Showing 92 of total 92 results (show query)
andrewzm
IDE:Integro-Difference Equation Spatio-Temporal Models
The Integro-Difference Equation model is a linear, dynamical model used to model phenomena that evolve in space and in time; see, for example, Cressie and Wikle (2011, ISBN:978-0-471-69274-4) or Dewar et al. (2009) <doi:10.1109/TSP.2008.2005091>. At the heart of the model is the kernel, which dictates how the process evolves from one time point to the next. Both process and parameter reduction are used to facilitate computation, and spatially-varying kernels are allowed. Data used to estimate the parameters are assumed to be readings of the process corrupted by Gaussian measurement error. Parameters are fitted by maximum likelihood, and estimation is carried out using an evolution algorithm.
Maintained by Andrew Zammit-Mangion. Last updated 3 years ago.
66.2 match 1 stars 3.70 score 9 scripts
sparklyr
sparklyr:R Interface to Apache Spark
R interface to Apache Spark, a fast and general engine for big data processing, see <https://spark.apache.org/>. This package supports connecting to local and remote Apache Spark clusters, provides a 'dplyr' compatible back-end, and provides an interface to Spark's built-in machine learning algorithms.
Maintained by Edgar Ruiz. Last updated 8 days ago.
apache-sparkdistributeddplyridelivymachine-learningremote-clusterssparksparklyr
12.8 match 959 stars 15.16 score 4.0k scripts 21 dependents
mrc-ide
EpiEstim:Estimate Time Varying Reproduction Numbers from Epidemic Curves
Tools to quantify transmissibility throughout an epidemic from the analysis of time series of incidence as described in Cori et al. (2013) <doi:10.1093/aje/kwt133> and Wallinga and Teunis (2004) <doi:10.1093/aje/kwh255>.
Maintained by Anne Cori. Last updated 7 months ago.
15.0 match 95 stars 12.00 score 1.0k scripts 7 dependentsmrc-ide
odin:ODE Generation and Integration
Generate systems of ordinary differential equations (ODE) and integrate them, using a domain specific language (DSL). The DSL uses R's syntax, but compiles to C in order to efficiently solve the system. A solver is not provided, but instead interfaces to the packages 'deSolve' and 'dde' are generated. With these, while solving the differential equations, no allocations are done and the calculations remain entirely in compiled code. Alternatively, a model can be transpiled to R for use in contexts where a C compiler is not present. After compilation, models can be inspected to return information about parameters and outputs, or intermediate values after calculations. 'odin' is not targeted at any particular domain and is suitable for any system that can be expressed primarily as mathematical expressions. Additional support is provided for working with delays (delay differential equations, DDE), using interpolated functions during interpolation, and for integrating quantities that represent arrays.
Maintained by Rich FitzJohn. Last updated 9 months ago.
15.0 match 106 stars 9.74 score 290 scripts 3 dependentsmrc-ide
orderly2:Orderly Next Generation
Distributed reproducible computing framework, adopting ideas from git, docker and other software. By defining a lightweight interface around the inputs and outputs of an analysis, a lot of the repetitive work for reproducible research can be automated. We define a simple format for organising and describing work that facilitates collaborative reproducible research and acknowledges that all analyses are run multiple times over their lifespans.
Maintained by Rich FitzJohn. Last updated 2 months ago.
15.0 match 8 stars 8.30 score 49 scripts 2 dependentsmrc-ide
malariasimulation:An individual based model for malaria
Specifies the latest and greatest malaria model.
Maintained by Giovanni Charles. Last updated 26 days ago.
15.0 match 16 stars 8.17 score 146 scriptsmrc-ide
dust:Iterate Multiple Realisations of Stochastic Models
An Engine for simulation of stochastic models. Includes support for running stochastic models in parallel, either with shared or varying parameters. Simulations are run efficiently in compiled code and can be run with a fraction of simulated states returned to R, allowing control over memory usage. Support is provided for building bootstrap particle filter for performing Sequential Monte Carlo (e.g., Gordon et al. 1993 <doi:10.1049/ip-f-2.1993.0015>). The core of the simulation engine is the 'xoshiro256**' algorithm (Blackman and Vigna <arXiv:1805.01407>), and the package is further described in FitzJohn et al 2021 <doi:10.12688/wellcomeopenres.16466.2>.
Maintained by Rich FitzJohn. Last updated 5 months ago.
15.0 match 18 stars 7.84 score 60 scripts 3 dependentsmrc-ide
naomi:Naomi Model for Subnational HIV Estimates
This package implements the Naomi model for subnational HIV estimates.
