R-universe search: ecology

adeverse

ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintained by Aurélie Siberchicot. Last updated 9 days ago.

openblas cpp

46.6 match 40 stars 15.10 score 2.2k scripts 257 dependents

vegandevs

vegan:Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Maintained by Jari Oksanen. Last updated 29 days ago.

ecological-modelling ecology ordination fortran openblas

26.5 match 472 stars 19.41 score 15k scripts 440 dependents

cmerow

rangeModelMetadata:Provides Templates for Metadata Files Associated with Species Range Models

Range Modeling Metadata Standards (RMMS) address three challenges: they (i) are designed for convenience to encourage use, (ii) accommodate a wide variety of applications, and (iii) are extensible to allow the community of range modelers to steer it as needed. RMMS are based on a data dictionary that specifies a hierarchical structure to catalog different aspects of the range modeling process. The dictionary balances a constrained, minimalist vocabulary to improve standardization with flexibility for users to provide their own values. Merow et al. (2019) <DOI:10.1111/geb.12993> describe the standards in more detail. Note that users who prefer to use the R package 'ecospat' can obtain it from <https://github.com/ecospat/ecospat>.

Maintained by Cory Merow. Last updated 8 months ago.

ecological-metadata-language ecological-modelling ecological-models ecology species-distribution-modelling species-distributions

31.7 match 6 stars 6.96 score 16 scripts 3 dependents

mspinillos

ecoregime:Analysis of Ecological Dynamic Regimes

A toolbox for implementing the Ecological Dynamic Regime framework (Sánchez-Pinillos et al., 2023 <doi:10.1002/ecm.1589>) to characterize and compare groups of ecological trajectories in multidimensional spaces defined by state variables. The package includes the RETRA-EDR algorithm to identify representative trajectories, functions to generate, summarize, and visualize representative trajectories, and several metrics to quantify the distribution and heterogeneity of trajectories in an ecological dynamic regime and quantify the dissimilarity between two or more ecological dynamic regimes. The package also includes a set of functions to assess ecological resilience based on ecological dynamic regimes (Sánchez-Pinillos et al., 2024 <doi:10.1016/j.biocon.2023.110409>).

Maintained by Martina Sánchez-Pinillos. Last updated 12 months ago.

31.8 match 7 stars 5.32 score 8 scripts

andrewljackson

SIBER:Stable Isotope Bayesian Ellipses in R

Fits bi-variate ellipses to stable isotope data using Bayesian inference with the aim being to describe and compare their isotopic niche.

Maintained by Andrew Jackson. Last updated 10 months ago.

community-ecology ecology niche-modelling stable-isotopes jags cpp

17.5 match 37 stars 9.15 score 187 scripts 1 dependents

confoobio

GMSE:Generalised Management Strategy Evaluation Simulator

Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.

Maintained by A. Bradley Duthie. Last updated 3 years ago.

adaptive-management agricultural-modelling conflict conflict-resolution conservation ecological-modelling ecological-models ecology food-security game-theory genetic-algorithm genetic-algorithms management-decisions management-strategy-evaluation population-model simulation wildlife-management

25.8 match 10 stars 5.43 score 178 scripts

rekyt

funrar:Functional Rarity Indices Computation

Computes functional rarity indices as proposed by Violle et al. (2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed using both regional and local information. Functional Rarity combines both the functional aspect of rarity as well as the extent aspect of rarity. 'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.

Maintained by Matthias Grenié. Last updated 12 months ago.

ecological-models ecology rarity traits

17.5 match 17 stars 7.85 score 233 scripts 1 dependents

sciviews

pastecs:Package for Analysis of Space-Time Ecological Series

Regularisation, decomposition and analysis of space-time series. The pastecs R package is a PNEC-Art4 and IFREMER (Benoit Beliaeff <Benoit.Beliaeff@ifremer.fr>) initiative to bring PASSTEC 2000 functionalities to R.

Maintained by Philippe Grosjean. Last updated 1 years ago.

ecology time-series

12.9 match 4 stars 10.34 score 2.1k scripts 13 dependents

weecology

portalr:Create Useful Summaries of the Portal Data

Download and generate summaries for the rodent, plant, ant, and weather data from the Portal Project. Portal is a long-term (and ongoing) experimental monitoring site in the Chihuahuan desert. The raw data files can be found at <https://github.com/weecology/portaldata>.

Maintained by Glenda M. Yenni. Last updated 4 months ago.

community-ecology ecology small-mammal-trapping

17.5 match 11 stars 7.48 score 63 scripts

project-gen3sis

gen3sis:General Engine for Eco-Evolutionary Simulations

Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.

Maintained by Oskar Hagen. Last updated 1 years ago.

biodiversity ecology evolution mechanistic model modeling simulation cpp

17.3 match 29 stars 7.56 score 69 scripts

jeffreyevans

spatialEco:Spatial Analysis and Modelling Utilities

Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.

Maintained by Jeffrey S. Evans. Last updated 26 days ago.

biodiversity conservation ecology r-spatial raster spatial vector

12.8 match 110 stars 9.55 score 736 scripts 2 dependents

ropensci

phylocomr:Interface to 'Phylocom'

Interface to 'Phylocom' (<https://phylodiversity.net/phylocom/>), a library for analysis of 'phylogenetic' community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like 'aot', 'ecovolve', 'bladj', 'phylomatic', and more.

Maintained by Luna Luisa Sanchez Reyes. Last updated 2 years ago.

phylogeny phylocom phylodiversity community structure character evolution species community-ecology ecology evolution

17.5 match 15 stars 6.81 score 19 scripts 3 dependents

stscl

gdverse:Analysis of Spatial Stratified Heterogeneity

Analyzing spatial factors and exploring spatial associations based on the concept of spatial stratified heterogeneity, while also taking into account local spatial dependencies, spatial interpretability, complex spatial interactions, and robust spatial stratification. Additionally, it supports the spatial stratified heterogeneity family established in academic literature.

Maintained by Wenbo Lv. Last updated 3 days ago.

geographical-detector geoinformatics geospatial-analysis spatial-statistics spatial-stratified-heterogeneity cpp

12.9 match 33 stars 9.10 score 41 scripts 2 dependents

nowosad

motif:Local Pattern Analysis

Describes spatial patterns of categorical raster data for any defined regular and irregular areas. Patterns are described quantitatively using built-in signatures based on co-occurrence matrices but also allows for any user-defined functions. It enables spatial analysis such as search, change detection, and clustering to be performed on spatial patterns (Nowosad (2021) <doi:10.1007/s10980-020-01135-0>).

Maintained by Jakub Nowosad. Last updated 7 months ago.

categorical-raster global-ecology landscape-ecology spatial cpp

15.0 match 63 stars 7.48 score 48 scripts

pbs-assess

sdmTMB:Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

Implements spatial and spatiotemporal GLMMs (Generalized Linear Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial Differential Equation) Gaussian Markov random field approximation to Gaussian random fields. One common application is for spatially explicit species distribution models (SDMs). See Anderson et al. (2024) <doi:10.1101/2022.03.24.485545>.

Maintained by Sean C. Anderson. Last updated 3 days ago.

ecology glmm spatial-analysis species-distribution-modelling tmb cpp

10.0 match 205 stars 11.04 score 848 scripts 1 dependents

biometris

douconca:Double Constrained Correspondence Analysis for Trait-Environment Analysis in Ecology

Double constrained correspondence analysis (dc-CA) analyzes (multi-)trait (multi-)environment ecological data by using the 'vegan' package and native R code. Throughout the two step algorithm of ter Braak et al. (2018) is used. This algorithm combines and extends community- (sample-) and species-level analyses, i.e. the usual community weighted means (CWM)-based regression analysis and the species-level analysis of species-niche centroids (SNC)-based regression analysis. The two steps use canonical correspondence analysis to regress the abundance data on to the traits and (weighted) redundancy analysis to regress the CWM of the orthonormalized traits on to the environmental predictors. The function dc_CA() has an option to divide the abundance data of a site by the site total, giving equal site weights. This division has the advantage that the multivariate analysis corresponds with an unweighted (multi-trait) community-level analysis, instead of being weighted. The first step of the algorithm uses vegan::cca(). The second step uses wrda() but vegan::rda() if the site weights are equal. This version has a predict() function. For details see ter Braak et al. 2018 <doi:10.1007/s10651-017-0395-x>.

Maintained by Bart-Jan van Rossum. Last updated 4 months ago.

correspondence-analysis ecology ecology-modeling multi-environment multi-trait

22.0 match 5.02 score 6 scripts

lance-waller-lab

envi:Environmental Interpolation using Spatial Kernel Density Estimation

Estimates an ecological niche using occurrence data, covariates, and kernel density-based estimation methods. For a single species with presence and absence data, the 'envi' package uses the spatial relative risk function that is estimated using the 'sparr' package. Details about the 'sparr' package methods can be found in the tutorial: Davies et al. (2018) <doi:10.1002/sim.7577>. Details about kernel density estimation can be found in J. F. Bithell (1990) <doi:10.1002/sim.4780090616>. More information about relative risk functions using kernel density estimation can be found in J. F. Bithell (1991) <doi:10.1002/sim.4780101112>.

Maintained by Ian D. Buller. Last updated 5 months ago.

ecological-niche ecological-niche-modelling geospatial geospatial-analysis kernel-density-estimation niche-modeling niche-modelling non-euclidean-spaces point-pattern point-pattern-analysis principal-component-analysis spatial-analysis species-distribution-modeling species-distribution-modelling

24.9 match 1 stars 4.22 score 33 scripts

jamiemkass

ENMeval:Automated Tuning and Evaluations of Ecological Niche Models

Runs ecological niche models over all combinations of user-defined settings (i.e., tuning), performs cross validation to evaluate models, and returns data tables to aid in selection of optimal model settings that balance goodness-of-fit and model complexity. Also has functions to partition data spatially (or not) for cross validation, to plot multiple visualizations of results, to run null models to estimate significance and effect sizes of performance metrics, and to calculate range overlap between model predictions, among others. The package was originally built for Maxent models (Phillips et al. 2006, Phillips et al. 2017), but the current version allows possible extensions for any modeling algorithm. The extensive vignette, which guides users through most package functionality but unfortunately has a file size too big for CRAN, can be found here on the package's Github Pages website: <https://jamiemkass.github.io/ENMeval/articles/ENMeval-2.0-vignette.html>.

Maintained by Jamie M. Kass. Last updated 2 months ago.

8.5 match 49 stars 11.16 score 332 scripts 2 dependents

r-spatialecology

landscapemetrics:Landscape Metrics for Categorical Map Patterns

Calculates landscape metrics for categorical landscape patterns in a tidy workflow. 'landscapemetrics' reimplements the most common metrics from 'FRAGSTATS' (<https://www.fragstats.org/>) and new ones from the current literature on landscape metrics. This package supports 'terra' SpatRaster objects as input arguments. It further provides utility functions to visualize patches, select metrics and building blocks to develop new metrics.

Maintained by Maximilian H.K. Hesselbarth. Last updated 2 months ago.

landscape-ecology landscape-metrics raster spatial cpp

7.5 match 240 stars 12.47 score 584 scripts 4 dependents

adamlilith

enmSdmX:Species Distribution Modeling and Ecological Niche Modeling

Implements species distribution modeling and ecological niche modeling, including: bias correction, spatial cross-validation, model evaluation, raster interpolation, biotic "velocity" (speed and direction of movement of a "mass" represented by a raster), interpolating across a time series of rasters, and use of spatially imprecise records. The heart of the package is a set of "training" functions which automatically optimize model complexity based number of available occurrences. These algorithms include MaxEnt, MaxNet, boosted regression trees/gradient boosting machines, generalized additive models, generalized linear models, natural splines, and random forests. To enhance interoperability with other modeling packages, no new classes are created. The package works with 'PROJ6' geodetic objects and coordinate reference systems.

Maintained by Adam B. Smith. Last updated 1 months ago.

bias-correction biogeography ecological-niche-modeling ecological-niche-modelling niche-modeling niche-modelling species-distribution-modeling openjdk

16.8 match 25 stars 5.57 score 37 scripts

covaruber

sommer:Solving Mixed Model Equations in R

Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.

Maintained by Giovanny Covarrubias-Pazaran. Last updated 3 days ago.

average-information mixed-models rcpparmadillo openblas cpp openmp

7.2 match 44 stars 12.63 score 300 scripts 10 dependents

ncss-tech

soilDB:Soil Database Interface

A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.

Maintained by Andrew Brown. Last updated 2 days ago.

kssl nasis nrcs soil soil-data-access soil-survey soilweb sql usda

7.8 match 86 stars 11.18 score 1.0k scripts 1 dependents

ecospat

ecospat:Spatial Ecology Miscellaneous Methods

Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.

Maintained by Olivier Broennimann. Last updated 2 months ago.

9.3 match 32 stars 9.35 score 418 scripts 1 dependents

mobiodiv

mobr:Measurement of Biodiversity

Functions for calculating metrics for the measurement biodiversity and its changes across scales, treatments, and gradients. The methods implemented in this package are described in: Chase, J.M., et al. (2018) <doi:10.1111/ele.13151>, McGlinn, D.J., et al. (2019) <doi:10.1111/2041-210X.13102>, McGlinn, D.J., et al. (2020) <doi:10.1101/851717>, and McGlinn, D.J., et al. (2023) <doi:10.1101/2023.09.19.558467>.

