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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.

32 stars 9.35 score 418 scripts 1 dependents

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

133 stars 8.36 score 96 scripts

green-striped-gecko

dartR:Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Functions are provided that facilitate the import and analysis of 'SNP' (single nucleotide polymorphism) and 'silicodart' (presence/absence) data. The main focus is on data generated by 'DarT' (Diversity Arrays Technology), however, data from other sequencing platforms can be used once 'SNP' or related fragment presence/absence data from any source is imported. Genetic datasets are stored in a derived 'genlight' format (package 'adegenet'), that allows for a very compact storage of data and metadata. Functions are available for importing and exporting of 'SNP' and 'silicodart' data, for reporting on and filtering on various criteria (e.g. 'CallRate', heterozygosity, reproducibility, maximum allele frequency). Additional functions are available for visualization (e.g. Principle Coordinate Analysis) and creating a spatial representation using maps. 'dartR' supports also the analysis of 3rd party software package such as 'newhybrid', 'structure', 'NeEstimator' and 'blast'. Since version 2.0.3 we also implemented simulation functions, that allow to forward simulate 'SNP' dynamics under different population and evolutionary dynamics. Comprehensive tutorials and support can be found at our 'github' repository: github.com/green-striped-gecko/dartR/. If you want to cite 'dartR', you find the information by typing citation('dartR') in the console.

Maintained by Bernd Gruber. Last updated 2 days ago.

34 stars 7.41 score

consbiol-unibern

SDMtune:Species Distribution Model Selection

User-friendly framework that enables the training and the evaluation of species distribution models (SDMs). The package implements functions for data driven variable selection and model tuning and includes numerous utilities to display the results. All the functions used to select variables or to tune model hyperparameters have an interactive real-time chart displayed in the 'RStudio' viewer pane during their execution.

Maintained by Sergio Vignali. Last updated 3 months ago.

hyperparameter-tuningspecies-distribution-modellingvariable-selectioncpp

25 stars 7.37 score 155 scripts

green-striped-gecko

PopGenReport:A Simple Framework to Analyse Population and Landscape Genetic Data

Provides beginner friendly framework to analyse population genetic data. Based on 'adegenet' objects it uses 'knitr' to create comprehensive reports on spatial genetic data. For detailed information how to use the package refer to the comprehensive tutorials or visit <http://www.popgenreport.org/>.

Maintained by Bernd Gruber. Last updated 1 years ago.

5 stars 7.27 score 82 scripts 1 dependents

sylvainschmitt

SSDM:Stacked Species Distribution Modelling

Allows to map species richness and endemism based on stacked species distribution models (SSDM). Individuals SDMs can be created using a single or multiple algorithms (ensemble SDMs). For each species, an SDM can yield a habitat suitability map, a binary map, a between-algorithm variance map, and can assess variable importance, algorithm accuracy, and between- algorithm correlation. Methods to stack individual SDMs include summing individual probabilities and thresholding then summing. Thresholding can be based on a specific evaluation metric or by drawing repeatedly from a Bernoulli distribution. The SSDM package also provides a user-friendly interface.

Maintained by Sylvain Schmitt. Last updated 11 months ago.

44 stars 6.99 score 44 scripts

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 3 months ago.

105 stars 6.91 score 126 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 21 hours ago.

ecological-modellinglandscape-ecosystem-modellingspades

17 stars 6.09 score 12 scripts 4 dependents

simondedman

gbm.auto:Automated Boosted Regression Tree Modelling and Mapping Suite

Automates delta log-normal boosted regression tree abundance prediction. Loops through parameters provided (LR (learning rate), TC (tree complexity), BF (bag fraction)), chooses best, simplifies, & generates line, dot & bar plots, & outputs these & predictions & a report, makes predicted abundance maps, and Unrepresentativeness surfaces. Package core built around 'gbm' (gradient boosting machine) functions in 'dismo' (Hijmans, Phillips, Leathwick & Jane Elith, 2020 & ongoing), itself built around 'gbm' (Greenwell, Boehmke, Cunningham & Metcalfe, 2020 & ongoing, originally by Ridgeway). Indebted to Elith/Leathwick/Hastie 2008 'Working Guide' <doi:10.1111/j.1365-2656.2008.01390.x>; workflow follows Appendix S3. See <https://www.simondedman.com/> for published guides and papers using this package.