Maintained by Jeff Eaton. Last updated 5 days ago.
15.0 match 9 stars 7.74 score 54 scripts 2 dependentsmrc-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.
15.0 match 3 stars 7.52 score 29 scripts 3 dependentsmrc-ide
rrq:Simple Redis Queue
Simple Redis queue in R.
Maintained by Rich FitzJohn. Last updated 4 months ago.
15.0 match 24 stars 7.40 score 14 scripts 3 dependentsmrc-ide
mcstate:Monte Carlo Methods for State Space Models
Implements Monte Carlo methods for state-space models such as 'SIR' models in epidemiology. Particle MCMC (pmcmc) and SMC2 methods are planned. This package is particularly designed to work with odin/dust models, but we will see how general it becomes.
Maintained by Rich FitzJohn. Last updated 9 months ago.
15.0 match 19 stars 7.08 score 87 scriptsmrc-ide
epireview:Tools to update and summarise the latest pathogen data from the Pathogen Epidemiology Review Group (PERG)
Contains the latest open access pathogen data from the Pathogen Epidemiology Review Group (PERG). Tools are available to update pathogen databases with new peer-reviewed data as it becomes available, and to summarise the latest data using tables and figures.
Maintained by Sangeeta Bhatia. Last updated 22 hours ago.
15.0 match 30 stars 6.76 score 6 scriptsmrc-ide
dust2:Next Generation dust
Experimental sources for the next generation of dust, which will properly adopt the particle filter, have support for partial parameter updates, support for multiple parameter sets and hopefully better GPU/MPI support.
Maintained by Rich FitzJohn. Last updated 8 days ago.
15.0 match 6.66 score 32 scripts 2 dependentsmrc-ide
context:Contexts for evaluating R expressions
Contexts for evaluating R expressions.
Maintained by Rich FitzJohn. Last updated 2 years ago.
15.0 match 5 stars 6.59 score 1.7k scripts 1 dependentsmrc-ide
hipercow:High Performance Computing
Set up cluster environments and jobs. Moo.
Maintained by Rich FitzJohn. Last updated 10 days ago.
15.0 match 1 stars 6.53 score 45 scripts 1 dependentsmrc-ide
odin2:Next generation odin
Temporary package for rewriting odin.
Maintained by Rich FitzJohn. Last updated 2 months ago.
15.0 match 5 stars 6.32 score 22 scriptsmrc-ide
drjacoby:Flexible Markov Chain Monte Carlo via Reparameterization
drjacoby is an R package for performing Bayesian inference via Markov chain monte carlo (MCMC). In addition to being highly flexible it implements some advanced techniques that can improve mixing in tricky situations.
Maintained by Bob Verity. Last updated 9 months ago.
15.0 match 12 stars 6.27 score 77 scriptsmrc-ide
dde:Solve Delay Differential Equations
Solves ordinary and delay differential equations, where the objective function is written in either R or C. Suitable only for non-stiff equations, the solver uses a 'Dormand-Prince' method that allows interpolation of the solution at any point. This approach is as described by Hairer, Norsett and Wanner (1993) <ISBN:3540604529>. Support is also included for iterating difference equations.
Maintained by Rich FitzJohn. Last updated 6 months ago.
15.0 match 15 stars 6.20 score 35 scripts 1 dependentsmrc-ide
hintr:R API for calling naomi district level HIV model
R API for calling naomi district level HIV model.
Maintained by Robert Ashton. Last updated 4 days ago.
15.0 match 2 stars 5.80 score 2 scripts 1 dependentsmrc-ide
odin.dust:Compile Odin to Dust
Less painful than it sounds, this package compiles an odin model to use dust, our new stochastic model system. Supports only a subset of odin models (discrete time stochastic models with no interpolation and no delays).
Maintained by Rich FitzJohn. Last updated 5 months ago.
15.0 match 3 stars 5.71 score 122 scriptsmrc-ide
cinterpolate:Interpolation From C
Simple interpolation methods designed to be used from C code. Supports constant, linear and spline interpolation. An R wrapper is included but this package is primarily designed to be used from C code using 'LinkingTo'. The spline calculations are classical cubic interpolation, e.g., Forsythe, Malcolm and Moler (1977) <ISBN: 9780131653320>.
Maintained by Rich FitzJohn. Last updated 6 months ago.
15.0 match 9 stars 5.66 score 1 scripts 3 dependentsmrc-ide
eppasm:Age-structured EPP Model for HIV Epidemic Estimates
What the package does (one paragraph).
