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r-daagxtras
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various data sets used in additional exercises for the book Maindonald, J.H. and Braun, W.J. (3rd edn 2010) "Data Analysis and Graphics Using R", and for a 'Data Mining' course. Note that a number of datasets that were in earlier versions of this package have been transferred to the DAAG package.
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2023-06-16 |
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r-arf3ds4
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Activated Region Fitting (ARF) is an analysis method for fMRI data.
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2023-06-16 |
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r-crrp
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In competing risks regression, the proportional subdistribution hazards(PSH) model is popular for its direct assessment of covariate effects on the cumulative incidence function. This package allows for penalized variable selection for the PSH model. Penalties include LASSO, SCAD, MCP, and their group versions.
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2023-06-16 |
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r-corporacoco
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A set of functions used to compare co-occurrence between two corpora.
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2023-06-16 |
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r-compoisson
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Provides routines for density and moments of the Conway-Maxwell-Poisson distribution as well as functions for fitting the COM-Poisson model for over/under-dispersed count data.
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2023-06-16 |
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r-compboost
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C++ implementation of component-wise boosting implementation of component-wise boosting written in C++ to obtain high runtime performance and full memory control. The main idea is to provide a modular class system which can be extended without editing the source code. Therefore, it is possible to use R functions as well as C++ functions for custom base-learners, losses, logging mechanisms or stopping criteria.
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2023-06-16 |
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r-coxboost
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This package provides routines for fitting Cox models by likelihood based boosting for a single endpoint or in presence of competing risks
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2023-06-16 |
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r-coretdt
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Use to analysis case-parent trio sequencing studies. Test the compound heterozygous and recessive disease models
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2023-06-16 |
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r-concor
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The four functions svdcp (cp for column partitioned), svdbip or svdbip2 (bip for bi-partitioned), and svdbips (s for a simultaneous optimization of one set of r solutions), correspond to a "SVD by blocks" notion, by supposing each block depending on relative subspaces, rather than on two whole spaces as usual SVD does. The other functions, based on this notion, are relative to two column partitioned data matrices x and y defining two sets of subsets xi and yj of variables and amount to estimate a link between xi and yj for the pair (xi, yj) relatively to the links associated to all the other pairs.
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2023-06-16 |
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r-cwhmisc
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Miscellaneous useful or interesting functions.
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2023-06-16 |
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r-cvcalibration
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Statistical inferences for estimating the calibration equation with error-in observations
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2023-06-16 |
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r-datastructures
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Implementation of advanced data structures such as hashmaps, heaps, or queues. Advanced data structures are essential in many computer science and statistics problems, for example graph algorithms or string analysis. The package uses 'Boost' and 'STL' data types and extends these to R with 'Rcpp' modules.
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2023-06-16 |
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r-cpk
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The package cpk provides simplified clinical pharmacokinetic functions for dose regimen design and modification at the point-of-care. Currently, the following functions are available: (1) ttc.fn for target therapeutic concentration, (2) dr.fn for dose rate, (3) di.fn for dosing interval, (4) dm.fn for maintenance dose, (5) bc.ttc.fn for back calculation, (6) ar.fn for accumulation ratio, (7) dpo.fn for orally administered dose, (8) cmax.fn for peak concentration, (9) css.fn for steady-state concentration, (10) cmin.fn for trough,(11) ct.fn for concentration-time predictions, (12) dlcmax.fn for calculating loading dose based on drug's maximum concentration, (13) dlar.fn for calculating loading dose based on drug's accumulation ratio, and (14) R0.fn for calculating drug infusion rate. Reference: Linares O, Linares A. Computational opioid prescribing: A novel application of clinical pharmacokinetics. J Pain Palliat Care Pharmacother 2011;25:125-135.
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2023-06-16 |
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r-cvq2
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The external prediction capability of quantitative structure-activity relationship (QSAR) models is often quantified using the predictive squared correlation coefficient. This value can be calculated with an external data set or by cross validation.
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2023-06-16 |
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r-cuttlefish.model
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This package can be used to standardize abundance indices using the delta-GLM method and to model the English Channel cuttlefish stock using a two-stage biomass model
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2023-06-16 |
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r-beginr
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Useful functions for R beginners, including hints for the arguments of the 'plot()' function, self-defined functions for error bars, user-customized pair plots and hist plots, enhanced linear regression figures, etc.. This package could be helpful to R experts as well.
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2023-06-16 |
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r-cssam
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Cell-type specific differential expression of a microarray experiment of heterogeneous tissue samples, using SAM.
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2023-06-16 |
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r-cptec
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Allows to retrieve data from the 'CPTEC/INPE' weather forecast API. 'CPTEC' stands for 'Centro de Previsão de Tempo e Estudos Climáticos' and 'INPE' for 'Instituto Nacional de Pesquisas Espaciais'. 'CPTEC' is the most advanced numerical weather and climate forecasting center in Latin America, with high-precision short and medium-term weather forecasting since the beginning of 1995. See <http://www.cptec.inpe.br/> for more information.