Maintained by Daniel McGlinn. Last updated 9 days ago.

biodiversity conservation ecology rarefaction species statistics

10.0 match 23 stars 8.65 score 93 scripts

tguillerme

dispRity:Measuring Disparity

A modular package for measuring disparity (multidimensional space occupancy). Disparity can be calculated from any matrix defining a multidimensional space. The package provides a set of implemented metrics to measure properties of the space and allows users to provide and test their own metrics. The package also provides functions for looking at disparity in a serial way (e.g. disparity through time) or per groups as well as visualising the results. Finally, this package provides several statistical tests for disparity analysis.

Maintained by Thomas Guillerme. Last updated 11 days ago.

disparity ecology multidimensionality palaeobiology

10.0 match 26 stars 8.65 score 220 scripts 1 dependents

femiguez

nlraa:Nonlinear Regression for Agricultural Applications

Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is the Beta growth function proposed by Yin et al. (2003) <doi:10.1093/aob/mcg029>. There are several other functions with breakpoints (e.g. linear-plateau, plateau-linear, exponential-plateau, plateau-exponential, quadratic-plateau, plateau-quadratic and bilinear), a non-rectangular hyperbola and a bell-shaped curve. Twenty eight (28) new self-start (SS) functions in total. This package also supports the publication 'Nonlinear regression Models and applications in agricultural research' by Archontoulis and Miguez (2015) <doi:10.2134/agronj2012.0506>, a book chapter with similar material <doi:10.2134/appliedstatistics.2016.0003.c15> and a publication by Oddi et. al. (2019) in Ecology and Evolution <doi:10.1002/ece3.5543>. The function 'nlsLMList' uses 'nlsLM' for fitting, but it is otherwise almost identical to 'nlme::nlsList'.In addition, this release of the package provides functions for conducting simulations for 'nlme' and 'gnls' objects as well as bootstrapping. These functions are intended to work with the modeling framework of the 'nlme' package. It also provides four vignettes with extended examples.

Maintained by Fernando Miguez. Last updated 11 months ago.

agricultural ecology nonlinear-mixed-models nonlinear-regression

10.5 match 23 stars 8.19 score 112 scripts 2 dependents

psolymos

ResourceSelection:Resource Selection (Probability) Functions for Use-Availability Data

Resource Selection (Probability) Functions for use-availability wildlife data based on weighted distributions as described in Lele and Keim (2006) <doi:10.1890/0012-9658(2006)87%5B3021:WDAEOR%5D2.0.CO;2>, Lele (2009) <doi:10.2193/2007-535>, and Solymos & Lele (2016) <doi:10.1111/2041-210X.12432>.

Maintained by Peter Solymos. Last updated 10 months ago.

ecology estimation lele rsf rspf solymos weighted-distributions

10.0 match 8 stars 8.37 score 752 scripts 3 dependents

lter

lterdatasampler:Educational Dataset Examples from the Long Term Ecological Research Program

Curated datasets from US Long Term Ecological Research sites.

Maintained by Allison Horst. Last updated 1 years ago.

data-science ecology lter-science

13.4 match 50 stars 6.26 score 240 scripts

pnovack-gottshall

ecospace:Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks

Implements stochastic simulations of community assembly (ecological diversification) using customizable ecospace frameworks (functional trait spaces). Provides a wrapper to calculate common ecological disparity and functional ecology statistical dynamics as a function of species richness. Functions are written so they will work in a parallel-computing environment.

Maintained by Phil Novack-Gottshall. Last updated 5 years ago.

17.9 match 5 stars 4.51 score 13 scripts

cran

MASS:Support Functions and Datasets for Venables and Ripley's MASS

Functions and datasets to support Venables and Ripley, "Modern Applied Statistics with S" (4th edition, 2002).

Maintained by Brian Ripley. Last updated 29 days ago.

7.5 match 19 stars 10.53 score 11k dependents

adrientaudiere

MiscMetabar:Miscellaneous Functions for Metabarcoding Analysis

Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.

Maintained by Adrien Taudière. Last updated 8 days ago.

sequencing microbiome metagenomics clustering classification visualization amplicon amplicon-sequencing biodiversity-informatics ecology illumina metabarcoding ngs-analysis

12.2 match 17 stars 6.44 score 23 scripts

florianhartig

BayesianTools:General-Purpose MCMC and SMC Samplers and Tools for Bayesian Statistics

General-purpose MCMC and SMC samplers, as well as plots and diagnostic functions for Bayesian statistics, with a particular focus on calibrating complex system models. Implemented samplers include various Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential Monte Carlo (SMC) particle filter.

Maintained by Florian Hartig. Last updated 1 years ago.

bayes ecological-models mcmc optimization smc systems-biology cpp

7.5 match 124 stars 10.18 score 580 scripts 5 dependents

traitecoevo

plant:A Package for Modelling Forest Trait Ecology and Evolution

Solves trait, size and patch structured model from (Falster et al. 2016) using either method of characteristics or as stochastic, finite-sized population.

Maintained by Daniel Falster. Last updated 20 days ago.

c-plus-plus demography dynamic ecology evolution forests plant-physiology science-research simulation trait cpp

12.9 match 53 stars 5.87 score

nicholasjclark

mvgam:Multivariate (Dynamic) Generalized Additive Models

Fit Bayesian Dynamic Generalized Additive Models to multivariate observations. Users can build nonlinear State-Space models that can incorporate semiparametric effects in observation and process components, using a wide range of observation families. Estimation is performed using Markov Chain Monte Carlo with Hamiltonian Monte Carlo in the software 'Stan'. References: Clark & Wells (2023) <doi:10.1111/2041-210X.13974>.

Maintained by Nicholas J Clark. Last updated 2 days ago.

bayesian-statistics dynamic-factor-models ecological-modelling forecasting gaussian-process generalised-additive-models generalized-additive-models joint-species-distribution-modelling multilevel-models multivariate-timeseries stan time-series-analysis timeseries vector-autoregression vectorautoregression cpp

7.5 match 146 stars 9.90 score 117 scripts

julianfaraway

faraway:Datasets and Functions for Books by Julian Faraway

Books are "Linear Models with R" published 1st Ed. August 2004, 2nd Ed. July 2014, 3rd Ed. February 2025 by CRC press, ISBN 9781439887332, and "Extending the Linear Model with R" published by CRC press in 1st Ed. December 2005 and 2nd Ed. March 2016, ISBN 9781584884248 and "Practical Regression and ANOVA in R" contributed documentation on CRAN (now very dated).

Maintained by Julian Faraway. Last updated 2 months ago.

data

7.6 match 29 stars 9.43 score 1.7k scripts 1 dependents

cont-limno

LAGOSNE:Interface to the Lake Multi-Scaled Geospatial and Temporal Database

Client for programmatic access to the Lake Multi-scaled Geospatial and Temporal database <https://lagoslakes.org>, with functions for accessing lake water quality and ecological context data for the US.

Maintained by Jemma Stachelek. Last updated 2 years ago.

ecology geoscience limnology water-quality

10.5 match 15 stars 6.77 score 98 scripts

neon-biodiversity

Ostats:O-Stats, or Pairwise Community-Level Niche Overlap Statistics

O-statistics, or overlap statistics, measure the degree of community-level trait overlap. They are estimated by fitting nonparametric kernel density functions to each species’ trait distribution and calculating their areas of overlap. For instance, the median pairwise overlap for a community is calculated by first determining the overlap of each species pair in trait space, and then taking the median overlap of each species pair in a community. This median overlap value is called the O-statistic (O for overlap). The Ostats() function calculates separate univariate overlap statistics for each trait, while the Ostats_multivariate() function calculates a single multivariate overlap statistic for all traits. O-statistics can be evaluated against null models to obtain standardized effect sizes. 'Ostats' is part of the collaborative Macrosystems Biodiversity Project "Local- to continental-scale drivers of biodiversity across the National Ecological Observatory Network (NEON)." For more information on this project, see the Macrosystems Biodiversity Website (<https://neon-biodiversity.github.io/>). Calculation of O-statistics is described in Read et al. (2018) <doi:10.1111/ecog.03641>, and a teaching module for introducing the underlying biological concepts at an undergraduate level is described in Grady et al. (2018) <http://tiee.esa.org/vol/v14/issues/figure_sets/grady/abstract.html>.

Maintained by Quentin D. Read. Last updated 4 months ago.

ecology

10.5 match 7 stars 6.69 score 28 scripts

cboettig

neonstore:NEON Data Store

The National Ecological Observatory Network (NEON) provides access to its numerous data products through its REST API, <https://data.neonscience.org/data-api/>. This package provides a high-level user interface for downloading and storing NEON data products. Unlike 'neonUtilities', this package will avoid repeated downloading, provides persistent storage, and improves performance. 'neonstore' can also construct a local 'duckdb' database of stacked tables, making it possible to work with tables that are far to big to fit into memory.

Maintained by Carl Boettiger. Last updated 12 months ago.

database ecology neon-data provenance

10.5 match 9 stars 6.67 score 143 scripts 11 dependents

mpio-be

rangeMapper:A Platform for the Study of Macro-Ecology of Life History Traits

Tools for generation of (life-history) traits and diversity maps on hexagonal or square grids. Valcu et al.(2012) <doi:10.1111/j.1466-8238.2011.00739.x>.

Maintained by Mihai Valcu. Last updated 2 years ago.

assemblage-level ecology global life-history-traits raster-cell species

12.9 match 8 stars 5.38 score 30 scripts

ropensci

EDIutils:An API Client for the Environmental Data Initiative Repository

A client for the Environmental Data Initiative repository REST API. The 'EDI' data repository <https://portal.edirepository.org/nis/home.jsp> is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the 'PASTA+' software stack <https://pastaplus-core.readthedocs.io/en/latest/index.html#> and was developed in collaboration with the US 'LTER' Network <https://lternet.edu/>. 'EDIutils' includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users.

Maintained by Colin Smith. Last updated 1 years ago.

ecology eml-metadata open-access open-data research-data-management research-data-repository

10.5 match 10 stars 6.47 score 117 scripts

seananderson

glmmfields:Generalized Linear Mixed Models with Robust Random Fields for Spatiotemporal Modeling

Implements Bayesian spatial and spatiotemporal models that optionally allow for extreme spatial deviations through time. 'glmmfields' uses a predictive process approach with random fields implemented through a multivariate-t distribution instead of the usual multivariate normal. Sampling is conducted with 'Stan'. References: Anderson and Ward (2019) <doi:10.1002/ecy.2403>.

Maintained by Sean C. Anderson. Last updated 1 years ago.

ecology extremes spatial-analysis spatiotemporal cpp

10.0 match 50 stars 6.74 score 55 scripts

ropensci

rfishbase:R Interface to 'FishBase'

A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'

Maintained by Carl Boettiger. Last updated 3 months ago.

fish fishbase taxonomy

6.5 match 116 stars 10.11 score 764 scripts 2 dependents

adokter

bioRad:Biological Analysis and Visualization of Weather Radar Data

Extract, visualize and summarize aerial movements of birds and insects from weather radar data. See Dokter, A. M. et al. (2018) "bioRad: biological analysis and visualization of weather radar data" <doi:10.1111/ecog.04028> for a software paper describing package and methodologies.

Maintained by Adriaan M. Dokter. Last updated 4 days ago.

aeroecology enram eumetnet-opera lifewatch movement-ecology nexrad oscibio radar weather-radar wsr-88d

7.5 match 29 stars 8.70 score 56 scripts

ropensci

NLMR:Simulating Neutral Landscape Models

Provides neutral landscape models (<doi:10.1007/BF02275262>, <http://sci-hub.tw/10.1007/bf02275262>). Neutral landscape models range from "hard" neutral models (completely random distributed), to "soft" neutral models (definable spatial characteristics) and generate landscape patterns that are independent of ecological processes. Thus, these patterns can be used as null models in landscape ecology. 'NLMR' combines a large number of algorithms from other published software for simulating neutral landscapes. The simulation results are obtained in a spatial data format (raster* objects from the 'raster' package) and can, therefore, be used in any sort of raster data operation that is performed with standard observation data.

Maintained by Marco Sciaini. Last updated 7 months ago.

landscape-ecology neutral-landscape-model peer-reviewed spatial cpp

8.3 match 65 stars 7.74 score 193 scripts

paternogbc

sensiPhy:Sensitivity Analysis for Comparative Methods

An implementation of sensitivity analysis for phylogenetic comparative methods. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PCM: (i) Species Sampling uncertainty (sample size; influential species and clades). (ii) Phylogenetic uncertainty (different topologies and/or branch lengths). (iii) Data uncertainty (intraspecific variation and measurement error).

Maintained by Gustavo Paterno. Last updated 5 years ago.

comparative-methods ecology evolution phylogenetics sensitivity-analysis

10.0 match 13 stars 6.38 score 61 scripts

ropensci

pangaear:Client for the 'Pangaea' Database

Tools to interact with the 'Pangaea' Database (<https://www.pangaea.de>), including functions for searching for data, fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea' 'OAI-PMH' service.

