ggjoy - Joyplots in 'ggplot2'
Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Last updated 9 days ago
archivedpackagesr-universe
4.78 score 5 stars 1 dependents 495 downloadsflowTraceR - Tracing Information Flow for Inter-Software Comparisons in Mass Spectrometry-Based Bottom-Up Proteomics
Useful functions to standardize software outputs from ProteomeDiscoverer, Spectronaut, DIA-NN and MaxQuant on precursor, modified peptide and proteingroup level and to trace software differences for identifications such as varying proteingroup denotations for common precursor.
Last updated 24 days ago
archivedpackagesr-universe
4.35 score 5 stars 1 dependents 282 downloads
DataFakeR - Generate Fake Data for Relational Databases
Based on provided database description and/or database connection generate data sample preserving source structure.
Last updated 12 days ago
archivedpackagesr-universe
4.24 score 5 stars 249 downloadsBchron - Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling
Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); age-depth modelling as per the algorithm of Haslett and Parnell (2008) <DOI:10.1111/j.1467-9876.2008.00623.x>; Relative sea level rate estimation incorporating time uncertainty in polynomial regression models (Parnell and Gehrels 2015) <DOI:10.1002/9781118452547.ch32>; non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM; currently unpublished), and reverse calibration of dates from calibrated into un-calibrated years (also unpublished).
Last updated 21 hours ago
archivedpackagesr-universe
4.18 score 5 stars 1 dependents 960 downloadsscDHA - Single-Cell Decomposition using Hierarchical Autoencoder
Provides a fast and accurate pipeline for single-cell analyses. The 'scDHA' software package can perform clustering, dimension reduction and visualization, classification, and time-trajectory inference on single-cell data (Tran et.al. (2021) <DOI:10.1038/s41467-021-21312-2>).
Last updated 19 days ago
archivedpackagesr-universecpp
4.18 score 5 stars 2 dependents 264 downloadsspectralGraphTopology - Learning Graphs from Data via Spectral Constraints
In the era of big data and hyperconnectivity, learning high-dimensional structures such as graphs from data has become a prominent task in machine learning and has found applications in many fields such as finance, health care, and networks. 'spectralGraphTopology' is an open source, documented, and well-tested R package for learning graphs from data. It provides implementations of state of the art algorithms such as Combinatorial Graph Laplacian Learning (CGL), Spectral Graph Learning (SGL), Graph Estimation based on Majorization-Minimization (GLE-MM), and Graph Estimation based on Alternating Direction Method of Multipliers (GLE-ADMM). In addition, graph learning has been widely employed for clustering, where specific algorithms are available in the literature. To this end, we provide an implementation of the Constrained Laplacian Rank (CLR) algorithm.
Last updated 1 months ago
archivedpackagesr-universeopenblascpp
4.18 score 5 stars 2 dependents 279 downloadstabnet - Fit 'TabNet' Models for Classification and Regression
Implements the 'TabNet' model by Sercan O. Arik et al. (2019) <doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical Multi-label Classification Networks' by Giunchiglia et al. <doi:10.48550/arXiv.2010.10151> and provides a consistent interface for fitting and creating predictions. It's also fully compatible with the 'tidymodels' ecosystem.
Last updated 1 days ago
archivedpackagesr-universe
4.10 score 5 stars 593 downloadsMMRcaseselection - Case Classification and Selection Based on Regression Results
Researchers doing a mixed-methods analysis (nested analysis as developed by Lieberman (2005) <doi:10.1017/S0003055405051762>) can use the package for the classification of cases and case selection using results of a linear regression. One can designate cases as typical, deviant, extreme and pathway case and use different case selection strategies for the choice of a case belonging to one of these types.
Last updated 21 hours ago
archivedpackagesr-universe
4.00 score 5 stars 134 downloads
bayesCT - Simulation and Analysis of Adaptive Bayesian Clinical Trials
Simulation and analysis of Bayesian adaptive clinical trials for binomial, Gaussian, and time-to-event data types, incorporates historical data and allows early stopping for futility or early success. The package uses novel and efficient Monte Carlo methods for estimating Bayesian posterior probabilities, evaluation of loss to follow up, and imputation of incomplete data. The package has the functionality for dynamically incorporating historical data into the analysis via the power prior or non-informative priors.
Last updated 21 hours ago
archivedpackagesr-universe
4.00 score 5 stars 270 downloads
greatR - Gene Registration from Expression and Time-Courses in R
A tool for registering (aligning) gene expression profiles between reference and query data.
Last updated 14 days ago
archivedpackagesr-universe
4.00 score 5 stars 284 downloadsmpwR - Standardized Comparison of Workflows in Mass Spectrometry-Based Bottom-Up Proteomics
Useful functions to analyze proteomic workflows including number of identifications, data completeness, missed cleavages, quantitative and retention time precision etc. Various software outputs are supported such as 'ProteomeDiscoverer', 'Spectronaut', 'DIA-NN' and 'MaxQuant'.
