PKPDsim - Tools for Performing Pharmacokinetic-Pharmacodynamic Simulations

Simulate dose regimens for pharmacokinetic-pharmacodynamic (PK-PD) models described by differential equation (DE) systems. Simulation using ADVAN-style analytical equations is also supported (Abuhelwa et al. (2015) <doi:10.1016/j.vascn.2015.03.004>).

Last updated 7 hours ago

archivedpackagesr-universecpp

4.35 score 5 stars 755 downloads

Bchron - Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate Estimation, and Non-Parametric Phase Modelling

Enables quick calibration of radiocarbon dates under various calibration curves (including user generated ones); age-depth modelling as per the algorithm of Haslett and Parnell (2008) <DOI:10.1111/j.1467-9876.2008.00623.x>; Relative sea level rate estimation incorporating time uncertainty in polynomial regression models (Parnell and Gehrels 2015) <DOI:10.1002/9781118452547.ch32>; non-parametric phase modelling via Gaussian mixtures as a means to determine the activity of a site (and as an alternative to the Oxcal function SUM; currently unpublished), and reverse calibration of dates from calibrated into un-calibrated years (also unpublished).

Last updated 2 days ago

archivedpackagesr-universe

4.18 score 5 stars 1 dependents 960 downloads

tabnet - Fit 'TabNet' Models for Classification and Regression

Implements the 'TabNet' model by Sercan O. Arik et al. (2019) <doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical Multi-label Classification Networks' by Giunchiglia et al. <doi:10.48550/arXiv.2010.10151> and provides a consistent interface for fitting and creating predictions. It's also fully compatible with the 'tidymodels' ecosystem.

Last updated 2 days ago

archivedpackagesr-universe

4.10 score 5 stars 593 downloads

MMRcaseselection - Case Classification and Selection Based on Regression Results

Researchers doing a mixed-methods analysis (nested analysis as developed by Lieberman (2005) <doi:10.1017/S0003055405051762>) can use the package for the classification of cases and case selection using results of a linear regression. One can designate cases as typical, deviant, extreme and pathway case and use different case selection strategies for the choice of a case belonging to one of these types.

Last updated 2 days ago

archivedpackagesr-universe

4.00 score 5 stars 134 downloads

QCAcluster - Tools for the Analysis of Clustered Data in QCA

Clustered set-relational data in Qualitative Comparative Analysis (QCA) can have a hierarchical structure, a panel structure or repeated cross sections. 'QCAcluster' allows QCA researchers to supplement the analysis of pooled the data with a disaggregated perspective focusing on selected partitions of the data. The pooled data can be partitioned along the dimensions of the clustered data (individual cross sections or time series) to perform partition-specific truth table minimizations. Empirical researchers can further calculate the weight that each partition has on the parameters of the pooled solution and the diversity of the cases under analysis within and across partitions (see <https://ingorohlfing.github.io/QCAcluster/>).

Last updated 2 days ago

archivedpackagesr-universe

4.00 score 5 stars 185 downloads

bayesCT - Simulation and Analysis of Adaptive Bayesian Clinical Trials

Simulation and analysis of Bayesian adaptive clinical trials for binomial, Gaussian, and time-to-event data types, incorporates historical data and allows early stopping for futility or early success. The package uses novel and efficient Monte Carlo methods for estimating Bayesian posterior probabilities, evaluation of loss to follow up, and imputation of incomplete data. The package has the functionality for dynamically incorporating historical data into the analysis via the power prior or non-informative priors.

Last updated 2 days ago

archivedpackagesr-universe

4.00 score 5 stars 270 downloads

MethEvolSIM - Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies

DNA methylation is an epigenetic modification involved in genomic stability, gene regulation, development and disease. DNA methylation occurs mainly through the addition of a methyl group to cytosines, for example to cytosines in a CpG dinucleotide context (CpG stands for a cytosine followed by a guanine). Tissue-specific methylation patterns lead to genomic regions with different characteristic methylation levels. E.g. in vertebrates CpG islands (regions with high CpG content) that are associated to promoter regions of expressed genes tend to be unmethylated. 'MethEvolSIM' is a model-based simulation software for the generation and modification of cytosine methylation patterns along a given tree, which can be a genealogy of cells within an organism, a coalescent tree of DNA sequences sampled from a population, or a species tree. The simulations are based on an extension of the model of Grosser & Metzler (2020) <doi:10.1186/s12859-020-3438-5> and allows for changes of the methylation states at single cytosine positions as well as simultaneous changes of methylation frequencies in genomic structures like CpG islands.

Last updated 3 days ago

archivedpackagesr-universe

3.88 score 5 stars 287 downloads

gyro - Hyperbolic Geometry

Hyperbolic geometry in the Minkowski model and the Poincaré model. The methods are based on the gyrovector space theory developed by A. A. Ungar that can be found in the book 'Analytic Hyperbolic Geometry: Mathematical Foundations And Applications' <doi:10.1142/5914>. The package provides functions to plot three-dimensional hyperbolic polyhedra and to plot hyperbolic tilings of the Poincaré disk.

