httpgd - A 'HTTP' Server Graphics Device

A graphics device for R that is accessible via network protocols. This package was created to make it easier to embed live R graphics in integrated development environments and other applications. The included 'HTML/JavaScript' client (plot viewer) aims to provide a better overall user experience when dealing with R graphics. The device asynchronously serves graphics via 'HTTP' and 'WebSockets'.

Last updated 3 days ago

archivedpackagesr-universecpp

6.68 score 5 stars 1 dependents 280 scripts 3.8k 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 5 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 5 days ago

archivedpackagesr-universe

5.10 score 5 stars 3 dependents 430 scripts 1.3k downloads

unigd - Universal Graphics Device

A unified R graphics backend. Render R graphics fast and easy to many common file formats. Provides a thread safe 'C' interface for asynchronous rendering of R graphics.

Last updated 3 days ago

archivedpackagesr-universecairotifflibpngzlibcpp

5.01 score 5 stars 2 dependents 6 scripts 3.4k downloads

FeatureHashing - Creates a Model Matrix via Feature Hashing with a Formula Interface

Feature hashing, also called as the hashing trick, is a method to transform features of a instance to a vector. Thus, it is a method to transform a real dataset to a matrix. Without looking up the indices in an associative array, it applies a hash function to the features and uses their hash values as indices directly. The method of feature hashing in this package was proposed in Weinberger et al. (2009) <arXiv:0902.2206>. The hashing algorithm is the murmurhash3 from the 'digest' package. Please see the README in <https://github.com/wush978/FeatureHashing> for more information.

Last updated 29 days ago

archivedpackagesr-universecpp

4.85 score 5 stars 141 scripts 294 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 8 days ago

archivedpackagesr-universecpp

4.37 score 5 stars 4 dependents 39 scripts 342 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 8 days ago

archivedpackagesr-universe

4.35 score 5 stars 1 dependents 30 scripts 302 downloads

onemap - Construction of Genetic Maps in Experimental Crosses

Analysis of molecular marker data from model (backcrosses, F2 and recombinant inbred lines) and non-model systems (i. e. outcrossing species). For the later, it allows statistical analysis by simultaneously estimating linkage and linkage phases (genetic map construction) according to Wu et al. (2002) <doi:10.1006/tpbi.2002.1577>. All analysis are based on multipoint approaches using hidden Markov models.

Last updated 23 days ago

archivedpackagesr-universecpp

4.15 score 5 stars 556 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 8 days ago

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

3.95 score 5 stars 18 scripts 202 downloads

readwritesqlite - Enhanced Reading and Writing for 'SQLite' Databases

Reads and writes data frames to 'SQLite' databases while preserving time zones (for POSIXct columns), projections (for 'sfc' columns), units (for 'units' columns), levels (for factors and ordered factors) and classes for logical, Date and 'hms' columns. It also logs changes to tables and provides more informative error messages.

Last updated 1 months ago

archivedpackagesr-universe

3.92 score 5 stars 1 dependents 11 scripts 204 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 5 days ago

archivedpackagesr-universecpp

3.89 score 5 stars 78 scripts 485 downloads

databraryr - Interact with the 'Databrary.org' API

'Databrary.org' is a restricted access repository for research data, especially video and audio. This package provides commands to interact with the data stored on 'Databrary.org'.

Last updated 21 days ago

archivedpackagesr-universe

3.88 score 5 stars 323 downloads

openmpt - Open 'ModPlug' Tracker Port

Tracker music uses audio samples and pattern tables to organise musical compositions. Such music is stored in module files. This package reads, renders and plays module files using the 'libopenmpt' library <https://lib.openmpt.org/>.

Last updated 22 days ago

archivedpackagesr-universelibopenmptportaudio19cpp

3.88 score 5 stars 189 downloads

cppcontainers - 'C++' Standard Template Library Containers

Use 'C++' Standard Template Library containers interactively in R. Includes sets, unordered sets, multisets, unordered multisets, maps, unordered maps, multimaps, unordered multimaps, stacks, queues, priority queues, vectors, deques, forward lists, and lists.