Last updated 24 days ago
archivedpackagesr-universe
4.00 score 5 stars 292 downloadsgyro - Hyperbolic Geometry
Hyperbolic geometry in the Minkowski model and the Poincaré model. The methods are based on the gyrovector space theory developed by A. A. Ungar that can be found in the book 'Analytic Hyperbolic Geometry: Mathematical Foundations And Applications' <doi:10.1142/5914>. The package provides functions to plot three-dimensional hyperbolic polyhedra and to plot hyperbolic tilings of the Poincaré disk.
Last updated 7 days ago
archivedpackagesr-universecpp
3.88 score 5 stars 1 dependents 669 downloads
nestedmodels - Tidy Modelling for Nested Data
A modelling framework for nested data using the 'tidymodels' ecosystem. Specify how to nest data using the 'recipes' package, create testing and training splits using 'rsample', and fit models to this data using the 'parsnip' and 'workflows' packages. Allows any model to be fit to nested data.
Last updated 12 days ago
archivedpackagesr-universe
3.70 score 5 stars 657 downloadswebqueue - Multicore HTTP Server
Distributes HTTP requests among a pool of background R processes. Supports timeouts and interrupts of requests to ensure that CPU cores are utilized effectively.
Last updated 16 days ago
archivedpackagesr-universe
3.70 score 5 stars 12 downloadscxhull - Convex Hull
Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.
Last updated 7 days ago
archivedpackagesr-universe
3.57 score 5 stars 5 dependents 903 downloadsgdm - Generalized Dissimilarity Modeling
A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models. Mokany K, Ware C, Woolley SNC, Ferrier S, Fitzpatrick MC (2022) <doi:10.1111/geb.13459> Ferrier S, Manion G, Elith J, Richardson K (2007) <doi:10.1111/j.1472-4642.2007.00341.x>.
Last updated 2 days ago
archivedpackagesr-universecpp
3.40 score 5 stars 811 downloadsRcppPlanc - Parallel Low-Rank Approximation with Nonnegativity Constraints
'Rcpp' bindings for 'PLANC', a highly parallel and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library. Wraps algorithms described in Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and Eswar et. al (2021) <doi:10.1145/3432185>. Implements algorithms described in Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>, Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.
Last updated 3 days ago
archivedpackagesr-universecppopenmp
3.40 score 5 stars 78 downloadsPerseusR - Perseus R Interop
Enables the interoperability between the Perseus platform for omics data analysis (Tyanova et al. 2016) <doi:10.1038/nmeth.3901> and R. It provides the foundation for developing and running Perseus plugins implemented in R by providing all required input and output handling, including data and parameter parsing as described in Rudolph and Cox 2018 <doi:10.1101/447268>.
Last updated 9 days ago
archivedpackagesr-universe
3.40 score 5 stars 163 downloadsrTorch - R Bindings to 'PyTorch'
'R' implementation and interface of the Machine Learning platform 'PyTorch' <https://pytorch.org/> developed in 'Python'. It requires a 'conda' environment with 'torch' and 'torchvision' Python packages to provide 'PyTorch' functions, methods and classes. The key object in 'PyTorch' is the tensor which is in essence a multidimensional array. These tensors are fairly flexible in performing calculations in CPUs as well as 'GPUs' to accelerate tensor operations.
Last updated 9 days ago
archivedpackagesr-universe
3.40 score 5 stars 189 downloadstorchaudio - R Interface to 'pytorch''s 'torchaudio'
Provides access to datasets, models and processing facilities for deep learning in audio.
Last updated 13 days ago
archivedpackagesr-universe
3.40 score 5 stars 203 downloadsscCAN - Single-Cell Clustering using Autoencoder and Network Fusion
A single-cell Clustering method using 'Autoencoder' and Network fusion ('scCAN') Bang Tran (2022) <doi:10.1038/s41598-022-14218-6> for segregating the cells from the high-dimensional 'scRNA-Seq' data. The software automatically determines the optimal number of clusters and then partitions the cells in a way such that the results are robust to noise and dropouts. 'scCAN' is fast and it supports Windows, Linux, and Mac OS.
Last updated 19 days ago
archivedpackagesr-universe
3.40 score 5 stars 540 downloadsMicroSEC - Sequence Error Filter for Formalin-Fixed and Paraffin-Embedded Samples
Clinical sequencing of tumor is usually performed on formalin-fixed and paraffin-embedded samples and have many sequencing errors. We found that the majority of these errors are detected in chimeric read caused by single-strand DNA with micro-homology. Our filtering pipeline focuses on the uneven distribution of the artifacts in each read and removes such errors in formalin-fixed and paraffin-embedded samples without over-eliminating the true mutations detected in fresh frozen samples.
Last updated 20 days ago
archivedpackagesr-universe
3.40 score 5 stars 182 downloadspolyhedralCubature - Multiple Integration over Convex Polyhedra
Evaluation of multiple integrals over convex polyhedra. This is useful when the bounds of the integrals are some linear combinations of the variables.
Last updated 21 days ago
archivedpackagesr-universe
3.40 score 5 stars 198 downloadstern.rbmi - Create Interface for 'RBMI' and 'tern'
'RBMI' implements standard and reference based multiple imputation methods for continuous longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). This package provides an interface for 'RBMI' uses the 'tern' <https://cran.r-project.org/package=tern> framework by Zhu et al. (2023) and tabulate results easily using 'rtables' <https://cran.r-project.org/package=rtables> by Becker et al. (2023).