Last updated 8 days ago

archivedpackagesr-universecpp

3.88 score 5 stars 1 dependents 669 downloads

kibior - A Simple Data Management and Sharing Tool

An interface to store, retrieve, search, join and share datasets, based on Elasticsearch (ES) API. As a decentralized, FAIR and collaborative search engine and database effort, it proposes a simple push/pull/search mechanism only based on ES, a tool which can be deployed on nearly any hardware. It is a high-level R-ES binding to ease data usage using 'elastic' package (S. Chamberlain (2020)) <https://docs.ropensci.org/elastic/>, extends joins from 'dplyr' package (H. Wickham et al. (2020)) <https://dplyr.tidyverse.org/> and integrates specific biological format importation with Bioconductor packages such as 'rtracklayer' (M. Lawrence and al. (2009) <doi:10.1093/bioinformatics/btp328>) <http://bioconductor.org/packages/rtracklayer>, 'Biostrings' (H. Pagès and al. (2020) <doi:10.18129/B9.bioc.Biostrings>) <http://bioconductor.org/packages/Biostrings>, and 'Rsamtools' (M. Morgan and al. (2020) <doi:10.18129/B9.bioc.Rsamtools>) <http://bioconductor.org/packages/Rsamtools>, but also a long list of more common ones with 'rio' (C-h. Chan and al. (2018)) <https://cran.r-project.org/package=rio>.

Last updated 2 days ago

dataimportdatarepresentationthirdpartyclientarchivedpackagesr-universe

3.70 score 5 stars 204 downloads

cxhull - Convex Hull

Computes the convex hull in arbitrary dimension, based on the Qhull library (<http://www.qhull.org>). The package provides a complete description of the convex hull: edges, ridges, facets, adjacencies. Triangulation is optional.

Last updated 8 days ago

archivedpackagesr-universe

3.57 score 5 stars 5 dependents 903 downloads

ropenmeteo - Wrappers for 'Open-Meteo' API

Wrappers for the Application Programming Interface from the <https://open-meteo.com> project along with helper functions. The <https://open-meteo.com> project streamlines access to a range of publicly historical and forecast meteorology data from agencies across the world.

Last updated 1 days ago

archivedpackagesr-universe

3.40 score 5 stars 373 downloads

crplyr - A 'dplyr' Interface for Crunch

In order to facilitate analysis of datasets hosted on the Crunch data platform <https://crunch.io/>, the 'crplyr' package implements 'dplyr' methods on top of the Crunch backend. The usual methods 'select', 'filter', 'group_by', 'summarize', and 'collect' are implemented in such a way as to perform as much computation on the server and pull as little data locally as possible.

Last updated 1 days ago

archivedpackagesr-universe

3.40 score 5 stars 454 downloads

gdm - Generalized Dissimilarity Modeling

A toolkit with functions to fit, plot, summarize, and apply Generalized Dissimilarity Models. Mokany K, Ware C, Woolley SNC, Ferrier S, Fitzpatrick MC (2022) <doi:10.1111/geb.13459> Ferrier S, Manion G, Elith J, Richardson K (2007) <doi:10.1111/j.1472-4642.2007.00341.x>.

Last updated 3 days ago

archivedpackagesr-universecpp

3.40 score 5 stars 811 downloads

RcppPlanc - Parallel Low-Rank Approximation with Nonnegativity Constraints

'Rcpp' bindings for 'PLANC', a highly parallel and extensible NMF/NTF (Non-negative Matrix/Tensor Factorization) library. Wraps algorithms described in Kannan et. al (2018) <doi:10.1109/TKDE.2017.2767592> and Eswar et. al (2021) <doi:10.1145/3432185>. Implements algorithms described in Welch et al. (2019) <doi:10.1016/j.cell.2019.05.006>, Gao et al. (2021) <doi:10.1038/s41587-021-00867-x>, and Kriebel & Welch (2022) <doi:10.1038/s41467-022-28431-4>.

Last updated 4 days ago

archivedpackagesr-universecppopenmp

3.40 score 5 stars 78 downloads

stelfi - Hawkes and Log-Gaussian Cox Point Processes Using Template Model Builder

Fit Hawkes and log-Gaussian Cox process models with extensions. Introduced in Hawkes (1971) <doi:10.2307/2334319> a Hawkes process is a self-exciting temporal point process where the occurrence of an event immediately increases the chance of another. We extend this to consider self-inhibiting process and a non-homogeneous background rate. A log-Gaussian Cox process is a Poisson point process where the log-intensity is given by a Gaussian random field. We extend this to a joint likelihood formulation fitting a marked log-Gaussian Cox model. In addition, the package offers functionality to fit self-exciting spatiotemporal point processes. Models are fitted via maximum likelihood using 'TMB' (Template Model Builder). Where included 1) random fields are assumed to be Gaussian and are integrated over using the Laplace approximation and 2) a stochastic partial differential equation model, introduced by Lindgren, Rue, and Lindström. (2011) <doi:10.1111/j.1467-9868.2011.00777.x>, is defined for the field(s).

Last updated 1 days ago

archivedpackagesr-universecpp

2.70 score 5 stars 183 downloads

addScales - Adds Labeled Center Line and Scale Lines/Regions to Trellis Plots

Modifies trellis objects by adding horizontal and/or vertical reference lines or shaded regions that provide visual scaling information. This is mostly useful in multi-panel plots that use the relation = 'free' option in their 'scales' argument list.

