twitteR - R Based Twitter Client

Provides an interface to the Twitter web API.

Last updated 25 days ago

archivedpackagesr-universe

6.24 score 5 stars 1 dependents 2.0k scripts 1.3k downloads

choroplethr - Simplify the Creation of Choropleth Maps in R

Choropleths are thematic maps where geographic regions, such as states, are colored according to some metric, such as the number of people who live in that state. This package simplifies this process by 1. Providing ready-made functions for creating choropleths of common maps. 2. Providing data and API connections to interesting data sources for making choropleths. 3. Providing a framework for creating choropleths from arbitrary shapefiles. 4. Overlaying those maps over reference maps from Google Maps.

Last updated 30 days ago

archivedpackagesr-universe

5.61 score 5 stars 1 dependents 860 scripts 1.3k downloads

acs - Download, Manipulate, and Present American Community Survey and Decennial Data from the US Census

Provides a general toolkit for downloading, managing, analyzing, and presenting data from the U.S. Census (<https://www.census.gov/data/developers/data-sets.html>), including SF1 (Decennial short-form), SF3 (Decennial long-form), and the American Community Survey (ACS). Confidence intervals provided with ACS data are converted to standard errors to be bundled with estimates in complex acs objects. Package provides new methods to conduct standard operations on acs objects and present/plot data in statistically appropriate ways.

Last updated 30 days ago

archivedpackagesr-universe

5.10 score 5 stars 3 dependents 430 scripts 1.3k downloads

flowTraceR - 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 5 days ago

archivedpackagesr-universe

4.35 score 5 stars 1 dependents 282 downloads

sparsevar - Sparse VAR/VECM Models Estimation

A wrapper for sparse VAR/VECM time series models estimation using penalties like ENET (Elastic Net), SCAD (Smoothly Clipped Absolute Deviation) and MCP (Minimax Concave Penalty). Based on the work of Sumanta Basu and George Michailidis <doi:10.1214/15-AOS1315>.

Last updated 1 months ago

archivedpackagesr-universe

4.35 score 5 stars 1 dependents 30 scripts 198 downloads

picasso - Pathwise Calibrated Sparse Shooting Algorithm

Computationally efficient tools for fitting generalized linear model with convex or non-convex penalty. Users can enjoy the superior statistical property of non-convex penalty such as SCAD and MCP which has significantly less estimation error and overfitting compared to convex penalty such as lasso and ridge. Computation is handled by multi-stage convex relaxation and the PathwIse CAlibrated Sparse Shooting algOrithm (PICASSO) which exploits warm start initialization, active set updating, and strong rule for coordinate preselection to boost computation, and attains a linear convergence to a unique sparse local optimum with optimal statistical properties. The computation is memory-optimized using the sparse matrix output.

Last updated 1 months ago

archivedpackagesr-universecpp

4.07 score 5 stars 2 dependents 39 scripts 246 downloads

mpwR - 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 5 days ago

archivedpackagesr-universe

4.00 score 5 stars 292 downloads

getCRUCLdata - 'CRU' 'CL' v. 2.0 Climatology Client

Provides functions that automate downloading and importing University of East Anglia Climate Research Unit ('CRU') 'CL' v. 2.0 climatology data, facilitates the calculation of minimum temperature and maximum temperature and formats the data into a data.table object or a list of 'terra' 'rast' objects for use. 'CRU' 'CL' v. 2.0 data are a gridded climatology of 1961-1990 monthly means released in 2002 and cover all land areas (excluding Antarctica) at 10 arc minutes (0.1666667 degree) resolution. For more information see the description of the data provided by the University of East Anglia Climate Research Unit, <https://crudata.uea.ac.uk/cru/data/hrg/tmc/readme.txt>.

Last updated 1 months ago

anglia-cruclimate-datacru-cl2temperaturerainfallelevationdata-accesswindrelative-humiditysolar-radiationdiurnal-temperaturefrostarchivedpackagesr-universe

3.95 score 5 stars 18 scripts 445 downloads

synthACS - Synthetic Microdata and Spatial MicroSimulation Modeling for ACS Data

Provides access to curated American Community Survey (ACS) base tables via a wrapper to library(acs). Builds synthetic micro-datasets at any user-specified geographic level with ten default attributes; and, conducts spatial microsimulation modeling (SMSM) via simulated annealing. SMSM is conducted in parallel by default. Lastly, we provide functionality for data-extensibility of micro-datasets <doi:10.18637/jss.v104.i07>.

