R packages for Ecology

A list of useful R packages for ecology, biodiversity and conservation.

Abhishek Kumar https://akumar.netlify.app (Panjab University, Chandigarh)https://puchd.ac.in
08-13-2021
Package Description Reference Links
adiv analyse biodiversity in ecology Pavoine (2020)
BAT measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity Cardoso, Rigal, and Carvalho (2014)
betapart partitioning beta diversity into turnover and nestedness components Baselga and Orme (2012)
bien Botanical Information and Ecology Network (BIEN) database Maitner et al. (2017)
biodivMapR mapping \(\alpha\) and \(\beta\) diversity from remotely sensed images Féret and Boissieu (2019) https://jbferet.github.io/biodivMapR/
biomass estimating above-ground biomass and its uncertainty in tropical forests Réjou-Méchain et al. (2017)
ConR large-scale multispecies preliminary conservation assessments using distribution data Dauby et al. (2017)
ecospat spatial analyses and modeling of species niches and distributions Cola et al. (2017) https://www.unil.ch/ecospat/home/menuguid/ecospat-resources/tools.html
Distance Distance Sampling Detection Function and Abundance Estimation Miller et al. (2019) https://distancesampling.org/
ENMTools toolbox for ecological niche modelling in comparative ecological biogeography Warren et al. (2021) https://github.com/danlwarren/ENMTools
ForestFit bayesian modeling for plant height diameter data Teimouri, Doser, and Finley (2020)
ForestGapR forest gap analysis from canopy height models Silva et al. (2019)
GapAnalysis calculation of conservation indicators using spatial information Carver et al. (2021) https://github.com/CIAT-DAPA/GapAnalysis
geodiv gradient surface metrics to provide continuous measures of landscape heterogeneity Smith et al. (2021)
geoorigin trait mapping and geographic provenancing of specimens without categorical constraints Hulme-Beaman et al. (2020)
GerminaR germination analysis for plants Lozano-Isla, Benites-Alfaro, and Pompelli (2019)
HistMapR Rapid digitization of historical land-use maps in R Auffret et al. (2017) https://github.com/AGAuffret/HistMapR
Hmsc Hierarchical Modelling of Species Communities with Joint species distribution models Tikhonov et al. (2020) https://github.com/hmsc-r/HMSC
letsR data handling and analysis in macroecology Vilela and Villalobos (2015)
MBHdesign Efficient spatial survey design Foster (2020)
MIAmaxent Variable transformation and model selection for species distribution models Vollering, Halvorsen, and Mazzoni (2019)
mobsim simulation and measurement of biodiversity across spatial scales May et al. (2018)
NicheMapR biophysical modelling: the microclimate model Kearney and Porter (2016) https://mrke.github.io/
nlstimedist quantification of unimodal phenology distributions Steer, Ramsay, and Franco (2019)
ntbox modelling and evaluating multidimensional ecological niches Osorio-Olvera et al. (2020) https://luismurao.github.io/ntbox_user_guide.html
phyloregion biogeographical regionalization and macroecology Daru, Karunarathne, and Schliep (2020) https://phyloregion.com/
phyr phylogenetic species-distribution modelling in ecological communities Li et al. (2020) https://daijiang.github.io/phyr/
R2MCDS analysis of multi-species datasets collected using distance sampling Bolduc, Roy, and Rousseu (2018) https://github.com/RoyChristian/R2MCDS
RangeShiftR individual-based simulation of spatial eco-evolutionary dynamics and species’ responses to environmental changes Malchow et al. (2021) https://rangeshifter.github.io/RangeshiftR-tutorials/
rasterdiv measuring ecosystem heterogeneity from space Rocchini et al. (2021) https://github.com/mattmar/rasterdiv
red
sars fitting, evaluating and comparing species–area relationship models Matthews et al. (2019)
segRDA piecewise redundancy analysis Vieira et al. (2019)
spatialwarnings Monitoring ecosystem degradation using spatial data Génin et al. (2018)
ssdm predict distribution of species richness and composition based on stacked species distribution models Schmitt et al. (2017) https://github.com/sylvainschmitt/SSDM
SSP estimation of sampling effort in studies of ecological communities Guerra-Castro et al. (2021) https://github.com/edlinguerra/SSP
V.PhyloMaker generate very large phylogenies for vascular plants Jin and Qian (2019)
VoCC velocity of climate change and related climatic metrics Molinos et al. (2019)
wallace reproducible modeling of species niches and distributions Kass et al. (2018) https://wallaceecomod.github.io/
zoon reproducible and shareable species distribution modelling Golding et al. (2017) 
library(gt)

rbind(
  
  c("`adiv`", "analyse biodiversity in ecology", md("Pavoine et al. [2020](https://doi.org/10.1111/2041-210x.13430)"), ""),
  