Last updated 11 days ago

archivedpackagesr-universecpp

3.70 score 5 stars 431 downloads

ondisc - Fast, Universal, and Intuitive Computing on Large-Scale Single-Cell Data

Single-cell datasets are growing in size, posing challenges as well as opportunities for biology researchers. 'ondisc' (short for "on-disk single cell") enables users to easily and efficiently analyze large-scale single-cell data. 'ondisc' makes computing on large-scale single-cell data FUN: Fast, Universal, and iNtuitive.

Last updated 15 days ago

archivedpackagesr-universezlibcpp

3.70 score 5 stars 246 downloads

SI - Stochastic Integrating

An implementation of four stochastic methods of integrating in R, including: 1. Stochastic Point Method (or Monte Carlo Method); 2. Mean Value Method; 3. Important Sampling Method; 4. Stratified Sampling Method. It can be used to estimate one-dimension or multi-dimension integration by Monte Carlo methods. And the estimated variance (precision) is given. Reference: Caflisch, R. E. (1998) <doi:10.1017/S0962492900002804>.

Last updated 22 days ago

archivedpackagesr-universe

3.70 score 5 stars 149 downloads

ExpImage - Analysis of Images in Experiments

Tools created for image analysis in researches. There are functions associated with image editing, segmentation, and obtaining biometric measurements (Este pacote foi idealizado para para a analise de imagens em pesquisas. Ha funcoes associadas a edicao de imagens, segmentacao, e obtencao de medidas biometricas) <https://www.expstat.com/pacotes-do-r/expimage>.

Last updated 15 days ago

archivedpackagesr-universe

3.48 score 5 stars 323 downloads

LncPath - Identifying the Pathways Regulated by LncRNA Sets of Interest

Identifies pathways synergisticly regulated by the interested lncRNA(long non-coding RNA) sets based on a lncRNA-mRNA(messenger RNA) interaction network. 1) The lncRNA-mRNA interaction network was built from the protein-protein interactions and the lncRNA-mRNA co-expression relationships in 28 RNA-Seq data sets. 2) The interested lncRNAs can be mapped into networks as seed nodes and a random walk strategy will be performed to evaluate the rate of each coding genes influenced by the seed lncRNAs. 3) Pathways regulated by the lncRNA set will be evaluated by a weighted Kolmogorov-Smirnov statistic as an ES Score. 4) The p value and false discovery rate value will also be calculated through a permutation analysis. 5) The running score of each pathway can be plotted and the heat map of each pathway can also be plotted if an expression profile is provided. 6) The rank and scores of the gene list of each pathway can be printed.

Last updated 22 days ago

archivedpackagesr-universe

3.48 score 5 stars 156 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 3 days ago

archivedpackagesr-universecpp

3.40 score 5 stars 4 scripts 345 downloads

coil - Contextualization and Evaluation of COI-5P Barcode Data

Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences against nucleotide and amino acid profile hidden Markov models (PHMMs) (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted analysis of barcode data.

Last updated 15 days ago

archivedpackagesr-universe

3.40 score 5 stars 347 downloads

nimbleAPT - Adaptive Parallel Tempering for 'NIMBLE'

Functions for adaptive parallel tempering (APT) with NIMBLE models. Adapted from 'Lacki' & 'Miasojedow' (2016) <DOI:10.1007/s11222-015-9579-0> and 'Miasojedow, Moulines and Vihola' (2013) <DOI:10.1080/10618600.2013.778779>.

Last updated 15 days ago

archivedpackagesr-universe

3.40 score 5 stars 238 downloads

PPtreeregViz - Projection Pursuit Regression Tree Visualization

It was developed as a tool for exploring 'PPTreereg' (Projection Pursuit TREE of REGression). It uses various projection pursuit indexes and 'XAI' (eXplainable Artificial Intelligence) methods to help understand the model by finding connections between the input variables and prediction values of the model. The 'KernelSHAP' (Aas, Jullum and Løland (2019) <arXiv:1903.10464>) algorithm was modified to fit ‘PPTreereg’, and some codes were modified from the 'shapr' package (Sellereite, Nikolai, and Martin Jullum (2020) <doi:10.21105/joss.02027>). The implemented methods help to explore the model at the single instance level as well as at the whole dataset level. Users can compare with other machine learning models by applying it to the 'DALEX' package of 'R'.

