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r-ctv
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None |
Infrastructure for task views to CRAN-style repositories: Querying task views and installing the associated packages (client-side tools), generating HTML pages and storing task view information in the repository (server-side tools).
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2024-01-16 |
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r-csem
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public |
Estimate, assess, test, and study linear, nonlinear, hierarchical and multigroup structural equation models using composite-based approaches and procedures, including estimation techniques such as partial least squares path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc), generalized structured component analysis (GSCA), generalized structured component analysis with uniqueness terms (GSCAm), generalized canonical correlation analysis (GCCA), principal component analysis (PCA), factor score regression (FSR) using sum score, regression or bartlett scores (including bias correction using Croon’s approach), as well as several tests and typical postestimation procedures (e.g., verify admissibility of the estimates, assess the model fit, test the model fit etc.).
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2024-01-16 |
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r-cub
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public |
For ordinal rating data, estimate and test models within the family of CUB models and their extensions (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions). Simulation routines, plotting facilities and fitting measures are also provided.
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2024-01-16 |
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r-cttinshiny
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public |
A Shiny interface developed in close coordination with the CTT package, providing a GUI that guides the user through CTT analyses.
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2024-01-16 |
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r-cstime
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public |
Provides easy and consistent time conversion for public health purposes. The time conversion functions provided here are between date, ISO week, ISO yearweek, ISO year, calendar month/year, season, season week.
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2024-01-16 |
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r-ctt
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public |
A collection of common test and item analyses from a classical test theory (CTT) framework. Analyses can be applied to both dichotomous and polytomous data. Functions provide reliability analyses (alpha), item statistics, disctractor analyses, disattenuated correlations, scoring routines, and empirical ICCs.
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2024-01-16 |
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r-ctrlgene
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public |
A simple way to assess the stability of candidate housekeeping genes is implemented in this package.
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2024-01-16 |
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r-ctrdata
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public |
A system for querying, retrieving and analyzing protocol- and results-related information on clinical trials from four public registers, the 'European Union Clinical Trials Register' ('EUCTR', <https://www.clinicaltrialsregister.eu/>), 'ClinicalTrials.gov' ('CTGOV', using the classic interface at <https://classic.clinicaltrials.gov/>, and 'CTGOV2', using the current interface at <https://www.clinicaltrials.gov/>), the 'ISRCTN' (<http://www.isrctn.com/>) and the 'European Union Clinical Trials Information System' ('CTIS', <https://euclinicaltrials.eu/>). Trial information is downloaded, converted and stored in a database ('PostgreSQL', 'SQLite', 'DuckDB' or 'MongoDB'; via package 'nodbi'). All documents in registers associated with trials can also be downloaded. Other functions identify deduplicated records, easily find and extract variables (fields) of interest even from complex nested data as used by the registers, merge variables and update queries. The package can be used for meta-analysis and trend-analysis of the design and conduct as well as of the results of clinical trials.
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2024-01-16 |
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r-cthresher
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public |
Estimation and inference methods for the continuous threshold expectile regression. It can fit the continuous threshold expectile regression and test the existence of change point, for the paper, "Feipeng Zhang and Qunhua Li (2016). A continuous threshold expectile regression, submitted."
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2024-01-16 |
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r-csdata
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public |
Datasets relating to population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2020.
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2024-01-16 |
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r-csvy
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public |
Support for import from and export to the CSVY file format. CSVY is a file format that combines the simplicity of CSV (comma-separated values) with the metadata of other plain text and binary formats (JSON, XML, Stata, etc.) by placing a YAML header on top of a regular CSV.
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2024-01-16 |
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r-csv
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public |
Reads and writes CSV with selected conventions. Uses the same generic function for reading and writing to promote consistent formats.
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2024-01-16 |
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r-crunch
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public |
The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.
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2024-01-16 |
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r-csn
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public |
Provides functions for computing the density and the log-likelihood function of closed-skew normal variates, and for generating random vectors sampled from this distribution. See Gonzalez-Farias, G., Dominguez-Molina, J., and Gupta, A. (2004). The closed skew normal distribution, Skew-elliptical distributions and their applications: a journey beyond normality, Chapman and Hall/CRC, Boca Raton, FL, pp. 25-42.
