R-universe search: needs:roxygen2

r-lib

devtools:Tools to Make Developing R Packages Easier

Collection of package development tools.

Maintained by Jennifer Bryan. Last updated 6 months ago.

package-creation

2.4k stars 19.55 score 51k scripts 150 dependents

thinkr-open

attachment:Deal with Dependencies

Manage dependencies during package development. This can retrieve all dependencies that are used in ".R" files in the "R/" directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2' documentation of functions. There is a function to update the "DESCRIPTION" file of your package with 'CRAN' packages or any other remote package. All functions to retrieve dependencies of ".R" scripts and ".Rmd" or ".qmd" files can be used independently of a package development.

Maintained by Vincent Guyader. Last updated 17 days ago.

hacktoberfest

110 stars 10.44 score 48 scripts 5 dependents

reditorsupport

languageserver:Language Server Protocol

An implementation of the Language Server Protocol for R. The Language Server protocol is used by an editor client to integrate features like auto completion. See <https://microsoft.github.io/language-server-protocol/> for details.

Maintained by Randy Lai. Last updated 1 years ago.

language-server-protocol

607 stars 9.93 score 207 scripts 1 dependents

dataoneorg

dataone:R Interface to the DataONE REST API

Provides read and write access to data and metadata from the DataONE network <https://www.dataone.org> of data repositories. Each DataONE repository implements a consistent repository application programming interface. Users call methods in R to access these remote repository functions, such as methods to query the metadata catalog, get access to metadata for particular data packages, and read the data objects from the data repository. Users can also insert and update data objects on repositories that support these methods.

Maintained by Matthew B. Jones. Last updated 3 years ago.

36 stars 9.93 score 472 scripts 3 dependents

ropensci

rdflib:Tools to Manipulate and Query Semantic Data

The Resource Description Framework, or 'RDF' is a widely used data representation model that forms the cornerstone of the Semantic Web. 'RDF' represents data as a graph rather than the familiar data table or rectangle of relational databases. The 'rdflib' package provides a friendly and concise user interface for performing common tasks on 'RDF' data, such as reading, writing and converting between the various serializations of 'RDF' data, including 'rdfxml', 'turtle', 'nquads', 'ntriples', and 'json-ld'; creating new 'RDF' graphs, and performing graph queries using 'SPARQL'. This package wraps the low level 'redland' R package which provides direct bindings to the 'redland' C library. Additionally, the package supports the newer and more developer friendly 'JSON-LD' format through the 'jsonld' package. The package interface takes inspiration from the Python 'rdflib' library.

Maintained by Carl Boettiger. Last updated 8 months ago.

peer-reviewed

57 stars 9.59 score 123 scripts 7 dependents

thinkr-open

fusen:Build a Package from Rmarkdown Files

Use Rmarkdown First method to build your package. Start your package with documentation, functions, examples and tests in the same unique file. Everything can be set from the Rmarkdown template file provided in your project, then inflated as a package. Inflating the template copies the relevant chunks and sections in the appropriate files required for package development.

Maintained by Vincent Guyader. Last updated 2 months ago.

hacktoberfest rmd-first

163 stars 9.45 score 35 scripts

ropensci

DataPackageR:Construct Reproducible Analytic Data Sets as R Packages

A framework to help construct R data packages in a reproducible manner. Potentially time consuming processing of raw data sets into analysis ready data sets is done in a reproducible manner and decoupled from the usual 'R CMD build' process so that data sets can be processed into R objects in the data package and the data package can then be shared, built, and installed by others without the need to repeat computationally costly data processing. The package maintains data provenance by turning the data processing scripts into package vignettes, as well as enforcing documentation and version checking of included data objects. Data packages can be version controlled on 'GitHub', and used to share data for manuscripts, collaboration and reproducible research.

Maintained by Dave Slager. Last updated 7 months ago.

peer-reviewed reproducibility

156 stars 9.38 score 72 scripts

briencj

asremlPlus:Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The 'asreml' package provides a computationally efficient algorithm for fitting a wide range of linear mixed models using Residual Maximum Likelihood. It is a commercial package and a license for it can be purchased from 'VSNi' <https://vsni.co.uk/> as 'asreml-R', who will supply a zip file for local installation/updating (see <https://asreml.kb.vsni.co.uk/>). It is not needed for functions that are methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be installed from <http://chris.brien.name/rpackages/>.

Maintained by Chris Brien. Last updated 1 months ago.

asreml mixed-models

19 stars 9.37 score 200 scripts

whipson

maestro:Orchestration of Data Pipelines

Framework for creating and orchestrating data pipelines. Organize, orchestrate, and monitor multiple pipelines in a single project. Use tags to decorate functions with scheduling parameters and configuration.

Maintained by Will Hipson. Last updated 6 days ago.

119 stars 9.20 score 150 scripts

r-spatial

link2GI:Linking Geographic Information Systems, Remote Sensing and Other Command Line Tools

Functions and tools for using open GIS and remote sensing command-line interfaces in a reproducible environment.

Maintained by Chris Reudenbach. Last updated 4 months ago.

26 stars 8.99 score 78 scripts 1 dependents

pharmar

riskmetric:Risk Metrics to Evaluating R Packages

Facilities for assessing R packages against a number of metrics to help quantify their robustness.

Maintained by Eli Miller. Last updated 7 days ago.

166 stars 8.98 score 43 scripts

ajrgodfrey

BrailleR:Improved Access for Blind Users

Blind users do not have access to the graphical output from R without printing the content of graphics windows to an embosser of some kind. This is not as immediate as is required for efficient access to statistical output. The functions here are created so that blind people can make even better use of R. This includes the text descriptions of graphs, convenience functions to replace the functionality offered in many GUI front ends, and experimental functionality for optimising graphical content to prepare it for embossing as tactile images.

Maintained by A. Jonathan R. Godfrey. Last updated 12 months ago.

123 stars 8.90 score 143 scripts

pik-piam

remind2:The REMIND R package (2nd generation)

Contains the REMIND-specific routines for data and model output manipulation.

Maintained by Renato Rodrigues. Last updated 3 days ago.

8.87 score 161 scripts 5 dependents

cynkra

fledge:Smoother Change Tracking and Versioning for R Packages

Streamlines the process of updating changelogs (NEWS.md) and versioning R packages developed in git repositories.

Maintained by Kirill Müller. Last updated 3 months ago.

changelog git package-creation

188 stars 8.73 score 10 scripts

ropensci

datapack:A Flexible Container to Transport and Manipulate Data and Associated Resources

Provides a flexible container to transport and manipulate complex sets of data. These data may consist of multiple data files and associated meta data and ancillary files. Individual data objects have associated system level meta data, and data files are linked together using the OAI-ORE standard resource map which describes the relationships between the files. The OAI- ORE standard is described at <https://www.openarchives.org/ore/>. Data packages can be serialized and transported as structured files that have been created following the BagIt specification. The BagIt specification is described at <https://tools.ietf.org/html/draft-kunze-bagit-08>.

Maintained by Matthew B. Jones. Last updated 3 years ago.

43 stars 8.55 score 195 scripts 4 dependents

eblondel

zen4R:Interface to 'Zenodo' REST API

Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by 'Zenodo' and upload and download of files.

Maintained by Emmanuel Blondel. Last updated 1 months ago.

api datacite depositions deposits doi fair zenodo

45 stars 8.25 score 76 scripts 1 dependents

ramikrispin

coronavirus:The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Dataset

Provides a daily summary of the Coronavirus (COVID-19) cases by state/province. Data source: Johns Hopkins University Center for Systems Science and Engineering (JHU CCSE) Coronavirus <https://systems.jhu.edu/research/public-health/ncov/>.

Maintained by Rami Krispin. Last updated 2 years ago.

covid-19 covid19 covid19-data dataset

499 stars 8.25 score 716 scripts

nceas

metajam:Easily Download Data and Metadata from 'DataONE'

A set of tools to foster the development of reproducible analytical workflow by simplifying the download of data and metadata from 'DataONE' (<https://www.dataone.org>) and easily importing this information into R.

Maintained by Julien Brun. Last updated 7 months ago.

data data-analysis metadata repositories

16 stars 8.13 score 75 scripts

mazamascience

MazamaSpatialUtils:Spatial Data Download and Utility Functions

A suite of conversion functions to create internally standardized spatial polygons data frames. Utility functions use these data sets to return values such as country, state, time zone, watershed, etc. associated with a set of longitude/latitude pairs. (They also make cool maps.)

Maintained by Jonathan Callahan. Last updated 5 months ago.

5 stars 8.01 score 282 scripts 2 dependents

dasonk

docstring:Provides Docstring Capabilities to R Functions

Provides the ability to display something analogous to Python's docstrings within R. By allowing the user to document their functions as comments at the beginning of their function without requiring putting the function into a package we allow more users to easily provide documentation for their functions. The documentation can be viewed just like any other help files for functions provided by packages as well.

Maintained by Dason Kurkiewicz. Last updated 3 years ago.

devtools docstring documentation documentation-tool roxygen-style

58 stars 7.96 score 305 scripts 1 dependents

matloff

dsld:Data Science Looks at Discrimination

Statistical and graphical tools for detecting and measuring discrimination and bias, be it racial, gender, age or other. Detection and remediation of bias in machine learning algorithms. 'Python' interfaces available.

Maintained by Norm Matloff. Last updated 2 months ago.

12 stars 7.81 score 35 scripts

mazamascience

MazamaCoreUtils:Utility Functions for Production R Code

A suite of utility functions providing functionality commonly needed for production level projects such as logging, error handling, cache management and date-time parsing. Functions for date-time parsing and formatting require that time zones be specified explicitly, avoiding a common source of error when working with environmental time series.

Maintained by Jonathan Callahan. Last updated 4 months ago.

4 stars 7.76 score 119 scripts 5 dependents

ropensci

redland:RDF Library Bindings in R

Provides methods to parse, query and serialize information stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>. This package supports RDF by implementing an R interface to the Redland RDF C library, described at <https://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph consisting of Statements composed of Subject, Predicate, and Object Nodes.

Maintained by Matthew B. Jones. Last updated 1 years ago.

redland

16 stars 7.76 score 98 scripts 13 dependents

sciviews

SciViews:'SciViews' - Data Processing and Visualization with the 'SciViews::R' Dialect

The 'SciViews::R' dialect provides a set of functions that streamlines data input, process, analysis and visualization especially, but not exclusively, for beginners or occasional users. It mixes base R and tidyverse, plus another set of CRAN packages for an easy and coherent use of R.

Maintained by Philippe Grosjean. Last updated 7 months ago.

sciviews

8 stars 7.62 score 116 scripts 1 dependents

bioc

cogena:co-expressed gene-set enrichment analysis

cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.

