Using a time-varying random parameters model developed in Koutchade et al., (2024) <https://hal.science/hal-04318163>, this package allows allocating variable input costs among crops produced by farmers based on panel data including information on input expenditure aggregated at the farm level and acreage shares. It also considers in fairly way the weighting data and can allow integrating time-varying and time-constant control variables.

Pqsfinder detects DNA and RNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, pqsfinder is able to detect G4s folded from imperfect G-runs containing bulges or mismatches or G4s having long loops. Pqsfinder also assigns an integer score to each hit that was fitted on G4 sequencing data and corresponds to expected stability of the folded G4.

For a multisite replication project, computes the consistency metric P_orig, which is the probability that the original study would observe an estimated effect size as extreme or more extreme than it actually did, if in fact the original study were statistically consistent with the replications. Other recommended metrics are: (1) the probability of a true effect of scientifically meaningful size in the same direction as the estimate the original study; and (2) the probability of a true effect of meaningful size in the direction opposite the original study's estimate. These two can be computed using the package \codeMetaUtility::prop_stronger. Additionally computes older metrics used in replication projects (namely expected agreement in "statistical significance" between an original study and replication studies as well as prediction intervals for the replication estimates). See Mathur and VanderWeele (under review; <https://osf.io/apnjk/>) for details.

One and two sample mean and variance tests (differences and ratios) are considered. The test statistics are all expressed in the same form as the Student t-test, which facilitates their presentation in the classroom. This contribution also fills the gap of a robust (to non-normality) alternative to the chi-square single variance test for large samples, since no such procedure is implemented in standard statistical software.

This package provides the ability to display something analogous to Python's docstrings within R. By allowing the user to document their functions as comments at the beginning of their function without requiring putting the function into a package we allow more users to easily provide documentation for their functions. The documentation can be viewed just like any other help files for functions provided by packages as well.

Calculation and plotting of instantaneous unavailabilities of basic events along with the top event of fault trees are issues important in reliability analysis of complex systems. Here, a fault tree is provided in terms of its minimal cut sets, along with reliability and maintainability distribution functions of the basic events. All the methods are derived from Horton (2002, ISBN: 3-936150-21-4), Niloofar and Lazarova-Molnar (2022).

It provides an effective, efficient, and fast way to explore the Gene Ontology (GO). Given a set of genes, the package contains functions to assess the GO and obtain the terms associated with the genes and the levels of the GO terms. The package provides functions for the three different GO ontology. We discussed the methods explicitly in the following article <doi:10.1038/s41598-020-73326-3>.

This package provides utility functions that are simply, frequently used, but may require higher performance that what can be obtained from base R. Incidentally provides support for reverse geocoding', such as matching a point with its nearest neighbour in another array. Used as a complement to package hutils by sacrificing compilation or installation time for higher running speeds. The name is a portmanteau of the author and Rcpp'.

This package provides a systematic framework for integrating multiple modalities of assays profiled on the same set of samples. The goal is to identify genes that are altered in cancer either marginally or consistently across different assays. The heterogeneity among different platforms and different samples are automatically adjusted so that the overall alteration magnitude can be accurately inferred. See Tong and Coombes (2012) <doi:10.1093/bioinformatics/bts561>.

This package provides a convenience tool to create HTML with inline styles using juicyjuice and markdown packages. It is particularly useful when working on a content management system (CMS) whose code editor eliminates style and link tags. The main use case of the package is the learning management system, Moodle'. Additional helper functions for teaching purposes are provided. Learn more about juicedown at <https://kenjisato.github.io/juicedown/>.

Estimate agreement of a group of raters with a gold standard rating on a nominal scale. For a single gold standard rater the average pairwise agreement of raters with this gold standard is provided. For a group of (gold standard) raters the approach of S. Vanbelle, A. Albert (2009) <doi:10.1007/s11336-009-9116-1> is implemented. Bias and standard error are estimated via delete-1 jackknife.