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2024-01-16 |
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r-cshapes
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public |
Package for CShapes 2.0, a GIS dataset of country borders (1886-today). Includes functions for data extraction and the computation of distance matrices and -lists.
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2024-01-16 |
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r-cseqpat
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public |
Mines contiguous sequential patterns in text.
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2024-01-16 |
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r-crosstable
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public |
Create descriptive tables for continuous and categorical variables. Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'. You can also compute effect sizes and statistical tests if needed.
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2024-01-16 |
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r-crwrm
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public |
To re-calculate the coefficients and the standard deviation when changing the reference group.
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2024-01-16 |
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r-crul
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public |
A simple HTTP client, with tools for making HTTP requests, and mocking HTTP requests. The package is built on R6, and takes inspiration from Ruby's 'faraday' gem (<https://rubygems.org/gems/faraday>). The package name is a play on curl, the widely used command line tool for HTTP, and this package is built on top of the R package 'curl', an interface to 'libcurl' (<https://curl.se/libcurl/>).
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2024-01-16 |
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r-crew
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public |
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <https://CRAN.R-project.org/package=mirai> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>.
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2024-01-16 |
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r-crtsize
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public |
Sample size estimation in cluster (group) randomized trials. Contains traditional power-based methods, empirical smoothing (Rotondi and Donner, 2009), and updated meta-analysis techniques (Rotondi and Donner, 2012).
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2024-01-16 |
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r-crso
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public |
An algorithm for identifying candidate driver combinations in cancer. CRSO is based on a theoretical model of cancer in which a cancer rule is defined to be a collection of two or more events (i.e., alterations) that are minimally sufficient to cause cancer. A cancer rule set is a set of cancer rules that collectively are assumed to account for all of ways to cause cancer in the population. In CRSO every event is designated explicitly as a passenger or driver within each patient. Each event is associated with a patient-specific, event-specific passenger penalty, reflecting how unlikely the event would have happened by chance, i.e., as a passenger. CRSO evaluates each rule set by assigning all samples to a rule in the rule set, or to the null rule, and then calculating the total statistical penalty from all unassigned event. CRSO uses a three phase procedure find the best rule set of fixed size K for a range of Ks. A core rule set is then identified from among the best rule sets of size K as the rule set that best balances rule set size and statistical penalty. Users should consult the 'crso' vignette for an example walk through of a full CRSO run. The full description, of the CRSO algorithm is presented in: Klein MI, Cannataro V, Townsend J, Stern DF and Zhao H. "Identifying combinations of cancer driver in individual patients." BioRxiv 674234 [Preprint]. June 19, 2019. <doi:10.1101/674234>. Please cite this article if you use 'crso'.
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2024-01-16 |
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r-crsnls
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public |
Functions for nonlinear regression parameters estimation by algorithms based on Controlled Random Search algorithm. Both functions (crs4hc(), crs4hce()) adapt current search strategy by four heuristics competition. In addition, crs4hce() improves adaptability by adaptive stopping condition.
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2024-01-16 |
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r-crsmeta
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public |
Obtain coordinate system metadata from various data formats. There are functions to extract a 'CRS' (coordinate reference system, <https://en.wikipedia.org/wiki/Spatial_reference_system>) in 'EPSG' (European Petroleum Survey Group, <http://www.epsg.org/>), 'PROJ4' <https://proj.org/>, or 'WKT2' (Well-Known Text 2, <http://docs.opengeospatial.org/is/12-063r5/12-063r5.html>) forms. This is purely for getting simple metadata from in-memory formats, please use other tools for out of memory data sources.
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2024-01-16 |
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r-crseeventstudy
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public |
Based on Dutta et al. (2018) <doi:10.1016/j.jempfin.2018.02.004>, this package provides their standardized test for abnormal returns in long-horizon event studies. The methods used improve the major weaknesses of size, power, and robustness of long-run statistical tests described in Kothari/Warner (2007) <doi:10.1016/B978-0-444-53265-7.50015-9>. Abnormal returns are weighted by their statistical precision (i.e., standard deviation), resulting in abnormal standardized returns. This procedure efficiently captures the heteroskedasticity problem. Clustering techniques following Cameron et al. (2011) <doi:10.1198/jbes.2010.07136> are adopted for computing cross-sectional correlation robust standard errors. The statistical tests in this package therefore accounts for potential biases arising from returns' cross-sectional correlation, autocorrelation, and volatility clustering without power loss.