Last updated 30 days ago

archivedpackagesr-universecpp

3.89 score 5 stars 78 scripts 485 downloads

CohortSurvival - Estimate Survival from Common Data Model Cohorts

Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.

Last updated 7 days ago

archivedpackagesr-universe

3.88 score 5 stars 867 downloads

spectralGraphTopology - 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 14 days ago

archivedpackagesr-universeopenblascpp

3.88 score 5 stars 1 dependents 852 downloads

MiscMetabar - Miscellaneous Functions for Metabarcoding Analysis

Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.

Last updated 22 days ago

sequencingmicrobiomemetagenomicsclusteringclassificationvisualizationarchivedpackagesr-universe

3.76 score 5 stars 23 scripts 766 downloads

btb - Beyond the Border - Kernel Density Estimation for Urban Geography

The kernelSmoothing() function allows you to square and smooth geolocated data. It calculates a classical kernel smoothing (conservative) or a geographically weighted median. There are four major call modes of the function. The first call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth) for a classical kernel smoothing and automatic grid. The second call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, quantiles) for a geographically weighted median and automatic grid. The third call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, centroids) for a classical kernel smoothing and user grid. The fourth call mode is kernelSmoothing(obs, epsg, cellsize, bandwidth, quantiles, centroids) for a geographically weighted median and user grid. Geographically weighted summary statistics : a framework for localised exploratory data analysis, C.Brunsdon & al., in Computers, Environment and Urban Systems C.Brunsdon & al. (2002) <doi:10.1016/S0198-9715(01)00009-6>, Statistical Analysis of Spatial and Spatio-Temporal Point Patterns, Third Edition, Diggle, pp. 83-86, (2003) <doi:10.1080/13658816.2014.937718>.

Last updated 14 days ago

archivedpackagesr-universecpp

3.70 score 5 stars 418 downloads

OwenQ - Owen Q-Function

Evaluates the Owen Q-function for an integer value of the degrees of freedom, by applying Owen's algorithm (1965) <doi:10.1093/biomet/52.3-4.437>. It is useful for the calculation of the power of equivalence tests.

Last updated 25 days ago

archivedpackagesr-universecpp

3.70 score 5 stars 10 scripts 352 downloads

DDoutlier - Distance & Density-Based Outlier Detection

Outlier detection in multidimensional domains. Implementation of notable distance and density-based outlier algorithms. Allows users to identify local outliers by comparing observations to their nearest neighbors, reverse nearest neighbors, shared neighbors or natural neighbors. For distance-based approaches, see Knorr, M., & Ng, R. T. (1997) <doi:10.1145/782010.782021>, Angiulli, F., & Pizzuti, C. (2002) <doi:10.1007/3-540-45681-3_2>, Hautamaki, V., & Ismo, K. (2004) <doi:10.1109/ICPR.2004.1334558> and Zhang, K., Hutter, M. & Jin, H. (2009) <doi:10.1007/978-3-642-01307-2_84>. For density-based approaches, see Tang, J., Chen, Z., Fu, A. W. C., & Cheung, D. W. (2002) <doi:10.1007/3-540-47887-6_53>, Jin, W., Tung, A. K. H., Han, J., & Wang, W. (2006) <doi:10.1007/11731139_68>, Schubert, E., Zimek, A. & Kriegel, H-P. (2014) <doi:10.1137/1.9781611973440.63>, Latecki, L., Lazarevic, A. & Prokrajac, D. (2007) <doi:10.1007/978-3-540-73499-4_6>, Papadimitriou, S., Gibbons, P. B., & Faloutsos, C. (2003) <doi:10.1109/ICDE.2003.1260802>, Breunig, M. M., Kriegel, H.-P., Ng, R. T., & Sander, J. (2000) <doi:10.1145/342009.335388>, Kriegel, H.-P., Kröger, P., Schubert, E., & Zimek, A. (2009) <doi:10.1145/1645953.1646195>, Zhu, Q., Feng, Ji. & Huang, J. (2016) <doi:10.1016/j.patrec.2016.05.007>, Huang, J., Zhu, Q., Yang, L. & Feng, J. (2015) <doi:10.1016/j.knosys.2015.10.014>, Tang, B. & Haibo, He. (2017) <doi:10.1016/j.neucom.2017.02.039> and Gao, J., Hu, W., Zhang, X. & Wu, Ou. (2011) <doi:10.1007/978-3-642-20847-8_23>.

