Showing 135 of total 135 results (show query)
ropensci
rebird:R Client for the eBird Database of Bird Observations
A programmatic client for the eBird database (<https://ebird.org/home>), including functions for searching for bird observations by geographic location (latitude, longitude), eBird hotspots, location identifiers, by notable sightings, by region, and by taxonomic name.
Maintained by Sebastian Pardo. Last updated 1 months ago.
birdsbirdingebirddatabasedatabiologyobservationssightingsornithologyebird-apiebird-webservicesspocc
25.2 match 90 stars 10.43 score 73 scripts 6 dependents
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 1 days ago.
11.8 match 4 stars 13.03 score 652 scripts 12 dependents
emmanuelparadis
ape:Analyses of Phylogenetics and Evolution
Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Maintained by Emmanuel Paradis. Last updated 14 hours ago.
7.2 match 64 stars 17.22 score 13k scripts 599 dependents
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 13 days ago.
7.8 match 39 stars 14.96 score 2.2k scripts 256 dependents
luomus
fbi:Finnish Biodiversity Indicators
Finnish biodiversity indicators is a service providing time series of abundance indices and related metrics for Finland. The input data for the indices are provided by the Finnish Biodiversity Information Facility.
Maintained by William K. Morris. Last updated 3 days ago.
19.7 match 5.89 score 60 scripts
vegandevs
vegan:Community Ecology Package
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Maintained by Jari Oksanen. Last updated 16 days ago.
ecological-modellingecologyordinationfortranopenblas
5.4 match 472 stars 19.41 score 15k scripts 440 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
15.2 match 6 stars 6.78 score 24 scripts
bayesball
LearnBayes:Learning Bayesian Inference
Contains functions for summarizing basic one and two parameter posterior distributions and predictive distributions. It contains MCMC algorithms for summarizing posterior distributions defined by the user. It also contains functions for regression models, hierarchical models, Bayesian tests, and illustrations of Gibbs sampling.
Maintained by Jim Albert. Last updated 7 years ago.
7.5 match 38 stars 11.34 score 690 scripts 31 dependents
psolymos
bSims:Agent-Based Bird Point Count Simulator
A highly scientific and utterly addictive bird point count simulator to test statistical assumptions, aid survey design, and have fun while doing it (Solymos 2024 <doi:10.1007/s42977-023-00183-2>). The simulations follow time-removal and distance sampling models based on Matsuoka et al. (2012) <doi:10.1525/auk.2012.11190>, Solymos et al. (2013) <doi:10.1111/2041-210X.12106>, and Solymos et al. (2018) <doi:10.1650/CONDOR-18-32.1>, and sound attenuation experiments by Yip et al. (2017) <doi:10.1650/CONDOR-16-93.1>.
Maintained by Peter Solymos. Last updated 10 months ago.
biasbirdsdetectabilityshinysimulationsurvey-design
13.4 match 4 stars 5.36 score 38 scripts
emf-creaf
indicspecies:Relationship Between Species and Groups of Sites
Functions to assess the strength and statistical significance of the relationship between species occurrence/abundance and groups of sites [De Caceres & Legendre (2009) <doi:10.1890/08-1823.1>]. Also includes functions to measure species niche breadth using resource categories [De Caceres et al. (2011) <doi:10.1111/J.1600-0706.2011.19679.x>].
Maintained by Miquel De Cáceres. Last updated 24 days ago.
7.5 match 10 stars 9.49 score 386 scripts 4 dependents
jeromeecoac
seewave:Sound Analysis and Synthesis
Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses. See Sueur et al. (2008) <doi:10.1080/09524622.2008.9753600> and Sueur (2018) <doi:10.1007/978-3-319-77647-7>.
Maintained by Jerome Sueur. Last updated 1 years ago.
7.5 match 18 stars 8.88 score 880 scripts 23 dependents
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.
3dbirdsconditional-empirical-random-walkgliding-and-soaringmachine-learningmovement-ecologyrandom-trajectory-generatorrandom-walksimulationtrajectory-generation
11.5 match 6 stars 5.71 score 19 scripts
marcoklh
afpt:Tools for Modelling of Animal Flight Performance
Allows estimation and modelling of flight costs in animal (vertebrate) flight, implementing the aerodynamic power model described in Klein Heerenbrink et al. (2015) <doi:10.1098/rspa.2014.0952>. Taking inspiration from the program 'Flight', developed by Colin Pennycuick (Pennycuick (2008) "Modelling the flying bird". Amsterdam: Elsevier. ISBN 0-19-857721-4), flight performance is estimated based on basic morphological measurements such as body mass, wingspan and wing area. 'afpt' can be used to make predictions on how animals should adjust their flight behaviour and wingbeat kinematics to varying flight conditions.
Maintained by Marco KleinHeerenbrink. Last updated 1 years ago.
15.4 match 2 stars 4.14 score 23 scripts
middleton-lab
abd:The Analysis of Biological Data
The abd package contains data sets and sample code for The Analysis of Biological Data by Michael Whitlock and Dolph Schluter (2009; Roberts & Company Publishers).
Maintained by Kevin M. Middleton. Last updated 11 months ago.
11.5 match 6 stars 5.53 score 182 scripts 1 dependents
charvey23
AvInertia:Calculate the Inertial Properties of a Flying Bird
Tools to compute the center of gravity and moment of inertia tensor of any flying bird. The tools function by modeling a bird as a composite structure of simple geometric objects. This requires detailed morphological measurements of bird specimens although those obtained for the associated paper have been included in the package for use. Refer to the vignettes and supplementary material for detailed information on the package function.
Maintained by Christina Harvey. Last updated 3 years ago.
12.3 match 6 stars 5.00 score 33 scripts
paulesantos
avesperu:Access to the List of Birds Species of Peru
Allows access to the data found in the species list featured in the renowned 'List of the Birds of Peru' Plenge, M. A. (2023) <https://sites.google.com/site/boletinunop/checklist>. This publication stands as one of Peru's most comprehensive reviews of bird diversity. The dataset incorporates detailed species accounts and has been meticulously structured for effortless utilization within the R environment.
Maintained by Paul E. Santos Andrade. Last updated 3 months ago.
17.7 match 1 stars 3.45 score 14 scripts
joe-wayman
avotrex:A Global Dataset of Anthropogenic Extinct Birds and their Traits: Phylogeny Builder
Grafts the extinct bird species from the 'Avotrex' database (Sayol et al., in review) on to the 'BirdTree' phylogenies <https://birdtree.org>, using a set of different commands.
Maintained by Joseph Wayman. Last updated 7 months ago.
12.7 match 4.74 score 8 scripts
rsetienne
DAISIE:Dynamical Assembly of Islands by Speciation, Immigration and Extinction
Simulates and computes the (maximum) likelihood of a dynamical model of island biota assembly through speciation, immigration and extinction. See Valente et al. (2015) <doi:10.1111/ele.12461>.
Maintained by Rampal S. Etienne. Last updated 1 months ago.