Last updated 18 days ago

archivedpackagesr-universeopenblascpp

3.40 score 5 stars 229 downloads

COCONUT - COmbat CO-Normalization Using conTrols (COCONUT)

Allows for pooled analysis of microarray data by batch-correcting control samples, and then applying the derived correction parameters to non-control samples to obtain bias-free, inter-dataset corrected data.

Last updated 22 days ago

archivedpackagesr-universe

3.40 score 5 stars 523 downloads

IsotopeR - Stable Isotope Mixing Model

Estimates diet contributions from isotopic sources using JAGS. Includes estimation of concentration dependence and measurement error.

Last updated 22 days ago

archivedpackagesr-universejagscpp

3.40 score 5 stars 391 downloads

dhis2r - Client for the 'DHIS2' Web API

Connect and pull data from a 'DHIS2 (District Health Information Software 2)' instance into R.

Last updated 24 days ago

archivedpackagesr-universe

3.40 score 5 stars 294 downloads

forestdynR - Calculate Forest Dynamics

Determines the dynamics of tree species communities (mortality rates, recruitment, loss and gain in basal area, net changes and turnover). Important notes are a) The 'forest_df' argument (data) must contain the columns 'plot' (plot identification), 'spp' (species identification), DBH_1 (Diameter at breast height in first year of measure) and DBH_2 (Diameter at breast height in second year of measure). DBH_1 and DBH_2 must be numeric values; b) example input file in 'data(forest_df_example)'; c) The argument 'inv_time' represents the time between inventories, in years; d) The 'coord' argument must be of the type 'c(longitude, latitude)', with decimal degree values; e) Argument 'add_wd' represents a dataframe with wood density values (g cm-3) format with three columns ('genus', 'species', 'wd'). This argument is set to NULL by default, and if isn't provided, the wood density will be estimated with the getWoodDensity() function from the 'BIOMASS' package.

Last updated 27 days ago

archivedpackagesr-universe

3.40 score 5 stars 4 scripts 444 downloads

RFCCA - Random Forest with Canonical Correlation Analysis

Random Forest with Canonical Correlation Analysis (RFCCA) is a random forest method for estimating the canonical correlations between two sets of variables depending on the subject-related covariates. The trees are built with a splitting rule specifically designed to partition the data to maximize the canonical correlation heterogeneity between child nodes. The method is described in Alakus et al. (2021) <doi:10.1093/bioinformatics/btab158>. 'RFCCA' uses 'randomForestSRC' package (Ishwaran and Kogalur, 2020) by freezing at the version 2.9.3. The custom splitting rule feature is utilised to apply the proposed splitting rule. The 'randomForestSRC' package implements 'OpenMP' by default, contingent upon the support provided by the target architecture and operating system. In this package, 'LAPACK' and 'BLAS' libraries are used for matrix decompositions.

Last updated 27 days ago

archivedpackagesr-universeopenblasopenmp

3.40 score 5 stars 3 scripts 131 downloads

CovRegRF - Covariance Regression with Random Forests

Covariance Regression with Random Forests (CovRegRF) is a random forest method for estimating the covariance matrix of a multivariate response given a set of covariates. Random forest trees are built with a new splitting rule which is designed to maximize the distance between the sample covariance matrix estimates of the child nodes. The method is described in Alakus et al. (2023) <doi:10.1186/s12859-023-05377-y>. 'CovRegRF' uses 'randomForestSRC' package (Ishwaran and Kogalur, 2022) <https://cran.r-project.org/package=randomForestSRC> by freezing at the version 3.1.0. The custom splitting rule feature is utilised to apply the proposed splitting rule. The 'randomForestSRC' package implements 'OpenMP' by default, contingent upon the support provided by the target architecture and operating system. In this package, 'LAPACK' and 'BLAS' libraries are used for matrix decompositions.

Last updated 30 days ago

archivedpackagesr-universeopenblasopenmp

3.40 score 5 stars 3 scripts 103 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 5 days ago

archivedpackagesr-universeopenblas

3.30 score 5 stars 20 scripts 611 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 5 days ago

archivedpackagesr-universe

3.20 score 5 stars 16 scripts 300 downloads

Dodge - Acceptance Sampling Ideas Originated by H.F. Dodge

A variety of sampling plans are able to be compared using evaluations of their operating characteristics (OC), average outgoing quality (OQ), average total inspection (ATI) etc.