Maintained by Scott Chamberlain. Last updated 2 years ago.

pangaea environmental science earth science archive paleontology ecology chemistry atmosphere api-client data paleobiology scientific webservice-client

10.0 match 21 stars 6.27 score 29 scripts

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.

ecology metacommunity

10.5 match 11 stars 5.95 score 27 scripts 1 dependents

npechl

acoRn:Exclusion-Based Parentage Assignment Using Multilocus Genotype Data

Exclusion-based parentage assignment is essential for studies in biodiversity conservation and breeding programs - Kang Huang, Rui Mi, Derek W Dunn, Tongcheng Wang, Baoguo Li, (2018), <doi:10.1534/genetics.118.301592>. The tool compares multilocus genotype data of potential parents and offspring, identifying likely parentage relationships while accounting for genotyping errors, missing data, and duplicate genotypes. 'acoRn' includes two algorithms: one generates synthetic genotype data based on user-defined parameters, while the other analyzes existing genotype data to identify parentage patterns. The package is versatile, applicable to diverse organisms, and offers clear visual outputs, making it a valuable resource for researchers.

Maintained by Nikos Pechlivanis. Last updated 6 months ago.

ecology ecology-modelling parental-assignment

17.5 match 3.54 score 3 scripts

eldarrak

FLightR:Reconstruct Animal Paths from Solar Geolocation Loggers Data

Spatio-temporal locations of an animal are computed from annotated data with a hidden Markov model via particle filter algorithm. The package is relatively robust to varying degrees of shading. The hidden Markov model is described in Movement Ecology - Rakhimberdiev et al. (2015) <doi:10.1186/s40462-015-0062-5>, general package description is in the Methods in Ecology and Evolution - Rakhimberdiev et al. (2017) <doi:10.1111/2041-210X.12765> and package accuracy assessed in the Journal of Avian Biology - Rakhimberdiev et al. (2016) <doi:10.1111/jav.00891>.

Maintained by Eldar Rakhimberdiev. Last updated 6 months ago.

movement-ecology solar-geolocation-loggers solar-geolocator

8.3 match 23 stars 7.28 score 111 scripts

bafuentes

rassta:Raster-Based Spatial Stratification Algorithms

Algorithms for the spatial stratification of landscapes, sampling and modeling of spatially-varying phenomena. These algorithms offer a simple framework for the stratification of geographic space based on raster layers representing landscape factors and/or factor scales. The stratification process follows a hierarchical approach, which is based on first level units (i.e., classification units) and second-level units (i.e., stratification units). Nonparametric techniques allow to measure the correspondence between the geographic space and the landscape configuration represented by the units. These correspondence metrics are useful to define sampling schemes and to model the spatial variability of environmental phenomena. The theoretical background of the algorithms and code examples are presented in Fuentes, Dorantes, and Tipton (2021). <doi:10.31223/X50S57>.

Maintained by Bryan A. Fuentes. Last updated 3 years ago.

ecology geoinformatics hierarchical modeling sampling spatial

10.0 match 16 stars 5.96 score 19 scripts

ltrr-arizona-edu

burnr:Forest Fire History Analysis

Tools to read, write, parse, and analyze forest fire history data (e.g. FHX). Described in Malevich et al. (2018) <doi:10.1016/j.dendro.2018.02.005>.

Maintained by Steven Malevich. Last updated 3 years ago.

citation dendrochronology ecology forestfire plot scientific statistics

10.0 match 15 stars 5.95 score 59 scripts

skembel

picante:Integrating Phylogenies and Ecology

Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.

Maintained by Steven W. Kembel. Last updated 2 years ago.

5.2 match 34 stars 11.42 score 1.1k scripts 16 dependents

biometry

bipartite:Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.

Maintained by Carsten F. Dormann. Last updated 19 days ago.

cpp

5.3 match 37 stars 10.93 score 592 scripts 15 dependents

edlinguerra

SSP:Simulated Sampling Procedure for Community Ecology

Simulation-based sampling protocol (SSP) is an R package design to estimate sampling effort in studies of ecological communities based on the definition of pseudo-multivariate standard error (MultSE) (Anderson & Santana-Garcon, 2015) <doi:10.1111/ele.12385> and simulation of ecological data. The theoretical background is described in Guerra-Castro et al. (2020) <doi:10.1101/2020.03.19.996991>.

Maintained by Edlin Guerra-Castro. Last updated 5 years ago.

10.3 match 2 stars 5.48 score 9 scripts 1 dependents

mattmar

dynamAedes:A Unified Mechanistic Model for the Population Dynamics of Invasive Aedes Mosquitoes

Generalised model for population dynamics of invasive Aedes mosquitoes. Rationale and model structure are described here: Da Re et al. (2021) <doi:10.1016/j.ecoinf.2020.101180> and Da Re et al. (2022) <doi:10.1101/2021.12.21.473628>.

Maintained by Matteo Marcantonio. Last updated 1 years ago.

ecology invasive-species modelling mosquitoes pathogens

10.0 match 7 stars 5.59 score 11 scripts

forestgeo

fgeo:Analyze Forest Diversity and Dynamics

To help you access, transform, analyze, and visualize ForestGEO data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to install and load the entire package-collection with a single R command, and provides convenient ways to find relevant documentation. Most commonly, you should not worry about the individual packages that make up the package-collection as you can access all features via this package. To learn more about ForestGEO visit <http://www.forestgeo.si.edu/>.

Maintained by Mauro Lepore. Last updated 5 years ago.

abundance demography dynamic dynamics ecology fgeo forestgeo forests habitat metapackage tree

10.0 match 33 stars 5.53 score 12 scripts

funecology

fundiversity:Easy Computation of Functional Diversity Indices

Computes six functional diversity indices. These are namely, Functional Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic), Functional Richness intersections (FRic_intersect), Functional Dispersion (FDis), and Rao's entropy (Q) (reviewed in Villéger et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and parallel functions to compute functional diversity indices (Grenié & Gruson 2023 <doi:10.1111/ecog.06585>).

Maintained by Matthias Grenié. Last updated 9 months ago.

biodiversity biodiversity-indicators biodiversity-informatics functional-diversity functional-ecology functional-trait functional-traits trait trait-based traits

7.5 match 38 stars 7.34 score 38 scripts

psolymos

mefa4:Multivariate Data Handling with S4 Classes and Sparse Matrices

An S4 update of the 'mefa' package using sparse matrices for enhanced efficiency. Sparse array-like objects are supported via lists of sparse matrices.

Maintained by Peter Solymos. Last updated 6 months ago.

data-manipulation ecology sparse-matrices

10.0 match 5.34 score 368 scripts 2 dependents

frmunoz

ecolottery:Coalescent-Based Simulation of Ecological Communities

Coalescent-Based Simulation of Ecological Communities as proposed by Munoz et al. (2018) <doi:10.1111/2041-210X.12918>. The package includes a tool for estimating parameters of community assembly by using Approximate Bayesian Computation.

Maintained by François Munoz. Last updated 2 years ago.

8.6 match 15 stars 6.18 score 17 scripts 1 dependents

ropensci

rmangal:'Mangal' Client

An interface to the 'Mangal' database - a collection of ecological networks. This package includes functions to work with the 'Mangal RESTful API' methods (<https://mangal-interactions.github.io/mangal-api/>).

Maintained by Kevin Cazelles. Last updated 1 years ago.

ecology networks food webs interactions data publications open access

10.5 match 14 stars 5.07 score 28 scripts

spatial-ews

spatialwarnings:Spatial Early Warning Signals of Ecosystem Degradation

Tools to compute and assess significance of early-warnings signals (EWS) of ecosystem degradation on raster data sets. EWS are spatial metrics derived from raster data -- e.g. spatial autocorrelation -- that increase before an ecosystem undergoes a non-linear transition (Genin et al. (2018) <doi:10.1111/2041-210X.13058>).

Maintained by Alexandre Genin. Last updated 7 months ago.

catastrophic critical ecology indicators points shifts space transitions cpp

10.0 match 15 stars 5.32 score 46 scripts

phiala

ecodist:Dissimilarity-Based Functions for Ecological Analysis

Dissimilarity-based analysis functions including ordination and Mantel test functions, intended for use with spatial and community ecological data. The original package description is in Goslee and Urban (2007) <doi:10.18637/jss.v022.i07>, with further statistical detail in Goslee (2010) <doi:10.1007/s11258-009-9641-0>.

Maintained by Sarah Goslee. Last updated 1 years ago.

openblas

5.3 match 9 stars 9.84 score 566 scripts 9 dependents

ivaughan

econullnetr:Null Model Analysis for Ecological Networks

Tools for using null models to analyse ecological networks (e.g. food webs, flower-visitation networks, seed-dispersal networks) and detect resource preferences or non-random interactions among network nodes. Tools are provided to run null models, test for and plot preferences, plot and analyse bipartite networks, and export null model results in a form compatible with other network analysis packages. The underlying null model was developed by Agusti et al. (2003) Molecular Ecology <doi:10.1046/j.1365-294X.2003.02014.x> and the full application to ecological networks by Vaughan et al. (2018) econullnetr: an R package using null models to analyse the structure of ecological networks and identify resource selection. Methods in Ecology & Evolution, <doi:10.1111/2041-210X.12907>.

Maintained by Ian Vaughan. Last updated 4 years ago.

10.4 match 7 stars 5.04 score 31 scripts

scollinselliott

lakhesis:Consensus Seriation for Binary Data

Determining consensus seriations for binary incidence matrices, using a two-step process of Procrustes-fit correspondence analysis for heuristic selection of partial seriations and iterative regression to establish a single consensus. Contains the Lakhesis Calculator, a graphical platform for identifying seriated sequences. Collins-Elliott (2024) <https://volweb.utk.edu/~scolli46/sceLakhesis.pdf>.

Maintained by Stephen A. Collins-Elliott. Last updated 4 months ago.

archaeology binary-data correspondence-analysis ecology seriation

10.0 match 5 stars 5.18 score 2 scripts

roelandkindt

BiodiversityR:Package for Community Ecology and Suitability Analysis

Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.

Maintained by Roeland Kindt. Last updated 2 months ago.

7.2 match 17 stars 7.13 score 390 scripts 2 dependents

miguel-porto

SiMRiv:Simulating Multistate Movements in River/Heterogeneous Landscapes

Provides functions to generate and analyze spatially-explicit individual-based multistate movements in rivers, heterogeneous and homogeneous spaces. This is done by incorporating landscape bias on local behaviour, based on resistance rasters. Although originally conceived and designed to simulate trajectories of species constrained to linear habitats/dendritic ecological networks (e.g. river networks), the simulation algorithm is built to be highly flexible and can be applied to any (aquatic, semi-aquatic or terrestrial) organism, independently on the landscape in which it moves. Thus, the user will be able to use the package to simulate movements either in homogeneous landscapes, heterogeneous landscapes (e.g. semi-aquatic animal moving mainly along rivers but also using the matrix), or even in highly contrasted landscapes (e.g. fish in a river network). The algorithm and its input parameters are the same for all cases, so that results are comparable. Simulated trajectories can then be used as mechanistic null models (Potts & Lewis 2014, <DOI:10.1098/rspb.2014.0231>) to test a variety of 'Movement Ecology' hypotheses (Nathan et al. 2008, <DOI:10.1073/pnas.0800375105>), including landscape effects (e.g. resources, infrastructures) on animal movement and species site fidelity, or for predictive purposes (e.g. road mortality risk, dispersal/connectivity). The package should be relevant to explore a broad spectrum of ecological phenomena, such as those at the interface of animal behaviour, management, landscape and movement ecology, disease and invasive species spread, and population dynamics.

Maintained by Miguel Porto. Last updated 7 months ago.

animal-movement heterogeneous-landscapes movement-ecology river-networks simulation

8.5 match 15 stars 6.08 score 27 scripts 1 dependents

r-spatialecology

shar:Species-Habitat Associations

Analyse species-habitat associations in R. Therefore, information about the location of the species (as a point pattern) is needed together with environmental conditions (as a categorical raster). To test for significance habitat associations, one of the two components is randomized. Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.

Maintained by Maximilian H.K. Hesselbarth. Last updated 1 months ago.

habitat-association landscape-ecology point-pattern-analysis spatial-analysis

7.5 match 20 stars 6.83 score 28 scripts

fmestre1

MetaLandSim:Landscape and Range Expansion Simulation

Tools to generate random landscape graphs, evaluate species occurrence in dynamic landscapes, simulate future landscape occupation and evaluate range expansion when new empty patches are available (e.g. as a result of climate change). References: Mestre, F., Canovas, F., Pita, R., Mira, A., Beja, P. (2016) <doi:10.1016/j.envsoft.2016.03.007>; Mestre, F., Risk, B., Mira, A., Beja, P., Pita, R. (2017) <doi:10.1016/j.ecolmodel.2017.06.013>; Mestre, F., Pita, R., Mira, A., Beja, P. (2020) <doi:10.1186/s12898-019-0273-5>.