6.8 match 9 stars 8.59 score 55 scripts 1 dependents
philipmostert
PointedSDMs:Fit Models Derived from Point Processes to Species Distributions using 'inlabru'
Integrated species distribution modeling is a rising field in quantitative ecology thanks to significant rises in the quantity of data available, increases in computational speed and the proven benefits of using such models. Despite this, the general software to help ecologists construct such models in an easy-to-use framework is lacking. We therefore introduce the R package 'PointedSDMs': which provides the tools to help ecologists set up integrated models and perform inference on them. There are also functions within the package to help run spatial cross-validation for model selection, as well as generic plotting and predicting functions. An introduction to these methods is discussed in Issac, Jarzyna, Keil, Dambly, Boersch-Supan, Browning, Freeman, Golding, Guillera-Arroita, Henrys, Jarvis, Lahoz-Monfort, Pagel, Pescott, Schmucki, Simmonds and O’Hara (2020) <doi:10.1016/j.tree.2019.08.006>.
Maintained by Philip Mostert. Last updated 2 months ago.
6.6 match 25 stars 8.57 score 50 scripts 1 dependents
schochastics
networkdata:Repository of Network Datasets
The package contains a large collection of network dataset with different context. This includes social networks, animal networks and movie networks. All datasets are in 'igraph' format.
Maintained by David Schoch. Last updated 12 months ago.
10.5 match 143 stars 5.01 score 143 scripts
hidef-aerial-surveying
stochLAB:Stochastic Collision Risk Model
Collision Risk Models for avian fauna (seabird and migratory birds) at offshore wind farms. The base deterministic model is derived from Band (2012) <https://tethys.pnnl.gov/publications/using-collision-risk-model-assess-bird-collision-risks-offshore-wind-farms>. This was further expanded on by Masden (2015) <doi:10.7489/1659-1> and code used here is heavily derived from this work with input from Dr A. Cook at the British Trust for Ornithology. These collision risk models are useful for marine ornithologists who are working in the offshore wind industry, particularly in UK waters. However, many of the species included in the stochastic collision risk models (stoch_crm) can also be found in the North Atlantic in the United States and Canada, and could be applied there.
Maintained by Grant Humphries. Last updated 2 years ago.
collision-riskmigratoryspeciesoffshore-windseabirds
11.0 match 6 stars 4.78 score 10 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 8 months ago.
biodiversitybiodiversity-indicatorsbiodiversity-informaticsfunctional-diversityfunctional-ecologyfunctional-traitfunctional-traitstraittrait-basedtraits
6.9 match 38 stars 7.34 score 38 scripts
tslumley
rimu:Responses in Multiplex
Tools for manipulating, exploring, and visualising multiple-response data, including scored or ranked responses. Conversions to and from factors, lists, strings, matrices; reordering, lumping, flattening; set operations; tables; frequency and co-occurrence plots.
Maintained by Thomas Lumley. Last updated 12 months ago.
10.4 match 4 stars 4.78 score 10 scripts
jamesramsay5
fda:Functional Data Analysis
These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer and in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions are available by ftp from <https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Maintained by James Ramsay. Last updated 4 months ago.
4.0 match 3 stars 12.29 score 2.0k scripts 143 dependents
gavinsimpson
gratia:Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'
Graceful 'ggplot'-based graphics and utility functions for working with generalized additive models (GAMs) fitted using the 'mgcv' package. Provides a reimplementation of the plot() method for GAMs that 'mgcv' provides, as well as 'tidyverse' compatible representations of estimated smooths.
Maintained by Gavin L. Simpson. Last updated 12 hours ago.
distributional-regressiongamgammgeneralized-additive-mixed-modelsgeneralized-additive-modelsggplot2glmlmmgcvpenalized-splinerandom-effectssmoothingsplines
3.8 match 217 stars 12.99 score 1.6k scripts 2 dependentsropensci
birdsize:Estimate Avian Body Size Distributions
Generate estimated body size distributions for populations or communities of birds, given either species ID or species' mean body size. Designed to work naturally with the North American Breeding Bird Survey, or with any dataset of bird species, abundance, and/or mean size data.
Maintained by Renata Diaz. Last updated 1 years ago.
12.4 match 3 stars 3.78 score 8 scripts
nicholasjclark
MRFcov:Markov Random Fields with Additional Covariates
Approximate node interaction parameters of Markov Random Fields graphical networks. Models can incorporate additional covariates, allowing users to estimate how interactions between nodes in the graph are predicted to change across covariate gradients. The general methods implemented in this package are described in Clark et al. (2018) <doi:10.1002/ecy.2221>.
Maintained by Nicholas J Clark. Last updated 12 months ago.
conditional-random-fieldsgraphical-modelsmachine-learningmarkov-random-fieldmultivariate-analysismultivariate-statisticsnetwork-analysisnetworks
7.6 match 24 stars 6.03 score 30 scripts
cran
asnipe:Animal Social Network Inference and Permutations for Ecologists
Implements several tools that are used in animal social network analysis, as described in Whitehead (2007) Analyzing Animal Societies <University of Chicago Press> and Farine & Whitehead (2015) <doi: 10.1111/1365-2656.12418>. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Maintained by Damien R. Farine. Last updated 2 years ago.
10.4 match 2 stars 4.36 score 173 scripts 2 dependents
bmasinde
FlyingR:Simulation of Bird Flight Range
Functions for range estimation in birds based on Pennycuick (2008) and Pennycuick (1975), 'Flight' program which compliments Pennycuick (2008) requires manual entry of birds which can be tedious when there are hundreds of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975) and time-marching computation methods as in Pennycuick (1998) and Pennycuick (2008). See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>, and Pennycuick (2008, ISBN:9780080557816).
Maintained by Brian Masinde. Last updated 3 years ago.
11.0 match 2 stars 4.00 score 5 scripts
rdinnager
phyf:Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs
The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.
Maintained by Russell Dinnage. Last updated 7 months ago.
10.3 match 1 stars 4.20 score 53 scripts 1 dependents
martinbozon
Rmolt:Graphic Visualization of the Birds' Molt
Graphical visualization of the birds' molt to facilitate the creation of molting graph for passerines having 9 (Rmolt(data,9)) or 10 primaries (Rmolt(data,10)), and also only for the 10 first primaries (Rmolt(data,"10_0")).
Maintained by Martin Bozon. Last updated 2 years ago.
14.1 match 3.00 score 2 scripts
fcharte
mldr:Exploratory Data Analysis and Manipulation of Multi-Label Data Sets
Exploratory data analysis and manipulation functions for multi- label data sets along with an interactive Shiny application to ease their use.
Maintained by David Charte. Last updated 5 years ago.
6.0 match 23 stars 7.07 score 168 scripts 2 dependentsbiodiverse
spAbundance:Univariate and Multivariate Spatial Modeling of Species Abundance
Fits single-species (univariate) and multi-species (multivariate) non-spatial and spatial abundance models in a Bayesian framework using Markov Chain Monte Carlo (MCMC). Spatial models are fit using Nearest Neighbor Gaussian Processes (NNGPs). Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2022) <doi:10.18637/jss.v103.i05>. Fits single-species and multi-species spatial and non-spatial versions of generalized linear mixed models (Gaussian, Poisson, Negative Binomial), N-mixture models (Royle 2004 <doi:10.1111/j.0006-341X.2004.00142.x>) and hierarchical distance sampling models (Royle, Dawson, Bates (2004) <doi:10.1890/03-3127>). Multi-species spatial models are fit using a spatial factor modeling approach with NNGPs for computational efficiency.
Maintained by Jeffrey Doser. Last updated 17 days ago.
6.5 match 17 stars 6.15 score 43 scripts 1 dependents
zdebruine
RcppML:Rcpp Machine Learning Library
Fast machine learning algorithms including matrix factorization and divisive clustering for large sparse and dense matrices.
