/rowley2019.rda
data/rruff.sample.rda
data/sierraTransect.rda
data/soil_minerals.rda
data/soiltexture.rda
data/sp1.rda
data/sp2.rda
data/sp3.rda
data/sp4.rda
data/sp5.rda
data/sp6.rda
data/spectral.reference.rda
data/traditionalColorNames.rda
data/us.state.soils.rda
demo/00Index
demo/aqp.R demo/slope_effect_hz_thickness.R
docs/404.html
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inst/WORDLIST
inst/_pkgdown.yml
inst/example-data/jacobs2000-hz-data.csv
inst/example-data/jacobs2000-site-data.csv
man/HzDepthLogicSubset.Rd man/L1_profiles.Rd man/PMS2Munsell.Rd man/ROSETTA.centroids.Rd man/SoilProfileCollection-class.Rd man/SoilProfileCollection-plotting-methods.Rd man/SoilTextureLevels.Rd man/addBracket.Rd man/addDiagnosticBracket.Rd man/addVolumeFraction.Rd man/aggregateColor.Rd man/aggregateSoilDepth.Rd man/alignTransect.Rd man/allocate.Rd man/aqp-package.Rd man/aqp_df_class.Rd man/argillic.clay.increase.depth.Rd man/barron.torrent.redness.LAB.Rd man/bootstrapSoilTexture.Rd man/brierScore.Rd man/buntley.westin.index.Rd man/ca630.Rd man/checkHzDepthLogic.Rd man/checkSPC.Rd man/coercion-methods.Rd man/colorContrast.Rd man/colorContrastPlot.Rd man/colorQuantiles.Rd man/combine-SoilProfileCollection-method.Rd man/compositeSPC.Rd man/confusionIndex.Rd man/contrastChart.Rd man/contrastClass.Rd man/coordinates.Rd man/correctAWC.Rd man/crit.clay.argillic.Rd man/denormalize.Rd man/depthOf.Rd man/depthWeights.Rd man/depth_units.Rd man/depths.Rd man/diagnostic_hz-set.Rd man/diagnostic_hz.Rd man/dice.Rd man/dollarsign-set.Rd man/dollarsign.Rd man/dot-HSD.Rd man/dot-as.data.frame.aqp.Rd man/dot-data_dots.Rd man/dot-makeEquivalentMunsellLUT.Rd man/dot-parseGrouped_formula.Rd man/doublebracket-set.Rd man/doublebracket.Rd man/duplicate.Rd man/equivalentMunsellChips.Rd man/equivalent_munsell.Rd man/estimateAWC.Rd man/estimatePSCS.Rd man/estimateSoilDepth.Rd man/evalGenHZ.Rd man/evalMissingData.Rd man/explainPlotSPC.Rd man/f.noise.Rd man/fillHzGaps.Rd man/findOverlap.Rd man/fixOverlap.Rd man/generalize.hz.Rd man/get.increase.depths.Rd man/get.increase.matrix.Rd man/get.ml.hz.Rd man/getArgillicBounds.Rd man/getCambicBounds.Rd man/getClosestMunsellChip.Rd man/getLastHorizonID.Rd man/getSoilDepthClass.Rd man/getSurfaceHorizonDepth.Rd man/glom-SoilProfileCollection-method.Rd man/glomApply.Rd man/grepSPC.Rd man/groupSPC.Rd man/groupedProfilePlot.Rd man/guessGenHzLevels.Rd man/guessHzAttrName.Rd man/guessHzDesgnName.Rd man/guessHzTexClName.Rd man/harden.melanization.Rd man/harden.rubification.Rd man/harmonize-SoilProfileCollection-method.Rd man/hasDarkColors.Rd man/horizonColorIndices.Rd man/horizonDepths.Rd man/horizonNames.Rd man/horizons.Rd man/huePosition.Rd man/hurst.redness.Rd man/hzDepthTests.Rd man/hzDesgn.Rd man/hzDistinctnessCodeToOffset.Rd man/hzID.Rd man/hzTopographyCodeToLineType.Rd man/hzTopographyCodeToOffset.Rd man/hzTransitionProbabilities.Rd man/hzdesgnname-set.Rd man/hzdesgnname.Rd man/hzidname.Rd