Estimates the intraclass correlation coefficient for trajectory data using a matrix of distances between trajectories. The distances implemented are the extended Hausdorff distances (Min et al. 2007) <doi:10.1080/13658810601073315> and the discrete Fréchet distance (Magdy et al. 2015) <doi:10.1109/IntelCIS.2015.7397286>.

Geostatistical interpolation has traditionally been done by manually fitting a variogram and then interpolating. Here, we introduce classes and methods that can do this interpolation automatically. Pebesma et al (2010) gives an overview of the methods behind and possible usage <doi:10.1016/j.cageo.2010.03.019>.

It allows to cluster communication networks using the Stochastic Topic Block Model <doi:10.1007/s11222-016-9713-7> by posting jobs through the API of the linkage.fr server, which implements the clustering method. The package also allows to visualize the clustering results returned by the server.

PDF is a standard file format for laying out text and images in documents. At its core, these documents are sequences of objects defined in plain text. This package allows for the creation of PDF documents at a very low level without any library or graphics device dependencies.

Run flexible mediation analyses using natural effect models as described in Lange, Vansteelandt and Bekaert (2012) <DOI:10.1093/aje/kwr525>, Vansteelandt, Bekaert and Lange (2012) <DOI:10.1515/2161-962X.1014> and Loeys, Moerkerke, De Smet, Buysse, Steen and Vansteelandt (2013) <DOI:10.1080/00273171.2013.832132>.

Calculate the precision in mean differences (raw or Cohen's D) and correlation coefficients for different sample sizes. Uses permutations of the collected functional magnetic resonance imaging (fMRI) region of interest data. Method described in Klapwijk, Jongerling, Hoijtink and Crone (2024) <doi:10.31234/osf.io/cz32t>.

This package provides methods to detect genetic markers involved in biological adaptation. pcadapt provides statistical tools for outlier detection based on Principal Component Analysis. Implements the method described in (Luu, 2016) <DOI:10.1111/1755-0998.12592> and later revised in (Privé, 2020) <DOI:10.1093/molbev/msaa053>.

Based on (but not identical to) the no-longer-maintained package phyext', provides enhancements to phylobase classes, specifically for use by package SigTree'; provides classes and methods which help users manipulate branch-annotated trees (as in SigTree'); also provides support for a few other extra features.

This package provides tools for downloading, reading and analyzing the National Survey of Health - PNS, a household survey from Brazilian Institute of Geography and Statistics - IBGE. The data must be downloaded from the official website <https://www.ibge.gov.br/>. Further analysis must be made using package survey'.

Generates random values from a univariate and multivariate continuous distribution by using kernel density estimation based on a sample. Duong (2017) <doi:10.18637/jss.v021.i07>, Christian P. Robert and George Casella (2010 ISBN:978-1-4419-1575-7) <doi:10.1007/978-1-4419-1576-4>.

Implementation of hybrid STL decomposition based time delay neural network model for univariate time series forecasting. For method details see Jha G K, Sinha, K (2014). <doi:10.1007/s00521-012-1264-z>, Xiong T, Li C, Bao Y (2018). <doi:10.1016/j.neucom.2017.11.053>.

Programmatic interface to the SNOTEL snow data (<https://www.nrcs.usda.gov/programs-initiatives/sswsf-snow-survey-and-water-supply-forecasting-program>). Provides easy downloads of snow data into your R work space or a local directory. Additional post-processing routines to extract snow season indexes are provided.

It can be useful to temporarily hide some text or other HTML elements in Shiny applications. Building on Spoiler-Alert.js', it is possible to select the elements to hide at startup, to partially reveal them by hovering them, and to completely show them when clicking on them.

Provide regularized maximum covariance analysis incorporating smoothness, sparseness and orthogonality of couple patterns by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D (Wang and Huang, 2018 <doi:10.1002/env.2481>).

Create rich and fully interactive timeline visualizations. Timelines can be included in Shiny apps or R markdown documents. timevis includes an extensive API to manipulate a timeline after creation, and supports getting data out of the visualization into R. Based on the vis.js Timeline JavaScript library.

Facilitate the movement between data frames to xts'. Particularly useful when moving from tidyverse to the widely used xts package, which is the input format of choice to various other packages. It also allows the user to use a spread_by argument for a character column xts conversion.

This package provides functions that compute predictions from Generalised Additive Models (GAMs) fitted with mgcv and return them as a tibble. These can be plotted with a generic plot()-method that uses ggplot2 or plotted as any other data frame. The main function is predict_gam().

Feasible Multivariate Generalized Autoregressive Conditional Heteroscedasticity (GARCH) models including Dynamic Conditional Correlation (DCC), Copula GARCH and Generalized Orthogonal GARCH with Generalized Hyperbolic distribution. A review of some of these models can be found in Boudt, Galanos, Payseur and Zivot (2019) <doi:10.1016/bs.host.2019.01.001>.

This package provides methods and tools for implementing regularized multivariate functional principal component analysis ('ReMFPCA') for multivariate functional data whose variables might be observed over different dimensional domains. ReMFPCA is an object-oriented interface leveraging the extensibility and scalability of R6. It employs a parameter vector to control the smoothness of each functional variable. By incorporating smoothness constraints as penalty terms within a regularized optimization framework, ReMFPCA generates smooth multivariate functional principal components, offering a concise and interpretable representation of the data. For detailed information on the methods and techniques used in ReMFPCA', please refer to Haghbin et al. (2023) <doi:10.48550/arXiv.2306.13980>.

Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at https://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.

This package provides a platform-independent API to access the operating system's credential store. It currently supports Keychain on macOS, Credential Store on Windows, the Secret Service API on GNU/Linux, and a simple, platform independent store implemented with environment variables. Additional storage back-ends can be added easily.

This package implements an efficient O(n) algorithm based on bucket-sorting for fast computation of standard clustering comparison measures. Available measures include adjusted Rand index (ARI), normalized information distance (NID), normalized mutual information (NMI), adjusted mutual information (AMI), normalized variation information (NVI) and entropy.

Libretro is a simple but powerful development interface that allows for the easy creation of emulators, games and multimedia applications that can plug straight into any libretro-compatible frontend. RetroArch is the official reference frontend for the libretro API, currently used by most as a modular multi-system game/emulator system.

This package provides functionality for processing and statistical analysis of multiplexed assays of variant effect (MAVE) and similar data. The package contains functions covering the full workflow from raw FASTQ files to publication-ready visualizations. A broad range of library designs can be processed with a single, unified interface.