Maintained by Jeff Eaton. Last updated 3 months ago.
15.0 match 6 stars 5.04 score 34 scripts 3 dependentsmrc-ide
first90:The first90 model
Implements the Shiny90 model for estimating progress towards the UNAIDS "first 90" target for HIV awareness of status in sub-Saharan Africa.
Maintained by Jeffrey Eaton. Last updated 4 months ago.
15.0 match 5 stars 4.53 score 2 scripts 3 dependents
rstudio
rstudioapi:Safely Access the RStudio API
Access the RStudio API (if available) and provide informative error messages when it's not.
Maintained by Kevin Ushey. Last updated 4 months ago.
3.5 match 172 stars 18.81 score 3.6k scripts 2.1k dependentsmrc-ide
popim:POPulation IMmunity: Run a Demographic Model of Vaccine Exposure Over Time
Tools for setting up an age-structured population, applying vaccination activities to it, and tracking vaccine-induced immunity through time.
Maintained by Tini Garske. Last updated 2 months ago.
15.0 match 1 stars 4.15 score 4 scriptsmrc-ide
beers:Calculate Beers Ordinary Interpolation
Calculate Beers Interpolation (both Ordinary and Modified method); a six-term formula which minimizes the fifth differences of the interpolated results. See p877 of The Methods and Materials of Demography, Volume 2, referring to Beers, The Record of the American Institute of Actuaries, 34, Part I (69):59-60, June 1945.
Maintained by Wes Hinsley. Last updated 4 years ago.
demographyinterpolationsubdivision
15.0 match 2 stars 3.95 score 5 scripts 3 dependentsmrc-ide
didehpc:DIDE HPC Support
Previous DIDE HPC support. Don't use this, use hipercow instead.
Maintained by Rich FitzJohn. Last updated 4 months ago.
15.0 match 10 stars 3.94 score 58 scriptsmrc-ide
specio:Read Spectrum Files
Read data from Spectrum PJNZ file into R consumable format for EPP.
Maintained by Robert Ashton. Last updated 4 years ago.
15.0 match 1 stars 3.78 score 1 scripts 2 dependents
richdeto
geouy:Geographic Information of Uruguay
The toolbox have functions to load and process geographic information for Uruguay. And extra-function to get address coordinates and orthophotos through the uruguayan 'IDE' API <https://www.gub.uy/infraestructura-datos-espaciales/tramites-y-servicios/servicios/sistema-unico-direcciones-geograficas>.
Maintained by Richard Detomasi. Last updated 11 months ago.
9.5 match 14 stars 5.83 score 32 scripts 1 dependentsmrc-ide
naomi.options:Contains model and calibration options and helper functions for Naomi
Contains model and calibration option JSON and default values and helper functions for Naomi.
Maintained by Robert Ashton. Last updated 4 months ago.
15.0 match 3.43 score 1 scripts 3 dependentsmrc-ide
hipercow.windows:DIDE HPC Support for Windows
Driver for using the DIDE windows cluster, via the hipercow package. Typically the user will install that package directly and this once they are requested to.
Maintained by Rich FitzJohn. Last updated 10 days ago.
15.0 match 1 stars 3.32 score 2 scripts
ropensci
rix:Reproducible Data Science Environments with 'Nix'
Simplifies the creation of reproducible data science environments using the 'Nix' package manager, as described in Dolstra (2006) <ISBN 90-393-4130-3>. The included `rix()` function generates a complete description of the environment as a `default.nix` file, which can then be built using 'Nix'. This results in project specific software environments with pinned versions of R, packages, linked system dependencies, and other tools. Additional helpers make it easy to run R code in 'Nix' software environments for testing and production.
Maintained by Bruno Rodrigues. Last updated 3 days ago.
nixpeer-reviewedreproducibilityreproducible-research
4.5 match 235 stars 10.54 score 67 scriptsmrc-ide
provisionr:Provision a Library
Provision a set of packages into a new library, possibly for use on a different architecture.
Maintained by Rich FitzJohn. Last updated 5 years ago.
15.0 match 27 stars 3.13 score 1 scriptsmrc-ide
orderly.db:Database Support for 'orderly2'
Access databases from 'orderly2' while running reports. Includes the basic 'SQL' support originally included in 'orderly' for establishing connections and setting up data for use within a report.
Maintained by Rich FitzJohn. Last updated 1 years ago.
