Showing 200 of total 571 results (show query)
nanxstats
ggsci:Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2'
A collection of 'ggplot2' color palettes inspired by plots in scientific journals, data visualization libraries, science fiction movies, and TV shows.
Maintained by Nan Xiao. Last updated 7 months ago.
color-palettesdata-visualizationggplot2ggscisci-fiscientific-journalsvisualization
35.8 match 676 stars 17.83 score 25k scripts 414 dependentsrstudio
rticles:Article Formats for R Markdown
A suite of custom R Markdown formats and templates for authoring journal articles and conference submissions.
Maintained by Christophe Dervieux. Last updated 14 days ago.
40.5 match 1.5k stars 11.50 score 188 scripts 2 dependentscrsh
papaja:Prepare American Psychological Association Journal Articles with R Markdown
Tools to create dynamic, submission-ready manuscripts, which conform to American Psychological Association manuscript guidelines. We provide R Markdown document formats for manuscripts (PDF and Word) and revision letters (PDF). Helper functions facilitate reporting statistical analyses or create publication-ready tables and plots.
Maintained by Frederik Aust. Last updated 3 months ago.
apaapa-guidelinesjournalmanuscriptpsychologyreproducible-paperreproducible-researchrmarkdown
18.5 match 658 stars 11.45 score 1.6k scripts 1 dependentsrjournal
rjtools:Preparing, Checking, and Submitting Articles to the 'R Journal'
Create an 'R Journal' 'Rmarkdown' template article, that will generate html and pdf versions of your paper. Check that the paper folder has all the required components needed for submission. Examples of 'R Journal' publications can be found at <https://journal.r-project.org>.
Maintained by Di Cook. Last updated 2 days ago.
22.7 match 32 stars 8.63 score 37 scripts 1 dependentspgomba
MDPIexploreR:Web Scraping and Bibliometric Analysis of MDPI Journals
Provides comprehensive tools to scrape and analyze data from the MDPI journals. It allows users to extract metrics such as submission-to-acceptance times, article types, and whether articles are part of special issues. The package can also visualize this information through plots. Additionally, 'MDPIexploreR' offers tools to explore patterns of self-citations within articles and provides insights into guest-edited special issues.
Maintained by Pablo Gómez Barreiro. Last updated 2 months ago.
analysisdata-analysisdata-visualizationmdpimetricsscientific-journalsvisualizationweb-scraping
26.0 match 20 stars 6.41 score 8 scriptsmassimoaria
bibliometrix:Comprehensive Science Mapping Analysis
Tool for quantitative research in scientometrics and bibliometrics. It implements the comprehensive workflow for science mapping analysis proposed in Aria M. and Cuccurullo C. (2017) <doi:10.1016/j.joi.2017.08.007>. 'bibliometrix' provides various routines for importing bibliographic data from 'SCOPUS', 'Clarivate Analytics Web of Science' (<https://www.webofknowledge.com/>), 'Digital Science Dimensions' (<https://www.dimensions.ai/>), 'OpenAlex' (<https://openalex.org/>), 'Cochrane Library' (<https://www.cochranelibrary.com/>), 'Lens' (<https://lens.org>), and 'PubMed' (<https://pubmed.ncbi.nlm.nih.gov/>) databases, performing bibliometric analysis and building networks for co-citation, coupling, scientific collaboration and co-word analysis.
Maintained by Massimo Aria. Last updated 1 months ago.
bibliometric-analysisbibliometricscitationcitation-networkcitationsco-authorsco-occurenceco-word-analysiscorrespondence-analysiscouplingisi-webjournalmanuscriptquantitative-analysisscholarssciencescience-mappingscientificscientometricsscopus
11.0 match 530 stars 12.33 score 514 scripts 2 dependentsrempsyc
pubDashboard:Creating Publication Data Visualization Dashboards
Package to facilitate the creation of data visualization dashboards through the flexdashboard and openalexR packages.
Maintained by Rémi Thériault. Last updated 1 months ago.
43.6 match 2.54 score 7 scriptsrempsyc
pubmedDashboard:Creating PubMed Data Visualization Dashboards
Package to facilitate the creation of data visualization dashboards through the flexdashboard and easyPubMed packages. This package is now deprecated in favour of the pubDashboard package.
Maintained by Rémi Thériault. Last updated 8 months ago.