Maintained by Zhilong Jia. Last updated 5 months ago.

clustering genesetenrichment geneexpression visualization pathways kegg go microarray sequencing systemsbiology datarepresentation dataimport bioconductor bioinformatics

12 stars 7.36 score 32 scripts

hoxo-m

githubinstall:A Helpful Way to Install R Packages Hosted on GitHub

Provides an helpful way to install packages hosted on GitHub.

Maintained by Koji Makiyama. Last updated 7 years ago.

r-language

49 stars 7.29 score 177 scripts

yihui

Rd2roxygen:Convert Rd to 'Roxygen' Documentation

Functions to convert Rd to 'roxygen' documentation. It can parse an Rd file to a list, create the 'roxygen' documentation and update the original R script (e.g. the one containing the definition of the function) accordingly. This package also provides utilities that can help developers build packages using 'roxygen' more easily. The 'formatR' package can be used to reformat the R code in the examples sections so that the code will be more readable.

Maintained by Yihui Xie. Last updated 12 months ago.

roxygen-documentation

32 stars 7.26 score 82 scripts 1 dependents

soerenpannier

emdi:Estimating and Mapping Disaggregated Indicators

Functions that support estimating, assessing and mapping regional disaggregated indicators. So far, estimation methods comprise direct estimation, the model-based unit-level approach Empirical Best Prediction (see "Small area estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>), the area-level model (see "Estimates of income for small places: An application of James-Stein procedures to Census Data" by Fay and Herriot (1979) <doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance estimation methods, log and arcsin transformation, spatial, robust and measurement error models), as well as their precision estimates. The assessment of the used model is supported by a summary and diagnostic plots. For a suitable presentation of estimates, map plots can be easily created. Furthermore, results can easily be exported to excel. For a detailed description of the package and the methods used see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07> and the second package vignette "A Framework for Producing Small Area Estimates Based on Area-Level Models in R".

Maintained by Soeren Pannier. Last updated 1 years ago.

15 stars 7.26 score 45 scripts 1 dependents

inbo

checklist:A Thorough and Strict Set of Checks for R Packages and Source Code

An opinionated set of rules for R packages and R source code projects.

Maintained by Thierry Onkelinx. Last updated 1 months ago.

checklist continuous-integration continuous-testing quality-assurance

19 stars 7.24 score 21 scripts 2 dependents

pik-piam

lucode2:Code Manipulation and Analysis Tools

A collection of tools which allow to manipulate and analyze code.

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

7.22 score 364 scripts 8 dependents

ropensci

pkgcheck:rOpenSci Package Checks

Check whether a package is ready for submission to rOpenSci's peer review system.

Maintained by Mark Padgham. Last updated 20 days ago.

compliance-automation software-analysis software-checking

19 stars 7.13 score 29 scripts 1 dependents

ropensci

mregions2:Access Data from Marineregions.org: Gazetteer & Data Products

Explore and retrieve marine geospatial data from the Marine Regions Gazetteer <https://marineregions.org/gazetteer.php?p=webservices> and the Marine Regions Data Products <https://marineregions.org/webservices.php>.

Maintained by Salvador Jesús Fernández Bejarano. Last updated 7 days ago.

9 stars 7.03 score 40 scripts

r-lib

roxygen2md:'Roxygen' to 'Markdown'

Converts elements of 'roxygen' documentation to 'markdown'.

Maintained by Kirill Müller. Last updated 4 months ago.

documentation markdown

68 stars 7.00 score 11 scripts 2 dependents

thinkr-open

thinkr:Tools for Cleaning Up Messy Files

Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.

Maintained by Vincent Guyader. Last updated 3 years ago.

hacktoberfest thinkr-not-maintained

29 stars 6.96 score 45 scripts

pik-piam

edgeTransport:Prepare EDGE Transport Data for the REMIND model

EDGE-T is a fork of the GCAM transport module https://jgcri.github.io/gcam-doc/energy.html#transportation with a high level of detail in its representation of technological and modal options. It is a partial equilibrium model with a nested multinomial logit structure and relies on the modified logit formulation. Most of the sources are not publicly available. PIK-internal users can find the sources in the distributed file system in the folder `/p/projects/rd3mod/inputdata/sources/EDGE-Transport-Standalone`.

Maintained by Johanna Hoppe. Last updated 2 days ago.

5 stars 6.84 score 16 scripts 2 dependents

raymondbalise

rUM:R Templates from the University of Miami

This holds some r markdown and quarto templates and a template to create a research project in "R Studio".

Maintained by Raymond Balise. Last updated 10 days ago.

rmarkdown

9 stars 6.84 score 16 scripts

kozodoi

fairness:Algorithmic Fairness Metrics

Offers calculation, visualization and comparison of algorithmic fairness metrics. Fair machine learning is an emerging topic with the overarching aim to critically assess whether ML algorithms reinforce existing social biases. Unfair algorithms can propagate such biases and produce predictions with a disparate impact on various sensitive groups of individuals (defined by sex, gender, ethnicity, religion, income, socioeconomic status, physical or mental disabilities). Fair algorithms possess the underlying foundation that these groups should be treated similarly or have similar prediction outcomes. The fairness R package offers the calculation and comparisons of commonly and less commonly used fairness metrics in population subgroups. These methods are described by Calders and Verwer (2010) <doi:10.1007/s10618-010-0190-x>, Chouldechova (2017) <doi:10.1089/big.2016.0047>, Feldman et al. (2015) <doi:10.1145/2783258.2783311> , Friedler et al. (2018) <doi:10.1145/3287560.3287589> and Zafar et al. (2017) <doi:10.1145/3038912.3052660>. The package also offers convenient visualizations to help understand fairness metrics.

Maintained by Nikita Kozodoi. Last updated 2 years ago.

algorithmic-discrimination algorithmic-fairness discrimination disparate-impact fairness fairness-ai fairness-ml machine-learning

32 stars 6.82 score 69 scripts 1 dependents

thinkr-open

checkhelper:Deal with Check Outputs

Deal with packages 'check' outputs and reduce the risk of rejection by 'CRAN' by following policies.

Maintained by Sebastien Rochette. Last updated 1 years ago.

34 stars 6.74 score 18 scripts

frbcesab

rcompendium:Create a Package or Research Compendium Structure

Makes easier the creation of R package or research compendium (i.e. a predefined files/folders structure) so that users can focus on the code/analysis instead of wasting time organizing files. A full ready-to-work structure is set up with some additional features: version control, remote repository creation, CI/CD configuration (check package integrity under several OS, test code with 'testthat', and build and deploy website using 'pkgdown'). This package heavily relies on the R packages 'devtools' and 'usethis' and follows recommendations made by Wickham H. (2015) <ISBN:9781491910597> and Marwick B. et al. (2018) <doi:10.7287/peerj.preprints.3192v2>.

Maintained by Nicolas Casajus. Last updated 2 months ago.

reproducible-research research-compendium

40 stars 6.72 score 22 scripts

correlaid

newsanchor:Client for the News API

Interface to gather news from the 'News API', based on a multilevel query <https://newsapi.org/>. A personal API key is required.

Maintained by Yannik Buhl. Last updated 5 years ago.

36 stars 6.70 score 40 scripts

wahani

dat:Tools for Data Manipulation

An implementation of common higher order functions with syntactic sugar for anonymous function. Provides also a link to 'dplyr' and 'data.table' for common transformations on data frames to work around non standard evaluation by default.

Maintained by Sebastian Warnholz. Last updated 4 years ago.

16 stars 6.66 score 32 scripts 1 dependents

wahani

aoos:Another Object Orientation System

Another implementation of object-orientation in R. It provides syntactic sugar for the S4 class system and two alternative new implementations. One is an experimental version built around S4 and the other one makes it more convenient to work with lists as objects.

Maintained by Sebastian Warnholz. Last updated 8 years ago.

5 stars 6.66 score 17 scripts 6 dependents

rorynolan

exampletestr:Help for Writing Unit Tests Based on Function Examples

Take the examples written in your documentation of functions and use them to create shells (skeletons which must be manually completed by the user) of test files to be tested with the 'testthat' package. Sort of like python 'doctests' for R.

Maintained by Rory Nolan. Last updated 6 months ago.

37 stars 6.63 score 8 scripts

mazamascience

AirMonitor:Air Quality Data Analysis

Utilities for working with hourly air quality monitoring data with a focus on small particulates (PM2.5). A compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Algorithms to calculate NowCast and the associated Air Quality Index (AQI) are defined at the US Environmental Projection Agency AirNow program: <https://document.airnow.gov/technical-assistance-document-for-the-reporting-of-daily-air-quailty.pdf>.

Maintained by Jonathan Callahan. Last updated 6 months ago.

7 stars 6.57 score 178 scripts

jakesherman

easypackages:Easy Loading and Installing of Packages

Easily load and install multiple packages from different sources, including CRAN and GitHub. The libraries function allows you to load or attach multiple packages in the same function call. The packages function will load one or more packages, and install any packages that are not installed on your system (after prompting you). Also included is a from_import function that allows you to import specific functions from a package into the global environment.

Maintained by Jake Sherman. Last updated 7 years ago.

packages

11 stars 6.52 score 490 scripts

gisma

uavRmp:UAV Mission Planner

The Unmanned Aerial Vehicle Mission Planner provides an easy to use work flow for planning autonomous obstacle avoiding surveys of ready to fly unmanned aerial vehicles to retrieve aerial or spot related data. It creates either intermediate flight control files for the DJI-Litchi supported series or ready to upload control files for the pixhawk-based flight controller as used in the 3DR-Solo or Yuneec series. Additionally it contains some useful tools for digitizing and data manipulation.

Maintained by Chris Reudenbach. Last updated 10 months ago.

cultural-heritage dji drone flight-planning forest-mapping litchi low-budget-uav mission-planning photogrammetry pixhawk pixhawk-controller qgroundcontrol2litchi solo survey terrain-following terrain-mapping uavs yuneec

25 stars 6.48 score 6 scripts

ai4ci

interfacer:Define and Enforce Contracts for Dataframes as Function Parameters

A dataframe validation framework for package builders who use dataframes as function parameters. It performs checks on column names, coerces data-types, and checks grouping to make sure user inputs conform to a specification provided by the package author. It provides a mechanism for package authors to automatically document supported dataframe inputs and selectively dispatch to functions depending on the format of a dataframe much like S3 does for classes. It also contains some developer tools to make working with and documenting dataframe specifications easier. It helps package developers to improve their documentation and simplifies parameter validation where dataframes are used as function parameters.

Maintained by Robert Challen. Last updated 2 months ago.

2 stars 6.43 score 2 dependents

luckinet

ontologics:Code-Logics to Handle Ontologies

Provides tools to build and work with an ontology of linked (open) data in a tidy workflow. It is inspired by the Food and Agrilculture Organizations (FAO) caliper platform <https://www.fao.org/statistics/caliper/web/> and makes use of the Simple Knowledge Organisation System (SKOS).

