Package: nichevol 0.1.20

Marlon E. Cobos

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:Marlon E. Cobos [aut, cre], Hannah L. Owens [aut], A. Townsend Peterson [aut]

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)
nichevol_0.1.20.tgz(r-4.4-emscripten)nichevol_0.1.20.tgz(r-4.3-emscripten)
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'))

Peer review:

Bug tracker:https://github.com/marlonecobos/nichevol/issues

Datasets:
  • 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

On CRAN:

26 exports 14 stars 1.91 score 66 dependencies 1 mentions 2 scripts 189 downloads

Last updated 1 years agofrom:e3a1112b80. Checks:OK: 3 NOTE: 4. Indexed: no.

TargetResultDate
Doc / VignettesOKAug 31 2024
R-4.5-winNOTEAug 31 2024
R-4.5-linuxNOTEAug 01 2024
R-4.4-winNOTEAug 31 2024
R-4.4-macNOTEAug 31 2024
R-4.3-winOKAug 31 2024
R-4.3-macOKAug 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

Readme and manuals

Help Manual

Help pageTopics
Helper function to prepare bin tablesbin_env
Maximum likelihood reconstruction of ancestral character statesbin_ml_rec
Maximum parsimony reconstruction of ancestral character statesbin_par_rec
Bin table of environmental conditions in M and for occurrencesbin_table
Bin tables of environmental conditions in M and for occurrences from objectsbin_tables
Bin tables of environmental conditions in M and for occurrences from databin_tables0
Example of character table for six speciescharacter_table
Histograms of environmental conditions in M and for occurrences (one species)hist_evalues
Histograms of environmental conditions in M and for occurrenceshistograms_env
Example of accessible areas for a speciesm m1 m2 m3 m4 m5 m6
Maps of niche reconstructions and changes detectedmap_nichevol
PNG bar figures to represent ecological niches of distinct taxaniche_bars
Labels to represent niches of tips and ancestorsniche_labels
Legends for niche labels in phylogenetic treesniche_legend
nichevol: Assessment of Species’ Ecological Niche Evolution Considering Uncertainty in Reconstructionsnichevol
PNG bar figures for representing niche evolutionnichevol_bars
Labels to represent changes of niche characteristics between ancestors and descendantsnichevol_labels
Legends for niche evolution labels in phylogenetic treesnichevol_legend
Example of occurrence records for six speciesocc_list
Example of table with results from parsimony reconstructionspar_rec_table
Helper function to create PDF files with histogramspdf_histograms
Read tables of binary niche characters from directoryread_bin_table read_bin_tables
Helper function to rename tips of trees for simulationsrename_tips
Helper function to calculate the median bin score for a given speciesscore_tip
Helper function to assign bin scores to every tip in a given treescore_tree
Set values of uncertainty towards one or both ends of the variableset_uncertainty
Helper function to get sigma squared values for a given datasetsig_sq
Smooth character table values resulted from ancestral character state reconstructionssmooth_rec
Statistics of environmental conditions in M and for occurrences (one variable)stats_eval
Statistics of environmental conditions in M and for occurrences (multiple variables)stats_evalues
Example of an environmental variable used in analysistemp
Example of a phylogenetic tree for six speciestree
Example of a list containing a tree and a table of characters for six speciestree_data
Example of a phylogenetic tree for five speciestree5