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2023-06-16 |
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r-conics
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plot conics (ellipses, hyperbolas, parabolas)
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2023-06-16 |
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r-coloredica
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It implements colored Independent Component Analysis (Lee et al., 2011) and spatial colored Independent Component Analysis (Shen et al., 2014). They are two algorithms to perform ICA when sources are assumed to be temporal or spatial stochastic processes, respectively.
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2023-06-16 |
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r-clustmmdd
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An implementation of a variable selection procedure in clustering by mixture models for discrete data (clustMMDD). Genotype data are examples of such data with two unordered observations (alleles) at each locus for diploid individual. The two-fold problem of variable selection and clustering is seen as a model selection problem where competing models are characterized by the number of clusters K, and the subset S of clustering variables. Competing models are compared by penalized maximum likelihood criteria. We considered asymptotic criteria such as Akaike and Bayesian Information criteria, and a family of penalized criteria with penalty function to be data driven calibrated.
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2023-06-16 |
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r-collectargs
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We often want to take all (or most) of the objects in one environment (such as the parameter values of a function) and pass them to another. This might be calling a second function, or iterating over a list, calling the same function. These functions wrap often repeated code. Current stable version (committed on October 14, 2017).
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2023-06-16 |
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r-clusternor
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The clustering 'NUMA' Optimized Routines package or 'clusternor' is a highly optimized package for performing clustering in parallel with accelerations specifically targeting multi-core Non-Uniform Memory Access ('NUMA') hardware architectures. Disa Mhembere, Da Zheng, Carey E. Priebe, Joshua T. Vogelstein, Randal Burns (2019) <arXiv:1902.09527>.
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2023-06-16 |
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r-commontrend
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Directly extract and plot stochastic common trends from a cointegration system using different approaches, currently including Kasa (1992) and Gonzalo and Granger (1995). The approach proposed by Gonzalo and Granger, also known as Permanent-Transitory Decomposition, is widely used in macroeconomics and market microstructure literature. Kasa's approach, on the other hand, has a nice property that it only uses the super consistent estimator: the cointegration vector 'beta'. This package also provides functions calculate P-value from Johansen Statistics according to the approximation method proposed by Doornik (1998). Update: 0.7-1: Fix bugs in calculation alpha. Add formulas and more explanations. 0.6-1: Rewrite the description file. 0.5-1: Add functions to calculate P-value from Johansen statistic, and vice versa.
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2023-06-16 |
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r-combinepvalue
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We offer two statistical tests to combine p-values: selfcontained.test vs competitive.test. The goal is to test whether a vector of pvalues are jointly significant when we combine them together.
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2023-06-16 |
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r-coindeskr
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Extract real-time Bitcoin price details by accessing 'CoinDesk' Bitcoin price Index API <https://www.coindesk.com/api/>.
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2023-06-16 |
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r-clustergenomics
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The Partitioning Algorithm based on Recursive Thresholding (PART) is used to recursively uncover clusters and subclusters in the data. Functionality is also available for visualization of the clustering.
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2023-06-16 |
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r-clusteval
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An R package that provides a suite of tools to evaluate clustering algorithms, clusterings, and individual clusters.
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2023-06-16 |
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r-codadiags
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Markov chain Monte Carlo burn-in based on "bridge" statistics, in the way of coda::heidel.diag, but including non asymptotic tabulated statistics.
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2023-06-16 |
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r-compactr
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Creates empty plots with compact axis notation to which users can add whatever they like (points, lines, text, etc.) The notation is more compact in the sense that the axis-labels and tick-labels are closer to the axis and the tick-marks are shorter. Also, if the plot appears as part of a matrix, the x-axis notation is suppressed unless the plot appears along the bottom row and the y-axis notation is suppress unless the plot appears along the left column.
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2023-06-16 |
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r-colr
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Powerful functions to select and rename columns in dataframes, lists and numeric types by 'Perl' regular expression. Regular expression ('regex') are a very powerful grammar to match strings, such as column names.
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2023-06-16 |
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r-clustsig
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A complimentary package for use with hclust; simprof tests to see which (if any) clusters are statistically different. The null hypothesis is that there is no a priori group structure. See Clarke, K.R., Somerfield, P.J., and Gorley R.N. 2008. Testing of null hypothesis in exploratory community analyses: similarity profiles and biota-environment linkage. J. Exp. Mar. Biol. Ecol. 366, 56-69.