man/hztexclname-set.Rd man/hztexclname.Rd man/idname.Rd man/invertLabelColor.Rd man/jacobs2000.Rd man/length.Rd man/lunique.Rd man/max.Rd man/metadata.Rd man/min.Rd man/missingDataGrid.Rd man/mixMunsell.Rd man/mollic.thickness.requirement.Rd man/munsell.Rd man/munsell.spectra.Rd man/munsell2rgb.Rd man/munsell2spc-SoilProfileCollection-method.Rd man/mutate_profile.Rd man/names.Rd man/nrow.Rd man/overlapMetrics.Rd man/panel.depth_function.Rd man/parseMunsell.Rd man/pbindlist.Rd man/pc.Rd man/perturb.Rd man/plotColorMixture.Rd man/plotColorQuantiles.Rd man/plotMultipleSPC.Rd man/plot_distance_graph.Rd man/pms.munsell.lut.Rd man/previewColors.Rd man/profileApply.Rd man/profileGroupLabels.Rd man/profile_id.Rd man/proj4string-SoilProfileCollection-method.Rd man/proj4string-set-SoilProfileCollection-ANY-method.Rd man/random_profile.Rd man/rebuildSPC.Rd man/reorderHorizons.Rd man/repairMissingHzDepths.Rd man/replaceHorizons.Rd man/resample.twotheta.Rd man/restrictions-set.Rd man/restrictions.Rd man/rgb2munsell.Rd man/rowley2019.Rd man/rruff.sample.Rd man/segment.Rd man/shannonEntropy.Rd man/show.Rd man/sierraTransect.Rd man/sim.Rd man/singlebracket.Rd man/site.Rd man/siteNames.Rd man/slab-methods.Rd man/slice-methods.Rd man/slicedHSD.Rd man/soilColorSignature.Rd man/soilPalette.Rd man/soil_minerals.Rd man/soiltexture.Rd man/sp1.Rd man/sp2.Rd man/sp3.Rd man/sp4.Rd man/sp5.Rd man/sp6.Rd man/spc2mpspline-SoilProfileCollection-method.Rd man/spc_in_sync.Rd man/spec2Munsell.Rd man/spectral.reference.Rd man/split-SoilProfileCollection-method.Rd man/splitLogicErrors.Rd man/subApply.Rd man/subset-SoilProfileCollection-method.Rd man/subsetHz-SoilProfileCollection-method.Rd man/subsetProfiles.Rd man/summarizeSPC.Rd man/tauW.Rd man/texture.Rd man/textureTriangleSummary.Rd man/thompson.bell.darkness.Rd man/traditionalColorNames.Rd man/transform.Rd man/trunc-SoilProfileCollection-method.Rd man/unique.Rd man/unroll.Rd man/us.state.soils.Rd man/validSpatialData.Rd man/xtableTauW.Rd
misc/.travis.yml.bak
misc/aqp-spellcheck-allowed.csv
misc/aqp2/aqp-nse.R misc/aqp2/big_random.R misc/aqp2/coalesce.R misc/aqp2/df_test.R misc/aqp2/function-dependencies.R misc/aqp2/glomDepthOfDemo.R misc/aqp2/jindex-benchmarks.R
misc/aqp2/man_deprecated/SPC-split-methods.Rd
misc/aqp2/man_deprecated/SPC-unique-methods.Rd
misc/aqp2/man_deprecated/SPC-utils.Rd
misc/aqp2/man_deprecated/SoilProfileCollection-class.Rd misc/aqp2/man_deprecated/checkHzDepthLogic.Rd
misc/aqp2/man_deprecated/profileApply-methods.Rd
misc/aqp2/man_deprecated/union.Rd
misc/aqp2/multiglomDT.R misc/aqp2/new_splines.R misc/aqp2/pipes_test.R misc/aqp2/robust-union.R misc/aqp2/spc_integrity.Rmd misc/aqp2/spline_assessments.R misc/aqp2/test-k-keywords.R
misc/example-data/OSACA/OSACA-example_soil_data.csv
misc/example-data/OSACA/process_OSACA-data.R
misc/example-data/redox-jacobs-et-al-2000/hz.txt
misc/example-data/redox-jacobs-et-al-2000/process.R
misc/example-data/redox-jacobs-et-al-2000/site.txt