Maintained by Zach DeBruine. Last updated 2 years ago.
clusteringmatrix-factorizationnmfrcpprcppeigensparse-matrixcppopenmp
3.8 match 104 stars 10.53 score 125 scripts 46 dependents
davidorme
caper:Comparative Analyses of Phylogenetics and Evolution in R
Functions for performing phylogenetic comparative analyses.
Maintained by David Orme. Last updated 1 years ago.
5.3 match 1 stars 7.41 score 928 scripts 5 dependents
openintrostat
openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs
Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.
Maintained by Mine Çetinkaya-Rundel. Last updated 3 months ago.
3.4 match 240 stars 11.39 score 6.0k scripts
johnsonhsieh
iNEXT:Interpolation and Extrapolation for Species Diversity
Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation curves for species diversity (Hill numbers) based on individual-based abundance data or sampling-unit- based incidence data; see Chao and others (2014, Ecological Monographs) for pertinent theory and methodologies, and Hsieh, Ma and Chao (2016, Methods in Ecology and Evolution) for an introduction of the R package.
Maintained by T. C. Hsieh. Last updated 12 months ago.
3.8 match 57 stars 10.18 score 598 scripts 3 dependentsadeverse
adephylo:Exploratory Analyses for the Phylogenetic Comparative Method
Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.
Maintained by Aurélie Siberchicot. Last updated 3 days ago.
3.8 match 9 stars 10.05 score 312 scripts 4 dependents
statmanrobin
Stat2Data:Datasets for Stat2
Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.
Maintained by Robin Lock. Last updated 6 years ago.
7.2 match 5 stars 4.94 score 544 scriptsropensci
phylotaR:Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
Maintained by Shixiang Wang. Last updated 8 months ago.
blastngenbankpeer-reviewedphylogeneticssequence-alignment
6.0 match 23 stars 5.86 score 156 scripts
bayes-rules
bayesrules:Datasets and Supplemental Functions from Bayes Rules! Book
Provides datasets and functions used for analysis and visualizations in the Bayes Rules! book (<https://www.bayesrulesbook.com>). The package contains a set of functions that summarize and plot Bayesian models from some conjugate families and another set of functions for evaluation of some Bayesian models.
Maintained by Mine Dogucu. Last updated 3 years ago.
4.0 match 72 stars 8.06 score 466 scripts
rbgramacy
maptree:Mapping, Pruning, and Graphing Tree Models
Functions with example data for graphing, pruning, and mapping models from hierarchical clustering, and classification and regression trees.
Maintained by Robert B. Gramacy. Last updated 3 years ago.
7.1 match 4.42 score 132 scripts 15 dependents
rjknell
Biostatistics:Statistics Tutorials for Biologists
Tutorials for statistics, aimed at biological scientists. Subjects range from basic descriptive statistics through to complex linear modelling. The tutorials include text, videos, interactive coding exercises and multiple choice quizzes. The package also includes 19 datasets which are used in the tutorials.
Maintained by Rob Knell. Last updated 3 years ago.
6.9 match 4.54 score 5 scriptsropensci
rdataretriever:R Interface to the Data Retriever
Provides an R interface to the Data Retriever <https://retriever.readthedocs.io/en/latest/> via the Data Retriever's command line interface. The Data Retriever automates the tasks of finding, downloading, and cleaning public datasets, and then stores them in a local database.
Maintained by Henry Senyondo. Last updated 8 months ago.
datadata-sciencedatabasedatasetsscience
4.0 match 46 stars 7.70 score 36 scriptsropensci
traits:Species Trait Data from Around the Web
Species trait data from many different sources, including sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>), plant trait data from 'BETYdb', data from 'EOL' 'Traitbank', 'Birdlife' International, and more.
Maintained by David LeBauer. Last updated 2 months ago.
traitsapiweb-servicesspeciestaxonomyapi-client
3.5 match 41 stars 8.65 score 82 scripts 11 dependentsbmasinde
flying:Simulation of Bird Flight Range
Functions for range estimation in birds based on Pennycuick (2008) and Pennycuick (1975), 'Flight' program which compliments Pennycuick (2008) requires manual entry of birds which can be tedious when there are thousands of birds to estimate. Implemented are two ODE methods discussed in Pennycuick (1975) and time-marching computation method "constant muscle mass" as in Pennycuick (1998). See Pennycuick (1975, ISBN:978-0-12-249405-5), Pennycuick (1998) <doi:10.1006/jtbi.1997.0572>, and Pennycuick (2008, ISBN:9780080557816).
Maintained by Brian Masinde. Last updated 5 years ago.
11.2 match 2.70 score 5 scripts
thothorn
TH.data:TH's Data Archive
Contains data sets used in other packages Torsten Hothorn maintains.
Maintained by Torsten Hothorn. Last updated 2 months ago.
3.6 match 8.28 score 137 scripts 370 dependents
pilaboratory
sads:Maximum Likelihood Models for Species Abundance Distributions
Maximum likelihood tools to fit and compare models of species abundance distributions and of species rank-abundance distributions.
Maintained by Paulo I. Prado. Last updated 1 years ago.
3.4 match 23 stars 8.66 score 244 scripts 3 dependents
bbsbayes
bbsBayes2:Hierarchical Bayesian Analysis of North American BBS Data
The North American Breeding Bird Survey (BBS) is a long-running program that seeks to monitor the status and trends of the breeding birds in North America. Since its start in 1966, the BBS has accumulated over 50 years of data for over 500 species of North American Birds. Given the temporal and spatial structure of the data, hierarchical Bayesian models are used to assess the status and trends of these 500+ species of birds. 'bbsBayes2' allows you to perform hierarchical Bayesian analysis of BBS data. You can run a full model analysis for one or more species that you choose, or you can take more control and specify how the data should be stratified, prepared for 'Stan', or modelled.
Maintained by Brandon P.M. Edwards. Last updated 2 months ago.
6.3 match 8 stars 4.64 score 121 scripts
mamaz7
AICcmodavg:Model Selection and Multimodel Inference Based on (Q)AIC(c)
Functions to implement model selection and multimodel inference based on Akaike's information criterion (AIC) and the second-order AIC (AICc), as well as their quasi-likelihood counterparts (QAIC, QAICc) from various model object classes. The package implements classic model averaging for a given parameter of interest or predicted values, as well as a shrinkage version of model averaging parameter estimates or effect sizes. The package includes diagnostics and goodness-of-fit statistics for certain model types including those of 'unmarkedFit' classes estimating demographic parameters after accounting for imperfect detection probabilities. Some functions also allow the creation of model selection tables for Bayesian models of the 'bugs', 'rjags', and 'jagsUI' classes. Functions also implement model selection using BIC. Objects following model selection and multimodel inference can be formatted to LaTeX using 'xtable' methods included in the package.
Maintained by Marc J. Mazerolle. Last updated 10 days ago.
3.8 match 1 stars 7.83 score 1.8k scripts 8 dependents
rachel-greenlee
AtlasMaker:Make Multiple 'leaflet' Maps in 'Shiny'
Simplify creating multiple, related 'leaflet' maps across tabs for a 'shiny' application. Users build lists of any polygons, points, and polylines needed for the project, use the map_server() function to assign built lists and other chosen aesthetics into each tab, and the package leverages modules to generate all map tabs.
