This package provides a simple method to display and characterise the multidimensional ecological niche of a species. The method also estimates the optimums and amplitudes along each niche dimension. Give also an estimation of the degree of niche overlapping between species. See Kleparski and Beaugrand (2022) <doi:10.1002/ece3.8830> for further details.

The main purpose of waterquality is to quickly and easily convert satellite-based reflectance imagery into one or many well-known water quality algorithms designed for the detection of harmful algal blooms or the following pigment proxies: chlorophyll-a, blue-green algae (phycocyanin), and turbidity. Johansen et al. (2019) <doi:10.21079/11681/35053>.

This package implements a method to rapidly assess cell type identity using both functional and random gene sets and it allows users to quantify cell type replicability across datasets using neighbor voting. MetaNeighbor works on the basis that cells of the same type should have more similar gene expression profiles than cells of different types.

This package is designed to improve and simplify the analysis of scRNA-seq data. It uses the Seurat object for this purpose. It provides an array of enhanced visualization tools, an integrated functional and pathway analysis pipeline, seamless integration with popular Python tools, and a suite of utility functions to aid in data manipulation and presentation.

Uses support vector machines to identify a perfectly separating hyperplane (linear or curvilinear) between two entities in high-dimensional space. If this plane exists, the entities do not overlap. Applications include overlap detection in morphological, resource or environmental dimensions. More details can be found in: Brown et al. (2020) <doi:10.1111/2041-210X.13363> .

An RStudio Addin wrapper for the mergen package. This package employs artificial intelligence to convert data analysis questions into executable code, explanations, and algorithms. This package makes it easier to use Large Language Models in your development environment by providing a chat-like interface, while also allowing you to inspect and execute the returned code.

This package provides a set of basic and extensible data structures and functions for multivariate analysis, including dimensionality reduction techniques, projection methods, and preprocessing functions. The aim of this package is to offer a flexible and user-friendly framework for multivariate analysis that can be easily extended for custom requirements and specific data analysis tasks.

Conduct inference on the sample average treatment effect for a matched (observational) dataset with a continuous treatment. Equipped with calipered non-bipartite matching, bias-corrected sample average treatment effect estimation, and covariate-adjusted variance estimation. Matching, estimation, and inference methods are described in Frazier, Heng and Zhou (2024) <doi:10.48550/arXiv.2409.11701>.

The PROMETHEE method is a multi-criteria decision-making method addressing with outranking problems. The method establishes a preference structure between the alternatives, having a preference function for each criterion. IN this context, three variants of the method is carried out: PROMETHEE I (Partial Outranking), PROMETHEE II (Total Outranking), and PROMETHEE III (Outranking by Intervals).

This package provides confidence intervals in least-squares regressions when the variable of interest has a shift-share structure, and in instrumental variables regressions when the instrument has a shift-share structure. The confidence intervals implement the AKM and AKM0 methods developed in Adão, Kolesár, and Morales (2019) <doi:10.1093/qje/qjz025>.

This package performs simulations of binary spatial raster data using the Ising model (Ising (1925) <doi:10.1007/BF02980577>; Onsager (1944) <doi:10.1103/PhysRev.65.117>). It allows to set a few parameters that represent internal and external pressures, and the number of simulations (Stepinski and Nowosad (2023) <doi:10.1098/rsos.231005>).

This package provides a curated set of colors that are called using a standardized syntax: saturation + hue + lightness. For example, "brightblue4" and "mutedred2". Functions exists to return individual colors by name or to build palettes across or within hues. Most functions allow you to visualize the palettes in addition to returning the desired hex codes.

This package provides tools for constructing and analyzing two-phase experimental designs under correlated error structures. Version 1.1.1 includes improved efficiency factor classification with tolerance control, updated plot visualizations, and improved clarity of the results. The conceptual framework and the term two-phase were introduced by McIntyre (1955) <doi:10.2307/3001770>).

Handle genomic data within data frames just as you would with GRanges'. This packages provides method to deal with genomic intervals the "tidy-way" which makes it simpler to integrate in the the general data munging process. The API is inspired by the popular bedtools and the genome_join() method from the fuzzyjoin package.

Archive and manage times series data from official statistics. The timeseriesdb package was designed to manage a large catalog of time series from official statistics which are typically published on a monthly, quarterly or yearly basis. Thus timeseriesdb is optimized to handle updates caused by data revision as well as elaborate, multi-lingual meta information.

This package provides a client package that makes the KorAP web service API accessible from R. The corpus analysis platform KorAP has been developed as a scientific tool to make potentially large, stratified and multiply annotated corpora, such as the German Reference Corpus DeReKo or the Corpus of the Contemporary Romanian Language CoRoLa', accessible for linguists to let them verify hypotheses and to find interesting patterns in real language use. The RKorAPClient package provides access to KorAP and the corpora behind it for user-created R code, as a programmatic alternative to the KorAP web user-interface. You can learn more about KorAP and use it directly on DeReKo at <https://korap.ids-mannheim.de/>.

Record your test suite's HTTP interactions and replay them during future test runs for fast, deterministic, accurate tests. This is an older version of VCR that is free software under the Expat license. The project later switched to the Hippocratic license, which is non-free. Do not use it in new free software projects.

mkmf-lite is a light version of Ruby's mkmf.rb designed for use as a library. It does not create packages, builds, or log files of any kind. Instead, it provides mixin methods that you can use in FFI or tests to check for the presence of header files, constants, and so on.

AnVILBilling helps monitor AnVIL-related costs in R, using queries to a BigQuery table to which costs are exported daily. Functions are defined to help categorize tasks and associated expenditures, and to visualize and explore expense profiles over time. This package will be expanded to help users estimate costs for specific task sets.

This package provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported.

This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.

This package provides tools to analyze point patterns in space occurring over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks. This package is based on the following research: Eckardt and Mateu (2018) <doi:10.1080/10618600.2017.1391695>. Eckardt and Mateu (2021) <doi:10.1007/s11749-020-00720-4>.

Lattice functions for drawing folded empirical cumulative distribution plots, or mountain plots. A mountain plot is similar to an empirical CDF plot, except that the curve increases from 0 to 0.5, then decreases from 0.5 to 1 using an inverted scale at the right side. See Monti (1995) <doi:10.1080/00031305.1995.10476179>.

Streamlines the steps for adding colour scales and associated legends when working with base R graphics, especially for interactive use. Popular palettes are included and pretty legends produced when mapping a large variety of vector classes to a colour scale. An additional helper for adding axes and grid lines complements the base::plot() work flow.