Last updated 25 days ago

archivedpackagesr-universe

3.62 score 5 stars 1 dependents 56 scripts 446 downloads

mr.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 13 days ago

archivedpackagesr-universe

3.53 score 5 stars 2 dependents 2.2k downloads

tableschema.r - Table Schema 'Frictionless Data'

Allows to work with 'Table Schema' (<https://specs.frictionlessdata.io/table-schema/>). 'Table Schema' is well suited for use cases around handling and validating tabular data in text formats such as 'csv', but its utility extends well beyond this core usage, towards a range of applications where data benefits from a portable schema format. The 'tableschema.r' package can load and validate any table schema descriptor, allow the creation and modification of descriptors, expose methods for reading and streaming data that conforms to a 'Table Schema' via the 'Tabular Data Resource' abstraction.

Last updated 21 days ago

archivedpackagesr-universe

3.40 score 5 stars 101 scripts 184 downloads

MicroSEC - 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 19 hours ago

archivedpackagesr-universe

3.40 score 5 stars 182 downloads

polyhedralCubature - 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 2 days ago

archivedpackagesr-universe

3.40 score 5 stars 198 downloads

tern.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 3 days ago

archivedpackagesr-universe

3.40 score 5 stars 258 downloads

mapping - Automatic Download, Linking, Manipulating Coordinates for Maps

Maps are an important tool to visualise variables distribution across different spatial objects. The mapping process requires to link the data with coordinates and then generate the correspondent map. This package provide coordinates, linking and mapping functions for an automatic, flexible and easy approach of external functions. The package provides an easy, flexible and automatic unit. Geographical coordinates are provided in the package and automatically linked with the input data to generate maps with internal provided functions or external functions. Provide an easy, flexible and automatic approach to potentially download updated coordinates, to link statistical units with coordinates and to aggregate variables based on the spatial hierarchy of units. The object returned from the package can be used for thematic maps with the build-in functions provided in mapping or with other packages already available.

Last updated 5 days ago

archivedpackagesr-universe

3.40 score 5 stars 351 downloads

rock - 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 5 days ago

archivedpackagesr-universe

3.40 score 5 stars 425 downloads

STRMPS - 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 7 days ago

biostringspwalignshortreadirangesarchivedpackagesr-universe

3.40 score 5 stars 232 downloads

finreportr - 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 8 days ago

archivedpackagesr-universe

3.40 score 5 stars 411 downloads

Pandora - Retrieve Data using the API of the 'Pandora' Data Platform

API wrapper that contains functions to retrieve data from the 'Pandora' databases. Web services for API: <https://pandora.earth/>.

Last updated 23 days ago

archivedpackagesr-universe

3.40 score 5 stars 2 scripts 259 downloads

TwitterAutomatedTrading - Automated Trading Using Tweets

Provides an integration to the 'metatrader 5'. The functionalities carry out automated trading using sentiment indexes computed from 'twitter' and/or 'stockwits'. The sentiment indexes are based on the ph.d. dissertation "Essays on Economic Forecasting Models" (Godeiro,2018) <https://repositorio.ufpb.br/jspui/handle/123456789/15198> The integration between the 'R' and the 'metatrader 5' allows sending buy/sell orders to the brokerage.