Maintained by Rachel Greenlee. Last updated 2 years ago.
7.3 match 4.00 score 4 scripts
raydanner
SongEvo:An Individual-Based Model of Bird Song Evolution
Simulates the cultural evolution of quantitative traits of bird song. 'SongEvo' is an individual- (agent-) based model. 'SongEvo' is spatially-explicit and can be parameterized with, and tested against, measured song data. Functions are available for model implementation, sensitivity analyses, parameter optimization, model validation, and hypothesis testing.
Maintained by Raymond Danner. Last updated 5 years ago.
6.5 match 2 stars 4.51 score 16 scripts
jknape
poptrend:Estimate Smooth and Linear Trends from Population Count Survey Data
Functions to estimate and plot smooth or linear population trends, or population indices, from animal or plant count survey data.
Maintained by Jonas Knape. Last updated 1 years ago.
7.2 match 10 stars 4.00 score 4 scripts
liamdbailey
climwin:Climate Window Analysis
Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response. Please see van de Pol et al. (2016) <doi:10.1111/2041-210X.12590> and Bailey and van de Pol (2016) <doi:10.1371/journal.pone.0167980> for details.
Maintained by Liam D. Bailey. Last updated 5 years ago.
3.6 match 12 stars 7.42 score 138 scripts
ghislainv
jSDM:Joint Species Distribution Models
Fits joint species distribution models ('jSDM') in a hierarchical Bayesian framework (Warton and al. 2015 <doi:10.1016/j.tree.2015.09.007>). The Gibbs sampler is written in 'C++'. It uses 'Rcpp', 'Armadillo' and 'GSL' to maximize computation efficiency.
Maintained by Ghislain Vieilledent. Last updated 2 years ago.
4.5 match 11 stars 5.87 score 68 scripts
clbustos
dominanceanalysis:Dominance Analysis
Dominance analysis is a method that allows to compare the relative importance of predictors in multiple regression models: ordinary least squares, generalized linear models, hierarchical linear models, beta regression and dynamic linear models. The main principles and methods of dominance analysis are described in Budescu, D. V. (1993) <doi:10.1037/0033-2909.114.3.542> and Azen, R., & Budescu, D. V. (2003) <doi:10.1037/1082-989X.8.2.129> for ordinary least squares regression. Subsequently, the extensions for multivariate regression, logistic regression and hierarchical linear models were described in Azen, R., & Budescu, D. V. (2006) <doi:10.3102/10769986031002157>, Azen, R., & Traxel, N. (2009) <doi:10.3102/1076998609332754> and Luo, W., & Azen, R. (2013) <doi:10.3102/1076998612458319>, respectively.
Maintained by Claudio Bustos Navarrete. Last updated 1 years ago.
4.6 match 25 stars 5.75 score 45 scripts
yonicd
jsTree:Create Interactive Trees with the 'jQuery' 'jsTree' Plugin
Create and customize interactive trees using the 'jQuery' 'jsTree' <https://www.jstree.com/> plugin library and the 'htmlwidgets' package. These trees can be used directly from the R console, from 'RStudio', in Shiny apps and R Markdown documents.
Maintained by Jonathan Sidi. Last updated 4 years ago.
3.8 match 31 stars 6.92 score 18 scripts 2 dependents
mdsr-book
mdsr:Complement to 'Modern Data Science with R'
A complement to all editions of *Modern Data Science with R* (ISBN: 978-0367191498, publisher URL: <https://www.routledge.com/Modern-Data-Science-with-R/Baumer-Kaplan-Horton/p/book/9780367191498>). This package contains data and code to complete exercises and reproduce examples from the text. It also facilitates connections to the SQL database server used in the book. All editions of the book are supported by this package.
Maintained by Benjamin S. Baumer. Last updated 7 months ago.
3.5 match 38 stars 7.21 score 504 scriptsthothorn
HSAUR3:A Handbook of Statistical Analyses Using R (3rd Edition)
Functions, data sets, analyses and examples from the third edition of the book ''A Handbook of Statistical Analyses Using R'' (Torsten Hothorn and Brian S. Everitt, Chapman & Hall/CRC, 2014). The first chapter of the book, which is entitled ''An Introduction to R'', is completely included in this package, for all other chapters, a vignette containing all data analyses is available. In addition, Sweave source code for slides of selected chapters is included in this package (see HSAUR3/inst/slides). The publishers web page is '<https://www.routledge.com/A-Handbook-of-Statistical-Analyses-using-R/Hothorn-Everitt/p/book/9781482204582>'.
Maintained by Torsten Hothorn. Last updated 7 months ago.
3.8 match 6 stars 6.72 score 120 scripts 2 dependents
r-forge
Sleuth3:Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.
Maintained by Berwin A Turlach. Last updated 1 years ago.
3.8 match 6.38 score 522 scripts
inbo
territoria:Clustering Observations from Breeding Birds into Territoria
Clusters individual observations based on breeding indication and distance between observations.
Maintained by Thierry Onkelinx. Last updated 2 years ago.
birdbreedingclusterhome-rangeterritory
14.0 match 1.70 score 4 scripts
smbc-nzp
MigConnectivity:Estimate Migratory Connectivity for Migratory Animals
Allows the user to estimate transition probabilities for migratory animals between any two phases of the annual cycle, using a variety of different data types. Also quantifies the strength of migratory connectivity (MC), a standardized metric to quantify the extent to which populations co-occur between two phases of the annual cycle. Includes functions to estimate MC and the more traditional metric of migratory connectivity strength (Mantel correlation) incorporating uncertainty from multiple sources of sampling error. For cross-species comparisons, methods are provided to estimate differences in migratory connectivity strength, incorporating uncertainty. See Cohen et al. (2018) <doi:10.1111/2041-210X.12916>, Cohen et al. (2019) <doi:10.1111/ecog.03974>, and Roberts et al. (2023) <doi:10.1002/eap.2788> for details on some of these methods.
Maintained by Jeffrey A. Hostetler. Last updated 12 months ago.
3.4 match 8 stars 6.77 score 41 scriptsropensci
auk:eBird Data Extraction and Processing in R
Extract and process bird sightings records from eBird (<http://ebird.org>), an online tool for recording bird observations. Public access to the full eBird database is via the eBird Basic Dataset (EBD; see <http://ebird.org/ebird/data/download> for access), a downloadable text file. This package is an interface to AWK for extracting data from the EBD based on taxonomic, spatial, or temporal filters, to produce a manageable file size that can be imported into R.
Maintained by Matthew Strimas-Mackey. Last updated 2 months ago.
2.5 match 143 stars 9.04 score 254 scripts
mikemeredith
overlap:Estimates of Coefficient of Overlapping for Animal Activity Patterns
Provides functions to fit kernel density functions to data on temporal activity patterns of animals; estimate coefficients of overlapping of densities for two species; and calculate bootstrap estimates of confidence intervals.
Maintained by Liz Campbell. Last updated 2 years ago.
3.5 match 2 stars 6.42 score 265 scripts 1 dependents
wavx
bioacoustics:Analyse Audio Recordings and Automatically Extract Animal Vocalizations
Contains all the necessary tools to process audio recordings of various formats (e.g., WAV, WAC, MP3, ZC), filter noisy files, display audio signals, detect and extract automatically acoustic features for further analysis such as classification.
Maintained by Jean Marchal. Last updated 1 years ago.