misc/example-data/rosetta/AWC-by-texture-class-ROSETTA.R
misc/example-data/rosetta/centroids-edited.csv
misc/example-data/rosetta/centroids.csv
misc/example-data/rosetta/format-and-save.R misc/example-data/rosetta/get-centroids.R misc/example-data/rosetta/prep-VG-curves-and-sim-quantiles.R
misc/example-data/rowley-et-al-2019/ca-res.txt
misc/example-data/rowley-et-al-2019/geochem.txt
misc/example-data/rowley-et-al-2019/hz.txt
misc/example-data/rowley-et-al-2019/min.txt
misc/example-data/rowley-et-al-2019/process.R
misc/example-data/sierra-transect/dahlgren-granitics.csv
misc/example-data/sierra-transect/processing.R
misc/example-data/sierra-transect/rasmussen-andisitic-lahar-site.csv
misc/example-data/sierra-transect/rasmussen-andisitic-lahar.csv
misc/example-data/sierra-transect/transect-GIS-data.csv
misc/example-data/soiltexture/first-draft-LUT.R misc/example-data/soiltexture/make-SSC-to-texture-LUT.R
misc/example-data/state-soils/state_soils.csv
misc/example-data/state-soils/us-state-soils.R misc/fixOverlap-SANN.R misc/harden-color-PDI.R
misc/hexstickers/aqp_sticker_v1.png
misc/hexstickers/aqp_sticker_v2.png
misc/hexstickers/minify-SPC-hex.R
misc/hexstickers/sharpshootR_sticker_v1.png
misc/hexstickers/soilDB_sticker_v1.png
misc/hexstickers/static/sharpshootR_spade.png
misc/hexstickers/static/soildb_flattening.png
misc/make_R_from_Rd.R
misc/old-CITATION
misc/profiling/munsell2rgb-DT-merge.R misc/profiling/random_profile-benchmarks.R misc/sandbox/CIELAB-demonstration.R misc/sandbox/DT-testing-plotSPC.R misc/sandbox/IPA-algorithm-test.R
misc/sandbox/KSSL-full-texture-distribution.png
misc/sandbox/L1-slab-eval-by-GG.R misc/sandbox/Polychrome-example.R misc/sandbox/RMF-examples.R misc/sandbox/SPC_brick.R misc/sandbox/SVG-TT-for-NASIS.R
misc/sandbox/TT.svg
misc/sandbox/TX-ideas.R misc/sandbox/USFS-modal-pedon-style-sketches.R
misc/sandbox/VNIR-example-spectra.rds
misc/sandbox/VNIR-spectra-soil-color.R misc/sandbox/animate-OSD-colors-with-depth.R misc/sandbox/animate-fixOverlap.R misc/sandbox/bootstrap-texture-eval.R misc/sandbox/checkHzDepthLogic-byhz.R misc/sandbox/clarksville.R misc/sandbox/color-by-series.R misc/sandbox/color-distance-with-depth.R misc/sandbox/color-mixture-ternary.R misc/sandbox/color-quantiles-L1-median.R misc/sandbox/color-spiral.R misc/sandbox/colordistance-leon-example.R misc/sandbox/colorspace-specplot-example.R misc/sandbox/contrastChart-check.R misc/sandbox/datatable-checkHzDepthLogic.R misc/sandbox/demo-perturb-interface.R misc/sandbox/dice.R misc/sandbox/eval-mixMunsell-candidates.R misc/sandbox/fancySoilColorStyle.R misc/sandbox/find-fix-NA-depths.R misc/sandbox/findNormalizableVars.R misc/sandbox/fixOhorizons.R misc/sandbox/font-test.R misc/sandbox/gap-filling.R misc/sandbox/hz-distinctness-demo.R misc/sandbox/minify-SPC-ideas.R misc/sandbox/mix-all-hues.R misc/sandbox/mix-soil-pigments.R misc/sandbox/mixing-color-depths-mollic.R misc/sandbox/moist-to-dry-color-via-OSDs.R
