Package: nichevol 0.1.20
nichevol: Tools for Ecological Niche Evolution Assessment Considering Uncertainty
A collection of tools that allow users to perform critical steps in the process of assessing ecological niche evolution over phylogenies, with uncertainty incorporated explicitly in reconstructions. The method proposed here for ancestral reconstruction of ecological niches characterizes species' niches using a bin-based approach that incorporates uncertainty in estimations. Compared to other existing methods, the approaches presented here reduce risk of overestimation of amounts and rates of ecological niche evolution. The main analyses include: initial exploration of environmental data in occurrence records and accessible areas, preparation of data for phylogenetic analyses, executing comparative phylogenetic analyses of ecological niches, and plotting for interpretations. Details on the theoretical background and methods used can be found in: Owens et al. (2020) <doi:10.1002/ece3.6359>, Peterson et al. (1999) <doi:10.1126/science.285.5431.1265>, Soberón and Peterson (2005) <doi:10.17161/bi.v2i0.4>, Peterson (2011) <doi:10.1111/j.1365-2699.2010.02456.x>, Barve et al. (2011) <doi:10.1111/ecog.02671>, Machado-Stredel et al. (2021) <doi:10.21425/F5FBG48814>, Owens et al. (2013) <doi:10.1016/j.ecolmodel.2013.04.011>, Saupe et al. (2018) <doi:10.1093/sysbio/syx084>, and Cobos et al. (2021) <doi:10.1111/jav.02868>.
Authors:
nichevol_0.1.20.tar.gz
nichevol_0.1.20.zip(r-4.5)nichevol_0.1.20.zip(r-4.4)nichevol_0.1.20.zip(r-4.3)
nichevol_0.1.20.tgz(r-4.4-any)nichevol_0.1.20.tgz(r-4.3-any)
nichevol_0.1.20.tar.gz(r-4.5-noble)nichevol_0.1.20.tar.gz(r-4.4-noble)
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nichevol.pdf |nichevol.html✨
nichevol/json (API)
NEWS
# Install 'nichevol' in R: |
install.packages('nichevol', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/marlonecobos/nichevol/issues
- character_table - Example of character table for six species
- occ_list - Example of occurrence records for six species
- par_rec_table - Example of table with results from parsimony reconstructions
- tree - Example of a phylogenetic tree for six species
- tree5 - Example of a phylogenetic tree for five species
- tree_data - Example of a list containing a tree and a table of characters for six species
Last updated 1 years agofrom:e3a1112b80. Checks:OK: 3 NOTE: 4. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Aug 31 2024 |
R-4.5-win | NOTE | Aug 31 2024 |
R-4.5-linux | NOTE | Aug 01 2024 |
R-4.4-win | NOTE | Aug 31 2024 |
R-4.4-mac | NOTE | Aug 31 2024 |
R-4.3-win | OK | Aug 31 2024 |
R-4.3-mac | OK | Aug 31 2024 |
Exports:bin_envbin_ml_recbin_par_recbin_tablebin_tablesbin_tables0hist_evalueshistograms_envmap_nichevolniche_barsniche_labelsniche_legendnichevol_barsnichevol_labelsnichevol_legendpdf_histogramsread_bin_tableread_bin_tablesrename_tipsscore_tipscore_treeset_uncertaintysig_sqsmooth_recstats_evalstats_evalues
Dependencies:apecastorcliclusterGenerationcodacodetoolscolorspacecombinatcpp11DEoptimdeSolvedigestdoParallelexpmfansifarverfastmatchforeachgeigergenericsggplot2ggseqlogogluegtableigraphisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmnormtmunsellmvtnormnaturalsortncbitnlmenumDerivoptimParallelphangornphytoolspillarpkgconfigquadprogR6RColorBrewerRcppRcppEigenrlangRSpectrascalesscatterplot3dstringistringrsubplexterratibbleutf8vctrsviridisLitewithr