Maintained by Simon Dedman. Last updated 19 days ago.

18 stars 5.77 score 13 scripts

giopogg

webSDM:Including Known Interactions in Species Distribution Models

A collection of tools to fit and work with trophic Species Distribution Models. Trophic Species Distribution Models combine knowledge of trophic interactions with Bayesian structural equation models that model each species as a function of its prey (or predators) and environmental conditions. It exploits the topological ordering of the known trophic interaction network to predict species distribution in space and/or time, where the prey (or predator) distribution is unavailable. The method implemented by the package is described in Poggiato, Andréoletti, Pollock and Thuiller (2022) <doi:10.22541/au.166853394.45823739/v1>.

Maintained by Giovanni Poggiato. Last updated 9 months ago.

17 stars 5.71 score 9 scripts

predictiveecology

CBMutils:Utilities for modelling carbon based on CBM-CFS3

Implementation of several components of the Carbon Budget Model of the Canadian Forest Service (v3).

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

4.54 score 3 scripts

vascobranco

red:IUCN Redlisting Tools

Includes algorithms to facilitate the assessment of extinction risk of species according to the IUCN (International Union for Conservation of Nature, see <https://www.iucn.org/> for more information) red list criteria.

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

biodiversityextinction-risk

1 stars 4.54 score 29 scripts 1 dependents

predictiveecology

fireSenseUtils:Utilities for Working With the 'fireSense' Group of 'SpaDES' Modules

Utilities for working with the 'fireSense' group of 'SpaDES' modules.

Maintained by Eliot J B McIntire. Last updated 1 months ago.

1 stars 4.51 score 2 scripts

predictiveecology

map:Defines a meta class of geographical objects, the 'map' class, and associated tools

The 'map' class is a collection of geospatial objects (e.g., from the 'sp', 'raster', 'sf', and 'terra' packages), with a number of metadata additions to enable powerful methods, e.g., for leaflet, reproducible GIS etc.

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

2 stars 4.33 score 178 scripts 1 dependents

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

1 stars 4.18 score 7 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-ecologysimulation-modeling

1 stars 3.91 score 3 scripts 6 dependents

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-scienceecologyspatial-analysis

5 stars 3.40 score 4 scripts

nowosad

geostatbook:Geostatystyka w R

Materialy do skryptu Geostatystyka w R.

Maintained by Jakub Nowosad. Last updated 3 years ago.

6 stars 2.88 score 25 scripts

predictiveecology

LandWebUtils:Helper functions for the LandWeb project

Additional utilities for LandWeb analyses.

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

landscape-ecologysimulation-modeling

2 stars 2.60 score 2 scripts

fchianucci

hemispheR:Processing Hemispherical Canopy Images

Import and classify canopy fish-eye images, estimate angular gap fraction and derive canopy attributes like leaf area index and openness. Additional information is provided in the study by Chianucci F., Macek M. (2023) <doi:10.1016/j.agrformet.2023.109470>.

Maintained by Francesco Chianucci. Last updated 12 months ago.

3 stars 2.18 score 7 scripts

predictiveecology

usefulFuns:Useful functions for my modules and packages

A few functions and wrappers around useful code.

Maintained by Tati Micheletti. Last updated 4 months ago.

1.70 score 1 scripts

predictiveecology

mpbutils:Utilities for Mountain Pine Beetle Simulation Modelling

Utilities for mountain pine beetle (MPB) simulation modelling.

Maintained by Eliot J B McIntire. Last updated 9 months ago.

1.70 score

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