Files in hallucigenia-sparsa/seqtime

Time Series Analysis of Sequencing Data

.DS_Store

.Rbuildignore

.gitignore

.travis.yml

DESCRIPTION

LICENSE

NAMESPACE

R/.DS_Store

R/.Rapp.history

R/addNoise.R R/analyseTSComparison.R R/analyseTaxaInA.R R/assignTaxonLevelsToA.R R/autocorVsTaxonNum.R R/binByMemory.R R/caporaso_F4FecesL6.R R/caporaso_F4LPalmL6.R R/caporaso_F4RPalmL6.R R/caporaso_F4TongueL6.R R/caporaso_M3FecesL6.R R/compareFit.R R/compareTS.R R/david_stoolA_metadata.R R/david_stoolA_otus.R R/david_stoolB_metadata.R R/david_stoolB_otus.R R/david_stool_lineages.R R/doc.R R/envGrowthChanges.R R/filterTaxonMatrix.R R/firstlib.R R/generateA.R R/generateAbundances.R R/generateDataSet.R R/generateTS.R R/getAStats.R R/getConnectance.R R/getPep.R R/getTaxonomy.R R/glv.R R/hill.R R/identifyNoisetypes.R R/interpolate.R R/klemm.game.R R/limits.R R/limitsQuality.R R/modifyA.R R/noisetypes.R R/normalize.R R/perturbation.R R/plotA.R R/plotAbundanceVsNoisetypes.R R/plotNoisetypes.R R/plotNoisetypesVsHurst.R R/plotTSComparison.R R/powerspec.R R/rad.R R/rarefyFilter.R R/removeLowAbundance.R R/ricker.R R/seqtime.R R/sheldon.R R/simCountMat.R R/simDecay.R R/simHubbell.R R/simNoiseMat.R R/simuntb.R R/sliceTS.R R/soi.R R/taylor.R R/testStability.R R/timeDecay.R R/tsDiagnostic.R R/tsJumpStats.R R/tsplot.R R/tsubsample.R R/varEvol.R README.md

data/caporaso_F4FecesL6.rda

data/caporaso_F4LPalmL6.rda

data/caporaso_F4RPalmL6.rda

data/caporaso_F4TongueL6.rda

data/caporaso_M3FecesL6.rda

data/david_stoolA_metadata.rda

data/david_stoolA_otus.rda

data/david_stoolB_metadata.rda

data/david_stoolB_otus.rda

data/david_stool_lineages.rda

docs/404.html

docs/LICENSE-text.html

docs/articles/dataset_generation.html

docs/articles/dataset_generation_files/figure-html/unnamed-chunk-2-1.png

docs/articles/dataset_generation_files/figure-html/unnamed-chunk-3-1.png

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docs/articles/figure_noise_simulations/noise_simu-1.png

docs/articles/figure_seqtime_tour/unnamed-chunk-10-1.png

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docs/articles/figure_seqtime_tour/unnamed-chunk-9-1.png

