R-universe search: expand

joachim-gassen

ExPanDaR:Explore Your Data Interactively

Provides a shiny-based front end (the 'ExPanD' app) and a set of functions for exploratory data analysis. Run as a web-based app, 'ExPanD' enables users to assess the robustness of empirical evidence without providing them access to the underlying data. You can export a notebook containing the analysis of 'ExPanD' and/or use the functions of the package to support your exploratory data analysis workflow. Refer to the vignettes of the package for more information on how to use 'ExPanD' and/or the functions of this package.

Maintained by Joachim Gassen. Last updated 4 years ago.

accounting eda exploratory-data-analysis finance open-science replication shiny shiny-apps

28.9 match 156 stars 7.80 score 203 scripts

causal-lda

TrialEmulation:Causal Analysis of Observational Time-to-Event Data

Implements target trial emulation methods to apply randomized clinical trial design and analysis in an observational setting. Using marginal structural models, it can estimate intention-to-treat and per-protocol effects in emulated trials using electronic health records. A description and application of the method can be found in Danaei et al (2013) <doi:10.1177/0962280211403603>.

Maintained by Isaac Gravestock. Last updated 24 days ago.

causal-inference longitudinal-data survival-analysis cpp

23.0 match 25 stars 7.72 score 29 scripts

spatstat

spatstat.random:Random Generation Functionality for the 'spatstat' Family

Functionality for random generation of spatial data in the 'spatstat' family of packages. Generates random spatial patterns of points according to many simple rules (complete spatial randomness, Poisson, binomial, random grid, systematic, cell), randomised alteration of patterns (thinning, random shift, jittering), simulated realisations of random point processes including simple sequential inhibition, Matern inhibition models, Neyman-Scott cluster processes (using direct, Brix-Kendall, or hybrid algorithms), log-Gaussian Cox processes, product shot noise cluster processes and Gibbs point processes (using Metropolis-Hastings birth-death-shift algorithm, alternating Gibbs sampler, or coupling-from-the-past perfect simulation). Also generates random spatial patterns of line segments, random tessellations, and random images (random noise, random mosaics). Excludes random generation on a linear network, which is covered by the separate package 'spatstat.linnet'.

Maintained by Adrian Baddeley. Last updated 2 days ago.

point-processes random-generation simulation spatial-sampling spatial-simulation cpp

14.0 match 5 stars 10.81 score 84 scripts 175 dependents

tidyverse

ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics

A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.

Maintained by Thomas Lin Pedersen. Last updated 10 days ago.

data-visualisation visualisation

5.3 match 6.6k stars 25.10 score 645k scripts 7.5k dependents

tidyverse

tidyr:Tidy Messy Data

Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).

Maintained by Hadley Wickham. Last updated 13 days ago.

tidy-data cpp

5.0 match 1.4k stars 22.88 score 168k scripts 5.5k dependents

bioc

ggtree:an R package for visualization of tree and annotation data

'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

Maintained by Guangchuang Yu. Last updated 5 months ago.

alignment annotation clustering dataimport multiplesequencealignment phylogenetics reproducibleresearch software visualization annotations ggplot2 phylogenetic-trees

6.6 match 864 stars 16.86 score 5.1k scripts 109 dependents

ludvigolsen

rearrr:Rearranging Data

Arrange data by a set of methods. Use rearrangers to reorder data points and mutators to change their values. From basic utilities, to centering the greatest value, to swirling in 3-dimensional space, 'rearrr' enables creativity when plotting and experimenting with data.

Maintained by Ludvig Renbo Olsen. Last updated 10 days ago.

arrange cluster expand forming generate ggplot2 order plotting-in-r roll rotate shaping swirl transformations

14.9 match 24 stars 7.26 score 128 scripts 8 dependents

jmpsteen

medflex:Flexible Mediation Analysis Using Natural Effect Models

Run flexible mediation analyses using natural effect models as described in Lange, Vansteelandt and Bekaert (2012) <DOI:10.1093/aje/kwr525>, Vansteelandt, Bekaert and Lange (2012) <DOI:10.1515/2161-962X.1014> and Loeys, Moerkerke, De Smet, Buysse, Steen and Vansteelandt (2013) <DOI:10.1080/00273171.2013.832132>.

Maintained by Johan Steen. Last updated 2 years ago.

causal-inference flexible-modeling mediation-analysis

14.6 match 23 stars 7.09 score 54 scripts

r-forge

Matrix:Sparse and Dense Matrix Classes and Methods

A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.

Maintained by Martin Maechler. Last updated 7 days ago.

openblas

5.3 match 1 stars 17.23 score 33k scripts 12k dependents

bioc

S4Vectors:Foundation of vector-like and list-like containers in Bioconductor

The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).

Maintained by Hervé Pagès. Last updated 1 months ago.

infrastructure datarepresentation bioconductor-package core-package

5.6 match 18 stars 16.05 score 1.0k scripts 1.9k dependents

bioc

GenomicDataCommons:NIH / NCI Genomic Data Commons Access

Programmatically access the NIH / NCI Genomic Data Commons RESTful service.

Maintained by Sean Davis. Last updated 1 months ago.

dataimport sequencing api-client bioconductor bioinformatics cancer core-services data-science genomics nci tcga vignette

7.2 match 87 stars 11.94 score 238 scripts 12 dependents

r-cas

caracas:Computer Algebra

Computer algebra via the 'SymPy' library (<https://www.sympy.org/>). This makes it possible to solve equations symbolically, find symbolic integrals, symbolic sums and other important quantities.

Maintained by Mikkel Meyer Andersen. Last updated 15 days ago.

11.6 match 24 stars 6.80 score 87 scripts 1 dependents

hadley

reshape:Flexibly Reshape Data

Flexibly restructure and aggregate data using just two functions: melt and cast.

Maintained by Hadley Wickham. Last updated 3 years ago.

7.6 match 9.83 score 21k scripts 231 dependents

metrumresearchgroup

mrgsolve:Simulate from ODE-Based Models

Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.

Maintained by Kyle T Baron. Last updated 1 months ago.

mrgsolve ode openblas cpp

6.8 match 138 stars 10.90 score 1.2k scripts 3 dependents

datashield

DSLite:'DataSHIELD' Implementation on Local Datasets

'DataSHIELD' is an infrastructure and series of R packages that enables the remote and 'non-disclosive' analysis of sensitive research data. This 'DataSHIELD Interface' implementation is for analyzing datasets living in the current R session. The purpose of this is primarily for lightweight 'DataSHIELD' analysis package development.

Maintained by Yannick Marcon. Last updated 2 years ago.

13.9 match 4 stars 5.03 score 53 scripts

hputter

mstate:Data Preparation, Estimation and Prediction in Multi-State Models

Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models, see Putter, Fiocco, Geskus (2007) <doi:10.1002/sim.2712>.

Maintained by Hein Putter. Last updated 29 days ago.

5.7 match 11 stars 12.13 score 322 scripts 55 dependents

adeckmyn

maps:Draw Geographical Maps

Display of maps. Projection code and larger maps are in separate packages ('mapproj' and 'mapdata').

Maintained by Alex Deckmyn. Last updated 2 months ago.

4.5 match 24 stars 14.70 score 19k scripts 490 dependents

rstudio

gt:Easily Create Presentation-Ready Display Tables

Build display tables from tabular data with an easy-to-use set of functions. With its progressive approach, we can construct display tables with a cohesive set of table parts. Table values can be formatted using any of the included formatting functions. Footnotes and cell styles can be precisely added through a location targeting system. The way in which 'gt' handles things for you means that you don't often have to worry about the fine details.

Maintained by Richard Iannone. Last updated 12 days ago.

docx easy-to-use html latex rtf summary-tables

3.6 match 2.1k stars 18.36 score 20k scripts 112 dependents

jojo-

mipfp:Multidimensional Iterative Proportional Fitting and Alternative Models

An implementation of the iterative proportional fitting (IPFP), maximum likelihood, minimum chi-square and weighted least squares procedures for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multidimensional). The package also provides an application of the IPFP to simulate multivariate Bernoulli distributions.

Maintained by Johan Barthelemy. Last updated 4 years ago.

9.7 match 24 stars 6.79 score 86 scripts 3 dependents

friendly

vcdExtra:'vcd' Extensions and Additions

Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data and the 'gnm' package for Generalized Nonlinear Models. In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of 'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by Michael Friendly and David Meyer.

Maintained by Michael Friendly. Last updated 5 months ago.

categorical-data-visualization generalized-linear-models mosaic-plots

6.3 match 24 stars 10.34 score 472 scripts 3 dependents

philchalmers

mirt:Multidimensional Item Response Theory

Analysis of discrete response data using unidimensional and multidimensional item analysis models under the Item Response Theory paradigm (Chalmers (2012) <doi:10.18637/jss.v048.i06>). Exploratory and confirmatory item factor analysis models are estimated with quadrature (EM) or stochastic (MHRM) methods. Confirmatory bi-factor and two-tier models are available for modeling item testlets using dimension reduction EM algorithms, while multiple group analyses and mixed effects designs are included for detecting differential item, bundle, and test functioning, and for modeling item and person covariates. Finally, latent class models such as the DINA, DINO, multidimensional latent class, mixture IRT models, and zero-inflated response models are supported, as well as a wide family of probabilistic unfolding models.

Maintained by Phil Chalmers. Last updated 11 days ago.

irt mirt openblas cpp openmp

4.0 match 210 stars 14.98 score 2.5k scripts 40 dependents

detlew

PowerTOST:Power and Sample Size for (Bio)Equivalence Studies

Contains functions to calculate power and sample size for various study designs used in bioequivalence studies. Use known.designs() to see the designs supported. Power and sample size can be obtained based on different methods, amongst them prominently the TOST procedure (two one-sided t-tests). See README and NEWS for further information.

Maintained by Detlew Labes. Last updated 12 months ago.

6.3 match 20 stars 9.61 score 112 scripts 4 dependents

insightsengineering

rbmi:Reference Based Multiple Imputation

Implements standard and reference based multiple imputation methods for continuous longitudinal endpoints (Gower-Page et al. (2022) <doi:10.21105/joss.04251>). In particular, this package supports deterministic conditional mean imputation and jackknifing as described in Wolbers et al. (2022) <doi:10.1002/pst.2234>, Bayesian multiple imputation as described in Carpenter et al. (2013) <doi:10.1080/10543406.2013.834911>, and bootstrapped maximum likelihood imputation as described in von Hippel and Bartlett (2021) <doi: 10.1214/20-STS793>.

Maintained by Isaac Gravestock. Last updated 24 days ago.

6.8 match 18 stars 8.78 score 33 scripts 1 dependents

bioc

goProfiles:goProfiles: an R package for the statistical analysis of functional profiles

The package implements methods to compare lists of genes based on comparing the corresponding 'functional profiles'.

Maintained by Alex Sanchez. Last updated 5 months ago.

annotation go geneexpression genesetenrichment graphandnetwork microarray multiplecomparison pathways software

10.6 match 5.48 score 6 scripts 1 dependents

markfairbanks

tidytable:Tidy Interface to 'data.table'

A tidy interface to 'data.table', giving users the speed of 'data.table' while using tidyverse-like syntax.

Maintained by Mark Fairbanks. Last updated 2 months ago.

5.1 match 458 stars 11.41 score 732 scripts 10 dependents

jasonjfoster

roll:Rolling and Expanding Statistics

Fast and efficient computation of rolling and expanding statistics for time-series data.

Maintained by Jason Foster. Last updated 1 months ago.

algorithms rcpp statistics openblas cpp openmp

5.9 match 116 stars 9.76 score 318 scripts 13 dependents

dmpe

urlshorteneR:R Wrapper for the 'Bit.ly' and 'Is.gd'/'v.gd' URL Shortening Services

Allows using two URL shortening services, which also provide expanding and analytic functions. Specifically developed for 'Bit.ly' (which requires OAuth 2.0) and 'is.gd' (no API key).

