Package: lirrr 0.0.2
lirrr: Functions collected/wrote by Daijiang Li
To keep all my functions in one place, and to use them more easily.
Authors:
lirrr_0.0.2.tar.gz
lirrr_0.0.2.zip(r-4.5)lirrr_0.0.2.zip(r-4.4)lirrr_0.0.2.zip(r-4.3)
lirrr_0.0.2.tgz(r-4.4-any)lirrr_0.0.2.tgz(r-4.3-any)
lirrr_0.0.2.tar.gz(r-4.5-noble)lirrr_0.0.2.tar.gz(r-4.4-noble)
lirrr_0.0.2.tgz(r-4.4-emscripten)lirrr_0.0.2.tgz(r-4.3-emscripten)
lirrr.pdf |lirrr.html✨
lirrr/json (API)
| # Install 'lirrr' in R: |
| install.packages('lirrr', repos = c('https://daijiang.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/daijiang/lirrr/issues
Last updated 8 months agofrom:8162955869. Checks:OK: 1 ERROR: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Sep 16 2024 |
| R-4.5-win | ERROR | Sep 16 2024 |
| R-4.5-linux | ERROR | Sep 16 2024 |
| R-4.4-win | ERROR | Sep 16 2024 |
| R-4.4-mac | ERROR | Sep 16 2024 |
| R-4.3-win | ERROR | Sep 16 2024 |
| R-4.3-mac | ERROR | Sep 16 2024 |
Exports:cap_first_letterdist_to_dfget_n_polytomyget_pd_alphalogit_tranmvpdpanel.corpanel.histpd2phylo_betapartrand_testrm_site_noobsrm_sp_noobstnrs_match_names_2unifrac2var_to_rownames
Dependencies:apeaplotaskpasscliclustercolorspacecpp11crayoncurldigestdplyrfansifarverfsgenericsggfunggplot2ggplotifyggtreegluegridGraphicsgtablehmshttrisobandjsonlitelabelinglatticelazyevallifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpatchworkpermutephylocomrPhyloMeasurespicantepillarpkgconfigplyrprettyunitsprogresspurrrR6RColorBrewerRcpprentrezreshape2rlangrnclrotlscalesstringistringrsystibbletidyrtidyselecttidytreetreeioutf8vctrsveganviridisLitewithrXMLyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Make the first letter upper case | cap_first_letter |
| Example community data | comm_a |
| #' Example community data | comm_b |
| Change a distance matrix or a matrix to a data frame | dist_to_df |
| Calculate number of polytomies | get_n_polytomy |
| Calculate alpha phylogenetic diversity | get_pd_alpha |
| Highlight all branches linking a subset of species in a phylogeny | highlight_subset_sp_in_phylogeny |
| Logit transformation | logit_tran |
| MPD and VPD (mean and variance of pairwise distance) | mvpd |
| 'panel.cor' to plot absolute value of correlations | panel.cor |
| 'panel.hist' to plot absolute value of correlations | panel.hist |
| Faith's PD | pd2 |
| Phylogenetic beta diversity partition | phylo_betapart |
| Randomization tests | rand_test |
| Remove site that has no observations (site by sp matrix) | rm_site_noobs |
| Remove sp that not observed at any site (site by sp matrix) | rm_sp_noobs |
| Match taxa names with the Open Tree of Life | tnrs_match_names_2 |
| #' Example phylogeny | tree |
| unifrac | unifrac2 |
| Function to add a column as row names, and remove it from columns | var_to_rownames |