Maintained by Steffen Ehrmann. Last updated 2 months ago.

interoperability ontology

3 stars 6.39 score 17 scripts 1 dependents

ices-tools-prod

icesTAF:Functions to Support the ICES Transparent Assessment Framework

Functions to support the ICES Transparent Assessment Framework <https://taf.ices.dk> to organize data, methods, and results used in ICES assessments. ICES is an organization facilitating international collaboration in marine science.

Maintained by Colin Millar. Last updated 2 years ago.

5 stars 6.37 score 1.1k scripts 1 dependents

pik-piam

mrremind:MadRat REMIND Input Data Package

The mrremind packages contains data preprocessing for the REMIND model.

Maintained by Lavinia Baumstark. Last updated 3 days ago.

4 stars 6.25 score 15 scripts 1 dependents

johncoene

packer:An Opinionated Framework for Using 'JavaScript'

Enforces good practice and provides convenience functions to make work with 'JavaScript' not just easier but also scalable. It is a robust wrapper to 'NPM', 'yarn', and 'webpack' that enables to compartmentalize 'JavaScript' code, leverage 'NPM' and 'yarn' packages, include 'TypeScript', 'React', or 'Vue' in web applications, and much more.

Maintained by John Coene. Last updated 8 months ago.

javascript webpack

148 stars 6.25 score 1 scripts 2 dependents

mikldk

roxytest:Various Tests with 'roxygen2'

Various tests as 'roxygen2' roclets: e.g. 'testthat' and 'tinytest' tests. Also other static analysis tools as checking parameter documentation consistency and others.

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

95 stars 6.15 score 3 scripts

patzaw

TKCat:Tailored Knowledge Catalog

Facilitate the management of data from knowledge resources that are frequently used alone or together in research environments. In 'TKCat', knowledge resources are manipulated as modeled database (MDB) objects. These objects provide access to the data tables along with a general description of the resource and a detail data model documenting the tables, their fields and their relationships. These MDBs are then gathered in catalogs that can be easily explored an shared. Finally, 'TKCat' provides tools to easily subset, filter and combine MDBs and create new catalogs suited for specific needs.

Maintained by Patrice Godard. Last updated 5 days ago.

5 stars 6.13 score 27 scripts

geocompx

geocompkg:Geocomputation with R Metapackage

Package supporting the book Geocomputation with R (\url{https://r.geocompx.org}). The packages in the Imports are required to build the first chapter of the book. The packages in Suggests are required for Part II and III.

Maintained by Jakub Nowosad. Last updated 6 months ago.

geocomputation spatial

21 stars 6.10 score 2 scripts

ramikrispin

covid19italy:The 2019 Novel Coronavirus COVID-19 (2019-nCoV) Italy Dataset

Provides a daily summary of the Coronavirus (COVID-19) cases in Italy by country, region and province level. Data source: Presidenza del Consiglio dei Ministri - Dipartimento della Protezione Civile <https://www.protezionecivile.it/>.

Maintained by Rami Krispin. Last updated 2 years ago.

47 stars 6.07 score 25 scripts

kforner

srcpkgs:R Source Packages Manager

Manage a collection/library of R source packages. Discover, document, load, test source packages. Enable to use those packages as if they were actually installed. Quickly reload only what is needed on source code change. Run tests and checks in parallel.

Maintained by Karl Forner. Last updated 10 months ago.

11 stars 6.04 score 6 scripts

bioc

INDEED:Interactive Visualization of Integrated Differential Expression and Differential Network Analysis for Biomarker Candidate Selection Package

An R package for integrated differential expression and differential network analysis based on omic data for cancer biomarker discovery. Both correlation and partial correlation can be used to generate differential network to aid the traditional differential expression analysis to identify changes between biomolecules on both their expression and pairwise association levels. A detailed description of the methodology has been published in Methods journal (PMID: 27592383). An interactive visualization feature allows for the exploration and selection of candidate biomarkers.

Maintained by Ressom group. Last updated 5 months ago.

immunooncology software researchfield biologicalquestion statisticalmethod differentialexpression massspectrometry metabolomics

5 stars 6.02 score 10 scripts

bioc

PathoStat:PathoStat Statistical Microbiome Analysis Package

The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.

Maintained by Solaiappan Manimaran. Last updated 5 months ago.

microbiome metagenomics graphandnetwork microarray patternlogic principalcomponent sequencing software visualization rnaseq immunooncology

8 stars 5.90 score 8 scripts

simonpcouch

anyflights:Query 'nycflights13'-Like Air Travel Data for Given Years and Airports

Supplies a set of functions to query air travel data for user- specified years and airports. Datasets include on-time flights, airlines, airports, planes, and weather.

Maintained by Simon P. Couch. Last updated 3 months ago.

49 stars 5.90 score 23 scripts

modeloriented

modelDown:Make Static HTML Website for Predictive Models

Website generator with HTML summaries for predictive models. This package uses 'DALEX' explainers to describe global model behavior. We can see how well models behave (tabs: Model Performance, Auditor), how much each variable contributes to predictions (tabs: Variable Response) and which variables are the most important for a given model (tabs: Variable Importance). We can also compare Concept Drift for pairs of models (tabs: Drifter). Additionally, data available on the website can be easily recreated in current R session. Work on this package was financially supported by the NCN Opus grant 2017/27/B/ST6/01307 at Warsaw University of Technology, Faculty of Mathematics and Information Science.

Maintained by Kamil Romaszko. Last updated 4 years ago.

121 stars 5.80 score 15 scripts

bioc

MetID:Network-based prioritization of putative metabolite IDs

This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.

Maintained by Zhenzhi Li. Last updated 5 months ago.

assaydomain biologicalquestion infrastructure researchfield statisticalmethod technology workflowstep network kegg

1 stars 5.74 score 110 scripts

tiago-simoes

EvoPhylo:Pre- And Postprocessing of Morphological Data from Relaxed Clock Bayesian Phylogenetics

Performs automated morphological character partitioning for phylogenetic analyses and analyze macroevolutionary parameter outputs from clock (time-calibrated) Bayesian inference analyses, following concepts introduced by Simões and Pierce (2021) <doi:10.1038/s41559-021-01532-x>.

Maintained by Tiago Simoes. Last updated 2 years ago.

4 stars 5.66 score 19 scripts

mazamascience

MazamaLocationUtils:Manage Spatial Metadata for Known Locations

Utility functions for discovering and managing metadata associated with spatially unique "known locations". Applications include all fields of environmental monitoring (e.g. air and water quality) where data are collected at stationary sites.

Maintained by Jonathan Callahan. Last updated 4 months ago.

5.64 score 108 scripts

kinto-b

makepipe:Pipeline Tools Inspired by 'GNU Make'

A suite of tools for transforming an existing workflow into a self-documenting pipeline with very minimal upfront costs. Segments of the pipeline are specified in much the same way a 'Make' rule is, by declaring an executable recipe (which might be an R script), along with the corresponding targets and dependencies. When the entire pipeline is run through, only those recipes that need to be executed will be. Meanwhile, execution metadata is captured behind the scenes for later inspection.

Maintained by Kinto Behr. Last updated 3 months ago.

make pipeline

33 stars 5.60 score 12 scripts

tomzylkin

penppml:Penalized Poisson Pseudo Maximum Likelihood Regression

A set of tools that enables efficient estimation of penalized Poisson Pseudo Maximum Likelihood regressions, using lasso or ridge penalties, for models that feature one or more sets of high-dimensional fixed effects. The methodology is based on Breinlich, Corradi, Rocha, Ruta, Santos Silva, and Zylkin (2021) <http://hdl.handle.net/10986/35451> and takes advantage of the method of alternating projections of Gaure (2013) <doi:10.1016/j.csda.2013.03.024> for dealing with HDFE, as well as the coordinate descent algorithm of Friedman, Hastie and Tibshirani (2010) <doi:10.18637/jss.v033.i01> for fitting lasso regressions. The package is also able to carry out cross-validation and to implement the plugin lasso of Belloni, Chernozhukov, Hansen and Kozbur (2016) <doi:10.1080/07350015.2015.1102733>.

Maintained by Joao Cruz. Last updated 2 months ago.

cpp

12 stars 5.56 score 10 scripts

hughjonesd

doctest:Generate Tests from Examples Using 'roxygen' and 'testthat'

Creates 'testthat' tests from 'roxygen' examples using simple tags.

Maintained by David Hugh-Jones. Last updated 1 years ago.

33 stars 5.52 score 4 scripts

bioc

methylclock:Methylclock - DNA methylation-based clocks

This package allows to estimate chronological and gestational DNA methylation (DNAm) age as well as biological age using different methylation clocks. Chronological DNAm age (in years) : Horvath's clock, Hannum's clock, BNN, Horvath's skin+blood clock, PedBE clock and Wu's clock. Gestational DNAm age : Knight's clock, Bohlin's clock, Mayne's clock and Lee's clocks. Biological DNAm clocks : Levine's clock and Telomere Length's clock.

Maintained by Dolors Pelegri-Siso. Last updated 5 months ago.

dnamethylation biologicalquestion preprocessing statisticalmethod normalization cpp

39 stars 5.52 score 28 scripts

ropensci

mcbette:Model Comparison Using 'babette'

'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'mcbette' allows to do a Bayesian model comparison over some site and clock models, using 'babette' (<https://github.com/ropensci/babette/>).

Maintained by Richèl J.C. Bilderbeek. Last updated 8 months ago.

openjdk

7 stars 5.50 score 18 scripts

thinkr-open

lozen:Management tools for missions

Management tools for missions (internal and external). Includes weekly, GL projects, etc.

Maintained by Sébastien Rochette. Last updated 12 months ago.

experimental

7 stars 5.42 score 14 scripts

luckinet

arealDB:Harmonise and Integrate Heterogeneous Areal Data

Many relevant applications in the environmental and socioeconomic sciences use areal data, such as biodiversity checklists, agricultural statistics, or socioeconomic surveys. For applications that surpass the spatial, temporal or thematic scope of any single data source, data must be integrated from several heterogeneous sources. Inconsistent concepts, definitions, or messy data tables make this a tedious and error-prone process. 'arealDB' tackles those problems and helps the user to integrate a harmonised databases of areal data. Read the paper at Ehrmann, Seppelt & Meyer (2020) <doi:10.1016/j.envsoft.2020.104799>.

Maintained by Steffen Ehrmann. Last updated 2 months ago.

areal-data database

2 stars 5.41 score 15 scripts

simon-smart88

shinyscholar:A Template for Creating Reproducible 'shiny' Applications

Create a skeleton 'shiny' application with create_template() that is reproducible, can be saved and meets academic standards for attribution. Forked from 'wallace'. Code is split into modules that are loaded and linked together automatically and each call one function. Guidance pages explain modules to users and flexible logging informs them of any errors. Options enable asynchronous operations, viewing of source code, interactive maps and data tables. Use to create complex analytical applications, following best practices in open science and software development. Includes functions for automating repetitive development tasks and an example application at run_shinyscholar() that requires install.packages("shinyscholar", dependencies = TRUE). A guide to developing applications can be found on the package website.