Maintained by John Malc. Last updated 29 days ago.

bitly isgd shorten-urls shortener shorturl url

8.4 match 21 stars 6.70 score 53 scripts 1 dependents

symengine

symengine:Interface to the 'SymEngine' Library

Provides an R interface to 'SymEngine' <https://github.com/symengine/>, a standalone 'C++' library for fast symbolic manipulation. The package has functionalities for symbolic computation like calculating exact mathematical expressions, solving systems of linear equations and code generation.

Maintained by Jialin Ma. Last updated 1 years ago.

mpfr4 gmp cpp

6.8 match 26 stars 8.20 score 33 scripts 10 dependents

liamrevell

phytools:Phylogenetic Tools for Comparative Biology (and Other Things)

A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.

Maintained by Liam J. Revell. Last updated 28 days ago.

4.0 match 218 stars 13.85 score 4.8k scripts 76 dependents

aphalo

photobiology:Photobiological Calculations

Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima: peaks, valleys and spikes. Conversion between energy-and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.

Maintained by Pedro J. Aphalo. Last updated 3 days ago.

light photobiology quantification r4photobiology-suite radiation spectra sun-position

5.5 match 4 stars 9.35 score 604 scripts 12 dependents

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 4 hours ago.

3.8 match 845 stars 13.60 score 264 scripts 2 dependents

edzer

intervals:Tools for Working with Points and Intervals

Tools for working with and comparing sets of points and intervals.

Maintained by Edzer Pebesma. Last updated 7 months ago.

cpp

5.3 match 11 stars 9.40 score 122 scripts 90 dependents

spatstat

spatstat.utils:Utility Functions for 'spatstat'

Contains utility functions for the 'spatstat' family of packages which may also be useful for other purposes.

Maintained by Adrian Baddeley. Last updated 2 days ago.

spatial-analysis spatial-data spatstat

4.1 match 5 stars 11.66 score 134 scripts 248 dependents

animint

animint2:Animated Interactive Grammar of Graphics

Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.

Maintained by Toby Hocking. Last updated 28 days ago.

5.4 match 64 stars 8.87 score 173 scripts

cvxgrp

CVXR:Disciplined Convex Optimization

An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

3.6 match 207 stars 12.89 score 768 scripts 51 dependents

hesim-dev

hesim:Health Economic Simulation Modeling and Decision Analysis

A modular and computationally efficient R package for parameterizing, simulating, and analyzing health economic simulation models. The package supports cohort discrete time state transition models (Briggs et al. 1998) <doi:10.2165/00019053-199813040-00003>, N-state partitioned survival models (Glasziou et al. 1990) <doi:10.1002/sim.4780091106>, and individual-level continuous time state transition models (Siebert et al. 2012) <doi:10.1016/j.jval.2012.06.014>, encompassing both Markov (time-homogeneous and time-inhomogeneous) and semi-Markov processes. Decision uncertainty from a cost-effectiveness analysis is quantified with standard graphical and tabular summaries of a probabilistic sensitivity analysis (Claxton et al. 2005, Barton et al. 2008) <doi:10.1002/hec.985>, <doi:10.1111/j.1524-4733.2008.00358.x>. Use of C++ and data.table make individual-patient simulation, probabilistic sensitivity analysis, and incorporation of patient heterogeneity fast.

Maintained by Devin Incerti. Last updated 6 months ago.

health-economic-evaluation microsimulation simulation-modeling cpp

5.6 match 67 stars 8.12 score 41 scripts

kaneplusplus

bigmemory:Manage Massive Matrices with Shared Memory and Memory-Mapped Files

Create, store, access, and manipulate massive matrices. Matrices are allocated to shared memory and may use memory-mapped files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and 'bigalgebra' provide advanced functionality.

Maintained by Michael J. Kane. Last updated 1 years ago.

cpp

3.8 match 127 stars 11.87 score 920 scripts 64 dependents

tidyverts

fabletools:Core Tools for Packages in the 'fable' Framework

Provides tools, helpers and data structures for developing models and time series functions for 'fable' and extension packages. These tools support a consistent and tidy interface for time series modelling and analysis.

Maintained by Mitchell OHara-Wild. Last updated 1 months ago.

3.6 match 91 stars 12.18 score 396 scripts 18 dependents

bioc

KEGGgraph:KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.

Maintained by Jitao David Zhang. Last updated 5 months ago.

pathways graphandnetwork visualization kegg

5.5 match 7.76 score 114 scripts 23 dependents

jvbraun

AlgDesign:Algorithmic Experimental Design

Algorithmic experimental designs. Calculates exact and approximate theory experimental designs for D,A, and I criteria. Very large designs may be created. Experimental designs may be blocked or blocked designs created from a candidate list, using several criteria. The blocking can be done when whole and within plot factors interact.

Maintained by Jerome Braun. Last updated 3 years ago.

4.5 match 12 stars 9.52 score 119 scripts 41 dependents

nlmixr2

rxode2:Facilities for Simulating from ODE-Based Models

Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.

Maintained by Matthew L. Fidler. Last updated 30 days ago.

fortran openblas cpp openmp

3.8 match 40 stars 11.24 score 220 scripts 13 dependents

kkholst

lava:Latent Variable Models

A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.

Maintained by Klaus K. Holst. Last updated 2 months ago.

latent-variable-models simulation statistics structural-equation-models

3.3 match 33 stars 12.85 score 610 scripts 476 dependents

great-northern-diver

zenplots:Zigzag Expanded Navigation Plots

Graphical tools for visualizing high-dimensional data along a path of alternating one- and two-dimensional plots. Note that this includes interactive graphics plots based on 'loon' in turn based on 'tcltk' (included as part of the standard R distribution). It also requires 'graph' from Bioconductor. For more detail on use and algorithms, see <doi:10.18637/jss.v095.i04>.

Maintained by Wayne Oldford. Last updated 1 years ago.

dimensional-data dimensional-plots graphical-systems pairs zigzag

7.7 match 3 stars 5.33 score 12 scripts 1 dependents

mrdwab

splitstackshape:Stack and Reshape Datasets After Splitting Concatenated Values

Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The concat.split (cSplit) family of functions splits such data into separate cells. The package also includes functions to stack groups of columns and to reshape wide data, even when the data are "unbalanced"---something which reshape (from base R) does not handle, and which melt and dcast from reshape2 do not easily handle.

Maintained by Ananda Mahto. Last updated 6 years ago.

4.0 match 59 stars 10.25 score 2.1k scripts 21 dependents

guyabel

tidycat:Expand Tidy Output for Categorical Parameter Estimates

Create additional rows and columns on broom::tidy() output to allow for easier control on categorical parameter estimates.

Maintained by Guy J. Abel. Last updated 1 years ago.

data-visualization data-viz glm model-comparison regression-analysis regression-models statistical-analysis statistical-modeling

7.4 match 4 stars 5.53 score 56 scripts 1 dependents

oobianom

r2resize:In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents

Automatic resizing toolbar for containers, images and tables. Various resizer or expandable container functionalities are also included. Most suitable to include in 'shiny', 'markdown' and 'quarto' documents.

Maintained by Obinna Obianom. Last updated 4 months ago.

card resize rmarkdown shiny

6.2 match 15 stars 6.44 score 23 scripts

nashjc

optimx:Expanded Replacement and Extension of the 'optim' Function

Provides a replacement and extension of the optim() function to call to several function minimization codes in R in a single statement. These methods handle smooth, possibly box constrained functions of several or many parameters. Note that function 'optimr()' was prepared to simplify the incorporation of minimization codes going forward. Also implements some utility codes and some extra solvers, including safeguarded Newton methods. Many methods previously separate are now included here. This is the version for CRAN.

Maintained by John C Nash. Last updated 2 months ago.

3.0 match 2 stars 12.87 score 1.8k scripts 89 dependents

bioc

tidyCoverage:Extract and aggregate genomic coverage over features of interest

`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.

Maintained by Jacques Serizay. Last updated 5 months ago.

software sequencing coverage

6.6 match 21 stars 5.80 score 6 scripts

luisdva

annotater:Annotate Package Load Calls

Provides non-invasive annotation of package load calls such as \code{library()}, \code{p_load()}, and \code{require()} so that we can have an idea of what the packages we are loading are meant for.

Maintained by Luis D. Verde Arregoitia. Last updated 5 months ago.

5.6 match 102 stars 6.81 score 21 scripts

ropensci

drake:A Pipeline Toolkit for Reproducible Computation at Scale

A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://docs.ropensci.org/drake/> and the online manual <https://books.ropensci.org/drake/>.

Maintained by William Michael Landau. Last updated 3 months ago.

data-science drake high-performance-computing makefile peer-reviewed pipeline reproducibility reproducible-research ropensci workflow

3.3 match 1.3k stars 11.49 score 1.7k scripts 1 dependents

bioc

VariantAnnotation:Annotation of Genetic Variants

Annotate variants, compute amino acid coding changes, predict coding outcomes.

Maintained by Bioconductor Package Maintainer. Last updated 2 months ago.

dataimport sequencing snp annotation genetics variantannotation curl bzip2 xz-utils zlib

3.3 match 11.39 score 1.9k scripts 152 dependents

cran

coxme:Mixed Effects Cox Models

Fit Cox proportional hazards models containing both fixed and random effects. The random effects can have a general form, of which familial interactions (a "kinship" matrix) is a particular special case. Note that the simplest case of a mixed effects Cox model, i.e. a single random per-group intercept, is also called a "frailty" model. The approach is based on Ripatti and Palmgren, Biometrics 2002.

Maintained by Terry M. Therneau. Last updated 7 months ago.

4.3 match 2 stars 8.78 score 562 scripts 15 dependents

r-lib

scales:Scale Functions for Visualization

Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.

Maintained by Thomas Lin Pedersen. Last updated 5 months ago.

ggplot2

1.8 match 419 stars 19.88 score 88k scripts 7.9k dependents

dcousin3

superb:Summary Plots with Adjusted Error Bars

Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.

Maintained by Denis Cousineau. Last updated 2 months ago.

error-bars plotting statistics summary-plots summary-statistics visualization

3.7 match 19 stars 9.55 score 155 scripts 2 dependents

lme4

lme4:Linear Mixed-Effects Models using 'Eigen' and S4

Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".

Maintained by Ben Bolker. Last updated 3 days ago.

cpp

1.7 match 647 stars 20.69 score 35k scripts 1.5k dependents

r-spatial

stars:Spatiotemporal Arrays, Raster and Vector Data Cubes

Reading, manipulating, writing and plotting spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL' bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.

Maintained by Edzer Pebesma. Last updated 1 months ago.

raster satellite-images spatial

1.9 match 571 stars 18.27 score 7.2k scripts 137 dependents

r-cas

Ryacas0:Legacy 'Ryacas' (Interface to 'Yacas' Computer Algebra System)

A legacy version of 'Ryacas', an interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).

