R packages

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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.


Likelihood based optimal partitioning for indicator species analysis

Finding the best binary partition for each species based on model selection, possibly controlling for modifying/confounding variables.


Relational operators for intervals

Evaluating if values of vectors are within different open/closed intervals ('x %[]% c(a, b)'), or if two closed intervals overlap ('c(a1, b1) %[o]% c(a2, b2)'). Operators for negation and directional relations also implemented.


Adding progress bar to '*apply' functions

A lightweight package that adds progress bar to vectorized R functions ('*apply'). The implementation can easily be added to functions where showing the progress is useful (e.g. bootstrap). The type and style of the progress bar (with percentages or remaining time) can be set through options.


Community ecology package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists. A collaborative project with Jari Oksanen as lead developer. Contributing to the package with diversity analysis and community nullmodels.


Resource selection (probability) functions for use-availability data

Resource Selection (Probability) Functions for use-availability wildlife data.


Multivariate data handling with S4 classes and sparse matrices

Multivariate data handling using sparse matrices for big data problems.


Analyzing wildlife data with detection error

Analyzing wildlife data with detection error. Zero inflated models for single visit data when the probability of detection is less than one. Provides hands-on formula interface with inferences based on numerical optimization and data cloning


Data cloning and MCMC tools for maximum likelihood methods

Low level functions for implementing maximum likelihood estimating procedures for complex models using data cloning and Bayesian Markov chain Monte Carlo methods with support for JAGS, WinBUGS, OpenBUGS (and STAN). It contains features for parallel computing. Read mode on datacloning.org


Hierarchical models made easy with data cloning

Hierarchical models made easy with data cloning: S4 classes around infrastructure provided by the dclone package to make package development with data cloning for hierarchical models easy as a breeze. Read mode on datacloning.org


Population viability analysis with data cloning

Likelihood based population viability analysis in the presence of observation error and missing data. The package can be used to fit, compare, predict, and forecast various growth model types using data cloning.


Models and data sets for the study of species-area relationships

Data sets and models for the sudy of species-area relationships.


Multivariate data handling in ecology and biogeography

Standardized computational environment for ecological data manipulation.

Other contributions

Statistical computing meets biodiversity conservation and natural resource management

How many birds are out there?

In a recent paper entitled “Lessons learned from comparing spatially explicit models and the Partners in Flight approach to estimate population sizes of boreal birds in Alberta, Canada” we developed improved, spatially explicit models for 81 land bird species in northern Alberta, Canada. We then compared these estimates of bird abundance to a commonly-used but non-spatially explicit estimate by Partners in Flight (PIF v 3.0) that’s based on the North American Breeding Bird Survey (BBS) data set. The publication is a result of years of collaboration between the ABMI, Boreal Avian Modelling (BAM) project, Canadian Wildlife Service (Environment and Climate Change Canada), and United States Geological Survey.

ABMI (7) ARU (1) Alberta (1) BAM (1) C (1) CRAN (1) Hungary (2) JOSM (2) PVA (2) PVAClone (1) QPAD (3) R (20) R packages (1) abundance (1) bioacoustics (1) biodiversity (1) birds (2) course (2) data (1) data cloning (4) dclone (3) density (1) dependencies (1) detect (3) detectability (3) footprint (3) forecasting (1) functions (3) intrval (4) lhreg (1) mefa4 (1) monitoring (2) pbapply (5) phylogeny (1) plyr (1) poster (2) processing time (2) progress bar (4) publications (2) report (1) sector effects (1) shiny (1) single visit (1) site (1) slider (1) slides (2) special (3) species (1) trend (1) tutorials (2) video (4)