Last updated 25 days ago

archivedpackagesr-universe

3.40 score 5 stars 4 scripts 181 downloads

MALDIcellassay - Automated MALDI Cell Assays Using Dose-Response Curve Fitting

Conduct automated cell-based assays using Matrix-Assisted Laser Desorption/Ionization (MALDI) methods for high-throughput screening of signals responsive to treatments. The package efficiently identifies high variance signals and fits dose-response curves to them. Quality metrics such as Z', V', log2FC, and CRS are provided for evaluating the potential of signals as biomarkers. The methodologies were introduced by Weigt et al. (2018) <doi:10.1038/s41598-018-29677-z> and refined by Unger et al. (2021) <doi:10.1038/s41596-021-00624-z>.

Last updated 25 days ago

archivedpackagesr-universe

3.40 score 5 stars 9 scripts 181 downloads

unnest - Unnest Hierarchical Data Structures

Fast flattening of hierarchical data structures (e.g. JSON, XML) into data.frames with a flexible spec language.

Last updated 28 days ago

archivedpackagesr-universecpp

3.40 score 5 stars 4 scripts 345 downloads

SFSI - Sparse Family and Selection Index

Here we provide tools for the estimation of coefficients in penalized regressions when the (co)variance matrix of predictors and the covariance vector between predictors and response, are provided. These methods are extended to the context of a Selection Index (commonly used for breeding value prediction). The approaches offer opportunities such as the integration of high-throughput traits in genetic evaluations ('Lopez-Cruz et al., 2020') <doi:10.1038/s41598-020-65011-2> and solutions for training set optimization in Genomic Prediction ('Lopez-Cruz & de los Campos, 2021') <doi:10.1093/genetics/iyab030>.

Last updated 29 days ago

archivedpackagesr-universeopenblas

3.30 score 5 stars 20 scripts 611 downloads

TukeyC - Conventional Tukey Test

Perform the conventional Tukey test from formula, lm, aov, aovlist and lmer objects.

Last updated 6 days ago

archivedpackagesr-universe

3.24 score 5 stars 599 downloads

PResiduals - Probability-Scale Residuals and Residual Correlations

Computes probability-scale residuals and residual correlations for continuous, ordinal, binary, count, and time-to-event data <doi:10.18637/jss.v094.i12>.

Last updated 18 days ago

archivedpackagesr-universe

3.22 score 5 stars 67 scripts 408 downloads

noaastormevents - Explore NOAA Storm Events Database

Allows users to explore and plot data from the National Oceanic and Atmospheric Administration (NOAA) Storm Events database through R for United States counties. Functionality includes matching storm event listings by time and location to hurricane best tracks data. This work was supported by grants from the Colorado Water Center, the National Institute of Environmental Health Sciences (R00ES022631) and the National Science Foundation (1331399).

Last updated 30 days ago

archivedpackagesr-universe

3.20 score 5 stars 16 scripts 300 downloads

figpatch - Easily Arrange External Figures with Patchwork Alongside 'ggplot2' Figures

For including external figures into an assembled {patchwork}. This enables the creation of more complex figures that include images alongside plots.

Last updated 25 days ago

archivedpackagesr-universe

3.18 score 5 stars 61 scripts 260 downloads

clinDataReview - 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 6 days ago

archivedpackagesr-universe

3.18 score 5 stars 678 downloads

D4TAlink.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 4 days ago

archivedpackagesr-universe

3.00 score 5 stars 344 downloads

seeker - Simplified Fetching and Processing of Microarray and RNA-Seq Data

Wrapper around various existing tools and command-line interfaces, providing a standard interface, simple parallelization, and detailed logging. For microarray data, maps probe sets to standard gene IDs, building on 'GEOquery' Davis and Meltzer (2007) <doi:10.1093/bioinformatics/btm254>, 'ArrayExpress' Kauffmann et al. (2009) <doi:10.1093/bioinformatics/btp354>, Robust multi-array average 'RMA' Irizarry et al. (2003) <doi:10.1093/biostatistics/4.2.249>, and 'BrainArray' Dai et al. (2005) <doi:10.1093/nar/gni179>. For RNA-seq data, fetches metadata and raw reads from National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA), performs standard adapter and quality trimming using 'TrimGalore' Krueger <https://github.com/FelixKrueger/TrimGalore>, performs quality control checks using 'FastQC' Andrews <https://github.com/s-andrews/FastQC>, quantifies transcript abundances using 'salmon' Patro et al. (2017) <doi:10.1038/nmeth.4197> and potentially 'refgenie' Stolarczyk et al. (2020) <doi:10.1093/gigascience/giz149>, aggregates the results using 'MultiQC' Ewels et al. (2016) <doi:10.1093/bioinformatics/btw354>, maps transcripts to genes using 'biomaRt' Durinkck et al. (2009) <doi:10.1038/nprot.2009.97>, and summarizes transcript-level quantifications for gene-level analyses using 'tximport' Soneson et al. (2015) <doi:10.12688/f1000research.7563.2>.

