This package implements an approximate string matching version of R's native match function. It can calculate various string distances based on edits (Damerau-Levenshtein, Hamming, Levenshtein, optimal string alignment), qgrams (q- gram, cosine, jaccard distance) or heuristic metrics (Jaro, Jaro-Winkler). An implementation of soundex is provided as well. Distances can be computed between character vectors while taking proper care of encoding or between integer vectors representing generic sequences.

Juniper makes it possible to write GraphQL servers in Rust that are type-safe and fast. It also tries to make declaring and resolving GraphQL schemas convenient.

Juniper does not include a web server. Instead it provides building blocks to make integration with existing servers straightforward. It optionally provides a pre-built integration for the Actix, Hyper, Iron, Rocket, and Warp frameworks, including embedded Graphiql and GraphQL Playground for easy debugging.

Juniper makes it possible to write GraphQL servers in Rust that are type-safe and fast. It also tries to make declaring and resolving GraphQL schemas convenient.

Juniper does not include a web server. Instead it provides building blocks to make integration with existing servers straightforward. It optionally provides a pre-built integration for the Actix, Hyper, Iron, Rocket, and Warp frameworks, including embedded Graphiql and GraphQL Playground for easy debugging.

The Racket BC (``before Chez'' or ``bytecode'') implementation was the default before Racket 8.0. It uses a compiler written in C targeting architecture-independent bytecode, plus a JIT compiler on most platforms. Racket BC has a different C API than the current default runtime system, Racket CS (based on ``Chez Scheme'').

This package is the normal implementation of Racket BC with a precise garbage collector, 3M (``Moving Memory Manager'').

The fonts provide uppercase formal script letters for use as symbols in scientific and mathematical typesetting (in contrast to the informal script fonts such as that used for the calligraphic symbols in the TeX maths symbol font). The fonts are provided as Metafont source, and as derived Adobe Type 1 format. LaTeX support, for using these fonts in mathematics, is available via one of the packages calrsfs and mathrsfs.

Construct the admissible exact intervals for the binomial proportion, the Poisson mean and the total number of subjects with a certain attribute or the total number of the subjects for the hypergeometric distribution. Both one-sided and two-sided intervals are of interest. This package can be used to calculate the intervals constructed methods developed by Wang (2014) <doi:10.5705/ss.2012.257> and Wang (2015) <doi:10.1111/biom.12360>.

This package provides classes and methods for handling networks or graphs whose nodes are geographical (i.e. locations in the globe). The functionality includes the creation of objects of class geonetwork as a graph with node coordinates, the computation of network measures, the support of spatial operations (projection to different Coordinate Reference Systems, handling of bounding boxes, etc.) and the plotting of the geonetwork object combined with supplementary cartography for spatial representation.

Analysis of kin-cohort studies. kin.cohort provides estimates of age-specific cumulative risk of a disease for carriers and noncarriers of a mutation. The cohorts are retrospectively built from relatives of probands for whom the genotype is known. Currently the method of moments and marginal maximum likelihood are implemented. Confidence intervals are calculated from bootstrap samples. Most of the code is a translation from previous MATLAB code by N. Chatterjee.

This package contains kidney care oriented functions. Current version contains functions for calculation of: - Estimated glomerular filtration rate by CKD-EPI (2021 and 2009), MDRD, CKiD, FAS, EKFC, etc. - Kidney Donor Risk Index and Kidney Donor Profile Index for kidney transplant donors. - Citation: Bikbov B. kidney.epi: Kidney-Related Functions for Clinical and Epidemiological Research. Scientific-Tools.Org, <https://Scientific-Tools.Org>. <doi:10.32614/CRAN.package.kidney.epi>.

This package provides a single function options.ifunset(...) is contained herewith, which allows the user to set a global option ONLY if it is not already set. By this token, for package maintainers this function can be used in preference to the standard options(...) function, making provision for THEIR end user to place options(...) directives within their .Rprofile file, which will not be overridden at the point when a package is loaded.

