Files in hallucigenia-sparsa/seqtime
Time Series Analysis of Sequencing Data

.DS_Store
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/.DS_Store
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/LICENSE
docs/LICENSE.html
docs/articles/README.md docs/articles/dataset_generation.R
docs/articles/dataset_generation.html
docs/articles/dataset_generation.md
docs/articles/dataset_generation_files/figure-html/unnamed-chunk-2-1.png
docs/articles/dataset_generation_files/figure-html/unnamed-chunk-3-1.png
docs/articles/dataset_generation_files/figure-html/unnamed-chunk-4-1.png
docs/articles/figure_network_inference/unnamed-chunk-10-1.png
docs/articles/figure_network_inference/unnamed-chunk-12-1.png
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docs/articles/figure_network_inference/unnamed-chunk-7-1.png
docs/articles/figure_network_inference/unnamed-chunk-9-1.png
docs/articles/figure_noise_simulations/noise_simu-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-10-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-11-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-12-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-13-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-14-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-15-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-16-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-3-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-4-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-5-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-6-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-7-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-8-1.png
docs/articles/figure_seqtime_tour/unnamed-chunk-9-1.png
docs/articles/index.html
docs/articles/main.R
docs/articles/network_inference.html
docs/articles/network_inference.md
docs/articles/noise_simulations.html
docs/articles/noise_simulations.md
docs/articles/seqtime_tour.html
docs/articles/seqtime_tour.md
docs/authors.html
docs/index.html
docs/jquery.sticky-kit.min.js
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/reference/addNoise.html
docs/reference/assignTaxonLevelsToA-1.png
docs/reference/assignTaxonLevelsToA-2.png
docs/reference/assignTaxonLevelsToA-5.png
docs/reference/assignTaxonLevelsToA-7.png
docs/reference/assignTaxonLevelsToA.html
docs/reference/autocorVsTaxonNum.html
docs/reference/binByMemory-1.png
docs/reference/binByMemory-2.png
docs/reference/binByMemory-4.png
docs/reference/binByMemory.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-2.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-2.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-2.png
docs/reference/glv-3.png
docs/reference/glv.html
docs/reference/hill.html
docs/reference/identifyNoisetypes-1.png
docs/reference/identifyNoisetypes-2.png
docs/reference/identifyNoisetypes-6.png
docs/reference/identifyNoisetypes-9.png
docs/reference/identifyNoisetypes.html
docs/reference/index.html
docs/reference/interpolate-1.png
docs/reference/interpolate-2.png
docs/reference/interpolate-3.png
docs/reference/interpolate.html
docs/reference/limits.html
docs/reference/limitsQuality.html
docs/reference/modifyA.html
docs/reference/noisetypes.html
docs/reference/noisetypesHurst.html
docs/reference/normalize.html
docs/reference/perturbation.html
docs/reference/plotA-1.png
docs/reference/plotA-2.png
docs/reference/plotA-3.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-2.png
docs/reference/powerspec.html
docs/reference/rad-1.png
docs/reference/rad-2.png
docs/reference/rad-3.png
docs/reference/rad-4.png
docs/reference/rad-5.png
docs/reference/rad-8.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-3.png
docs/reference/ricker-4.png
docs/reference/ricker-6.png
docs/reference/ricker.html
docs/reference/seqtime.html
docs/reference/sheldon.html
docs/reference/simCountMat-1.png
docs/reference/simCountMat-2.png
docs/reference/simCountMat.html
docs/reference/simDecay-1.png
docs/reference/simDecay-2.png
docs/reference/simDecay-3.png
docs/reference/simDecay-4.png
docs/reference/simDecay-6.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-4.png
docs/reference/simNoiseMat-5.png
docs/reference/simNoiseMat-6.png
docs/reference/simNoiseMat-7.png
docs/reference/simNoiseMat-8.png
docs/reference/simNoiseMat.html
docs/reference/simUntb-1.png
docs/reference/simUntb-2.png
docs/reference/simUntb.html
docs/reference/sliceTS.html
docs/reference/soi-4.png
docs/reference/soi.html
docs/reference/taylor.html
docs/reference/testStability.html
docs/reference/timeDecay-1.png
docs/reference/timeDecay-2.png
docs/reference/timeDecay-4.png
docs/reference/timeDecay.html
docs/reference/tsDiagnostic-2.png
docs/reference/tsDiagnostic-4.png
docs/reference/tsDiagnostic-6.png
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-395.png
docs/reference/tsplot-4.png
docs/reference/tsplot-5.png
docs/reference/tsplot-6.png
docs/reference/tsplot-8.png
docs/reference/tsplot.html
docs/reference/tsubsample.html
docs/reference/varEvol-1.png
docs/reference/varEvol-2.png
docs/reference/varEvol-4.png
docs/reference/varEvol.html
inst/doc/.DS_Store
inst/doc/dataset_generation.R inst/doc/dataset_generation.Rmd
inst/doc/dataset_generation.html
inst/doc/network_inference.R inst/doc/network_inference.Rmd
inst/doc/network_inference.html
inst/doc/noise_simulations.R inst/doc/noise_simulations.Rmd
inst/doc/noise_simulations.html
inst/doc/seqtime_tour.R inst/doc/seqtime_tour.Rmd
inst/doc/seqtime_tour.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/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/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/.gitignore
vignettes/README.md vignettes/dataset_generation.Rmd vignettes/dataset_generation.md vignettes/main.R vignettes/network_inference.Rmd vignettes/network_inference.md vignettes/noise_simulations.Rmd vignettes/noise_simulations.md vignettes/seqtime_tour.Rmd vignettes/seqtime_tour.md
hallucigenia-sparsa/seqtime documentation built on June 16, 2018, 1:49 p.m.