Maintained by Frederico Mestre. Last updated 2 years ago.

biogeography ecology metapopulation species

10.0 match 3 stars 5.10 score 28 scripts

spluque

diveMove:Dive Analysis and Calibration

Utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided.

Maintained by Sebastian P. Luque. Last updated 6 months ago.

animal-behavior behavioural-ecology biology diving science

7.5 match 6 stars 6.75 score 55 scripts

mjg211

phaseR:Phase Plane Analysis of One- And Two-Dimensional Autonomous ODE Systems

Performs a qualitative analysis of one- and two-dimensional autonomous ordinary differential equation systems, using phase plane methods. Programs are available to identify and classify equilibrium points, plot the direction field, and plot trajectories for multiple initial conditions. In the one-dimensional case, a program is also available to plot the phase portrait. Whilst in the two-dimensional case, programs are additionally available to plot nullclines and stable/unstable manifolds of saddle points. Many example systems are provided for the user. For further details can be found in Grayling (2014) <doi:10.32614/RJ-2014-023>.

Maintained by Michael J Grayling. Last updated 3 years ago.

biological-modeling differential-equations dynamical-systems ecological-modelling lotka-volterra manifolds modeling-dynamic-systems morris-lecar perturbation-analysis phase-plane sir-model species-interactions van-der-pol

7.5 match 15 stars 6.63 score 94 scripts 1 dependents

ropensci

landscapetools:Landscape Utility Toolbox

Provides utility functions for some of the less-glamorous tasks involved in landscape analysis. It includes functions to coerce raster data to the common tibble format and vice versa, it helps with flexible reclassification tasks of raster data and it provides a function to merge multiple raster. Furthermore, 'landscapetools' helps landscape scientists to visualize their data by providing optional themes and utility functions to plot single landscapes, rasterstacks, -bricks and lists of raster.

Maintained by Marco Sciaini. Last updated 2 years ago.

landscape landscape-ecology raster visualization workflow

7.5 match 47 stars 6.61 score 191 scripts

plant-data

ritalic:Interface to the ITALIC Database of Lichen Biodiversity

A programmatic interface to the Web Service methods provided by ITALIC (<https://italic.units.it>). ITALIC is a database of lichen data in Italy and bordering European countries. 'ritalic' includes functions for retrieving information about lichen scientific names, geographic distribution, ecological data, morpho-functional traits and identification keys. More information about the data is available at <https://italic.units.it/?procedure=base&t=59&c=60>. The API documentation is available at <https://italic.units.it/?procedure=api>.

Maintained by Matteo Conti. Last updated 27 days ago.

biodiversity ecology fungi italic lichen

12.2 match 2 stars 4.04 score 6 scripts

xinghuq

DA:Discriminant Analysis for Evolutionary Inference

Discriminant Analysis (DA) for evolutionary inference (Qin, X. et al, 2020, <doi:10.22541/au.159256808.83862168>), especially for population genetic structure and community structure inference. This package incorporates the commonly used linear and non-linear, local and global supervised learning approaches (discriminant analysis), including Linear Discriminant Analysis of Kernel Principal Components (LDAKPC), Local (Fisher) Linear Discriminant Analysis (LFDA), Local (Fisher) Discriminant Analysis of Kernel Principal Components (LFDAKPC) and Kernel Local (Fisher) Discriminant Analysis (KLFDA). These discriminant analyses can be used to do ecological and evolutionary inference, including demography inference, species identification, and population/community structure inference.

Maintained by Xinghu Qin. Last updated 4 years ago.

biomedicalinformatics chipseq clustering coverage dnamethylation differentialexpression differentialmethylation software differentialsplicing epigenetics functionalgenomics geneexpression genesetenrichment genetics immunooncology multiplecomparison normalization pathways qualitycontrol rnaseq regression sage sequencing systemsbiology timecourse transcription transcriptomics dapc discriminant-analysis ecological kernel kernel-local kernel-principle-components population-structure-inference principal-components

10.5 match 1 stars 4.70 score 1 scripts

bioc

LEA:LEA: an R package for Landscape and Ecological Association Studies

LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.

Maintained by Olivier Francois. Last updated 18 days ago.

software statistical method clustering regression openblas

7.4 match 6.63 score 534 scripts

admahood

neonPlantEcology:Process NEON Plant Data for Ecological Analysis

Downloading and organizing plant presence and percent cover data from the National Ecological Observatory Network <https://www.neonscience.org>.

Maintained by Adam Mahood. Last updated 3 months ago.

9.7 match 8 stars 5.08 score 7 scripts

yiluheihei

RevEcoR:Reverse Ecology Analysis on Microbiome

An implementation of the reverse ecology framework. Reverse ecology refers to the use of genomics to study ecology with no a priori assumptions about the organism(s) under consideration, linking organisms to their environment. It allows researchers to reconstruct the metabolic networks and study the ecology of poorly characterized microbial species from their genomic information, and has substantial potentials for microbial community ecological analysis.

Maintained by Yang Cao. Last updated 6 years ago.

8.5 match 6 stars 5.77 score 22 scripts 1 dependents

mlysy

nicheROVER:Niche Region and Niche Overlap Metrics for Multidimensional Ecological Niches

Implementation of a probabilistic method to calculate 'nicheROVER' (_niche_ _r_egion and niche _over_lap) metrics using multidimensional niche indicator data (e.g., stable isotopes, environmental variables, etc.). The niche region is defined as the joint probability density function of the multidimensional niche indicators at a user-defined probability alpha (e.g., 95%). Uncertainty is accounted for in a Bayesian framework, and the method can be extended to three or more indicator dimensions. It provides directional estimates of niche overlap, accounts for species-specific distributions in multivariate niche space, and produces unique and consistent bivariate projections of the multivariate niche region. The article by Swanson et al. (2015) <doi:10.1890/14-0235.1> provides a detailed description of the methodology. See the package vignette for a worked example using fish stable isotope data.

Maintained by Martin Lysy. Last updated 1 years ago.

7.2 match 9 stars 6.80 score 47 scripts 1 dependents

pzhaonet

rarestR:Rarefaction-Based Species Richness Estimator

Calculate rarefaction-based alpha- and beta-diversity. Offer parametric extrapolation to estimate the total expected species in a single community and the total expected shared species between two communities. Visualize the curve-fitting for these estimators.

Maintained by Peng Zhao. Last updated 5 months ago.

biodiversity ecology

10.0 match 2 stars 4.89 score 13 scripts

predictiveecology

LandR:Landscape Ecosystem Modelling in R

Utilities for 'LandR' suite of landscape simulation models. These models simulate forest vegetation dynamics based on LANDIS-II, and incorporate fire and insect disturbance, as well as other important ecological processes. Models are implemented as 'SpaDES' modules.

Maintained by Eliot J B McIntire. Last updated 2 days ago.

ecological-modelling landscape-ecosystem-modelling spades

8.0 match 17 stars 6.09 score 12 scripts 4 dependents

robitalec

distanceto:Calculate Distance to Features

Calculates distances from point locations to features. The usual approach for eg. resource selection function analyses is to generate a complete distance to features surface then sample it with your observed and random points. Since these raster based approaches can be pretty costly with large areas, and often lead to memory issues in R, the distanceto package opts to compute these distances using efficient, vector based approaches. As a helper, there's a decidedly low-res raster based approach for visually inspecting your region's distance surface. But the workhorse is distance_to.

Maintained by Alec L. Robitaille. Last updated 2 years ago.

animal distance-to ecology resource-selection rsf spatial

10.0 match 5 stars 4.88 score 10 scripts 1 dependents

forestgeo

fgeo.tool:Import and Manipulate 'ForestGEO' Data

To help you access, transform, analyze, and visualize 'ForestGEO' data, we developed a collection of R packages (<https://forestgeo.github.io/fgeo/>). This package, in particular, helps you to easily import, filter, and modify 'ForestGEO' data. To learn more about 'ForestGEO' visit <https://forestgeo.si.edu/>.

Maintained by Mauro Lepore. Last updated 3 years ago.

dynamics ecology fgeo forestgeo miscelaneas tools tree utils

10.0 match 2 stars 4.86 score 27 scripts 3 dependents

jenniniku

gllvm:Generalized Linear Latent Variable Models

Analysis of multivariate data using generalized linear latent variable models (gllvm). Estimation is performed using either the Laplace method, variational approximations, or extended variational approximations, implemented via TMB (Kristensen et al. (2016), <doi:10.18637/jss.v070.i05>).

Maintained by Jenni Niku. Last updated 1 days ago.

cpp openmp

4.4 match 52 stars 10.56 score 176 scripts 1 dependents

alexhroom

rshift:Paleoecology Functions for Regime Shift Analysis

Contains a variety of functions, based around regime shift analysis of paleoecological data. Citations: Rodionov() from Rodionov (2004) <doi:10.1029/2004GL019448> Lanzante() from Lanzante (1996) <doi:10.1002/(SICI)1097-0088(199611)16:11%3C1197::AID-JOC89%3E3.0.CO;2-L> Hellinger_trans from Numerical Ecology, Legendre & Legendre (ISBN 9780444538680) rolling_autoc from Liu, Gao & Wang (2018) <doi:10.1016/j.scitotenv.2018.06.276> Sample data sets lake_data & lake_RSI processed from Bush, Silman & Urrego (2004) <doi:10.1126/science.1090795> Sample data set January_PDO from NOAA: <https://www.ncei.noaa.gov/access/monitoring/pdo/>.

Maintained by Alex H. Room. Last updated 2 months ago.

ecology paleoecology regime-shift rust cargo

10.5 match 4 stars 4.38 score 8 scripts

vascobranco

gecko:Geographical Ecology and Conservation Knowledge Online

Includes a collection of geographical analysis functions aimed primarily at ecology and conservation science studies, allowing processing of both point and raster data. Now integrates SPECTRE (<https://biodiversityresearch.org/spectre/>), a dataset of global geospatial threat data, developed by the authors.

Maintained by Vasco V. Branco. Last updated 3 months ago.

conservation-science ecology spatial-analysis

13.5 match 5 stars 3.40 score 4 scripts

munterfi

eRTG3D:Empirically Informed Random Trajectory Generation in 3-D

Creates realistic random trajectories in a 3-D space between two given fix points, so-called conditional empirical random walks (CERWs). The trajectory generation is based on empirical distribution functions extracted from observed trajectories (training data) and thus reflects the geometrical movement characteristics of the mover. A digital elevation model (DEM), representing the Earth's surface, and a background layer of probabilities (e.g. food sources, uplift potential, waterbodies, etc.) can be used to influence the trajectories. Unterfinger M (2018). "3-D Trajectory Simulation in Movement Ecology: Conditional Empirical Random Walk". Master's thesis, University of Zurich. <https://www.geo.uzh.ch/dam/jcr:6194e41e-055c-4635-9807-53c5a54a3be7/MasterThesis_Unterfinger_2018.pdf>. Technitis G, Weibel R, Kranstauber B, Safi K (2016). "An algorithm for empirically informed random trajectory generation between two endpoints". GIScience 2016: Ninth International Conference on Geographic Information Science, 9, online. <doi:10.5167/uzh-130652>.

Maintained by Merlin Unterfinger. Last updated 3 years ago.

3d birds conditional-empirical-random-walk gliding-and-soaring machine-learning movement-ecology random-trajectory-generator random-walk simulation trajectory-generation

8.0 match 6 stars 5.71 score 19 scripts

robinhankin

untb:Ecological Drift under the UNTB

Hubbell's Unified Neutral Theory of Biodiversity.

Maintained by Robin K. S. Hankin. Last updated 4 months ago.

6.9 match 4 stars 6.53 score 80 scripts

chabert-liddell

robber:Using Block Model to Estimate the Robustness of Ecological Network

Implementation of a variety of methods to compute the robustness of ecological interaction networks with binary interactions as described in <doi:10.1002/env.2709>. In particular, using the Stochastic Block Model and its bipartite counterpart, the Latent Block Model to put a parametric model on the network, allows the comparison of the robustness of networks differing in species richness and number of interactions. It also deals with networks that are partially sampled and/or with missing values.

Maintained by Saint-Clair Chabert-Liddell. Last updated 1 years ago.

ecological-network robber robustness

12.1 match 1 stars 3.70 score 4 scripts

clementcalenge

adehabitatHS:Analysis of Habitat Selection by Animals

A collection of tools for the analysis of habitat selection.

Maintained by Clement Calenge. Last updated 7 months ago.

9.3 match 1 stars 4.77 score 51 scripts

dvrbts

labdsv:Ordination and Multivariate Analysis for Ecology

A variety of ordination and community analyses useful in analysis of data sets in community ecology. Includes many of the common ordination methods, with graphical routines to facilitate their interpretation, as well as several novel analyses.