Last updated 1 days ago

archivedpackagesr-universe

2.70 score 5 stars 251 downloads

twangRDC - Gradient Boosting for Linkage Failure in FSRDCs

Provides functions for gradient boosted weighting to correct linkage failures or generate comparison groups.

Last updated 2 days ago

archivedpackagesr-universe

2.70 score 5 stars 191 downloads

EFS - Tool for Ensemble Feature Selection

Provides a function to check the importance of a feature based on a dependent classification variable. An ensemble of feature selection methods is used to determine the normalized importance value of all features. Combining these methods in one function (building the cumulative importance values) provides a stable feature selection tool. This selection can also be viewed in a barplot using the barplot_fs() function and proved using the evaluation function efs_eval().

Last updated 3 days ago

archivedpackagesr-universe

2.70 score 5 stars 168 downloads

portsort - Factor-Based Portfolio Sorts

Designed to aid both academic researchers and asset managers in conducting factor based portfolio sorts. Provides functionality to sort assets into portfolios for up to three factors via a conditional or unconditional sorting procedure.

Last updated 9 days ago

archivedpackagesr-universe

2.70 score 5 stars 253 downloads

PEACH - Pareto Enrichment Analysis for Combining Heterogeneous Datasets

A meta gene set analysis tool developed based on principles of Pareto dominance (William B T Mock (2011) <doi:10.1007/978-1-4020-9160-5_341>). It is designed to combine gene set analysis p-values from multiple transcriptome datasets (e.g., microarray and RNA-Seq). The novel Pareto method for p-value combination allows PEACH to properly model heterogeneity and correlation in Omics datasets.

Last updated 9 days ago

archivedpackagesr-universe

2.70 score 5 stars 137 downloads

MVLM - Multivariate Linear Model with Analytic p-Values

Allows a user to conduct multivariate multiple regression using analytic p-values rather than classic approximate F-tests.

Last updated 10 days ago

archivedpackagesr-universe

2.70 score 5 stars 417 downloads

LW1949 - An Automated Approach to Evaluating Dose-Effect Experiments Following Litchfield and Wilcoxon (1949)

The manual approach of Litchfield and Wilcoxon (1949) <http://jpet.aspetjournals.org/content/96/2/99.abstract> for evaluating dose-effect experiments is automated so that the computer can do the work.

Last updated 10 days ago

archivedpackagesr-universe

2.70 score 5 stars 131 downloads

dirmcmc - Directional Metropolis Hastings Algorithm

Implementation of Directional Metropolis Hastings Algorithm for MCMC.

Last updated 10 days ago

archivedpackagesr-universe

2.70 score 5 stars 408 downloads

kpcalg - Kernel PC Algorithm for Causal Structure Detection

Kernel PC (kPC) algorithm for causal structure learning and causal inference using graphical models. kPC is a version of PC algorithm that uses kernel based independence criteria in order to be able to deal with non-linear relationships and non-Gaussian noise.

Last updated 10 days ago

archivedpackagesr-universe

2.70 score 5 stars 196 downloads

FuzzyStatProb - Fuzzy Stationary Probabilities from a Sequence of Observations of an Unknown Markov Chain

An implementation of a method for computing fuzzy numbers representing stationary probabilities of an unknown Markov chain, from which a sequence of observations along time has been obtained. The algorithm is based on the proposal presented by James Buckley in his book on Fuzzy probabilities (Springer, 2005), chapter 6. Package 'FuzzyNumbers' is used to represent the output probabilities.

Last updated 10 days ago

archivedpackagesr-universe

2.70 score 5 stars 220 downloads

FarmSelect - Factor Adjusted Robust Model Selection

Implements a consistent model selection strategy for high dimensional sparse regression when the covariate dependence can be reduced through factor models. By separating the latent factors from idiosyncratic components, the problem is transformed from model selection with highly correlated covariates to that with weakly correlated variables. It is appropriate for cases where we have many variables compared to the number of samples. Moreover, it implements a robust procedure to estimate distribution parameters wherever possible, hence being suitable for cases when the underlying distribution deviates from Gaussianity. See the paper on the 'FarmSelect' method, Fan et al.(2017) <arXiv:1612.08490>, for detailed description of methods and further references.

Last updated 10 days ago

archivedpackagesr-universeopenblascpp

2.70 score 5 stars 178 downloads

tigerstats - R Functions for Elementary Statistics

A collection of data sets and functions that are useful in the teaching of statistics at an elementary level to students who may have little or no previous experience with the command line. The functions for elementary inferential procedures follow a uniform interface for user input. Some of the functions are instructional applets that can only be run on the R Studio integrated development environment with package 'manipulate' installed. Other instructional applets are Shiny apps that may be run locally. In teaching the package is used alongside of package 'mosaic', 'mosaicData' and 'abd', which are therefore listed as dependencies.

Last updated 1 days ago

archivedpackagesr-universe

2.61 score 5 stars 1.6k downloads

brulee - High-Level Modeling Functions with 'torch'

Provides high-level modeling functions to define and train models using the 'torch' R package. Models include linear, logistic, and multinomial regression as well as multilayer perceptrons.