Last updated 22 days ago

archivedpackagesr-universe

3.10 score 5 stars 179 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 6 days ago

archivedpackagesr-universe

3.00 score 5 stars 1 scripts 357 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 4 days ago

archivedpackagesr-universe

2.74 score 5 stars 11 scripts 392 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 4 days ago

archivedpackagesr-universe

2.70 score 5 stars 2 scripts 217 downloads

MissCP - Change Point Detection with Missing Values

A four step change point detection method that can detect break points with the presence of missing values proposed by Liu and Safikhani (2023) <https://drive.google.com/file/d/1a8sV3RJ8VofLWikTDTQ7W4XJ76cEj4Fg/view?usp=drive_link>.

Last updated 8 days ago

archivedpackagesr-universeopenblascpp

2.70 score 5 stars 2 scripts 144 downloads

sharpshootR - A Soil Survey Toolkit

Miscellaneous soil data management, summary, visualization, and conversion utilities to support soil survey.

Last updated 14 days ago

archivedpackagesr-universe

2.70 score 5 stars 934 downloads

MRS - Multi-Resolution Scanning for Cross-Sample Differences

An implementation of the MRS algorithm for comparison across distributions, as described in Jacopo Soriano, Li Ma (2017) <doi:10.1111/rssb.12180>. The model is based on a nonparametric process taking the form of a Markov model that transitions between a "null" and an "alternative" state on a multi-resolution partition tree of the sample space. MRS effectively detects and characterizes a variety of underlying differences. These differences can be visualized using several plotting functions.

Last updated 14 days ago

archivedpackagesr-universecpp

2.70 score 5 stars 301 downloads

dartR.captive - Analysing 'SNP' Data to Support Captive Breeding

Functions are provided that facilitate the analysis of SNP (single nucleotide polymorphism) data to answer questions regarding captive breeding and relatedness between individuals. 'dartR.captive' is part of the 'dartRverse' suit of packages. Gruber et al. (2018) <doi:10.1111/1755-0998.12745>. Mijangos et al. (2022) <doi:10.1111/2041-210X.13918>.

Last updated 15 days ago

archivedpackagesr-universe

2.70 score 5 stars 271 downloads

CRM - Continual Reassessment Method (CRM) for Phase I Clinical Trials

Functions for phase I clinical trials using the continual reassessment method.

Last updated 19 days ago

archivedpackagesr-universe

2.70 score 5 stars 262 downloads

dhh - A Heavy-Headed Distribution

The density, cumulative distribution, quantiles, and i.i.d random variables of a heavy-headed distribution. For more information, please see the vignette.

Last updated 22 days ago

archivedpackagesr-universe

2.70 score 5 stars 133 downloads

NetSwan - Network Strengths and Weaknesses Analysis

A set of functions for studying network robustness, resilience and vulnerability.

Last updated 22 days ago

archivedpackagesr-universe

2.54 score 5 stars 521 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 5 days ago

archivedpackagesr-universecpp

2.51 score 5 stars 13 scripts 161 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 3 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 6 days ago

archivedpackagesr-universe

2.40 score 5 stars 6 scripts 238 downloads

complex - Time Series Analysis and Forecasting Using Complex Variables

Set of function implementing the instruments for complex-valued modelling, including time series analysis and forecasting. This is based on the monograph by Svetunkov Sergey and Svetunkov Ivan "Complex-valued Econometrics with Examples in R" which is in press by Springer (expected to be published in 2024).

Last updated 15 days ago

archivedpackagesr-universeopenblascpp

2.40 score 5 stars 255 downloads

BigDataPE - Secure and Intuitive Access to 'BigDataPE' 'API' Datasets

Designed to simplify the process of retrieving datasets from the 'BigDataPE' platform using secure token-based authentication. It provides functions for securely storing, retrieving, and managing tokens associated with specific datasets, as well as fetching and processing data using the 'httr2' package. The integration with 'keyring' ensures that tokens are stored securely within the system’s credential manager.