Maintained by Simon E. H. Smart. Last updated 7 days ago.

22 stars 5.40 score 5 scripts

ropensci

srr:'rOpenSci' Review Roclets

Companion package to 'rOpenSci' statistical software review project.

Maintained by Mark Padgham. Last updated 5 months ago.

compliance-automation statistical-software cpp

5 stars 5.38 score 3 scripts 2 dependents

mazamascience

MazamaTimeSeries:Core Functionality for Environmental Time Series

Utility functions for working with environmental time series data from known locations. The compact data model is structured as a list with two dataframes. A 'meta' dataframe contains spatial and measuring device metadata associated with deployments at known locations. A 'data' dataframe contains a 'datetime' column followed by columns of measurements associated with each "device-deployment". Ephemerides calculations are based on code originally found in NOAA's "Solar Calculator" <https://gml.noaa.gov/grad/solcalc/>.

Maintained by Jonathan Callahan. Last updated 1 years ago.

timeseries

5.27 score 62 scripts 1 dependents

ropensci

roreviewapi:Plumber API to report package structure and function

Plumber API to report package structure and function.

Maintained by Mark Padgham. Last updated 1 months ago.

4 stars 5.26 score

insightsengineering

roxy.shinylive:A 'roxygen2' Extension for 'Shinylive'

An extension for 'roxygen2' to embed 'Shinylive' applications in the package documentation.

Maintained by Pawel Rucki. Last updated 4 months ago.

documentation roxygen2 shiny shinylive webr

10 stars 5.24 score

pik-piam

modelstats:Run Analysis Tools

A collection of tools to analyze model runs.

Maintained by Anastasis Giannousakis. Last updated 14 days ago.

1 stars 5.19 score 2 scripts

ramikrispin

covid19sf:The Covid19 San Francisco Dataset

Provides a verity of summary tables of the Covid19 cases in San Francisco. Data source: San Francisco, Department of Public Health - Population Health Division <https://datasf.org/opendata/>.

Maintained by Rami Krispin. Last updated 2 years ago.

12 stars 5.16 score 12 scripts

larsenlab

hlaR:Tools for HLA Data

A streamlined tool for eplet analysis of donor and recipient HLA (human leukocyte antigen) mismatch. Messy, low-resolution HLA typing data is cleaned, and imputed to high-resolution using the NMDP (National Marrow Donor Program) haplotype reference database <https://haplostats.org/haplostats>. High resolution data is analyzed for overall or single antigen eplet mismatch using a reference table (currently supporting 'HLAMatchMaker' <http://www.epitopes.net> versions 2 and 3). Data can enter or exit the workflow at different points depending on the user's aims and initial data quality.

Maintained by Joan Zhang. Last updated 2 years ago.

7 stars 5.15 score 9 scripts

miriamesteve

GSSTDA:Progression Analysis of Disease with Survival using Topological Data Analysis

Mapper-based survival analysis with transcriptomics data is designed to carry out. Mapper-based survival analysis is a modification of Progression Analysis of Disease (PAD) where survival data is taken into account in the filtering function. More details in: J. Fores-Martos, B. Suay-Garcia, R. Bosch-Romeu, M.C. Sanfeliu-Alonso, A. Falco, J. Climent, "Progression Analysis of Disease with Survival (PAD-S) by SurvMap identifies different prognostic subgroups of breast cancer in a large combined set of transcriptomics and methylation studies" <doi:10.1101/2022.09.08.507080>.

Maintained by Miriam Esteve. Last updated 8 months ago.

2 stars 5.15 score 7 scripts

s-fleck

testthis:Utils and 'RStudio' Addins to Make Testing Even More Fun

Utility functions and 'RStudio' addins for writing, running and organizing automated tests. Integrates tightly with the packages 'testthat', 'devtools' and 'usethis'. Hotkeys can be assigned to the 'RStudio' addins for running tests in a single file or to switch between a source file and the associated test file. In addition, testthis provides function to manage and run tests in subdirectories of the test/testthat directory.

Maintained by Stefan Fleck. Last updated 3 years ago.

rstudio rstudio-addin rstudio-addins testing testthat

33 stars 5.12 score 20 scripts

yanrong-stacy-song

creditr:Credit Default Swaps

Price credit default swaps using 'C' code from the International Swaps and Derivatives Association CDS Standard Model. See <https://www.cdsmodel.com/cdsmodel/documentation.html> for more information about the model and <https://www.cdsmodel.com/cdsmodel/cds-disclaimer.html> for license details for the 'C' code.

Maintained by Yanrong Song. Last updated 8 days ago.

5.05 score 32 scripts

dieghernan

pkgdev:Helpers to Develop a Package using GitHub Actions

A small set of functions that takes advantage of GitHub Actions for making your life easier as a R package developer. This package is primarily intended for personal use, however feel free to use it (at your own risk :)).

Maintained by Diego Hernangómez. Last updated 7 days ago.

developer-tools experimental github-actions

4 stars 5.00 score 7 scripts

ryan-riggs

RivRetrieve:Retrieve Global River Gauge Data

Provides access to global river gauge data from a variety of national-level river agencies. The package interfaces with the national-level agency websites to provide access to river gauge locations, river discharge, and river stage. Currently, the package is available for the following countries: Australia, Brazil, Canada, Chile, France, Japan, South Africa, the United Kingdom, and the United States.

Maintained by Ryan Riggs. Last updated 3 months ago.

9 stars 4.95 score 7 scripts

openwashdata

washr:Publication Toolkit for Water, Sanitation and Hygiene (WASH) Data

A toolkit to set up an R data package in a consistent structure. Automates tasks like tidy data export, data dictionary documentation, README and website creation, and citation management.

Maintained by Colin Walder. Last updated 5 months ago.

2 stars 4.95 score 7 scripts

qile0317

FastUtils:Fast, Readable Utility Functions

A wide variety of tools for general data analysis, wrangling, spelling, statistics, visualizations, package development, and more. All functions have vectorized implementations whenever possible. Exported names are designed to be readable, with longer names possessing short aliases.

Maintained by Qile Yang. Last updated 4 months ago.

scientific-computing utilities utility cpp

2 stars 4.95 score 2 scripts

vincentguyader

shiny2docker:Generate Dockerfiles for 'Shiny' Applications

Automates the creation of Dockerfiles for deploying 'Shiny' applications. By integrating with 'renv' for dependency management and leveraging Docker-based solutions, it simplifies the process of containerizing 'Shiny' apps, ensuring reproducibility and consistency across different environments. Additionally, it facilitates the setup of CI/CD pipelines for building Docker images on both GitLab and GitHub.

Maintained by Vincent Guyader. Last updated 2 months ago.

8 stars 4.90 score

mazamascience

MazamaSpatialPlots:Thematic Plots for Mazama Spatial Datasets

A suite of convenience functions for generating US state and county thematic maps using datasets from the MazamaSpatialUtils package.

Maintained by Jonathan Callahan. Last updated 2 months ago.

4.84 score 23 scripts

fvafrcu

document:Run 'roxygen2' on (Chunks of) Single Code Files

Have you ever been tempted to create 'roxygen2'-style documentation comments for one of your functions that was not part of one of your packages (yet)? This is exactly what this package is about: running 'roxygen2' on (chunks of) a single code file.

Maintained by Andreas Dominik Cullmann. Last updated 2 years ago.

4.80 score 127 scripts

mkearney

pkgverse:Build a Meta-Package Universe

Build your own universe of packages similar to the 'tidyverse' package <https://tidyverse.org/> with this meta-package creator. Create a package-verse, or meta package, by supplying a custom name for the collection of packages and the vector of desired package names to include– and optionally supply a destination directory, an indicator of whether to keep the created package directory, and/or a vector of verbs implement via the 'usethis' <http://usethis.r-lib.org/> package.

Maintained by Michael Wayne Kearney. Last updated 6 years ago.

package-manager tidyverse

121 stars 4.78 score 6 scripts

seewe

dataCompare:A 'shiny' App to Compare Two Data Frames

A tool developed with the 'Golem' framework which provides an easier way to check cells differences between two data frames. The user provides two data frames for comparison, selects IDs variables identifying each row of input data, then clicks a button to perform the comparison. Several 'R' package functions are used to describe the data and perform the comparison in the server of the application. The main ones are comparedf() from 'arsenal' and skim() from 'skimr'. For more details see the description of comparedf() from the 'arsenal' package and that of skim() from the 'skimr' package.

Maintained by Sergio Ewane Ebouele. Last updated 3 months ago.

2 stars 4.78 score 4 scripts

gadenbuie

shrtcts:Make Anything an RStudio Shortcut

An easily customizable method for creating RStudio addins from arbitrary R code. Use your own functions or call functions from other packages. Your shortcuts are stored in a YAML file in your home directory.

Maintained by Garrick Aden-Buie. Last updated 2 months ago.

addins-menu keyboard-shortcuts rstudio rstudio-addin rstudio-shortcut shortcuts

118 stars 4.77 score 3 scripts

bioc

methodical:Discovering genomic regions where methylation is strongly associated with transcriptional activity

DNA methylation is generally considered to be associated with transcriptional silencing. However, comprehensive, genome-wide investigation of this relationship requires the evaluation of potentially millions of correlation values between the methylation of individual genomic loci and expression of associated transcripts in a relatively large numbers of samples. Methodical makes this process quick and easy while keeping a low memory footprint. It also provides a novel method for identifying regions where a number of methylation sites are consistently strongly associated with transcriptional expression. In addition, Methodical enables housing DNA methylation data from diverse sources (e.g. WGBS, RRBS and methylation arrays) with a common framework, lifting over DNA methylation data between different genome builds and creating base-resolution plots of the association between DNA methylation and transcriptional activity at transcriptional start sites.

Maintained by Richard Heery. Last updated 2 months ago.

dnamethylation methylationarray transcription genomewideassociation software openjdk

4.65 score 14 scripts

techtonique

ahead:Time Series Forecasting with uncertainty quantification

Univariate and multivariate time series forecasting with uncertainty quantification.

Maintained by T. Moudiki. Last updated 1 months ago.

forecasting machine-learning predictive-modeling statistical-learning time-series time-series-forecasting uncertainty-quantification cpp

21 stars 4.63 score 51 scripts

ssa-statistical-team-projects

povmap:Extension to the 'emdi' Package

The R package 'povmap' supports small area estimation of means and poverty headcount rates. It adds several new features to the 'emdi' package (see "The R Package emdi for Estimating and Mapping Regionally Disaggregated Indicators" by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07>). These include new options for incorporating survey weights, ex-post benchmarking of estimates, two additional transformations, several new convenient functions to assist with reporting results, and a wrapper function to facilitate access from 'Stata'.

