This package provides sf data for Chinese provinces and cities, methods for plotting shape maps of Chinese provinces and cities, Convert Coordinates Between Different Systems, and a layer for leaflet with Gaode tiles. It is designed to facilitate geographical data visualization in China.

Create legends for maps and other graphics. Thematic maps need to be accompanied by legible legends to be fully comprehensible. This package offers a wide range of legends useful for cartography, some of which may also be useful for other types of graphics.

Model fitting and simulation for Gaussian and logistic inner product MultiNeSS models for multiplex networks. The package implements a convex fitting algorithm with fully adaptive parameter tuning, including options for edge cross-validation. For more details see MacDonald et al. (2020).

User-friendly, clear and simple statistics, primarily for publication in psychological science. The main functions are wrappers for other packages, but there are various additions as well. Every relevant step from data aggregation to reportable printed statistics is covered for basic experimental designs.

Calculation and presentation of decision-invariant bias adjustment thresholds and intervals for Network Meta-Analysis, as described by Phillippo et al. (2018) <doi:10.1111/rssa.12341>. These describe the smallest changes to the data that would result in a change of decision.

Implementation of the NetCutter algorithm described in Müller and Mancuso (2008) <doi:10.1371/journal.pone.0003178>. The package identifies co-occurring terms in a list of containers. For example, it may be used to detect genes that co-occur across genomes.

An R6 class to set up, run, monitor, collate, and debug large simulation studies comprising many small independent replications and treatment configurations. Parallel processing, reproducibility, fault- and error-tolerance, and ability to resume an interrupted or timed-out simulation study are built in.

Interface to Phylocom (<https://phylodiversity.net/phylocom/>), a library for analysis of phylogenetic community structure and character evolution. Includes low level methods for interacting with the three executables, as well as higher level interfaces for methods like aot', ecovolve', bladj', phylomatic', and more.

This package provides a collection of functions for constructing large pairwised comparisons and rating them using Elo rating system with supporting parallel processing. The method of random sample pairs is based on Reservoir Sampling proposed by JVitter (1985) <doi:10.1145/3147.3165>.

This package produces ANOVA tables in the format used by Judd, McClelland, and Ryan (2017, ISBN: 978-1138819832) in their introductory textbook, Data Analysis. This includes proportional reduction in error and formatting to improve ease the transition between the book and R.

Simplifies the process of generating samples from a variety of probability distributions, allowing users to quickly create data frames for demonstrations, troubleshooting, or teaching purposes. Data is available in multiple sizesâ small, medium, and large. For more information, refer to the package documentation.

Randomization of presence/absence species distribution raster data with or without including spatial structure for calculating standardized effect sizes and testing null hypothesis. The randomization algorithms are based on classical algorithms for matrices (Gotelli 2000, <doi:10.2307/177478>) implemented for raster data.

Description: Implementation of topological data analysis methods based on graph-theoretic approaches for discovering topological structures in data. The core algorithm constructs topological spaces from graphs following Nada et al. (2018) <doi:10.1002/mma.5096> "New types of topological structures via graphs".

Construct and analyse indexes in a pipeline tidy workflow. tidyindex contains modules for transforming variables, aggregating variables across time, reducing data dimension through weighting, and fitting distributions. A manuscript describing the methodology can be found at <https://github.com/huizezhang-sherry/paper-tidyindex>.

Streamline the process of accessing fundamental financial data from the United States Securities and Exchange Commission's ('SEC') Electronic Data Gathering, Analysis, and Retrieval system ('EDGAR') API <https://www.sec.gov/edgar/sec-api-documentation>, transforming it into a tidy, analysis-ready format.

Create United Nations High Commissioner for Refugees (UNHCR) branded documents, presentations, and reports using R Markdown templates. This package provides customized formats that align with UNHCR's official brand guidelines for creating professional PDF reports, Word documents, PowerPoint presentations, and HTML outputs.

The biodbNcbi library provides access to the NCBI databases CCDS, Gene, Pubchem Comp and Pubchem Subst, using biodb package framework. It allows to retrieve entries by their accession number. Web services can be accessed for searching the database by name or mass.

Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.

KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build PWM models of kinase-subtrates, statistically infer PWM:substrate matches, and integrate these data to infer kinase activity.

This package provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.

This package generates a Miami plot with centered chromosome labels. The output is a ggplot2 object. Users can specify which data they want plotted on top vs. bottom, whether to display significance line(s), what colors to give chromosomes, and what points to label.

This package provides three functions for dealing with dates: parse_iso_8601 recognizes and parses all valid ISO 8601 date and time formats, parse_date parses dates in unspecified formats, and format_iso_8601 formats a date in ISO 8601 format.

This package provides tools for capturing logic in a Shiny app and exposing it as code that can be run outside of Shiny (e.g., from an R console). It also provides tools for bundling both the code and results to the end user.