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2023-06-16 |
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r-cobra
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This package performs prediction for regression-oriented problems, aggregating in a nonlinear scheme any basic regression machines suggested by the context and provided by the user. If the user has no valuable knowledge on the data, four defaults machines wrappers are implemented so as to cover a minimal spectrum of prediction methods. If necessary, the computations may be parallelized. The method is described in Biau, Fischer, Guedj and Malley (2013), "COBRA: A Nonlinear Aggregation Strategy".
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2023-06-16 |
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r-colorfulvennplot
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Given 2-,3- or 4-dimensional data, plots a Venn diagram, i.e. 'crossing circles'. The user can specify values, labels for each circle-group and unique colors for each plotted part. Here is what it would look like for a 3-dimensional plot: http://elliotnoma.files.wordpress.com/2011/02/venndiagram.png. To see what the 4-dimensional plot looks like, go to http://elliotnoma.files.wordpress.com/2013/03/4dplot.png.
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2023-06-16 |
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r-commentr
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Functions to produce nicely formatted comments to use in R-scripts (or Latex/HTML/markdown etc). A comment with formatting is printed to the console and can then be copied to a script.
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2023-06-16 |
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r-cmc
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Calculation and plot of the stepwise Cronbach-Mesbah Curve
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2023-06-16 |
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r-colorpalette
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Different methods to generate a color palette based on a specified base color and a number of colors that should be created.
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2023-06-16 |
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r-clustercrit
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Compute clustering validation indices.
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2023-06-16 |
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r-commandr
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An S4 representation of the Command design pattern. The Operation class is a simple implementation using closures and supports forward and reverse (undo) evaluation. The more complicated Protocol framework represents each type of command (or analytical protocol) by a formal S4 class. Commands may be grouped and consecutively executed using the Pipeline class. Example use cases include logging, do/undo, analysis pipelines, GUI actions, parallel processing, etc.
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2023-06-16 |
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r-cde
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Facilitates searching, download and plotting of Water Framework Directive (WFD) reporting data for all waterbodies within the UK Environment Agency area. The types of data that can be downloaded are: WFD status classification data, Reasons for Not Achieving Good (RNAG) status, objectives set for waterbodies, measures put in place to improve water quality and details of associated protected areas. The site accessed is <https://environment.data.gov.uk/catchment-planning/>. The data are made available under the Open Government Licence v3.0 <https://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/>. This package has been peer-reviewed by rOpenSci (v. 0.4.0).
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2023-06-16 |
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r-compareodm
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Input: 2 ODM files (ODM version 1.3) Output: list of identical, matching, similar and differing data items
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2023-06-16 |
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r-combmsc
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Functions for computing optimal convex combinations of model selection criteria based on ranks, along with utility functions for constructing model lists, MSCs, and priors on model lists.
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2023-06-16 |
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r-colortools
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R package with handy functions to help users select and play with color schemes in an HSV color model
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2023-06-16 |
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r-coexist
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species coexistence modeling under asymmetric dispersal and fluctuating source-sink dynamics;testing the proportion of coexistence scenarios driven by neutral and niche processes
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2023-06-16 |
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r-clusterpower
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Calculate power for cluster randomized trials (CRTs) including multi-arm trials, individually randomized group treatment trials (IGRTTs), stepped wedge trials (SWTs) and others using closed-form (analytic) solutions, and estimates power using Monte Carlo methods.
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2023-06-16 |
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r-collesslike
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Computation of Colless-Like, Sackin and cophenetic balance indices of a phylogenetic tree and study of the distribution of these balance indices under the alpha-gamma model. For more details see A. Mir, F. Rossello, L. Rotger (2013) <doi:10.1016/j.mbs.2012.10.005>, M. J. Sackin (1972) <doi:10.1093/sysbio/21.2.225>, D. H. Colless (1982) <doi:10.2307/2413420>.
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2023-06-16 |
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r-cluer
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CLUster Evaluation (CLUE) is a computational method for identifying optimal number of clusters in a given time-course dataset clustered by cmeans or kmeans algorithms and subsequently identify key kinases or pathways from each cluster. Its implementation in R is called ClueR. See README on <https://github.com/PengyiYang/ClueR> for more details. P Yang et al. (2015) <doi:10.1371/journal.pcbi.1004403>.
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2023-06-16 |
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r-clinutidna
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This package provides the estimation of an index measuring the clinical utility of DNA testing in the context of gene-environment interactions on a disease. The corresponding gene-environment interaction effect on the additive scale can also be obtained. The estimation is based on case-control or cohort data. The method was developed by Nguyen et al. 2013.
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2023-06-16 |
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r-chcn
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A compilation of historical through contemporary climate measurements scraped from the Environment Canada Website Including tools for scraping data, creating metadata and formating temperature files.
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2023-06-16 |
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r-cifsmry
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Estimate of cumulative incidence function in two samples. Provide weighted summary statistics based on various methods and weights.
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2023-06-16 |
