Package: philr 1.33.0
Justin Silverman
philr: Phylogenetic partitioning based ILR transform for metagenomics data
PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.
Authors:
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philr.pdf |philr.html✨
philr/json (API)
NEWS
| # Install 'philr' in R: |
| install.packages('philr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jsilve24/philr/issues
On BioConductor:philr-1.33.0(bioc 3.21)philr-1.32.0(bioc 3.20)
immunooncologysequencingmicrobiomemetagenomicssoftware
Last updated 22 days agofrom:9061ebc2a4. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 31 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | OK | Oct 31 2024 |
| R-4.3-mac | OK | Oct 31 2024 |
Exports:annotate_balancebuildilrBasepcalculate.blwclrpclrpInvconvert_to_longilrpilrpInvmean_dist_to_tipsminicloname.balancename.to.nnnamed_rtreenn.to.namephilrphilrInvphylo2sbpshiftpshiftpInv
Dependencies:apeaplotclicolorspacecpp11digestdplyrfansifarverfastmatchfsgenericsggfunggplot2ggplotifyggtreegluegridGraphicsgtableigraphisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmunsellnlmepatchworkphangornpillarpkgconfigpurrrquadprogR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselecttidytreetreeioutf8vctrsviridisLitewithryulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| annotate_balance | annotate_balance |
| Weighted ILR Contrast Matrix | buildilrBasep |
| Calculate Branch Length Weightings for ILR Coordinates | calc.blw calculate.blw |
| Weighted CLR Transform | clrp clrpInv |
| Converts wide format ILR transformed data to long format | convert_to_long |
| Geometric Means of Columns | g.colMeans |
| Weighted Geometric Means of Rows | g.rowMeans |
| Weighted ILR Transform | ilrp ilrpInv |
| Mean distance from internal nodes to descendant tips | mean_dist_to_tips |
| miniclo | miniclo |
| Convert between node/tip labels and integer node numbers | name.to.nn name_nodenumber_conversion nn.to.name |
| Name a balance (coordinate) based on taxonomy | name.balance |
| Generate random tree with named internal nodes | named_rtree |
| Data transformation and driver of PhILR. | build.phylo.ilr philr |
| Inverse of PhILR Transform | philrInv |
| Create Sequential Binary Partition from Phylogenetic Tree | phylo2sbp |
| Shift data to origin given by p | shift shiftp shiftpInv |
