This package provides tools to more conveniently perform tasks associated with add-on packages. pacman conveniently wraps library and package related functions and names them in an intuitive and consistent fashion. It seeks to combine functionality from lower level functions which can speed up workflow.

This package provides maximally selected rank statistics with several p-value approximations.

This package provides a simple yet powerful logging utility. Based loosely on log4j, futile.logger takes advantage of R idioms to make logging a convenient and easy to use replacement for cat and print statements.

This package provides a simple set of wrapper functions for data.table::fread() that allows subsetting or filtering rows and selecting columns of table-formatted files too large for the available RAM.

This package provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. It is designed to work with FlowSOM and flow-cytometry use-cases.

This tool provides methods for aggregating ranked lists, especially lists of genes. It implements the Robust Rank Aggregation and other simple algorithms for the task. RRA method uses a probabilistic model for aggregation that is robust to noise and also facilitates the calculation of significance probabilities for all the elements in the final ranking.

This package provides string and binary representations of objects for several formats and MIME types.

This package implements an approximate string matching version of R's native match function. It can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.

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 converts between R and Simple Feature sf objects, without depending on the Simple Feature library. Conversion functions are available at both the R level, and through Rcpp.

Imports plain-text ASC data files from EyeLink eye trackers into (relatively) tidy data frames for analysis and visualization.

A workflow is a combination of a model and preprocessors (e.g, a formula, recipe, etc.). In order to try different combinations of these, an object can be created that contains many workflows. There are functions to create workflows en masse as well as training them and visualizing the results.

The r-nleqslv package solves a system of nonlinear equations using a Broyden or a Newton method with a choice of global strategies such as line search and trust region. There are options for using a numerical or user supplied Jacobian, for specifying a banded numerical Jacobian and for allowing a singular or ill-conditioned Jacobian.

This package provides a set of restricted permutation designs for freely exchangeable, line transects (time series), spatial grid designs and permutation of blocks (groups of samples). permute also allows split-plot designs, in which the whole-plots or split-plots or both can be freely exchangeable.

This package provides a Davidian curve defines a seminonparametric density, whose shape and flexibility can be tuned by easy to estimate parameters. Since a special case of a Davidian curve is the standard normal density, Davidian curves can be used for relaxing normality assumption in statistical applications (Zhang & Davidian, 2001) <doi:10.1111/j.0006-341X.2001.00795.x>. This package provides the density function, the gradient of the loglikelihood and a random generator for Davidian curves.

In order to smoothly animate the transformation of polygons and paths, many aspects needs to be taken into account, such as differing number of control points, changing center of rotation, etc. The transformr package provides an extensive framework for manipulating the shapes of polygons and paths and can be seen as the spatial brother to the tweenr package.

This package provides an implementation of scale functions for setting axis breaks of a ggplot.

This package provides utilities to work with indices of effect size and standardized parameters for a wide variety of models, allowing computation and conversion of indices such as Cohen's d, r, odds, etc.

Sensitivity (or recall or true positive rate), false positive rate, specificity, precision (or positive predictive value), negative predictive value, misclassification rate, accuracy, F-score---these are popular metrics for assessing performance of binary classifiers for certain thresholds. These metrics are calculated at certain threshold values. Receiver operating characteristic (ROC) curve is a common tool for assessing overall diagnostic ability of the binary classifier. Unlike depending on a certain threshold, area under ROC curve (also known as AUC), is a summary statistic about how well a binary classifier performs overall for the classification task. The ROCit package provides flexibility to easily evaluate threshold-bound metrics.

This package offers classes and functions to contact web servers while enforcing scheduling rules required by the sites. The URL class makes it easy to construct a URL by providing parameters as a vector. The Request class allows to describe Simple Object Access Protocol (SOAP) or standard requests: URL, method (POST or GET), header, body. The Scheduler class controls the request frequency for each server address by means of rules (Rule class). The RequestResult class permits to get the request status to handle error cases and the content.

This package provides some functions for sample classification in microarrays.

This package provides a collection of functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.

Tools for performing model selection and model averaging. Automated model selection through subsetting the maximum model, with optional constraints for model inclusion. Model parameter and prediction averaging based on model weights derived from information criteria (AICc and alike) or custom model weighting schemes.

This package provides a collection of perceptually uniform color maps made by Peter Kovesi (2015) "Good Colour Maps: How to Design Them" <arXiv:1509.03700> at the Centre for Exploration Targeting (CET).