34.2 match 4 stars 3.20 score 6 scriptsrobjhyndman
rcademy:Tools to assist with academic promotions
Ideas and tools to help with preparing documentation for promotions at universities.
Maintained by Rob Hyndman. Last updated 4 months ago.
24.0 match 14 stars 4.23 score 9 scriptsjrnold
ggthemes:Extra Themes, Scales and Geoms for 'ggplot2'
Some extra themes, geoms, and scales for 'ggplot2'. Provides 'ggplot2' themes and scales that replicate the look of plots by Edward Tufte, Stephen Few, 'Fivethirtyeight', 'The Economist', 'Stata', 'Excel', and 'The Wall Street Journal', among others. Provides 'geoms' for Tufte's box plot and range frame.
Maintained by Jeffrey B. Arnold. Last updated 11 months ago.
data-visualisationggplot2ggplot2-themesplotplottingthemevisualization
5.9 match 1.3k stars 16.18 score 40k scripts 97 dependentscovaruber
sommer:Solving Mixed Model Equations in R
Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>; Jensen et al., 1997). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the Henderson-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available.
Maintained by Giovanny Covarrubias-Pazaran. Last updated 19 days ago.
average-informationmixed-modelsrcpparmadilloopenblascppopenmp
7.7 match 40 stars 12.34 score 280 scripts 9 dependentsglobeandmail
upstartr:Utilities Powering the Globe and Mail's Data Journalism Template
Core functions necessary for using The Globe and Mail's R data journalism template, 'startr', along with utilities for day-to-day data journalism tasks, such as reading and writing files, producing graphics and cleaning up datasets.
Maintained by Tom Cardoso. Last updated 1 years ago.
datadata-analysisdata-journalismdata-visualizationjournalismnews
21.2 match 6 stars 4.13 score 45 scriptsjessesadler
debkeepr:Analysis of Non-Decimal Currencies and Double-Entry Bookkeeping
Analysis of historical non-decimal currencies and value systems that use tripartite or tetrapartite systems such as pounds, shillings, and pence. It introduces new vector classes to represent non-decimal currencies, making them compatible with numeric classes, and provides functions to work with these classes in data frames in the context of double-entry bookkeeping.
Maintained by Jesse Sadler. Last updated 2 years ago.
accountingdigital-humanitieseconomic-historyhistory
14.5 match 9 stars 5.51 score 24 scriptsenricoschumann
PMwR:Portfolio Management with R
Tools for the practical management of financial portfolios: backtesting investment and trading strategies, computing profit/loss and returns, analysing trades, handling lists of transactions, reporting, and more. The package provides a small set of reliable, efficient and convenient tools for processing and analysing trade/portfolio data. The manual provides all the details; it is available from <https://enricoschumann.net/R/packages/PMwR/manual/PMwR.html>. Examples and descriptions of new features are provided at <https://enricoschumann.net/notes/PMwR/>.
Maintained by Enrico Schumann. Last updated 3 months ago.
12.6 match 6.16 score 30 scriptsglobeandmail
tgamtheme:Globe and Mail Graphics Theme for 'ggplot2'
Theme and colour palettes for The Globe and Mail's graphics. Includes colour and fill scale functions, colour palette helpers and a Globe-styled 'ggplot2' theme object.
Maintained by Tom Cardoso. Last updated 4 years ago.
datadata-journalismdata-visualizationjournalismnews
17.5 match 6 stars 3.95 score 2 scripts 1 dependentsgesistsa
oolong:Create Validation Tests for Automated Content Analysis
Intended to create standard human-in-the-loop validity tests for typical automated content analysis such as topic modeling and dictionary-based methods. This package offers a standard workflow with functions to prepare, administer and evaluate a human-in-the-loop validity test. This package provides functions for validating topic models using word intrusion, topic intrusion (Chang et al. 2009, <https://papers.nips.cc/paper/3700-reading-tea-leaves-how-humans-interpret-topic-models>) and word set intrusion (Ying et al. 2021) <doi:10.1017/pan.2021.33> tests. This package also provides functions for generating gold-standard data which are useful for validating dictionary-based methods. The default settings of all generated tests match those suggested in Chang et al. (2009) and Song et al. (2020) <doi:10.1080/10584609.2020.1723752>.
