Man pages for hallucigenia-sparsa/seqtime
Time Series Analysis of Sequencing Data

addNoiseAdd Noise
analyseTaxaInACompute edge statistics for an interaction matrix with...
assignTaxonLevelsToAAssign Taxon Levels
autocorVsTaxonNumCompute slope for increasing number of taxa versus their...
binaryToPerturbGiven a binary vector, build a perturbation object
binByMemoryBin rows in a matrix by memory.
caporaso_F4FecesL6Caporaso Stool Sequencing Data for Subject F4 on level 6
caporaso_F4LPalmL6Caporaso Left Palm Sequencing Data for Subject F4 on level 6
caporaso_F4RPalmL6Caporaso Right Palm Sequencing Data for Subject F4 on level 6
caporaso_F4TongueL6Caporaso Tongue Sequencing Data for Subject F4 on level 6
caporaso_M3FecesL6Caporaso Stool Sequencing Data for Subject M3 on level 6
compareTSCommunity Time Series Comparison
david_stoolA_metadataDavid et al. stool sample metadata object of subject A
david_stoolA_otusDavid Stool Sequencing Data for Subject A
david_stoolB_metadataDavid et al. stool sample metadata object of subject B
david_stoolB_otusDavid Stool Sequencing Data for Subject B
david_stool_lineagesDavid et al. stool OTU lineages
docDissimilarity-Overlap Curve (DOC)
envGrowthChangesGenerate growth changes induced by environment
filterTaxonMatrixFilter taxa in an abundance matrix
generateAGenerate an interaction matrix
generateAbundancesGenerate Abundance Vector
generateDataSetGenerate a dataset
generateTSGenerate community time series
getAStatsAnalyse an interaction matrix
getPepPositive Edge Percentage
getTaxonomyGet the taxonomy given OTU names and lineage information
glvSimulate time series with the generalized Lotka-Volterra...
hillHill numbers
identifyNoisetypesIdentify Noise Types
interpolateTime Series Interpolation
limitsQualityQuality scores and plot for estimated interaction matrices
modifyAModify the interaction matrix
noisetypesConstructor for S3 noisetypes class
normalizeNormalize a matrix
perturbToBinaryGiven a perturbation object, extract a binary vector
plotAPlot an interaction matrix.
plotAbundanceVsNoisetypesPlot taxon abundances classified by noise type
plotNoisetypesDo a barplot of the noise types
plotNoisetypesVsHurstPlot noise types versus their range of Hurst exponents
powerspecReport slope of periodogram in log scale
radRank abundance distribution curve
rarefyFilterRarefaction combined with sample filtering
removeLowAbundanceRemove lowest abundance species
rickerGenerate time series with the Ricker model
seqtimeTime Series Analysis of Sequencing Data
sheldonCompute evenness using Sheldon's index
simCountMatSimulate a count matrix
simDecayPlot community similarity decay against selected taxa or...
simHubbellHubbell Simulation
simNoiseMatSimulate Noise
simUntbRun the Unified Neutral Theory of Biodiversity (UNTB) model
sliceTSSlice time series
soiSelf-organized instable model
taylorPlot relationship between row mean and row variance
testStabilityStability test for interaction matrix
timeDecayPlot the time decay.
tsDiagnosticDiagnostics for Community Simulation
tsJumpStatsCompute statistics on jumps through community space
tsplotTime Series Plot
tsubsampleSubsample Time Series
varEvolPlot mean variance versus the number of time points.
hallucigenia-sparsa/seqtime documentation built on Oct. 25, 2018, 2:12 p.m.