Man pages for hallucigenia-sparsa/seqtime
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. |