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2024-01-16 |
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r-crrstep
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public |
Performs forward and backwards stepwise regression for the Proportional subdistribution hazards model in competing risks (Fine & Gray 1999). Procedure uses AIC, BIC and BICcr as selection criteria. BICcr has a penalty of k = log(n*), where n* is the number of primary events.
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2024-01-16 |
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r-crov
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public |
Fits a constrained regression model for an ordinal response with ordinal predictors and possibly others, Espinosa and Hennig (2019) <DOI:10.1007/s11222-018-9842-2>. The parameter estimates associated with an ordinal predictor are constrained to be monotonic. If a monotonicity direction (isotonic or antitonic) is not specified for an ordinal predictor by the user, then one of the available methods will either establish it or drop the monotonicity assumption. Two monotonicity tests are also available to test the null hypothesis of monotonicity over a set of parameters associated with an ordinal predictor.
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2024-01-16 |
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r-crossval
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public |
Contains generic functions for performing cross validation and for computing diagnostic errors.
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2024-01-16 |
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r-crossva
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public |
Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (versions 1.4.1 & 1.5.1) or the WHO 2014 questionnaire for automated coding of Cause of Death using the InSilicoVA (data.type = "WHO2016") and InterVA5 algorithms. Previous versions of this package supported user-supplied mappings (via the map_records function), but this functionality has been removed. This package is made available by WHO and the Bloomberg Data for Health Initiative.
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2024-01-16 |
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r-crosstalk
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public |
Provides building blocks for allowing HTML widgets to communicate with each other, with Shiny or without (i.e. static .html files). Currently supports linked brushing and filtering.
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2024-01-16 |
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r-crossdes
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public |
Contains functions for the construction of carryover balanced crossover designs. In addition contains functions to check given designs for balance.
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2024-01-16 |
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r-cropdatape
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public |
Provides peruvian agricultural production data from the Agriculture Minestry of Peru (MINAGRI). The first version includes 6 crops: rice, quinoa, potato, sweet potato, tomato and wheat; all of them across 24 departments. Initially, in excel files which has been transformed and assembled using tidy data principles, i.e. each variable is in a column, each observation is a row and each value is in a cell. The variables variables are sowing and harvest area per crop, yield, production and price per plot, every one year, from 2004 to 2014.
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2024-01-16 |
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r-crop
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public |
A device closing function which is able to crop graphics (e.g., PDF, PNG files) on Unix-like operating systems with the required underlying command-line tools installed.
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2024-01-16 |
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r-crone
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public |
Functions to carry out the most important crystallographic calculations for crystal structures made of 1d Gaussian-shaped atoms, especially useful for methods development. Main reference: E. Smith, G. Evans, J. Foadi (2017) <doi:10.1088/1361-6404/aa8188>.
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2024-01-16 |
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r-crochet
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public |
Functions to help implement the extraction / subsetting / indexing function '[' and replacement function '[<-' of custom matrix-like types (based on S3, S4, etc.), modeled as closely to the base matrix class as possible (with tests to prove it).
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2024-01-16 |
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r-crisp
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public |
Implements convex regression with interpretable sharp partitions (CRISP), which considers the problem of predicting an outcome variable on the basis of two covariates, using an interpretable yet non-additive model. CRISP partitions the covariate space into blocks in a data-adaptive way, and fits a mean model within each block. Unlike other partitioning methods, CRISP is fit using a non-greedy approach by solving a convex optimization problem, resulting in low-variance fits. More details are provided in Petersen, A., Simon, N., and Witten, D. (2016). Convex Regression with Interpretable Sharp Partitions. Journal of Machine Learning Research, 17(94): 1-31 <http://jmlr.org/papers/volume17/15-344/15-344.pdf>.
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2024-01-16 |
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r-credsubs
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public |
Functions for constructing simultaneous credible bands and identifying subsets via the "credible subsets" (also called "credible subgroups") method. Package documentation includes the vignette included in this package, and the paper by Schnell, Fiecas, and Carlin (2020, <doi:10.18637/jss.v094.i07>).