Maintained by Ifeanyi Edochie. Last updated 5 months ago.

1 stars 4.60 score 10 scripts

pik-piam

reporttransport:Reporting package for edgeTransport

This package contains edgeTransport-specific routines to report model results. The main functionality is to generate transport reporting variables in MIF format from a given edgeTransport model run folder or REMIND input data.

Maintained by Johanna Hoppe. Last updated 2 months ago.

4.60 score 9 scripts 3 dependents

inbo

INBOmd:Markdown Templates for INBO

Several templates to generate reports, presentations and posters.

Maintained by Thierry Onkelinx. Last updated 1 years ago.

bookdown rmarkdown xelatex

12 stars 4.52 score 11 scripts

pik-piam

piamValidation:Validation Tools for PIK-PIAM

The piamValidation package provides validation tools for the Potsdam Integrated Assessment Modelling environment.

Maintained by Pascal Weigmann. Last updated 4 days ago.

1 stars 4.49 score 13 scripts

hubverse-org

hubDevs:Utilities for Creating and Standardising Hubverse Packages

What the package does (one paragraph).

Maintained by Anna Krystalli. Last updated 3 months ago.

hubverse

4.43 score 3 scripts

anthonynorth

roxyglobals:'Roxygen2' Global Variable Declarations

Generate utils::globalVariables() from 'roxygen2' @global and @autoglobal tags.

Maintained by Anthony North. Last updated 2 years ago.

roxygen2

53 stars 4.42 score 2 scripts

setempler

miscset:Miscellaneous Tools Set

A collection of miscellaneous methods to simplify various tasks, including plotting, data.frame and matrix transformations, environment functions, regular expression methods, and string and logical operations, as well as numerical and statistical tools. Most of the methods are simple but useful wrappers of common base R functions, which extend S3 generics or provide default values for important parameters.

Maintained by Sven E. Templer. Last updated 8 years ago.

miscellaneous cpp

1 stars 4.40 score 50 scripts

annechao

MF.beta4:Measuring Ecosystem Multi-Functionality and Its Decomposition

Provide simple functions to (i) compute a class of multi-functionality measures for a single ecosystem for given function weights, (ii) decompose gamma multi-functionality for pairs of ecosystems and K ecosystems (K can be greater than 2) into a within-ecosystem component (alpha multi-functionality) and an among-ecosystem component (beta multi-functionality). In each case, the correlation between functions can be corrected for. Based on biodiversity and ecosystem function data, this software also facilitates graphics for assessing biodiversity-ecosystem functioning relationships across scales.

Maintained by Anne Chao. Last updated 4 months ago.

4.40 score 3 scripts

michbur

AmpGram:Prediction of Antimicrobial Peptides

Predicts antimicrobial peptides using random forests trained on the n-gram encoded peptides (10.3390/ijms21124310). The implemented algorithm can be accessed from both the command line and shiny-based GUI. The AmpGram model is too large for CRAN and it has to be downloaded separately from the repository: <https://github.com/michbur/AmpGramModel>.

Maintained by Michal Burdukiewicz. Last updated 3 years ago.

4 stars 4.38 score 5 scripts

helske

changer:Change R Package Name

Changing the name of an existing R package is annoying but common task especially in the early stages of package development. This package (mostly) automates this task.

Maintained by Jouni Helske. Last updated 3 years ago.

47 stars 4.37 score 2 scripts

rmi-pacta

pacta.data.preparation:Prepare Data for PACTA for Investors

This package provides tools to prepare input datasets to be run in the PACTA_analysis tool.

Maintained by CJ Yetman. Last updated 5 months ago.

climate-change pacta pactaverse sustainable-finance

1 stars 4.36 score 11 scripts 1 dependents

thinkr-open

papillon:Build And Highlight Package Documentation With Customized Templates

Helps creating company visual identity. Build your templates for your package vignettes, reports with {bookdown}, package presentation with {pkgdown}. Highlight your documentation in your projects. Allow for code folding.

Maintained by Sébastien Rochette. Last updated 2 years ago.

11 stars 4.34 score 4 scripts

kserkcho

SCEM:Splitting-Coalescence-Estimation Method

We introduce improved methods for statistically assessing birth seasonality and intra-annual variation. The first method we propose is a new idea that uses a nonparametric clustering procedure to group individuals with similar time series data and estimate birth seasonality based on the clusters. One can use the function SCEM() to implement this method. The second method estimates input parameters for use with a previously-developed parametric approach (Tornero et al., 2013). The relevant code for this approach is makeFits_OLS(), while makeFits_initial() is the code to implement the same method but with given initial conditions for two parameters. The latter can be used to show the disadvantage of the existing approach. One can use the function makeFits() to generate parametric birth seasonality estimates using either initialization. Detailed description can be found here: Chazin Hannah, Soudeep Deb, Joshua Falk, and Arun Srinivasan. (2019) "New Statistical Approaches to Intra-Individual Isotopic Analysis and Modeling Birth Seasonality in Studies of Herd Animals." <doi:10.1111/arcm.12432>.

Maintained by Kyung Serk Cho. Last updated 4 years ago.

scem

4.30 score 3 scripts

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 2 months ago.

1 stars 4.30 score

bioc

oppti:Outlier Protein and Phosphosite Target Identifier

The aim of oppti is to analyze protein (and phosphosite) expressions to find outlying markers for each sample in the given cohort(s) for the discovery of personalized actionable targets.

Maintained by Abdulkadir Elmas. Last updated 5 months ago.

proteomics regression differentialexpression biomedicalinformatics genetarget geneexpression network

2 stars 4.30 score 2 scripts

green-striped-gecko

dartRverse:Install and Load the 'dartRverse' Suits of Packages

Provides a single function that supports the installation of all packages belonging to the 'dartRverse'. The 'dartRverse' is a set of packages that work together to analyse SNP (single nuclear polymorphism) data. All packages aim to have a similar 'look and feel' and are based on the same type of data structure ('genlight'), with additional metadata for loci and individuals (samples). For more information visit the 'GitHub' pages <https://github.com/green-striped-gecko/dartRverse>.

Maintained by Bernd Gruber. Last updated 18 days ago.

2 stars 4.27 score 47 scripts

eblondel

atom4R:Tools to Handle and Publish Metadata as 'Atom' XML Format

Provides tools to read/write/publish metadata based on the 'Atom' XML syndication format. This includes support of 'Dublin Core' XML implementation, and a client to API(s) implementing the 'AtomPub' - 'SWORD' API specification.

Maintained by Emmanuel Blondel. Last updated 1 months ago.

5 stars 4.18 score 3 scripts 2 dependents

ingorohlfing

qcapower:Estimate Power and Required Sample Size in QCA

Researchers working with Qualitative Comparative Analysis (QCA) can use the package to estimate power of a sufficient term using permutation tests. A term can be anything: A condition, conjunction or disjunction of any combination of these. The package further allows users to plot the estimation results and to estimate the number of cases required to achieve a certain level of power, given a prespecified null and alternative hypothesis. Reference for the article introducing power estimation for QCA is: Rohlfing, Ingo (2018) <doi:10.1017/pan.2017.30> (ungated version: <doi:10.17605/OSF.IO/PC4DF>).

Maintained by Ingo Rohlfing. Last updated 5 years ago.

3 stars 4.18 score 7 scripts

bioc

BUMHMM:Computational pipeline for computing probability of modification from structure probing experiment data

This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.

Maintained by Alina Selega. Last updated 5 months ago.

immunooncology geneticvariability transcription geneexpression generegulation coverage genetics structuralprediction transcriptomics bayesian classification featureextraction hiddenmarkovmodel regression rnaseq sequencing

4.15 score 14 scripts

inbo

protocolhelper:Helper Functions to Manage Protocols

Helper functions to manage INBO protocols.

Maintained by Hans Van Calster. Last updated 12 days ago.

5 stars 4.09 score 55 scripts

devopifex

component:Components for 'Shiny'

'Components' for 'Shiny', similar to 'Shiny' modules.

Maintained by John Coene. Last updated 1 years ago.

27 stars 4.04 score 82 scripts

wahani

saeRobust:Robust Small Area Estimation

Methods to fit robust alternatives to commonly used models used in Small Area Estimation. The methods here used are based on best linear unbiased predictions and linear mixed models. At this time available models include area level models incorporating spatial and temporal correlation in the random effects.

Maintained by Sebastian Warnholz. Last updated 1 years ago.

openblas cpp

1 stars 4.03 score 12 scripts 3 dependents

bioc

rifiComparative:'rifiComparative' compares the output of rifi from two different conditions.

'rifiComparative' is a continuation of rifi package. It compares two conditions output of rifi using half-life and mRNA at time 0 segments. As an input for the segmentation, the difference between half-life of both condtions and log2FC of the mRNA at time 0 are used. The package provides segmentation, statistics, summary table, fragments visualization and some additional useful plots for further anaylsis.

Maintained by Loubna Youssar. Last updated 5 months ago.

rnaseq differentialexpression generegulation transcriptomics microarray software

4.00 score

bioc

biocroxytest:Handle Long Tests in Bioconductor Packages

This package provides a roclet for roxygen2 that identifies and processes code blocks in your documentation marked with `@longtests`. These blocks should contain tests that take a long time to run and thus cannot be included in the regular test suite of the package. When you run `roxygen2::roxygenise` with the `longtests_roclet`, it will extract these long tests from your documentation and save them in a separate directory. This allows you to run these long tests separately from the rest of your tests, for example, on a continuous integration server that is set up to run long tests.

Maintained by Francesc Catala-Moll. Last updated 5 months ago.

software infrastructure

1 stars 4.00 score 3 scripts

covid19r

covid19swiss:COVID-19 Cases in Switzerland and Principality of Liechtenstein

Provides a daily summary of the Coronavirus (COVID-19) cases in Switzerland cantons and Principality of Liechtenstein. Data source: Specialist Unit for Open Government Data Canton of Zurich <https://www.zh.ch/de/politik-staat/opendata.html>.

Maintained by Rami Krispin. Last updated 4 years ago.

4.00 score 8 scripts

openpharma

roxylint:Lint 'roxygen2'-Generated Documentation

Provides formatting linting to 'roxygen2' tags. Linters report 'roxygen2' tags that do not conform to a standard style. These linters can be a helpful check for building more consistent documentation and to provide reminders about best practices or checks for typos. Default linting suites are provided for common style guides such as the one followed by the 'tidyverse', though custom linters can be registered by other packages or be custom-tailored to a specific package.

Maintained by Doug Kelkhoff. Last updated 1 years ago.

linter roxygen2

17 stars 3.93 score

ices-tools-prod

msy:Estimation of Equilibrium Reference Points for Fsisheries

Methods to estimate equilibrium reference points for fisheries data. Currently data must be converted into FLStock objects of the FLR (Fisheries Library in R) style, defined in the R package FLCore.

Maintained by Colin Millar. Last updated 2 years ago.

