Showing 31 of total 31 results (show query)
jniedballa
camtrapR:Camera Trap Data Management and Preparation of Occupancy and Spatial Capture-Recapture Analyses
Management of and data extraction from camera trap data in wildlife studies. The package provides a workflow for storing and sorting camera trap photos (and videos), tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it can visualise species activity data and provides simple mapping functions with GIS export.
Maintained by Juergen Niedballa. Last updated 3 months ago.
occupancy-modelingspatial-capture-recapturewildlife
10.5 match 35 stars 8.65 score 178 scripts
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.
4.0 match 240 stars 11.39 score 6.0k scripts
jedalong
wildlifeDI:Calculate Indices of Dynamic Interaction for Wildlife Tracking Data
Dynamic interaction refers to spatial-temporal associations in the movements of two (or more) animals. This package provides tools for calculating a suite of indices used for quantifying dynamic interaction with wildlife telemetry data. For more information on each of the methods employed see the references within. The package (as of version >= 0.3) also has new tools for automating contact analysis in large tracking datasets. The package (as of version 1.0) uses the 'move2' class of objects for working with tracking dataset.
Maintained by Jed Long. Last updated 10 months ago.
6.2 match 16 stars 6.70 score 31 scripts
confoobio
GMSE:Generalised Management Strategy Evaluation Simulator
Integrates game theory and ecological theory to construct social-ecological models that simulate the management of populations and stakeholder actions. These models build off of a previously developed management strategy evaluation (MSE) framework to simulate all aspects of management: population dynamics, manager observation of populations, manager decision making, and stakeholder responses to management decisions. The newly developed generalised management strategy evaluation (GMSE) framework uses genetic algorithms to mimic the decision-making process of managers and stakeholders under conditions of change, uncertainty, and conflict. Simulations can be run using gmse(), gmse_apply(), and gmse_gui() functions.
Maintained by A. Bradley Duthie. Last updated 3 years ago.
adaptive-managementagricultural-modellingconflictconflict-resolutionconservationecological-modellingecological-modelsecologyfood-securitygame-theorygenetic-algorithmgenetic-algorithmsmanagement-decisionsmanagement-strategy-evaluationpopulation-modelsimulationwildlife-management
7.5 match 10 stars 5.43 score 178 scripts
rkbauer
RchivalTag:Analyzing and Interactive Visualization of Archival Tagging Data
A set of functions to generate, access and analyze standard data products from archival tagging data.
Maintained by Robert K. Bauer. Last updated 2 months ago.
data-visualidepthdepth-temperature-profilesdygraphsggpotleafletminipatpelagicplotlysatellitesensorspatialstar-odditemperaturetime-seriestrackswildlife-computers
7.5 match 1 stars 3.59 score 26 scripts
jfieberg
SightabilityModel:Wildlife Sightability Modeling
Uses logistic regression to model the probability of detection as a function of covariates. This model is then used with observational survey data to estimate population size, while accounting for uncertain detection. See Steinhorst and Samuel (1989).
Maintained by Schwarz Carl James. Last updated 2 years ago.
5.3 match 1 stars 4.96 score 23 scripts
robitalec
camtrapmonitoring:Camera Trap Monitoring For Estimating Wildlife Density
Evaluating potential camera trap locations. Potential locations are evaluated using relevant spatial layers producing a dataset of selected locations with covariates that can be used to quantify sampling bias. Soon - density estimation methods.
Maintained by Alec L. Robitaille. Last updated 9 months ago.
camera-trapcamera-trapsspatialwildlife
12.9 match 2 stars 2.00 score 2 scripts
mikemeredith
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.
5.2 match 2 stars 4.84 score 115 scripts 1 dependents
psolymos
detect:Analyzing Wildlife Data with Detection Error
Models for analyzing site occupancy and count data models with detection error, including single-visit based models (Lele et al. 2012 <doi:10.1093/jpe/rtr042>, Moreno et al. 2010 <doi:10.1890/09-1073.1>, Solymos et al. 2012 <doi:10.1002/env.1149>, Denes et al. 2016 <doi:10.1111/1365-2664.12818>), conditional distance sampling and time-removal models (Solymos et al. 2013 <doi:10.1111/2041-210X.12106>, Solymos et al. 2018 <doi:10.1650/CONDOR-18-32.1>). Package development was supported by the Alberta Biodiversity Monitoring Institute and the Boreal Avian Modelling Project.
Maintained by Peter Solymos. Last updated 10 months ago.
4.8 match 5 stars 5.27 score 123 scripts
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.