Maintained by David W. Roberts. Last updated 2 years ago.

fortran

7.2 match 3 stars 6.05 score 452 scripts 12 dependents

andrewmarx

samc:Spatial Absorbing Markov Chains

Implements functions for working with absorbing Markov chains. The implementation is based on the framework described in "Toward a unified framework for connectivity that disentangles movement and mortality in space and time" by Fletcher et al. (2019) <doi:10.1111/ele.13333>, which applies them to spatial ecology. This framework incorporates both resistance and absorption with spatial absorbing Markov chains (SAMC) to provide several short-term and long-term predictions for metrics related to connectivity in landscapes. Despite the ecological context of the framework, this package can be used in any application of absorbing Markov chains.

Maintained by Andrew Marx. Last updated 5 months ago.

absorbing-markov-chains connectivity landscape-ecology landscape-metrics markov-chain cpp

8.3 match 12 stars 5.26 score 15 scripts

predictiveecology

pemisc:Miscellaneous Utilities Developed by the Predictive Ecology Group

Miscellaneous utilities developed by the Predictive Ecology Group (<http://predictiveecology.org>).

Maintained by Eliot J B McIntire. Last updated 3 months ago.

landscape-ecology simulation-modeling

11.0 match 1 stars 3.91 score 3 scripts 6 dependents

dimitri-justeau

restoptr:Ecological Restoration Planning

Flexible framework for ecological restoration planning. It aims to identify priority areas for restoration efforts using optimization algorithms (based on Justeau-Allaire et al. 2021 <doi:10.1111/1365-2664.13803>). Priority areas can be identified by maximizing landscape indices, such as the effective mesh size (Jaeger 2000 <doi:10.1023/A:1008129329289>), or the integral index of connectivity (Pascual-Hortal & Saura 2006 <doi:10.1007/s10980-006-0013-z>). Additionally, constraints can be used to ensure that priority areas exhibit particular characteristics (e.g., ensure that particular places are not selected for restoration, ensure that priority areas form a single contiguous network). Furthermore, multiple near-optimal solutions can be generated to explore multiple options in restoration planning. The package leverages the 'Choco-solver' software to perform optimization using constraint programming (CP) techniques (<https://choco-solver.org/>).

Maintained by Dimitri Justeau-Allaire. Last updated 9 months ago.

openjdk

8.5 match 11 stars 5.04 score 6 scripts

cmerow

meteR:Fitting and Plotting Tools for the Maximum Entropy Theory of Ecology (METE)

Fit and plot macroecological patterns predicted by the Maximum Entropy Theory of Ecology (METE).

Maintained by Cory Merow. Last updated 6 years ago.

cpp

8.0 match 11 stars 5.35 score 41 scripts

bbolker

emdbook:Support Functions and Data for "Ecological Models and Data"

Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).

Maintained by Ben Bolker. Last updated 9 months ago.

5.2 match 4 stars 8.04 score 656 scripts 21 dependents

godrigos

forams:Foraminifera and Community Ecology Analyses

SHE, FORAM Index and ABC Method analyses and custom plot functions for community data.

Maintained by Rodrigo Aluizio. Last updated 1 years ago.

ecology statistics

15.0 match 2.78 score 12 scripts

ropensci

EML:Read and Write Ecological Metadata Language Files

Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.

Maintained by Carl Boettiger. Last updated 3 years ago.

eml eml-metadata metadata-standard

3.7 match 97 stars 11.19 score 378 scripts 7 dependents

ropensci

emld:Ecological Metadata as Linked Data

This is a utility for transforming Ecological Metadata Language ('EML') files into 'JSON-LD' and back into 'EML.' Doing so creates a list-based representation of 'EML' in R, so that 'EML' data can easily be manipulated using standard 'R' tools. This makes this package an effective backend for other 'R'-based tools working with 'EML.' By abstracting away the complexity of 'XML' Schema, developers can build around native 'R' list objects and not have to worry about satisfying many of the additional constraints of set by the schema (such as element ordering, which is handled automatically). Additionally, the 'JSON-LD' representation enables the use of developer-friendly 'JSON' parsing and serialization that may facilitate the use of 'EML' in contexts outside of 'R,' as well as the informatics-friendly serializations such as 'RDF' and 'SPARQL' queries.

Maintained by Carl Boettiger. Last updated 4 years ago.

5.4 match 13 stars 7.63 score 69 scripts 8 dependents

haddonm

MQMF:Modelling and Quantitative Methods in Fisheries

Complements the book "Using R for Modelling and Quantitative Methods in Fisheries" ISBN 9780367469894, published in 2021 by Chapman & Hall in their "Using R series". There are numerous functions and data-sets that are used in the book's many practical examples.

Maintained by Malcolm Haddon. Last updated 2 years ago.

ecology fisheries haddon quantitative-methods uncertainty

10.0 match 11 stars 4.14 score 25 scripts

emf-creaf

ecotraj:Ecological Trajectory Analysis

Assists ecologists in the analysis of temporal changes of ecosystems, defined as trajectories on a chosen multivariate space, by providing a set of trajectory metrics and visual representations [De Caceres et al. (2019) <doi:10.1002/ecm.1350>; and Sturbois et al. (2021) <doi:10.1016/j.ecolmodel.2020.109400>]. Includes functions to estimate metrics for individual trajectories (length, directionality, angles, ...) as well as metrics to relate pairs of trajectories (dissimilarity and convergence). Functions are also provided to estimate the ecological quality of ecosystem with respect to reference conditions [Sturbois et al. (2023) <doi:10.1002/ecs2.4726>].

Maintained by Miquel De Cáceres. Last updated 2 days ago.

cpp

7.6 match 4 stars 5.25 score 21 scripts 1 dependents

efernandezpascual

seedr:Hydro and Thermal Time Seed Germination Models in R

Analysis of seed germination data using the physiological time modelling approach. Includes functions to fit hydrotime and thermal-time models with the traditional approaches of Bradford (1990) <doi:10.1104/pp.94.2.840> and Garcia-Huidobro (1982) <doi:10.1093/jxb/33.2.288>. Allows to fit models to grouped datasets, i.e. datasets containing multiple species, seedlots or experiments.

Maintained by Fernández-Pascual Eduardo. Last updated 4 years ago.

agronomy botany ecology germination seeds

10.0 match 2 stars 4.00 score 6 scripts

psolymos

opticut:Likelihood Based Optimal Partitioning and Indicator Species Analysis

Likelihood based optimal partitioning and indicator species analysis. Finding the best binary partition for each species based on model selection, with the possibility to take into account modifying/confounding variables as described in Kemencei et al. (2014) <doi:10.1556/ComEc.15.2014.2.6>. The package implements binary and multi-level response models, various measures of uncertainty, Lorenz-curve based thresholding, with native support for parallel computations.

Maintained by Peter Solymos. Last updated 10 months ago.

ecology indicator-species-analysis likelihood optimal-partitioning species

10.0 match 2 stars 3.91 score 82 scripts

ljvillanueva

soundecology:Soundscape Ecology

Functions to calculate indices for soundscape ecology and other ecology research that uses audio recordings.

Maintained by Luis J. Villanueva-Rivera. Last updated 6 years ago.

6.9 match 24 stars 5.53 score 95 scripts

quicklizard99

cheddar:Analysis and Visualisation of Ecological Communities

Provides a flexible, extendable representation of an ecological community and a range of functions for analysis and visualisation, focusing on food web, body mass and numerical abundance data. Allows inter-web comparisons such as examining changes in community structure over environmental, temporal or spatial gradients.

Maintained by Lawrence Hudson. Last updated 8 months ago.

cpp

5.5 match 15 stars 6.86 score 195 scripts

ogarciav

siplab:Spatial Individual-Plant Modelling

A platform for computing competition indices and experimenting with spatially explicit individual-based vegetation models.

Maintained by Oscar Garcia. Last updated 3 years ago.

plant-ecology plant-growth simulation

7.5 match 3 stars 4.97 score 31 scripts

covaruber

lme4breeding:Relationship-Based Mixed-Effects Models

Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the 'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.

Maintained by Giovanny Covarrubias-Pazaran. Last updated 1 months ago.

7.2 match 5 stars 5.15 score 7 scripts

cran

ei:Ecological Inference

Software accompanying Gary King's book: A Solution to the Ecological Inference Problem. (1997). Princeton University Press. ISBN 978-0691012407.

Maintained by James Honaker. Last updated 8 years ago.

18.2 match 1 stars 2.00 score

ropensci

ReLTER:An Interface for the eLTER Community

ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the [ODSEurope](maps.opendatascience.eu) starting with the dataset shared by [DEIMS-SDR](https://deims.org/) (see e.g. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function); - improve the quality of the dataset (see e.g. get_id_worms). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.

Maintained by Alessandro Oggioni. Last updated 1 years ago.

biodiversity-informatics data-science ecology elter research-infrastructure

10.5 match 12 stars 3.38 score 4 scripts

chiliubio

microeco:Microbial Community Ecology Data Analysis

A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity analysis, beta diversity analysis, differential abundance test, null model analysis, network analysis, machine learning, environmental data analysis and functional analysis.

Maintained by Chi Liu. Last updated 1 days ago.

3.5 match 222 stars 10.07 score 211 scripts 3 dependents

pecanproject

PEcAn.DB:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

2.9 match 216 stars 11.89 score 127 scripts 27 dependents

agrdatasci

climatrends:Climate Variability Indices for Ecological Modelling

Supports analysis of trends in climate change, ecological and crop modelling.

Maintained by Kauê de Sousa. Last updated 11 months ago.

climate-data climatology timeseries-analysis

6.7 match 5 stars 5.18 score 8 scripts

miguel-porto

eicm:Explicit Interaction Community Models

Model fitting and species biotic interaction network topology selection for explicit interaction community models. Explicit interaction community models are an extension of binomial linear models for joint modelling of species communities, that incorporate both the effects of species biotic interactions and the effects of missing covariates. Species interactions are modelled as direct effects of each species on each of the others, and are estimated alongside the effects of missing covariates, modelled as latent factors. The package includes a penalized maximum likelihood fitting function, and a genetic algorithm for selecting the most parsimonious species interaction network topology.

Maintained by Miguel Porto. Last updated 2 years ago.

community-modeling ecological-modelling interaction-network joint-models jsdm missing-covariates species-distribution-modelling species-interactions

7.5 match 6 stars 4.48 score 2 scripts

nimble-dev

nimbleEcology:Distributions for Ecological Models in 'nimble'

Common ecological distributions for 'nimble' models in the form of nimbleFunction objects. Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, dynamic hidden Markov, and N-mixture models. (Jolly (1965) <DOI: 10.2307/2333826>, Seber (1965) <DOI: 10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).

Maintained by Benjamin R. Goldstein. Last updated 3 months ago.

4.8 match 18 stars 7.01 score 94 scripts

hrlai

novelforestSG:Dataset from the Novel Forests of Singapore

The raw dataset and model used in Lai et al. (2021) Decoupled responses of native and exotic tree diversities to distance from old-growth forest and soil phosphorous in novel secondary forests. Applied Vegetation Science, 24, e12548.

Maintained by Hao Ran Lai. Last updated 1 years ago.

data diversity ecology forest singapore

10.0 match 2 stars 3.30 score 4 scripts

lter

ltertools:Tools Developed by the Long Term Ecological Research Community

Set of the data science tools created by various members of the Long Term Ecological Research (LTER) community. These functions were initially written largely as standalone operations and have later been aggregated into this package.

Maintained by Nicholas Lyon. Last updated 2 days ago.

data-science lter-science

6.9 match 3 stars 4.78 score 4 scripts

elaliberte

FD:Measuring Functional Diversity (FD) from Multiple Traits, and Other Tools for Functional Ecology

Computes different multidimensional FD indices. Implements a distance-based framework to measure FD that allows any number and type of functional traits, and can also consider species relative abundances. Also contains other useful tools for functional ecology.

Maintained by Etienne Laliberté. Last updated 1 years ago.

fortran

5.0 match 4 stars 6.54 score 586 scripts 15 dependents

bluegreen-labs

igrf:International Geomagnetic Reference Field

The 13th generation International Geomagnetic Reference Field (IGRF). A standard spherical harmonic representation of the Earth's main field.

Maintained by Koen Hufkens. Last updated 1 years ago.

geomagnetic-field movement-ecology fortran

7.5 match 4 stars 4.30 score 3 scripts

pecanproject

PEcAn.utils:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Rob Kooper. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

2.9 match 216 stars 10.94 score 218 scripts 35 dependents

jongheepark

MCMCpack:Markov Chain Monte Carlo (MCMC) Package

Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return 'coda' mcmc objects that can then be summarized using the 'coda' package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.

Maintained by Jong Hee Park. Last updated 7 months ago.

cpp

3.3 match 13 stars 9.47 score 2.6k scripts 149 dependents

grosssbm

sbm:Stochastic Blockmodels

A collection of tools and functions to adjust a variety of stochastic blockmodels (SBM). Supports at the moment Simple, Bipartite, 'Multipartite' and Multiplex SBM (undirected or directed with Bernoulli, Poisson or Gaussian emission laws on the edges, and possibly covariate for Simple and Bipartite SBM). See Léger (2016) <doi:10.48550/arXiv.1602.07587>, 'Barbillon et al.' (2020) <doi:10.1111/rssa.12193> and 'Bar-Hen et al.' (2020) <doi:10.48550/arXiv.1807.10138>.

