Time Series Analysis of Sequencing Data

addNoise | Add Noise |

analyseTaxaInA | Compute edge statistics for an interaction matrix with... |

assignTaxonLevelsToA | Assign Taxon Levels |

autocorVsTaxonNum | Compute slope for increasing number of taxa versus their... |

binaryToPerturb | Given a binary vector, build a perturbation object |

binByMemory | Bin rows in a matrix by memory. |

caporaso_F4FecesL6 | Caporaso Stool Sequencing Data for Subject F4 on level 6 |

caporaso_F4LPalmL6 | Caporaso Left Palm Sequencing Data for Subject F4 on level 6 |

caporaso_F4RPalmL6 | Caporaso Right Palm Sequencing Data for Subject F4 on level 6 |

caporaso_F4TongueL6 | Caporaso Tongue Sequencing Data for Subject F4 on level 6 |

caporaso_M3FecesL6 | Caporaso Stool Sequencing Data for Subject M3 on level 6 |

compareTS | Community Time Series Comparison |

david_stoolA_metadata | David et al. stool sample metadata object of subject A |

david_stoolA_otus | David Stool Sequencing Data for Subject A |

david_stoolB_metadata | David et al. stool sample metadata object of subject B |

david_stoolB_otus | David Stool Sequencing Data for Subject B |

david_stool_lineages | David et al. stool OTU lineages |

doc | Dissimilarity-Overlap Curve (DOC) |

envGrowthChanges | Generate growth changes induced by environment |

filterTaxonMatrix | Filter taxa in an abundance matrix |

generateA | Generate an interaction matrix |

generateAbundances | Generate Abundance Vector |

generateDataSet | Generate a dataset |

generateTS | Generate community time series |

getAStats | Analyse an interaction matrix |

getConnectance | Connectance |

getPep | Positive Edge Percentage |

getTaxonomy | Get the taxonomy given OTU names and lineage information |

glv | Simulate time series with the generalized Lotka-Volterra... |

hill | Hill numbers |

identifyNoisetypes | Identify Noise Types |

interpolate | Time Series Interpolation |

limits | LIMITS |

limitsQuality | Quality scores and plot for estimated interaction matrices |

modifyA | Modify the interaction matrix |

noisetypes | Constructor for S3 noisetypes class |

normalize | Normalize a matrix |

perturbation | Perturbation |

perturbToBinary | Given a perturbation object, extract a binary vector |

plotA | Plot an interaction matrix. |

plotAbundanceVsNoisetypes | Plot taxon abundances classified by noise type |

plotNoisetypes | Do a barplot of the noise types |

plotNoisetypesVsHurst | Plot noise types versus their range of Hurst exponents |

powerspec | Report slope of periodogram in log scale |

rad | Rank abundance distribution curve |

rarefyFilter | Rarefaction combined with sample filtering |

removeLowAbundance | Remove lowest abundance species |

ricker | Generate time series with the Ricker model |

seqtime | Time Series Analysis of Sequencing Data |

sheldon | Compute evenness using Sheldon's index |

simCountMat | Simulate a count matrix |

simDecay | Plot community similarity decay against selected taxa or... |

simHubbell | Hubbell Simulation |

simNoiseMat | Simulate Noise |

simUntb | Run the Unified Neutral Theory of Biodiversity (UNTB) model |

sliceTS | Slice time series |

soi | Self-organized instable model |

taylor | Plot relationship between row mean and row variance |

testStability | Stability test for interaction matrix |

timeDecay | Plot the time decay. |

tsDiagnostic | Diagnostics for Community Simulation |

tsJumpStats | Compute statistics on jumps through community space |

tsplot | Time Series Plot |

tsubsample | Subsample Time Series |

varEvol | Plot mean variance versus the number of time points. |

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