2.9 match 47 stars 7.71 score 72 scripts 5 dependents
rpruim
fastR2:Foundations and Applications of Statistics Using R (2nd Edition)
Data sets and utilities to accompany the second edition of "Foundations and Applications of Statistics: an Introduction using R" (R Pruim, published by AMS, 2017), a text covering topics from probability and mathematical statistics at an advanced undergraduate level. R is integrated throughout, and access to all the R code in the book is provided via the snippet() function.
Maintained by Randall Pruim. Last updated 1 years ago.
3.8 match 13 stars 5.85 score 108 scripts
r-a-dobson
dynamicSDM:Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution
A collection of novel tools for generating species distribution and abundance models (SDM) that are dynamic through both space and time. These highly flexible functions incorporate spatial and temporal aspects across key SDM stages; including when cleaning and filtering species occurrence data, generating pseudo-absence records, assessing and correcting sampling biases and autocorrelation, extracting explanatory variables and projecting distribution patterns. Throughout, functions utilise Google Earth Engine and Google Drive to minimise the computing power and storage demands associated with species distribution modelling at high spatio-temporal resolution.
Maintained by Rachel Dobson. Last updated 27 days ago.
dynamicsdmgoogle-earth-enginegoogledrivesdmspatiotemporalspatiotemporal-data-analysisspatiotemporal-forecastingspecies-distribution-modellingspecies-distributions
3.5 match 6 stars 6.16 score 20 scriptsr-forge
Sleuth2:Data Sets from Ramsey and Schafer's "Statistical Sleuth (2nd Ed)"
Data sets from Ramsey, F.L. and Schafer, D.W. (2002), "The Statistical Sleuth: A Course in Methods of Data Analysis (2nd ed)", Duxbury.
Maintained by Berwin A Turlach. Last updated 1 years ago.
3.8 match 5.70 score 191 scripts
birgiterni
moult:Models for Analysing Moult in Birds
Functions to estimate start and duration of moult from moult data, based on models developed in Underhill and Zucchini (1988, 1990).
Maintained by Birgit Erni. Last updated 3 years ago.
6.7 match 3.08 score 20 scripts 2 dependents
tesselle
tabula:Analysis and Visualization of Archaeological Count Data
An easy way to examine archaeological count data. This package provides several tests and measures of diversity: heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.), richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and similarity (Brainerd-Robinson, etc.). It allows to easily visualize count data and statistical thresholds: rank vs abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.
Maintained by Nicolas Frerebeau. Last updated 13 days ago.
data-visualizationarchaeologyarchaeological-science
4.0 match 5.10 score 38 scripts 1 dependents
pbiecek
PogromcyDanych:DataCrunchers (PogromcyDanych) is the Massive Online Open Course that Brings R and Statistics to the People
The data sets used in the online course ,,PogromcyDanych''. You can process data in many ways. The course Data Crunchers will introduce you to this variety. For this reason we will work on datasets of different size (from several to several hundred thousand rows), with various level of complexity (from two to two thousand columns) and prepared in different formats (text data, quantitative data and qualitative data). All of these data sets were gathered in a single big package called PogromcyDanych to facilitate access to them. It contains all sorts of data sets such as data about offer prices of cars, results of opinion polls, information about changes in stock market indices, data about names given to newborn babies, ski jumping results or information about outcomes of breast cancer patients treatment.
Maintained by Przemyslaw Biecek. Last updated 2 years ago.
3.8 match 8 stars 5.41 score 215 scripts 1 dependents
peterkdunn
GLMsData:Generalized Linear Model Data Sets
Data sets from the book Generalized Linear Models with Examples in R by Dunn and Smyth.
Maintained by Peter K. Dunn. Last updated 3 years ago.
7.8 match 2.61 score 220 scripts
tgouhier
synchrony:Methods for Computing Spatial, Temporal, and Spatiotemporal Statistics
Methods for computing spatial, temporal, and spatiotemporal statistics as described in Gouhier and Guichard (2014) [https://doi.org/10.1111/2041-210X.12188]. These methods include empirical univariate, bivariate and multivariate variograms; fitting variogram models; phase locking and synchrony analysis; generating autocorrelated and cross-correlated matrices.
Maintained by Tarik C. Gouhier. Last updated 5 years ago.
4.0 match 10 stars 4.84 score 46 scriptsmikemeredith
wiqid:Quick and Dirty Estimates for Wildlife Populations
Provides simple, fast functions for maximum likelihood and Bayesian estimates of wildlife population parameters, suitable for use with simulated data or bootstraps. Early versions were indeed quick and dirty, but optional error-checking routines and meaningful error messages have been added. Includes single and multi-season occupancy, closed capture population estimation, survival, species richness and distance measures.
Maintained by Ngumbang Juat. Last updated 2 years ago.
4.0 match 2 stars 4.84 score 115 scripts 1 dependentspsolymos
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-manipulationecologysparse-matrices
3.6 match 5.34 score 368 scripts 2 dependents
jakobbossek
smoof:Single and Multi-Objective Optimization Test Functions
Provides generators for a high number of both single- and multi- objective test functions which are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.
Maintained by Jakob Bossek. Last updated 1 years ago.
benchmark-functionsmulti-objective-optimizationsingle-objective-optimizationcpp
2.3 match 36 stars 8.54 score 261 scripts 9 dependentscran
zetadiv:Functions to Compute Compositional Turnover Using Zeta Diversity
Functions to compute compositional turnover using zeta-diversity, the number of species shared by multiple assemblages. The package includes functions to compute zeta-diversity for a specific number of assemblages and to compute zeta-diversity for a range of numbers of assemblages. It also includes functions to explain how zeta-diversity varies with distance and with differences in environmental variables between assemblages, using generalised linear models, linear models with negative constraints, generalised additive models,shape constrained additive models, and I-splines.
Maintained by Guillaume Latombe. Last updated 3 years ago.
6.5 match 3 stars 2.89 score 64 scripts
macroecology
letsR:Data Handling and Analysis in Macroecology
Handling, processing, and analyzing geographic data on species' distributions and environmental variables. Read Vilela & Villalobos (2015) <doi:10.1111/2041-210X.12401> for details.
Maintained by Bruno Vilela. Last updated 2 months ago.
2.0 match 29 stars 8.87 score 104 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.
3.3 match 1 stars 5.26 score 9 scripts 4 dependents
daijiang
megatrees:Subsets of randomly selected phylogenies from existing mega-phylogenies
There are an increasing number of mega-phylogenies available nowadays, with many of them being sets of thousands of posterior distribution phylogenies. For ecological studies, we may need to randomly select many such posterior phylogeneies to conduct analyses. This data package serves this purpose by providing a small number (100) of randomly selected posterior phylogenies (if available) so that we can readily use them for our downstream analyses without repeating the downloading and selecting processes.
Maintained by Daijiang Li. Last updated 2 months ago.
5.6 match 4 stars 3.08 score 2 scripts 1 dependents
txm676
gambin:Fit the Gambin Model to Species Abundance Distributions
Fits unimodal and multimodal gambin distributions to species-abundance distributions from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>. 'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are also provided to generate the gambin distribution and for calculating likelihood statistics.
Maintained by Thomas Matthews. Last updated 2 years ago.