Last updated 17 days ago

archivedpackagesr-universe

2.40 score 5 stars 503 downloads

rflexscan - The Flexible Spatial Scan Statistic

Functions for the detection of spatial clusters using the flexible spatial scan statistic developed by Tango and Takahashi (2005) <doi:10.1186/1476-072X-4-11>. This package implements a wrapper for the C routine used in the FleXScan 3.1.2 <https://sites.google.com/site/flexscansoftware/home> developed by Takahashi, Yokoyama, and Tango. For details, see Otani et al. (2021) <doi:10.18637/jss.v099.i13>.

Last updated 22 days ago

archivedpackagesr-universecpp

2.40 score 5 stars 218 downloads

klexdatr - Kootenay Lake Exploitation Study Data

Six relational 'tibbles' from the Kootenay Lake Large Trout Exploitation study. The study which ran from 2008 to 2014 caught, tagged and released large Rainbow Trout and Bull Trout in Kootenay Lake by boat angling. The fish were tagged with internal acoustic tags and/or high reward external tags and subsequently detected by an acoustic receiver array as well as reported by anglers. The data are analysed by Thorley and Andrusak (1994) <doi:10.7717/peerj.2874> to estimate the natural and fishing mortality of both species.

Last updated 1 months ago

archivedpackagesr-universe

2.40 score 5 stars 7 scripts 80 downloads

epigrowthfit - Nonlinear Mixed Effects Models of Epidemic Growth

Maximum likelihood estimation of nonlinear mixed effects models of epidemic growth using Template Model Builder ('TMB'). Enables joint estimation for collections of disease incidence time series, including time series that describe multiple epidemic waves. Supports a set of widely used phenomenological models: exponential, logistic, Richards (generalized logistic), subexponential, and Gompertz. Provides methods for interrogating model objects and several auxiliary functions, including one for computing basic reproduction numbers from fitted values of the initial exponential growth rate. Preliminary versions of this software were applied in Ma et al. (2014) <doi:10.1007/s11538-013-9918-2> and in Earn et al. (2020) <doi:10.1073/pnas.2004904117>.

Last updated 8 days ago

archivedpackagesr-universecppopenmp

2.35 score 5 stars 45 scripts 144 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 8 days ago

archivedpackagesr-universe

2.18 score 5 stars 1 dependents 4 scripts 178 downloads

MultAlloc - Optimal Allocation in Stratified Sampling

Integer Programming Formulations Applied to Univariate and Multivariate Allocation Problems.

Last updated 22 days ago

archivedpackagesr-universe

2.18 score 5 stars 1 dependents 219 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 5 days ago

archivedpackagesr-universegmpcpp

2.00 score 5 stars 20 scripts 512 downloads

pco - Panel Cointegration Tests

Computation of the Pedroni (1999) panel cointegration test statistics. Reported are the empirical and the standardized values.

Last updated 22 days ago

archivedpackagesr-universe

2.00 score 5 stars 296 downloads

RClickhouse - 'Yandex Clickhouse' Interface for R with Basic 'dplyr' Support

'Yandex Clickhouse' (<https://clickhouse.com/>) is a high-performance relational column-store database to enable big data exploration and 'analytics' scaling to petabytes of data. Methods are provided that enable working with 'Yandex Clickhouse' databases via 'DBI' methods and using 'dplyr'/'dbplyr' idioms.

Last updated 3 days ago

archivedpackagesr-universecpp

1.74 score 5 stars 11 scripts 446 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 8 days ago

archivedpackagesr-universeopenblascppopenmp

1.70 score 5 stars 1 scripts 256 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 8 days ago

archivedpackagesr-universecpp

1.70 score 5 stars 3 scripts 299 downloads

ccml - Consensus Clustering for Different Sample Coverage Data

Consensus clustering, also called meta-clustering or cluster ensembles, has been increasingly used in clinical data. Current consensus clustering methods tend to ensemble a number of different clusters from mathematical replicates with similar sample coverage. As the fact of common variety of sample coverage in the real-world data, a new consensus clustering strategy dealing with such biological replicates is required. This is a two-step consensus clustering package, which is used to input multiple predictive labels with different sample coverage (missing labels).