Last updated 1 days ago

archivedpackagesr-universe

2.40 score 5 stars 742 downloads

clusterability - Performs Tests for Cluster Tendency of a Data Set

Test for cluster tendency (clusterability) of a data set. The methods implemented - reducing the data set to a single dimension using principal component analysis or computing pairwise distances, and performing a multimodality test like the Dip Test or Silverman's Critical Bandwidth Test - are described in Adolfsson, Ackerman, and Brownstein (2019) <doi:10.1016/j.patcog.2018.10.026>. Such methods can inform whether clustering algorithms are appropriate for a data set.

Last updated 2 days ago

archivedpackagesr-universe

2.40 score 5 stars 218 downloads

MonetDB.R - Connect MonetDB to R

Allows to pull data from MonetDB into R.

Last updated 2 days ago

archivedpackagesr-universe

2.40 score 5 stars 253 downloads

RITCH - R Parser for the ITCH-Protocol

Allows to efficiently parse, filter, and write binary ITCH Files (Version 5.0) containing detailed financial transactions as distributed by NASDAQ to an R data.table.

Last updated 4 days ago

archivedpackagesr-universecpp

2.40 score 5 stars 231 downloads

Apollonius - 2D Apollonius Graphs

Computation of the Apollonius diagram of given 2D points and its dual the Apollonius graph, also known as the additively weighted Voronoï diagram, and which is a generalization of the classical Voronoï diagram. For references, see the bibliography in the CGAL documentation at <https://doc.cgal.org/latest/Apollonius_graph_2/citelist.html>.

Last updated 8 days ago

archivedpackagesr-universegmpcpp

2.40 score 5 stars 234 downloads

ggplotlyExtra - Extra Convenience Functions for 'Plotly'

Convenience functions for smooth conversion from 'ggplot' to 'plotly' where the conversion using ggplotly() usually gives an unexpected labels. The package ease the process of making a 'plotly' figures generated from 'ggplot2' object more aesthetic in terms of labels and customizability.

Last updated 10 days ago

archivedpackagesr-universe

2.40 score 5 stars 477 downloads

spsh - Estimation and Prediction of Parameters of Various Soil Hydraulic Property Models

Estimates model parameters of soil hydraulic property functions by inverting measured data. A wide range of hydraulic models, weighting schemes, global optimization algorithms, Markov chain Monte Carlo samplers, and extended statistical analyses of results are provided. Prediction of soil hydraulic property model parameters and common soil properties using pedotransfer functions is facilitated. Parameter estimation is based on identically and independentally distributed (weighted) model residuals, and simple model selection criteria (Hoege, M., Woehling, T., and Nowak, W. (2018) <doi:10.1002/2017WR021902>) can be calculated. The included models are the van Genuchten-Mualem in its unimodal, bimodal and trimodal form, the the Kosugi 2 parametric-Mualem model, and the Fredlund-Xing model. All models can be extended to account for non-capillary water storage and conductivity (Weber, T.K.D., Durner, W., Streck, T. and Diamantopoulos, E. (2019) <doi:10.1029/2018WR024584>. The isothermal vapour conductivity (Saito, H., Simunek, J. and Mohanty, B.P. (2006) <doi:10.2136/vzj2006.0007>) is calculated based on volumetric air space and a selection of different tortuosity models: (Grable, A.R., Siemer, E.G. (1968) <doi:10.2136/sssaj1968.03615995003200020011x>, Lai, S.H., Tiedje J.M., Erickson, E. (1976) <doi:10.2136/sssaj1976.03615995004000010006x>, Moldrup, P., Olesen, T., Rolston, D.E., and Yamaguchi, T. (1997) <doi:10.1097/00010694-199709000-00004>, Moldrup, P., Olesen, T., Yoshikawa, S., Komatsu, T., and Rolston, D.E. (2004) <doi:10.2136/sssaj2004.7500>, Moldrup, P., Olesen, T., Yoshikawa, S., Komatsu, T., and Rolston, D.E. (2005) <doi:10.1097/01.ss.0000196768.44165.1f>, Millington, R.J., Quirk, J.P. (1961) <doi:10.1039/TF9615701200>, Penman, H.L. (1940) <doi:10.1017/S0021859600048164>, and Xu, X, Nieber, J.L. Gupta, S.C. (1992) <doi:10.2136/sssaj1992.03615995005600060014x>).

Last updated 2 days ago

archivedpackagesr-universe

1.70 score 5 stars 135 downloads

InDisc - Obtaining and Estimating Unidimensional and Multidimensional IRT Dual Models

Performs a unified approach for obtaining and estimating unidimensional and multidimensional Item Response Theory (IRT) Dual Models (DMs), proposed by Ferrando (2019 <doi:10.1177/0146621618817779>).

Last updated 2 days ago

archivedpackagesr-universe

1.70 score 5 stars 181 downloads

geovol - Geopolitical Volatility (GEOVOL) Modelling

Simulation, estimation and inference for the geopolitical volatility (GEOVOL) model of Engle and Campos-Martins (2020) <doi:10.2139/ssrn.3685213>, where GEOVOL is modelled as a latent multiplicative volatility factor with heterogeneous factor loadings. Estimation is carried out as a maximization-maximization procedure, where GEOVOL and the GEOVOL loadings are estimated iteratively until convergence.

