Package: CommEcol 1.8.1

CommEcol: Community Ecology Analyses

Autosimilarity curves, standardization of spatial extent, dissimilarity indexes that overweight rare species, phylogenetic and functional (pairwise and multisample) dissimilarity indexes and nestedness for phylogenetic, functional and other diversity metrics. The methods for phylogenetic and functional nestedness is described in Melo, Cianciaruso and Almeida-Neto (2014) <doi:10.1111/2041-210X.12185>. This should be a complement to available packages, particularly 'vegan'.

Authors:Adriano Sanches Melo [aut, cre]

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CommEcol.pdf |CommEcol.html✨
CommEcol/json (API)

# Install 'CommEcol' in R:

install.packages('CommEcol', repos = c('https://a-s-melo.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

japi - Macroinvertebrate morphospecies living on stones of a stream in southeast Brazil
sites4.6 - Artificial dataset containing 4 samples [rows] and 6 species[columns].
sites5.6 - Artificial dataset containing 5 samples [rows] and 6 species[columns].
sites6.6 - Artificial dataset containing 6 samples [rows] and 6 species[columns].
stairs6 - Example of phylogenetic tree containing 6 species.
tree6 - Example of phylogenetic tree containing 6 species.

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.36 score 1 stars 1 packages 38 scripts 350 downloads 2 mentions 13 exports 127 dependencies

Last updated 4 months agofrom:35b6772685. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 27 2024
R-4.5-win	OK	Oct 27 2024
R-4.5-linux	OK	Oct 27 2024
R-4.4-win	OK	Oct 27 2024
R-4.4-mac	OK	Oct 27 2024
R-4.3-win	OK	Oct 27 2024
R-4.3-mac	OK	Oct 27 2024

Exports:autosimi betaRegDisp compas dis.chao dis.goodall dis.nness dis.nness.find.m part.m.tree part.p.tree select.window standExtent treeNodf treeNodfTest

Dependencies:abind ade4 adegenet adegraphics adephylo adespatial ape askpass base64enc betapart boot bslib cachem class classInt cli cluster codetools colorspace commonmark cpp11 crayon curl DBI deldir digest doSNOW dplyr e1071 fansi farver fastmap fastmatch fontawesome foreach fs generics geometry ggplot2 glue gmp gtable hms htmltools httpuv httr igraph interp isoband iterators itertools jpeg jquerylib jsonlite KernSmooth labeling later lattice latticeExtra lifecycle linprog lpSolve magic magrittr MASS Matrix memoise mgcv mime minpack.lm munsell nlme openssl permute phylobase picante pillar pixmap pkgconfig plyr png prettyunits progress promises proxy purrr R6 rappdirs rcdd RColorBrewer Rcpp RcppArmadillo RcppEigen RcppProgress reshape2 rlang rncl RNeXML s2 sass scales segmented seqinr sf shiny snow sourcetools sp spData spdep stringi stringr sys tibble tidyr tidyselect units utf8 uuid vctrs vegan viridisLite withr wk XML xml2 xtable

Help page	Topics
Community Ecology Analyses	CommEcol-package CommEcol
Autosimilarity curve of species community data	autosimi
Beta diversity metrics between sites in a moving window along environmental gradients	betaRegDisp
Simulation of species community data along gradients	compas
Chao et al. dissimilarity indices	dis.chao
Goodall dissimilarity index	dis.goodall
NNESS and NESS dissimilarity indices	dis.nness dis.nness.find.m
Macroinvertebrate morphospecies living on stones of a stream in southeast Brazil	japi
Partition of multi-sample dissimilarity indices using phylogenetic/functional data	part.m.tree
Partition of pair-wise dissimilarity indices using phylogenetic/functional data	part.p.tree
Select cells inside a defined window of a gridded dataset	select.window
Artificial dataset containing 4 samples [rows] and 6 species[columns].	sites4.6
Artificial dataset containing 5 samples [rows] and 6 species[columns].	sites5.6
Artificial dataset containing 6 samples [rows] and 6 species[columns].	sites6.6
Example of phylogenetic tree containing 6 species.	stairs6
Standardization of spatial extent for two metacommunities by subsampling	standExtent
Example of phylogenetic tree containing 6 species.	tree6
Tree-like Nestedness of Ecological Metacommunities	treeNodf treeNodfTest

Package: CommEcol 1.8.1

CommEcol: Community Ecology Analyses

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