Maintained by Chung-hong Chan. Last updated 22 days ago.
textanalysistopicmodelingvalidation
7.5 match 54 stars 7.55 score 22 scriptsestedeahora
guri:~!gurí_: Unified Format Manager for Research Journals
~gurí_ (Gestor Unificado de formatos para Revistas de Investigación / Unified Format Manager for Research Journals) facilitates the generation of final documents for scientific journals from documents obtained in the 'proofreading' stage. The proposal seeks to solve the difficulties of some academic journals in generating final documents in different formats in a consistent way and without generating duplicated processes. It also takes into account that many scientific journals use docx documents as the basis of their workflows.
Maintained by Pablo Santiago Serrati. Last updated 3 months ago.
18.0 match 2 stars 3.11 score 4 scriptsyulab-smu
scholar:Analyse Citation Data from Google Scholar
Provides functions to extract citation data from Google Scholar. Convenience functions are also provided for comparing multiple scholars and predicting future h-index values.
Maintained by Guangchuang Yu. Last updated 1 years ago.
5.5 match 42 stars 9.59 score 454 scripts 3 dependentskcuilla
reactablefmtr:Streamlined Table Styling and Formatting for Reactable
Provides various features to streamline and enhance the styling of interactive reactable tables with easy-to-use and highly-customizable functions and themes. Apply conditional formatting to cells with data bars, color scales, color tiles, and icon sets. Utilize custom table themes inspired by popular websites such and bootstrap themes. Apply sparkline line & bar charts (note this feature requires the 'dataui' package which can be downloaded from <https://github.com/timelyportfolio/dataui>). Increase the portability and reproducibility of reactable tables by embedding images from the web directly into cells. Save the final table output as a static image or interactive file.
Maintained by Kyle Cuilla. Last updated 2 years ago.
customizationdata-visualizationeasy-to-usereproducibletables
5.6 match 209 stars 8.67 score 460 scripts 4 dependentsatahk
pscl:Political Science Computational Laboratory
Bayesian analysis of item-response theory (IRT) models, roll call analysis; computing highest density regions; maximum likelihood estimation of zero-inflated and hurdle models for count data; goodness-of-fit measures for GLMs; data sets used in writing and teaching; seats-votes curves.
Maintained by Simon Jackman. Last updated 1 years ago.
3.4 match 65 stars 13.66 score 2.7k scripts 53 dependentsropensci
EDIutils:An API Client for the Environmental Data Initiative Repository
A client for the Environmental Data Initiative repository REST API. The 'EDI' data repository <https://portal.edirepository.org/nis/home.jsp> is for publication and reuse of ecological data with emphasis on metadata accuracy and completeness. It is built upon the 'PASTA+' software stack <https://pastaplus-core.readthedocs.io/en/latest/index.html#> and was developed in collaboration with the US 'LTER' Network <https://lternet.edu/>. 'EDIutils' includes functions to search and access existing data, evaluate and upload new data, and assist other data management tasks common to repository users.
Maintained by Colin Smith. Last updated 1 years ago.
ecologyeml-metadataopen-accessopen-dataresearch-data-managementresearch-data-repository
7.1 match 10 stars 6.49 score 123 scriptschristophergandrud
networkD3:D3 JavaScript Network Graphs from R
Creates 'D3' 'JavaScript' network, tree, dendrogram, and Sankey graphs from 'R'.
Maintained by Christopher Gandrud. Last updated 6 years ago.
3.3 match 653 stars 13.57 score 3.4k scripts 31 dependentsbioc
swfdr:Estimation of the science-wise false discovery rate and the false discovery rate conditional on covariates
This package allows users to estimate the science-wise false discovery rate from Jager and Leek, "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the false discovery rate conditional on covariates, using a regression framework, as per Boca and Leek, "A direct approach to estimating false discovery rates conditional on covariates," 2018, PeerJ.
Maintained by Simina M. Boca. Last updated 3 months ago.
multiplecomparisonstatisticalmethodsoftware
7.1 match 3 stars 6.25 score 37 scriptsabhi-1u
texor:Converting 'LaTeX' 'R Journal' Articles into 'RJ-web-articles'
Articles in the 'R Journal' were first authored in 'LaTeX', which performs admirably for 'PDF' files but is less than ideal for modern online interfaces. The 'texor' package does all the transitional chores and conversions necessary to move to the online versions.
Maintained by Abhishek Ulayil. Last updated 1 months ago.