3.3 match 47 stars 7.71 score 72 scripts 5 dependents
mstrimas
colorist:Coloring Wildlife Distributions in Space-Time
Color and visualize wildlife distributions in space-time using raster data. In addition to enabling display of sequential change in distributions through the use of small multiples, 'colorist' provides functions for extracting several features of interest from a sequence of distributions and for visualizing those features using HCL (hue-chroma-luminance) color palettes. Resulting maps allow for "fair" visual comparison of intensity values (e.g., occurrence, abundance, or density) across space and time and can be used to address questions about where, when, and how consistently a species, group, or individual is likely to be found.
Maintained by Matthew Strimas-Mackey. Last updated 11 months ago.
3.5 match 14 stars 5.60 score 19 scripts
torstax
amregtest:Runs Allelematch Regression Tests
Automates regression testing of package 'allelematch'. Over 2500 tests covers all functions in 'allelematch', reproduces the examples from the documentation and includes negative tests. The implementation is based on 'testthat'.
Maintained by Torvald Staxler. Last updated 11 months ago.
6.0 match 3.18 score 3 scripts
viralemergence
epizootic:Spatially Explicit Population Models of Disease Transmission in Wildlife
This extension of the pattern-oriented modeling framework of the 'poems' package provides a collection of modules and functions customized for modeling disease transmission on a population scale in a spatiotemporally explicit manner. This includes seasonal time steps, dispersal functions that track disease state of dispersers, results objects that store disease states, and a population simulator that includes disease dynamics.
Maintained by July Pilowsky. Last updated 6 months ago.
2.9 match 4 stars 5.45 score 5 scripts
clementcalenge
adehabitatHS:Analysis of Habitat Selection by Animals
A collection of tools for the analysis of habitat selection.
Maintained by Clement Calenge. Last updated 6 months ago.
2.9 match 1 stars 4.77 score 51 scripts
inbo
camtraptor:Read, Explore and Visualize Camera Trap Data Packages
Read, explore and visualize Camera Trap Data Packages (Camtrap DP). 'Camtrap DP' (<https://camtrap-dp.tdwg.org>) is a community developed data exchange format for this type of data. With camtraptor you can read and filter data, create overviews of observed species, relative abundance or effort, and plot these data on a map.
Maintained by Damiano Oldoni. Last updated 28 days ago.
1.9 match 12 stars 6.27 score 16 scripts
rhedley
locaR:A Set of Tools for Sound Localization
A set of functions and tools to conduct acoustic source localization, as well as organize and check localization data and results. The localization functions implement the modified steered response power algorithm described by Cobos et al. (2010) <doi:10.1109/LSP.2010.2091502>.
Maintained by Richard Hedley. Last updated 2 years ago.
1.8 match 1 stars 4.78 score 24 scripts
dsjohnson
ctmmUtils:Auxillary functions for using the {ctmm} package efficiently
Utility functions to augment the the {ctmm} package. The additional function are targeted toward analysis of marine mammal telemetry, but can be used or easily modified for other situations.
Maintained by Devin S. Johnson. Last updated 3 months ago.
3.3 match 2.40 score
ecodynizw
imageseg:Deep Learning Models for Image Segmentation
A general-purpose workflow for image segmentation using TensorFlow models based on the U-Net architecture by Ronneberger et al. (2015) <arXiv:1505.04597> and the U-Net++ architecture by Zhou et al. (2018) <arXiv:1807.10165>. We provide pre-trained models for assessing canopy density and understory vegetation density from vegetation photos. In addition, the package provides a workflow for easily creating model input and model architectures for general-purpose image segmentation based on grayscale or color images, both for binary and multi-class image segmentation.
Maintained by Juergen Niedballa. Last updated 1 years ago.
image-segmentationkerastensorflow
1.6 match 18 stars 4.95 score 9 scripts
sjbonner
RWildbook:Interface for the 'Wildbook' Wildlife Data Management Framework
Provides an interface with the 'Wildbook' mark-recapture ecological database framework. It helps users to pull data from the 'Wildbook' framework and format data for further analysis with mark-recapture applications like 'Program MARK' (which can be accessed via the 'RMark' package in 'R'). Further information on the 'Wildbook' framework is available at: <http://www.wildbook.org/doku.php>.
Maintained by Simon Bonner. Last updated 7 years ago.
2.9 match 1 stars 2.30 score 4 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 scriptspsolymos
WildLift:An Open-source Tool to Guide Decisions for Wildlife Conservation
Compare alternative recovery actions: Linear Feature Restoration, Linear Feature Deactivation, Maternal Penning, Conservation Breeding, Predator Exclosure, Wolf Reduction, and Moose Reduction. Quantifying the trade-offs associated with alternative recovery actions for threatened species. The tool consists of a generalized matrix population model that is parametrized based on information from the published literature or ongoing experiments. Users can input population parameters (e.g., population size and survival rates) or choose from pre-set caribou subpopulations to estimate changes to populations from implementing recovery actions as described in Nagy-Reis et al. (2020) <doi:10.3389/fevo.2020.564508>.