15.0 match 3.00 score 1 scriptsmrc-ide
demogsurv:Demographic analysis of DHS and other household surveys
This package includes tools for calculating demographic indicators from household survey data. Initially developed for for processing and analysis from Demographic and Health Surveys (DHS) and Multiple Indicator Cluster Surveys (MICS). The package provides tools to calculate standard child mortality, adult mortality, and fertility indicators stratified arbitrarily by age group, calendar period, pre-survey time periods, birth cohorts and other survey variables (e.g. residence, region, wealth status, education, etc.). Design-based standard errors and sample correlations are available for all indicators via Taylor linearisation or jackknife.
Maintained by Jeff Eaton. Last updated 3 years ago.
15.0 match 6 stars 2.92 score 28 scriptsmrc-ide
odin.js:'odin' 'JavaScript' support
Create 'JavaScript' differential equation models from an 'odin' model specification.
Maintained by Rich FitzJohn. Last updated 2 years ago.
15.0 match 5 stars 2.88 score 3 scriptsmrc-ide
queuer:Queue Tasks
Queue tasks to number of backends.
Maintained by Rich FitzJohn. Last updated 2 years ago.
15.0 match 4 stars 2.78 score 4 scriptsmrc-ide
syncr:Synchronise Directories
Syncronise directories using rsync.
Maintained by Rich FitzJohn. Last updated 7 years ago.
15.0 match 9 stars 2.65 score 2 scriptsmrc-ide
testthat.buildkite:A testthat reporter for buildkite
A testthat reporter that prints progress output in a format for use in buildkite logs.
Maintained by Robert Ashton. Last updated 2 years ago.
15.0 match 2.54 score 1 scriptsmrc-ide
conan2:Conan the Librarian
Create libraries. For us, there is no spring. Just the wind that smells fresh before the storm.
Maintained by Rich FitzJohn. Last updated 16 days ago.
15.0 match 2.48 score 1 scripts 1 dependentsmrc-ide
threemc:(Matt's) Multi-Level Model of Male Circumcision in Sub-Saharan Africa
Functions and datasets to support, and extend to other Sub-Saharan African countries, Thomas, M. et. al., 2021, A multi-level model for estimating region-age-time-type specific male circumcision coverage from household survey and health system data in South Africa, <arXiv:2108.091422>.
Maintained by Patrick OToole. Last updated 1 years ago.
15.0 match 2.38 score 16 scriptsmrc-ide
assessr:Performance metrics for probabilitic forecasts
This package implements various metrics for assessing the performance of probabilitic forecasts.
Maintained by Sangeeta Bhatia. Last updated 5 years ago.
15.0 match 2.35 score 15 scripts 1 dependents
r-lib
devtools:Tools to Make Developing R Packages Easier
Collection of package development tools.
Maintained by Jennifer Bryan. Last updated 6 months ago.
1.8 match 2.4k stars 19.51 score 51k scripts 148 dependentsmrc-ide
moz.utils:Utility functions
Utility functions, for useful utilitarian uses.
Maintained by Oli Stevens. Last updated 2 months ago.
15.0 match 2.26 score 18 scriptsmrc-ide
naomi.resources:Data dependencies for Naomi output generation
Makes data for Naomi output generation as an R package.
Maintained by Rachel Esra. Last updated 1 years ago.
15.0 match 2.18 score 1 scriptsmrc-ide
mode:Solve Multiple ODEs
Solve multiple ODEs in parallel.
Maintained by Rich FitzJohn. Last updated 2 years ago.
15.0 match 2.10 score 25 scriptsmrc-ide
jointlyr:Joint estimation of initial incidence and reproduction number
Provides a Stan implementation of a method to jointly estimate incidence and reproduction number.
Maintained by Sangeeta Bhatia. Last updated 3 years ago.
15.0 match 2.00 score 1 scriptsmrc-ide
orderly.sharedfile:Package Title Here
Access files in shared locations from orderly.
Maintained by Rich FitzJohn. Last updated 5 months ago.
15.0 match 1 stars 2.00 score 2 scriptsmrc-ide
heartbeatr:Heartbeat Support using 'Redis'
Simple heartbeat support for R using 'Redis'. A heartbeat is a background thread that acts as a dead-man's switch. It will create a key on Redis that will automatically expire after a number of seconds and then periodically refresh that key, even when the R process is busy. If the process dies for some reason, then the key will disappear. A heartbeat can be used to detect loss of worker processes on shared systems.
Maintained by Rich FitzJohn. Last updated 4 years ago.
15.0 match 2 stars 2.00 score 4 scripts
yihui
formatR:Format R Code Automatically
Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package (see tidy_app()).
Maintained by Yihui Xie. Last updated 1 years ago.