7.0 match 7 stars 6.28 score 8 scriptsirworkshop
campfin:Wrangle Campaign Finance Data
Explore and normalize American campaign finance data. Created by the Investigative Reporting Workshop to facilitate work on The Accountability Project, an effort to collect public data into a central, standard database that is more easily searched: <https://publicaccountability.org/>.
Maintained by Kiernan Nicholls. Last updated 1 years ago.
campaign-financedata-journalism
7.5 match 17 stars 5.66 score 54 scriptsropensci
jstor:Read Data from JSTOR/DfR
Functions and helpers to import metadata, ngrams and full-texts delivered by Data for Research by JSTOR.
Maintained by Thomas Klebel. Last updated 6 months ago.
jstorpeer-reviewedtext-analysistext-mining
5.4 match 47 stars 7.29 score 55 scriptsropensci
refsplitr:author name disambiguation, author georeferencing, and mapping of coauthorship networks with 'Web of Science' data
Tools to parse and organize reference records downloaded from the 'Web of Science' citation database into an R-friendly format, disambiguate the names of authors, geocode their locations, and generate/visualize coauthorship networks. This package has been peer-reviewed by rOpenSci (v. 1.0).
Maintained by Emilio Bruna. Last updated 5 months ago.
name disambiguationbibliometricscoauthorshipcollaborationgeoreferencingmetasciencereferencesscientometricsscience of scienceweb of science
6.9 match 55 stars 5.64 score 16 scriptsbioc
annotate:Annotation for microarrays
Using R enviroments for annotation.
Maintained by Bioconductor Package Maintainer. Last updated 3 months ago.
3.3 match 11.73 score 800 scripts 252 dependentscarloscinelli
benford.analysis:Benford Analysis for Data Validation and Forensic Analytics
Provides tools that make it easier to validate data using Benford's Law.
Maintained by Carlos Cinelli. Last updated 5 years ago.
6.8 match 61 stars 5.66 score 75 scriptscsgillespie
poweRlaw:Analysis of Heavy Tailed Distributions
An implementation of maximum likelihood estimators for a variety of heavy tailed distributions, including both the discrete and continuous power law distributions. Additionally, a goodness-of-fit based approach is used to estimate the lower cut-off for the scaling region.
Maintained by Colin Gillespie. Last updated 5 years ago.
3.1 match 109 stars 12.06 score 332 scripts 31 dependentsalexander-pastukhov
BiDimRegression:Calculates the Bidimensional Regression Between Two 2D Configurations
Calculates the bidimensional regression between two 2D configurations following the approach by Tobler (1965).
Maintained by Alexander Pastukhov. Last updated 3 years ago.
9.3 match 4.00 score 20 scriptscovaruber
lme4breeding:Relationship-Based Mixed-Effects Models
Fit relationship-based and customized mixed-effects models with complex variance-covariance structures using the 'lme4' machinery. The core computational algorithms are implemented using the 'Eigen' 'C++' library for numerical linear algebra and 'RcppEigen' 'glue'.
Maintained by Giovanny Covarrubias-Pazaran. Last updated 4 days ago.
7.2 match 6 stars 5.16 score 5 scriptskwstat
agridat:Agricultural Datasets
Datasets from books, papers, and websites related to agriculture. Example graphics and analyses are included. Data come from small-plot trials, multi-environment trials, uniformity trials, yield monitors, and more.
Maintained by Kevin Wright. Last updated 1 months ago.
2.7 match 124 stars 11.22 score 1.7k scripts 4 dependentshturner
BradleyTerry2:Bradley-Terry Models
Specify and fit the Bradley-Terry model, including structured versions in which the parameters are related to explanatory variables through a linear predictor and versions with contest-specific effects, such as a home advantage.
Maintained by Heather Turner. Last updated 6 years ago.
bradley-terry-modelspaired-comparisonsstatistical-models
3.5 match 19 stars 7.88 score 167 scripts 1 dependentssbgraves237
Ecdat:Data Sets for Econometrics
Data sets for econometrics, including political science.
Maintained by Spencer Graves. Last updated 2 months ago.
3.8 match 2 stars 7.16 score 740 scripts 3 dependentsbenyamindsmith
igraphwalshdata:'igraph' Datasets from Melanie Walsh
Interesting 'igraph' datasets from Melanie Walsh's sample social network datasets repository <https://github.com/melaniewalsh/sample-social-network-datasets>.
