R packages

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EDMAinR

Euclidean distance matrix analysis in R

A coordinate-free approach for comparing biological shapes using landmark data.

moosecounter

Adaptive moose surveys

The R package and Shiny app implements count models to aid in estimating Moose populations and composition.

clickrup

Interacting with the ClickUp v2 API from R

ClickUp is a cloud-based collaboration and project management tool. The clickrup R package wraps the ClickUp API v2.

WildLift

A Tool to Guide Decisions for Wildlife Conservation

WildLift can be used to quantitatively compare the costs and demographic benefits of recovery actions for an iconic threatened species.

tryr

Client/Server Error Handling for HTTP API Frameworks

Differentiate client errors (4xx) from server errors (5xx) for the 'plumber' and 'RestRserve' HTTP API frameworks. The package also includes a built-in logging mechanism to standard output (STDOUT) or standard error (STDERR) depending on the log level.

deps

Dependency Management with roxygen-style Comments

Manage your source code dependencies by decorating your existing R code with special, roxygen-style comments.

rconfig

Manage R configuration at the command line

Manage R configuration using files (JSON, YAML, separated text) JSON strings and command line arguments. Command line arguments can be used to override configuration. Period-separated command line flags are parsed as hierarchical lists.

bSims

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.

opticut

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.

intrval

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.

pbapply

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.

vegan

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.

ResourceSelection

Resource selection (probability) functions for use-availability data

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

mefa4

Multivariate data handling with S4 classes and sparse matrices

Multivariate data handling using sparse matrices for big data problems.

detect

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

dclone

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

dcmle

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

PVAClone

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.