  c("`BAT`", "measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity", "@cardoso2014", "")) |>
  as.data.frame() |>
  gt()
V1 V2 V3 V4
`adiv` analyse biodiversity in ecology Pavoine et al. [2020](https://doi.org/10.1111/2041-210x.13430)
`BAT` measurement and estimation of alpha and beta taxon, phylogenetic and functional diversity @cardoso2014
Auffret, Alistair G., Adam Kimberley, Jan Plue, Helle Skånes, Simon Jakobsson, Emelie Waldén, Marika Wennbom, et al. 2017. “HistMapR: Rapid Digitization of Historical Land-Use Maps in R.” Methods in Ecology and Evolution 8 (11): 1453–57. https://doi.org/10.1111/2041-210x.12788.
Baselga, Andrés, and C. David L. Orme. 2012. “betapart: An R Package for the Study of Beta Diversity.” Methods in Ecology and Evolution 3 (5): 808–12. https://doi.org/10.1111/j.2041-210x.2012.00224.x.
Bolduc, François, Christian Roy, and François Rousseu. 2018. “R2mcds: An R Package for the Analysis of Multi-Species Datasets Collected Using Distance Sampling.” Ecological Informatics 47: 23–25. https://doi.org/10.1016/j.ecoinf.2017.10.003.
Cardoso, Pedro, François Rigal, and José C. Carvalho. 2014. “BAT Biodiversity Assessment Tools, an R Package for the Measurement and Estimation of Alpha and Beta Taxon, Phylogenetic and Functional Diversity.” Methods in Ecology and Evolution 6 (2): 232–36. https://doi.org/10.1111/2041-210x.12310.
Carver, Daniel, Chrystian C. Sosa, Colin K. Khoury, Harold A. Achicanoy, Maria Victoria Diaz, Steven Sotelo, Nora P. Castañeda-Álvarez, and Julian Ramirez-Villegas. 2021. “GapAnalysis: An R Package to Calculate Conservation Indicators Using Spatial Information.” Ecography 44 (7): 1000–1009. https://doi.org/10.1111/ecog.05430.
Cola, Valeria Di, Olivier Broennimann, Blaise Petitpierre, Frank T. Breiner, Manuela DAmen, Christophe Randin, Robin Engler, et al. 2017. “ecospat: An R Package to Support Spatial Analyses and Modeling of Species Niches and Distributions.” Ecography 40 (6): 774–87. https://doi.org/10.1111/ecog.02671.
Daru, Barnabas H., Piyal Karunarathne, and Klaus Schliep. 2020. “phyloregion: R Package for Biogeographical Regionalization and Macroecology.” Methods in Ecology and Evolution 11 (11): 1483–91. https://doi.org/10.1111/2041-210x.13478.
Dauby, Gilles, Tariq Stévart, Vincent Droissart, Ariane Cosiaux, Vincent Deblauwe, Murielle Simo-Droissart, Marc S. M. Sosef, et al. 2017. “ConR: An R Package to Assist Large-Scale Multispecies Preliminary Conservation Assessments Using Distribution Data.” Ecology and Evolution 7 (24): 11292–303. https://doi.org/10.1002/ece3.3704.
Féret, Jean-Baptiste, and Florian Boissieu. 2019. “biodivMapR: An R Package for \(\alpha\)- and \(\beta\)-Diversity Mapping Using Remotely Sensed Images.” Methods in Ecology and Evolution 11 (1): 64–70. https://doi.org/10.1111/2041-210x.13310.
Foster, Scott D. 2020. “MBHdesign: An R-package for Efficient Spatial Survey Designs.” Methods in Ecology and Evolution 12 (3): 415–20. https://doi.org/10.1111/2041-210x.13535.
Génin, Alexandre, Sabiha Majumder, Sumithra Sankaran, Alain Danet, Vishwesha Guttal, Florian D. Schneider, and Sonia Kéfi. 2018. “Monitoring Ecosystem Degradation Using Spatial Data and the R Package spatialwarnings.” Methods in Ecology and Evolution 9 (10): 2067–75. https://doi.org/10.1111/2041-210x.13058.
Golding, Nick, Tom A. August, Tim C. D. Lucas, David J. Gavaghan, E. Emiel Loon, and Greg McInerny. 2017. “The zoon R Package for Reproducible and Shareable Species Distribution Modelling.” Methods in Ecology and Evolution 9 (2): 260–68. https://doi.org/10.1111/2041-210x.12858.
Guerra-Castro, Edlin J., Juan Carlos Cajas, Nuno Simões, Juan J. Cruz-Motta, and Maite Mascaró. 2021. “SSP: An R Package to Estimate Sampling Effort in Studies of Ecological Communities.” Ecography 44 (4): 561–73. https://doi.org/10.1111/ecog.05284.