3.4 match 3 stars 5.03 score 12 scripts
tathey
VLF:Frequency Matrix Approach for Assessing Very Low Frequency Variants in Sequence Records
Using frequency matrices, very low frequency variants (VLFs) are assessed for amino acid and nucleotide sequences. The VLFs are then compared to see if they occur in only one member of a species, singleton VLFs, or if they occur in multiple members of a species, shared VLFs. The amino acid and nucleotide VLFs are then compared to see if they are concordant with one another. Amino acid VLFs are also assessed to determine if they lead to a change in amino acid residue type, and potential changes to protein structures. Based on Stoeckle and Kerr (2012) <doi:10.1371/journal.pone.0043992>.
Maintained by Taryn B. T. Athey. Last updated 3 years ago.
7.8 match 2.16 score 48 scripts 1 dependentsfcharte
mldr.datasets:R Ultimate Multilabel Dataset Repository
Large collection of multilabel datasets along with the functions needed to export them to several formats, to make partitions, and to obtain bibliographic information.
Maintained by David Charte. Last updated 6 years ago.
3.5 match 8 stars 4.68 score 120 scripts
eriqande
gaiah:Genetic and Isotopic Assignment Accounting for Habitat Suitability
Tools for using genetic markers, stable isotope data, and habitat suitability data to calculate posterior probabilities of breeding origin of migrating birds.
Maintained by Eric C. Anderson. Last updated 2 years ago.
5.9 match 1 stars 2.74 score 11 scriptsbayesball
ProbBayes:Probability and Bayesian Modeling
Functions and datasets to accompany J. Albert and J. Hu, "Probability and Bayesian Modeling", CRC Press, (2019, ISBN: 1138492566).
Maintained by Jim Albert. Last updated 4 years ago.
3.8 match 5 stars 4.30 score 80 scriptscran
TSA:Time Series Analysis
Contains R functions and datasets detailed in the book "Time Series Analysis with Applications in R (second edition)" by Jonathan Cryer and Kung-Sik Chan.
Maintained by Kung-Sik Chan. Last updated 3 years ago.
3.6 match 2 stars 4.47 score 5 dependentspsolymos
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.
ecologyindicator-species-analysislikelihoodoptimal-partitioningspecies
4.0 match 2 stars 3.91 score 82 scripts
dwarton
ecostats:Code and Data Accompanying the Eco-Stats Text (Warton 2022)
Functions and data supporting the Eco-Stats text (Warton, 2022, Springer), and solutions to exercises. Functions include tools for using simulation envelopes in diagnostic plots, and a function for diagnostic plots of multivariate linear models. Datasets mentioned in the package are included here (where not available elsewhere) and there is a vignette for each chapter of the text with solutions to exercises.
Maintained by David Warton. Last updated 1 years ago.
2.3 match 8 stars 6.58 score 53 scripts
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
6.6 match 2.28 score 38 scripts
jcoliver
lifeR:Identify Sites for Your Bird List
A suite of tools to use the 'eBird' database (<https://ebird.org/home/>) and APIs to compare users' species lists to recent observations and create a report of the top sites to visit to see new species.
Maintained by Jeffrey Oliver. Last updated 1 months ago.
3.1 match 4 stars 4.78 score 6 scripts
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 20 days ago.
aeroecologyenrameumetnet-operalifewatchmovement-ecologynexradoscibioradarweather-radarwsr-88d
1.7 match 29 stars 8.65 score 56 scriptstesselle
folio:Datasets for Teaching Archaeology and Paleontology
Datasets for teaching quantitative approaches and modeling in archaeology and paleontology. This package provides several types of data related to broad topics (cultural evolution, radiocarbon dating, paleoenvironments, etc.), which can be used to illustrate statistical methods in the classroom (multivariate data analysis, compositional data analysis, diversity measurement, etc.).
Maintained by Nicolas Frerebeau. Last updated 1 months ago.
archaeologyarchaeological-sciencepaleontologydatasets
4.5 match 3.02 score 2 scripts 1 dependents
ldbk
m2b:Movement to Behaviour Inference using Random Forest
Prediction of behaviour from movement characteristics using observation and random forest for the analyses of movement data in ecology. From movement information (speed, bearing...) the model predicts the observed behaviour (movement, foraging...) using random forest. The model can then extrapolate behavioural information to movement data without direct observation of behaviours. The specificity of this method relies on the derivation of multiple predictor variables from the movement data over a range of temporal windows. This procedure allows to capture as much information as possible on the changes and variations of movement and ensures the use of the random forest algorithm to its best capacity. The method is very generic, applicable to any set of data providing movement data together with observation of behaviour.
Maintained by Laurent Dubroca. Last updated 8 years ago.
3.2 match 2 stars 4.08 score 12 scripts
moderndive
moderndive:Tidyverse-Friendly Introductory Linear Regression
Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Maintained by Albert Y. Kim. Last updated 3 months ago.
1.1 match 88 stars 11.35 score 1.8k scripts
ddalthorp
GenEst:Generalized Mortality Estimator
Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Maintained by Daniel Dalthorp. Last updated 2 years ago.
1.6 match 7 stars 7.81 score 55 scripts 2 dependents
prabhanjan-tattar
gpk:100 Data Sets for Statistics Education
Collection of datasets as prepared by Profs. A.P. Gore, S.A. Paranjape, and M.B. Kulkarni of Department of Statistics, Poona University, India. With their permission, first letter of their names forms the name of this package, the package has been built by me and made available for the benefit of R users. This collection requires a rich class of models and can be a very useful building block for a beginner.
Maintained by Prabhanjan Tattar. Last updated 12 years ago.
7.3 match 1.69 score 49 scriptsluomus
haahka:Haahka bird migration browser
Bird Migration browser.
Maintained by William K. Morris. Last updated 11 days ago.
3.8 match 3.15 score
bart1
moveWindSpeed:Estimate Wind Speeds from Bird Trajectories
Estimating wind speed from trajectories of individually tracked birds using a maximum likelihood approach from Weinzierl et al., 2016 <doi.org:10.1002/ece3.2585>.
Maintained by Bart Kranstauber. Last updated 2 years ago.
3.5 match 3.38 score 12 scripts
joblion
MixAll:Clustering and Classification using Model-Based Mixture Models
Algorithms and methods for model-based clustering and classification. It supports various types of data: continuous, categorical and counting and can handle mixed data of these types. It can fit Gaussian (with diagonal covariance structure), gamma, categorical and Poisson models. The algorithms also support missing values.
Maintained by Serge Iovleff. Last updated 10 months ago.
3.6 match 3.29 score 97 scripts
tyee001
VGAMdata:Data Supporting the 'VGAM' Package
Mainly data sets to accompany the VGAM package and the book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) <DOI:10.1007/978-1-4939-2818-7>. These are used to illustrate vector generalized linear and additive models (VGLMs/VGAMs), and associated models (Reduced-Rank VGLMs, Quadratic RR-VGLMs, Row-Column Interaction Models, and constrained and unconstrained ordination models in ecology). This package now contains some old VGAM family functions which have been replaced by newer ones (often because they are now special cases).
Maintained by Thomas Yee. Last updated 1 months ago.
4.0 match 1 stars 2.94 score 95 scripts 1 dependents
mlverse
torchdatasets:Ready to Use Extra Datasets for Torch
Provides datasets in a format that can be easily consumed by torch 'dataloaders'. Handles data downloading from multiple sources, caching and pre-processing so users can focus only on their model implementations.
Maintained by Daniel Falbel. Last updated 5 days ago.