Maintained by Mikkel Meyer Andersen. Last updated 2 years ago.

cpp

4.8 match 2 stars 7.11 score 36 scripts 6 dependents

alexanderrobitzsch

miceadds:Some Additional Multiple Imputation Functions, Especially for 'mice'

Contains functions for multiple imputation which complements existing functionality in R. In particular, several imputation methods for the mice package (van Buuren & Groothuis-Oudshoorn, 2011, <doi:10.18637/jss.v045.i03>) are implemented. Main features of the miceadds package include plausible value imputation (Mislevy, 1991, <doi:10.1007/BF02294457>), multilevel imputation for variables at any level or with any number of hierarchical and non-hierarchical levels (Grund, Luedtke & Robitzsch, 2018, <doi:10.1177/1094428117703686>; van Buuren, 2018, Ch.7, <doi:10.1201/9780429492259>), imputation using partial least squares (PLS) for high dimensional predictors (Robitzsch, Pham & Yanagida, 2016), nested multiple imputation (Rubin, 2003, <doi:10.1111/1467-9574.00217>), substantive model compatible imputation (Bartlett et al., 2015, <doi:10.1177/0962280214521348>), and features for the generation of synthetic datasets (Reiter, 2005, <doi:10.1111/j.1467-985X.2004.00343.x>; Nowok, Raab, & Dibben, 2016, <doi:10.18637/jss.v074.i11>).

Maintained by Alexander Robitzsch. Last updated 16 days ago.

missing-data multiple-imputation openblas cpp

3.7 match 16 stars 9.16 score 542 scripts 9 dependents

tidyverse

dbplyr:A 'dplyr' Back End for Databases

A 'dplyr' back end for databases that allows you to work with remote database tables as if they are in-memory data frames. Basic features works with any database that has a 'DBI' back end; more advanced features require 'SQL' translation to be provided by the package author.

Maintained by Hadley Wickham. Last updated 3 months ago.

database

1.7 match 481 stars 19.72 score 5.2k scripts 736 dependents

hrbrmstr

longurl:Expand Short 'URLs'

Tools are provided to expand vectors of short URLs into long 'URLs'. No 'API' services are used, which may mean that this operates more slowly than 'API' services do (since they usually cache results of expansions that every user of the service requests). You can setup your own caching layer with the 'memoise' package if you wish to have a speedup during single sessions or add larger dependencies, such as 'Redis', to gain a longer-term performance boost at the expense of added complexity.

Maintained by Bob Rudis. Last updated 5 years ago.

r-cyber url url-shortener

7.4 match 33 stars 4.56 score 22 scripts

stephenmilborrow

earth:Multivariate Adaptive Regression Splines

Build regression models using the techniques in Friedman's papers "Fast MARS" and "Multivariate Adaptive Regression Splines" <doi:10.1214/aos/1176347963>. (The term "MARS" is trademarked and thus not used in the name of the package.)

Maintained by Stephen Milborrow. Last updated 5 months ago.

fortran openblas

4.0 match 5 stars 8.40 score 3.9k scripts 26 dependents

bxc147

Epi:Statistical Analysis in Epidemiology

Functions for demographic and epidemiological analysis in the Lexis diagram, i.e. register and cohort follow-up data. In particular representation, manipulation, rate estimation and simulation for multistate data - the Lexis suite of functions, which includes interfaces to 'mstate', 'etm' and 'cmprsk' packages. Contains functions for Age-Period-Cohort and Lee-Carter modeling and a function for interval censored data and some useful functions for tabulation and plotting, as well as a number of epidemiological data sets.

Maintained by Bendix Carstensen. Last updated 2 months ago.

3.3 match 4 stars 9.65 score 708 scripts 11 dependents

helmut01

replicateBE:Average Bioequivalence with Expanding Limits (ABEL)

Performs comparative bioavailability calculations for Average Bioequivalence with Expanding Limits (ABEL). Implemented are 'Method A' / 'Method B' and the detection of outliers. If the design allows, assessment of the empiric Type I Error and iteratively adjusting alpha to control the consumer risk. Average Bioequivalence - optionally with a tighter (narrow therapeutic index drugs) or wider acceptance range (South Africa: Cmax) - is implemented as well.

Maintained by Helmut Schütz. Last updated 3 years ago.

bioequivalence biostatistics

6.8 match 9 stars 4.65 score 10 scripts

bioc

seqsetvis:Set Based Visualizations for Next-Gen Sequencing Data

seqsetvis enables the visualization and analysis of sets of genomic sites in next gen sequencing data. Although seqsetvis was designed for the comparison of mulitple ChIP-seq samples, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files pileups from bam file). seqsetvis has multiple functions for fetching data from regions into a tidy format for analysis in data.table or tidyverse and visualization via ggplot2.

Maintained by Joseph R Boyd. Last updated 3 months ago.

software chipseq multiplecomparison sequencing visualization

5.4 match 5.82 score 82 scripts

renkun-ken

rlist:A Toolbox for Non-Tabular Data Manipulation

Provides a set of functions for data manipulation with list objects, including mapping, filtering, grouping, sorting, updating, searching, and other useful functions. Most functions are designed to be pipeline friendly so that data processing with lists can be chained.

Maintained by Kun Ren. Last updated 2 years ago.

2.3 match 206 stars 13.73 score 2.2k scripts 123 dependents

asmahani

RegressionFactory:Expander Functions for Generating Full Gradient and Hessian from Single-Slot and Multi-Slot Base Distributions

The expander functions rely on the mathematics developed for the Hessian-definiteness invariance theorem for linear projection transformations of variables, described in authors' paper, to generate the full, high-dimensional gradient and Hessian from the lower-dimensional derivative objects. This greatly relieves the computational burden of generating the regression-function derivatives, which in turn can be fed into any optimization routine that utilizes such derivatives. The theorem guarantees that Hessian definiteness is preserved, meaning that reasoning about this property can be performed in the low-dimensional space of the base distribution. This is often a much easier task than its equivalent in the full, high-dimensional space. Definiteness of Hessian can be useful in selecting optimization/sampling algorithms such as Newton-Raphson optimization or its sampling equivalent, the Stochastic Newton Sampler. Finally, in addition to being a computational tool, the regression expansion framework is of conceptual value by offering new opportunities to generate novel regression problems.

Maintained by Alireza S. Mahani. Last updated 4 years ago.

13.4 match 2.30 score 20 scripts

trinker

lexicon:Lexicons for Text Analysis

A collection of lexical hash tables, dictionaries, and word lists.

Maintained by Tyler Rinker. Last updated 3 years ago.

hash lexicon lookup names-frequent stopwords text-dictionaries text-mining

3.4 match 111 stars 8.80 score 224 scripts 25 dependents

canmod

macpan2:Fast and Flexible Compartmental Modelling

Fast and flexible compartmental modelling with Template Model Builder.

Maintained by Steve Walker. Last updated 3 days ago.

compartmental-models epidemiology forecasting mixed-effects model-fitting optimization simulation simulation-modeling cpp

3.4 match 4 stars 8.89 score 246 scripts 1 dependents

bioc

RCy3:Functions to Access and Control Cytoscape

Vizualize, analyze and explore networks using Cytoscape via R. Anything you can do using the graphical user interface of Cytoscape, you can now do with a single RCy3 function.

Maintained by Alex Pico. Last updated 5 months ago.

visualization graphandnetwork thirdpartyclient network

2.3 match 52 stars 13.39 score 628 scripts 15 dependents

egenn

rtemis:Machine Learning and Visualization

Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.

Maintained by E.D. Gennatas. Last updated 1 months ago.

data-science data-visualization machine-learning machine-learning-library visualization

4.3 match 145 stars 7.09 score 50 scripts 2 dependents

shaunpwilkinson

insect:Informatic Sequence Classification Trees

Provides tools for probabilistic taxon assignment with informatic sequence classification trees. See Wilkinson et al (2018) <doi:10.7287/peerj.preprints.26812v1>.

Maintained by Shaun Wilkinson. Last updated 4 years ago.

5.2 match 14 stars 5.80 score 91 scripts

gavinsimpson

coenocliner:Coenocline Simulation

Simulate species occurrence and abundances (counts) along gradients.

Maintained by Gavin L. Simpson. Last updated 4 years ago.

4.9 match 12 stars 6.03 score 15 scripts 1 dependents

maxconway

fbar:An Extensible Approach to Flux Balance Analysis

A toolkit for Flux Balance Analysis and related metabolic modeling techniques. Functions are provided for: parsing models in tabular format, converting parsed metabolic models to input formats for common linear programming solvers, and evaluating and applying gene-protein-reaction mappings. In addition, there are wrappers to parse a model, select a solver, find the metabolic fluxes, and return the results applied to the original model. Compared to other packages in this field, this package puts a much heavier focus on providing reusable components that can be used in the design of new implementation of new techniques, in particular those that involve large parameter sweeps. For a background on the theory, see What is Flux Balance Analysis <doi:10.1038/nbt.1614>.

Maintained by Max Conway. Last updated 5 years ago.

5.4 match 9 stars 5.49 score 23 scripts

lrberge

fixest:Fast Fixed-Effects Estimations

Fast and user-friendly estimation of econometric models with multiple fixed-effects. Includes ordinary least squares (OLS), generalized linear models (GLM) and the negative binomial. The core of the package is based on optimized parallel C++ code, scaling especially well for large data sets. The method to obtain the fixed-effects coefficients is based on Berge (2018) <https://github.com/lrberge/fixest/blob/master/_DOCS/FENmlm_paper.pdf>. Further provides tools to export and view the results of several estimations with intuitive design to cluster the standard-errors.

Maintained by Laurent Berge. Last updated 7 months ago.

cpp openmp

2.0 match 387 stars 14.69 score 3.8k scripts 25 dependents

flr

FLCore:Core Package of FLR, Fisheries Modelling in R

Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.

Maintained by Iago Mosqueira. Last updated 10 days ago.

fisheries flr fisheries-modelling

3.3 match 16 stars 8.78 score 956 scripts 23 dependents

brodieg

oshka:Recursive Quoted Language Expansion

Expands quoted language by recursively replacing any symbol that points to quoted language with the language it points to. The recursive process continues until only symbols that point to non-language objects remain. The resulting quoted language can then be evaluated normally. This differs from the traditional 'quote'/'eval' pattern because it resolves intermediate language objects that would interfere with evaluation.

Maintained by Brodie Gaslam. Last updated 7 years ago.

nse-functions

5.6 match 14 stars 5.15 score 9 scripts

tidyverse

dtplyr:Data Table Back-End for 'dplyr'

Provides a data.table backend for 'dplyr'. The goal of 'dtplyr' is to allow you to write 'dplyr' code that is automatically translated to the equivalent, but usually much faster, data.table code.

Maintained by Hadley Wickham. Last updated 2 months ago.

datatable dplyr

1.7 match 671 stars 16.27 score 2.5k scripts 147 dependents

mlverse

torch:Tensors and Neural Networks with 'GPU' Acceleration

Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.

Maintained by Daniel Falbel. Last updated 6 days ago.

autograd deep-learning torch cpp

1.7 match 520 stars 16.52 score 1.4k scripts 38 dependents

mucollective

multiverse:Create 'multiverse analysis' in R

Implement 'multiverse' style analyses (Steegen S., Tuerlinckx F, Gelman A., Vanpaemal, W., 2016) <doi:10.1177/1745691616658637> to show the robustness of statistical inference. 'Multiverse analysis' is a philosophy of statistical reporting where paper authors report the outcomes of many different statistical analyses in order to show how fragile or robust their findings are. The 'multiverse' package (Sarma A., Kale A., Moon M., Taback N., Chevalier F., Hullman J., Kay M., 2021) <doi:10.31219/osf.io/yfbwm> allows users to concisely and flexibly implement 'multiverse-style' analysis, which involve declaring alternate ways of performing an analysis step, in R and R Notebooks.

Maintained by Abhraneel Sarma. Last updated 4 months ago.

3.3 match 62 stars 8.37 score 42 scripts

kwb-r

kwb.utils:General Utility Functions Developed at KWB

This package contains some small helper functions that aim at improving the quality of code developed at Kompetenzzentrum Wasser gGmbH (KWB).

Maintained by Hauke Sonnenberg. Last updated 12 months ago.