Last updated 2 days ago

archivedpackagesr-universe

1.70 score 5 stars 138 downloads

vampyr - Factor Analysis Controlling the Effects of Response Bias

Vampirize the response biases from a dataset! Performs factor analysis controlling the effects of social desirability and acquiescence using the method described in Ferrando, Lorenzo-Seva & Chico (2009) <doi:10.1080/10705510902751374>.

Last updated 2 days ago

archivedpackagesr-universe

1.70 score 5 stars 148 downloads

SparseTSCGM - Sparse Time Series Chain Graphical Models

Computes sparse vector autoregressive coefficients and precision matrices for time series chain graphical models. Fentaw Abegaz and Ernst Wit (2013) <doi:10.1093/biostatistics/kxt005>.

Last updated 2 days ago

archivedpackagesr-universe

1.70 score 5 stars 187 downloads

ggjoy - Joyplots in 'ggplot2'

Joyplots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.

Last updated 10 days ago

archivedpackagesr-universe

4.78 score 5 stars 1 dependents 495 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 25 days ago

archivedpackagesr-universe

4.35 score 5 stars 1 dependents 282 downloads

DataFakeR - Generate Fake Data for Relational Databases

Based on provided database description and/or database connection generate data sample preserving source structure.

Last updated 13 days ago

archivedpackagesr-universe

4.24 score 5 stars 249 downloads

scDHA - Single-Cell Decomposition using Hierarchical Autoencoder

Provides a fast and accurate pipeline for single-cell analyses. The 'scDHA' software package can perform clustering, dimension reduction and visualization, classification, and time-trajectory inference on single-cell data (Tran et.al. (2021) <DOI:10.1038/s41467-021-21312-2>).

Last updated 20 days ago

archivedpackagesr-universecpp

4.18 score 5 stars 2 dependents 264 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 1 months ago

archivedpackagesr-universeopenblascpp

4.18 score 5 stars 2 dependents 279 downloads

greatR - Gene Registration from Expression and Time-Courses in R

A tool for registering (aligning) gene expression profiles between reference and query data.

Last updated 15 days ago

archivedpackagesr-universe

4.00 score 5 stars 284 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 25 days ago

archivedpackagesr-universe

4.00 score 5 stars 292 downloads

nestedmodels - Tidy Modelling for Nested Data

A modelling framework for nested data using the 'tidymodels' ecosystem. Specify how to nest data using the 'recipes' package, create testing and training splits using 'rsample', and fit models to this data using the 'parsnip' and 'workflows' packages. Allows any model to be fit to nested data.

Last updated 13 days ago

archivedpackagesr-universe

3.70 score 5 stars 657 downloads

MOCHA - Modeling for Single-Cell Open Chromatin Analysis

A statistical framework and analysis tool for open chromatin analysis designed specifically for single cell ATAC-seq (Assay for Transposase-Accessible Chromatin) data, after cell type/cluster identification. These novel modules remove unwanted technical variation, identify open chromatin, robustly models repeated measures in single cell data, implement advanced statistical frameworks to model zero-inflation for differential and co-accessibility analyses, and integrate with existing databases and modules for downstream analyses to reveal biological insights. MOCHA provides a statistical foundation for complex downstream analysis to help advance the potential of single cell ATAC-seq for applied studies. Methods for zero-inflated statistics are as described in: Ghazanfar, S., Lin, Y., Su, X. et al. (2020) <doi:10.1038/s41592-020-0885-x>. Pimentel, Ronald Silva, "Kendall's Tau and Spearman's Rho for Zero-Inflated Data" (2009) <https://scholarworks.wmich.edu/dissertations/721/>.

Last updated 14 days ago

archivedpackagesr-universe

3.70 score 5 stars 192 downloads

webqueue - Multicore HTTP Server

Distributes HTTP requests among a pool of background R processes. Supports timeouts and interrupts of requests to ensure that CPU cores are utilized effectively.

Last updated 17 days ago

archivedpackagesr-universe

3.70 score 5 stars 12 downloads

rTorch - R Bindings to 'PyTorch'

'R' implementation and interface of the Machine Learning platform 'PyTorch' <https://pytorch.org/> developed in 'Python'. It requires a 'conda' environment with 'torch' and 'torchvision' Python packages to provide 'PyTorch' functions, methods and classes. The key object in 'PyTorch' is the tensor which is in essence a multidimensional array. These tensors are fairly flexible in performing calculations in CPUs as well as 'GPUs' to accelerate tensor operations.

Last updated 10 days ago

archivedpackagesr-universe

3.40 score 5 stars 189 downloads

PerseusR - Perseus R Interop

Enables the interoperability between the Perseus platform for omics data analysis (Tyanova et al. 2016) <doi:10.1038/nmeth.3901> and R. It provides the foundation for developing and running Perseus plugins implemented in R by providing all required input and output handling, including data and parameter parsing as described in Rudolph and Cox 2018 <doi:10.1101/447268>.