2.0 match 15 stars 5.65 score 99 scripts
andburch
rabi:Generate Codes to Uniquely and Robustly Identify Individuals for Animal Behavior Studies
Facilitates the design and generation of optimal color (or symbol) codes that can be used to mark and identify individual animals. These codes are made such that the IDs are robust to partial erasure: even if sections of the code are lost, the entire identity of the animal can be reconstructed. Thus, animal subjects are not confused and no ambiguity is introduced.
Maintained by Andrew Taylor Burchill. Last updated 3 years ago.
animal-behaviorcollective-behavior
2.9 match 3.70 score 7 scripts
agroscope-ch
OpenFoodTox:EFSA OpenFoodTox Data Made Accessible as an R Package
Provides convenient access to data extracted from some of the spreadsheet files made available by the chemical hazards database of the European Food Safety Authority (EFSA), accessible via <https://www.efsa.europa.eu/en/data-report/chemical-hazards-database-openfoodtox>.
Maintained by Johannes Ranke. Last updated 8 months ago.
3.0 match 1 stars 3.48 score 2 scripts
hanmingwu1103
dataSDA:Data Sets for Symbolic Data Analysis
Collects a diverse range of symbolic data and offers a comprehensive set of functions that facilitate the conversion of traditional data into the symbolic data format.
Maintained by Han-Ming Wu. Last updated 2 years ago.
3.8 match 2.70 score 2 scripts
nschiett
fishualize:Color Palettes Based on Fish Species
Implementation of color palettes based on fish species.
Maintained by Nina M. D. Schiettekatte. Last updated 11 months ago.
1.1 match 155 stars 8.54 score 370 scripts
birdscanada
naturecounts:Access and download data on plant and animal populations from NatureCounts
Access and download data on plant and animal populations from various databases through NatureCounts, a service managed by Bird Studies Canada.
Maintained by Denis Lepage. Last updated 6 months ago.
2.3 match 14 stars 4.11 score 46 scriptscran
gamair:Data for 'GAMs: An Introduction with R'
Data sets and scripts used in the book 'Generalized Additive Models: An Introduction with R', Wood (2006,2017) CRC.
Maintained by Simon Wood. Last updated 6 years ago.
3.8 match 2.43 score 162 scriptscran
Rcapture:Loglinear Models for Capture-Recapture Experiments
Estimation of abundance and other demographic parameters for closed populations, open populations and the robust design in capture-recapture experiments using loglinear models.
Maintained by Louis-Paul Rivest. Last updated 3 years ago.
3.3 match 1 stars 2.53 score 1 dependents
adrian-bowman
rpanel:Simple Interactive Controls for R using the 'tcltk' Package
A set of functions to build simple GUI controls for R functions. These are built on the 'tcltk' package. Uses could include changing a parameter on a graph by animating it with a slider or a "doublebutton", up to more sophisticated control panels. Some functions for specific graphical tasks, referred to as 'cartoons', are provided.
Maintained by Adrian Bowman. Last updated 2 years ago.
1.9 match 1 stars 4.30 score 157 scripts 9 dependents
ebird
ebirdst:Access and Analyze eBird Status and Trends Data Products
Tools for accessing and analyzing eBird Status and Trends Data Products (<https://science.ebird.org/en/status-and-trends>). eBird (<https://ebird.org/home>) is a global database of bird observations collected by member of the public. eBird Status and Trends uses these data to model global bird distributions, abundances, and population trends at a high spatial and temporal resolution.
Maintained by Matthew Strimas-Mackey. Last updated 20 days ago.
0.8 match 26 stars 8.85 score 228 scripts
aschleg
PetfindeR:'Petfinder' API Wrapper
Wrapper of the 'Petfinder API' <https://www.petfinder.com/developers/v2/docs/> that implements methods for interacting with and extracting data from the 'Petfinder' database. The 'Petfinder REST API' allows access to the 'Petfinder' database, one of the largest online databases of adoptable animals and animal welfare organizations across North America.
Maintained by Aaron Schlegel. Last updated 5 years ago.
animal-shelteranimal-welfare-organizationsanimalsapi-wrapperpetfinderpetfinder-apipetfinder-database
1.5 match 6 stars 4.48 score 6 scripts
kenkellner
IPMbook:Functions and Data for the Book 'Integrated Population Models'
Provides functions and data sets to accompany the book 'Integrated Population Models: Theory and Ecological Applications with R and JAGS' by Michael Schaub and Marc Kéry (ISBN: 9780128205648).
Maintained by Ken Kellner. Last updated 1 months ago.
1.5 match 1 stars 3.95 score 177 scripts
rvhulst
evidence:Analysis of Scientific Evidence Using Bayesian and Likelihood Methods
Bayesian (and some likelihoodist) functions as alternatives to hypothesis-testing functions in R base using a user interface patterned after those of R's hypothesis testing functions. See McElreath (2016, ISBN: 978-1-4822-5344-3), Gelman and Hill (2007, ISBN: 0-521-68689-X) (new edition in preparation) and Albert (2009, ISBN: 978-0-387-71384-7) for good introductions to Bayesian analysis and Pawitan (2002, ISBN: 0-19-850765-8) for the Likelihood approach. The functions in the package also make extensive use of graphical displays for data exploration and model comparison.
Maintained by Robert van Hulst. Last updated 7 years ago.
3.4 match 1.63 score 43 scripts
rvalavi
disdat:Data for Comparing Species Distribution Modeling Methods
Easy access to species distribution data for 6 regions in the world, for a total of 226 anonymised species. These data are described and made available by Elith et al (2020) <doi:10.17161/bi.v15i2.13384> to compare species distribution modelling methods.
Maintained by Roozbeh Valavi. Last updated 2 years ago.
1.8 match 2.92 score 42 scriptscran
birdring:Methods to Analyse Ring Re-Encounter Data
R functions to read EURING data and analyse re-encounter data of birds marked by metal rings. For a tutorial, go to <doi:10.1080/03078698.2014.933053>.
Maintained by Fraenzi Korner-Nievergelt. Last updated 1 years ago.
4.0 match 1.30 scorecran
placer:PLastic ACcumulation Estimate using R (PLACER)
Assessment of the prevalence of plastic debris in bird nests based on bootstrap replicates. The package allows for calculating bootstrapped 95% confidence intervals for the estimated prevalence of debris. Combined with a Bayesian approach, the resampling simulations can be also used to define appropriate sample sizes to detect prevalence of plastics. The method has wide application, and can also be applied to estimate confidence intervals and define sample sizes for the prevalence of plastics ingested by any other organisms. The method is described in Tavares et al. (Submitted).
Maintained by Davi Castro-Tavares. Last updated 6 years ago.
2.2 match 2.00 score
jangraffelman
MLpreemption:Maximum Likelihood Estimation of the Niche Preemption Model
Provides functions for obtaining estimates of the parameter of the niche preemption model (also known as the geometric series), in particular a maximum likelihood estimator (Graffelman, 2021) <doi:10.1101/2021.01.27.428381>. The niche preemption model is a widely used model in ecology and biodiversity studies.
Maintained by Jan Graffelman. Last updated 4 years ago.
4.0 match 1.00 score
gaborcsardi
rcorpora:A Collection of Small Text Corpora of Interesting Data
A collection of small text corpora of interesting data. It contains all data sets from 'dariusk/corpora'. Some examples: names of animals: birds, dinosaurs, dogs; foods: beer categories, pizza toppings; geography: English towns, rivers, oceans; humans: authors, US presidents, occupations; science: elements, planets; words: adjectives, verbs, proverbs, US president quotes.