misc/sandbox/morphologic-grid/examples/hv4-site.csv
misc/sandbox/morphologic-grid/examples/hv4-smu.csv
misc/sandbox/morphologic-grid/examples/hv4.tif
misc/sandbox/morphologic-grid/examples/hv4.tif.aux.xml
misc/sandbox/morphologic-grid/examples/hv4.tif.vat.cpg
misc/sandbox/morphologic-grid/examples/hv4.tif.vat.dbf
misc/sandbox/morphologic-grid/experiments.R misc/sandbox/morphologic-grid/soil-color-grid/colordistance-package.R
misc/sandbox/morphologic-grid/soil-color-grid/leaf-john-kelley.jpg
misc/sandbox/morphologic-grid/soil-color-grid/notes.R misc/sandbox/mps-functions.R misc/sandbox/mps-vs-slab.R misc/sandbox/mps2-eval.R misc/sandbox/new-classes/accessors.r misc/sandbox/new-classes/benchmark-new-classes.r misc/sandbox/new-classes/classes-rebooted.r misc/sandbox/new-classes/coerce.r misc/sandbox/new-classes/init.r misc/sandbox/new-classes/overloads.r misc/sandbox/new-classes/setters.r misc/sandbox/new-classes/spatial.r misc/sandbox/new-classes/test-rebooted.r misc/sandbox/optimizing-fillHzGaps.R misc/sandbox/pedon-RMF-colors.R misc/sandbox/plot-single-SPC-notes.R misc/sandbox/pretty-soil-jars.R misc/sandbox/profile_compare-k-medoids.R misc/sandbox/slabPlot.R misc/sandbox/slice-wise-Tukey-HSD.R misc/sandbox/slice-wise-entropy-example.R misc/sandbox/soil-color-betadisp.R misc/sandbox/soil-color-opinions.R misc/sandbox/soil-colors-legos.R misc/sandbox/soil-texture-separate-sim-by-class.R misc/sandbox/soilColorSignature-testing.R misc/sandbox/spec2Munsell-examples.R
misc/sandbox/spilled-paint.png
misc/sandbox/spilled-paint2.png
misc/sandbox/spring-colors.R
misc/sandbox/spring-colors.csv
misc/sandbox/state-soils.R misc/sandbox/swatchplot-ideas.R misc/sandbox/test-aqp2.R misc/sandbox/test-rgb2munsell-with-dE00.R misc/sandbox/traditional-color-names.R misc/sandbox/transect-OSD-viz.R
misc/sketches/hz-boundary-ideas-01.png
misc/sketches/hz-boundary-ideas-02.png
misc/sp5-old.rda
misc/spellcheck.R misc/test_suite/AQP-dylan-S4-hacking.R misc/test_suite/AQP_parallel.R misc/test_suite/aggregateColor-dev.R misc/test_suite/check_mean_sd_quantiles.R misc/test_suite/check_profile_compare.R misc/test_suite/compiler-benchmarking.R misc/test_suite/load-dummy-examples.R misc/test_suite/nasis-metadata-dev.R misc/test_suite/new_S4_examples.R
misc/test_suite/nssl/CA630-pedon.csv
misc/test_suite/nssl/CA630-site.csv
misc/test_suite/nssl/MLRA_18_22-lab_data.csv
misc/test_suite/nssl/ca630-CEC_and_Bases.csv
misc/test_suite/nssl/ca630-new.Rda
misc/test_suite/nssl/ca630.rda
misc/test_suite/nssl/ca630_b.dbf
misc/test_suite/nssl/ca630_b.prj
misc/test_suite/nssl/ca630_b.sbn
misc/test_suite/nssl/ca630_b.sbx
misc/test_suite/nssl/ca630_b.shp
misc/test_suite/nssl/ca630_b.shp.xml
misc/test_suite/nssl/ca630_b.shx
misc/test_suite/nssl/notes.R misc/test_suite/pcs_wt_mean_test.R misc/test_suite/profiling.R misc/test_suite/sda_soilweb_comparison.R misc/test_suite/segment-reprex.R misc/test_suite/slab-data.table-test.R misc/test_suite/slab-profiling.R misc/test_suite/slab2.R