1.8 match 259 stars 15.07 score 1.4k scripts 1.2k dependents
pik-piam
mrcommons:MadRat commons Input Data Library
Provides useful functions and a common structure to all the input data required to run models like MAgPIE and REMIND of model input data.
Maintained by Jan Philipp Dietrich. Last updated 2 days ago.
3.9 match 1 stars 6.67 score 16 scripts 15 dependentsmrc-ide
weighter:Model averaging
This package implementes model averaging.
Maintained by Sangeeta Bhatia. Last updated 5 years ago.
15.0 match 1 stars 1.70 score 1 scriptsmrc-ide
cart:Malaria Cartographic Information
Extract population, prevalence and vector cartographic information for use with malarisimulation.
Maintained by Pete Winskill. Last updated 3 years ago.
15.0 match 1 stars 1.70 score 8 scriptsrstudio
renv:Project Environments
A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.
Maintained by Kevin Ushey. Last updated 2 days ago.
1.3 match 1.0k stars 18.55 score 1.5k scripts 113 dependentsmrc-ide
naomi.utils:Utility Functions For Naomi Datasets
This package contains utility functions for creating and manipulating datasets for the Naomi model and related projects.
Maintained by Jeffrey Eaton. Last updated 12 months ago.
15.0 match 1 stars 1.64 score 11 scripts
brodieg
diffobj:Diffs for R Objects
Generate a colorized diff of two R objects for an intuitive visualization of their differences.
Maintained by Brodie Gaslam. Last updated 3 years ago.
1.8 match 232 stars 13.12 score 107 scripts 486 dependents
bioc
sevenbridges:Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.
Maintained by Phil Webster. Last updated 5 months ago.
softwaredataimportthirdpartyclientapi-clientbioconductorbioinformaticscloudcommon-workflow-languagesevenbridges
2.9 match 35 stars 7.40 score 24 scripts
nx10
httpgd:A 'HTTP' Server Graphics Device
A graphics device for R that is accessible via network protocols. This package was created to make it easier to embed live R graphics in integrated development environments and other applications. The included 'HTML/JavaScript' client (plot viewer) aims to provide a better overall user experience when dealing with R graphics. The device asynchronously serves graphics via 'HTTP' and 'WebSockets'.
Maintained by Florian Rupprecht. Last updated 7 hours ago.
1.9 match 428 stars 11.01 score 280 scripts 1 dependents
michelnivard
gptstudio:Use Large Language Models Directly in your Development Environment
Large language models are readily accessible via API. This package lowers the barrier to use the API inside of your development environment. For more on the API, see <https://platform.openai.com/docs/introduction>.
Maintained by James Wade. Last updated 5 days ago.
chatgptgpt-3rstudiorstudio-addin
1.9 match 924 stars 10.83 score 43 scripts 1 dependentsmrc-ide
ascertainr:Case Ascertainment Model
This pacakge implements a case asecertainment model.
Maintained by Sangeeta Bhatia. Last updated 5 years ago.
15.0 match 2 stars 1.30 score 1 scriptsrstudio
tfruns:Training Run Tools for 'TensorFlow'
Create and manage unique directories for each 'TensorFlow' training run. Provides a unique, time stamped directory for each run along with functions to retrieve the directory of the latest run or latest several runs.
Maintained by Tomasz Kalinowski. Last updated 11 months ago.
1.5 match 34 stars 11.80 score 325 scripts 77 dependents
cran
varitas:Variant Calling in Targeted Analysis Sequencing Data
Multi-caller variant analysis pipeline for targeted analysis sequencing (TAS) data. Features a modular, automated workflow that can start with raw reads and produces a user-friendly PDF summary and a spreadsheet containing consensus variant information.
Maintained by Adam Mills. Last updated 4 years ago.
7.7 match 2.30 scoremrc-ide
dfertility:District level estimation of age-specific fertility
This package estimates district-level estimates of age-specific fertility from nationally representative household survey data.
Maintained by Oli Stevens. Last updated 1 years ago.
15.0 match 1 stars 1.18 score 15 scripts
rexyai
RestRserve:A Framework for Building HTTP API
Allows to easily create high-performance full featured HTTP APIs from R functions. Provides high-level classes such as 'Request', 'Response', 'Application', 'Middleware' in order to streamline server side application development. Out of the box allows to serve requests using 'Rserve' package, but flexible enough to integrate with other HTTP servers such as 'httpuv'.