13 stars 3.91 score 42 scripts

repboxr

repboxDB:Functions for exported repbox data

Functions for exported repbox data

Maintained by Sebastian Kranz. Last updated 4 months ago.

3.91 score 8 scripts 9 dependents

biogenies

CancerGram:Prediction of Anticancer Peptides

Predicts anticancer peptides using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI. The CancerGram model is too large for CRAN and it has to be downloaded separately from the repository: <https://github.com/BioGenies/CancerGramModel>. For more information see: Burdukiewicz et al. (2020) <doi:10.3390/pharmaceutics12111045>.

Maintained by Michal Burdukiewicz. Last updated 4 years ago.

anticancer-peptides bioinformatics k-mer n-gram peptide-identification random-forests

4 stars 3.90 score 3 scripts

richelbilderbeek

pureseqtmr:Predict Transmembrane Protein Topology

Proteins reside in either the cell plasma or in the cell membrane. A membrane protein goes through the membrane at least once. Given the amino acid sequence of a membrane protein, the tool 'PureseqTM' (<https://github.com/PureseqTM/pureseqTM_package>, as described in "Efficient And Accurate Prediction Of Transmembrane Topology From Amino acid sequence only.", Wang, Qing, et al (2019), <doi:10.1101/627307>), can predict the topology of a membrane protein. This package allows one to use 'PureseqTM' from R.

Maintained by Richèl J.C. Bilderbeek. Last updated 2 years ago.

cpp

1 stars 3.90 score 16 scripts

wch

bisectr:Tools to Find Bad Commits with 'git bisect'

Tools to find bad commits with git bisect. See https://github.com/wch/bisectr for examples and test script templates.

Maintained by Winston Chang. Last updated 10 years ago.

16 stars 3.90 score 2 scripts

openpharma

roxytypes:Typed Parameter Tags for Integration with 'roxygen2'

Provides typed parameter documentation tags for integration with 'roxygen2'. Typed parameter tags provide a consistent interface for annotating expected types for parameters and returned values. Tools for converting from existing styles are also provided to easily adapt projects which implement typed documentation by convention rather than tag. Use the default format or provide your own.

Maintained by Doug Kelkhoff. Last updated 6 months ago.

roxygen2 type-hints

5 stars 3.88 score 1 scripts

mrcaseb

personalr:Automated Personal Package Setup

Functions to setup a personal R package that attaches given libraries and exports personal helper functions.

Maintained by Sebastian Carl. Last updated 3 years ago.

13 stars 3.81 score 1 scripts

undocumeantit

roxyPackage:Utilities to Automate Package Builds

The intention of this package is to make packaging R code as easy as possible. 'roxyPackage' uses tools from the 'roxygen2' package to generate documentation. It also automatically generates and updates files like *-package.R, DESCRIPTION, CITATION, ChangeLog and NEWS.Rd. Building packages supports source format, as well as several binary formats (MS Windows, Mac OS X, Debian GNU/Linux) if the package contains pure R code only. The packages built are stored in a fully functional local R package repository which can be synced to a web server to share them with others. This includes the generation of browsable HTML pages similar to CRAN, with support for RSS feeds from the ChangeLog. Please read the vignette for a more detailed explanation by example.

Maintained by m.eik michalke. Last updated 8 months ago.

11 stars 3.74 score 1 scripts

rmi-pacta

pactaverse:Easily Install and Load the 'PACTA-verse'

The 'pactaverse' is a set of packages that work to help R users implement various functionality related to the PACTA open source project.

Maintained by Jackson Hoffart. Last updated 4 months ago.

6 stars 3.73 score 3 scripts

jimhester

autoinst:Auto Install Packages

Automatically install packages when they are missing.

Maintained by Jim Hester. Last updated 7 years ago.

53 stars 3.72 score

pik-piam

mredgebuildings:Prepare data to be used by the EDGE-Buildings model

Prepare data to be used by the EDGE-Buildings model.

Maintained by Robin Hasse. Last updated 17 days ago.

3.72 score

repboxr

repboxReg:Repbox module for analysing regressions

Repbox module for analysing regressions

Maintained by Sebastian Kranz. Last updated 2 months ago.

3.71 score 6 scripts 2 dependents

sigbertklinke

smvgraph:Visualization and Clustering of Data in a Shiny App

Various visualisations of univariate and multivariate graphs (e.g. mosaic diagram, scatterplot matrix, Andrews curves, parallel coordinate diagram, radar diagram and Chernoff plots) as well as clustering methods (e.g. k-means, agglomerative, EM clustering and DBSCAN) are implemented as a Shiny app. The app allows interactive changes, e.g. of the order of variables. It is intended for use in teaching.

Maintained by Sigbert Klinke. Last updated 2 years ago.

3.70 score

kelliejarcher

ordinalbayes:Bayesian Ordinal Regression for High-Dimensional Data

Provides a function for fitting various penalized Bayesian cumulative link ordinal response models when the number of parameters exceeds the sample size. These models have been described in Zhang and Archer (2021) <doi:10.1186/s12859-021-04432-w>.

Maintained by Kellie J. Archer. Last updated 3 years ago.

jags cpp

1 stars 3.70 score 1 scripts

norawuerz

saeTrafo:Transformations for Unit-Level Small Area Models

The aim of this package is to offer new methodology for unit-level small area models under transformations and limited population auxiliary information. In addition to this new methodology, the widely used nested error regression model without transformations (see "An Error-Components Model for Prediction of County Crop Areas Using Survey and Satellite Data" by Battese, Harter and Fuller (1988) <doi:10.1080/01621459.1988.10478561>) and its well-known uncertainty estimate (see "The estimation of the mean squared error of small-area estimators" by Prasad and Rao (1990) <doi:10.1080/01621459.1995.10476570>) are provided. In this package, the log transformation and the data-driven log-shift transformation are provided. If a transformation is selected, an appropriate method is chosen depending on the respective input of the population data: Individual population data (see "Empirical best prediction under a nested error model with log transformation" by Molina and Martín (2018) <doi:10.1214/17-aos1608>) but also aggregated population data (see "Estimating regional income indicators under transformations and access to limited population auxiliary information" by Würz, Schmid and Tzavidis <unpublished>) can be entered. Especially under limited data access, new methodologies are provided in saeTrafo. Several options are available to assess the used model and to judge, present and export its results. For a detailed description of the package and the methods used see the corresponding vignette.

Maintained by Nora Würz. Last updated 10 months ago.

1 stars 3.70 score

drordas

D2MCS:Data Driving Multiple Classifier System

Provides a novel framework to able to automatically develop and deploy an accurate Multiple Classifier System based on the feature-clustering distribution achieved from an input dataset. 'D2MCS' was developed focused on four main aspects: (i) the ability to determine an effective method to evaluate the independence of features, (ii) the identification of the optimal number of feature clusters, (iii) the training and tuning of ML models and (iv) the execution of voting schemes to combine the outputs of each classifier comprising the Multiple Classifier System.

Maintained by Miguel Ferreiro-Díaz. Last updated 3 years ago.

openjdk

3.70 score

vasileioskarapoulios

LDNN:Longitudinal Data Neural Network

This is a Neural Network regression model implementation using 'Keras', consisting of 10 Long Short-Term Memory layers that are fully connected along with the rest of the inputs.

Maintained by Vasileios Karapoulios. Last updated 4 years ago.

3.70 score 6 scripts

thinkr-open

testdown:'testhat' Results to Bookdown

Turn your 'testthat' results a Bookdown.

Maintained by Colin Fay. Last updated 2 years ago.

27 stars 3.61 score 3 scripts

melodyaowen

crt2power:Designing Cluster-Randomized Trials with Two Continuous Co-Primary Outcomes

Provides methods for powering cluster-randomized trials with two continuous co-primary outcomes using five key design techniques. Includes functions for calculating required sample size and statistical power. For more details on methodology, see Owen et al. (2025) <doi:10.1002/sim.70015>, Yang et al. (2022) <doi:10.1111/biom.13692>, Pocock et al. (1987) <doi:10.2307/2531989>, Vickerstaff et al. (2019) <doi:10.1186/s12874-019-0754-4>, and Li et al. (2020) <doi:10.1111/biom.13212>.

Maintained by Melody Owen. Last updated 17 days ago.

3.60 score 2 scripts

bryanhanson

roxut:Document Unit Tests Roxygen-Style

Much as 'roxygen2' allows one to document functions in the same file as the function itself, 'roxut' allows one to write the unit tests in the same file as the function. Once processed, the unit tests are moved to the appropriate directory. Currently supports 'testthat' and 'tinytest' frameworks. The 'roxygen2' package provides much of the infrastructure.

Maintained by Bryan A. Hanson. Last updated 2 years ago.

8 stars 3.60 score

repboxr

repboxHtml:HTML reports for repbox

HTML reports for repbox

Maintained by Sebastian Kranz. Last updated 2 months ago.

3.59 score 10 scripts 2 dependents

jfwambaugh

invivoPKfit:Fits Toxicokinetic Models to In Vivo PK Data Sets

Takes in vivo toxicokinetic concentration-time data and fits parameters of 1-compartment and 2-compartment models for each chemical. These methods are described in detail in "Informatics for Toxicokinetics" (submitted).

Maintained by John Wambaugh. Last updated 7 days ago.

3.48 score 4 scripts

achateigner

anyLib:Install and Load Any Package from CRAN, Bioconductor or Github

Made to make your life simpler with packages, by installing and loading a list of packages, whether they are on CRAN, Bioconductor or github. For github, if you do not have the full path, with the maintainer name in it (e.g. "achateigner/topReviGO"), it will be able to load it but not to install it.

Maintained by Aurelien Chateigner. Last updated 6 years ago.

3 stars 3.48 score 7 scripts

flalom

drugsens:Automated Analysis of 'QuPath' Output Data and Metadata Extraction

A comprehensive toolkit for analyzing microscopy data output from 'QuPath' software. Provides functionality for automated data processing, metadata extraction, and statistical analysis of imaging results. The methodology implemented in this package is based on Labrosse et al. (2024) <doi:10.1016/j.xpro.2024.103274> "Protocol for quantifying drug sensitivity in 3D patient-derived ovarian cancer models", which describes the complete workflow for drug sensitivity analysis in patient-derived cancer models.

Maintained by Flavio Lombardo. Last updated 2 months ago.

data-analysis image-processing qupath workflow

3.48 score 1 scripts

fastgitorg

fgitR:Using 'FastGit' to Accelerate the Access to 'GitHub'

'FastGit' <https://doc.fastgit.org/> works like a mirror of 'GitHub' to make significant acceleration. 'fgitR' is a package to do git operation with 'FastGit' automatically.

Maintained by Han Chen. Last updated 3 years ago.

6 stars 3.48 score 4 scripts

ifpri

GFSir:Global Food Security analysis using IMPACT model and R

Global Food Security analysis using IMPACT model and R.

