This package provides a WebSocket client interface for R. WebSocket is a protocol for low-overhead real-time communication: <https://en.wikipedia.org/wiki/WebSocket>.

Application to estimate statistical values using properties provided by a group of individuals to describe concepts using shiny'. It estimates the underlying distribution to generate new descriptive words Canessa et al. (2023) <doi:10.3758/s13428-022-01811-w>, applies a new clustering model, and uses simulations to estimate the probability that two persons describe the same words based on their descriptions Canessa et al. (2022) <doi:10.3758/s13428-022-02030-z>.

This package provides a series of tools to compute and plot quantities related to classical and robust wavelet variance for time series and regular lattices. More details can be found, for example, in Serroukh, A., Walden, A.T., & Percival, D.B. (2000) <doi:10.2307/2669537> and Guerrier, S. & Molinari, R. (2016) <doi:10.48550/arXiv.1607.05858>.

Calculates the WEGE (Weighted Endemism including Global Endangerment index) index for a particular area. Additionally it also calculates rasters of KBA's (Key Biodiversity Area) criteria (A1a, A1b, A1e, and B1), Weighted endemism (WE), the EDGE (Evolutionarily Distinct and Globally Endangered) score, Evolutionary Distinctiveness (ED) and Extinction risk (ER). Farooq, H., Azevedo, J., Belluardo F., Nanvonamuquitxo, C., Bennett, D., Moat, J., Soares, A., Faurby, S. & Antonelli, A. (2020) <doi:10.1101/2020.01.17.910299>.

This package performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

This package provides a prediction model is calibrated if, roughly, for any percentage x we can expect that x subjects out of 100 experience the event among all subjects that have a predicted risk of x%. A calibration plot provides a simple, yet useful, way of assessing the calibration assumption. The Wally plot consists of a sequence of usual calibration plots. Among the plots contained within the sequence, one is the actual calibration plot which has been obtained from the data and the others are obtained from similar simulated data under the calibration assumption. It provides the investigator with a direct visual understanding of the shape and sampling variability that are common under the calibration assumption. The original calibration plot from the data is included randomly among the simulated calibration plots, similarly to a police lineup. If the original calibration plot is not easily identified then the calibration assumption is not contradicted by the data. The method handles the common situations in which the data contain censored observations and occurrences of competing events.

Generate continuous maps of genetic diversity using moving windows with options for rarefaction, interpolation, and masking as described in Bishop et al. (2023) <doi:10.1111/2041-210X.14090>.

This package provides a collection of utility functions, themes, and templates to support personal data analysis workflows. Includes functions for formatting numeric values as text, custom themes and color scales for ggplot2', and automatic formatting for tables created with gt'.

This package provides a toolkit to set up an R data package in a consistent structure. Automates tasks like tidy data export, data dictionary documentation, README and website creation, and citation management.

Converts pathways from WikiPathways GPML format or KEGG KGML format into igraph objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).

This package provides the functions to perform a Welch's one-way Anova with fixed effects based on summary statistics (sample size, means, standard deviation) and the Games-Howell post hoc test for multiple comparisons and provides the effect size estimator adjusted omega squared. In addition sample size estimation can be computed based on Levy's method, and a Monte Carlo simulation is included to bootstrap residual normality and homoscedasticity Welch, B. L. (1951) <doi:10.1093/biomet/38.3-4.330> Kirk, R. E. (1996) <doi:10.1177/0013164496056005002> Carroll, R. M., & Nordholm, L. A. (1975) <doi:10.1177/001316447503500304> Albers, C., & Lakens, D. (2018) <doi:10.1016/j.jesp.2017.09.004> Games, P. A., & Howell, J. F. (1976) <doi:10.2307/1164979> Levy, K. J. (1978a) <doi:10.1080/00949657808810246> Show-Li, J., & Gwowen, S. (2014) <doi:10.1111/bmsp.12006>.

Easily override the default visual choices in ggplot2 to make your time series plots look more like the Wall Street Journal. Specific theme design choices include omitting x-axis grid lines and displaying sparse light grey y-axis grid lines. Additionally, this allows to label the y-axis scales with your units only displayed on the top-most number, while also removing the bottom most number (unless specifically overridden). The goal is visual simplicity, because who has time to waste looking at a cluttered graph?

This package provides functions for determining the effect of data weights on the variance of survey data: users will load a data set which has a weights column, and the package will calculate the design effect (DEFF), weighting loss, root design effect (DEFT), effective sample size (ESS), and/or weighted margin of error.