3.7 match 8 stars 7.33 score 12 scripts 78 dependents

braverock

PerformanceAnalytics:Econometric Tools for Performance and Risk Analysis

Collection of econometric functions for performance and risk analysis. In addition to standard risk and performance metrics, this package aims to aid practitioners and researchers in utilizing the latest research in analysis of non-normal return streams. In general, it is most tested on return (rather than price) data on a regular scale, but most functions will work with irregular return data as well, and increasing numbers of functions will work with P&L or price data where possible.

Maintained by Brian G. Peterson. Last updated 3 months ago.

1.7 match 222 stars 15.93 score 4.8k scripts 20 dependents

eitsupi

neopolars:R Bindings for the 'polars' Rust Library

Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.

Maintained by Tatsuya Shima. Last updated 2 days ago.

rust cargo

5.4 match 40 stars 4.86 score 1 scripts

globalgov

messydates:A Flexible Class for Messy Dates

Contains a set of tools for constructing and coercing into and from the "mdate" class. This date class implements ISO 8601-2:2019(E) and allows regular dates to be annotated to express unspecified date components, approximate or uncertain date components, date ranges, and sets of dates. This is useful for describing and analysing temporal information, whether historical or recent, where date precision may vary.

Maintained by James Hollway. Last updated 10 days ago.

dates

5.1 match 15 stars 5.08 score

bioc

OmicsMLRepoR:Search harmonized metadata created under the OmicsMLRepo project

This package provides functions to browse the harmonized metadata for large omics databases. This package also supports data navigation if the metadata incorporates ontology.

Maintained by Sehyun Oh. Last updated 1 months ago.

software infrastructure datarepresentation

4.8 match 5.40 score 14 scripts

easystats

datawizard:Easy Data Wrangling and Statistical Transformations

A lightweight package to assist in key steps involved in any data analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) <doi:10.21105/joss.04684>.

Maintained by Etienne Bacher. Last updated 10 days ago.

data dplyr hacktoberfest janitor manipulation reshape tidyr wrangling

1.8 match 222 stars 14.71 score 436 scripts 119 dependents

cbroeckl

RAMClustR:Mass Spectrometry Metabolomics Feature Clustering and Interpretation

A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectrometry <DOI: 10.1021/ac501530d> data.

Maintained by Helge Hecht. Last updated 7 months ago.

massspectrometry metabolomics

3.8 match 12 stars 6.78 score 20 scripts

jeinbeck-code

npmlreg:Nonparametric Maximum Likelihood Estimation for Random Effect Models

Nonparametric maximum likelihood estimation or Gaussian quadrature for overdispersed generalized linear models and variance component models.

Maintained by Jochen Einbeck. Last updated 7 years ago.

7.8 match 3.26 score 30 scripts 1 dependents

wrathematics

kazaam:Tools for Tall Distributed Matrices

Many data science problems reduce to operations on very tall, skinny matrices. However, sometimes these matrices can be so tall that they are difficult to work with, or do not even fit into main memory. One strategy to deal with such objects is to distribute their rows across several processors. To this end, we offer an 'S4' class for tall, skinny, distributed matrices, called the 'shaq'. We also provide many useful numerical methods and statistics operations for operating on these distributed objects. The naming is a bit "tongue-in-cheek", with the class a play on the fact that 'Shaquille' 'ONeal' ('Shaq') is very tall, and he starred in the film 'Kazaam'.

Maintained by Drew Schmidt. Last updated 8 years ago.

openblas

6.6 match 3.82 score 133 scripts

matthewheun

matsindf:Matrices in Data Frames

Provides functions to collapse a tidy data frame into matrices in a data frame and expand a data frame of matrices into a tidy data frame.

Maintained by Matthew Heun. Last updated 9 days ago.

4.6 match 5 stars 5.48 score 40 scripts

dusadrian

admisc:Adrian Dusa's Miscellaneous

Contains functions used across packages 'DDIwR', 'QCA' and 'venn'. Interprets and translates, factorizes and negates SOP - Sum of Products expressions, for both binary and multi-value crisp sets, and extracts information (set names, set values) from those expressions. Other functions perform various other checks if possibly numeric (even if all numbers reside in a character vector) and coerce to numeric, or check if the numbers are whole. It also offers, among many others, a highly versatile recoding routine and some more flexible alternatives to the base functions 'with()' and 'within()'. SOP simplification functions in this package use related minimization from package 'QCA', which is recommended to be installed despite not being listed in the Imports field, due to circular dependency issues.

Maintained by Adrian Dusa. Last updated 4 days ago.

3.3 match 2 stars 7.61 score 20 scripts 92 dependents

aphalo

ggpmisc:Miscellaneous Extensions to 'ggplot2'

Extensions to 'ggplot2' respecting the grammar of graphics paradigm. Statistics: locate and tag peaks and valleys; label plot with the equation of a fitted polynomial or other types of models; labels with P-value, R^2 or adjusted R^2 or information criteria for fitted models; label with ANOVA table for fitted models; label with summary for fitted models. Model fit classes for which suitable methods are provided by package 'broom' and 'broom.mixed' are supported. Scales and stats to build volcano and quadrant plots based on outcomes, fold changes, p-values and false discovery rates.

Maintained by Pedro J. Aphalo. Last updated 4 months ago.

data-analysis dataviz ggplot2-annotations ggplot2-stats statistics

1.9 match 105 stars 13.32 score 4.4k scripts 14 dependents

bioc

MSnbase:Base Functions and Classes for Mass Spectrometry and Proteomics

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

Maintained by Laurent Gatto. Last updated 3 days ago.

immunooncology infrastructure proteomics massspectrometry qualitycontrol dataimport bioconductor bioinformatics mass-spectrometry proteomics-data visualisation cpp

1.9 match 130 stars 12.81 score 772 scripts 36 dependents

projectmosaic

mosaic:Project MOSAIC Statistics and Mathematics Teaching Utilities

Data sets and utilities from Project MOSAIC (<http://www.mosaic-web.org>) used to teach mathematics, statistics, computation and modeling. Funded by the NSF, Project MOSAIC is a community of educators working to tie together aspects of quantitative work that students in science, technology, engineering and mathematics will need in their professional lives, but which are usually taught in isolation, if at all.

Maintained by Randall Pruim. Last updated 1 years ago.

1.8 match 93 stars 13.32 score 7.2k scripts 7 dependents

bioc

QFeatures:Quantitative features for mass spectrometry data

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

Maintained by Laurent Gatto. Last updated 13 days ago.

infrastructure massspectrometry proteomics metabolomics bioconductor mass-spectrometry

2.0 match 27 stars 11.87 score 278 scripts 49 dependents

bioc

CellNOptR:Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

Maintained by Attila Gabor. Last updated 5 months ago.

cellbasedassays cellbiology proteomics pathways network timecourse immunooncology

3.5 match 6.72 score 98 scripts 6 dependents

irworkshop

campfin:Wrangle Campaign Finance Data

Explore and normalize American campaign finance data. Created by the Investigative Reporting Workshop to facilitate work on The Accountability Project, an effort to collect public data into a central, standard database that is more easily searched: <https://publicaccountability.org/>.

Maintained by Kiernan Nicholls. Last updated 1 years ago.

campaign-finance data-journalism

4.1 match 17 stars 5.66 score 54 scripts

joaomacalos

sfcr:Simulate Stock-Flow Consistent Models

Routines to write, simulate, and validate stock-flow consistent (SFC) models. The accounting structure of SFC models are described in Godley and Lavoie (2007, ISBN:978-1-137-08599-3). The algorithms implemented to solve the models (Gauss-Seidel and Broyden) are described in Kinsella and O'Shea (2010) <doi:10.2139/ssrn.1729205> and Peressini and Sullivan (1988, ISBN:0-387-96614-5).

Maintained by Joao Macalos. Last updated 3 years ago.

openblas cpp

4.1 match 24 stars 5.66 score 38 scripts

frictionlessdata

tableschema.r:Table Schema 'Frictionless Data'

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

Maintained by Kleanthis Koupidis. Last updated 2 years ago.

4.0 match 25 stars 5.70 score 101 scripts

statisfactions

simpr:Flexible 'Tidyverse'-Friendly Simulations

A general, 'tidyverse'-friendly framework for simulation studies, design analysis, and power analysis. Specify data generation, define varying parameters, generate data, fit models, and tidy model results in a single pipeline, without needing loops or custom functions.

Maintained by Ethan Brown. Last updated 8 months ago.

3.3 match 43 stars 6.89 score 30 scripts

bioc

plyranges:A fluent interface for manipulating GenomicRanges

A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.

Maintained by Michael Love. Last updated 5 months ago.

infrastructure datarepresentation workflowstep coverage bioconductor data-analysis dplyr genomic-ranges genomics tidy-data

1.8 match 143 stars 12.60 score 1.9k scripts 20 dependents

dsy109

HoRM:Supplemental Functions and Datasets for "Handbook of Regression Methods"

Supplement for the book "Handbook of Regression Methods" by D. S. Young. Some datasets used in the book are included and documented. Wrapper functions are included that simplify the examples in the textbook, such as code for constructing a regressogram and expanding ANOVA tables to reflect the total sum of squares.

Maintained by Derek S. Young. Last updated 9 months ago.

regression-analysis regression-models shiny-apps

6.3 match 3.56 score 73 scripts

henrikbengtsson

R.utils:Various Programming Utilities

Utility functions useful when programming and developing R packages.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

1.6 match 63 stars 13.74 score 5.7k scripts 814 dependents

config-i1

greybox:Toolbox for Model Building and Forecasting

Implements functions and instruments for regression model building and its application to forecasting. The main scope of the package is in variables selection and models specification for cases of time series data. This includes promotional modelling, selection between different dynamic regressions with non-standard distributions of errors, selection based on cross validation, solutions to the fat regression model problem and more. Models developed in the package are tailored specifically for forecasting purposes. So as a results there are several methods that allow producing forecasts from these models and visualising them.

Maintained by Ivan Svetunkov. Last updated 3 days ago.

forecasting model-selection model-selection-and-evaluation regression regression-models statistics cpp

2.0 match 30 stars 11.03 score 97 scripts 34 dependents

bioc

SynExtend:Tools for Working With Synteny Objects

Shared order between genomic sequences provide a great deal of information. Synteny objects produced by the R package DECIPHER provides quantitative information about that shared order. SynExtend provides tools for extracting information from Synteny objects.

Maintained by Nicholas Cooley. Last updated 3 days ago.

genetics clustering comparativegenomics dataimport fortran openmp

3.4 match 1 stars 6.42 score 77 scripts

quexiang

OpenMindat:Quickly Retrieve Datasets from the 'Mindat' API

The goal of OpenMindat R package is to provide functions for users or machines to quickly and easily retrieve datasets from the mindat.org API (<https://api.mindat.org/schema/redoc/>).

Maintained by Xiang Que. Last updated 2 months ago.

3.8 match 34 stars 5.83 score 3 scripts

urbananalyst

dodgr:Distances on Directed Graphs

Distances on dual-weighted directed graphs using priority-queue shortest paths (Padgham (2019) <doi:10.32866/6945>). Weighted directed graphs have weights from A to B which may differ from those from B to A. Dual-weighted directed graphs have two sets of such weights. A canonical example is a street network to be used for routing in which routes are calculated by weighting distances according to the type of way and mode of transport, yet lengths of routes must be calculated from direct distances.

Maintained by Mark Padgham. Last updated 6 days ago.

distance openstreetmap router shortest-paths street-networks cpp

1.9 match 129 stars 11.53 score 229 scripts 4 dependents

jokergoo

sfcurve:2x2, 3x3 and Nxn Space-Filling Curves

Implementation of all possible forms of 2x2 and 3x3 space-filling curves, i.e., the generalized forms of the Hilbert curve <https://en.wikipedia.org/wiki/Hilbert_curve>, the Peano curve <https://en.wikipedia.org/wiki/Peano_curve> and the Peano curve in the meander type (Figure 5 in <https://eudml.org/doc/141086>). It can generates nxn curves expanded from any specific level-1 units. It also implements the H-curve and the three-dimensional Hilbert curve.