Maintained by Dmitry Selivanov. Last updated 2 days ago.
http-serveropenapirest-apiswagger-uicpp
1.8 match 283 stars 9.56 score 95 scripts 1 dependents
klmr
box:Write Reusable, Composable and Modular R Code
A modern module system for R. Organise code into hierarchical, composable, reusable modules, and use it effortlessly across projects via a flexible, declarative dependency loading syntax.
Maintained by Konrad Rudolph. Last updated 11 days ago.
1.3 match 888 stars 12.39 score 47 scripts 4 dependents
t-kalinowski
keras: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 11 months ago.
1.5 match 10.82 score 10k scripts 54 dependents
insightsengineering
teal.code:Code Storage and Execution Class for 'teal' Applications
Introduction of 'qenv' S4 class, that facilitates code execution and reproducibility in 'teal' applications.
Maintained by Dawid Kaledkowski. Last updated 29 days ago.
1.7 match 11 stars 9.00 score 11 scripts 9 dependentsmrc-ide
rincewind:Utilities for processing forecasts matrices
This package contains utility functions for processing forecasts matrices.
Maintained by Sangeeta Bhatia. Last updated 3 years ago.
15.0 match 1 stars 1.00 score 1 scripts
julienide
PeriodicTable:Periodic Table of the Elements
Provides a dataset containing properties for chemical elements. Helper functions are also provided to access some atomic properties.
Maintained by Julien Idé. Last updated 8 years ago.
9.8 match 1 stars 1.48 score 10 scripts 1 dependents
bioboot
bio3d:Biological Structure Analysis
Utilities to process, organize and explore protein structure, sequence and dynamics data. Features include the ability to read and write structure, sequence and dynamic trajectory data, perform sequence and structure database searches, data summaries, atom selection, alignment, superposition, rigid core identification, clustering, torsion analysis, distance matrix analysis, structure and sequence conservation analysis, normal mode analysis, principal component analysis of heterogeneous structure data, and correlation network analysis from normal mode and molecular dynamics data. In addition, various utility functions are provided to enable the statistical and graphical power of the R environment to work with biological sequence and structural data. Please refer to the URLs below for more information.
Maintained by Barry Grant. Last updated 5 months ago.
1.6 match 5 stars 8.49 score 1.4k scripts 10 dependents
gallegoj
tfarima:Transfer Function and ARIMA Models
Building customized transfer function and ARIMA models with multiple operators and parameter restrictions. Functions for model identification, model estimation (exact or conditional maximum likelihood), model diagnostic checking, automatic outlier detection, calendar effects, forecasting and seasonal adjustment. See Bell and Hillmer (1983) <doi:10.1080/01621459.1983.10478005>, Box, Jenkins, Reinsel and Ljung <ISBN:978-1-118-67502-1>, Box, Pierce and Newbold (1987) <doi:10.1080/01621459.1987.10478430>, Box and Tiao (1975) <doi:10.1080/01621459.1975.10480264>, Chen and Liu (1993) <doi:10.1080/01621459.1993.10594321>.
Maintained by Jose L. Gallego. Last updated 12 months ago.
3.3 match 2 stars 4.04 score 11 scriptsrstudio
rscontract:Generic implementation of the 'RStudio' connections contract
Provides a generic implementation of the 'RStudio' connection contract to make it easier for database connections, and other type of connections, opened via R packages integrate with the connections pane inside the 'RStudio' interactive development environment (IDE).
Maintained by Nathan Stephens. Last updated 4 years ago.
2.3 match 22 stars 5.12 score 4 scripts 2 dependentsbioc
maaslin3:"Refining and extending generalized multivariate linear models for meta-omic association discovery"
MaAsLin 3 refines and extends generalized multivariate linear models for meta-omicron association discovery. It finds abundance and prevalence associations between microbiome meta-omics features and complex metadata in population-scale epidemiological studies. The software includes multiple analysis methods (including support for multiple covariates, repeated measures, and ordered predictors), filtering, normalization, and transform options to customize analysis for your specific study.
Maintained by William Nickols. Last updated 7 hours ago.
metagenomicssoftwaremicrobiomenormalizationmultiplecomparison
1.3 match 32 stars 8.12 score 34 scriptspik-piam
mrremind:MadRat REMIND Input Data Package
The mrremind packages contains data preprocessing for the REMIND model.
Maintained by Lavinia Baumstark. Last updated 2 days ago.
1.7 match 4 stars 6.25 score 15 scripts 1 dependentsr-lib
lintr:A 'Linter' for R Code
Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.
Maintained by Michael Chirico. Last updated 7 days ago.