Last updated 30 days ago

archivedpackagesr-universe

3.00 score 5 stars 1 scripts 253 downloads

tessellation - 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 2 days ago

archivedpackagesr-universe

2.88 score 5 stars 1 dependents 256 downloads

casabourse - Casablanca Stock Exchange Data

It provides real-time data from the Casablanca Stock Exchange. The objective is to facilitate access to data for all users of the R programming language. It includes a variety of data accessible just by function call.

Last updated 29 days ago

archivedpackagesr-universe

2.74 score 5 stars 11 scripts 392 downloads

kmeRs - 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 5 days ago

softwarearchivedpackagesr-universe

2.70 score 5 stars 192 downloads

hddplot - 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 5 days ago

archivedpackagesr-universe

2.70 score 5 stars 366 downloads

TEAM - 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 6 days ago

archivedpackagesr-universe

2.70 score 5 stars 128 downloads

TT - 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 6 days ago

archivedpackagesr-universe

2.70 score 5 stars 179 downloads

varycoef - Modeling Spatially Varying Coefficients

Implements a maximum likelihood estimation (MLE) method for estimation and prediction of Gaussian process-based spatially varying coefficient (SVC) models (Dambon et al. (2021a) <doi:10.1016/j.spasta.2020.100470>). Covariance tapering (Furrer et al. (2006) <doi:10.1198/106186006X132178>) can be applied such that the method scales to large data. Further, it implements a joint variable selection of the fixed and random effects (Dambon et al. (2021b) <doi:10.1080/13658816.2022.2097684>). The package and its capabilities are described in (Dambon et al. (2021c) <arXiv:2106.02364>).

Last updated 9 days ago

archivedpackagesr-universe

2.70 score 5 stars 259 downloads

nbfar - 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 14 days ago

archivedpackagesr-universeopenblascpp

2.70 score 5 stars 169 downloads

easyDifferentialGeneCoexpression - Easily Performs Differential Coexpression Analysis

A function that reads in the GEO code of a list of probesets or gene symbols, a gene expression dataset GEO accession code, the name of the dataset feature discriminating the two conditions for the differential coexpression, and the values of the two different conditions for the differential coexpression, and returns the significant pairs of genes/probesets with highest differential coexpression (p-value < 0.005). If the input gene list is made of gene symbols, this package associates the probesets to these gene symbols, if found. Platforms available: GPL80, GPL8300, GPL80, GPL96, GPL570, GPL571, GPL20115, GPL1293, GPL6102, GPL6104, GPL6883, GPL6884, GPL13497, GPL14550, GPL17077, GPL6480. GEO: Gene Expression Omnibus. ID: identifier code. The GEO datasets are downloaded from the URL <https://ftp.ncbi.nlm.nih.gov/geo/series/>.

Last updated 29 days ago

archivedpackagesr-universe

2.70 score 5 stars 2 scripts 217 downloads

exceedProb - Confidence Intervals for Exceedance Probability

Computes confidence intervals for the exceedance probability of normally distributed estimators. Currently only supports general linear models. Please see Segal (2019) <arXiv:1803.03356> for more information.

Last updated 29 days ago

archivedpackagesr-universecpp

2.51 score 5 stars 13 scripts 161 downloads

mbest - 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 4 days ago

archivedpackagesr-universe

2.48 score 5 stars 2 dependents 844 downloads

rehydratoR - 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 1 days ago

archivedpackagesr-universe

2.40 score 5 stars 146 downloads

bdsm - Bayesian Dynamic Systems Modeling

Implements methods for building and analyzing models based on panel data as described in the paper by Moral-Benito (2013, <doi:10.1080/07350015.2013.818003>). The package provides functions to estimate dynamic panel data models and analyze the results of the estimation.

