Showing 21 of total 21 results (show query)
mpi-bgc-functional-biogeography
rtry:Preprocessing Plant Trait Data
Designed to support the application of plant trait data providing easy applicable functions for the basic steps of data preprocessing, e.g. data import, data exploration, selection of columns and rows, excluding trait data according to different attributes, geocoding, long- to wide-table transformation, and data export. 'rtry' was initially developed as part of the TRY R project to preprocess trait data received via the TRY database.
Maintained by Olee Hoi Ying Lam. Last updated 2 years ago.
14.0 match 24 stars 5.94 score 24 scripts
globalecologylab
poems:Pattern-Oriented Ensemble Modeling System
A framework of interoperable R6 classes (Chang, 2020, <https://CRAN.R-project.org/package=R6>) for building ensembles of viable models via the pattern-oriented modeling (POM) approach (Grimm et al.,2005, <doi:10.1126/science.1116681>). The package includes classes for encapsulating and generating model parameters, and managing the POM workflow. The workflow includes: model setup; generating model parameters via Latin hyper-cube sampling (Iman & Conover, 1980, <doi:10.1080/03610928008827996>); running multiple sampled model simulations; collating summary results; and validating and selecting an ensemble of models that best match known patterns. By default, model validation and selection utilizes an approximate Bayesian computation (ABC) approach (Beaumont et al., 2002, <doi:10.1093/genetics/162.4.2025>), although alternative user-defined functionality could be employed. The package includes a spatially explicit demographic population model simulation engine, which incorporates default functionality for density dependence, correlated environmental stochasticity, stage-based transitions, and distance-based dispersal. The user may customize the simulator by defining functionality for translocations, harvesting, mortality, and other processes, as well as defining the sequence order for the simulator processes. The framework could also be adapted for use with other model simulators by utilizing its extendable (inheritable) base classes.
Maintained by July Pilowsky. Last updated 20 days ago.
biogeographypopulation-modelprocess-based
10.0 match 10 stars 8.05 score 59 scripts 2 dependents
ropensci
CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections
Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.
Maintained by Alexander Zizka. Last updated 1 years ago.
5.9 match 82 stars 10.93 score 306 scripts 3 dependents
joshwlambert
DAISIEprep:Extracts Phylogenetic Island Community Data from Phylogenetic Trees
Extracts colonisation and branching times of island species to be used for analysis in the R package 'DAISIE'. It uses phylogenetic and endemicity data to extract the separate island colonists and store them.
Maintained by Joshua W. Lambert. Last updated 1 months ago.
data-scienceisland-biogeographyphylogenetics
9.3 match 6 stars 6.78 score 24 scripts
biorgeo
bioregion:Comparison of Bioregionalisation Methods
The main purpose of this package is to propose a transparent methodological framework to compare bioregionalisation methods based on hierarchical and non-hierarchical clustering algorithms (Kreft & Jetz (2010) <doi:10.1111/j.1365-2699.2010.02375.x>) and network algorithms (Lenormand et al. (2019) <doi:10.1002/ece3.4718> and Leroy et al. (2019) <doi:10.1111/jbi.13674>).
Maintained by Maxime Lenormand. Last updated 10 days ago.
biogeographybioregionbioregionalizationcpp
10.0 match 7 stars 6.27 score 11 scripts
frbcesab
funbiogeo:Functional Biogeography Analyses
Helps users with analyses in functional biogeogeography by loading and combining data, computing trait coverage, as well as computing functional diversity indices, drawing maps, correlating them with the environment, and upscaling assemblages.
Maintained by Nicolas Casajus. Last updated 4 days ago.
functional-biogeographyfunctional-diversityfunctional-trait
10.8 match 11 stars 5.60 score 8 scripts
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 24 days ago.
bias-correctionbiogeographyecological-niche-modelingecological-niche-modellingniche-modelingniche-modellingspecies-distribution-modelingopenjdk
10.0 match 25 stars 5.62 score 37 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.
biogeographyecologymetapopulationspecies
10.0 match 3 stars 5.10 score 28 scripts
paicecode
PAICE:Phylogeographic Analysis of Island Colonization Events
Estimation of the number of colonization events between islands of the same archipelago for a species. It uses rarefaction curves to control for both field and genetic sample sizes as it was described in Coello et al. (2022) <doi:10.1111/jbi.14341>.