Last updated 22 days ago
archivedpackagesr-universe
3.40 score 5 stars 258 downloadsrock - Reproducible Open Coding Kit
The Reproducible Open Coding Kit ('ROCK', and this package, 'rock') was developed to facilitate reproducible and open coding, specifically geared towards qualitative research methods. Although it is a general-purpose toolkit, three specific applications have been implemented, specifically an interface to the 'rENA' package that implements Epistemic Network Analysis ('ENA'), means to process notes from Cognitive Interviews ('CIs'), and means to work with decentralized construct taxonomies ('DCTs'). The 'ROCK' and this 'rock' package are described in the ROCK book <https://rockbook.org> and more information, such as tutorials, is available at <https://rock.science>.
Last updated 24 days ago
archivedpackagesr-universe
3.40 score 5 stars 425 downloadsSTRMPS - Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data
Loading, identifying, aggregating, manipulating, and analysing short tandem repeat regions of massively parallel sequencing data in forensic genetics. The analyses and framework implemented in this package relies on the papers of Vilsen et al. (2017) <doi:10.1016/j.fsigen.2017.01.017> and Vilsen et al. (2018) <doi:10.1016/j.fsigen.2018.04.003>. Note: that the parallelisation in the package relies on mclapply() and, thus, speed-ups will only be seen on UNIX based systems.
Last updated 26 days ago
biostringspwalignshortreadirangesarchivedpackagesr-universe
3.40 score 5 stars 232 downloadsfinreportr - Financial Data from U.S. Securities and Exchange Commission
Download and display company financial data from the U.S. Securities and Exchange Commission's EDGAR database. It contains a suite of functions with web scraping and XBRL parsing capabilities that allows users to extract data from EDGAR in an automated and scalable manner. See <https://www.sec.gov/edgar/searchedgar/companysearch.html> for more information.
Last updated 27 days ago
archivedpackagesr-universe
3.40 score 5 stars 411 downloadsTukeyC - Conventional Tukey Test
Perform the conventional Tukey test from formula, lm, aov, aovlist and lmer objects.
Last updated 26 days ago
archivedpackagesr-universe
3.24 score 5 stars 599 downloadsclinDataReview - Clinical Data Review Tool
Creation of interactive tables, listings and figures ('TLFs') and associated report for exploratory analysis of data in a clinical trial, e.g. for clinical oversight activities. Interactive figures include sunburst, treemap, scatterplot, line plot and barplot of counts data. Interactive tables include table of summary statistics (as counts of adverse events, enrollment table) and listings. Possibility to compare data (summary table or listing) across two data batches/sets. A clinical data review report is created via study-specific configuration files and template 'R Markdown' reports contained in the package.
Last updated 25 days ago
archivedpackagesr-universe
3.18 score 5 stars 678 downloadsD4TAlink.light - FAIR Data - Workflow Management
Tools, methods and processes for the management of analysis workflows. These lightweight solutions facilitate structuring R&D activities. These solutions were developed to comply with Good Documentation Practice (GDP), with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>, and with ALCOA+ principles as proposed by the U.S. FDA.
Last updated 23 days ago
archivedpackagesr-universe
3.00 score 5 stars 344 downloadstabulate - Pretty Console Output for Tables
Generates pretty console output for tables allowing for full customization of cell colors, font type, borders and many others attributes. It also supports 'multibyte' characters and nested tables.
Last updated 13 days ago
archivedpackagesr-universecpp
2.88 score 5 stars 3.0k downloadstessellation - Delaunay and Voronoï Tessellations
Delaunay and Voronoï tessellations, with emphasis on the two-dimensional and the three-dimensional cases (the package provides functions to plot the tessellations for these cases). Delaunay tessellations are computed in C with the help of the 'Qhull' library <http://www.qhull.org/>.
Last updated 21 days ago
archivedpackagesr-universe
2.88 score 5 stars 1 dependents 256 downloadsmr.raps - Two Sample Mendelian Randomization using Robust Adjusted Profile Score
Mendelian randomization is a method of identifying and estimating a confounded causal effect using genetic instrumental variables. This packages implements methods for two-sample Mendelian randomization with summary statistics by using Robust Adjusted Profile Score (RAPS). References: Qingyuan Zhao, Jingshu Wang, Jack Bowden, Dylan S. Small. Statistical inference in two-sample summary-data Mendelian randomization using robust adjusted profile score. <arXiv:1801.09652>.
Last updated 1 months ago
archivedpackagesr-universe
2.88 score 5 stars 1 dependents 168 downloadsaddScales - Adds Labeled Center Line and Scale Lines/Regions to Trellis Plots
Modifies trellis objects by adding horizontal and/or vertical reference lines or shaded regions that provide visual scaling information. This is mostly useful in multi-panel plots that use the relation = 'free' option in their 'scales' argument list.
Last updated 9 hours ago
archivedpackagesr-universe
2.70 score 5 stars 251 downloadstwangRDC - Gradient Boosting for Linkage Failure in FSRDCs
Provides functions for gradient boosted weighting to correct linkage failures or generate comparison groups.
