Dockerize R Markdown Documents (liftr)
Dockerize R Markdown documents with support for Rabix (Portable Bioinformatics Pipelines).
Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests (spatstat)
Comprehensive open-source toolbox for analysing spatial data, mainly Spatial Point Patterns, including multitype/marked points and spatial covariates, in any two-dimensional spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, and point patterns on a linear network. Contains about 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference. Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks. Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Diggle-Cressie-Loosmore-Ford, Dao-Genton) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov) are also supported. Parametric models can be fitted to point pattern data using the functions ppm, kppm, slrm similar to glm. Types of models include Poisson, Gibbs, Cox and cluster point processes. Models may involve dependence on covariates, interpoint interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods. Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise, AIC). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
spatstat
shiny_spatstat
Open Location Code Handling in R (olctools)
Open Location Codes’ (http://openlocationcode.com) are a Google-created standard for identifying geographic locations. olctools provides utilities for validating, encoding and decoding entries that follow this standard.
Streamlined Plot Theme and Plot Annotations for ‘ggplot2’ (cowplot)
Some helpful extensions and modifications to the ‘ggplot2’ library. In particular, this package makes it easy to combine multiple ‘ggplot2’ plots into one and label them with letters, e.g. A, B, C, etc., as is often required for scientific publications. The package also provides a streamlined and clean theme that is used in the Wilke lab, hence the package name, which stands for Claus O. Wilke’s plot library.
Classification, Regression and Feature Evaluation (CORElearn)
This is a suite of machine learning algorithms written in C++ with R interface. It contains several machine learning model learning techniques in classification and regression, for example classification and regression trees with optional constructive induction and models in the leaves, random forests, kNN, naive Bayes, and locally weighted regression. It is especially strong in feature evaluation where it contains several variants of Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini, information gain, MDL, DKM. These methods can be used for example to discretize numeric attributes. Its additional strength is OrdEval algorithm and its visualization used for evaluation of data sets with ordinal features and class enabling analysis according to the Kano model. Several algorithms support parallel multithreaded execution via OpenMP. The top-level documentation is reachable through ?CORElearn.