This package offers extensive tools for phylogenetic analysis. It focuses on phylogenetic comparative biology but also includes methods for visualizing, analyzing, manipulating, reading, writing, and inferring phylogenetic trees. Functions for comparative biology include ancestral state reconstruction, model fitting, and phylogeny and trait data simulation. A broad range of plotting methods includes mapping trait evolution on trees, projecting trees into phenotype space or geographic maps, and visualizing correlated speciation between trees. Additional functions allow for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. Examples include computing consensus trees, simulating trees and data under various models, and attaching species or clades to a tree either randomly or non-randomly. This package provides numerous tools for tree manipulations and analyses that are valuable for phylogenetic research.

This package provides a set of tools for inspecting and understanding R data structures inspired by str. It includes ast for visualizing abstract syntax trees, ref for showing shared references, cst for showing call stack trees, and obj_size for computing object sizes.

This package provides template functions to assist in building friendly R packages that praise their users.

This package provides a minimal, unifying API for scripts and packages to report progress updates from anywhere including when using parallel processing. The package is designed such that the developer can to focus on what progress should be reported on without having to worry about how to present it. The end user has full control of how, where, and when to render these progress updates.

This package offers methods for estimating statistical changes in time series. These are used for identifying nearby critical transitions.

The DBI package provides a database interface (DBI) definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

This package provides a collection of R functions to perform nonparametric analysis of covariance for regression curves or surfaces. Testing the equality or parallelism of nonparametric curves or surfaces is equivalent to analysis of variance (ANOVA) or analysis of covariance (ANCOVA) for one-sample functional data. Three different testing methods are available in the package, including one based on L-2 distance, one based on an ANOVA statistic, and one based on variance estimators.

The ggcorrplot package can be used to visualize easily a correlation matrix using ggplot2. It provides a solution for reordering the correlation matrix and displays the significance level on the plot. It also includes a function for computing a matrix of correlation p-values.

There are three main goals to the vctrs package:

1. To propose vec_size() and vec_type() as alternatives to length() and class(). These definitions are paired with a framework for type-coercion and size-recycling.

2. To define type- and size-stability as desirable function properties, use them to analyse existing base function, and to propose better alternatives. This work has been particularly motivated by thinking about the ideal properties of c(), ifelse(), and rbind().

3. To provide a new vctr base class that makes it easy to create new S3 vectors. vctrs provides methods for many base generics in terms of a few new vctrs generics, making implementation considerably simpler and more robust.

Join tables together based not on whether columns match exactly, but whether they are similar by some comparison. Implementations include string distance and regular expression matching.

This package is a collection of data analysis tools. It includes tools for regression outlier detection in a fitted linear model, stationary bootstrap using a truncated geometric distribution, a comprehensive test for weak stationarity, column means by group, weighted biplots, and a heuristic to obtain a better initial configuration in non-metric MDS.

This package provides an interface to the C implementation of the random number generator with multiple independent streams developed by L'Ecuyer et al (2002). The main purpose of this package is to enable the use of this random number generator in parallel R applications.

This package lets you replace the standard x-axis in ggplots with a combination matrix to visualize complex set overlaps. UpSet has introduced a new way to visualize the overlap of sets as an alternative to Venn diagrams. This package provides a simple way to produce such plots using ggplot2. In addition it can convert any categorical axis into a combination matrix axis.

This package provides a replacement for the extract function from the raster package that is suitable for extracting raster values using sf polygons.

The main aim of the pander R package is to provide a minimal and easy tool for rendering R objects into Pandoc's markdown. The package is also capable of exporting/converting complex Pandoc documents (reports) in various ways.

This package provides implementations of the SHA-3 cryptographic hash and SHAKE256 extendable-output functions (XOF).

Create, read and write GEXF (Graph Exchange XML Format) graph files (used in Gephi and others). It allows the user to easily build/read graph files including attributes, GEXF visual attributes (such as color, size, and position), network dynamics (for both edges and nodes) and edge weighting. Users can build/handle graphs element-by-element or massively through data-frames, visualize the graph on a web browser through gexf-js (a JavaScript library) and interact with the igraph package.

This package models with sparse and dense matrix matrices, using modular prediction and response module classes.

The biglm package lets you create a linear model object that uses only codep^2 memory for p variables. It can be updated with more data using update. This allows linear regression on data sets larger than memory.

This package provides a library for rolling windows operations. The package enables full control over the window length, window lag, and time indices. With a runner one can apply any R function on rolling windows. The package eases work with equally and unequally spaced time series.

This package provides support for all calendars as specified in the Climate and Forecast (CF) Metadata Conventions for climate and forecasting data. The CF Metadata Conventions is widely used for distributing files with climate observations or projections, including the Coupled Model Intercomparison Project (CMIP) data used by climate change scientists and the Intergovernmental Panel on Climate Change (IPCC). This package specifically allows the user to work with any of the CF-compliant calendars (many of which are not compliant with POSIXt). The CF time coordinate is formally defined in the CF Metadata Conventions document.

This package implements an opinionated framework for building a production- ready Shiny application. Golem contains a series of tools like dependency management, version management, easy installation and deployment or documentation management.

This package lets you create in just a few lines of R code a nice user interface to modify the data or the graphical parameters of one or multiple interactive charts. It is useful to quickly explore visually some data or for package developers to generate user interfaces easy to maintain.

This package is a r-ggplot2 extension that provides flipped components:

1. horizontal versions of r-ggplot2 stats and r-ggplot2 geoms;

2. vertical versions of r-ggplot2 positions.