Last updated 21 hours ago
archivedpackagesr-universe
2.70 score 5 stars 191 downloadsEFS - Tool for Ensemble Feature Selection
Provides a function to check the importance of a feature based on a dependent classification variable. An ensemble of feature selection methods is used to determine the normalized importance value of all features. Combining these methods in one function (building the cumulative importance values) provides a stable feature selection tool. This selection can also be viewed in a barplot using the barplot_fs() function and proved using the evaluation function efs_eval().
Last updated 2 days ago
archivedpackagesr-universe
2.70 score 5 stars 168 downloadsportsort - Factor-Based Portfolio Sorts
Designed to aid both academic researchers and asset managers in conducting factor based portfolio sorts. Provides functionality to sort assets into portfolios for up to three factors via a conditional or unconditional sorting procedure.
Last updated 8 days ago
archivedpackagesr-universe
2.70 score 5 stars 253 downloadsPEACH - Pareto Enrichment Analysis for Combining Heterogeneous Datasets
A meta gene set analysis tool developed based on principles of Pareto dominance (William B T Mock (2011) <doi:10.1007/978-1-4020-9160-5_341>). It is designed to combine gene set analysis p-values from multiple transcriptome datasets (e.g., microarray and RNA-Seq). The novel Pareto method for p-value combination allows PEACH to properly model heterogeneity and correlation in Omics datasets.
Last updated 8 days ago
archivedpackagesr-universe
2.70 score 5 stars 137 downloadskpcalg - Kernel PC Algorithm for Causal Structure Detection
Kernel PC (kPC) algorithm for causal structure learning and causal inference using graphical models. kPC is a version of PC algorithm that uses kernel based independence criteria in order to be able to deal with non-linear relationships and non-Gaussian noise.
Last updated 9 days ago
archivedpackagesr-universe
2.70 score 5 stars 196 downloadsMVLM - Multivariate Linear Model with Analytic p-Values
Allows a user to conduct multivariate multiple regression using analytic p-values rather than classic approximate F-tests.
Last updated 9 days ago
archivedpackagesr-universe
2.70 score 5 stars 417 downloadsAcousticNDLCodeR - Coding Sound Files for Use with NDL
Make acoustic cues to use with the R packages 'ndl' or 'ndl2'. The package implements functions used in the PLoS ONE paper: Denis Arnold, Fabian Tomaschek, Konstantin Sering, Florence Lopez, and R. Harald Baayen (2017). Words from spontaneous conversational speech can be recognized with human-like accuracy by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit. PLoS ONE 12(4):e0174623 <doi:10.1371/journal.pone.0174623> More details can be found in the paper and the supplement. 'ndl' is available on CRAN. 'ndl2' is available by request from <[email protected]>.
Last updated 9 days ago
archivedpackagesr-universe
2.70 score 5 stars 286 downloadsFarmSelect - Factor Adjusted Robust Model Selection
Implements a consistent model selection strategy for high dimensional sparse regression when the covariate dependence can be reduced through factor models. By separating the latent factors from idiosyncratic components, the problem is transformed from model selection with highly correlated covariates to that with weakly correlated variables. It is appropriate for cases where we have many variables compared to the number of samples. Moreover, it implements a robust procedure to estimate distribution parameters wherever possible, hence being suitable for cases when the underlying distribution deviates from Gaussianity. See the paper on the 'FarmSelect' method, Fan et al.(2017) <arXiv:1612.08490>, for detailed description of methods and further references.
Last updated 9 days ago
archivedpackagesr-universeopenblascpp
2.70 score 5 stars 178 downloadsLW1949 - An Automated Approach to Evaluating Dose-Effect Experiments Following Litchfield and Wilcoxon (1949)
The manual approach of Litchfield and Wilcoxon (1949) <http://jpet.aspetjournals.org/content/96/2/99.abstract> for evaluating dose-effect experiments is automated so that the computer can do the work.
Last updated 9 days ago
archivedpackagesr-universe
2.70 score 5 stars 131 downloadsdirmcmc - Directional Metropolis Hastings Algorithm
Implementation of Directional Metropolis Hastings Algorithm for MCMC.
Last updated 9 days ago
archivedpackagesr-universe
2.70 score 5 stars 408 downloadsFuzzyStatProb - Fuzzy Stationary Probabilities from a Sequence of Observations of an Unknown Markov Chain
An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain, from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package 'FuzzyNumbers' is used to represent the output probabilities.
Last updated 9 days ago
archivedpackagesr-universe
2.70 score 5 stars 220 downloadsshiny.info - 'shiny' Info
Displays simple diagnostic information of the 'shiny' project in the user interface of the app.
Last updated 12 days ago
archivedpackagesr-universe
2.70 score 5 stars 159 downloadskmeRs - K-Mers Similarity Score Matrix and HeatMap
Similarity Score Matrix and HeatMap for nucleic and amino acid k-mers. Similarity score is evaluated by Point Accepted Mutation (PAM) and BLOcks SUbstitution Matrix (BLOSUM). The 30, 40, 70, 120, 250 and 62, 45, 50, 62, 80, 100 matrix versions are available for PAM and BLOSUM, respectively. Alignment is evaluated by local and global alignment.
