close

Showing 13 of total 13 results (show query)

ericmarcon

entropart:Entropy Partitioning to Measure Diversity

Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity. Estimation-bias corrections are available.

Maintained by Eric Marcon. Last updated 2 months ago.

biodiversitydiversityentropy-partitioningestimatormeasurespecies

25.1 match 9 stars 7.81 score 115 scripts 1 dependents

boydorr

rdiversity:Measurement and Partitioning of Similarity-Sensitive Biodiversity

Provides a framework for the measurement and partitioning of the (similarity-sensitive) biodiversity of a metacommunity and its constituent subcommunities. Richard Reeve, et al. (2016) <arXiv:1404.6520v3>.

Maintained by Richard Reeve. Last updated 3 years ago.

biodiversitydiversity-measurementpartitioning-diversity

27.8 match 8 stars 6.85 score 66 scripts 1 dependents

taddallas

metacom:Analysis of the 'Elements of Metacommunity Structure'

Functions to analyze coherence, boundary clumping, and turnover following the pattern-based metacommunity analysis of Leibold and Mikkelson 2002 <doi:10.1034/j.1600-0706.2002.970210.x>. The package also includes functions to visualize ecological networks, and to calculate modularity as a replacement to boundary clumping.

Maintained by Tad Dallas. Last updated 2 years ago.

ecologymetacommunity

23.8 match 11 stars 5.95 score 27 scripts 1 dependents

cran

iCAMP:Infer Community Assembly Mechanisms by Phylogenetic-Bin-Based Null Model Analysis

To implement a general framework to quantitatively infer Community Assembly Mechanisms by Phylogenetic-bin-based null model analysis, abbreviated as 'iCAMP' (Ning et al 2020) <doi:10.1038/s41467-020-18560-z>. It can quantitatively assess the relative importance of different community assembly processes, such as selection, dispersal, and drift, for both communities and each phylogenetic group ('bin'). Each bin usually consists of different taxa from a family or an order. The package also provides functions to implement some other published methods, including neutral taxa percentage (Burns et al 2016) <doi:10.1038/ismej.2015.142> based on neutral theory model and quantifying assembly processes based on entire-community null models ('QPEN', Stegen et al 2013) <doi:10.1038/ismej.2013.93>. It also includes some handy functions, particularly for big datasets, such as phylogenetic and taxonomic null model analysis at both community and bin levels, between-taxa niche difference and phylogenetic distance calculation, phylogenetic signal test within phylogenetic groups, midpoint root of big trees, etc. Version 1.3.x mainly improved the function for 'QPEN' and added function 'icamp.cate()' to summarize 'iCAMP' results for different categories of taxa (e.g. core versus rare taxa).

Maintained by Daliang Ning. Last updated 3 years ago.

19.9 match 2 stars 2.26 score 1 dependents

theoreticalecology

sjSDM:Scalable Joint Species Distribution Modeling

A scalable and fast method for estimating joint Species Distribution Models (jSDMs) for big community data, including eDNA data. The package estimates a full (i.e. non-latent) jSDM with different response distributions (including the traditional multivariate probit model). The package allows to perform variation partitioning (VP) / ANOVA on the fitted models to separate the contribution of environmental, spatial, and biotic associations. In addition, the total R-squared can be further partitioned per species and site to reveal the internal metacommunity structure, see Leibold et al., <doi:10.1111/oik.08618>. The internal structure can then be regressed against environmental and spatial distinctiveness, richness, and traits to analyze metacommunity assembly processes. The package includes support for accounting for spatial autocorrelation and the option to fit responses using deep neural networks instead of a standard linear predictor. As described in Pichler & Hartig (2021) <doi:10.1111/2041-210X.13687>, scalability is achieved by using a Monte Carlo approximation of the joint likelihood implemented via 'PyTorch' and 'reticulate', which can be run on CPUs or GPUs.

Maintained by Maximilian Pichler. Last updated 25 days ago.

deep-learninggpu-accelerationmachine-learningspecies-distribution-modellingspecies-interactions

3.9 match 69 stars 7.64 score 70 scripts

ericmarcon

divent:Entropy Partitioning to Measure Diversity

Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>. 'divent' provides functions to estimate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.

Maintained by Eric Marcon. Last updated 22 days ago.

cpp

5.0 match 1 stars 4.81 score 1 scripts

vanderleidebastiani

SYNCSA:Analysis of Functional and Phylogenetic Patterns in Metacommunities

Analysis of metacommunities based on functional traits and phylogeny of the community components. The functions that are offered here implement for the R environment methods that have been available in the SYNCSA application written in C++ (by Valerio Pillar, available at <http://ecoqua.ecologia.ufrgs.br/SYNCSA.html>).

Maintained by Vanderlei Julio Debastiani. Last updated 5 years ago.

3.5 match 3 stars 5.36 score 28 scripts 1 dependents

pilaboratory

sads:Maximum Likelihood Models for Species Abundance Distributions

Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.

Maintained by Paulo I. Prado. Last updated 1 years ago.

1.8 match 23 stars 8.66 score 244 scripts 3 dependents

frareb

inpdfr:Analyse Text Documents Using Ecological Tools

A set of functions to analyse and compare texts, using classical text mining functions, as well as those from theoretical ecology.

Maintained by Rebaudo Francois. Last updated 2 years ago.

2.3 match 2 stars 4.41 score 26 scripts

a-s-melo

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'.

Maintained by Adriano Sanches Melo. Last updated 9 months ago.

3.5 match 1 stars 2.39 score 41 scripts 1 dependents

vanderleidebastiani

PCPS:Principal Coordinates of Phylogenetic Structure

Set of functions for analysis of Principal Coordinates of Phylogenetic Structure (PCPS).

Maintained by Vanderlei Julio Debastiani. Last updated 4 years ago.

1.8 match 1 stars 3.65 score 7 scripts

cran

comsimitv:Flexible Framework for Simulating Community Assembly

Flexible framework for trait-based simulation of community assembly, where components could be replaced by user-defined function and that allows variation of traits within species.

Maintained by Zoltan Botta-Dukat. Last updated 4 years ago.

2.0 match 2.00 score 3 scripts

rsetienne

SADISA:Species Abundance Distributions with Independent-Species Assumption

Computes the probability of a set of species abundances of a single or multiple samples of individuals with one or more guilds under a mainland-island model. One must specify the mainland (metacommunity) model and the island (local) community model. It assumes that species fluctuate independently. The package also contains functions to simulate under this model. See Haegeman, B. & R.S. Etienne (2017). A general sampling formula for community structure data. Methods in Ecology & Evolution 8: 1506-1519 <doi:10.1111/2041-210X.12807>.

Maintained by Rampal S. Etienne. Last updated 5 years ago.

0.5 match 3.00 score 6 scripts

: