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 dependentsboydorr
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 dependentstaddallas
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.
23.8 match 11 stars 5.95 score 27 scripts 1 dependentstheoreticalecology
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 scriptsericmarcon
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.
5.0 match 1 stars 4.81 score 1 scriptsvanderleidebastiani
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 dependentspilaboratory
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 dependentsfrareb
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 scriptsa-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 dependentsvanderleidebastiani
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 scriptscran
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 scriptsrsetienne
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