Maintained by Zuguang Gu. Last updated 6 months ago.

cpp

4.6 match 1 stars 4.66 score 13 scripts

bioc

DESeq2:Differential gene expression analysis based on the negative binomial distribution

Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

Maintained by Michael Love. Last updated 11 days ago.

sequencing rnaseq chipseq geneexpression transcription normalization differentialexpression bayesian regression principalcomponent clustering immunooncology openblas cpp

1.3 match 375 stars 16.11 score 17k scripts 115 dependents

pik-piam

gdx:Interface package for GDX files in R

A wrapper package for the gdxrrw extending its functionality and allowing to read and write GDX files directly in R.

Maintained by Jan Philipp Dietrich. Last updated 10 months ago.

4.5 match 1 stars 4.71 score 128 scripts 9 dependents

ygeunkim

bvhar:Bayesian Vector Heterogeneous Autoregressive Modeling

Tools to model and forecast multivariate time series including Bayesian Vector heterogeneous autoregressive (VHAR) model by Kim & Baek (2023) (<doi:10.1080/00949655.2023.2281644>). 'bvhar' can model Vector Autoregressive (VAR), VHAR, Bayesian VAR (BVAR), and Bayesian VHAR (BVHAR) models.

Maintained by Young Geun Kim. Last updated 17 days ago.

bayesian bayesian-econometrics bvar eigen forecasting har pybind11 python rcppeigen time-series vector-autoregression cpp openmp

3.3 match 6 stars 6.42 score 25 scripts

jmbarbone

mark:Miscellaneous, Analytic R Kernels

Miscellaneous functions and wrappers for development in other packages created, maintained by Jordan Mark Barbone.

Maintained by Jordan Mark Barbone. Last updated 1 months ago.

4.3 match 6 stars 4.95 score 9 scripts

spatstat

spatstat.model:Parametric Statistical Modelling and Inference for the 'spatstat' Family

Functionality for parametric statistical modelling and inference for spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Supports parametric modelling, formal statistical inference, and model validation. Parametric models include Poisson point processes, Cox point processes, Neyman-Scott cluster processes, Gibbs point processes and determinantal point processes. Models can be fitted to data using maximum likelihood, maximum pseudolikelihood, maximum composite likelihood and the method of minimum contrast. Fitted models can be simulated and predicted. Formal inference includes hypothesis tests (quadrat counting tests, Cressie-Read tests, Clark-Evans test, Berman test, Diggle-Cressie-Loosmore-Ford test, scan test, studentised permutation test, segregation test, ANOVA tests of fitted models, adjusted composite likelihood ratio test, envelope tests, Dao-Genton test, balanced independent two-stage test), confidence intervals for parameters, and prediction intervals for point counts. Model validation techniques include leverage, influence, partial residuals, added variable plots, diagnostic plots, pseudoscore residual plots, model compensators and Q-Q plots.

Maintained by Adrian Baddeley. Last updated 8 days ago.

analysis-of-variance cluster-process confidence-intervals cox-process determinantal-point-processes gibbs-process influence leverage model-diagnostics neyman-scott parameter-estimation poisson-process spatial-analysis spatial-modelling spatial-point-processes statistical-inference

2.3 match 5 stars 9.09 score 6 scripts 46 dependents

tiledb-inc

tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.

Maintained by Isaiah Norton. Last updated 5 days ago.

array hdfs s3 storage-manager tiledb cpp

1.7 match 107 stars 11.96 score 306 scripts 4 dependents

winvector

wrapr:Wrap R Tools for Debugging and Parametric Programming

Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.

Maintained by John Mount. Last updated 2 years ago.

1.8 match 137 stars 11.11 score 390 scripts 12 dependents

fishr-core-team

FSA:Simple Fisheries Stock Assessment Methods

A variety of simple fish stock assessment methods.

Maintained by Derek H. Ogle. Last updated 2 months ago.

fish fisheries fisheries-management fisheries-stock-assessment population-dynamics stock-assessment

1.8 match 68 stars 11.08 score 1.7k scripts 6 dependents

pbreheny

grpreg:Regularization Paths for Regression Models with Grouped Covariates

Efficient algorithms for fitting the regularization path of linear regression, GLM, and Cox regression models with grouped penalties. This includes group selection methods such as group lasso, group MCP, and group SCAD as well as bi-level selection methods such as the group exponential lasso, the composite MCP, and the group bridge. For more information, see Breheny and Huang (2009) <doi:10.4310/sii.2009.v2.n3.a10>, Huang, Breheny, and Ma (2012) <doi:10.1214/12-sts392>, Breheny and Huang (2015) <doi:10.1007/s11222-013-9424-2>, and Breheny (2015) <doi:10.1111/biom.12300>, or visit the package homepage <https://pbreheny.github.io/grpreg/>.

Maintained by Patrick Breheny. Last updated 17 days ago.

1.8 match 34 stars 11.38 score 192 scripts 34 dependents

cran

MuMIn:Multi-Model Inference

Tools for model selection and model averaging with support for a wide range of statistical models. Automated model selection through subsets of the maximum model, with optional constraints for model inclusion. Averaging of model parameters and predictions based on model weights derived from information criteria (AICc and alike) or custom model weighting schemes.

Maintained by Kamil Bartoń. Last updated 9 months ago.

2.3 match 8 stars 8.84 score 5.6k scripts 27 dependents

chrisaberson

pwr2ppl:Power Analyses for Common Designs (Power to the People)

Statistical power analysis for designs including t-tests, correlations, multiple regression, ANOVA, mediation, and logistic regression. Functions accompany Aberson (2019) <doi:10.4324/9781315171500>.

Maintained by Chris Aberson. Last updated 3 years ago.

4.7 match 17 stars 4.16 score 17 scripts

ewenharrison

finalfit:Quickly Create Elegant Regression Results Tables and Plots when Modelling

Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.

Maintained by Ewen Harrison. Last updated 7 months ago.

1.7 match 270 stars 11.43 score 1.0k scripts

dmurdoch

plotrix:Various Plotting Functions

Lots of plots, various labeling, axis and color scaling functions. The author/maintainer died in September 2023.

Maintained by Duncan Murdoch. Last updated 1 years ago.

1.7 match 5 stars 11.31 score 9.2k scripts 361 dependents

cran

epitools:Epidemiology Tools

Tools for training and practicing epidemiologists including methods for two-way and multi-way contingency tables.

Maintained by Adam Omidpanah. Last updated 5 years ago.

4.0 match 2 stars 4.89 score 12 dependents

seankross

swirl:Learn R, in R

Use the R console as an interactive learning environment. Users receive immediate feedback as they are guided through self-paced lessons in data science and R programming.

Maintained by Sean Kross. Last updated 5 years ago.

3.4 match 5.73 score 1.8k scripts 1 dependents

cjvanlissa

tidySEM:Tidy Structural Equation Modeling

A tidy workflow for generating, estimating, reporting, and plotting structural equation models using 'lavaan', 'OpenMx', or 'Mplus'. Throughout this workflow, elements of syntax, results, and graphs are represented as 'tidy' data, making them easy to customize. Includes functionality to estimate latent class analyses, and to plot 'dagitty' and 'igraph' objects.

Maintained by Caspar J. van Lissa. Last updated 8 days ago.

1.8 match 58 stars 10.69 score 330 scripts 1 dependents

richfitz

diversitree:Comparative 'Phylogenetic' Analyses of Diversification

Contains a number of comparative 'phylogenetic' methods, mostly focusing on analysing diversification and character evolution. Contains implementations of 'BiSSE' (Binary State 'Speciation' and Extinction) and its unresolved tree extensions, 'MuSSE' (Multiple State 'Speciation' and Extinction), 'QuaSSE', 'GeoSSE', and 'BiSSE-ness' Other included methods include Markov models of discrete and continuous trait evolution and constant rate 'speciation' and extinction.

Maintained by Richard G. FitzJohn. Last updated 6 months ago.

fftw3 gsl openblas cpp

2.3 match 33 stars 8.51 score 524 scripts 4 dependents

kurthornik

chron:Chronological Objects which Can Handle Dates and Times

Provides chronological objects which can handle dates and times.

Maintained by Kurt Hornik. Last updated 3 months ago.

2.3 match 8.51 score 2.5k scripts 115 dependents

tagteam

Publish:Format Output of Various Routines in a Suitable Way for Reports and Publication

A bunch of convenience functions that transform the results of some basic statistical analyses into table format nearly ready for publication. This includes descriptive tables, tables of logistic regression and Cox regression results as well as forest plots.

Maintained by Thomas A. Gerds. Last updated 11 days ago.

1.9 match 15 stars 10.11 score 274 scripts 36 dependents

bradleyjeck

epanetReader:Read Epanet Files into R

Reads water network simulation data in 'Epanet' text-based '.inp' and '.rpt' formats into R. Also reads results from 'Epanet-msx'. Provides basic summary information and plots. The README file has a quick introduction. See <http://www2.epa.gov/water-research/epanet> for more information on the Epanet software for modeling hydraulic and water quality behavior of water piping systems.

Maintained by Bradley Eck. Last updated 7 years ago.

epanet epanet-simulation water

3.9 match 17 stars 4.86 score 43 scripts

eagerai

fastai:Interface to 'fastai'

The 'fastai' <https://docs.fast.ai/index.html> library simplifies training fast and accurate neural networks using modern best practices. It is based on research in to deep learning best practices undertaken at 'fast.ai', including 'out of the box' support for vision, text, tabular, audio, time series, and collaborative filtering models.

Maintained by Turgut Abdullayev. Last updated 11 months ago.

audio collaborative-filtering darknet darknet-image-classification fastai medical object-detection tabular text vision

2.0 match 118 stars 9.40 score 76 scripts

vpnagraj

twoxtwo:Work with Two-by-Two Tables

A collection of functions for data analysis with two-by-two contingency tables. The package provides tools to compute measures of effect (odds ratio, risk ratio, and risk difference), calculate impact numbers and attributable fractions, and perform hypothesis testing. Statistical analysis methods are oriented towards epidemiological investigation of relationships between exposures and outcomes.

Maintained by VP Nagraj. Last updated 3 years ago.

4.0 match 2 stars 4.68 score 12 scripts

bluegreen-labs

phenocamr:Facilitates 'PhenoCam' Data Access and Time Series Post-Processing

Programmatic interface to the 'PhenoCam' web services (<https://phenocam.nau.edu/webcam>). Allows for easy downloading of 'PhenoCam' data directly to your R workspace or your computer and provides post-processing routines for consistent and easy timeseries outlier detection, smoothing and estimation of phenological transition dates. Methods for this package are described in detail in Hufkens et. al (2018) <doi:10.1111/2041-210X.12970>.

Maintained by Koen Hufkens. Last updated 1 years ago.

phenocam phenocam-data phenology-modelling remote-sensing

2.8 match 22 stars 6.69 score 75 scripts 1 dependents

pepijn-devries

csquares:Concise Spatial Query and Representation System (c-Squares)

Encode and decode c-squares, from and to simple feature (sf) or spatiotemporal arrays (stars) objects. Use c-squares codes to quickly join or query spatial data.

Maintained by Pepijn de Vries. Last updated 7 months ago.