0.5 match 1.2k stars 17.00 score 916 scripts 33 dependents
discoleo
Rpdb:Read, Write, Visualize and Manipulate PDB Files
Provides tools to read, write, visualize Protein Data Bank (PDB) files and perform some structural manipulations.
Maintained by Leonard Mada. Last updated 24 days ago.
1.7 match 4.43 score 68 scripts
phgrosjean
svIDE:Functions to Ease Interactions Between R and IDE or Code Editors
Function for the GUI API to interact with external IDE/code editors.
Maintained by Philippe Grosjean. Last updated 7 years ago.
6.8 match 1.04 score 11 scriptsphgrosjean
svTools:Wrappers for Tools in Other Packages for IDE Friendliness
Set of tools aimed at wrapping some of the functionalities of the packages tools, utils and codetools into a nicer format so that an IDE can use them.
Maintained by Philippe Grosjean. Last updated 7 years ago.
5.3 match 1.20 score 16 scriptsropensci
aeolus:Unleash Useful Linebreaks in Markdown Documents
Add linebreaks at the end of sentences and remove other linebreaks.
Maintained by Maëlle Salmon. Last updated 1 months ago.
1.7 match 14 stars 3.45 score 3 scripts
wlandau
crew:A Distributed Worker Launcher Framework
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'NNG'-powered 'mirai' R package by Gao (2023) <doi:10.5281/zenodo.7912722> is a sleek and sophisticated scheduler that efficiently processes these intense workloads. The 'crew' package extends 'mirai' with a unifying interface for third-party worker launchers. Inspiration also comes from packages. 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischel, and Surmann (2017) <doi:10.21105/joss.00135>.
Maintained by William Michael Landau. Last updated 11 hours ago.
0.5 match 136 stars 11.19 score 243 scripts 2 dependentscran
BayesGP:Efficient Implementation of Gaussian Process in Bayesian Hierarchical Models
Implements Bayesian hierarchical models with flexible Gaussian process priors, focusing on Extended Latent Gaussian Models and incorporating various Gaussian process priors for Bayesian smoothing. Computations leverage finite element approximations and adaptive quadrature for efficient inference. Methods are detailed in Zhang, Stringer, Brown, and Stafford (2023) <doi:10.1177/09622802221134172>; Zhang, Stringer, Brown, and Stafford (2024) <doi:10.1080/10618600.2023.2289532>; Zhang, Brown, and Stafford (2023) <doi:10.48550/arXiv.2305.09914>; and Stringer, Brown, and Stafford (2021) <doi:10.1111/biom.13329>.
Maintained by Ziang Zhang. Last updated 4 months ago.
1.8 match 3.18 score
mlverse
chattr:Interact with Large Language Models in 'RStudio'
Enables user interactivity with large-language models ('LLM') inside the 'RStudio' integrated development environment (IDE). The user can interact with the model using the 'shiny' app included in this package, or directly in the 'R' console. It comes with back-ends for 'OpenAI', 'GitHub' 'Copilot', and 'LlamaGPT'.
Maintained by Edgar Ruiz. Last updated 1 months ago.
0.5 match 215 stars 10.55 score 71 scripts 1 dependentswlandau
crew.cluster:Crew Launcher Plugins for Traditional High-Performance Computing Clusters
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.cluster' package extends the 'mirai'-powered 'crew' package with worker launcher plugins for traditional high-performance computing systems. Inspiration also comes from packages 'mirai' by Gao (2023) <https://github.com/shikokuchuo/mirai>, 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>.
Maintained by William Michael Landau. Last updated 1 months ago.
crewhigh-performance-computing
0.5 match 28 stars 6.81 score 68 scripts
jreps
OhdsiShinyAppBuilder:Viewing Observational Health Data Sciences and Informatics Results via 'shiny' Modules
Users can build a single 'shiny' app for exploring population characterization, population-level causal effect estimation, and patient-level prediction results generated via the R analyses packages in 'HADES' (see <https://ohdsi.github.io/Hades/>). Learn more about 'OhdsiShinyAppBuilder' at <https://ohdsi.github.io/OhdsiShinyAppBuilder/>.
Maintained by Jenna Reps. Last updated 3 months ago.
1.6 match 2.00 score 1 scripts
deboerk
cocor:Comparing Correlations
Statistical tests for the comparison between two correlations based on either independent or dependent groups. Dependent correlations can either be overlapping or nonoverlapping. A web interface is available on the website <http://comparingcorrelations.org>. A plugin for the R GUI and IDE RKWard is included. Please install RKWard from <https://rkward.kde.org> to use this feature. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard.