Last updated 24 days ago
softwarearchivedpackagesr-universe
2.70 score 5 stars 192 downloadshddplot - Use Known Groups in High-Dimensional Data to Derive Scores for Plots
Cross-validated linear discriminant calculations determine the optimum number of features. Test and training scores from successive cross-validation steps determine, via a principal components calculation, a low-dimensional global space onto which test scores are projected, in order to plot them. Further functions are included that are intended for didactic use. The package implements, and extends, methods described in J.H. Maindonald and C.J. Burden (2005) <https://journal.austms.org.au/V46/CTAC2004/Main/home.html>.
Last updated 24 days ago
archivedpackagesr-universe
2.70 score 5 stars 366 downloadsTT - Display Tree Structured Data using Datatable Widget (DT)
Wrapper of datatable widget, allowing display of data.tree objects. All arguments of the data.tree become columns and each node is a row. Adds column with buttons allowing folding and unfolding the levels.
Last updated 25 days ago
archivedpackagesr-universe
2.70 score 5 stars 179 downloadsTEAM - Multiple Hypothesis Testing on an Aggregation Tree Method
An implementation of the TEAM algorithm to identify local differences between two (e.g. case and control) independent, univariate distributions, as described in J Pura, C Chan, and J Xie (2019) <arXiv:1906.07757>. The algorithm is based on embedding a multiple-testing procedure on a hierarchical structure to identify high-resolution differences between two distributions. The hierarchical structure is designed to identify strong, short-range differences at lower layers and weaker, but long-range differences at increasing layers. TEAM yields consistent layer-specific and overall false discovery rate control.
Last updated 25 days ago
archivedpackagesr-universe
2.70 score 5 stars 128 downloadsnbfar - Negative Binomial Factor Regression Models ('nbfar')
We developed a negative binomial factor regression model to estimate structured (sparse) associations between a feature matrix X and overdispersed count data Y. With 'nbfar', microbiome count data Y can be used, for example, to associate host or environmental covariates with microbial abundances. Currently, two models are available: a) Negative Binomial reduced rank regression (NB-RRR), b) Negative Binomial co-sparse factor regression (NB-FAR). Please refer the manuscript 'Mishra, A. K., & Müller, C. L. (2021). Negative Binomial factor regression with application to microbiome data analysis. bioRxiv.' for more details.
Last updated 1 months ago
archivedpackagesr-universeopenblascpp
2.70 score 5 stars 45 downloadstigerstats - R Functions for Elementary Statistics
A collection of data sets and functions that are useful in the teaching of statistics at an elementary level to students who may have little or no previous experience with the command line. The functions for elementary inferential procedures follow a uniform interface for user input. Some of the functions are instructional applets that can only be run on the R Studio integrated development environment with package 'manipulate' installed. Other instructional applets are Shiny apps that may be run locally. In teaching the package is used alongside of package 'mosaic', 'mosaicData' and 'abd', which are therefore listed as dependencies.
Last updated 9 hours ago
archivedpackagesr-universe
2.61 score 5 stars 1.6k downloadsIBDsim - Simulation of Chromosomal Regions Shared by Family Members
Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Kong et. al (2010) <doi:10.1038/nature09525>), phased chromosomes are simulated for all pedigree members, either by unconditional gene dropping or conditional on a specified IBD pattern. Additional functions provide summaries and further analysis of the simulated genomes.
Last updated 9 days ago
archivedpackagesr-universe
2.48 score 5 stars 242 downloadsmbest - Moment-Based Estimation for Hierarchical Models
Fast moment-based hierarchical model fitting. Implements methods from the papers "Fast Moment-Based Estimation for Hierarchical Models," by Perry (2017) and "Fitting a Deeply Nested Hierarchical Model to a Large Book Review Dataset Using a Moment-Based Estimator," by Zhang, Schmaus, and Perry (2018).
Last updated 23 days ago
archivedpackagesr-universe
2.48 score 5 stars 2 dependents 844 downloadsMonetDB.R - Connect MonetDB to R
Allows to pull data from MonetDB into R.
Last updated 21 hours ago
archivedpackagesr-universe
2.40 score 5 stars 253 downloadsclusterability - Performs Tests for Cluster Tendency of a Data Set
Test for cluster tendency (clusterability) of a data set. The methods implemented - reducing the data set to a single dimension using principal component analysis or computing pairwise distances, and performing a multimodality test like the Dip Test or Silverman's Critical Bandwidth Test - are described in Adolfsson, Ackerman, and Brownstein (2019) <doi:10.1016/j.patcog.2018.10.026>. Such methods can inform whether clustering algorithms are appropriate for a data set.
Last updated 21 hours ago
archivedpackagesr-universe
2.40 score 5 stars 218 downloadsRITCH - R Parser for the ITCH-Protocol
Allows to efficiently parse, filter, and write binary ITCH Files (Version 5.0) containing detailed financial transactions as distributed by NASDAQ to an R data.table.
Last updated 3 days ago
archivedpackagesr-universecpp
2.40 score 5 stars 231 downloadsApollonius - 2D Apollonius Graphs
Computation of the Apollonius diagram of given 2D points and its dual the Apollonius graph, also known as the additively weighted Voronoï diagram, and which is a generalization of the classical Voronoï diagram. For references, see the bibliography in the CGAL documentation at <https://doc.cgal.org/latest/Apollonius_graph_2/citelist.html>.