Last updated 10 days ago

archivedpackagesr-universe

3.40 score 5 stars 163 downloads

torchaudio - R Interface to 'pytorch''s 'torchaudio'

Provides access to datasets, models and processing facilities for deep learning in audio.

Last updated 14 days ago

archivedpackagesr-universe

3.40 score 5 stars 203 downloads

scCAN - Single-Cell Clustering using Autoencoder and Network Fusion

A single-cell Clustering method using 'Autoencoder' and Network fusion ('scCAN') Bang Tran (2022) <doi:10.1038/s41598-022-14218-6> for segregating the cells from the high-dimensional 'scRNA-Seq' data. The software automatically determines the optimal number of clusters and then partitions the cells in a way such that the results are robust to noise and dropouts. 'scCAN' is fast and it supports Windows, Linux, and Mac OS.

Last updated 20 days ago

archivedpackagesr-universe

3.40 score 5 stars 540 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 21 days 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 22 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 23 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 25 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 25 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 27 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 28 days ago

archivedpackagesr-universe

3.40 score 5 stars 411 downloads

TukeyC - Conventional Tukey Test

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

Last updated 27 days ago

archivedpackagesr-universe

3.24 score 5 stars 599 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 26 days ago

archivedpackagesr-universe

3.18 score 5 stars 678 downloads

tabulate - Pretty Console Output for Tables

Generates pretty console output for tables allowing for full customization of cell colors, font type, borders and many others attributes. It also supports 'multibyte' characters and nested tables.

Last updated 14 days ago

archivedpackagesr-universecpp

2.88 score 5 stars 3.0k 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 22 days ago

archivedpackagesr-universe

2.88 score 5 stars 1 dependents 256 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 1 months ago

archivedpackagesr-universe

2.88 score 5 stars 1 dependents 168 downloads

AcousticNDLCodeR - Coding Sound Files for Use with NDL

Make acoustic cues to use with the R packages 'ndl' or 'ndl2'. The package implements functions used in the PLoS ONE paper: Denis Arnold, Fabian Tomaschek, Konstantin Sering, Florence Lopez, and R. Harald Baayen (2017). Words from spontaneous conversational speech can be recognized with human-like accuracy by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit. PLoS ONE 12(4):e0174623 <doi:10.1371/journal.pone.0174623> More details can be found in the paper and the supplement. 'ndl' is available on CRAN. 'ndl2' is available by request from <[email protected]>.

Last updated 10 days ago

archivedpackagesr-universe

2.70 score 5 stars 286 downloads

shiny.info - 'shiny' Info

Displays simple diagnostic information of the 'shiny' project in the user interface of the app.

Last updated 13 days ago

archivedpackagesr-universe

2.70 score 5 stars 159 downloads

miWQS - Multiple Imputation Using Weighted Quantile Sum Regression

The miWQS package handles the uncertainty due to below the detection limit in a correlated component mixture problem. Researchers want to determine if a set/mixture of continuous and correlated components/chemicals is associated with an outcome and if so, which components are important in that mixture. These components share a common outcome but are interval-censored between zero and low thresholds, or detection limits, that may be different across the components. This package applies the multiple imputation (MI) procedure to the weighted quantile sum regression (WQS) methodology for continuous, binary, or count outcomes (Hargarten & Wheeler (2020) <doi:10.1016/j.envres.2020.109466>). The imputation models are: bootstrapping imputation (Lubin et.al (2004) <doi:10.1289/ehp.7199>), univariate Bayesian imputation (Hargarten & Wheeler (2020) <doi:10.1016/j.envres.2020.109466>), and multivariate Bayesian regression imputation.

Last updated 13 days ago

archivedpackagesr-universe

2.70 score 5 stars 245 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 25 days ago

archivedpackagesr-universe

2.70 score 5 stars 366 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 25 days ago

softwarearchivedpackagesr-universe

2.70 score 5 stars 192 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 26 days ago

archivedpackagesr-universe

2.70 score 5 stars 179 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 1 months ago

archivedpackagesr-universeopenblascpp

2.70 score 5 stars 45 downloads

IBDsim - Simulation of Chromosomal Regions Shared by Family Members

Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Kong et. al (2010) <doi:10.1038/nature09525>), phased chromosomes are simulated for all pedigree members, either by unconditional gene dropping or conditional on a specified IBD pattern. Additional functions provide summaries and further analysis of the simulated genomes.

Last updated 10 days ago

archivedpackagesr-universe

2.48 score 5 stars 242 downloads

predkmeans - Covariate Adaptive Clustering

Implements the predictive k-means method for clustering observations, using a mixture of experts model to allow covariates to influence cluster centers. Motivated by air pollution epidemiology settings, where cluster membership needs to be predicted across space. Includes functions for predicting cluster membership using spatial splines and principal component analysis (PCA) scores using either multinomial logistic regression or support vector machines (SVMs). For method details see Keller et al. (2017) <doi:10.1214/16-AOAS992>.