Maintained by Birk Diedenhofen. Last updated 3 years ago.
0.5 match 1 stars 5.15 score 151 scripts 9 dependentswlandau
crew.aws.batch:A Crew Launcher Plugin for AWS Batch
In computationally demanding analysis projects, statisticians and data scientists asynchronously deploy long-running tasks to distributed systems, ranging from traditional clusters to cloud services. The 'crew.aws.batch' package extends the 'mirai'-powered 'crew' package with a worker launcher plugin for AWS Batch. Inspiration also comes from packages 'mirai' by Gao (2023) <https://github.com/shikokuchuo/mirai>, 'future' by Bengtsson (2021) <doi:10.32614/RJ-2021-048>, 'rrq' by FitzJohn and Ashton (2023) <https://github.com/mrc-ide/rrq>, 'clustermq' by Schubert (2019) <doi:10.1093/bioinformatics/btz284>), and 'batchtools' by Lang, Bischl, and Surmann (2017). <doi:10.21105/joss.00135>.
Maintained by William Michael Landau. Last updated 1 months ago.
aws-batchcrewhigh-performance-computing
0.5 match 15 stars 4.99 score 6 scripts
rdinnager
slimr:Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations
Lets you write 'SLiM' scripts (population genomics simulation) using your favourite R IDE, using a syntax as close as possible to the original 'SLiM' language. It offer many tools to manipulate those scripts, as well as run them in the 'SLiM' software from R, as well as capture and post-process their output, after or even during a simulation.
Maintained by Russell Dinnage. Last updated 4 months ago.
0.5 match 8 stars 4.70 score 42 scripts
paulesantos
geoperu:Download Spatial Datasets of Peru
Provides convenient access to the official spatial datasets of Peru as 'sf' objects in R. This package includes a wide range of geospatial data covering various aspects of Peruvian geography, such as: administrative divisions (Source: INEI <https://ide.inei.gob.pe/>), protected natural areas (Source: GEO ANP - SERNANP <https://geo.sernanp.gob.pe/visorsernanp/>). All datasets are harmonized in terms of attributes, projection, and topology, ensuring consistency and ease of use for spatial analysis and visualization.
Maintained by Paul E. Santos Andrade. Last updated 4 months ago.
0.5 match 2 stars 3.95 score 5 scripts
hoxo-m
sGMRFmix:Sparse Gaussian Markov Random Field Mixtures for Anomaly Detection
An implementation of sparse Gaussian Markov random field mixtures presented by Ide et al. (2016) <doi:10.1109/ICDM.2016.0119>. It provides a novel anomaly detection method for multivariate noisy sensor data. It can automatically handle multiple operational modes. And it can also compute variable-wise anomaly scores.
Maintained by Koji Makiyama. Last updated 7 years ago.
0.5 match 1 stars 2.34 score 22 scripts
frankiethull
ggpal2:{pal} extension ggplot2 LLM assistant
Extension of {pal}, a LLM assistant add-in for RStudio and Positron IDEs built on {elmer}. {ggpal2} is an assistant designed to help with ggplot2.
Maintained by Frank Hull. Last updated 3 months ago.
0.5 match 1 stars 2.18 score 1 scriptsdeboerk
cocron:Statistical Comparisons of Two or more Alpha Coefficients
Statistical tests for the comparison between two or more alpha coefficients based on either dependent or independent groups of individuals. A web interface is available at http://comparingcronbachalphas.org. A plugin for the R GUI and IDE RKWard is included. Please install RKWard from https:// rkward.kde.org to use this feature. The respective R package 'rkward' cannot be installed directly from a repository, as it is a part of RKWard.
Maintained by Birk Diedenhofen. Last updated 9 years ago.
0.5 match 2.12 score 22 scripts
sonjakuhnt
fanovaGraph:Building Kriging Models from FANOVA Graphs
Estimation and plotting of a function's FANOVA graph to identify the interaction structure and fitting, prediction and simulation of a Kriging model modified by the identified structure. The interactive function plotManipulate() can only be run on the 'RStudio IDE' with 'RStudio' package 'manipulate' loaded. 'RStudio' is freely available (<https://rstudio.com/>), and includes package 'manipulate'. The equivalent function plotTk() bases on CRAN Repository packages only. For further information on the method see Fruth, J., Roustant, O., Kuhnt, S. (2014) <doi:10.1016/j.jspi.2013.11.007>.
Maintained by Sonja Kuhnt. Last updated 4 years ago.
0.5 match 1 stars 1.20 score 16 scripts