Last updated 7 days ago
archivedpackagesr-universegmpcpp
2.40 score 5 stars 234 downloadspredkmeans - Covariate Adaptive Clustering
Implements the predictive k-means method for clustering observations, using a mixture of experts model to allow covariates to influence cluster centers. Motivated by air pollution epidemiology settings, where cluster membership needs to be predicted across space. Includes functions for predicting cluster membership using spatial splines and principal component analysis (PCA) scores using either multinomial logistic regression or support vector machines (SVMs). For method details see Keller et al. (2017) <doi:10.1214/16-AOAS992>.
Last updated 9 days ago
archivedpackagesr-universeopenblascpp
2.40 score 5 stars 147 downloadsjsonStrings - Manipulation of JSON Strings
Fast manipulation of JSON strings. Allows to extract or delete an element in a JSON string, merge two JSON strings, and more.
Last updated 13 days ago
archivedpackagesr-universecpp
2.40 score 5 stars 178 downloadsrflashtext - FlashText Algorithm for Finding and Replacing Words
Implementation of the FlashText algorithm, by Singh (2017) <arXiv:1711.00046>. It can be used to find and replace words in a given text with only one pass over the document.
Last updated 13 days ago
archivedpackagesr-universecpp
2.40 score 5 stars 105 downloadsdatasailr - Row by Row Data Processing Tool, Using 'DataSailr' Script
A row by row data processing tool. You can write data processing code in 'DataSailr' script which is specially intended for data manipulation. The package uses 'libsailr' (C/C++ library) for its 'DataSailr' code parsing and its execution.
Last updated 13 days ago
archivedpackagesr-universecpp
2.40 score 5 stars 291 downloadsrehydratoR - Downloads Tweets from a List of Tweet IDs
Facilitates replication of Twitter-based research by handling common programming tasks needed when downloading tweets. Specifically, it ensures a user does not exceed Twitter’s rate limits, and it saves tweets in moderately sized files. While a user could perform these tasks in their own code, doing so may be beyond the capabilities of many users.
Last updated 21 days ago
archivedpackagesr-universe
2.40 score 5 stars 98 downloadsfingraph - Learning Graphs for Financial Markets
Learning graphs for financial markets with optimization algorithms. This package contains implementations of the algorithms described in the paper: Cardoso JVM, Ying J, and Palomar DP (2021) <https://papers.nips.cc/paper/2021/hash/a64a034c3cb8eac64eb46ea474902797-Abstract.html> "Learning graphs in heavy-tailed markets", Advances in Neural Informations Processing Systems (NeurIPS).
Last updated 1 months ago
archivedpackagesr-universe
2.40 score 5 stars 45 downloadsgtheory - Apply Generalizability Theory with R
Estimates variance components, generalizability coefficients, universe scores, and standard errors when observed scores contain variation from one or more measurement facets (e.g., items and raters).
Last updated 9 days ago
archivedpackagesr-universe
2.00 score 5 stars 382 downloadsnoegletalR - Tidy Tibbles of Noegletal
Work with data from <https://noegletal.dk> in a tidy manner. Tidy up previously downloaded data or retrieve new data directly from the comfort of R. You can also browse an up-to-date list of available data, including thorough variable descriptions.
Last updated 16 days ago
archivedpackagesr-universe
2.40 score 5 stars 78 downloadstidyformula - Build Formulas Using Tidy Selection Helpers
Provides the function 'tidyformula()', which translates formulas containing 'tidyselect'-style selection helpers. It expands these helpers by evaluating 'dplyr::select()' with the relevant selection helper and a supplied data frame. The package contains methods for traversing abstract syntax trees from Wickham, Hadley (2019) <doi:10.1201/9781351201315>.
Last updated 24 days ago
archivedpackagesr-universe
2.40 score 5 stars 193 downloadsmarp - Model-Averaged Renewal Process
To implement a model-averaging approach with different renewal models, with a primary focus on forecasting large earthquakes. Based on six renewal models (i.e., Poisson, Gamma, Log-Logistics, Weibull, Log-Normal and BPT), model-averaged point estimates are calculated using AIC (or BIC) weights. Additionally, both percentile and studentized bootstrapped model-averaged confidence intervals are constructed. In comparison, point and interval estimation from the individual or "best" model (determined via model selection) can be retrieved.
Last updated 1 months ago
archivedpackagesr-universe
2.40 score 5 stars 41 downloadsrllama - Access and Analyze Data from 'DeFiLlama'
Provides an interface to access and analyze data from 'DeFiLlama'<https://defillama.com>. This package simplifies the process of fetching and manipulating 'DeFiLlama' data for further analysis and visualization.
Last updated 1 months ago
archivedpackagesr-universe
2.40 score 5 stars 43 downloadsfinbipartite - Learning Bipartite Graphs: Heavy Tails and Multiple Components
Learning bipartite and k-component bipartite graphs from financial datasets. This package contains implementations of the algorithms described in the paper: Cardoso JVM, Ying J, and Palomar DP (2022). <https://openreview.net/pdf?id=WNSyF9qZaMd> "Learning bipartite graphs: heavy tails and multiple components, Advances in Neural Informations Processing Systems" (NeurIPS).