Last updated 3 days ago

archivedpackagesr-universe

2.40 score 5 stars 225 downloads

tidyformula - 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 5 days ago

archivedpackagesr-universe

2.40 score 5 stars 193 downloads

marp - 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 12 days ago

archivedpackagesr-universe

2.40 score 5 stars 184 downloads

rllama - 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 13 days ago

archivedpackagesr-universe

2.40 score 5 stars 265 downloads

finbipartite - 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 14 days ago

archivedpackagesr-universe

2.40 score 5 stars 206 downloads

fingraph - 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 14 days ago

archivedpackagesr-universe

2.40 score 5 stars 192 downloads

washex - Washington State Legislative Explorer

Gets data from the Washington State Legislature.

Last updated 18 days ago

archivedpackagesr-universe

2.40 score 5 stars 2 scripts 192 downloads

dataclass - Easily Create Structured Lists or Data Frames with Input Validation

Easily define templates for lists and data frames that validate each element. Specify the expected type (i.e., character, numeric, etc), expected length, minimum and maximum values, allowable values, and more for each element in your data. Decide whether violations of these expectations should throw an error or a warning. This package is useful for validating data within R processes which pull from dynamic data sources such as databases and web APIs to provide an extra layer of validation around input and output data.

Last updated 21 days ago

archivedpackagesr-universe

2.40 score 5 stars 1 scripts 337 downloads

squat - Statistics for Quaternion Temporal Data

An implementation of statistical tools for the analysis of rotation-valued time series and functional data. It relies on pre-existing quaternion data structure provided by the 'Eigen' 'C++' library.

Last updated 25 days ago

archivedpackagesr-universecppopenmp

2.40 score 5 stars 6 scripts 185 downloads

IOHexperimenter - Benchmarking Part of the 'IOHprofiler'

The benchmarking module for the Iterative Optimization Heuristics Profiler ('IOHprofiler'). This module provides benchmarking in the 'IOHprofiler' format, which can be visualized using the 'IOHanalyzer' module.

Last updated 28 days ago

archivedpackagesr-universecpp

2.40 score 5 stars 3 scripts 257 downloads

glottospace - Language Mapping and Geospatial Analysis of Linguistic and Cultural Data

Streamlined workflows for geolinguistic analysis, including: accessing global linguistic and cultural databases, data import, data entry, data cleaning, data exploration, mapping, visualization and export.

Last updated 1 months ago

archivedpackagesr-universe

2.40 score 5 stars 6 scripts 109 downloads

XBRL - 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 8 days ago

archivedpackagesr-universelibxml2cpp

2.18 score 5 stars 1 dependents 448 downloads

prefio - Structures for Preference Data

Convenient structures for creating, sourcing, reading, writing and manipulating ordinal preference data. Methods for writing to/from PrefLib formats. See Nicholas Mattei and Toby Walsh "PrefLib: A Library of Preference Data" (2013) <doi:10.1007/978-3-642-41575-3_20>.

Last updated 1 months ago

archivedpackagesr-universe

2.18 score 5 stars 1 dependents 4 scripts 77 downloads

FLSSS - Mining Rigs for Problems in the Subset Sum Family

Specialized solvers for combinatorial optimization problems in the Subset Sum family. The solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value multisets with predefined subset sum errors, (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The multi-threaded framework for the latter offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Historical updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) option of mapping floating-point instance to compressed 64-bit integer instance with user-controlled precision loss, which could yield substantial speedup due to the dimension reduction and efficient compressed integer arithmetic via bit-manipulations; (e) distributed computing infrastructure for multidimensional subset sum; (f) arbitrary-precision zero-margin-of-error multidimensional Subset Sum accelerated by a simplified Bloom filter. The package contains a copy of xxHash from <https://github.com/Cyan4973/xxHash>. Package vignette (<doi:10.48550/arXiv.1612.04484>) detailed a few historical updates. Functions prefixed with 'aux' (auxiliary) are independent implementations of published algorithms for solving optimization problems less relevant to Subset Sum.