Maintained by Abhijeet Mishra. Last updated 6 days ago.

3.40 score 1 scripts

bristol-vaccine-centre

testerror:Uncertainty in Multiplex Panel Testing

Provides methods to support the estimation of epidemiological parameters based on the results of multiplex panel tests.

Maintained by Robert Challen. Last updated 12 months ago.

1 stars 3.40 score 4 scripts

ropensci

ReLTER:An Interface for the eLTER Community

ReLTER provides access to DEIMS-SDR (https://deims.org/), and allows interaction with data and software implemented by eLTER Research Infrastructure (RI) thus improving data sharing among European LTER projects. ReLTER uses the R language to access and interact with the DEIMS-SDR archive of information shared by the Long Term Ecological Research (LTER) network. This package grew within eLTER H2020 as a major project that will help advance the development of European Long-Term Ecosystem Research Infrastructures (eLTER RI - https://elter-ri.eu). The ReLTER package functions in particular allow to: - retrieve the information about entities (e.g. sites, datasets, and activities) shared by DEIMS-SDR (see e.g. get_site_info function); - interact with the [ODSEurope](maps.opendatascience.eu) starting with the dataset shared by [DEIMS-SDR](https://deims.org/) (see e.g. [get_site_ODS](https://docs.ropensci.org/ReLTER/reference/get_site_ODS.html) function); - use the eLTER site informations to download and crop geospatial data from other platforms (see e.g. get_site_ODS function); - improve the quality of the dataset (see e.g. get_id_worms). Functions currently implemented are derived from discussions of the needs among the eLTER users community. The ReLTER package will continue to follow the progress of eLTER-RI and evolve, adding new tools and improvements as required.

Maintained by Alessandro Oggioni. Last updated 1 years ago.

biodiversity-informatics data-science ecology elter research-infrastructure

12 stars 3.38 score 4 scripts

repboxr

repboxRun:Run repbox analyses

Run repbox analyses

Maintained by Sebastian Kranz. Last updated 2 months ago.

3.36 score 11 scripts 1 dependents

wahani

REPLesentR:Presentations in the REPL

Create presentations and display them inside the R 'REPL' (Read-Eval-Print loop), aka the R console. Presentations can be written in 'RMarkdown' or any other text format. A set of convenient navigation options as well as code evaluation during a presentation is provided. It is great for tech talks with live coding examples and tutorials. While this is not a replacement for standard presentation formats, it's old-school looks might just be what sets it apart. This project has been inspired by the 'REPLesent' project for presentations in the 'Scala' 'REPL'.

Maintained by Sebastian Warnholz. Last updated 5 years ago.

4 stars 3.30 score 2 scripts

ehmarwan

Elja:Linear, Logistic and Generalized Linear Models Regressions for the EnvWAS/EWAS Approach

Tool for Environment-Wide Association Studies (EnvWAS / EWAS) which are repeated analysis. It includes three functions. One function for linear regression, a second for logistic regression and a last one for generalized linear models.

Maintained by Marwan El Homsi. Last updated 2 years ago.

2 stars 3.30 score 2 scripts

bioc

Rmmquant:RNA-Seq multi-mapping Reads Quantification Tool

RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.

Maintained by Zytnicki Matthias. Last updated 5 months ago.

geneexpression transcription zlib cpp

3.30 score 5 scripts

devopifex

windy:'Tailwind' for 'Shiny'

'Tailwind' for 'Shiny'.

Maintained by John Coene. Last updated 2 years ago.

38 stars 3.28 score

repboxr

repboxMap:Mapping information from article and run supplement. Mainly (regression) tables.

This package should use as input only information stored in regdb tables.

Maintained by Sebastian Kranz. Last updated 2 months ago.

3.26 score 1 scripts 2 dependents

jsta

nesRdata:National Eutrophication Survey Data

Serves data from the United States Environmental Protection Agency (USEPA) National Eutrophication Survey <https://www.epa.gov/national-aquatic-resource-surveys>.

Maintained by Jemma Stachelek. Last updated 1 years ago.

hydrology water-quality

3 stars 3.18 score 9 scripts

curycu

valuemap:Making Choropleth Map

You can easily visualize your 'sf' polygons or data.frame with h3 address. While 'leaflet' package is too raw for data analysis, this package can save data analysts' efforts & time with pre-set visualize options.

Maintained by Huncheol Ha. Last updated 2 years ago.

geospatial leaflet sf

3 stars 3.18 score 5 scripts

coreofscience

margaret:Scientometric Analysis Minciencias

The target of 'margaret' is help to extract data from Minciencias to analyze scientific production in Colombia.

Maintained by Bryan Arias. Last updated 2 years ago.

3 stars 3.18 score 4 scripts

ifpri

DOORMAT:Data processor for IMPACT model (Data prOcessor fOR iMpAcT)

Data processor for IMPACT model.

Maintained by Abhijeet Mishra. Last updated 10 months ago.

3.18 score 5 dependents

zhuxr11

roclang:Functions for Diffusing Function Documentations into 'Roxygen' Comments

Efficient diffusing of content across function documentations. Sections, parameters or dot parameters are extracted from function documentations and turned into valid Rd character strings, which are ready to diffuse into the 'roxygen' comments of another function by inserting inline code.

Maintained by Xiurui Zhu. Last updated 2 years ago.

2 stars 3.00 score 2 scripts

jimbrig

jimstools:Tools for R

What the package does (one paragraph).

Maintained by Jimmy Briggs. Last updated 3 years ago.

functions personal utility

2 stars 3.00 score 2 scripts

yhankcheng

psdr:Use Time Series to Generate and Compare Power Spectral Density

Functions that allow you to generate and compare power spectral density (PSD) plots given time series data. Fast Fourier Transform (FFT) is used to take a time series data, analyze the oscillations, and then output the frequencies of these oscillations in the time series in the form of a PSD plot.Thus given a time series, the dominant frequencies in the time series can be identified. Additional functions in this package allow the dominant frequencies of multiple groups of time series to be compared with each other. To see example usage with the main functions of this package, please visit this site: <https://yhhc2.github.io/psdr/articles/Introduction.html>. The mathematical operations used to generate the PSDs are described in these sites: <https://www.mathworks.com/help/matlab/ref/fft.html>. <https://www.mathworks.com/help/signal/ug/power-spectral-density-estimates-using-fft.html>.

Maintained by Yong-Han Hank Cheng. Last updated 4 years ago.

3.00 score 4 scripts

uribo

textlintr:Natural Language Linter Tools for 'R Markdown' and R Code

What the package does (one paragraph).

Maintained by Shinya Uryu. Last updated 2 years ago.

lint natural-language-processing

9 stars 2.95 score 4 scripts

zkamvar

beaverdown:An updated R Markdown thesis template for Oregon State University using the bookdown package

Using the bookdown package and LaTeX and Word thesis templates from Oregon State University, this package was derived from Chester Ismay's package "thesisdown"

Maintained by Zhian N. Kamvar. Last updated 8 years ago.

17 stars 2.93 score 2 scripts

iame-researchcenter

PFIM:Population Fisher Information Matrix

Evaluate or optimize designs for nonlinear mixed effects models using the Fisher Information matrix. Methods used in the package refer to Mentré F, Mallet A, Baccar D (1997) <doi:10.1093/biomet/84.2.429>, Retout S, Comets E, Samson A, Mentré F (2007) <doi:10.1002/sim.2910>, Bazzoli C, Retout S, Mentré F (2009) <doi:10.1002/sim.3573>, Le Nagard H, Chao L, Tenaillon O (2011) <doi:10.1186/1471-2148-11-326>, Combes FP, Retout S, Frey N, Mentré F (2013) <doi:10.1007/s11095-013-1079-3> and Seurat J, Tang Y, Mentré F, Nguyen TT (2021) <doi:10.1016/j.cmpb.2021.106126>.

Maintained by Romain Leroux. Last updated 5 months ago.

2.78 score 9 scripts

burgette

OVtool:Omitted Variable Tool

This tool was designed to assess the sensitivity of research findings to omitted variables when estimating causal effects using propensity score (PS) weighting. This tool produces graphics and summary results that will enable a researcher to quantify the impact an omitted variable would have on their results. Burgette et al. (2021) describe the methodology behind the primary function in this package, ov_sim. The method is demonstrated in Griffin et al. (2020) <doi:10.1016/j.jsat.2020.108075>.

Maintained by Lane Burgette. Last updated 3 years ago.

2.78 score 12 scripts

repboxr

repboxCodeText:Extracting purely text based information from supplement code

Extracting purely text based information from supplement code

Maintained by Sebastian Kranz. Last updated 11 months ago.

2.78 score 1 scripts 2 dependents

terminological

ggrrr:Addressing Annoyances and Irritations

Visualisation hacks, tabular data helpers, fonts, caching, tidy data functions. It is an swiss army knife, jack of all trades.

Maintained by Robert Challen. Last updated 10 months ago.

1 stars 2.74 score 11 scripts

repboxr

repboxStata:Repbox analysis of stata scripts in reproduction packages

Repbox analysis of stata scripts in reproduction packages

Maintained by Sebastian Kranz. Last updated 2 months ago.

2.73 score 4 scripts 2 dependents

ifpri

ARIA:App for IMPACT (App foR ImpAct)

App for IMPACT (App foR ImpAct).

Maintained by Abhijeet Mishra. Last updated 10 months ago.

2.70 score 6 scripts

sciviews

exploreit:Exploratory Data Analysis for 'SciViews::R'

Multivariate analysis and data exploration for the 'SciViews::R' dialect.

Maintained by Philippe Grosjean. Last updated 11 months ago.

multivariate-analysis sciviews statistical-methods

2.70 score 4 scripts

ifpri

KIRAN:Package for setting up Key IMPACT R-Archive Network suite of packages

Establishes the KIRAN suite of R based packages.

Maintained by Abhijeet Mishra. Last updated 2 years ago.

2.70 score

soodoku

rdomains:Get the Category of Content Hosted by a Domain

Get the category of content hosted by a domain. Use Shallalist <http://shalla.de/>, Virustotal (which provides access to lots of services) <https://www.virustotal.com/>, Alexa <https://aws.amazon.com/awis/>, DMOZ <https://curlie.org/>, University Domain list <https://github.com/Hipo/university-domains-list> or validated machine learning classifiers based on Shallalist data to learn about the kind of content hosted by a domain.

Maintained by Gaurav Sood. Last updated 3 years ago.

2.70 score 7 scripts

vtshen

AHM:Additive Heredity Model: Method for the Mixture-of-Mixtures Experiments

An implementation of the additive heredity model for the mixture-of-mixtures experiments of Shen et al. (2019) in Technometrics <doi:10.1080/00401706.2019.1630010>. The additive heredity model considers an additive structure to inherently connect the major components with the minor components. The additive heredity model has a meaningful interpretation for the estimated model because of the hierarchical and heredity principles applied and the nonnegative garrote technique used for variable selection.

