R packages

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.

sharx

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

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

mefa

Multivariate data handling in ecology and biogeography

Standardized computational environment for ecological data manipulation.

Other contributions

• adegenet: coords.monmonier CRAN GitHub
• plotrix: ladderplot, ruginv, draw.ellipse CRAN GitHub
• epiR: epi.occc CRAN GitHub

What is new in the intrval R package?

An update (v 0.1-1) of the intrval package was recently published on CRAN. The package simplifies interval related logical operations (read more about the motivation in this post). So what is new in this version? Some of the inconsistencies in the 1st CRAN release have been cleaned up, and I have been pushed hard (see GitHub issue to implement all the 16 interval-to-interval operators. These operators define the open/closed nature of the lower/upper limits of the intervals on the left and right hand side of the o in the middle as in c(a1, b1) %[]o[]% c(a2, b2).