Entropy weighted k-means (ewkm) by Liping Jing, Michael K. Ng and Joshua Zhexue Huang (2007) <doi:10.1109/TKDE.2007.1048> is a weighted subspace clustering algorithm that is well suited to very high dimensional data. Weights are calculated as the importance of a variable with regard to cluster membership. The two-level variable weighting clustering algorithm tw-k-means (twkm) by Xiaojun Chen, Xiaofei Xu, Joshua Zhexue Huang and Yunming Ye (2013) <doi:10.1109/TKDE.2011.262> introduces two types of weights, the weights on individual variables and the weights on variable groups, and they are calculated during the clustering process. The feature group weighted k-means (fgkm) by Xiaojun Chen, Yunminng Ye, Xiaofei Xu and Joshua Zhexue Huang (2012) <doi:10.1016/j.patcog.2011.06.004> extends this concept by grouping features and weighting the group in addition to weighting individual features.

An adaptation for estuaries (tidal waters) of weighted regression on time, discharge, and season to evaluate trends in water quality time series. Please see Beck and Hagy (2015) <doi:10.1007/s10666-015-9452-8> for details.

This package provides a set of utility function to prevent the spread of utility scripts in W4M (Workflow4Metabolomics) tools, and centralize them in a single package. To note, some are meant to be replaced by the use of dedicated packages in the future, like the parse_args() function: it is here only to prepare the ground for more global changes in W4M scripts and tools. This package is used by part of the W4M Galaxy modules, some of them being available on the community-maintained GitHub repository for Metabolomics Galaxy tools <https://github.com/workflow4metabolomics/tools-metabolomics>. See Delporte et al (2025) <doi:10.1002/cpz1.70095> for more details.

Search and download data from the World Bank Data API.

Computes the Weighted Topological Overlap with positive and negative signs (wTO) networks given a data frame containing the mRNA count/ expression/ abundance per sample, and a vector containing the interested nodes of interaction (a subset of the elements of the full data frame). It also computes the cut-off threshold or p-value based on the individuals bootstrap or the values reshuffle per individual. It also allows the construction of a consensus network, based on multiple wTO networks. The package includes a visualization tool for the networks. More about the methodology can be found at <doi:10.1186/s12859-018-2351-7>.

Converts weekly data to monthly data. Users can use three types of week formats: ISO week, epidemiology week (epi week) and calendar date.

Lossless webp images are 26% smaller in size compared to PNG. Lossy webp images are 25-34% smaller in size compared to JPEG. This package reads and writes webp images into a 3 (rgb) or 4 (rgba) channel bitmap array using conventions from the jpeg and png packages.

This package provides tools for simulating the biophysical effects of vessel-strikes on whales. The aim is to support the evaluation of marine policies limiting ship speeds through regions in which whales reside. This is important because ship strikes are a major source of lethality for several whale species, including the critically endangered North Atlantic right whale. In this analysis, whales are modelled with a four-layer system comprising skin, blubber, sub-layer (muscle or organ) and bone. Reasonable values for the material properties of these layers, along with other factors such as whale surface area and mass, are provided for a variety of whale species. Similarly, key values are provided for several ship types. The collision is modelled according to Newtonian dynamics, with stresses and strains within the whale layers being simulated over time. The simulation results are analyzed in the context of whale-strike data, to develop a Lethality Index for the whale in the modelled collision. For the underlying science, see Kelley and other "Assessing the Lethality of Ship Strikes on Whales Using Simple Biophysical Models." (2021) <doi:10.1111/mms.12745>. For more on the R code, see Kelley "`whalestrike`: An R package for simulating ship strikes on whales" (2024) <doi:10.21105/joss.06473>.

Color palettes taken from the landscapes and cities of Washington state. Colors were extracted from a set of photographs, and then combined to form a set of continuous and discrete palettes. Continuous palettes were designed to be perceptually uniform, while discrete palettes were chosen to maximize contrast at several different levels of overall brightness and saturation. Each palette has been evaluated to ensure colors are distinguishable by colorblind people.

Allows to turn standard R code into offensive programming code. Provides code instrumentation to ease this change and tools to assist and accelerate code production and tuning while using offensive programming code technics. Should improve code robustness and quality. Function calls can be easily verified on-demand or in batch mode to assess parameter types and length conformities. Should improve coders productivity as offensive programming reduces the code size due to reduced number of controls all along the call chain. Should speed up processing as many checks will be reduced to one single check.

Easily plot heat maps of the world, based on continuous or categorical data. Country labels can also be added to the map.