Last updated 10 days ago

archivedpackagesr-universeopenblascpp

2.40 score 5 stars 147 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 26 days ago

archivedpackagesr-universe

2.70 score 5 stars 128 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 24 days ago

archivedpackagesr-universe

2.48 score 5 stars 2 dependents 844 downloads

gradientPickerD3 - Interactive Color Gradient Picker Using 'htmlwidgets' and the Modified JS Script 'jquery-gradient-picker'

Widget for an interactive selection and modification of a color gradient. 'gradientPickerD3' allows addition, removement and replacement of color ticks. List of numeric values will automatically translate in their corresponding tick position within the numeric range. App returns a data.frame containing tick values, colors and the positions in percent (0.0 to 1.0) for each color tick in the gradient. The original JS 'jquery-gradient-picker' was implemented by Matt Crinklaw-Vogt (nick: tantaman) <https://github.com/tantaman/>. Widget and JS modifications were done by CD. Peikert.

Last updated 10 days ago

archivedpackagesr-universe

2.40 score 5 stars 393 downloads

jsonStrings - Manipulation of JSON Strings

Fast manipulation of JSON strings. Allows to extract or delete an element in a JSON string, merge two JSON strings, and more.

Last updated 14 days ago

archivedpackagesr-universecpp

2.40 score 5 stars 178 downloads

datasailr - Row by Row Data Processing Tool, Using 'DataSailr' Script

A row by row data processing tool. You can write data processing code in 'DataSailr' script which is specially intended for data manipulation. The package uses 'libsailr' (C/C++ library) for its 'DataSailr' code parsing and its execution.

Last updated 14 days ago

archivedpackagesr-universecpp

2.40 score 5 stars 291 downloads

rflashtext - FlashText Algorithm for Finding and Replacing Words

Implementation of the FlashText algorithm, by Singh (2017) <arXiv:1711.00046>. It can be used to find and replace words in a given text with only one pass over the document.

Last updated 14 days ago

archivedpackagesr-universecpp

2.40 score 5 stars 105 downloads

noegletalR - Tidy Tibbles of Noegletal

Work with data from <https://noegletal.dk> in a tidy manner. Tidy up previously downloaded data or retrieve new data directly from the comfort of R. You can also browse an up-to-date list of available data, including thorough variable descriptions.

Last updated 17 days ago

archivedpackagesr-universe

2.40 score 5 stars 78 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 22 days ago

archivedpackagesr-universe

2.40 score 5 stars 98 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 25 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 1 months ago

archivedpackagesr-universe

2.40 score 5 stars 41 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 1 months ago

archivedpackagesr-universe

2.40 score 5 stars 43 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 1 months ago

archivedpackagesr-universe

2.40 score 5 stars 45 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 1 months ago

archivedpackagesr-universe

2.40 score 5 stars 53 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 28 days ago

archivedpackagesr-universelibxml2cpp

2.18 score 5 stars 1 dependents 448 downloads

multinet - Analysis and mining of multilayer social networks

Functions for the creation/generation and analysis of multilayer social networks <doi:10.18637/jss.v098.i08>.

Last updated 14 days ago

archivedpackagesr-universecpp

2.06 score 5 stars 1.1k downloads

gtheory - Apply Generalizability Theory with R

Estimates variance components, generalizability coefficients, universe scores, and standard errors when observed scores contain variation from one or more measurement facets (e.g., items and raters).

Last updated 10 days ago

archivedpackagesr-universe

2.00 score 5 stars 382 downloads

hilldiv - Integral Analysis of Diversity Based on Hill Numbers

Tools for analysing, comparing, visualising and partitioning diversity based on Hill numbers. 'hilldiv' is an R package that provides a set of functions to assist analysis of diversity for diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses based on Hill numbers, using OTU/ASV tables and associated phylogenetic trees as inputs. The package includes functions for (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these grounded in abundance-based and incidence-based Hill numbers. The statistical framework developed around Hill numbers encompasses many of the most broadly employed diversity (e.g. richness, Shannon index, Simpson index), phylogenetic diversity (e.g. Faith's PD, Allen's H, Rao's quadratic entropy) and dissimilarity (e.g. Sorensen index, Unifrac distances) metrics. This enables the most common analyses of diversity to be performed while grounded in a single statistical framework. The methods are described in Jost et al. (2007) <DOI:10.1890/06-1736.1>, Chao et al. (2010) <DOI:10.1098/rstb.2010.0272> and Chiu et al. (2014) <DOI:10.1890/12-0960.1>; and reviewed in the framework of molecularly characterised biological systems in Alberdi & Gilbert (2019) <DOI:10.1111/1755-0998.13014>.

Last updated 3 days ago

archivedpackagesr-universe

1.70 score 5 stars 292 downloads

MiDA - Microarray Data Analysis

Set of functions designed to simplify transcriptome analysis and identification of marker molecules using microarrays data. The package includes a set of functions that allows performing full pipeline of analysis including data normalization, summarisation, binary classification, FDR (False Discovery Rate) multiple comparison and the definition of potential biological markers.

Last updated 3 days ago

archivedpackagesr-universe

1.70 score 5 stars 112 downloads

OHCSpackage - Prepare Housing Data for Analysis

Prepares census and core housing needs data, specifically designed for use with Statistics Canada data and standardized input data. The package offers functions for tidying, organizing, and splitting complex data tables, making it easier for users to perform analyses on the data. 'OHCSpackage''' is particularly useful for those working with census data that has a consistent format, number of rows, and number of columns. With this package, users can save time and streamline their data preparation processes.