Hulme-Beaman, Ardern, Anna Rudzinski, Joseph E. J. Cooper, Robert F. Lachlan, Keith Dobney, and Mark G. Thomas. 2020. “geoorigins: A New Method and R Package for Trait Mapping and Geographic Provenancing of Specimens Without Categorical Constraints.” Methods in Ecology and Evolution 11 (10): 1247–57. https://doi.org/10.1111/2041-210x.13444.
Jin, Yi, and Hong Qian. 2019. “V.PhyloMaker: An R Package That Can Generate Very Large Phylogenies for Vascular Plants.” Ecography 42 (8): 1353–59. https://doi.org/10.1111/ecog.04434.
Kass, Jamie M., Bruno Vilela, Matthew E. Aiello-Lammens, Robert Muscarella, Cory Merow, and Robert P. Anderson. 2018. “wallace: A Flexible Platform for Reproducible Modeling of Species Niches and Distributions Built for Community Expansion.” Methods in Ecology and Evolution 9 (4): 1151–56. https://doi.org/10.1111/2041-210x.12945.
Kearney, Michael R., and Warren P. Porter. 2016. “NicheMapR an R Package for Biophysical Modelling: The Microclimate Model.” Ecography 40 (5): 664–74. https://doi.org/10.1111/ecog.02360.
Li, Daijiang, Russell Dinnage, Lucas A. Nell, Matthew R. Helmus, and Anthony R. Ives. 2020. “phyr: An R Package for Phylogenetic Species-Distribution Modelling in Ecological Communities.” Methods in Ecology and Evolution 11 (11): 1455–63. https://doi.org/10.1111/2041-210x.13471.
Lozano-Isla, Flavio, Omar E. Benites-Alfaro, and Marcelo F. Pompelli. 2019. “GerminaR: An R Package for Germination Analysis with the Interactive Web Application “GerminaQuant for R”.” Ecological Research 34 (2): 339–46. https://doi.org/10.1111/1440-1703.1275.
Maitner, Brian S., Brad Boyle, Nathan Casler, Rick Condit, John Donoghue, Sandra M. Durán, Daniel Guaderrama, et al. 2017. “The bien R Package: A Tool to Access the Botanical Information and Ecology Network (BIEN) Database.” Methods in Ecology and Evolution 9 (2): 373–79. https://doi.org/10.1111/2041-210x.12861.
Malchow, Anne-Kathleen, Greta Bocedi, Stephen C. F. Palmer, Justin M. J. Travis, and Damaris Zurell. 2021. “RangeShiftR: An R Package for Individual-Based Simulation of Spatial Eco-Evolutionary Dynamics and Species Responses to Environmental Changes.” Ecography. https://doi.org/10.1111/ecog.05689.
Matthews, Thomas J., Kostas A. Triantis, Robert J. Whittaker, and François Guilhaumon. 2019. “sars: An R Package for Fitting, Evaluating and Comparing Speciesarea Relationship Models.” Ecography 42 (8): 1446–55. https://doi.org/10.1111/ecog.04271.
May, Felix, Katharina Gerstner, Daniel J. McGlinn, Xiao Xiao, and Jonathan M. Chase. 2018. “mobsim: An R Package for the Simulation and Measurement of Biodiversity Across Spatial Scales.” Methods in Ecology and Evolution 9 (6): 1401–8. https://doi.org/10.1111/2041-210x.12986.
Miller, David L., Eric Rexstad, Len Thomas, Laura Marshall, and Jeffrey L. Laake. 2019. “Distance Sampling in R.” Journal of Statistical Software 89 (1). https://doi.org/10.18637/jss.v089.i01.
Molinos, Jorge Garcı́a, David S. Schoeman, Christopher J. Brown, and Michael T. Burrows. 2019. “VoCC: An R Package for Calculating the Velocity of Climate Change and Related Climatic Metrics.” Methods in Ecology and Evolution 10 (12): 2195–2202. https://doi.org/10.1111/2041-210x.13295.
Osorio-Olvera, Luis, Andrés Lira-Noriega, Jorge Soberón, Andrew Townsend Peterson, Manuel Falconi, Rusby G. Contreras-Dı́az, Enrique Martı́nez-Meyer, Vijay Barve, and Narayani Barve. 2020. “ntbox: An R Package with Graphical User Interface for Modelling and Evaluating Multidimensional Ecological Niches.” Methods in Ecology and Evolution 11 (10): 1199–1206. https://doi.org/10.1111/2041-210x.13452.
Pavoine, Sandrine. 2020. “adiv: An R Package to Analyse Biodiversity in Ecology.” Methods in Ecology and Evolution 11 (9): 1106–12. https://doi.org/10.1111/2041-210x.13430.