Last updated 1 months ago
archivedpackagesr-universe
2.40 score 5 stars 53 downloadsXBRL - Extraction of Business Financial Information from 'XBRL' Documents
Functions to extract business financial information from an Extensible Business Reporting Language ('XBRL') instance file and the associated collection of files that defines its 'Discoverable' Taxonomy Set ('DTS').
Last updated 27 days ago
archivedpackagesr-universelibxml2cpp
2.18 score 5 stars 1 dependents 448 downloadsmultinet - Analysis and mining of multilayer social networks
Functions for the creation/generation and analysis of multilayer social networks <doi:10.18637/jss.v098.i08>.
Last updated 13 days ago
archivedpackagesr-universecpp
2.06 score 5 stars 1.1k downloadsvampyr - Factor Analysis Controlling the Effects of Response Bias
Vampirize the response biases from a dataset! Performs factor analysis controlling the effects of social desirability and acquiescence using the method described in Ferrando, Lorenzo-Seva & Chico (2009) <doi:10.1080/10705510902751374>.
Last updated 21 hours ago
archivedpackagesr-universe
1.70 score 5 stars 148 downloadsInDisc - Obtaining and Estimating Unidimensional and Multidimensional IRT Dual Models
Performs a unified approach for obtaining and estimating unidimensional and multidimensional Item Response Theory (IRT) Dual Models (DMs), proposed by Ferrando (2019 <doi:10.1177/0146621618817779>).
Last updated 21 hours ago
archivedpackagesr-universe
1.70 score 5 stars 181 downloadsgeovol - Geopolitical Volatility (GEOVOL) Modelling
Simulation, estimation and inference for the geopolitical volatility (GEOVOL) model of Engle and Campos-Martins (2020) <doi:10.2139/ssrn.3685213>, where GEOVOL is modelled as a latent multiplicative volatility factor with heterogeneous factor loadings. Estimation is carried out as a maximization-maximization procedure, where GEOVOL and the GEOVOL loadings are estimated iteratively until convergence.
Last updated 21 hours ago
archivedpackagesr-universe
1.70 score 5 stars 138 downloadsSparseTSCGM - Sparse Time Series Chain Graphical Models
Computes sparse vector autoregressive coefficients and precision matrices for time series chain graphical models. Fentaw Abegaz and Ernst Wit (2013) <doi:10.1093/biostatistics/kxt005>.
Last updated 21 hours ago
archivedpackagesr-universe
1.70 score 5 stars 187 downloadsgradientPickerD3 - Interactive Color Gradient Picker Using 'htmlwidgets' and the Modified JS Script 'jquery-gradient-picker'
Widget for an interactive selection and modification of a color gradient. 'gradientPickerD3' allows addition, removement and replacement of color ticks. List of numeric values will automatically translate in their corresponding tick position within the numeric range. App returns a data.frame containing tick values, colors and the positions in percent (0.0 to 1.0) for each color tick in the gradient. The original JS 'jquery-gradient-picker' was implemented by Matt Crinklaw-Vogt (nick: tantaman) <https://github.com/tantaman/>. Widget and JS modifications were done by CD. Peikert.
Last updated 9 days ago
archivedpackagesr-universe
2.40 score 5 stars 393 downloadsggplotlyExtra - Extra Convenience Functions for 'Plotly'
Convenience functions for smooth conversion from 'ggplot' to 'plotly' where the conversion using ggplotly() usually gives an unexpected labels. The package ease the process of making a 'plotly' figures generated from 'ggplot2' object more aesthetic in terms of labels and customizability.
Last updated 9 days ago
archivedpackagesr-universe
2.40 score 5 stars 477 downloadsMiDA - Microarray Data Analysis
Set of functions designed to simplify transcriptome analysis and identification of marker molecules using microarrays data. The package includes a set of functions that allows performing full pipeline of analysis including data normalization, summarisation, binary classification, FDR (False Discovery Rate) multiple comparison and the definition of potential biological markers.
Last updated 2 days ago
archivedpackagesr-universe
1.70 score 5 stars 112 downloadsEmiStatR - Emissions and Statistics in R for Wastewater and Pollutants in Combined Sewer Systems
Provides a fast and parallelised calculator to estimate combined wastewater emissions. It supports the planning and design of urban drainage systems, without the requirement of extensive simulation tools. The 'EmiStatR' package implements modular R methods. This enables to add new functionalities through the R framework.
Last updated 8 days ago
archivedpackagesr-universe
1.70 score 5 stars 231 downloadsOHCSpackage - Prepare Housing Data for Analysis
Prepares census and core housing needs data, specifically designed for use with Statistics Canada data and standardized input data. The package offers functions for tidying, organizing, and splitting complex data tables, making it easier for users to perform analyses on the data. 'OHCSpackage''' is particularly useful for those working with census data that has a consistent format, number of rows, and number of columns. With this package, users can save time and streamline their data preparation processes.
Last updated 8 days ago
archivedpackagesr-universe
1.70 score 5 stars 165 downloadsINCATome - Internal Control Analysis of Translatome Studies by Microarrays
Data analysis, normalisation and differential expression for Translatome studies by microarrays (T Sbarrato et al. RNA. 2017 Aug 25; <DOI:10.1261/rna.060525.116>).