Last updated 15 days ago

archivedpackagesr-universe

1.70 score 5 stars 298 downloads

PlasmaMutationDetector2 - Tumor Mutation Detection in Plasma using Barcoding

Aims at detecting single nucleotide variation (SNV) and insertion/deletion (INDEL) in circulating tumor DNA (ctDNA), used as a surrogate marker for tumor, at each base position of an Next Generation Sequencing (NGS) analysis using barcoding. Mutations are assessed by comparing the minor-allele frequency at each position to the measured PER in control samples. This package has been used for Kjersti Tjensvoll, Morten Lapin, Bjørnar Gilje, Herish Garresori, Satu Oltedal, Rakel Brendsdal Forthun, Anders Molven, Yves Rozenholc and Oddmund N\o{o}rdgaard (2022) <https://www.nature.com/articles/s41598-022-09698-5>.

Last updated 15 days ago

archivedpackagesr-universe

1.70 score 5 stars 184 downloads

stratvns - Optimal Stratification in Stratified Sampling

An Optimization Algorithm Applied to Stratification Problem.This function aims at constructing optimal strata with an optimization algorithm based on a global optimisation technique called vns.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 226 downloads

ridittools - Useful Functions for Ridit Analysis

Functions to compute ridit scores of vectors, compute mean ridits and their standard errors for vectors compared to a reference vector, as described in Fleiss (1981, ISBN:0-471-06428-9), and compute means/SEs for multiple groups in matrices. Data can be either counts or proportions. Emphasis is on ridit analysis of ordered categorical data such as Likert items and pain-rating scales.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 124 downloads

wqs - Weighted Quantile Sum Regression

Fits weighted quantile sum regression models, calculates weighted quantile sum index and estimated component weights.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 199 downloads

fasjem - A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models

This is an R implementation of "A Fast and Scalable Joint Estimator for Learning Multiple Related Sparse Gaussian Graphical Models" (FASJEM). The FASJEM algorithm can be used to estimate multiple related precision matrices. For instance, it can identify context-specific gene networks from multi-context gene expression datasets. By performing data-driven network inference from high-dimensional and heterogonous data sets, this tool can help users effectively translate aggregated data into knowledge that take the form of graphs among entities. Please run demo(fasjem) to learn the basic functions provided by this package. For more details, please see <http://proceedings.mlr.press/v54/wang17e/wang17e.pdf>.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 184 downloads

lrmest - Different Types of Estimators to Deal with Multicollinearity

When multicollinearity exists among predictor variables of the linear model, least square estimators does not provide a better solution for estimating parameters. To deal with multicollinearity several estimators are proposed in the literature. Some of these estimators are Ordinary Least Square Estimator (OLSE), Ordinary Generalized Ordinary Least Square Estimator (OGOLSE), Ordinary Ridge Regression Estimator (ORRE), Ordinary Generalized Ridge Regression Estimator (OGRRE), Restricted Least Square Estimator (RLSE), Ordinary Generalized Restricted Least Square Estimator (OGRLSE), Ordinary Mixed Regression Estimator (OMRE), Ordinary Generalized Mixed Regression Estimator (OGMRE), Liu Estimator (LE), Ordinary Generalized Liu Estimator (OGLE), Restricted Liu Estimator (RLE), Ordinary Generalized Restricted Liu Estimator (OGRLE), Stochastic Restricted Liu Estimator (SRLE), Ordinary Generalized Stochastic Restricted Liu Estimator (OGSRLE), Type (1),(2),(3) Liu Estimator (Type-1,2,3 LTE), Ordinary Generalized Type (1),(2),(3) Liu Estimator (Type-1,2,3 OGLTE), Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 ALTE), Ordinary Generalized Type (1),(2),(3) Adjusted Liu Estimator (Type-1,2,3 OGALTE), Almost Unbiased Ridge Estimator (AURE), Ordinary Generalized Almost Unbiased Ridge Estimator (OGAURE), Almost Unbiased Liu Estimator (AULE), Ordinary Generalized Almost Unbiased Liu Estimator (OGAULE), Stochastic Restricted Ridge Estimator (SRRE), Ordinary Generalized Stochastic Restricted Ridge Estimator (OGSRRE), Restricted Ridge Regression Estimator (RRRE) and Ordinary Generalized Restricted Ridge Regression Estimator (OGRRRE). To select the best estimator in a practical situation the Mean Square Error (MSE) is used. Using this package scalar MSE value of all the above estimators and Prediction Sum of Square (PRESS) values of some of the estimators can be obtained, and the variation of the MSE and PRESS values for the relevant estimators can be shown graphically.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 211 downloads