3.2 match 2 stars 5.81 score 20 scripts

eth-mds

ricu:Intensive Care Unit Data with R

Focused on (but not exclusive to) data sets hosted on PhysioNet (<https://physionet.org>), 'ricu' provides utilities for download, setup and access of intensive care unit (ICU) data sets. In addition to functions for running arbitrary queries against available data sets, a system for defining clinical concepts and encoding their representations in tabular ICU data is presented.

Maintained by Nicolas Bennett. Last updated 10 months ago.

3.3 match 39 stars 5.65 score 77 scripts

ropensci

RNeXML:Semantically Rich I/O for the 'NeXML' Format

Provides access to phyloinformatic data in 'NeXML' format. The package should add new functionality to R such as the possibility to manipulate 'NeXML' objects in more various and refined way and compatibility with 'ape' objects.

Maintained by Carl Boettiger. Last updated 10 months ago.

metadata nexml phylogenetics linked-data

1.9 match 13 stars 9.92 score 100 scripts 19 dependents

cranhaven

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>.

Maintained by Gjalt-Jorn Peters. Last updated 8 days ago.

archived packages r-universe

5.5 match 5 stars 3.40 score

r-forge

agrmt:Calculate Concentration and Dispersion in Ordered Rating Scales

Calculates concentration and dispersion in ordered rating scales. It implements various measures of concentration and dispersion to describe what researchers variably call agreement, concentration, consensus, dispersion, or polarization among respondents in ordered data. It also implements other related measures to classify distributions. In addition to a generic city-block based concentration measure and a generic dispersion measure, the package implements various measures, including van der Eijk's (2001) <DOI: 10.1023/A:1010374114305> measure of agreement A, measures of concentration by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, Berry and Mielke, Reardon, and Garcia-Montalvo and Reynal-Querol. Furthermore, the package provides an implementation of Galtungs AJUS-system to classify distributions, as well as a function to identify the position of multiple modes.

Maintained by Didier Ruedin. Last updated 29 days ago.

5.2 match 3.58 score 38 scripts

pharmaverse

admiral:ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).

Maintained by Ben Straub. Last updated 5 days ago.

cdisc clinical-trials open-source

1.3 match 236 stars 13.89 score 486 scripts 4 dependents

murrayefford

secrdesign:Sampling Design for Spatially Explicit Capture-Recapture

Tools for designing spatially explicit capture-recapture studies of animal populations. This is primarily a simulation manager for package 'secr'. Extensions in version 2.5.0 include costing and evaluation of detector spacing.

Maintained by Murray Efford. Last updated 6 months ago.

cpp

4.3 match 4.35 score 56 scripts

bioc

annotatr:Annotation of Genomic Regions to Genomic Annotations

Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.

Maintained by Raymond G. Cavalcante. Last updated 5 months ago.

software annotation genomeannotation functionalgenomics visualization genome-annotation

1.9 match 26 stars 9.76 score 246 scripts 5 dependents

bodkan

slendr:A Simulation Framework for Spatiotemporal Population Genetics

A framework for simulating spatially explicit genomic data which leverages real cartographic information for programmatic and visual encoding of spatiotemporal population dynamics on real geographic landscapes. Population genetic models are then automatically executed by the 'SLiM' software by Haller et al. (2019) <doi:10.1093/molbev/msy228> behind the scenes, using a custom built-in simulation 'SLiM' script. Additionally, fully abstract spatial models not tied to a specific geographic location are supported, and users can also simulate data from standard, non-spatial, random-mating models. These can be simulated either with the 'SLiM' built-in back-end script, or using an efficient coalescent population genetics simulator 'msprime' by Baumdicker et al. (2022) <doi:10.1093/genetics/iyab229> with a custom-built 'Python' script bundled with the R package. Simulated genomic data is saved in a tree-sequence format and can be loaded, manipulated, and summarised using tree-sequence functionality via an R interface to the 'Python' module 'tskit' by Kelleher et al. (2019) <doi:10.1038/s41588-019-0483-y>. Complete model configuration, simulation and analysis pipelines can be therefore constructed without a need to leave the R environment, eliminating friction between disparate tools for population genetic simulations and data analysis.

Maintained by Martin Petr. Last updated 13 days ago.

popgen population-genetics simulations spatial-statistics

2.0 match 56 stars 9.15 score 88 scripts

bbolker

reformulas:Machinery for Processing Random Effect Formulas

Takes formulas including random-effects components (formatted as in 'lme4', 'glmmTMB', etc.) and processes them. Includes various helper functions.

Maintained by Ben Bolker. Last updated 5 months ago.

1.7 match 5 stars 10.92 score 24 scripts 1.5k dependents

pecanproject

PEcAn.settings:PEcAn Settings package

Contains functions to read PEcAn settings files.

Maintained by David LeBauer. Last updated 2 days ago.

bayesian cyberinfrastructure data-assimilation data-science ecosystem-model ecosystem-science forecasting meta-analysis national-science-foundation pecan plants

1.8 match 216 stars 10.00 score 54 scripts 17 dependents

djnavarro

lsr:Companion to "Learning Statistics with R"

A collection of tools intended to make introductory statistics easier to teach, including wrappers for common hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners, Version 0.6.

Maintained by Danielle Navarro. Last updated 3 years ago.

1.9 match 12 stars 9.55 score 1.7k scripts 11 dependents

stephanehess

apollo:Tools for Choice Model Estimation and Application

Choice models are a widely used technique across numerous scientific disciplines. The Apollo package is a very flexible tool for the estimation and application of choice models in R. Users are able to write their own model functions or use a mix of already available ones. Random heterogeneity, both continuous and discrete and at the level of individuals and choices, can be incorporated for all models. There is support for both standalone models and hybrid model structures. Both classical and Bayesian estimation is available, and multiple discrete continuous models are covered in addition to discrete choice. Multi-threading processing is supported for estimation and a large number of pre and post-estimation routines, including for computing posterior (individual-level) distributions are available. For examples, a manual, and a support forum, visit <http://www.ApolloChoiceModelling.com>. For more information on choice models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess, S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview of the field.

Maintained by Stephane Hess. Last updated 5 days ago.

openblas cpp openmp

3.8 match 1 stars 4.74 score 173 scripts

bioc

orthogene:Interspecies gene mapping

`orthogene` is an R package for easy mapping of orthologous genes across hundreds of species. It pulls up-to-date gene ortholog mappings across **700+ organisms**. It also provides various utility functions to aggregate/expand common objects (e.g. data.frames, gene expression matrices, lists) using **1:1**, **many:1**, **1:many** or **many:many** gene mappings, both within- and between-species.

Maintained by Brian Schilder. Last updated 5 months ago.

genetics comparativegenomics preprocessing phylogenetics transcriptomics geneexpression animal-models bioconductor bioconductor-package bioinformatics biomedicine comparative-genomics evolutionary-biology genes genomics ontologies translational-research

2.3 match 42 stars 7.85 score 31 scripts 2 dependents

hturner

gnm:Generalized Nonlinear Models

Functions to specify and fit generalized nonlinear models, including models with multiplicative interaction terms such as the UNIDIFF model from sociology and the AMMI model from crop science, and many others. Over-parameterized representations of models are used throughout; functions are provided for inference on estimable parameter combinations, as well as standard methods for diagnostics etc.

Maintained by Heather Turner. Last updated 2 years ago.

generalized-linear-models generalized-nonlinear-models statistical-models openblas

1.7 match 16 stars 10.51 score 290 scripts 21 dependents

poissonconsulting

ypr:Yield Per Recruit

An implementation of equilibrium-based yield per recruit methods. Yield per recruit methods can used to estimate the optimal yield for a fish population as described by Walters and Martell (2004) <isbn:0-691-11544-3>. The yield can be based on the number of fish caught (or harvested) or biomass caught for all fish or just large (trophy) individuals.

Maintained by Joe Thorley. Last updated 2 months ago.

yield-per-recruit

2.3 match 7 stars 7.84 score 55 scripts 1 dependents

jongheepark

MCMCpack:Markov Chain Monte Carlo (MCMC) Package

Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return 'coda' mcmc objects that can then be summarized using the 'coda' package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.

Maintained by Jong Hee Park. Last updated 7 months ago.

cpp

1.9 match 13 stars 9.40 score 2.6k scripts 150 dependents

enricoschumann

textutils:Utilities for Handling Strings and Text

Utilities for handling character vectors that store human-readable text (either plain or with markup, such as HTML or LaTeX). The package provides, in particular, functions that help with the preparation of plain-text reports, e.g. for expanding and aligning strings that form the lines of such reports. The package also provides generic functions for transforming R objects to HTML and to plain text.

Maintained by Enrico Schumann. Last updated 2 months ago.

html5 string-manipulation

2.4 match 11 stars 7.37 score 47 scripts 12 dependents

csids

cstidy:Helpful Functions for Cleaning Surveillance Data

Helpful functions for the cleaning and manipulation of surveillance data, especially with regards to the creation and validation of panel data from individual level surveillance data.

Maintained by Richard Aubrey White. Last updated 9 months ago.

csverse

3.8 match 4.65 score 1 dependents

plangfelder

WGCNA:Weighted Correlation Network Analysis

Functions necessary to perform Weighted Correlation Network Analysis on high-dimensional data as originally described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559>. Includes functions for rudimentary data cleaning, construction of correlation networks, module identification, summarization, and relating of variables and modules to sample traits. Also includes a number of utility functions for data manipulation and visualization.

Maintained by Peter Langfelder. Last updated 6 months ago.

cpp

1.8 match 54 stars 9.65 score 5.3k scripts 32 dependents

edsandorf

spdesign:Designing Stated Preference Experiments

Contemporary software commonly used to design stated preference experiments are expensive and the code is closed source. This is a free software package with an easy to use interface to make flexible stated preference experimental designs using state-of-the-art methods. For an overview of stated choice experimental design theory, see e.g., Rose, J. M. & Bliemer, M. C. J. (2014) in Hess S. & Daly. A. <doi:10.4337/9781781003152>. The package website can be accessed at <https://spdesign.edsandorf.me>. We acknowledge funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant INSPiRE (Grant agreement ID: 793163).

Maintained by Erlend Dancke Sandorf. Last updated 5 months ago.

3.8 match 4.60 score 20 scripts

ropensci

tidync:A Tidy Approach to 'NetCDF' Data Exploration and Extraction

Tidy tools for 'NetCDF' data sources. Explore the contents of a 'NetCDF' source (file or URL) presented as variables organized by grid with a database-like interface. The hyper_filter() interactive function translates the filter value or index expressions to array-slicing form. No data is read until explicitly requested, as a data frame or list of arrays via hyper_tibble() or hyper_array().

Maintained by Michael Sumner. Last updated 5 months ago.

1.8 match 93 stars 9.49 score 524 scripts 2 dependents

constantamateur

SoupX:Single Cell mRNA Soup eXterminator

Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.

Maintained by Matthew Daniel Young. Last updated 2 years ago.

1.7 match 264 stars 10.09 score 594 scripts 1 dependents

jienagu

dataMojo:Reshape Data Table

A grammar of data manipulation with 'data.table', providing a consistent a series of utility functions that help you solve the most common data manipulation challenges.

Maintained by Jiena McLellan. Last updated 2 years ago.

5.9 match 2.88 score 15 scripts

emmanuelparadis

pegas:Population and Evolutionary Genetics Analysis System

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Maintained by Emmanuel Paradis. Last updated 1 years ago.

2.3 match 7.53 score 576 scripts 18 dependents

inlabru-org

fmesher:Triangle Meshes and Related Geometry Tools

Generate planar and spherical triangle meshes, compute finite element calculations for 1- and 2-dimensional flat and curved manifolds with associated basis function spaces, methods for lines and polygons, and transparent handling of coordinate reference systems and coordinate transformation, including 'sf' and 'sp' geometries. The core 'fmesher' library code was originally part of the 'INLA' package, and implements parts of "Triangulations and Applications" by Hjelle and Daehlen (2006) <doi:10.1007/3-540-33261-8>.

