This package is for genomic regions processing using command line tools such as BEDTools, BEDOPS and Tabix. These tools offer scalable and efficient utilities to perform genome arithmetic e.g indexing, formatting and merging. The bedr package's API enhances access to these tools as well as offers additional utilities for genomic regions processing.

This package provides an R API to the Open Source Geometry Engine (GEOS) library and a vector format with which to efficiently store GEOS geometries. High-performance functions to extract information from, calculate relationships between, and transform geometries are provided. Finally, facilities to import and export geometry vectors to other spatial formats are provided.

Content-preserving transformations transformations of PDF files such as split, combine, and compress. This package interfaces directly to the qpdf C++ API and does not require any command line utilities. Note that qpdf does not read actual content from PDF files: to extract text and data you need the pdftools package.

This package contains some tools for testing, analyzing time series data and fitting popular time series models such as ARIMA, Moving Average and Holt Winters, etc. Most functions also provide nice and clear outputs like SAS does, such as identify, estimate and forecast, which are the same statements in PROC ARIMA in SAS.

An all-encompassing R toolkit designed to streamline the process of calling various bioinformatics software and then performing data analysis and visualization in R. With blit', users can easily integrate a wide array of bioinformatics command line tools into their workflows, leveraging the power of R for sophisticated data manipulation and graphical representation.

Package binr (pronounced as "binner") provides algorithms for cutting numerical values exhibiting a potentially highly skewed distribution into evenly distributed groups (bins). This functionality can be applied for binning discrete values, such as counts, as well as for discretization of continuous values, for example, during generation of features used in machine learning algorithms.

Learning the structure of graphical models from datasets with thousands of variables. More information about the research papers detailing the theory behind Chordalysis is available at <http://www.francois-petitjean.com/Research> (KDD 2016, SDM 2015, ICDM 2014, ICDM 2013). The R package development site is <https://github.com/HerrmannM/Monash-ChoR>.

Interface for Rcpp users to dlib <http://dlib.net> which is a C++ toolkit containing machine learning algorithms and computer vision tools. It is used in a wide range of domains including robotics, embedded devices, mobile phones, and large high performance computing environments. This package allows R users to use dlib through Rcpp'.

Automatic differentiation is achieved by using dual numbers without providing hand-coded gradient functions. The output value of a mathematical function is returned with the values of its exact first derivative (or gradient). For more details see Baydin, Pearlmutter, Radul, and Siskind (2018) <https://jmlr.org/papers/volume18/17-468/17-468.pdf>.

Efficient methods for computing distance covariance and relevant statistics. See Székely et al.(2007) <doi:10.1214/009053607000000505>; Székely and Rizzo (2013) <doi:10.1016/j.jmva.2013.02.012>; Székely and Rizzo (2014) <doi:10.1214/14-AOS1255>; Huo and Székely (2016) <doi:10.1080/00401706.2015.1054435>.

Enhance R help system by fuzzy search and preview interface, pseudo-postfix operators, and more. The `?.` pseudo-postfix operator and the `?` prefix operator displays documents and contents (source or structure) of objects simultaneously to help understanding the objects. The `?p` pseudo-postfix operator displays package documents, and is shorter than help(package = foo).

This package provides a C++ API for routinely used numerical tools such as integration, root-finding, and optimization, where function arguments are given as lambdas. This facilitates Rcpp programming, enabling the development of R'-like code in C++ where functions can be defined on the fly and use variables in the surrounding environment.

GEE estimation of the parameters in mean structures with possible correlation between the outcomes. User-specified mean link and variance functions are allowed, along with observation weighting. The M in the name geeM is meant to emphasize the use of the Matrix package, which allows for an implementation based fully in R.

This package provides a light-weight, dependency-free, application programming interface (API) to access system-level Git <https://git-scm.com/downloads> commands from within R'. Contains wrappers and defaults for common data science workflows as well as Zsh <https://github.com/ohmyzsh/ohmyzsh> plugin aliases. A generalized API syntax is also available.

Efficient sampling from high-dimensional truncated Gaussian distributions, or multivariate truncated normal (MTN). Techniques include zigzag Hamiltonian Monte Carlo as in Akihiko Nishimura, Zhenyu Zhang and Marc A. Suchard (2024) <doi:10.1080/01621459.2024.2395587>, and harmonic Monte Carlo in Ari Pakman and Liam Paninski (2014) <doi:10.1080/10618600.2013.788448>.

Estimate the orientation of an inertial measurement unit (IMU) with a 3-axis accelerometer and a 3-axis gyroscope using a complementary filter. imuf takes an IMU's accelerometer and gyroscope readings, time duration, its initial orientation, and a gain factor as inputs, and returns an estimate of the IMU's final orientation.

Calculates the RMS intrinsic and parameter-effects curvatures of a nonlinear regression model. The curvatures are global measures of assessing whether a model/data set combination is close-to-linear or not. See Bates and Watts (1980) <doi:10.1002/9780470316757> and Ratkowsky and Reddy (2017) <doi:10.1093/aesa/saw098> for details.

Fitting multivariate data patterns with local principal curves, including tools for data compression (projection) and measuring goodness-of-fit; with some additional functions for mean shift clustering. See Einbeck, Tutz and Evers (2005) <doi:10.1007/s11222-005-4073-8> and Ameijeiras-Alonso and Einbeck (2023) <doi:10.1007/s11634-023-00575-1>.

Distance between multivariate generalised Gaussian distributions, as presented by N. Bouhlel and A. Dziri (2019) <doi:10.1109/LSP.2019.2915000>. Manipulation of multivariate generalised Gaussian distributions (methods presented by Gomez, Gomez-Villegas and Marin (1998) <doi:10.1080/03610929808832115> and Pascal, Bombrun, Tourneret and Berthoumieu (2013) <doi:10.1109/TSP.2013.2282909>).

It performs the followings Multivariate Process Capability Indices: Shahriari et al. (1995) Multivariate Capability Vector, Taam et al. (1993) Multivariate Capability Index (MCpm), Pan and Lee (2010) proposal (NMCpm) and the followings based on Principal Component Analysis (PCA):Wang and Chen (1998), Xekalaki and Perakis (2002) and Wang (2005). Two datasets are included.

Model mixed integer linear programs in an algebraic way directly in R. The model is solver-independent and thus offers the possibility to solve a model with different solvers. It currently only supports linear constraints and objective functions. See the ompr website <https://dirkschumacher.github.io/ompr/> for more information, documentation and examples.

This package performs partial principal component analysis of a large sparse matrix. The matrix may be stored as a list of matrices to be concatenated (implicitly) horizontally. Useful application includes cases where the number of total nonzero entries exceed the capacity of 32 bit integers (e.g., with large Single Nucleotide Polymorphism data).

Formulates a sparse distance weighted discrimination (SDWD) for high-dimensional classification and implements a very fast algorithm for computing its solution path with the L1, the elastic-net, and the adaptive elastic-net penalties. More details about the methodology SDWD is seen on Wang and Zou (2016) (<doi:10.1080/10618600.2015.1049700>).

This package provides functions to implement the stability controlled quasi-experiment (SCQE) approach to study the effects of newly adopted treatments that were not assigned at random. This package contains tools to help users avoid making statistical assumptions that rely on infeasible assumptions. Methods developed in Hazlett (2019) <doi:10.1002/sim.8717>.