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2024-01-16 |
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r-credentials
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public |
Setup and retrieve HTTPS and SSH credentials for use with 'git' and other services. For HTTPS remotes the package interfaces the 'git-credential' utility which 'git' uses to store HTTP usernames and passwords. For SSH remotes we provide convenient functions to find or generate appropriate SSH keys. The package both helps the user to setup a local git installation, and also provides a back-end for git/ssh client libraries to authenticate with existing user credentials.
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2024-01-16 |
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r-cream
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public |
Provides a new method for identification of clusters of genomic regions within chromosomes. Primarily, it is used for calling clusters of cis-regulatory elements (COREs). 'CREAM' uses genome-wide maps of genomic regions in the tissue or cell type of interest, such as those generated from chromatin-based assays including DNaseI, ATAC or ChIP-Seq. 'CREAM' considers proximity of the elements within chromosomes of a given sample to identify COREs in the following steps: 1) It identifies window size or the maximum allowed distance between the elements within each CORE, 2) It identifies number of elements which should be clustered as a CORE, 3) It calls COREs, 4) It filters the COREs with lowest order which does not pass the threshold considered in the approach.
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2024-01-16 |
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r-crayon
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None |
The crayon package is now superseded. Please use the 'cli' package for new projects. Colored terminal output on terminals that support 'ANSI' color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI' color support is automatically detected. Colors and highlighting can be combined and nested. New styles can also be created easily. This package was inspired by the 'chalk' 'JavaScript' project.
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2024-01-16 |
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r-cranlogs
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public |
'API' to the database of 'CRAN' package downloads from the 'RStudio' 'CRAN mirror'. The database itself is at <http://cranlogs.r-pkg.org>, see <https://github.com/r-hub/cranlogs.app> for the raw 'API'.
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2024-01-16 |
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r-cptcity
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public |
Incorporates colour gradients from the 'cpt-city' web archive available at <http://soliton.vm.bytemark.co.uk/pub/cpt-city/>.
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2024-01-16 |
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r-crank
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public |
Functions for completing and recalculating rankings and sorting.
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2024-01-16 |
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r-cramer
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public |
Provides R routine for the so called two-sample Cramer-Test. This nonparametric two-sample-test on equality of the underlying distributions can be applied to multivariate data as well as univariate data. It offers two possibilities to approximate the critical value both of which are included in this package.
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2024-01-16 |
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r-cowsay
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public |
Allows printing of character strings as messages/warnings/etc. with ASCII animals, including cats, cows, frogs, chickens, ghosts, and more.
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2024-01-16 |
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r-cpt
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public |
Non-parametric test for equality of multivariate distributions. Trains a classifier to classify (multivariate) observations as coming from one of several distributions. If the classifier is able to classify the observations better than would be expected by chance (using permutation inference), then the null hypothesis that the distributions are equal is rejected.
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2024-01-16 |
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r-cpp11
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public |
Provides a header only, C++11 interface to R's C interface. Compared to other approaches 'cpp11' strives to be safe against long jumps from the C API as well as C++ exceptions, conform to normal R function semantics and supports interaction with 'ALTREP' vectors.
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2024-01-16 |
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r-cprr
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public |
Calculate date of birth, age, and gender, and generate anonymous sequence numbers from CPR numbers. <https://en.wikipedia.org/wiki/Personal_identification_number_(Denmark)>.
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2024-01-16 |
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r-cpmcglm
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public |
We propose to determine the correction of the significance level after multiple coding of an explanatory variable in Generalized Linear Model. The different methods of correction of the p-value are the Single step Bonferroni procedure, and resampling based methods developed by P.H.Westfall in 1993. Resampling methods are based on the permutation and the parametric bootstrap procedure. If some continuous, and dichotomous transformations are performed this package offers an exact correction of the p-value developed by B.Liquet & D.Commenges in 2005. The naive method with no correction is also available.
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2024-01-16 |
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r-cplots
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public |
Provides functions to produce some circular plots for circular data, in a height- or area-proportional manner. They include bar plots, smooth density plots, stacked dot plots, histograms, multi-class stacked smooth density plots, and multi-class stacked histograms.
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2024-01-16 |