Last updated 30 days ago

archivedpackagesr-universegmpcpp

2.00 score 5 stars 20 scripts 512 downloads

TukeyRegion - 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 2 days ago

archivedpackagesr-universecpp

1.70 score 5 stars 268 downloads

ohtadstats - 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 5 days ago

archivedpackagesr-universe

1.70 score 5 stars 263 downloads

ormBigData - Fitting Semiparametric Cumulative Probability Models for Big Data

A big data version for fitting cumulative probability models using the orm() function. See Liu et al. (2017) <DOI:10.1002/sim.7433> for details.

Last updated 18 days ago

archivedpackagesr-universe

1.70 score 5 stars 175 downloads

cpmBigData - Fitting Semiparametric Cumulative Probability Models for Big Data

A big data version for fitting cumulative probability models using the orm() function from the 'rms' package. See Liu et al. (2017) <DOI:10.1002/sim.7433> for details.

Last updated 18 days ago

archivedpackagesr-universe

1.70 score 5 stars 238 downloads

DATAstudio - The Research Data Warehouse of Miguel de Carvalho

Pulls together a collection of datasets from Miguel de Carvalho research articles. Including, for example: - de Carvalho (2012) <doi:10.1016/j.jspi.2011.08.016>; - de Carvalho et al (2012) <doi:10.1080/03610926.2012.709905>; - de Carvalho et al (2012) <doi:10.1016/j.econlet.2011.09.007>); - de Carvalho and Davison (2014) <doi:10.1080/01621459.2013.872651>; - de Carvalho and Rua (2017) <doi:10.1016/j.ijforecast.2015.09.004>.

Last updated 23 days ago

archivedpackagesr-universe

1.70 score 5 stars 2 scripts 285 downloads

fastQR - Fast QR Decomposition and Update

Efficient algorithms for performing, updating, and downdating the QR decomposition, R decomposition, or the inverse of the R decomposition of a matrix as rows or columns are added or removed. It also includes functions for solving linear systems of equations, normal equations for linear regression models, and normal equations for linear regression with a RIDGE penalty. For a detailed introduction to these methods, see the book by Golub and Van Loan (2013, <doi:10.1007/978-3-319-05089-8>) for complete introduction to the methods.

Last updated 24 days ago

archivedpackagesr-universecpp

1.70 score 5 stars 4 scripts 172 downloads

Statsomat - Shiny Apps for Automated Data Analysis and Automated Interpretation

Shiny apps for automated data analysis, annotated outputs and human-readable interpretation in natural language. Designed especially for learners and applied researchers. Currently available methods: EDA, EDA with Python, Correlation Analysis, Principal Components Analysis, Confirmatory Factor Analysis.

Last updated 25 days ago

archivedpackagesr-universe

1.70 score 5 stars 6 scripts 273 downloads

VARDetect - Multiple Change Point Detection in Structural VAR Models

Implementations of Thresholded Block Segmentation Scheme (TBSS) and Low-rank plus Sparse Two Step Procedure (LSTSP) algorithms for detecting multiple changes in structural VAR models. The package aims to address the problem of change point detection in piece-wise stationary VAR models, under different settings regarding the structure of their transition matrices (autoregressive dynamics); specifically, the following cases are included: (i) (weakly) sparse, (ii) structured sparse, and (iii) low rank plus sparse. It includes multiple algorithms and related extensions from Safikhani and Shojaie (2020) <doi:10.1080/01621459.2020.1770097> and Bai, Safikhani and Michailidis (2020) <doi:10.1109/TSP.2020.2993145>.

Last updated 1 months ago

archivedpackagesr-universeopenblascppopenmp

1.70 score 5 stars 1 scripts 174 downloads

elections.dtree - Ranked Voting Election Audits with Dirichlet-Trees

Perform ballot-polling Bayesian audits for ranked voting elections using Dirichlet-tree prior distributions. Everest et al. (2022) <arXiv:2206.14605>, <arXiv:2209.03881>.

Last updated 1 months ago

archivedpackagesr-universecpp

1.70 score 5 stars 3 scripts 160 downloads