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Weecology (@weecology)

weecology

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DeepForest

Python Package for Airborne RGB machine learning

retriever

Quickly download, clean up, and install public datasets into a database management system

NeonTreeEvaluation

Benchmark dataset for tree detection for airborne RGB, Hyperspectral and LIDAR imagery

ogrants

Open grants list

DeepTreeAttention

Implementation of Hang et al. 2020 "Hyperspectral Image Classification with Attention Aided CNNs" for tree species prediction

DeepLidar

LIDAR and RGB Deep Learning Model for Individual Tree Segmentation

data-sharing-paper

Paper on data sharing in ecology for IEE special issue

PortalData

Official Repo of the Portal Project Data

LDATS

Latent Dirichlet Allocation coupled with Bayesian Time Series analyses

NeonTreeEvaluation_package

R package for evaluating individual tree crown predictions against a diverse benchmark dataset

forecasting-course

Morgan Ernest & Ethan White's Ecological Forecasting & Dynamics Course

DeepForest-pytorch

Pytorch implementation of the deepforest model for tree crown RGB detection.

livedat

Template for living data workflow

portal-teachingdb

A simplified version of the Portal Project database designed for teaching

MATSS

R Package for Macroecological Analysis of Time Series Structure (MATSS)

white-etal-2012-ecology

Code for replicating "Characterizing species-abundance distributions across taxa and ecosystems using a simple maximum entropy model" by Ethan P. White, Katherine M. Thibault, and Xiao Xiao

portalr

A collection of functions to summarize the Portal Data

BirdDetector

A global bird detector model for the DeepForest-pytorch package

Jupyter Notebook

METE

Software for fitting and testing John Harte and colleagues' Maximum Entropy Theory of Ecology.

deepforestr

macroecotools

Tools for Macroecological Analyses Using Python

pydataweaver

The Pydata Weaver: A data Integration platform

portalPredictions

Using various models to forecast abundances at Portal

portalcasting

Model development, deployment, and evaluation for forecasting Portal ecosystem dynamics

TreeSegmentation

Reproducible analysis of tree segmentation methods in R.

sad-comparison

Elita Baldridge's dissertation repository

forecasting-dynamics-course

Morgan Ernest and Ethan White's course on Ecological Dynamics and Forecasting

MillionTrees

The MillionTreesBenchmark

abundance

zero-inflated negative binomial neural network with variational approximation to site-level & observer-level random effects

Jupyter Notebook

bibliometrics

Bibliometric research

bbs-forecasting

Research on forecasting using Breeding Bird Survey data

Jupyter Notebook

retrieverdash

Dashboard for retriever dataset status

MATSS-forecasting

Forecasting Analysis Comparison for Ecological Time Series

Retriever.jl

Julia wrapper for the Data Retriever software

mete-spatial

Research on the spatial predictions of METE

retriever-recipes

website

livedat-github-actions

experimental-rads

MATSS-LDATS

Macroecological LDA analysis of time series

NeonTreeEvaluation_python

python benchmark for individual tree crown methods

DeepForest_demos

DEPRECATED DeepForest demos

Jupyter Notebook

ratdat

R package version of Portal Project Teaching Database

branch-arch

neonwranglerpy

EvergladesWadingBird

Data from the Everglades breeding bird monitoring project

ecology-data-cache

lab-manual

mvgamportal

DeepForest_Model

Companion repo to DeepForest for training large models from DeepForest python package.

MATSSdemo

Automated build of a MATSS compendium

forecast_evaluation

Methods and tools for evaluating probabilistic forecasts

feasiblesets

Research code for understanding distributions of wealth in the context of all possible distributions

DoubleCounting

A repo for visualizing airborne imagery, making a prediction with a deepforest model and remove double counting among overlapping images.

mete-geog

Research on making geographic predictions for macroecological patterns using the Maximum Entropy Theory of Ecology

mcdb

Mammal community database updates

diversity-conservation

datawiki

Efforts related to http://ecologicaldata.org

portal-tools

Code for working with the Portal Project data

NEON_crown_maps

Generating tree crown maps for NEON sites

retriever-website

Website for the EcoData Retriever

retriever-site

http://www.data-retriever.org

portal-exploration

Exploration of the Portal data, using portalr

EvergladesSpeciesModel

A deepforest model for wading bird species prediction.

DeepTreeScape

Joint RGB and Deep Learning for individual tree detection

mete-energy

Research on the energetic predictions of METE

ESA_workshop_2022

lessons taught at the ESA workshop 2022 titled

NeonTreeEvaluation_analysis

This is the companion repo that presents analysis for methods tested on the NeonTreeEvaluation benchmark repo

NeonSpeciesBenchmark

A tree species classification benchmark for the National Ecological Observatory Network

NDVIning

sifting and comparing multiple NDVI sources and ensembles

forecasts

Archived forecasts for future analysis

portal-explorer

Shiny App for exploratory data analysis of the Portal Project

portal-experimental-macroeco

Code for reproducing the results from "An experimental test of the response of macroecological patterns to altered species interactions" by Sarah Supp et al. 2013 publishe in Ecology

bbc-data-rescue

Extracting data from Breeding Bird Census publications

portal-rodent-dispersal

Research on rodent dispersal patterns near Portal AZ

MATSS-startup

Macroecological Analysis of Time Series Structure

TreeDemo

Shiny app for tree detection in RGB imagery

wader

A collection of functions to retrieve and summarize the EvergladesWadingBird Data

AirborneBirds

The Airborne Birds benchmark

wiki

Weecology's Wiki - how to navigate life in the lab from choosing and pursuing a career path to using the printer