Maintained by Sumin Shen. Last updated 6 years ago.

2.70 score 2 scripts

obrienjoey

spRingsteen:All Things Data and Springsteen

An R data package containing setlists from all Bruce Springsteen concerts over 1973-2021. Also includes all his song details such as lyrics and albums. Data extracted from: <http://brucebase.wikidot.com/>.

Maintained by Joey OBrien. Last updated 1 years ago.

2.70 score 1 scripts

pik-piam

edgeTrpLib:Helper functions for EDGE transport calculations

This package is highly specialized and created solely to not duplicate helper functions.

Maintained by Alois Dirnaichner. Last updated 3 years ago.

2.54 score 5 scripts

stephenturner

Tverse:Meta package that installs my most commonly used packages

Meta package that installs my most commonly used packages.

Maintained by Stephen Turner. Last updated 7 months ago.

6 stars 2.48 score

repboxr

repboxR:Repbox for R code files in code supplements

Repbox for R code files in code supplements

Maintained by Sebastian Kranz. Last updated 1 years ago.

2.48 score 2 dependents

bentaylor1

miscFuncs:Miscellaneous Useful Functions Including LaTeX Tables, Kalman Filtering, QQplots with Simulation-Based Confidence Intervals, Linear Regression Diagnostics and Development Tools

Implementing various things including functions for LaTeX tables, the Kalman filter, QQ-plots with simulation-based confidence intervals, linear regression diagnostics, web scraping, development tools, relative risk and odds rati, GARCH(1,1) Forecasting.

Maintained by Benjamin M. Taylor. Last updated 5 months ago.

2.48 score 8 scripts

forecastingresearch

aggutils:Utilities for Aggregating Probabilistic Forecasts

Provides several methods for aggregating probabilistic forecasts. You have a group of people who have made probabilistic forecasts for the same event. You want to take advantage of the "wisdom of the crowd" and combine these forecasts in some sensible way. This package provides implementations of several strategies, including geometric mean of odds, an extremized aggregate (Neyman, Roughgarden (2021) <doi:10.1145/3490486.3538243>), and "high-density trimmed mean" (Powell et al. (2022) <doi:10.1037/dec0000191>).

Maintained by Molly Hickman. Last updated 1 years ago.

3 stars 2.48 score 3 scripts

barryzee

NoviceDeveloperResources:Resources to Assist Novice Developers

Assist novice developers when preparing a single package or a set of integrated packages to submit to CRAN. Automate the following individual or batch processing: check local source packages; build local .tar.gz source files; install packages from local .tar.gz files; detect conflicts between function names in the environment.

Maintained by Barry Zeeberg. Last updated 11 months ago.

2.48 score 1 dependents

ices-tools-prod

fisheryO:Fisheries Overviews for ICES Advice

Functions that work with International Council for the Exploration of the Sea (ICES) web services and databases to collate, aggregate, and plot Fisheries Overview products.

Maintained by Scott Large. Last updated 7 years ago.

3 stars 2.45 score 19 scripts

cran

wishmom:Compute Moments Related to Beta-Wishart and Inverse Beta-Wishart Distributions

Provides functions for computing moments and coefficients related to the Beta-Wishart and Inverse Beta-Wishart distributions. It includes functions for calculating the expectation of matrix-valued functions of the Beta-Wishart distribution, coefficient matrices C_k and H_k, expectation of matrix-valued functions of the inverse Beta-Wishart distribution, and coefficient matrices \tilde{C}_k and \tilde{H}_k. For more details, refer Hillier and Kan (2024) <https://www-2.rotman.utoronto.ca/~kan/papers/wishmom.pdf>, "On the Expectations of Equivariant Matrix-valued Functions of Wishart and Inverse Wishart Matrices".

Maintained by Raymond Kan. Last updated 7 months ago.

2.30 score

barryzee

SherlockHolmes:Building a Concordance of Terms in a Series of Texts

Compute the frequency distribution of a search term in a series of texts. For example, Arthur Conan Doyle wrote a total of 60 Sherlock Holmes stories, comprised of 54 short stories and 4 longer novels. I wanted to test my own subjective impression that, in many of the stories, Sherlock Holmes' popularity was used as bait to induce the reader to read a story that is essentially not primarily a Sherlock Holmes story. I used the term "Holmes" as a search pattern, since Watson would frequently address him by name, or use his name to describe something that he was doing. My hypothesis is that the frequency distribution of the search pattern "Holmes" is a good proxy for the degree to which a story is or is not truly a Sherlock Holmes story. The results are presented in a manuscript that is available as a vignette and online at <https://barryzee.github.io/Concordance/index.html>.

Maintained by Barry Zeeberg. Last updated 2 years ago.

2.30 score

cran

smarter:A Collection of Modified R Functions to Make Basic Coding More Convenient

A collection of recycled and modified R functions to aid in file manipulation, data exploration, wrangling, optimization, and object manipulation. Other functions aid in convenient data visualization, loop progression, software packaging, and installation.

Maintained by Paul Little. Last updated 1 months ago.

cpp openmp

2.26 score 3 dependents

davidruvolo51

rdConvert:Convert Rd files to Markdown files loaded with YAML

As R6 class for converting Rd files to markdown with YAML headers. This may be useful if you wish to use package documentation in static site generators outside of the R ecosystem (e.g., React, Vue, Svelte, Gatsby, etc.). By default, Rd files are rendered into their own directory with an independent `index.md` file. The Rd name is parsed and set as the child directory name.

Maintained by David Ruvolo. Last updated 4 years ago.

gatsby-template package-development rmarkdown rmarkdown-websites workflow

3 stars 2.18 score

pik-piam

mrtutorial:Tutorial Package For Madrat Package Library

Example package of mr- world libraries, in conjunction with MAgPIE MADRat tutorial. For more information please see: https://github.com/magpiemodel/tutorials/tree/master/madrat .

Maintained by David Meng-Chuen Chen. Last updated 12 months ago.

2.18 score 2 scripts

ifpri

reportIMPACT:IMPACT outputs R package for IMPACT version 3.x

Common output routines for extracting results from the IMPACT framework (versions 3.x).

Maintained by Abhijeet Mishra. Last updated 1 years ago.

2.18 score 1 dependents

craig-pal

activPAL:Advanced Processing and Chart Generation from activPAL Events Files

Contains functions to generate pre-defined summary statistics from activPAL events files <http:www.palt.com>. The package also contains functions to produce informative graphics that visualise physical activity behaviour and trends. This includes generating graphs that align physical activity behaviour with additional time based observations described by other data sets, such as sleep diaries and continuous glucose monitoring data.

Maintained by Craig Speirs. Last updated 6 years ago.

2.04 score 11 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 4 months ago.

openjdk

2.00 score 1 scripts

cran

SMASH:Subclone Multiplicity Allocation and Somatic Heterogeneity

Cluster user-supplied somatic read counts with corresponding allele-specific copy number and tumor purity to infer feasible underlying intra-tumor heterogeneity in terms of number of subclones, multiplicity, and allocation (Little et al. (2019) <doi:10.1186/s13073-019-0643-9>).

Maintained by Paul Little. Last updated 1 months ago.

openblas cpp openmp

2.00 score

barryzee

NoviceDeveloperResources2:Further Resources to Assist Novice Developers

Assist novice developers when preparing a single package or a set of integrated packages to submit to CRAN. Provide additional resources to facilitate the automation of the following individual or batch processing: check local source packages; build local .tar.gz source files; install packages from local .tar.gz files; detect conflicts between function names in the environment. The additional resources include determining the identity and ordering of the packages to process when updating an imported package.

Maintained by Barry Zeeberg. Last updated 11 months ago.

2.00 score

cran

CSeQTL:Cell Type-Specific Expression Quantitative Trail Loci Mapping

Perform bulk and cell type-specific expression quantitative trail loci mapping with our novel method (Little et al. (2023) <doi:10.1038/s41467-023-38795-w>).

Maintained by Paul Little. Last updated 25 days ago.

openblas cpp openmp

2.00 score

cwru-sdle

FAIRmaterials:Ontology Tools with Data FAIRification in Development

Translates several CSV files with ontological terms and corresponding data into RDF triples. These RDF triples are stored in OWL and JSON-LD files, facilitating data accessibility, interoperability, and knowledge unification. The triples are also visualized in a graph saved as an SVG. The input CSVs must be formatted with a template from a public Google Sheet; see README or vignette for more information. This is a tool is used by the SDLE Research Center at Case Western Reserve University to create and visualize material science ontologies, and it includes example ontologies to demonstrate its capabilities. This work was supported by the U.S. Department of Energy’s Office of Energy Efficiency and Renewable Energy (EERE) under Solar Energy Technologies Office (SETO) Agreement Numbers E-EE0009353 and DE-EE0009347, Department of Energy (National Nuclear Security Administration) under Award Number DE-NA0004104 and Contract number B647887, and U.S. National Science Foundation Award under Award Number 2133576.

Maintained by Roger H French. Last updated 9 months ago.

2.00 score 8 scripts

barryzee

runExamplesWrapper:Wrapper for 'run_examples()'

Captures errors encountered when running 'run_examples()', and processes and archives them. The function 'run_examples()' within the 'devtools' package allows batch execution of all of the examples within a given package. This is much more convenient than testing each example manually. However, a major inconvenience is that if an error is encountered, the program stops and does not complete testing the remaining examples. Also, there is not a systematic record of the results, namely which package functions had no examples, which had examples that failed, and which had examples that succeeded. The current package provides the missing functionality.

Maintained by Barry Zeeberg. Last updated 1 months ago.

2.00 score

cran

ROKET:Optimal Transport-Based Kernel Regression

Perform optimal transport on somatic point mutations and kernel regression hypothesis testing by integrating pathway level similarities at the gene level (Little et al. (2023) <doi:10.1111/biom.13769>). The software implements balanced and unbalanced optimal transport and omnibus tests with 'C++' across a set of tumor samples and allows for multi-threading to decrease computational runtime.

Maintained by Paul Little. Last updated 25 days ago.

openblas cpp openmp

2.00 score

danniyugithub

BEACH:Biometric Exploratory Analysis Creation House

A platform is provided for interactive analyses with a goal of totally easy to develop, deploy, interact, and explore (TEDDIE). Using this package, users can create customized analyses and make them available to end users who can perform interactive analyses and save analyses to RTF or HTML files. It allows developers to focus on R code for analysis, instead of dealing with html or shiny code.

Maintained by Danni Yu. Last updated 6 years ago.

openjdk

1 stars 2.00 score 3 scripts

konradkrahl

HanStat:Package for Easy Interpretation of Statistical Methods

A simple and time saving multiple linear regression function (OLS) with interpretation, optional bootstrapping, effect size calculation and all tested requirements.

Maintained by Konrad Krahl. Last updated 2 years ago.

2.00 score 1 scripts