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Community Ecology Package
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
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.
Fast Cross-Validation for Multi-Penalty Ridge Regression
Multi-penalty linear, logistic and cox ridge regression, including estimation of the penalty parameters by efficient (repeated) cross-validation and marginal likelihood maximization. Multiple high-dimensional data types that require penalization are allowed, as well as unpenalized variables. Paired and preferential data types can be specified. See Van de Wiel et al. (2021),
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
Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server (< https://overpass-api.de/>) and processed with very fast 'C++' routines for return to 'R'.
R Code for Mark Analysis
An interface to the software package MARK that constructs input files for MARK and extracts the output. MARK was developed by Gary White and is freely available at < http://www.phidot.org/software/mark/downloads/> but is not open source.
"Hit and Run" and "Shake and Bake" for Sampling Uniformly from Convex Shapes
The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints. Tervonen, T., van Valkenhoef, G., Basturk, N., and Postmus, D. (2012)
Classification and Regression Tests
Provides wrapper functions for running classification and regression tests using different machine learning techniques, such as Random Forests and decision trees. The package provides standardized methods for preparing data to suit the algorithm's needs, training a model, making predictions, and evaluating results. Also, some functions are provided to run multiple instances of a test.
Highly Adaptive Lasso Conditional Density Estimation
An algorithm for flexible conditional density estimation based on
application of pooled hazard regression to an artificial repeated measures
dataset constructed by discretizing the support of the outcome variable. To
facilitate non/semi-parametric estimation of the conditional density, the
highly adaptive lasso, a nonparametric regression function shown to reliably
estimate a large class of functions at a fast convergence rate, is utilized.
The pooled hazards data augmentation formulation implemented was first
described by Díaz and van der Laan (2011)
Vectorised Tools for URL Handling and Parsing
A toolkit for all URL-handling needs, including encoding and decoding, parsing, parameter extraction and modification. All functions are designed to be both fast and entirely vectorised. It is intended to be useful for people dealing with web-related datasets, such as server-side logs, although may be useful for other situations involving large sets of URLs.