Maintained by Julien Chiquet. Last updated 6 months ago.

network-analysis sbm stochastic-block-model cpp

3.8 match 16 stars 8.27 score 98 scripts 2 dependents

adeverse

adespatial:Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Maintained by Aurélie Siberchicot. Last updated 9 days ago.

fortran openblas

2.8 match 36 stars 11.16 score 398 scripts 2 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.

6.9 match 2 stars 4.41 score 26 scripts

cran

ei.Datasets:Real Datasets for Assessing Ecological Inference Algorithms

Provides more than 550 data sets of actual election results. Each of the data sets includes aggregate party and candidate outcomes at the voting unit (polling stations) level and two-way cross-tabulated results at the district level. These data sets can be used to assess ecological inference algorithms devised for estimating RxC (global) ecological contingency tables using exclusively aggregate results from voting units. Reference: Pavía (2022) <doi:10.1177/08944393211040808>.

Maintained by Jose M. Pavía. Last updated 3 years ago.

30.4 match 1.00 score

viralemergence

insectDisease:Ecological Database of the World's Insect Pathogens

David Onstad provided us with this insect disease database, sometimes referred to as the 'Ecological Database of the Worlds Insect Pathogens' or EDWIP. Files have been converted from 'SQL' to csv, and ported into 'R' for easy exploration and analysis. Thanks to the Macroecology of Infectious Disease Research Coordination Network (RCN) for funding and support. Data are also served online in a static format at <https://edwip.ecology.uga.edu/>.

Maintained by Tad Dallas. Last updated 2 months ago.

6.7 match 13 stars 4.41 score 2 scripts

calbertsen

argosTrack:Fit Movement Models to Argos Data for Marine Animals

Fits various state-space animal movement models to Argos data. Models are fitted by maximum likelihood with the Laplace approximation via 'TMB' and 'nlminb'. Functionality to visualize and simulate the models is available.

Maintained by Christoffer Moesgaard Albertsen. Last updated 4 years ago.

animal animal-behavior argos-data c-plus-plus gps-data movement movement-ecology solar-geolocator tracking cpp

7.5 match 12 stars 3.92 score 14 scripts

theomichelot

moveHMM:Animal Movement Modelling using Hidden Markov Models

Provides tools for animal movement modelling using hidden Markov models. These include processing of tracking data, fitting hidden Markov models to movement data, visualization of data and fitted model, decoding of the state process, etc. <doi:10.1111/2041-210X.12578>.

Maintained by Theo Michelot. Last updated 1 years ago.

openblas cpp

3.4 match 38 stars 8.63 score 112 scripts

pecanproject

PEcAn.assim.batch:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Istem Fer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

2.9 match 216 stars 9.96 score 20 scripts 2 dependents

mlammens

spThin:Functions for Spatial Thinning of Species Occurrence Records for Use in Ecological Models

A set of functions that can be used to spatially thin species occurrence data. The resulting thinned data can be used in ecological modeling, such as ecological niche modeling.

Maintained by Matthew E. Aiello-Lammens. Last updated 5 years ago.

3.6 match 2 stars 8.00 score 209 scripts 3 dependents

vda1r22

bbnet:Create Simple Predictive Models on Bayesian Belief Networks

A system to build, visualise and evaluate Bayesian belief networks. The methods are described in Stafford et al. (2015) <doi:10.12688/f1000research.5981.1>.

Maintained by Victoria Dominguez Almela. Last updated 2 months ago.

6.7 match 4.30 score 9 scripts

derek-corcoran-barrios

NetworkExtinction:Extinction Simulation in Ecological Networks

Simulates the extinction of species in ecological networks and it analyzes its cascading effects, described in Dunne et al. (2002) <doi:10.1073/pnas.192407699>.

Maintained by Derek Corcoran. Last updated 5 months ago.

5.5 match 5 stars 5.15 score 19 scripts

hankstevens

primer:Functions and Data for the Book, a Primer of Ecology with R

Functions are primarily functions for systems of ordinary differential equations, difference equations, and eigenanalysis and projection of demographic matrices; data are for examples.

Maintained by Hank Stevens. Last updated 4 years ago.

4.7 match 14 stars 5.92 score 118 scripts

g-rppl

movetrack:Estimate flight tracks from telemetry data

`movetrack` is an `R` package that provides simple functionality to estimate flight tracks from telemetry data using a hidden Markov model written in Stan.

Maintained by Georg Rüppel. Last updated 4 months ago.

hmm motus movement-ecology movement-modeling random-walk stan telemetry

7.5 match 1 stars 3.70 score 2 scripts

marlonecobos

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>.

Maintained by Marlon E. Cobos. Last updated 2 years ago.

7.2 match 14 stars 3.85 score 2 scripts

pecanproject

PEcAn.data.land:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

2.9 match 216 stars 9.33 score 19 scripts 10 dependents

desiquintans

electivity:Algorithms for Electivity Indices

Provides all electivity algorithms (including Vanderploeg and Scavia electivity) that were examined in Lechowicz (1982) <doi:10.1007/BF00349007>, plus the example data that were provided for moth resource utilisation.

Maintained by Desi Quintans. Last updated 6 years ago.

ecology electivity

10.0 match 1 stars 2.70 score 1 scripts

jsegrestin

comstab:Partitioning the Drivers of Stability of Ecological Communities

Contains the basic functions to apply the unified framework for partitioning the drivers of stability of ecological communities. Segrestin et al. (2024) <doi:10.1111/geb.13828>.

Maintained by Jules Segrestin. Last updated 8 months ago.

7.1 match 6 stars 3.78 score

bioc

MicrobiotaProcess:A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

MicrobiotaProcess is an R package for analysis, visualization and biomarker discovery of microbial datasets. It introduces MPSE class, this make it more interoperable with the existing computing ecosystem. Moreover, it introduces a tidy microbiome data structure paradigm and analysis grammar. It provides a wide variety of microbiome data analysis procedures under the unified and common framework (tidy-like framework).

Maintained by Shuangbin Xu. Last updated 5 months ago.

visualization microbiome software multiplecomparison featureextraction microbiome-analysis microbiome-data

2.7 match 183 stars 9.70 score 126 scripts 1 dependents

pecanproject

PEcAn.all:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

2.9 match 216 stars 9.00 score 266 scripts

tpetzoldt

simecol:Simulation of Ecological (and Other) Dynamic Systems

An object oriented framework to simulate ecological (and other) dynamic systems. It can be used for differential equations, individual-based (or agent-based) and other models as well. It supports structuring of simulation scenarios (to avoid copy and paste) and aims to improve readability and re-usability of code.

Maintained by Thomas Petzoldt. Last updated 8 months ago.

5.5 match 4.76 score 190 scripts

dwbapst

paleotree:Paleontological and Phylogenetic Analyses of Evolution

Provides tools for transforming, a posteriori time-scaling, and modifying phylogenies containing extinct (i.e. fossil) lineages. In particular, most users are interested in the functions timePaleoPhy, bin_timePaleoPhy, cal3TimePaleoPhy and bin_cal3TimePaleoPhy, which date cladograms of fossil taxa using stratigraphic data. This package also contains a large number of likelihood functions for estimating sampling and diversification rates from different types of data available from the fossil record (e.g. range data, occurrence data, etc). paleotree users can also simulate diversification and sampling in the fossil record using the function simFossilRecord, which is a detailed simulator for branching birth-death-sampling processes composed of discrete taxonomic units arranged in ancestor-descendant relationships. Users can use simFossilRecord to simulate diversification in incompletely sampled fossil records, under various models of morphological differentiation (i.e. the various patterns by which morphotaxa originate from one another), and with time-dependent, longevity-dependent and/or diversity-dependent rates of diversification, extinction and sampling. Additional functions allow users to translate simulated ancestor-descendant data from simFossilRecord into standard time-scaled phylogenies or unscaled cladograms that reflect the relationships among taxon units.

Maintained by David W. Bapst. Last updated 9 months ago.

3.5 match 21 stars 7.53 score 216 scripts 2 dependents

skstavroglou

patterncausality:Pattern Causality Algorithm

A comprehensive package for detecting and analyzing causal relationships in complex systems using pattern-based approaches. Key features include state space reconstruction, pattern identification, and causality strength evaluation.

Maintained by Hui Wang. Last updated 1 months ago.

4.0 match 3 stars 6.56 score 20 scripts

arturosp

ecocbo:Calculating Optimum Sampling Effort in Community Ecology

A system for calculating the optimal sampling effort, based on the ideas of "Ecological cost-benefit optimization" as developed by A. Underwood (1997, ISBN 0 521 55696 1). Data is obtained from simulated ecological communities with prep_data() which formats and arranges the initial data, and then the optimization follows the following procedure of four functions: (1) scompvar() calculates the variation components necessary for (2) sim_cbo() to calculate the optimal combination of number of sites and samples depending on either an economic budget or on a desired statistical accuracy. Additionally, (3) sim_beta() estimates statistical power and type 2 error by using Permutational Multivariate Analysis of Variance, and (6) plot_power() represents the results of the previous function.

Maintained by Arturo Sanchez-Porras. Last updated 7 months ago.

6.5 match 4.00 score 7 scripts

pecanproject

PEcAn.workflow:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PEcAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation. This package provides workhorse functions that can be used to run the major steps of a PEcAn analysis.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

2.9 match 216 stars 8.83 score 15 scripts 4 dependents

trenchproject

TrenchR:Tools for Microclimate and Biophysical Ecology

Tools for translating environmental change into organismal response. Microclimate models to vertically scale weather station data to organismal heights. The biophysical modeling tools include both general models for heat flows and specific models to predict body temperatures for a variety of ectothermic taxa. Additional functions model and temporally partition air and soil temperatures and solar radiation. Utility functions estimate the organismal and environmental parameters needed for biophysical ecology. 'TrenchR' focuses on relatively simple and modular functions so users can create transparent and flexible biophysical models. Many functions are derived from Gates (1980) <doi:10.1007/978-1-4612-6024-0> and Campbell and Norman (1988) <isbn:9780387949376>.

Maintained by Lauren Buckley. Last updated 1 years ago.

3.6 match 13 stars 6.89 score 43 scripts

pecanproject

PEcAn.uncertainty:PEcAn Functions Used for Propagating and Partitioning Uncertainties in Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

2.8 match 216 stars 8.93 score 15 scripts 5 dependents

pecanproject

PEcAn.SIPNET:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

2.9 match 216 stars 8.36 score 61 scripts

goldingn

BayesComm:Bayesian Community Ecology Analysis

Bayesian multivariate binary (probit) regression models for analysis of ecological communities.

Maintained by Nick Golding. Last updated 9 years ago.

openblas cpp

5.6 match 9 stars 4.35 score 25 scripts

jcdterry

cassandRa:Finds Missing Links and Metric Confidence Intervals in Ecological Bipartite Networks

Provides methods to deal with under sampling in ecological bipartite networks from Terry and Lewis (2020) Ecology <doi:10.1002/ecy.3047> Includes tools to fit a variety of statistical network models and sample coverage estimators to highlight most likely missing links. Also includes simple functions to resample from observed networks to generate confidence intervals for common ecological network metrics.

Maintained by Chris Terry. Last updated 10 months ago.

5.4 match 3 stars 4.48 score 4 scripts

bioc

phyloseq:Handling and analysis of high-throughput microbiome census data

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Maintained by Paul J. McMurdie. Last updated 5 months ago.

immunooncology sequencing microbiome metagenomics clustering classification multiplecomparison geneticvariability

1.7 match 597 stars 13.90 score 8.4k scripts 37 dependents

ausgis

GD:Geographical Detectors for Assessing Spatial Factors

Geographical detectors for measuring spatial stratified heterogeneity, as described in Jinfeng Wang (2010) <doi:10.1080/13658810802443457> and Jinfeng Wang (2016) <doi:10.1016/j.ecolind.2016.02.052>. Includes the optimal discretization of continuous data, four primary functions of geographical detectors, comparison of size effects of spatial unit and the visualizations of results. To use the package and to refer the descriptions of the package, methods and case datasets, please cite Yongze Song (2020) <doi:10.1080/15481603.2020.1760434>. The model has been applied in factor exploration of road performance and multi-scale spatial segmentation for network data, as described in Yongze Song (2018) <doi:10.3390/rs10111696> and Yongze Song (2020) <doi:10.1109/TITS.2020.3001193>, respectively.

Maintained by Wenbo Lv. Last updated 4 months ago.

geographical-detector spatial-stratified-heterogeneity

3.1 match 13 stars 7.74 score 51 scripts

pecanproject

PEcAnAssimSequential:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Mike Dietze. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants jags cpp

2.9 match 216 stars 8.12 score 35 scripts

wangnq111

LorMe:Lightening One-Code Resolving Microbial Ecology Solution

Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.

Maintained by Ningqi Wang. Last updated 17 days ago.

5.0 match 10 stars 4.70 score 1 scripts

pascoalf

ulrb:Unsupervised Learning Based Definition of Microbial Rare Biosphere

A tool to define rare biosphere. 'ulrb' solves the problem of the definition of rarity by replacing arbitrary thresholds with an unsupervised machine learning algorithm (partitioning around medoids, or k-medoids). This algorithm works for any type of microbiome data, provided there is a species abundance table. For validation of this method to different species abundance tables see Pascoal et al, 2024 (in peer-review). This method also works for non-microbiome data.

