Analytical methods and modeling tools
Software for viability, connectivity, occupancy, camera traps and acoustics.
19 resources
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Vortex
Free population viability analysis for extinction-risk simulation
Run a viability analysis to put a number on extinction risk under competing scenarios
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Circuitscape
Open-source circuit-theory tool for landscape connectivity and gene flow
Model where animals can actually move across a landscape, which is what a corridor argument needs
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Linkage Mapper
ArcGIS toolbox that maps and prioritizes wildlife corridors
Rank candidate corridors inside ArcGIS so a planner sees priorities, not a connectivity surface
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BOLD Systems
DNA barcode database and analysis workbench for species identification
Match a barcode sequence to a species, or check whether your taxon has reference barcodes at all
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TDWG Biodiversity Information Standards
The standards body for biodiversity data, and home of Darwin Core, the vocabulary everything from GBIF down uses to share occurrence and specimen records
Format occurrence data as Darwin Core so anyone else can publish or join it
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eBio Atlas
Open global eDNA biodiversity repository, freshwater focus
Deposit or reuse freshwater eDNA results where traditional survey coverage is simply impossible
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Maxent
Maximum-entropy species distribution modeling software
Run the distribution model reviewers still recognize, which works from presence records alone
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Wallace EcoMod
Guided R and Shiny platform for reproducible niche modeling
Build a niche model through a guided interface that writes reproducible R code as you go
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Program MARK
Capture-recapture survival and population parameter estimation
Estimate survival and abundance from capture histories, still the standard for mark-recapture work
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rOpenSci
Peer-reviewed hub for open-source R packages used in ecology
Pick an R package that passed peer review rather than gambling on an unmaintained one
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unmarked (R package)
Fits occupancy, distance sampling and N-mixture abundance models to survey data where detection is imperfect
Fit occupancy and abundance models that account for the animals you failed to detect
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camtrapR (R package)
Turns raw camera-trap images into detection histories, occupancy model inputs and activity patterns
Convert camera-trap folders into detection histories without hand-building the matrix yourself
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MegaDetector
Free AI model that finds animals, people and vehicles in camera-trap images so you never review a blank frame again
Strip blank frames from a camera-trap set before anyone spends time reviewing images
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AddaxAI
Runs MegaDetector and species classifiers through a desktop interface, with no coding required. Formerly EcoAssist
Run MegaDetector without writing code, and keep every image on your own machine
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Timelapse2
Free tool for reviewing and annotating large camera-trap image sets, and it imports MegaDetector results
Annotate a large image set fast, importing detector output so you only judge real frames
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Camelot
Free camera-trap database and classification tool that exports straight to camtrapR and PRESENCE
Manage camera-trap images and export straight into camtrapR or PRESENCE for analysis
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Raven
Cornell Lab sound analysis software for visualizing and measuring animal calls. Raven Lite is free, Raven Pro is paid
Start with free Raven Lite to measure calls, and buy Pro only when batch work demands it
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Kaleidoscope
Sorts and labels bird song, frog calls and bat echolocation across months of recordings. Lite edition is free
Sort months of recordings by species, trying the free Lite edition before paying for Pro
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bioacoustics (R package)
Free GPL-3 package that filters noisy audio and extracts acoustic features for classification, reading WAV, WAC, MP3 and ZC
Filter noisy recordings and extract features in R when commercial software is out of budget