eulerian - eulerian: A package to find eulerian paths from graphs

An eulerian path is a path in a graph which visits every edge exactly once. This package provides methods to handle eulerian paths or cycles.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 146 downloads

msgpackR - A library to serialize or unserialize data in MessagePack format

This is the library that can serialize or unserialize MessagePack format data.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 144 downloads

suRtex - LaTeX descriptive statistic reporting for survey data

suRtex was designed for easy descriptive statistic reporting of categorical survey data (e.g., Likert scales) in LaTeX. suRtex takes a matrix or data frame and produces the LaTeX code necessary for a sideways table creation. Mean, median, standard deviation, and sample size are optional.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 182 downloads

vfcp - Computation of v Values for U and Copula C(U, v)

Computation the value of one of two uniformly distributed marginals if the copula probability value is known and the value of the second marginal is also known. Computation and plotting corresponding cumulative distribution function or survival function. The numerical definition of a common area limited by lines of the cumulative distribution function and survival function. Approximate quantification of the probability of this area. In addition to 'amh', the copula dimension may be larger than 2.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 203 downloads

ConConPiWiFun - Optimisation with Continuous Convex Piecewise (Linear and Quadratic) Functions

Continuous convex piecewise linear (ccpl) resp. quadratic (ccpq) functions can be implemented with sorted breakpoints and slopes. This includes functions that are ccpl (resp. ccpq) on a convex set (i.e. an interval or a point) and infinite out of the domain. These functions can be very useful for a large class of optimisation problems. Efficient manipulation (such as log(N) insertion) of such data structure is obtained with map standard template library of C++ (that hides balanced trees). This package is a wrapper on such a class based on Rcpp modules.

Last updated 22 days ago

archivedpackagesr-universecpp

1.70 score 5 stars 272 downloads

TeachNet - Fits Neural Networks to Learn About Backpropagation

Can fit neural networks with up to two hidden layer and two different error functions. Also able to handle a weight decay. But just able to compute one output neuron and very slow.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 135 downloads

LRcontrast - Dose Response Signal Detection under Model Uncertainty

Provides functions for calculating test statistics, simulating quantiles and simulating p-values of likelihood ratio contrast tests in regression models with a lack of identifiability.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 183 downloads

CCTpack - Consensus Analysis, Model-Based Clustering, and Cultural Consensus Theory Applications

Consensus analysis, model-based clustering, and cultural consensus theory applications to response data (e.g. questionnaires). The models are applied using hierarchical Bayesian inference. The current package version supports binary, ordinal, and continuous data formats.

Last updated 22 days ago

archivedpackagesr-universejagscpp

1.70 score 5 stars 337 downloads

AssocAFC - Allele Frequency Comparison

When doing association analysis one does not always have the genotypes for the control population. In such cases it may be necessary to fall back on frequency based tests using well known sources for the frequencies in the control population, for instance, from the 1000 Genomes Project. The Allele Frequency Comparison ('AssocAFC') package performs multiple rare variant association analyses in both population and family-based GWAS (Genome-Wide Association Study) designs. It includes three score tests that are based on the difference of the sum of allele frequencies between cases and controls. Two of these tests, Wcorrected() and Wqls(), are collapsing-based tests and suffer from having protective and risk variants. The third test, afcSKAT(), is a score test that overcomes the mix of SNP (Single-Nucleotide Polymorphism) effect directions. For more details see Saad M and Wijsman EM (2017) <doi:10.1093/bib/bbx107>.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 271 downloads

NLRoot - searching for the root of equation

This is a package which can help you search for the root of a equation.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 178 downloads