Maintained by Francisco Pascoal. Last updated 5 days ago.

4.1 match 3 stars 5.78 score 9 scripts

luisagi

enmpa:Ecological Niche Modeling using Presence-Absence Data

A set of tools to perform Ecological Niche Modeling with presence-absence data. It includes algorithms for data partitioning, model fitting, calibration, evaluation, selection, and prediction. Other functions help to explore signals of ecological niche using univariate and multivariate analyses, and model features such as variable response curves and variable importance. Unique characteristics of this package are the ability to exclude models with concave quadratic responses, and the option to clamp model predictions to specific variables. These tools are implemented following principles proposed in Cobos et al., (2022) <doi:10.17161/bi.v17i.15985>, Cobos et al., (2019) <doi:10.7717/peerj.6281>, and Peterson et al., (2008) <doi:10.1016/j.ecolmodel.2007.11.008>.

Maintained by Luis F. Arias-Giraldo. Last updated 3 months ago.

cpp

5.3 match 5 stars 4.35 score 5 scripts

bioc

mina:Microbial community dIversity and Network Analysis

An increasing number of microbiome datasets have been generated and analyzed with the help of rapidly developing sequencing technologies. At present, analysis of taxonomic profiling data is mainly conducted using composition-based methods, which ignores interactions between community members. Besides this, a lack of efficient ways to compare microbial interaction networks limited the study of community dynamics. To better understand how community diversity is affected by complex interactions between its members, we developed a framework (Microbial community dIversity and Network Analysis, mina), a comprehensive framework for microbial community diversity analysis and network comparison. By defining and integrating network-derived community features, we greatly reduce noise-to-signal ratio for diversity analyses. A bootstrap and permutation-based method was implemented to assess community network dissimilarities and extract discriminative features in a statistically principled way.

Maintained by Rui Guan. Last updated 5 months ago.

software workflowstep cpp

4.7 match 5 stars 4.85 score 14 scripts

robitalec

ScaleInMultilayerNetworks:Package Accompanying: The Problem And Promise Of Scale In Multilayer Animal Social Networks.

Scale remains a foundational concept in ecology. Spatial scale, for instance, has become a central consideration in the way we understand landscape ecology and animal space use. Meanwhile, scale-dependent social processes can range from fine-scale interactions to co-occurrence and overlapping home ranges. Furthermore, sociality can vary within and across seasons. Multilayer networks promise the explicit integration of the social, spatial and, temporal contexts. Given the complex interplay of sociality and animal space use in heterogeneous landscapes, there remains an important gap in our understanding of the influence of scale on animal social networks. Using an empirical case study, we discuss ways of considering social, spatial and, temporal scale in the context of multilayer caribou social networks. Effective integration of social and spatial processes, including biologically meaningful scales, within the context of animal social networks is an emerging area of research. We incorporate perspectives that link the social environment to spatial processes across scales in a multilayer context.

Maintained by Alec L. Robitaille. Last updated 4 years ago.

ecology multilayer-networks social-network-analysis

10.8 match 1 stars 2.00 score

pecanproject

PEcAn.MAESPA:PEcAn Functions Used for Ecological Forecasts and Reanalysis using MAESPA

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.This package allows for MAESPA to be run through the PEcAN workflow.

Maintained by Tony Gardella. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

2.8 match 216 stars 7.58 score 2 scripts

yangcq-ivy

NicheBarcoding:Niche-model-Based Species Identification

Species Identification using DNA Barcodes Integrated with Environmental Niche Models.

Maintained by Cai-qing YANG. Last updated 8 months ago.

openjdk

5.0 match 1 stars 4.18 score 7 scripts

ahgroup

DSAIDE:Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)

Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios. The purpose of the package is to help individuals learn about infectious disease epidemiology (ecology/evolution) from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.

Maintained by Andreas Handel. Last updated 1 years ago.

3.3 match 26 stars 6.30 score 22 scripts

limnolab

diathor:Calculate Ecological Information and Diatom Based Indices

Calculate multiple biotic indices using diatoms from environmental samples. Diatom species are recognized by their species' name using a heuristic search, and their ecological data is retrieved from multiple sources. It includes number/shape of chloroplasts diversity indices, size classes, ecological guilds, and multiple biotic indices. It outputs both a dataframe with all the results and plots of all the obtained data in a defined output folder. - Sample data was taken from Nicolosi Gelis, Cochero & Gómez (2020, <doi:10.1016/j.ecolind.2019.105951>). - The package uses the 'Diat.Barcode' database to calculate morphological and ecological information by Rimet & Couchez (2012, <doi:10.1051/kmae/2012018>),and the combined classification of guilds and size classes established by B-Béres et al. (2017, <doi:10.1016/j.ecolind.2017.07.007>). - Current diatom-based biotic indices include the DES index by \href{<https://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=PASCAL8060205402>}{Descy (1979)} - EPID index by Dell'Uomo (1996, ISBN: 3950009002) - IDAP index by Prygiel & Coste (1993, <doi:10.1007/BF00028033>) - ID-CH index by Hürlimann & Niederhauser \href{, <https://www.bafu.admin.ch/bafu/fr/home/themes/eaux/publications/publications-eaux/methodes-analyse-appreciation-cours-eau-diatomees.html>)}{(2007)} - IDP index by Gómez & Licursi (2001, <doi:10.1023/A:1011415209445>) - ILM index by Leclercq & Maquet \href{<https://www.vliz.be/imisdocs/publications/286641.pdf>}{(1987)} - IPS index by Coste \href{<https://www.oieau.org/eaudoc/notice/ETUDE-DES-METHODES-BIOLOGIQUES-DAPPRECIATION-QUANTITATIVE-DE-LA-QUALITE-DES-EAUX>}{(1982)} - LOBO index by Lobo, Callegaro, & Bender (2002, ISBN:9788585869908) - SLA by Sládeček (1986, <doi:10.1002/aheh.19860140519>) - TDI index by Kelly, & Whitton (1995, <doi:10.1007/BF00003802>) - SPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019, <doi:10.1016/j.ecolind.2018.12.035>) - PBIDW index by Castro-Roa & Pinilla-Agudelo (2014) - DISP index by Stenger-Kovácsa et al. (2018)

Maintained by Joaquin Cochero. Last updated 8 months ago.

9.1 match 2 stars 2.30 score 4 scripts

bmaitner

BIEN:Tools for Accessing the Botanical Information and Ecology Network Database

Provides Tools for Accessing the Botanical Information and Ecology Network Database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <https://bien.nceas.ucsb.edu/bien/> for more Information). This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.

Maintained by Brian Maitner. Last updated 2 months ago.

3.4 match 6.04 score 205 scripts 5 dependents

predictiveecology

LandWebUtils:Helper functions for the LandWeb project

Additional utilities for LandWeb analyses.

Maintained by Alex M Chubaty. Last updated 2 months ago.

landscape-ecology simulation-modeling

7.5 match 2 stars 2.60 score 2 scripts

fraenzi

blmeco:Data Files and Functions Accompanying the Book "Bayesian Data Analysis in Ecology using R, BUGS and Stan"

Data files and functions accompanying the book Korner-Nievergelt, Roth, von Felten, Guelat, Almasi, Korner-Nievergelt (2015) "Bayesian Data Analysis in Ecology using R, BUGS and Stan", Elsevier, New York.

Maintained by Fraenzi Korner-Nievergelt. Last updated 5 years ago.

4.8 match 4.05 score 111 scripts

mindthegap-erc

StratPal:Stratigraphic Paleobiology Modeling Pipelines

The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.

Maintained by Niklas Hohmann. Last updated 1 days ago.

palaeobiology palaeontology paleobiology paleontology stratigraphic-paleobiology stratigraphy

3.2 match 1 stars 6.00 score 18 scripts

cran

EIEntropy:Ecological Inference Applying Entropy

Implements two estimations related to the foundations of info metrics applied to ecological inference. These methodologies assess the lack of disaggregated data and provide an approach to obtaining disaggregated territorial-level data. For more details, see the following references: Fernández-Vázquez, E., Díaz-Dapena, A., Rubiera-Morollón, F. et al. (2020) "Spatial Disaggregation of Social Indicators: An Info-Metrics Approach." <doi:10.1007/s11205-020-02455-z>. Díaz-Dapena, A., Fernández-Vázquez, E., Rubiera-Morollón, F., & Vinuela, A. (2021) "Mapping poverty at the local level in Europe: A consistent spatial disaggregation of the AROPE indicator for France, Spain, Portugal and the United Kingdom." <doi:10.1111/rsp3.12379>.

Maintained by Silvia María Franco Anaya. Last updated 12 days ago.

7.4 match 2.60 score

sandrinepavoine

adiv:Analysis of Diversity

Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.

Maintained by Sandrine Pavoine. Last updated 1 years ago.

8.3 match 1 stars 2.28 score 63 scripts

greta-dev

greta:Simple and Scalable Statistical Modelling in R

Write statistical models in R and fit them by MCMC and optimisation on CPUs and GPUs, using Google 'TensorFlow'. greta lets you write your own model like in BUGS, JAGS and Stan, except that you write models right in R, it scales well to massive datasets, and it’s easy to extend and build on. See the website for more information, including tutorials, examples, package documentation, and the greta forum.

Maintained by Nicholas Tierney. Last updated 18 days ago.

1.5 match 566 stars 12.53 score 396 scripts 6 dependents

mrkellermann

eiPack:Ecological Inference and Higher-Dimension Data Management

Provides methods for analyzing R by C ecological contingency tables using the extreme case analysis, ecological regression, and Multinomial-Dirichlet ecological inference models. Also provides tools for manipulating higher-dimension data objects.

Maintained by Michael Kellermann. Last updated 2 years ago.

9.6 match 1.92 score 28 scripts 1 dependents

jebyrnes

multifunc:Analysis of Ecological Drivers on Ecosystem Multifunctionality

Methods for the analysis of how ecological drivers affect the multifunctionality of an ecosystem based on methods of Byrnes et al. 2016 <doi:10.1111/2041-210X.12143> and Byrnes et al. 2022 <doi:10.1101/2022.03.17.484802>. Most standard methods in the literature are implemented (see vignettes) in a tidy format.

Maintained by Jarrett Byrnes. Last updated 3 years ago.

multifunctionality

3.5 match 16 stars 5.20 score 9 scripts

luismurao

tenm:Temporal Ecological Niche Models

Implements methods and functions to calibrate time-specific niche models (multi-temporal calibration), letting users execute a strict calibration and selection process of niche models based on ellipsoids, as well as functions to project the potential distribution in the present and in global change scenarios.The 'tenm' package has functions to recover information that may be lost or overlooked while applying a data curation protocol. This curation involves preserving occurrences that may appear spatially redundant (occurring in the same pixel) but originate from different time periods. A novel aspect of this package is that it might reconstruct the fundamental niche more accurately than mono-calibrated approaches. The theoretical background of the package can be found in Peterson et al. (2011)<doi:10.5860/CHOICE.49-6266>.

Maintained by Luis Osorio-Olvera. Last updated 8 months ago.

3.1 match 6 stars 5.79 score 34 scripts

jmzobitz

neonSoilFlux:Compute Soil Carbon Fluxes for the National Ecological Observatory Network Sites

Acquires and synthesizes soil carbon fluxes at sites located in the National Ecological Observatory Network (NEON). Provides flux estimates and associated uncertainty as well as key environmental measurements (soil water, temperature, CO2 concentration) that are used to compute soil fluxes.

Maintained by John Zobitz. Last updated 10 months ago.

3.3 match 6 stars 5.43 score 2 scripts

ambarbosa

ecotrends:Temporal Trends in Ecological Niche Models

Computes temporal trends in environmental suitability obtained from ecological niche models, based on a set of species presence point coordinates and predictor variables.

Maintained by A. Marcia Barbosa. Last updated 24 days ago.

3.5 match 12 stars 5.01 score

babaknaimi

sdm:Species Distribution Modelling

An extensible framework for developing species distribution models using individual and community-based approaches, generate ensembles of models, evaluate the models, and predict species potential distributions in space and time. For more information, please check the following paper: Naimi, B., Araujo, M.B. (2016) <doi:10.1111/ecog.01881>.

Maintained by Babak Naimi. Last updated 2 months ago.

1.9 match 24 stars 9.31 score 312 scripts 1 dependents

r-forge

cardidates:Identification of Cardinal Dates in Ecological Time Series

Identification of cardinal dates (begin, time of maximum, end of mass developments) in ecological time series using fitted Weibull functions.

Maintained by Thomas Petzoldt. Last updated 1 years ago.

5.2 match 3.34 score 22 scripts

biodiverse

unmarked:Models for Data from Unmarked Animals

Fits hierarchical models of animal abundance and occurrence to data collected using survey methods such as point counts, site occupancy sampling, distance sampling, removal sampling, and double observer sampling. Parameters governing the state and observation processes can be modeled as functions of covariates. References: Kellner et al. (2023) <doi:10.1111/2041-210X.14123>, Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.