Additions to party and partykit packages : tools for the interpretation of forests (surrogate trees, prototypes, etc.), feature selection (see Gregorutti et al (2017) <arXiv:1310.5726>, Hapfelmeier and Ulm (2013) <doi:10.1016/j.csda.2012.09.020>, Altmann et al (2010) <doi:10.1093/bioinformatics/btq134>) and parallelized versions of conditional forest and variable importance functions. Also modules and a shiny app for conditional inference trees.

Clinical reporting figures require to use consistent colors and configurations. As a part of the Roche open-source clinical reporting project, namely the NEST project, the nestcolor package specifies the color code and default theme with specifying ggplot2 theme parameters. Users can easily customize color and theme settings before using the reset of NEST packages to ensure consistent settings in both static and interactive output at the downstream.

Consists of custom wrapper functions using packages openxlsx', flextable', and officer to create highly formatted MS office friendly output of your data frames. These viewer friendly outputs are intended to match expectations of professional looking presentations in business and consulting scenarios. The functions are opinionated in the sense that they expect the input data frame to have certain properties in order to take advantage of the automated formatting.

Perform user-friendly power analyses for the random intercept cross-lagged panel model (RI-CLPM) and the bivariate stable trait autoregressive trait state (STARTS) model. The strategy as proposed by Mulder (2023) <doi:10.1080/10705511.2022.2122467> is implemented. Extensions include the use of parameter constraints over time, bounded estimation, generation of data with skewness and kurtosis, and the option to setup the power analysis for Mplus.

Quick Response codes (QR codes) are a type of matrix bar code and can be used to authenticate transactions, provide access to multi-factor authentication services and enable general data transfer in an image. QR codes use four standardized encoding modes (numeric, alphanumeric, byte/binary, and kanji) to efficiently store data. Matrix barcode generation is performed efficiently in C via the included libqrencoder library created by Kentaro Fukuchi.

This package provides a compilation of fish stock assessment methods for the analysis of length-frequency data in the context of data-poor fisheries. Includes methods and examples included in the FAO Manual by P. Sparre and S.C. Venema (1998), "Introduction to tropical fish stock assessment" (<https://openknowledge.fao.org/server/api/core/bitstreams/bc7c37b6-30df-49c0-b5b4-8367a872c97e/content>), as well as other more recent methods.

Umbrella for the alabaster suite, providing a single-line import for all alabaster.* packages. Installing this package ensures that all known alabaster.* packages are also installed, avoiding problems with missing packages when a staging method or loading function is dynamically requested. Obviously, this comes at the cost of needing to install more packages, so advanced users and application developers may prefer to install the required alabaster.* packages individually.

This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The synthetic hybridization data of “Tiling Arrays” can also be generated. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform. In addition, a visualization tool is provided to explore the synthetic nucleosome maps.

Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

Differential expression analysis of RNA-seq using the Poisson-Tweedie (PT) family of distributions. PT distributions are described by a mean, a dispersion and a shape parameter and include Poisson and NB distributions, among others, as particular cases. An important feature of this family is that, while the Negative Binomial (NB) distribution only allows a quadratic mean-variance relationship, the PT distributions generalizes this relationship to any orde.

In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomics hits and evolutionarily conserved start codons as the forms of evidence.

This package provides significance tests for second-order stationarity for time series using bootstrap wavelet packet tests. Provides functionality to visualize the time series with the results of the hypothesis tests superimposed. The methodology is described in Cardinali, A and Nason, G P (2016) "Practical powerful wavelet packet tests for second-order stationarity." Applied and Computational Harmonic Analysis, 44, 558-585 <doi:10.1016/j.acha.2016.06.006>.

Bayesian analysis of item-level hierarchical twin data using an integrated item response theory model. Analyses are based on Schwabe & van den Berg (2014) <doi:10.1007/s10519-014-9649-7>, Molenaar & Dolan (2014) <doi:10.1007/s10519-014-9647-9>, Schwabe, Jonker & van den Berg (2016) <doi:10.1007/s10519-015-9768-9> and Schwabe, Boomsma & van den Berg (2016) <doi:10.1016/j.lindif.2017.01.018>.