additiveDEA - Additive Data Envelopment Analysis Models

Provides functions for calculating efficiency with two types of additive Data Envelopment Analysis models: (i) Generalized Efficiency Measures: unweighted additive model (Cooper et al., 2007 <doi:10.1007/978-0-387-45283-8>), Range Adjusted Measure (Cooper et al., 1999, <doi:10.1023/A:1007701304281>), Bounded Adjusted Measure (Cooper et al., 2011 <doi:10.1007/s11123-010-0190-2>), Measure of Inefficiency Proportions (Cooper et al., 1999 <doi:10.1023/A:1007701304281>), and the Lovell-Pastor Measure (Lovell and Pastor, 1995 <doi:10.1016/0167-6377(95)00044-5>); and (ii) the Slacks-Based Measure (Tone, 2001 <doi:10.1016/S0377-2217(99)00407-5>). The functions provide several options: (i) constant and variable returns to scale; (ii) fixed (non-controllable) inputs and/or outputs; (iii) bounding the slacks so that unrealistically large slack values are avoided; and (iv) calculating the efficiency of specific Decision-Making Units (DMUs), rather than of the whole sample. Package additiveDEA also provides a function for reducing computation time when datasets are large.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 295 downloads

ABCp2 - Approximate Bayesian Computational Model for Estimating P2

Tests the goodness of fit of a distribution of offspring to the Normal, Poisson, and Gamma distribution and estimates the proportional paternity of the second male (P2) based on the best fit distribution.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 297 downloads

MultiRR - Bias, Precision, and Power for Multi-Level Random Regressions

Calculates bias, precision, and power for multi-level random regressions. Random regressions are types of hierarchical models in which data are structured in groups and (regression) coefficients can vary by groups. Tools to estimate model performance are designed mostly for scenarios where (regression) coefficients vary at just one level. 'MultiRR' provides simulation and analytical tools (based on 'lme4') to study model performance for random regressions that vary at more than one level (multi-level random regressions), allowing researchers to determine optimal sampling designs.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 176 downloads

RPPairwiseDesign - Resolvable partially pairwise balanced design and Space-filling design via association scheme

Using some association schemes to obtain a new series of resolvable partially pairwise balanced designs (RPPBD) and space-filling designs.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 189 downloads

DNLC - Differential Network Local Consistency Analysis

Using Local Moran's I for detection of differential network local consistency.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 238 downloads

CHFF - Closest History Flow Field Forecasting for Bivariate Time Series

The software matches the current history to the closest history in a time series to build a forecast.

Last updated 22 days ago

archivedpackagesr-universe

1.70 score 5 stars 151 downloads

nmadb - Network Meta-Analysis Database API

Set of functions for accessing database of network meta-analyses described in Petropoulou M, et al. Bibliographic study showed improving statistical methodology of network meta-analyses published between 1999 and 2015 <doi:10.1016/j.jclinepi.2016.11.002>. The database is hosted in a REDcap database at the Institute of Social and Preventive Medicine (ISPM) in the University of Bern.

Last updated 25 days ago

archivedpackagesr-universe

1.70 score 5 stars 179 downloads

boostmtree - Boosted Multivariate Trees for Longitudinal Data

Implements Friedman's gradient descent boosting algorithm for modeling longitudinal response using multivariate tree base learners. Longitudinal response could be continuous, binary, nominal or ordinal. A time-covariate interaction effect is modeled using penalized B-splines (P-splines) with estimated adaptive smoothing parameter. Although the package is design for longitudinal data, it can handle cross-sectional data as well. Implementation details are provided in Pande et al. (2017), Mach Learn <DOI:10.1007/s10994-016-5597-1>.

Last updated 29 days ago

archivedpackagesr-universe

1.70 score 5 stars 9 scripts 319 downloads

multilaterals - Transitive Index Numbers for Cross-Sections and Panel Data

Computing transitive (and non-transitive) index numbers (Coelli et al., 2005 <doi:10.1007/b136381>) for cross-sections and panel data. For the calculation of transitive indexes, the EKS (Coelli et al., 2005 <doi:10.1007/b136381>; Rao et al., 2002 <doi:10.1007/978-1-4615-0851-9_4>) and Minimum spanning tree (Hill, 2004 <doi:10.1257/0002828043052178>) methods are implemented. Traditional fixed-base and chained indexes, and their growth rates, can also be derived using the Paasche, Laspeyres, Fisher and Tornqvist formulas.

Last updated 1 months ago

archivedpackagesr-universe

1.70 score 5 stars 8 scripts 45 downloads

hasseDiagram - Drawing Hasse Diagram

Drawing Hasse diagram - visualization of transitive reduction of a finite partially ordered set.

Last updated 1 months ago

archivedpackagesr-universe

1.70 score 5 stars 3 scripts 137 downloads