Maintained by Benjamin Smith. Last updated 7 months ago.
6.6 match 3 stars 3.78 score 1 scriptsitalo-granato
snpReady:Preparing Genotypic Datasets in Order to Run Genomic Analysis
Three functions to clean, summarize and prepare genomic datasets to Genome Selection and Genome Association analysis and to estimate population genetic parameters.
Maintained by Italo Granato. Last updated 5 years ago.
4.2 match 3 stars 5.77 score 33 scriptskwb-r
kwb.endnote:Helper Functions for Analysing KWB Endnote Library (Exported as .xml)
Helper Functions For Analysing KWB Endnote Library (Exported As .XML).
Maintained by Michael Rustler. Last updated 4 years ago.
endnoteknowledge-repoliterature-data-managementproject-fakinpublication
7.7 match 3.00 score 2 scriptsingmarboeschen
JATSdecoder:A Metadata and Text Extraction and Manipulation Tool Set
Provides a function collection to extract metadata, sectioned text and study characteristics from scientific articles in 'NISO-JATS' format. Articles in PDF format can be converted to 'NISO-JATS' with the 'Content ExtRactor and MINEr' ('CERMINE', <https://github.com/CeON/CERMINE>). For convenience, two functions bundle the extraction heuristics: JATSdecoder() converts 'NISO-JATS'-tagged XML files to a structured list with elements title, author, journal, history, 'DOI', abstract, sectioned text and reference list. study.character() extracts multiple study characteristics like number of included studies, statistical methods used, alpha error, power, statistical results, correction method for multiple testing, software used. An estimation of the involved sample size is performed based on reports within the abstract and the reported degrees of freedom within statistical results. In addition, the package contains some useful functions to process text (text2sentences(), text2num(), ngram(), strsplit2(), grep2()). See Böschen, I. (2021) <doi:10.1007/s11192-021-04162-z> Böschen, I. (2021) <doi:10.1038/s41598-021-98782-3> and Böschen, I (2023) <doi:10.1038/s41598-022-27085-y>.
Maintained by Ingmar Böschen. Last updated 2 months ago.
cermineniso-jatspubmedcentraltext-extractiontext-miningxml-filesopenjdk
5.0 match 18 stars 4.56 score 7 scriptsjgregoriods
dispeRse:Simulation of Demic Diffusion with Environmental Constraints
Simulates demic diffusion building on models previously developed for the expansion of Neolithic and other food-producing economies during the Holocene (Fort et al. (2012) <doi:10.7183/0002-7316.77.2.203>, Souza et al. (2021) <doi:10.1098/rsif.2021.0499>). Growth and emigration are modelled as density-dependent processes using logistic growth and an asymptotic threshold model. Environmental and terrain layers, which can change over time, affect carrying capacity, growth and mobility. Multiple centres of origin with their respective starting times can be specified.
Maintained by Jonas Gregorio de Souza. Last updated 2 years ago.
agent-basedarchaeologydemicdiffusionsimulation
6.2 match 7 stars 3.54 score 4 scriptsmkoohafkan
rivr:Steady and Unsteady Open-Channel Flow Computation
A tool for undergraduate and graduate courses in open-channel hydraulics. Provides functions for computing normal and critical depths, steady-state water surface profiles (e.g. backwater curves) and unsteady flow computations (e.g. flood wave routing) as described in Koohafkan MC, Younis BA (2015). "Open-channel computation with R." The R Journal, 7(2), 249–262. <doi: 10.32614/RJ-2015-034>.
Maintained by Michael C Koohafkan. Last updated 5 months ago.
3.6 match 20 stars 5.71 score 17 scriptsrstudio
pagedown:Paginate the HTML Output of R Markdown with CSS for Print
Use the paged media properties in CSS and the JavaScript library 'paged.js' to split the content of an HTML document into discrete pages. Each page can have its page size, page numbers, margin boxes, and running headers, etc. Applications of this package include books, letters, reports, papers, business cards, resumes, and posters.
Maintained by Yihui Xie. Last updated 14 days ago.
csshtmlpaged-mediapdfprintingtypesetting
1.8 match 896 stars 11.47 score 350 scripts 16 dependentsgastonbecerra
ojsr:Crawler and Data Scraper for Open Journal System ('OJS')
Crawler for 'OJS' pages and scraper for meta-data from articles. You can crawl 'OJS' archives, issues, articles, galleys, and search results. You can scrape articles metadata from their head tag in html, or from Open Archives Initiative ('OAI') records. Most of these functions rely on 'OJS' routing conventions (<https://docs.pkp.sfu.ca/dev/documentation/en/architecture-routes>).