Maintained by Alberto J. Coello. Last updated 8 months ago.
biogeographycolonizationisland
10.0 match 1 stars 3.00 score 4 scripts
vjontiveros
island:Stochastic Island Biogeography Theory Made Easy
Develops stochastic models based on the Theory of Island Biogeography (TIB) of MacArthur and Wilson (1967) <doi:10.1023/A:1016393430551> and extensions. It implements methods to estimate colonization and extinction rates (including environmental variables) given presence-absence data, simulates community assembly, and performs model selection.
Maintained by Vicente Jimenez. Last updated 1 years ago.
8.9 match 3.10 score 42 scripts
pakillo
FloraIberica:Taxonomic and distribution data for all the vascular plants present in the Iberian Peninsula and Balearic Islands
Check which plant taxa are present and/or endemic, and get detailed (10x10 km) distribution maps for all the vascular plants present in the Iberian Peninsula and Balearic Islands, from genus to subspecies level, based on the AFLIBER database (<doi:10.1111/geb.13363>).
Maintained by Francisco Rodríguez-Sánchez. Last updated 2 years ago.
10.0 match 7 stars 2.54 score 4 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.
4.6 match 2 stars 3.89 score 77 scripts
thijsjanzen
GUILDS:Implementation of Sampling Formulas for the Unified Neutral Model of Biodiversity and Biogeography, with or without Guild Structure
A collection of sampling formulas for the unified neutral model of biogeography and biodiversity. Alongside the sampling formulas, it includes methods to perform maximum likelihood optimization of the sampling formulas, methods to generate data given the neutral model, and methods to estimate the expected species abundance distribution. Sampling formulas included in the GUILDS package are the Etienne Sampling Formula (Etienne 2005), the guild sampling formula, where guilds are assumed to differ in dispersal ability (Janzen et al. 2015), and the guilds sampling formula conditioned on guild size (Janzen et al. 2015).
Maintained by Thijs Janzen. Last updated 3 days ago.
3.2 match 2 stars 5.43 score 18 scripts 5 dependents
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
txm676
sars:Fit and Compare Species-Area Relationship Models Using Multimodel Inference
Implements the basic elements of the multi-model inference paradigm for up to twenty species-area relationship models (SAR), using simple R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>. The package is scalable and users can easily create their own model and data objects. Additional SAR related functions are provided.
Maintained by Thomas J. Matthews. Last updated 11 days ago.
1.8 match 9 stars 6.67 score 95 scripts
cran
EcoVirtual:Simulation of Ecological Models
Computer simulations of classical ecological models as a learning resource.
Maintained by Alexandre Adalardo de Oliveira. Last updated 6 years ago.
3.7 match 1.48 score 1 dependentscran
BAT:Biodiversity Assessment Tools
Includes algorithms to assess alpha and beta diversity in all their dimensions (taxonomic, phylogenetic and functional). It allows performing a number of analyses based on species identities/abundances, phylogenetic/functional distances, trees, convex-hulls or kernel density n-dimensional hypervolumes depicting species relationships. Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Maintained by Pedro Cardoso. Last updated 1 years ago.
1.7 match 3.17 score 3 dependents
darunabas
phyloregion:Biogeographic Regionalization and Macroecology
Computational infrastructure for biogeography, community ecology, and biodiversity conservation (Daru et al. 2020) <doi:10.1111/2041-210X.13478>. It is based on the methods described in Daru et al. (2020) <doi:10.1038/s41467-020-15921-6>. The original conceptual work is described in Daru et al. (2017) <doi:10.1016/j.tree.2017.08.013> on patterns and processes of biogeographical regionalization. Additionally, the package contains fast and efficient functions to compute more standard conservation measures such as phylogenetic diversity, phylogenetic endemism, evolutionary distinctiveness and global endangerment, as well as compositional turnover (e.g., beta diversity).
Maintained by Barnabas H. Daru. Last updated 5 months ago.
0.5 match 18 stars 7.21 score 50 scripts 1 dependents
danlwarren
ENMTools:Analysis of Niche Evolution using Niche and Distribution Models
Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Maintained by Dan Warren. Last updated 2 months ago.
0.5 match 105 stars 6.91 score 126 scripts
azizka
conserveR:Identifying Conservation Prioritization Methods Based on Data Availability
Helping biologists to choose the most suitable approach to link their research to conservation. After answering few questions on the data available, geographic and taxonomic scope, 'conserveR' ranks existing methods for conservation prioritization and systematic conservation planning by suitability. The methods data base of 'conserveR' contains 133 methods for conservation prioritization based on a systematic review of > 12,000 scientific publications from the fields of spatial conservation prioritization, systematic conservation planning, biogeography and ecology.
Maintained by Alexander Zizka. Last updated 4 years ago.
0.5 match 8 stars 3.60 score