Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

The R Package Ada for Stochastic Boosting

Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set. The package ada provides a straightforward, well-documented, and broad boosting routine for classification, ideally suited for small to moderate-sized data sets.

Efficient Plotting of Large-Sized Data

A tool to plot data with a large sample size using 'shiny' and 'plotly'. Relatively small samples are obtained from the original data using a specific algorithm. The samples are updated according to a user-defined x range. Jonas Van Der Donckt, Jeroen Van Der Donckt, Emiel Deprost (2022) < https://github.com/predict-idlab/plotly-resampler>.

Easily Work with 'Bootstrap' Icons

Easily use 'Bootstrap' icons inside 'Shiny' apps and 'R Markdown' documents. More generally, icons can be inserted in any 'htmltools' document through inline 'SVG'.

Functions for Optimal Matching

Distance based bipartite matching using minimum cost flow, oriented to matching of treatment and control groups in observational studies ('Hansen' and 'Klopfer' 2006 ). Routines are provided to generate distances from generalised linear models (propensity score matching), formulas giving variables on which to limit matched distances, stratified or exact matching directives, or calipers, alone or in combination.

Network Meta-Analysis Using Bayesian Methods

Network meta-analyses (mixed treatment comparisons) in the Bayesian framework using JAGS. Includes methods to assess heterogeneity and inconsistency, and a number of standard visualizations. van Valkenhoef et al. (2012) ; van Valkenhoef et al. (2015) .

Analyzing Dendrometer Data

Various functions to import, verify, process and plot high-resolution dendrometer data using daily and stem-cycle approaches as described in Deslauriers et al, 2007 . For more details about the package please see: Van der Maaten et al. 2016 .

Empirical Transition Matrix

The etm (empirical transition matrix) package permits to estimate the matrix of transition probabilities for any time-inhomogeneous multi-state model with finite state space using the Aalen-Johansen estimator. Functions for data preparation and for displaying are also included (Allignol et al., 2011 ). Functionals of the Aalen-Johansen estimator, e.g., excess length-of-stay in an intermediate state, can also be computed (Allignol et al. 2011 ).

Data Table Back-End for 'dplyr'

Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.

Bayesian Latent Variable Analysis

Fit a variety of Bayesian latent variable models, including confirmatory factor analysis, structural equation models, and latent growth curve models. References: Merkle & Rosseel (2018) ; Merkle et al. (2021) .