Maintained by Gaston Becerra. Last updated 2 months ago.
4.2 match 3 stars 4.83 score 15 scriptsnoaa-nwfsc
zoid:Bayesian Zero-and-One Inflated Dirichlet Regression Modelling
Fits Dirichlet regression and zero-and-one inflated Dirichlet regression with Bayesian methods implemented in Stan. These models are sometimes referred to as trinomial mixture models; covariates and overdispersion can optionally be included.
Maintained by Eric J. Ward. Last updated 9 months ago.
3.1 match 8 stars 6.58 score 12 scriptsmdplot
MDplot:Visualising Molecular Dynamics Analyses
Provides automatisation for plot generation succeeding common molecular dynamics analyses. This includes straightforward plots, such as RMSD (Root-Mean-Square-Deviation) and RMSF (Root-Mean-Square-Fluctuation) but also more sophisticated ones such as dihedral angle maps, hydrogen bonds, cluster bar plots and DSSP (Definition of Secondary Structure of Proteins) analysis. Currently able to load GROMOS, GROMACS and AMBER formats, respectively.
Maintained by Christian Margreitter. Last updated 3 years ago.
3.1 match 27 stars 6.46 score 36 scriptsropensci
rcrossref:Client for Various 'CrossRef' 'APIs'
Client for various 'CrossRef' 'APIs', including 'metadata' search with their old and newer search 'APIs', get 'citations' in various formats (including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs' to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to full text of articles when available.
Maintained by Najko Jahn. Last updated 2 years ago.
text-mingliteraturepdfxmlpublicationscitationsfull-texttdmcrossrefapiapi-wrappercrossref-apidoimetadata
2.0 match 170 stars 10.00 score 360 scripts 10 dependentsfutureverse
future.tools:Tools for Working with Futures
Tools for Working with Futures.
Maintained by Henrik Bengtsson. Last updated 8 months ago.
parallel-computingparallel-programming
6.9 match 2 stars 2.78 scorewenjie2wang
jds.rmd:R Markdown Templates for Journal of Data Science
Customized R Markdown templates for authoring articles for Journal of Data Science.
Maintained by Wenjie Wang. Last updated 8 months ago.
7.0 match 1 stars 2.70 scoreillinois-r
uiucthemes:'R' 'Markdown' Themes for 'UIUC' Documents and Presentations
A set of custom 'R' 'Markdown' templates for documents and presentations with the University of Illinois at Urbana-Champaign (UIUC) color scheme and identity standards.
Maintained by James Balamuta. Last updated 3 years ago.
3.4 match 51 stars 5.41 score 4 scriptsr-forge
tramME:Transformation Models with Mixed Effects
Likelihood-based estimation of mixed-effects transformation models using the Template Model Builder ('TMB', Kristensen et al., 2016) <doi:10.18637/jss.v070.i05>. The technical details of transformation models are given in Hothorn et al. (2018) <doi:10.1111/sjos.12291>. Likelihood contributions of exact, randomly censored (left, right, interval) and truncated observations are supported. The random effects are assumed to be normally distributed on the scale of the transformation function, the marginal likelihood is evaluated using the Laplace approximation, and the gradients are calculated with automatic differentiation (Tamasi & Hothorn, 2021) <doi:10.32614/RJ-2021-075>. Penalized smooth shift terms can be defined using 'mgcv'.
Maintained by Balint Tamasi. Last updated 1 days ago.
3.3 match 5.43 score 1 scriptsanestistouloumis
SimCorMultRes:Simulates Correlated Multinomial Responses
Simulates correlated multinomial responses conditional on a marginal model specification.
Maintained by Anestis Touloumis. Last updated 10 months ago.
binarylongitudinal-studiesmultinomialsimulation
3.0 match 7 stars 6.04 score 26 scripts 2 dependentsgraemeblair
rdss:Companion Datasets and Functions for Research Design in the Social Sciences
Helper functions to accompany the Blair, Coppock, and Humphreys (2022) "Research Design in the Social Sciences: Declaration, Diagnosis, and Redesign" <https://book.declaredesign.org>. 'rdss' includes datasets, helper functions, and plotting components to enable use and replication of the book.