docs/articles/index.html

docs/articles/network_inference.html

docs/articles/noise_simulations.html

docs/articles/seqtime_tour.html

docs/authors.html

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/addNoise.html

docs/reference/analyseTaxaInA.html

docs/reference/assignTaxonLevelsToA-1.png

docs/reference/assignTaxonLevelsToA.html

docs/reference/autocorVsTaxonNum.html

docs/reference/binByMemory-1.png

docs/reference/binByMemory.html

docs/reference/binaryToPerturb.html

docs/reference/caporaso_F4FecesL6.html

docs/reference/caporaso_F4LPalmL6.html

docs/reference/caporaso_F4RPalmL6.html

docs/reference/caporaso_F4TongueL6.html

docs/reference/caporaso_M3FecesL6.html

docs/reference/compareTS.html

docs/reference/david_stoolA_metadata.html

docs/reference/david_stoolA_otus-1.png

docs/reference/david_stoolA_otus.html

docs/reference/david_stoolB_metadata.html

docs/reference/david_stoolB_otus-1.png

docs/reference/david_stoolB_otus.html

docs/reference/david_stool_lineages.html

docs/reference/doc.html

docs/reference/envGrowthChanges.html

docs/reference/filterTaxonMatrix.html

docs/reference/generateA.html

docs/reference/generateAbundances.html

docs/reference/generateDataSet.html

docs/reference/generateTS.html

docs/reference/getAStats.html

docs/reference/getConnectance.html

docs/reference/getPep.html

docs/reference/getTaxonomy.html

docs/reference/glv-1.png

docs/reference/glv.html

docs/reference/hill.html

docs/reference/identifyNoisetypes-1.png

docs/reference/identifyNoisetypes.html

docs/reference/index.html

docs/reference/interpolate-1.png

docs/reference/interpolate.html

docs/reference/limits.html

docs/reference/limitsQuality.html

docs/reference/modifyA.html

docs/reference/noisetypes.html

docs/reference/normalize.html

docs/reference/perturbToBinary.html

docs/reference/perturbation.html

docs/reference/plotA-1.png

docs/reference/plotA.html

docs/reference/plotAbundanceVsNoisetypes.html

docs/reference/plotNoisetypes.html

docs/reference/plotNoisetypesVsHurst.html

docs/reference/powerspec-1.png

docs/reference/powerspec.html

docs/reference/rad-1.png

docs/reference/rad-2.png

docs/reference/rad.html

docs/reference/rarefyFilter.html

docs/reference/removeLowAbundance.html

docs/reference/ricker-1.png

docs/reference/ricker-2.png

docs/reference/ricker.html

docs/reference/seqtime.html

docs/reference/sheldon.html

docs/reference/simCountMat-1.png

docs/reference/simCountMat.html

docs/reference/simDecay-1.png

docs/reference/simDecay-2.png

docs/reference/simDecay.html

docs/reference/simHubbell.html

docs/reference/simNoiseMat-1.png

docs/reference/simNoiseMat-2.png

docs/reference/simNoiseMat-3.png

docs/reference/simNoiseMat.html

docs/reference/simUntb-1.png

docs/reference/simUntb.html

docs/reference/sliceTS.html

docs/reference/soi.html

docs/reference/taylor.html

docs/reference/testStability.html

docs/reference/timeDecay-1.png

docs/reference/timeDecay.html

docs/reference/tsDiagnostic.html

docs/reference/tsJumpStats.html

docs/reference/tsplot-1.png

docs/reference/tsplot-2.png

docs/reference/tsplot-3.png

docs/reference/tsplot.html

docs/reference/tsubsample.html

docs/reference/varEvol-1.png

docs/reference/varEvol.html

inst/extras/build.cran.sh

inst/extras/document.R

man/.DS_Store

man/addNoise.Rd man/analyseTaxaInA.Rd man/assignTaxonLevelsToA.Rd man/autocorVsTaxonNum.Rd man/binByMemory.Rd man/binaryToPerturb.Rd man/caporaso_F4FecesL6.Rd man/caporaso_F4LPalmL6.Rd man/caporaso_F4RPalmL6.Rd man/caporaso_F4TongueL6.Rd man/caporaso_M3FecesL6.Rd man/compareTS.Rd man/david_stoolA_metadata.Rd man/david_stoolA_otus.Rd man/david_stoolB_metadata.Rd man/david_stoolB_otus.Rd man/david_stool_lineages.Rd man/doc.Rd man/envGrowthChanges.Rd man/filterTaxonMatrix.Rd man/generateA.Rd man/generateAbundances.Rd man/generateDataSet.Rd man/generateTS.Rd man/getAStats.Rd man/getConnectance.Rd man/getPep.Rd man/getTaxonomy.Rd man/glv.Rd man/hill.Rd man/identifyNoisetypes.Rd man/interpolate.Rd man/limits.Rd man/limitsQuality.Rd man/modifyA.Rd man/noisetypes.Rd man/normalize.Rd man/perturbToBinary.Rd man/perturbation.Rd man/plotA.Rd man/plotAbundanceVsNoisetypes.Rd man/plotNoisetypes.Rd man/plotNoisetypesVsHurst.Rd man/powerspec.Rd man/rad.Rd man/rarefyFilter.Rd man/removeLowAbundance.Rd man/ricker.Rd man/seqtime.Rd man/sheldon.Rd man/simCountMat.Rd man/simDecay.Rd man/simHubbell.Rd man/simNoiseMat.Rd man/simUntb.Rd man/sliceTS.Rd man/soi.Rd man/taylor.Rd man/testStability.Rd man/timeDecay.Rd man/tsDiagnostic.Rd man/tsJumpStats.Rd man/tsplot.Rd man/tsubsample.Rd man/varEvol.Rd

seqtime.Rproj

tests/testthat.R tests/testthat/test-A.R

vignettes/.DS_Store

vignettes/.gitignore

vignettes/dataset_generation.Rmd vignettes/main.R vignettes/network_inference.Rmd vignettes/noise_simulations.Rmd vignettes/seqtime_tour.Rmd

vignettes/seqtime_tour.html

hallucigenia-sparsa/seqtime documentation built on Jan. 9, 2023, 11:53 p.m.