misc/utils/Munsell/SpectralReflectancesOf2007MunsellBookOfColorGlossy.txt.gz
misc/utils/Munsell/Spectrum00001.asd
misc/utils/Munsell/add-neutral-hue.R misc/utils/Munsell/automatic_conversion.R
misc/utils/Munsell/cie.15.2004.tables.xls
misc/utils/Munsell/color_conversion_functions.R misc/utils/Munsell/interpolate-spectra.R misc/utils/Munsell/main.R misc/utils/Munsell/make-spectral-reference-RDA.R
misc/utils/Munsell/munsell-all.dat.gz
misc/utils/Munsell/munsell.R misc/utils/Munsell/munsellinterpol-package-eval.R misc/utils/Munsell/prepare-simplfied-spectra-library.R
misc/utils/Munsell/spectral-reference-data.csv
misc/utils/Munsell/traditional-names-from-NASIS.csv
misc/utils/Munsell/traditional-names.R misc/utils/PMS/multiple-matches.R
misc/utils/PMS/notes.txt
misc/utils/PMS/pantone-coated.csv
misc/utils/PMS/pantone-uncoated.csv
misc/utils/PMS/prepare-LUT.R misc/utils/rebuild-aqp-soilDB-SPCs.R tests/testthat.R tests/testthat/test-DT-tbl.R tests/testthat/test-L1_profiles.R tests/testthat/test-PMS2Munsell.R tests/testthat/test-SPC-combine.R tests/testthat/test-SPC-k-keywords.R tests/testthat/test-SPC-objects.R tests/testthat/test-acc-unc.R tests/testthat/test-aggregateColor.R tests/testthat/test-aggregateSoilDepth.R tests/testthat/test-alignTransect.R tests/testthat/test-aqp.R tests/testthat/test-argillic.R tests/testthat/test-awc.R tests/testthat/test-bootstrapSoilTexture.R tests/testthat/test-cambic.R tests/testthat/test-checkHzDepthLogic.R tests/testthat/test-color-conversion.R tests/testthat/test-color-signature.R tests/testthat/test-colorContrast.R tests/testthat/test-colorIndices.R tests/testthat/test-colorQuantiles.R tests/testthat/test-denormalize.R tests/testthat/test-dice.R tests/testthat/test-dplyr-verbs.R tests/testthat/test-duplicate.R tests/testthat/test-estimateSoilDepth.R tests/testthat/test-evalMissingData.R tests/testthat/test-fillHzGaps.R tests/testthat/test-fix-find-overlap.R tests/testthat/test-genSlabLabels.R tests/testthat/test-genhz.R tests/testthat/test-getLastHorizonID.R tests/testthat/test-glom.R tests/testthat/test-guessColumnNames.R tests/testthat/test-harmonize.R tests/testthat/test-lunique.R tests/testthat/test-missingDataGrid.R tests/testthat/test-mixMunsell.R tests/testthat/test-mollic.R tests/testthat/test-overlap.R tests/testthat/test-plotSPC.R tests/testthat/test-profileApply.R tests/testthat/test-profile_compare.R tests/testthat/test-pscs.R tests/testthat/test-repairMissingHzDepths.R tests/testthat/test-segment.R tests/testthat/test-sim.R tests/testthat/test-similarMunsellChips.R tests/testthat/test-slab.R tests/testthat/test-slabPlot.R tests/testthat/test-slice.R tests/testthat/test-soil-depth.R tests/testthat/test-spc2mpspline.R tests/testthat/test-spec2Munsell.R tests/testthat/test-split.R tests/testthat/test-subsetHz.R tests/testthat/test-surface-thickness.R tests/testthat/test-textureTriangleSummary.R
ncss-tech/aqp documentation built on June 12, 2021, 2:48 p.m.