Last updated 8 days ago
archivedpackagesr-universe
1.70 score 5 stars 124 downloadssimest - Constrained Single Index Model Estimation
Estimation of function and index vector in single index model with and without shape constraints including different smoothness conditions.
Last updated 9 days ago
archivedpackagesr-universe
1.70 score 5 stars 143 downloadseivtools - Measurement Error Modeling Tools
This includes functions for analysis with error-prone covariates, including deconvolution, latent regression and errors-in-variables regression. It implements methods by Rabe-Hesketh et al. (2003) <doi:10.1191/1471082x03st056oa>, Lockwood and McCaffrey (2014) <doi:10.3102/1076998613509405>, and Lockwood and McCaffrey (2017) <doi:10.1007/s11336-017-9556-y>, among others.
Last updated 9 days ago
archivedpackagesr-universejagscpp
1.70 score 5 stars 179 downloadsrevgeo - Reverse Geocoding with the Photon Geocoder for OpenStreetMap, Google Maps, and Bing
Function revgeo() allows you to use the Photon geocoder for OpenStreetMap <http://photon.komoot.de>, Google Maps <http://maps.google.com>, and Bing <https://www.bingmapsportal.com> to reverse geocode coordinate pairs with minimal hassle.
Last updated 9 days ago
archivedpackagesr-universe
1.70 score 5 stars 310 downloadsSSrat - Two-Dimensional Sociometric Status Determination with Rating Scales
A set of functions for two-dimensional sociometric status determination with rating scales. For each person assessed, SSrat computes probability distributions of the total scores for `Sympathy' (S), `Antipathy' (A), social `Preference' (P) and social `Impact' (I), and applies a set of criteria for sociometric status categorization.
Last updated 9 days ago
archivedpackagesr-universe
1.70 score 5 stars 123 downloadsSizeEstimation - Estimating the Sizes of Populations at Risk of HIV Infection from Multiple Data Sources Using a Bayesian Hierarchical Model
This function develops an algorithm for presenting a Bayesian hierarchical model for estimating the sizes of local and national drug injected populations in Bangladesh. The model incorporates multiple commonly used data sources including mapping data, surveys, interventions, capture-recapture data, estimates or guesstimates from organizations, and expert opinion.
Last updated 9 days ago
archivedpackagesr-universe
1.70 score 5 stars 101 downloadsHETOP - MLE and Bayesian Estimation of Heteroskedastic Ordered Probit (HETOP) Model
Provides functions for maximum likelihood and Bayesian estimation of the Heteroskedastic Ordered Probit (HETOP) model, using methods described in Lockwood, Castellano and Shear (2018) <doi:10.3102/1076998618795124> and Reardon, Shear, Castellano and Ho (2017) <doi:10.3102/1076998616666279>. It also provides a general function to compute the triple-goal estimators of Shen and Louis (1998) <doi:10.1111/1467-9868.00135>.
Last updated 9 days ago
archivedpackagesr-universejagscpp
1.70 score 5 stars 152 downloadsin2extRemes - Into the extRemes Package
Graphical User Interface (GUI) to some of the functions in the package extRemes version >= 2.0 are included.
Last updated 9 days ago
archivedpackagesr-universe
1.70 score 5 stars 284 downloadsMargCond - Joint Marginal-Conditional Model
Fits joint marginal conditional models for multivariate longitudinal data, as in Proudfoot, Faig, Natarajan, and Xu (2018) <doi:10.1002/sim.7552>. Development of this package was supported by the UCSD Altman Translational Research Institute, NIH grant UL1TR001442. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.
Last updated 9 days ago
archivedpackagesr-universe
1.70 score 5 stars 129 downloadsScRNAIMM - Performing Single-Cell RNA-Seq Imputation by Using Mean/Median Imputation
Performing single-cell imputation in a way that preserves the biological variations in the data. The package clusters the input data to do imputation for each cluster, and do a distribution check using the Anderson-Darling normality test to impute dropouts using mean or median (Yazici, B., & Yolacan, S. (2007) <DOI:10.1080/10629360600678310>).
Last updated 19 days ago
archivedpackagesr-universe
1.70 score 5 stars 161 downloadsTukeyRegion - Tukey Region and Median
Tukey regions are polytopes in the Euclidean space, viz. upper-level sets of the Tukey depth function on given data. The bordering hyperplanes of a Tukey region are computed as well as its vertices, facets, centroid, and volume. In addition, the Tukey median set, which is the non-empty Tukey region having highest depth level, and its barycenter (= Tukey median) are calculated. Tukey regions are visualized in dimension two and three. For details see Liu, Mosler, and Mozharovskyi (2019, <doi:10.1080/10618600.2018.1546595>). See file LICENSE.note for additional license information.
Last updated 21 days ago
archivedpackagesr-universecpp
1.70 score 5 stars 268 downloadsohtadstats - Tomoka Ohta D Statistics
Calculate's Tomoka Ohta's partitioning of linkage disequilibrium, deemed D-statistics, for pairs of loci. Petrowski et al. (2019) <doi:10.5334/jors.250>.
Last updated 24 days ago
archivedpackagesr-universe
1.70 score 5 stars 263 downloads