Maintained by Finn Lindgren. Last updated 3 days ago.

cpp

1.5 match 16 stars 11.18 score 261 scripts 26 dependents

mclements

ascii:Export R Objects to Several Markup Languages

Coerce R object to 'asciidoc', 'txt2tags', 'restructuredText', 'org', 'textile' or 'pandoc' syntax. Package comes with a set of drivers for 'Sweave'.

Maintained by Mark Clements. Last updated 1 years ago.

3.3 match 8 stars 5.04 score 161 scripts 1 dependents

rqtl

qtl2:Quantitative Trait Locus Mapping in Experimental Crosses

Provides a set of tools to perform quantitative trait locus (QTL) analysis in experimental crosses. It is a reimplementation of the 'R/qtl' package to better handle high-dimensional data and complex cross designs. Broman et al. (2019) <doi:10.1534/genetics.118.301595>.

Maintained by Karl W Broman. Last updated 9 days ago.

cpp

1.8 match 34 stars 9.48 score 1.1k scripts 5 dependents

bhramdath

FEA:Finite Element Modeling for R

Finite element modeling of beam structures and 2D geometries using constant strain triangles. Applies material properties and boundary conditions (load and constraint) to generate a finite element model. The model produces stress, strain, and nodal displacements; a heat map is available to demonstrate regions where output variables are high or low. Also provides options for creating a triangular mesh of 2D geometries. Package developed with reference to: Bathe, K. J. (1996). Finite Element Procedures.[ISBN 978-0-9790049-5-7] -- Seshu, P. (2012). Textbook of Finite Element Analysis. [ISBN-978-81-203-2315-5] -- Mustapha, K. B. (2018). Finite Element Computations in Mechanics with R. [ISBN 9781315144474].

Maintained by Henna D. Bhramdat. Last updated 2 years ago.

16.5 match 1.00 score

bioc

clustifyr:Classifier for Single-cell RNA-seq Using Cell Clusters

Package designed to aid in classifying cells from single-cell RNA sequencing data using external reference data (e.g., bulk RNA-seq, scRNA-seq, microarray, gene lists). A variety of correlation based methods and gene list enrichment methods are provided to assist cell type assignment.

Maintained by Rui Fu. Last updated 5 months ago.

singlecell annotation sequencing microarray geneexpression assign-identities clusters marker-genes rna-seq single-cell-rna-seq

1.7 match 119 stars 9.63 score 296 scripts

kkholst

targeted:Targeted Inference

Various methods for targeted and semiparametric inference including augmented inverse probability weighted (AIPW) estimators for missing data and causal inference (Bang and Robins (2005) <doi:10.1111/j.1541-0420.2005.00377.x>), variable importance and conditional average treatment effects (CATE) (van der Laan (2006) <doi:10.2202/1557-4679.1008>), estimators for risk differences and relative risks (Richardson et al. (2017) <doi:10.1080/01621459.2016.1192546>), assumption lean inference for generalized linear model parameters (Vansteelandt et al. (2022) <doi:10.1111/rssb.12504>).

Maintained by Klaus K. Holst. Last updated 1 months ago.

causal-inference double-robust estimation semiparametric-estimation statistics openblas cpp openmp

2.3 match 11 stars 7.20 score 30 scripts 1 dependents

briencj

dae:Functions Useful in the Design and ANOVA of Experiments

The content falls into the following groupings: (i) Data, (ii) Factor manipulation functions, (iii) Design functions, (iv) ANOVA functions, (v) Matrix functions, (vi) Projector and canonical efficiency functions, and (vii) Miscellaneous functions. There is a vignette describing how to use the design functions for randomizing and assessing designs available as a vignette called 'DesignNotes'. The ANOVA functions facilitate the extraction of information when the 'Error' function has been used in the call to 'aov'. The package 'dae' can also be installed from <http://chris.brien.name/rpackages/>.

Maintained by Chris Brien. Last updated 4 months ago.

1.9 match 1 stars 8.62 score 356 scripts 7 dependents

uscbiostats

slurmR:A Lightweight Wrapper for 'Slurm'

'Slurm', Simple Linux Utility for Resource Management <https://slurm.schedmd.com/>, is a popular 'Linux' based software used to schedule jobs in 'HPC' (High Performance Computing) clusters. This R package provides a specialized lightweight wrapper of 'Slurm' with a syntax similar to that found in the 'parallel' R package. The package also includes a method for creating socket cluster objects spanning multiple nodes that can be used with the 'parallel' package.

Maintained by George Vega Yon. Last updated 1 years ago.

bioinformatics hpc slurm

2.0 match 59 stars 8.06 score 216 scripts 1 dependents

bioc

recount3:Explore and download data from the recount3 project

The recount3 package enables access to a large amount of uniformly processed RNA-seq data from human and mouse. You can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level with sample metadata and QC statistics. In addition we provide access to sample coverage BigWig files.

Maintained by Leonardo Collado-Torres. Last updated 3 months ago.

coverage differentialexpression geneexpression rnaseq sequencing software dataimport annotation-agnostic bioconductor count derfinder exon gene human illumina junction mouse recount recount3

2.0 match 33 stars 8.03 score 216 scripts

stephenturner

kgp:1000 Genomes Project Metadata

Metadata about populations and data about samples from the 1000 Genomes Project, including the 2,504 samples sequenced for the Phase 3 release and the expanded collection of 3,202 samples with 602 additional trios. The data is described in Auton et al. (2015) <doi:10.1038/nature15393> and Byrska-Bishop et al. (2022) <doi:10.1016/j.cell.2022.08.004>, and raw data is available at <http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/>. See Turner (2022) <doi:10.48550/arXiv.2210.00539> for more details.

Maintained by Stephen Turner. Last updated 2 years ago.

1000genomes bioinformatics genetics genomics metadata population-genetics sequencing

4.0 match 20 stars 4.00 score 3 scripts

bioc

DECIPHER:Tools for curating, analyzing, and manipulating biological sequences

A toolset for deciphering and managing biological sequences.

Maintained by Erik Wright. Last updated 6 days ago.

clustering genetics sequencing dataimport visualization microarray qualitycontrol qpcr alignment wholegenome microbiome immunooncology geneprediction openmp

1.9 match 8.40 score 1.1k scripts 14 dependents

akeyel

multirich:Calculate Multivariate Richness via UTC and sUTC

Functions to calculate Unique Trait Combinations (UTC) and scaled Unique Trait Combinations (sUTC) as measures of multivariate richness. The package can also calculate beta-diversity for trait richness and can partition this into nestedness-related and turnover components. The code will also calculate several measures of overlap. See Keyel and Wiegand (2016) <doi:10.1111/2041-210X.12558> for more details.

Maintained by Alexander Keyel. Last updated 4 years ago.

4.3 match 3.70 score 6 scripts

edonnachie

ICD10gm:Metadata Processing for the German Modification of the ICD-10 Coding System

Provides convenient access to the German modification of the International Classification of Diagnoses, 10th revision (ICD-10-GM). It provides functionality to aid in the identification, specification and historisation of ICD-10 codes. Its intended use is the analysis of routinely collected data in the context of epidemiology, medical research and health services research. The underlying metadata are released by the German Institute for Medical Documentation and Information <https://www.dimdi.de>, and are redistributed in accordance with their license.

Maintained by Ewan Donnachie. Last updated 1 years ago.

bfarm charlson comorbidities diagnoses dimdi icd-10 metadata routinedaten versorgungsforschung

3.0 match 10 stars 5.30 score 20 scripts

dkaschek

dMod:Dynamic Modeling and Parameter Estimation in ODE Models

The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.

Maintained by Daniel Kaschek. Last updated 10 days ago.

1.9 match 20 stars 8.35 score 251 scripts

rstudio

shinymeta:Export Domain Logic from Shiny using Meta-Programming

Provides tools for capturing logic in a Shiny app and exposing it as code that can be run outside of Shiny (e.g., from an R console). It also provides tools for bundling both the code and results to the end user.

Maintained by Carson Sievert. Last updated 11 months ago.

2.0 match 224 stars 7.80 score 62 scripts 5 dependents

atmoschem

vein:Vehicular Emissions Inventories

Elaboration of vehicular emissions inventories, consisting in four stages, pre-processing activity data, preparing emissions factors, estimating the emissions and post-processing of emissions in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>. Before using VEIN you need to know the vehicular composition of your study area, in other words, the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to start with the project to download a template to create a structure of directories and scripts.

Maintained by Sergio Ibarra-Espinosa. Last updated 1 months ago.

atmoschem atmospheric-chemistry atmospheric-science atmospheric-sciences emissions emissions-model vehicular-emissions-inventories vein fortran openmp

1.8 match 46 stars 8.65 score 137 scripts

modeloriented

fairmodels:Flexible Tool for Bias Detection, Visualization, and Mitigation

Measure fairness metrics in one place for many models. Check how big is model's bias towards different races, sex, nationalities etc. Use measures such as Statistical Parity, Equal odds to detect the discrimination against unprivileged groups. Visualize the bias using heatmap, radar plot, biplot, bar chart (and more!). There are various pre-processing and post-processing bias mitigation algorithms implemented. Package also supports calculating fairness metrics for regression models. Find more details in (Wiśniewski, Biecek (2021)) <arXiv:2104.00507>.

Maintained by Jakub Wiśniewski. Last updated 2 months ago.

explain-classifiers explainable-ml fairness fairness-comparison fairness-ml model-evaluation

2.0 match 86 stars 7.72 score 51 scripts 1 dependents

blue-matter

MSEtool:Management Strategy Evaluation Toolkit

Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).

Maintained by Adrian Hordyk. Last updated 26 days ago.

cpp

2.0 match 8 stars 7.69 score 163 scripts 3 dependents

jasonjfoster

rolltalk:Rolling and Expanding Statistics

Presentation for rolling and expanding statistics of time-series data.

Maintained by Jason Foster. Last updated 9 months ago.

algorithms presentation quarto statistics

5.9 match 2 stars 2.60 score 1 scripts

martin3141

spant:MR Spectroscopy Analysis Tools

Tools for reading, visualising and processing Magnetic Resonance Spectroscopy data. The package includes methods for spectral fitting: Wilson (2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018) <DOI:10.1002/mrm.27605>.

Maintained by Martin Wilson. Last updated 1 months ago.

brain mri mrs mrshub spectroscopy fortran

1.8 match 25 stars 8.52 score 81 scripts

philchalmers

SimDesign:Structure for Organizing Monte Carlo Simulation Designs

Provides tools to safely and efficiently organize and execute Monte Carlo simulation experiments in R. The package controls the structure and back-end of Monte Carlo simulation experiments by utilizing a generate-analyse-summarise workflow. The workflow safeguards against common simulation coding issues, such as automatically re-simulating non-convergent results, prevents inadvertently overwriting simulation files, catches error and warning messages during execution, implicitly supports parallel processing with high-quality random number generation, and provides tools for managing high-performance computing (HPC) array jobs submitted to schedulers such as SLURM. For a pedagogical introduction to the package see Sigal and Chalmers (2016) <doi:10.1080/10691898.2016.1246953>. For a more in-depth overview of the package and its design philosophy see Chalmers and Adkins (2020) <doi:10.20982/tqmp.16.4.p248>.

Maintained by Phil Chalmers. Last updated 3 hours ago.

monte-carlo-simulation simulation simulation-framework

1.1 match 62 stars 13.38 score 253 scripts 46 dependents

cran

sna:Tools for Social Network Analysis

A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.

Maintained by Carter T. Butts. Last updated 6 months ago.