Maintained by Graeme Blair. Last updated 12 days ago.
6.3 match 2.88 score 30 scriptsslee981
wsjplot:Style Time Series Plots Like the Wall Street Journal
Easily override the default visual choices in 'ggplot2' to make your time series plots look more like the Wall Street Journal. Specific theme design choices include omitting x-axis grid lines and displaying sparse light grey y-axis grid lines. Additionally, this allows to label the y-axis scales with your units only displayed on the top-most number, while also removing the bottom most number (unless specifically overridden). The goal is visual simplicity, because who has time to waste looking at a cluttered graph?
Maintained by Stephen Lee. Last updated 4 years ago.
6.6 match 2.70 score 6 scriptsflavjack
inti:Tools and Statistical Procedures in Plant Science
The 'inti' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. The mean aim of the package is to support researchers during the planning of experiments and data collection (tarpuy()), data analysis and graphics (yupana()) , and technical writing. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Maintained by Flavio Lozano-Isla. Last updated 25 days ago.
agricultureappsinkaverselmmplant-breedingplant-scienceshiny
2.0 match 5 stars 8.21 score 168 scriptstbates
umx:Structural Equation Modeling and Twin Modeling in R
Quickly create, run, and report structural equation models, and twin models. See '?umx' for help, and umx_open_CRAN_page("umx") for NEWS. Timothy C. Bates, Michael C. Neale, Hermine H. Maes, (2019). umx: A library for Structural Equation and Twin Modelling in R. Twin Research and Human Genetics, 22, 27-41. <doi:10.1017/thg.2019.2>.
Maintained by Timothy C. Bates. Last updated 3 days ago.
behavior-geneticsgeneticsopenmxpsychologysemstatisticsstructural-equation-modelingtutorialstwin-modelsumx
1.6 match 45 stars 9.25 score 466 scriptspwarncke77
ResIN:Response Item Networks
Contains various tools to perform and visualize Response Item Networks ('ResIN's'). 'ResIN' binarizes ordered-categorical and qualitative response choices from (survey) data, calculates pairwise associations and maps the location of each item response as a node in a force-directed network. Please refer to <https://www.resinmethod.net/> for more details.
Maintained by Philip Warncke. Last updated 4 months ago.
3.1 match 4.48 score 3 scriptspakillo
grateful:Facilitate Citation of R Packages
Facilitates the citation of R packages used in analysis projects. Scans project for packages used, gets their citations, and produces a document with citations in the preferred bibliography format, ready to be pasted into reports or manuscripts. Alternatively, 'grateful' can be used directly within an 'R Markdown' or 'Quarto' document.
Maintained by Francisco Rodriguez-Sanchez. Last updated 2 months ago.
citation-generatorsoftware-citation
1.7 match 230 stars 7.95 score 287 scriptseddelbuettel
pinp:'pinp' is not 'PNAS'
A 'PNAS'-alike style for 'rmarkdown', derived from the 'Proceedings of the National Academy of Sciences of the United States of America' ('PNAS') 'LaTeX' style, and adapted for use with 'markdown' and 'pandoc'.
Maintained by Dirk Eddelbuettel. Last updated 1 months ago.
1.8 match 148 stars 7.77 score 2 scripts 1 dependentszoushucai
journalabbr:Journal Abbreviations for BibTeX Documents
Since the reference management software (such as 'Zotero', 'Mendeley') exports Bib file journal abbreviation is not detailed enough, the 'journalabbr' package only abbreviates the journal field of Bib file, and then outputs a new Bib file for generating reference format with journal abbreviation on other software (such as 'texstudio'). The abbreviation table is from 'JabRef'. At the same time, 'Shiny' application is provided to generate 'thebibliography', a reference format that can be directly used for latex paper writing based on 'Rmd' files.
Maintained by ShuCai Zou. Last updated 2 months ago.
4.1 match 1 stars 3.34 score 11 scriptskosukehamazaki
RAINBOWR:Genome-Wide Association Study with SNP-Set Methods
By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our paper on PLOS Computational Biology: Kosuke Hamazaki and Hiroyoshi Iwata (2020) <doi:10.1371/journal.pcbi.1007663>.