Maintained by Gábor Csárdi. Last updated 7 years ago.
0.5 match 42 stars 6.83 score 36 scripts 2 dependentsadokter
vol2birdR:Vertical Profiles of Biological Signals in Weather Radar Data
'R' implementation of the 'vol2bird' software for generating vertical profiles of birds and other biological signals in weather radar data. See Dokter et al. (2011) <doi:10.1098/rsif.2010.0116> for a paper describing the methodology.
Maintained by Adriaan M. Dokter. Last updated 10 days ago.
0.5 match 6 stars 6.61 score 19 scripts
flowmapblue
flowmapblue:Flow Map Rendering
Create interactive flow maps using 'FlowmapBlue' 'TypeScript' library <https://github.com/FlowmapBlue/FlowmapBlue>, which is a free tool for representing aggregated numbers of movements between geographic locations as flow maps. It is used to visualize urban mobility, commuting behavior, bus, subway and air travels, bicycle sharing, human and bird migration, refugee flows, freight transportation, trade, supply chains, scientific collaboration, epidemiological and historical data and many other topics. The package allows to either create standalone flow maps in form of 'htmlwidgets' and save them in 'HTML' files, or integrate flow maps into 'Shiny' applications.
Maintained by Egor Kotov. Last updated 16 days ago.
datavismobilitymobility-datamovement-datarstudio
0.5 match 57 stars 6.70 score 22 scripts
clement-lee
crandep:Network Analysis of Dependencies of CRAN Packages
The dependencies of CRAN packages can be analysed in a network fashion. For each package we can obtain the packages that it depends, imports, suggests, etc. By iterating this procedure over a number of packages, we can build, visualise, and analyse the dependency network, enabling us to have a bird's-eye view of the CRAN ecosystem. One aspect of interest is the number of reverse dependencies of the packages, or equivalently the in-degree distribution of the dependency network. This can be fitted by the power law and/or an extreme value mixture distribution <doi:10.1111/stan.12355>, of which functions are provided.
Maintained by Clement Lee. Last updated 7 months ago.
0.5 match 8 stars 6.23 score 20 scripts
marinapapa
swaRmverse:Swarm Space Creation
Provides a pipeline for the comparative analysis of collective movement data (e.g. fish schools, bird flocks, baboon troops) by processing 2-dimensional positional data (x,y,t) from GPS trackers or computer vision tracking systems, discretizing events of collective motion, calculating a set of established metrics that characterize each event, and placing the events in a multi-dimensional swarm space constructed from these metrics. The swarm space concept, the metrics and data sets included are described in: Papadopoulou Marina, Furtbauer Ines, O'Bryan Lisa R., Garnier Simon, Georgopoulou Dimitra G., Bracken Anna M., Christensen Charlotte and King Andrew J. (2023) <doi:10.1098/rstb.2022.0068>.
Maintained by Marina Papadopoulou. Last updated 5 months ago.
0.5 match 2 stars 5.13 score 15 scripts
birdscancommunity
birdscanR:Migration Traffic Rate Calculation Package for 'Birdscan MR1' Radars
Extract data from 'Birdscan MR1' 'SQL' vertical-looking radar databases, filter, and process them to Migration Traffic Rates (#objects per hour and km) or density (#objects per km3) of, for example birds, and insects. Object classifications in the 'Birdscan MR1' databases are based on the dataset of Haest et al. (2021) <doi:10.5281/zenodo.5734960>). Migration Traffic Rates and densities can be calculated separately for different height bins (with a height resolution of choice) as well as over time periods of choice (e.g., 1/2 hour, 1 hour, 1 day, day/night, the full time period of observation, and anything in between). Two plotting functions are also included to explore the data in the 'SQL' databases and the resulting Migration Traffic Rate results. For details on the Migration Traffic Rate calculation procedures, see Schmid et al. (2019) <doi:10.1111/ecog.04025>.
Maintained by Birgen Haest. Last updated 3 months ago.
0.5 match 3 stars 4.86 score 3 scripts
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.
0.8 match 2.93 score 17 scriptsdaijiang
neonDivData:Standardized NEON Organismal Data for Biodiversity Research
Cleaned, simplified, and standardized NEON organismal data for biodiversity research. The following taxonomic groups are included so far: algae, beetles, birds, fish, herptiles, macroinvertebrates, mosquitoes, plants, small_mammals, ticks, tick_pathogens, and zooplankton. NEON input data (<https://data.neonscience.org>) were processed and standardized using R package `ecocomDP` (<https://github.com/EDIorg/ecocomDP>).
Maintained by Daijiang Li. Last updated 10 months ago.
0.5 match 15 stars 4.36 score 17 scripts
rrrlw
helixvis:Visualize Alpha-Helical Peptide Sequences
Create publication-quality, 2-dimensional visualizations of alpha-helical peptide sequences. Specifically, allows the user to programmatically generate helical wheels and wenxiang diagrams to provide a bird's eye, top-down view of alpha-helical oligopeptides. See Wadhwa RR, et al. (2018) <doi:10.21105/joss.01008> for more information.
Maintained by Raoul Wadhwa. Last updated 6 years ago.
biochemistryhelical-wheelspeptide-sequencesvisualizationwenxiang-diagrams
0.5 match 2 stars 4.00 score 3 scripts
biagolini
bwimage:Describe Image Patterns in Natural Structures
A computational tool to describe patterns in black and white images from natural structures. 'bwimage' implemented functions for exceptionally broad subject. For instance, 'bwimage' provide examples that range from calculation of canopy openness, description of patterns in vertical vegetation structure, to patterns in bird nest structure.
Maintained by Carlos Biagolini-Jr.. Last updated 5 years ago.
0.5 match 3.70 score
elipousson
bingmapr:Get Maps from Bing Maps Static Map API
Get static maps using aerial, bird's eye and other imagery from Bing Maps.
Maintained by Eli Pousson. Last updated 6 months ago.
bing-mapsbing-maps-apir-spatial
0.6 match 11 stars 3.04 score 6 scriptsddalthorp
dwp:Density-Weighted Proportion
Fit a Poisson regression to carcass distance data and integrate over the searched area at a wind farm to estimate the fraction of carcasses falling in the searched area and format the output for use as the dwp parameter in the 'GenEst' or 'eoa' package for estimating bird and bat mortality, following Dalthorp, et al. (2022) <arXiv:2201.10064>.
Maintained by Daniel Dalthorp. Last updated 2 years ago.
0.5 match 1 stars 2.70 scoreddalthorp
eoa3:Wildlife Mortality Estimator for Low Fatality Rates and Imperfect Detection
Evidence of Absence software (EoA) is a user-friendly application for estimating bird and bat fatalities at wind farms and designing search protocols. The software is particularly useful in addressing whether the number of fatalities has exceeded a given threshold and what search parameters are needed to give assurance that thresholds were not exceeded. The models are applicable even when zero carcasses have been found in searches, following Huso et al. (2015) <doi:10.1890/14-0764.1>, Dalthorp et al. (2017) <doi:10.3133/ds1055>, and Dalthorp and Huso (2015) <doi:10.3133/ofr20151227>.
Maintained by Daniel Dalthorp. Last updated 4 months ago.
0.5 match 1.00 score