2.3 match 8 stars 6.78 score 94 dependents

marinapapa

swaRmverse:Swarm Space Creation

Provides a pipeline for the comparative analysis of collective movement data (e.g. fish schools, bird flocks, baboon troops) by processing 2-dimensional positional data (x,y,t) from GPS trackers or computer vision tracking systems, discretizing events of collective motion, calculating a set of established metrics that characterize each event, and placing the events in a multi-dimensional swarm space constructed from these metrics. The swarm space concept, the metrics and data sets included are described in: Papadopoulou Marina, Furtbauer Ines, O'Bryan Lisa R., Garnier Simon, Georgopoulou Dimitra G., Bracken Anna M., Christensen Charlotte and King Andrew J. (2023) <doi:10.1098/rstb.2022.0068>.

Maintained by Marina Papadopoulou. Last updated 5 months ago.

3.0 match 2 stars 5.13 score 15 scripts

bioc

BiocCheck:Bioconductor-specific package checks

BiocCheck guides maintainers through Bioconductor best practicies. It runs Bioconductor-specific package checks by searching through package code, examples, and vignettes. Maintainers are required to address all errors, warnings, and most notes produced.

Maintained by Marcel Ramos. Last updated 24 days ago.

infrastructure bioconductor-package core-services

1.5 match 8 stars 10.07 score 114 scripts 6 dependents

nepem-ufsc

pliman:Tools for Plant Image Analysis

Tools for both single and batch image manipulation and analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>). The tools can be used for the quantification of leaf area, object counting, extraction of image indexes, shape measurement, object landmark identification, and Elliptical Fourier Analysis of object outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package also provides a comprehensive pipeline for generating shapefiles with complex layouts and supports high-throughput phenotyping of RGB, multispectral, and hyperspectral orthomosaics. This functionality facilitates field phenotyping using UAV- or satellite-based imagery.

Maintained by Tiago Olivoto. Last updated 3 hours ago.

openblas fftw3 cpp openmp

2.3 match 10 stars 6.70 score 476 scripts

peekxc

simplextree:Provides Tools for Working with General Simplicial Complexes

Provides an interface to a Simplex Tree data structure, which is a data structure aimed at enabling efficient manipulation of simplicial complexes of any dimension. The Simplex Tree data structure was originally introduced by Jean-Daniel Boissonnat and Clément Maria (2014) <doi:10.1007/s00453-014-9887-3>.

Maintained by Matt Piekenbrock. Last updated 1 years ago.

rcpp simplicial-complex topological-data-analysis topology cpp

3.3 match 15 stars 4.56 score 16 scripts 1 dependents

cran

hypergate:Machine Learning of Hyperrectangular Gating Strategies for High-Dimensional Cytometry

Given a high-dimensional dataset that typically represents a cytometry dataset, and a subset of the datapoints, this algorithm outputs an hyperrectangle so that datapoints within the hyperrectangle best correspond to the specified subset. In essence, this allows the conversion of clustering algorithms' outputs to gating strategies outputs.

Maintained by Etienne Becht. Last updated 1 years ago.

5.6 match 2.70 score

exaexa

scattermore:Scatterplots with More Points

C-based conversion of large scatterplot data to rasters plus other operations such as data blurring or data alpha blending. Speeds up plotting of data with millions of points.

Maintained by Mirek Kratochvil. Last updated 1 years ago.

performance plot scatterplot visualization cpp

1.3 match 244 stars 11.95 score 596 scripts 85 dependents

declaredesign

fabricatr:Imagine Your Data Before You Collect It

Helps you imagine your data before you collect it. Hierarchical data structures and correlated data can be easily simulated, either from random number generators or by resampling from existing data sources. This package is faster with 'data.table' and 'mvnfast' installed.

Maintained by Graeme Blair. Last updated 1 months ago.

1.8 match 93 stars 8.29 score 234 scripts 5 dependents

psychbruce

bruceR:Broadly Useful Convenient and Efficient R Functions

Broadly useful convenient and efficient R functions that bring users concise and elegant R data analyses. This package includes easy-to-use functions for (1) basic R programming (e.g., set working directory to the path of currently opened file; import/export data from/to files in any format; print tables to Microsoft Word); (2) multivariate computation (e.g., compute scale sums/means/... with reverse scoring); (3) reliability analyses and factor analyses; (4) descriptive statistics and correlation analyses; (5) t-test, multi-factor analysis of variance (ANOVA), simple-effect analysis, and post-hoc multiple comparison; (6) tidy report of statistical models (to R Console and Microsoft Word); (7) mediation and moderation analyses (PROCESS); and (8) additional toolbox for statistics and graphics.

Maintained by Han-Wu-Shuang Bao. Last updated 9 months ago.

anova data-analysis data-science linear-models linear-regression multilevel-models statistics toolbox

1.9 match 176 stars 7.87 score 316 scripts 3 dependents

ai4ci

ggoutbreak:Estimate Incidence, Proportions and Exponential Growth Rates

Simple statistical models and visualisations for calculating the incidence, proportion, exponential growth rate, and reproduction number of infectious disease case time series. This toolkit was largely developed during the COVID-19 pandemic.

Maintained by Robert Challen. Last updated 1 months ago.

3.4 match 1 stars 4.30 score

markbravington

mvbutils:General utilities, workspace organization, code and docu editing, live package maintenance, etc

Hierarchical workspace tree, code editing and backup, easy package prep, editing of packages while loaded, per-object lazy-loading, easy documentation, macro functions, and miscellaneous utilities. Needed by debug package.

Maintained by Mark V. Bravington. Last updated 6 days ago.

2.3 match 6.53 score 138 scripts 18 dependents

marberts

piar:Price Index Aggregation

Most price indexes are made with a two-step procedure, where period-over-period elemental indexes are first calculated for a collection of elemental aggregates at each point in time, and then aggregated according to a price index aggregation structure. These indexes can then be chained together to form a time series that gives the evolution of prices with respect to a fixed base period. This package contains a collection of functions that revolve around this work flow, making it easy to build standard price indexes, and implement the methods described by Balk (2008, <doi:10.1017/CBO9780511720758>), von der Lippe (2007, <doi:10.3726/978-3-653-01120-3>), and the CPI manual (2020, <doi:10.5089/9781484354841.069>) for bilateral price indexes.

Maintained by Steve Martin. Last updated 15 days ago.

economics inflation official-statistics statistics

2.0 match 4 stars 7.32 score 25 scripts

arg0naut91

neatRanges:Tidy Up Date/Time Ranges

Collapse, partition, combine, fill gaps in and expand date/time ranges.

Maintained by Aljaz Jelenko. Last updated 3 years ago.

collapse date-range intervals partitioning timestamp-ranges cpp

4.6 match 3 stars 3.18 score 2 scripts

nmautoverse

NMdata:Preparation, Checking and Post-Processing Data for PK/PD Modeling

Efficient tools for preparation, checking and post-processing of data in PK/PD (pharmacokinetics/pharmacodynamics) modeling, with focus on use of Nonmem. Attention is paid to ensure consistency, traceability, and Nonmem compatibility of Data. Rigorously checks final Nonmem datasets. Implemented in 'data.table', but easily integrated with 'base' and 'tidyverse'.

Maintained by Philip Delff. Last updated 3 days ago.

nonmem pharmacometrics

1.9 match 17 stars 7.69 score 88 scripts 2 dependents

bioc

CompoundDb:Creating and Using (Chemical) Compound Annotation Databases

CompoundDb provides functionality to create and use (chemical) compound annotation databases from a variety of different sources such as LipidMaps, HMDB, ChEBI or MassBank. The database format allows to store in addition MS/MS spectra along with compound information. The package provides also a backend for Bioconductor's Spectra package and allows thus to match experimetal MS/MS spectra against MS/MS spectra in the database. Databases can be stored in SQLite format and are thus portable.

Maintained by Johannes Rainer. Last updated 2 months ago.

massspectrometry metabolomics annotation databases mass-spectrometry

1.7 match 17 stars 8.40 score 69 scripts 1 dependents

josie-athens

pubh:A Toolbox for Public Health and Epidemiology

A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand 'ggplot2' plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.

Maintained by Josie Athens. Last updated 5 months ago.

2.5 match 5 stars 5.73 score 72 scripts

epiverse-trace

cfr:Estimate Disease Severity and Case Ascertainment

Estimate the severity of a disease and ascertainment of cases, as discussed in Nishiura et al. (2009) <doi:10.1371/journal.pone.0006852>.

Maintained by Adam Kucharski. Last updated 17 days ago.

case-fatality-rate epidemic-modelling epidemiology epiverse health-outcomes outbreak-analysis sdg-3

1.8 match 13 stars 8.15 score 35 scripts

gastonmaurodiaz

rcaiman:CAnopy IMage ANalysis

Tools for pre-processing and processing canopy photographs with support for raw data reading. Works with images taken with both regular and fisheye lenses (all types). Includes algorithms specifically designed to mitigate errors caused by direct sunlight.

Maintained by Gastón Mauro Díaz. Last updated 10 days ago.

4.0 match 1 stars 3.54 score 2 scripts

openanalytics

patientProfilesVis:Visualization of Patient Profiles

Creation of patient profile visualizations for exploration, diagnostic or monitoring purposes during a clinical trial. These static visualizations display a patient-specific overview of the evolution during the trial time frame of parameters of interest (as laboratory, ECG, vital signs), presence of adverse events, exposure to a treatment; associated with metadata patient information, as demography, concomitant medication. The visualizations can be tailored for specific domain(s) or endpoint(s) of interest. Visualizations are exported into patient profile report(s) or can be embedded in custom report(s).

Maintained by Laure Cougnaud. Last updated 9 months ago.

2.8 match 7 stars 5.15 score 9 scripts

mrc-ide

monty:Monte Carlo Models

Experimental sources for the next generation of mcstate, now called 'monty', which will support much of the old mcstate functionality but new things like better parameter interfaces, Hamiltonian Monte Carlo, and other features.

Maintained by Rich FitzJohn. Last updated 1 months ago.

cpp

1.9 match 3 stars 7.52 score 29 scripts 3 dependents

ddalthorp

GenEst:Generalized Mortality Estimator

Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.

Maintained by Daniel Dalthorp. Last updated 2 years ago.

cpp

1.8 match 7 stars 7.81 score 55 scripts 2 dependents

ekstroem

MESS:Miscellaneous Esoteric Statistical Scripts

A mixed collection of useful and semi-useful diverse statistical functions, some of which may even be referenced in The R Primer book. See Ekstrøm, C. T. (2016). The R Primer. 2nd edition. Chapman & Hall.

Maintained by Claus Thorn Ekstrøm. Last updated 30 days ago.

biostatistics power-analysis statistical-analysis statistical-methods statistical-models openblas cpp

1.8 match 4 stars 7.76 score 328 scripts 13 dependents

cran

meboot:Maximum Entropy Bootstrap for Time Series

Maximum entropy density based dependent data bootstrap. An algorithm is provided to create a population of time series (ensemble) without assuming stationarity. The reference paper (Vinod, H.D., 2004 <DOI: 10.1016/j.jempfin.2003.06.002>) explains how the algorithm satisfies the ergodic theorem and the central limit theorem.

Maintained by Fred Viole. Last updated 2 years ago.

4.1 match 2 stars 3.38 score 2 dependents

christophergandrud

DataCombine:Tools for Easily Combining and Cleaning Data Sets

Tools for combining and cleaning data sets, particularly with grouped and time series data. This includes functions for merging data while reporting duplicates, filling in columns with values of a column in another data frame, and creating continuous time data for interupted time series.

Maintained by Christopher Gandrud. Last updated 5 years ago.

1.6 match 55 stars 8.50 score 864 scripts 3 dependents