Maintained by Peter Solymos. Last updated 4 years ago.
2.9 match 1.70 score 5 scriptsdsjohnson
crawlUtils:Enhance And Integrate the {crawl} Package For Spatial Analysis Of Telemetry Output
Utility functions to augment the the {crawl} package and integrate it with the {sf} package for spatial analysis of telemetry model output. The additional function are targeted toward analysis of marine mammal telemetry, but can be used or easily modified for other situations.
Maintained by Devin S. Johnson. Last updated 6 months ago.
1.7 match 2 stars 2.60 score 1 scriptspsolymos
ResourceSelection:Resource Selection (Probability) Functions for Use-Availability Data
Resource Selection (Probability) Functions for use-availability wildlife data based on weighted distributions as described in Lele and Keim (2006) <doi:10.1890/0012-9658(2006)87%5B3021:WDAEOR%5D2.0.CO;2>, Lele (2009) <doi:10.2193/2007-535>, and Solymos & Lele (2016) <doi:10.1111/2041-210X.12432>.
Maintained by Peter Solymos. Last updated 10 months ago.
ecologyestimationlelersfrspfsolymosweighted-distributions
0.5 match 8 stars 8.29 score 752 scripts 3 dependents
poissonconsulting
klexdatr:Kootenay Lake Exploitation Study Data
Six relational 'tibbles' from the Kootenay Lake Large Trout Exploitation study. The study which ran from 2008 to 2014 caught, tagged and released large Rainbow Trout and Bull Trout in Kootenay Lake by boat angling. The fish were tagged with internal acoustic tags and/or high reward external tags and subsequently detected by an acoustic receiver array as well as reported by anglers. The data are analysed by Thorley and Andrusak (1994) <doi:10.7717/peerj.2874> to estimate the natural and fishing mortality of both species.
Maintained by Joe Thorley. Last updated 2 months ago.
1.5 match 2.30 score 7 scriptspoissonconsulting
curtisquadata:Curtis and Qua Creeks Productivity Study Data
Fifteen relational tibbles from the Curtis and Qua Creeks Productivity study. The study which ran from 2015 to 2017 collected data on the water quality and temperature, periphyton, benthic invertebrates and fish populations of Curtis and Qua Creeks in the Salmo Watershed, British Columbia.
Maintained by Joe Thorley. Last updated 2 months ago.
1.5 match 2.18 score 2 scripts
ddalthorp
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.
2.8 match 1.00 score
brianbattaile
TrackReconstruction:Reconstruct Animal Tracks from Magnetometer, Accelerometer, Depth and Optional Speed Data
Reconstructs animal tracks from magnetometer, accelerometer, depth and optional speed data. Designed primarily using data from Wildlife Computers Daily Diary tags deployed on northern fur seals.
Maintained by Brian Battaile. Last updated 3 years ago.
0.5 match 2.85 score 35 scripts
noreastermt
allelematch:Identifying Unique Multilocus Genotypes where Genotyping Error and Missing Data may be Present
Tools for the identification of unique of multilocus genotypes when both genotyping error and missing data may be present; targeted for use with large datasets and databases containing multiple samples of each individual (a common situation in conservation genetics, particularly in non-invasive wildlife sampling applications). Functions explicitly incorporate missing data and can tolerate allele mismatches created by genotyping error. If you use this package, please cite the original publication in Molecular Ecology Resources (Galpern et al., 2012), the details for which can be generated using citation('allelematch'). For a complete vignette, please access via the Data S1 Supplementary documentation and tutorials (PDF) located at <doi:10.1111/j.1755-0998.2012.03137.x>.
Maintained by Todd Cross. Last updated 12 months ago.
0.5 match 2.26 score 8 scripts 1 dependentsrobitalec
preparelocs:Prepares Relocations For The WEEL
Prepares animal relocation datasets for the Wildlife Evolutionary Ecology Lab at Memorial University.
Maintained by Alec L. Robitaille. Last updated 1 years ago.
animalanimal-movementgpstargets
0.6 match 1.70 score
skmckay
ecorest:Conducts Analyses Informing Ecosystem Restoration Decisions
Three sets of data and functions for informing ecosystem restoration decisions, particularly in the context of the U.S. Army Corps of Engineers. First, model parameters are compiled as a data set and associated metadata for over 300 habitat suitability models developed by the U.S. Fish and Wildlife Service (USFWS 1980, <https://www.fws.gov/policy-library/870fw1>). Second, functions for conducting habitat suitability analyses both for the models described above as well as generic user-specified model parameterizations. Third, a suite of decision support tools for conducting cost-effectiveness and incremental cost analyses (Robinson et al. 1995, IWR Report 95-R-1, U.S. Army Corps of Engineers).
Maintained by S. Kyle McKay. Last updated 6 months ago.
0.5 match 1.00 score 2 scripts