Réjou-Méchain, Maxime, Ariane Tanguy, Camille Piponiot, Jérôme Chave, and Bruno Hérault. 2017. “biomass: An R Package for Estimating Above-Ground Biomass and Its Uncertainty in Tropical Forests.” Methods in Ecology and Evolution 8 (9): 1163–67. https://doi.org/10.1111/2041-210x.12753.
Rocchini, Duccio, Elisa Thouverai, Matteo Marcantonio, Martina Iannacito, Daniele Da Re, Michele Torresani, Giovanni Bacaro, et al. 2021. “rasterdivan Information Theory Tailored R Package for Measuring Ecosystem Heterogeneity from Space: To the Origin and Back.” Methods in Ecology and Evolution 12 (6): 1093–1102. https://doi.org/10.1111/2041-210x.13583.
Schmitt, Sylvain, Robin Pouteau, Dimitri Justeau, Florian Boissieu, and Philippe Birnbaum. 2017. “ssdm: An R Package to Predict Distribution of Species Richness and Composition Based on Stacked Species Distribution Models.” Methods in Ecology and Evolution 8 (12): 1795–1803. https://doi.org/10.1111/2041-210x.12841.
Silva, Carlos A., Ruben Valbuena, Ekena R. Pinagé, Midhun Mohan, Danilo R. A. Almeida, Eben North Broadbent, Wan Shafrina Wan Mohd Jaafar, Daniel Papa, Adrian Cardil, and Carine Klauberg. 2019. “ForestGapR: An R Package for Forest Gap Analysis from Canopy Height Models.” Methods in Ecology and Evolution 10 (8): 1347–56. https://doi.org/10.1111/2041-210x.13211.
Smith, Annie C., Kyla M. Dahlin, Sydne Record, Jennifer K. Costanza, Adam M. Wilson, and Phoebe L. Zarnetske. 2021. “The geodiv R Package: Tools for Calculating Gradient Surface Metrics.” Methods in Ecology and Evolution. https://doi.org/10.1111/2041-210x.13677.
Steer, Nicola C., Paul M. Ramsay, and Miguel Franco. 2019. “nlstimedist: An R Package for the Biologically Meaningful Quantification of Unimodal Phenology Distributions.” Methods in Ecology and Evolution 10 (11): 1934–40. https://doi.org/10.1111/2041-210x.13293.
Teimouri, Mahdi, Jeffrey W. Doser, and Andrew O. Finley. 2020. “ForestFit: An R Package for Modeling Plant Size Distributions.” Environmental Modelling & Software 131: 104668. https://doi.org/10.1016/j.envsoft.2020.104668.
Tikhonov, Gleb, Øystein H. Opedal, Nerea Abrego, Aleksi Lehikoinen, Melinda M. J. Jonge, Jari Oksanen, and Otso Ovaskainen. 2020. “Joint Species Distribution Modelling with the R-package Hmsc.” Methods in Ecology and Evolution 11 (3): 442–47. https://doi.org/10.1111/2041-210x.13345.
Vieira, Danilo Cândido, Marco Colossi Brustolin, Fábio Cop Ferreira, and Gustavo Fonseca. 2019. “segRDA: An R Package for Performing Piecewise Redundancy Analysis.” Methods in Ecology and Evolution 10 (12): 2189–94. https://doi.org/10.1111/2041-210x.13300.
Vilela, Bruno, and Fabricio Villalobos. 2015. “letsR: A New R Package for Data Handling and Analysis in Macroecology.” Methods in Ecology and Evolution 6 (10): 1229–34. https://doi.org/10.1111/2041-210x.12401.
Vollering, Julien, Rune Halvorsen, and Sabrina Mazzoni. 2019. “The MIAmaxent R Package: Variable Transformation and Model Selection for Species Distribution Models.” Ecology and Evolution 9 (21): 12051–68. https://doi.org/10.1002/ece3.5654.
Warren, Dan L., Nicholas J. Matzke, Marcel Cardillo, John B. Baumgartner, Linda J. Beaumont, Michael Turelli, Richard E. Glor, et al. 2021. “ENMTools 1.0: An R Package for Comparative Ecological Biogeography.” Ecography 44 (4): 504–11. https://doi.org/10.1111/ecog.05485.

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Kumar (2021, Aug. 13). Abhishek Kumar: R packages for Ecology. Retrieved from https://abhikumar86.github.io/posts/2021-08-13-ecology-packages/

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@misc{kumar2021r,
  author = {Kumar, Abhishek},
  title = {Abhishek Kumar: R packages for Ecology},
  url = {https://abhikumar86.github.io/posts/2021-08-13-ecology-packages/},
  year = {2021}
}
© Copyright 2021 Abhishek Kumar