Last updated 9 days ago

archivedpackagesr-universe

1.70 score 5 stars 165 downloads

EmiStatR - Emissions and Statistics in R for Wastewater and Pollutants in Combined Sewer Systems

Provides a fast and parallelised calculator to estimate combined wastewater emissions. It supports the planning and design of urban drainage systems, without the requirement of extensive simulation tools. The 'EmiStatR' package implements modular R methods. This enables to add new functionalities through the R framework.

Last updated 9 days ago

archivedpackagesr-universe

1.70 score 5 stars 231 downloads

INCATome - Internal Control Analysis of Translatome Studies by Microarrays

Data analysis, normalisation and differential expression for Translatome studies by microarrays (T Sbarrato et al. RNA. 2017 Aug 25; <DOI:10.1261/rna.060525.116>).

Last updated 9 days ago

archivedpackagesr-universe

1.70 score 5 stars 124 downloads

simest - Constrained Single Index Model Estimation

Estimation of function and index vector in single index model with and without shape constraints including different smoothness conditions.

Last updated 10 days ago

archivedpackagesr-universe

1.70 score 5 stars 143 downloads

in2extRemes - Into the extRemes Package

Graphical User Interface (GUI) to some of the functions in the package extRemes version >= 2.0 are included.

Last updated 10 days ago

archivedpackagesr-universe

1.70 score 5 stars 284 downloads

eivtools - Measurement Error Modeling Tools

This includes functions for analysis with error-prone covariates, including deconvolution, latent regression and errors-in-variables regression. It implements methods by Rabe-Hesketh et al. (2003) <doi:10.1191/1471082x03st056oa>, Lockwood and McCaffrey (2014) <doi:10.3102/1076998613509405>, and Lockwood and McCaffrey (2017) <doi:10.1007/s11336-017-9556-y>, among others.

Last updated 10 days ago

archivedpackagesr-universejagscpp

1.70 score 5 stars 179 downloads

SizeEstimation - Estimating the Sizes of Populations at Risk of HIV Infection from Multiple Data Sources Using a Bayesian Hierarchical Model

This function develops an algorithm for presenting a Bayesian hierarchical model for estimating the sizes of local and national drug injected populations in Bangladesh. The model incorporates multiple commonly used data sources including mapping data, surveys, interventions, capture-recapture data, estimates or guesstimates from organizations, and expert opinion.

Last updated 10 days ago

archivedpackagesr-universe

1.70 score 5 stars 101 downloads

SSrat - Two-Dimensional Sociometric Status Determination with Rating Scales

A set of functions for two-dimensional sociometric status determination with rating scales. For each person assessed, SSrat computes probability distributions of the total scores for `Sympathy' (S), `Antipathy' (A), social `Preference' (P) and social `Impact' (I), and applies a set of criteria for sociometric status categorization.

Last updated 10 days ago

archivedpackagesr-universe

1.70 score 5 stars 123 downloads

HETOP - MLE and Bayesian Estimation of Heteroskedastic Ordered Probit (HETOP) Model

Provides functions for maximum likelihood and Bayesian estimation of the Heteroskedastic Ordered Probit (HETOP) model, using methods described in Lockwood, Castellano and Shear (2018) <doi:10.3102/1076998618795124> and Reardon, Shear, Castellano and Ho (2017) <doi:10.3102/1076998616666279>. It also provides a general function to compute the triple-goal estimators of Shen and Louis (1998) <doi:10.1111/1467-9868.00135>.

Last updated 10 days ago

archivedpackagesr-universejagscpp

1.70 score 5 stars 152 downloads

MargCond - Joint Marginal-Conditional Model

Fits joint marginal conditional models for multivariate longitudinal data, as in Proudfoot, Faig, Natarajan, and Xu (2018) <doi:10.1002/sim.7552>. Development of this package was supported by the UCSD Altman Translational Research Institute, NIH grant UL1TR001442. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH.

Last updated 10 days ago

archivedpackagesr-universe

1.70 score 5 stars 129 downloads

revgeo - Reverse Geocoding with the Photon Geocoder for OpenStreetMap, Google Maps, and Bing

Function revgeo() allows you to use the Photon geocoder for OpenStreetMap <http://photon.komoot.de>, Google Maps <http://maps.google.com>, and Bing <https://www.bingmapsportal.com> to reverse geocode coordinate pairs with minimal hassle.

Last updated 10 days ago

archivedpackagesr-universe

1.70 score 5 stars 310 downloads

ScRNAIMM - Performing Single-Cell RNA-Seq Imputation by Using Mean/Median Imputation

Performing single-cell imputation in a way that preserves the biological variations in the data. The package clusters the input data to do imputation for each cluster, and do a distribution check using the Anderson-Darling normality test to impute dropouts using mean or median (Yazici, B., & Yolacan, S. (2007) <DOI:10.1080/10629360600678310>).

Last updated 20 days ago

archivedpackagesr-universe

1.70 score 5 stars 161 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 22 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 25 days ago

archivedpackagesr-universe

1.70 score 5 stars 263 downloads