There are three sets of functions. The first produces basic properties of a graph and generates samples from multinomial distributions to facilitate the simulation functions (they maybe used for other purposes as well). The second provides various simulation functions for a Potts model in Potts, R. B. (1952) <doi:10.1017/S0305004100027419>. The third currently includes only one function which computes the normalizing constant of a Potts model based on simulation results.

Computes normalized cycle threshold (Ct) values (delta Ct) from raw quantitative polymerase chain reaction (qPCR) Ct values and conducts test of significance using t.test(). Plots expression values based from log2(2^(-1*delta delta Ct)) across groups per gene of interest. Methods for calculation of delta delta Ct and relative expression (2^(-1*delta delta Ct)) values are described in: Livak & Schmittgen, (2001) <doi:10.1006/meth.2001.1262>.

Empowers users to fuzzily-merge data frames with millions or tens of millions of rows in minutes with low memory usage. The package uses the locality sensitive hashing algorithms developed by Datar, Immorlica, Indyk and Mirrokni (2004) <doi:10.1145/997817.997857>, and Broder (1998) <doi:10.1109/SEQUEN.1997.666900> to avoid having to compare every pair of records in each dataset, resulting in fuzzy-merges that finish in linear time.

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

This package provides a shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.

Rustic is a fork of Rust mode. In addition to its predecessor, it offers the following features:

• Flycheck integration,

• Cargo popup,

• multiline error parsing,

• translation of ANSI control sequences through XTerm color,

• asynchronous Org Babel,

• custom compilation process,

• rustfmt errors in a Rust compilation mode,

• automatic LSP configuration with Eglot or LSP mode,

• optional Rust inline documentation,

• etc.

Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015)

Manage dependencies during package development. This can retrieve all dependencies that are used in ".R" files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and in roxygen2 documentation of functions. There is a function to update the "DESCRIPTION" file of your package with CRAN packages or any other remote package. All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can be used independently of a package development.

An implementation of the bridge distribution with logit-link in R. In Wang and Louis (2003) <DOI:10.1093/biomet/90.4.765>, such a univariate bridge distribution was derived as the distribution of the random intercept that bridged a marginal logistic regression and a conditional logistic regression. The conditional and marginal regression coefficients are a scalar multiple of each other. Such is not the case if the random intercept distribution was Gaussian.

Run other estimation and simulation software via the nlmixr2 (Fidler et al (2019) <doi:10.1002/psp4.12445>) interface including PKNCA', NONMEM and Monolix'. While not required, you can get/install the lixoftConnectors package in the Monolix installation, as described at the following url <https://monolixsuite.slp-software.com/r-functions/2024R1/installation-and-initialization>. When lixoftConnectors is available, Monolix can be run directly instead of setting up command line usage.

This package provides functions for the calculation and plotting of synchrony in tree growth from tree-ring width chronologies (TRW index). It combines variance-covariance (VCOV) mixed modelling with functions that quantify the degree to which the TRW chronologies contain a common temporal signal. It also implements temporal trends in spatial synchrony using a moving window. These methods can also be used with other kind of ecological variables that have temporal autocorrelation corrected.

Multiple Imputation has been shown to be a flexible method to impute missing values by Van Buuren (2007) <doi:10.1177/0962280206074463>. Expanding on this, random forests have been shown to be an accurate model by Stekhoven and Buhlmann <arXiv:1105.0828> to impute missing values in datasets. They have the added benefits of returning out of bag error and variable importance estimates, as well as being simple to run in parallel.

Data sets from a variety of biological sample matrices, analysed using a number of mass spectrometry based metabolomic analytical techniques. The example data sets are stored remotely using GitHub releases <https://github.com/aberHRML/metaboData/releases> which can be accessed from R using the package. The package also includes the abr1 FIE-MS data set from the FIEmspro package <https://users.aber.ac.uk/jhd/> <doi:10.1038/nprot.2007.511>.

This algorithm provides a numerical solution to the problem of unconstrained local minimization (or maximization). It is particularly suited for complex problems and more efficient than the Gauss-Newton-like algorithm when starting from points very far from the final minimum (or maximum). Each iteration is parallelized and convergence relies on a stringent stopping criterion based on the first and second derivatives. See Philipps et al, 2021 <doi:10.32614/RJ-2021-089>.