Maintained by Ken Kellner. Last updated 10 days ago.

openblas cpp openmp

1.3 match 4 stars 13.02 score 652 scripts 12 dependents

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.

7.1 match 1 stars 2.39 score 41 scripts 1 dependents

jarioksa

natto:An Extreme 'vegan' Package of Experimental Code

Random code that is too experimental or too weird to be included in the vegan package.

Maintained by Jari Oksanen. Last updated 1 months ago.

3.6 match 8 stars 4.68 score 1 scripts

biomodhub

biomod2:Ensemble Platform for Species Distribution Modeling

Functions for species distribution modeling, calibration and evaluation, ensemble of models, ensemble forecasting and visualization. The package permits to run consistently up to 10 single models on a presence/absences (resp presences/pseudo-absences) dataset and to combine them in ensemble models and ensemble projections. Some bench of other evaluation and visualisation tools are also available within the package.

Maintained by Maya Guéguen. Last updated 23 hours ago.

1.2 match 95 stars 13.85 score 536 scripts 7 dependents

neonscience

neonUtilities:Utilities for Working with NEON Data

NEON data packages can be accessed through the NEON Data Portal <https://www.neonscience.org> or through the NEON Data API (see <https://data.neonscience.org/data-api> for documentation). Data delivered from the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.

Maintained by Claire Lunch. Last updated 2 months ago.

1.6 match 57 stars 10.66 score 944 scripts 15 dependents

zhao-jun-yong

aelab:Data Processing for Aquatic Ecology

Facilitate the analysis of data related to aquatic ecology, specifically the establishment of carbon budget. Currently, the package allows the below analysis. (i) the calculation of greenhouse gas flux based on data obtained from trace gas analyzer using the method described in Lin et al. (2024). (ii) the calculation of Dissolved Oxygen (DO) metabolism based on data obtained from dissolved oxygen data logger using the method described in Staehr et al. (2010). Yong et al. (2024) <doi:10.5194/bg-21-5247-2024>. Staehr et al. (2010) <doi:10.4319/lom.2010.8.0628>.

Maintained by Zhao-Jun Yong. Last updated 3 months ago.

3.6 match 4.54 score 2 scripts

reumandc

wsyn:Wavelet Approaches to Studies of Synchrony in Ecology and Other Fields

Tools for a wavelet-based approach to analyzing spatial synchrony, principally in ecological data. Some tools will be useful for studying community synchrony. See, for instance, Sheppard et al (2016) <doi: 10.1038/NCLIMATE2991>, Sheppard et al (2017) <doi: 10.1051/epjnbp/2017000>, Sheppard et al (2019) <doi: 10.1371/journal.pcbi.1006744>.

Maintained by Daniel C. Reuman. Last updated 3 years ago.

3.4 match 1 stars 4.80 score 125 scripts

grosssbm

GREMLINS:Generalized Multipartite Networks

We define generalized multipartite networks as the joint observation of several networks implying some common pre-specified groups of individuals. The aim is to fit an adapted version of the popular stochastic block model to multipartite networks, as described in Bar-hen, Barbillon and Donnet (2020) <arXiv:1807.10138>.

Maintained by Sophie Donnet. Last updated 2 years ago.

2.9 match 1 stars 5.26 score 9 scripts 4 dependents

mrheath

StrathE2E2:End-to-End Marine Food Web Model

A dynamic model of the big-picture, whole ecosystem effects of hydrodynamics, temperature, nutrients, and fishing on continental shelf marine food webs. The package is described in: Heath, M.R., Speirs, D.C., Thurlbeck, I. and Wilson, R.J. (2020) <doi:10.1111/2041-210X.13510> StrathE2E2: An R package for modelling the dynamics of marine food webs and fisheries. 8pp.

Maintained by Michael Heath. Last updated 4 years ago.

4.9 match 3.10 score 25 scripts

reumandc

tsvr:Timescale-Specific Variance Ratio for Use in Community Ecology

Tools for timescale decomposition of the classic variance ratio of community ecology. Tools are as described in Zhao et al (in prep), extending commonly used methods introduced by Peterson et al (1975) <doi: 10.2307/1936306>.

Maintained by Daniel C. Reuman. Last updated 4 years ago.

3.4 match 2 stars 4.46 score 29 scripts

deankoch

rasterbc:Access Forest Ecology Layers for British Columbia in 2001-2018

R-based access to a large set of data variables relevant to forest ecology in British Columbia (BC), Canada. Layers are in raster format at 100m resolution in the BC Albers projection, hosted at the Federated Research Data Repository (FRDR) with <doi:10.20383/101.0283>. The collection includes: elevation; biogeoclimatic zone; wildfire; cutblocks; forest attributes from Hansen et al. (2013) <doi:10.1139/cjfr-2013-0401> and Beaudoin et al. (2017) <doi:10.1139/cjfr-2017-0184>; and rasterized Forest Insect and Disease Survey (FIDS) maps for a number of insect pest species, all covering the period 2001-2018. Users supply a polygon or point location in the province of BC, and 'rasterbc' will download the overlapping raster tiles hosted at FRDR, merging them as needed and returning the result in R as a 'SpatRaster' object. Metadata associated with these layers, and code for downloading them from their original sources can be found in the 'github' repository <https://github.com/deankoch/rasterbc_src>.

Maintained by Dean Koch. Last updated 1 years ago.

3.3 match 6 stars 4.52 score 11 scripts

wallaceecomod

wallace:A Modular Platform for Reproducible Modeling of Species Niches and Distributions

The 'shiny' application Wallace is a modular platform for reproducible modeling of species niches and distributions. Wallace guides users through a complete analysis, from the acquisition of species occurrence and environmental data to visualizing model predictions on an interactive map, thus bundling complex workflows into a single, streamlined interface. An extensive vignette, which guides users through most package functionality can be found on the package's GitHub Pages website: <https://wallaceecomod.github.io/wallace/articles/tutorial-v2.html>.

Maintained by Mary E. Blair. Last updated 22 days ago.

openjdk

1.8 match 133 stars 8.36 score 96 scripts

psolymos

mefa:Multivariate Data Handling in Ecology and Biogeography

A framework package aimed to provide standardized computational environment for specialist work via object classes to represent the data coded by samples, taxa and segments (i.e. subpopulations, repeated measures). It supports easy processing of the data along with cross tabulation and relational data tables for samples and taxa. An object of class `mefa' is a project specific compendium of the data and can be easily used in further analyses. Methods are provided for extraction, aggregation, conversion, plotting, summary and reporting of `mefa' objects. Reports can be generated in plain text or LaTeX format. Vignette contains worked examples.

Maintained by Peter Solymos. Last updated 10 months ago.

3.0 match 2 stars 4.82 score 111 scripts 2 dependents

fraenzi

carcass:Estimation of the Number of Fatalities from Carcass Searches

The number of bird or bat fatalities from collisions with buildings, towers or wind energy turbines can be estimated based on carcass searches and experimentally assessed carcass persistence times and searcher efficiency. Functions for estimating the probability that a bird or bat that died is found by a searcher are provided. Further functions calculate the posterior distribution of the number of fatalities based on the number of carcasses found and the estimated detection probability.

Maintained by Fraenzi Korner-Nievergelt. Last updated 1 years ago.

4.8 match 2.93 score 17 scripts

edwbaker

sonicscrewdriver:Bioacoustic Analysis and Publication Tools

Provides tools for manipulating sound files for bioacoustic analysis, and preparing analyses these for publication. The package validates that values are physically possible wherever feasible.

Maintained by Ed Baker. Last updated 3 days ago.

bioacoustics ecoacoustics

2.0 match 6 stars 7.04 score 26 scripts

haoranpopevo

ecode:Ordinary Differential Equation Systems in Ecology

A framework to simulate ecosystem dynamics through ordinary differential equations (ODEs). You create an ODE model, tells 'ecode' to explore its behaviour, and perform numerical simulations on the model. 'ecode' also allows you to fit model parameters by machine learning algorithms. Potential users include researchers who are interested in the dynamics of ecological community and biogeochemical cycles.

Maintained by Haoran Wu. Last updated 8 months ago.

3.5 match 7 stars 3.85 score 3 scripts

flare-forecast

ropenmeteo:Wrappers for 'Open-Meteo' API

Wrappers for the Application Programming Interface from the <https://open-meteo.com> project along with helper functions. The <https://open-meteo.com> project streamlines access to a range of publicly historical and forecast meteorology data from agencies across the world.

Maintained by Quinn Thomas. Last updated 7 months ago.

2.9 match 4.62 score 14 scripts

txm676

nos:Compute Node Overlap and Segregation in Ecological Networks

Calculate NOS (node overlap and segregation) and the associated metrics described in Strona and Veech (2015) <DOI:10.1111/2041-210X.12395> and Strona et al. (2017, In Press). The functions provided in the package enable assessment of structural patterns ranging from complete node segregation to perfect nestedness in a variety of network types. In addition, they provide a measure of network modularity.

Maintained by Thomas J. Matthews. Last updated 1 years ago.

4.6 match 2.88 score 15 scripts

anonymous-eco

phylosignalDB:Explore Phylogenetic Signals Using Distance-Based Methods

A unified method, called M statistic, is provided for detecting phylogenetic signals in continuous traits, discrete traits, and multi-trait combinations. Blomberg and Garland (2002) <doi:10.1046/j.1420-9101.2002.00472.x> provided a widely accepted statistical definition of the phylogenetic signal, which is the "tendency for related species to resemble each other more than they resemble species drawn at random from the tree". The M statistic strictly adheres to the definition of phylogenetic signal, formulating an index and developing a method of testing in strict accordance with the definition, instead of relying on correlation analysis or evolutionary models. The novel method equivalently expressed the textual definition of the phylogenetic signal as an inequality equation of the phylogenetic and trait distances and constructed the M statistic. Also, there are more distance-based methods under development.

Maintained by Liang Yao. Last updated 2 months ago.

3.8 match 3.40 score

nceas

rt:Interface to the 'Request Tracker' API

Provides a programmatic interface to the 'Request Tracker' (RT) HTTP API <https://rt-wiki.bestpractical.com/wiki/REST>. 'RT' is a popular ticket tracking system.

Maintained by Bryce Mecum. Last updated 4 years ago.

api request-tracker

1.6 match 6 stars 7.98 score 664 scripts

cxzdsa2332

idopNetwork:A Network Tool to Dissect Spatial Community Ecology

Most existing approaches for network reconstruction can only infer an overall network and, also, fail to capture a complete set of network properties. To address these issues, a new model has been developed, which converts static data into their 'dynamic' form. 'idopNetwork' is an 'R' interface to this model, it can inferring informative, dynamic, omnidirectional and personalized networks. For more information on functional clustering part, see Kim et al. (2008) <doi:10.1534/genetics.108.093690>, Wang et al. (2011) <doi:10.1093/bib/bbr032>. For more information on our model, see Chen et al. (2019) <doi:10.1038/s41540-019-0116-1>, and Cao et al. (2022) <doi:10.1080/19490976.2022.2106103>.

Maintained by Ang Dong. Last updated 2 years ago.

2.9 match 4 stars 4.30 score 3 scripts

cran

psy:Various Procedures Used in Psychometrics

Kappa, ICC, reliability coefficient, parallel analysis, multi-traits multi-methods, spherical representation of a correlation matrix.

Maintained by Bruno Falissard. Last updated 3 years ago.

3.8 match 3.32 score 4 dependents

cboettig

EcoNetGen:Simulate and Sample from Ecological Interaction Networks

Randomly generate a wide range of interaction networks with specified size, average degree, modularity, and topological structure. Sample nodes and links from within simulated networks randomly, by degree, by module, or by abundance. Simulations and sampling routines are implemented in 'FORTRAN', providing efficient generation times even for large networks. Basic visualization methods also included. Algorithms implemented here are described in de Aguiar et al. (2017) <arXiv:1708.01242>.

Maintained by Carl Boettiger. Last updated 2 years ago.

fortran

3.0 match 9 stars 4.00 score 11 scripts

kwstat

agridat:Agricultural Datasets

Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.

Maintained by Kevin Wright. Last updated 1 months ago.

data

1.1 match 126 stars 10.78 score 1.7k scripts 1 dependents

lter

lterpalettefinder:Extract Color Palettes from Photos and Pick Official LTER Palettes

Allows identification of palettes derived from LTER (Long Term Ecological Research) photographs based on user criteria. Also facilitates extraction of palettes from users' photos directly.

Maintained by Nicholas J Lyon. Last updated 2 years ago.

color-palette-generator data-science

2.2 match 27 stars 5.43 score 7 scripts

nschuwirth

ecoval:Procedures for Ecological Assessment of Surface Waters

Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.

Maintained by Nele Schuwirth. Last updated 3 years ago.

8.8 match 1.34 score 22 scripts

marcohlmann

metanetwork:Handling and Representing Trophic Networks in Space and Time

A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks. The package also implements network diversity indices at different aggregation levels and connectance computation.

Maintained by Marc Ohlmann. Last updated 2 years ago.

3.0 match 2 stars 3.89 score 77 scripts