Maintained by Kosuke Hamazaki. Last updated 2 months ago.
2.1 match 22 stars 6.29 score 22 scriptsinbo
INBOtheme:Themes for ggplot2
Several themes for the ggplot2 package. Among others themes complying with the style guide for the Research Institute for Nature and Forest (INBO) and Elsevier journals.
Maintained by Thierry Onkelinx. Last updated 2 years ago.
2.3 match 3 stars 5.21 score 358 scriptsmarcohlmann
metanetwork:Handling and Representing Trophic Networks in Space and Time
A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks. The package also implements network diversity indices at different aggregation levels and connectance computation.
Maintained by Marc Ohlmann. Last updated 2 years ago.
3.0 match 2 stars 3.89 score 77 scriptschr1swallace
coloc:Colocalisation Tests of Two Genetic Traits
Performs the colocalisation tests described in Giambartolomei et al (2013) <doi:10.1371/journal.pgen.1004383>, Wallace (2020) <doi:10.1371/journal.pgen.1008720>, Wallace (2021) <doi:10.1371/journal.pgen.1009440>.
Maintained by Chris Wallace. Last updated 2 months ago.
1.0 match 156 stars 12.21 score 888 scripts 3 dependentscran
blockmodeling:Generalized and Classical Blockmodeling of Valued Networks
This is primarily meant as an implementation of generalized blockmodeling for valued networks. In addition, measures of similarity or dissimilarity based on structural equivalence and regular equivalence (REGE algorithms) can be computed and partitioned matrices can be plotted: Žiberna (2007)<doi:10.1016/j.socnet.2006.04.002>, Žiberna (2008)<doi:10.1080/00222500701790207>, Žiberna (2014)<doi:10.1016/j.socnet.2014.04.002>.
Maintained by Aleš Žiberna. Last updated 1 years ago.
3.4 match 3.45 score 78 scripts 12 dependentscran
SDAResources:Datasets and Functions for 'Sampling: Design and Analysis, 3rd Edition'
Includes all the datasets of 'Sampling: Design and Analysis' (3rd edition by Sharon Lohr) in R format and additional functions for analyzing and graphing probability samples.
Maintained by Yan Lu. Last updated 3 years ago.
4.5 match 2.41 score 26 scriptscran
ILSM:Analyze Interconnection Structure of Multilayer Interaction Networks
In view of the analysis of the structural characteristics of the multilayer network has been complete, however, there is still a lack of a unified operation that can quickly obtain the corresponding characteristics of the multilayer network. To solve this insufficiency, 'ILSM' was designed for supporting calculating such metrics of multilayer networks by functions of this R package.
Maintained by WeiCheng Sun. Last updated 5 months ago.
3.3 match 3.30 score 5 scriptschiliubio
file2meco:Transform Files to 'microtable' Object with 'microeco' Package
Transform output files of some tools to the 'microtable' object of 'microtable' class in 'microeco' package. The 'microtable' class is the basic class in 'microeco' package and is necessary for the downstream microbial community data analysis.
Maintained by Chi Liu. Last updated 2 months ago.
1.6 match 23 stars 6.05 score 75 scriptscran
rmcfs:The MCFS-ID Algorithm for Feature Selection and Interdependency Discovery
MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M. Draminski, J. Koronacki (2018) <doi:10.18637/jss.v085.i12>.
Maintained by Michal Draminski. Last updated 5 months ago.
2.8 match 1 stars 3.37 score 26 scripts 1 dependentsrfastofficial
Rfast:A Collection of Efficient and Extremely Fast R Functions
A collection of fast (utility) functions for data analysis. Column and row wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. References: a) Tsagris M., Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>. b) Tsagris M. and Papadakis M. (2018). Forward regression in R: from the extreme slow to the extreme fast. Journal of Data Science, 16(4): 771--780. <doi:10.6339/JDS.201810_16(4).00006>. c) Chatzipantsiou C., Dimitriadis M., Papadakis M. and Tsagris M. (2020). Extremely Efficient Permutation and Bootstrap Hypothesis Tests Using Hypothesis Tests Using R. Journal of Modern Applied Statistical Methods, 18(2), eP2898. <doi:10.48550/arXiv.1806.10947>.
Maintained by Manos Papadakis. Last updated 1 years ago.
0.8 match 146 stars 12.33 score 1.2k scripts 162 dependentsropensci
suppdata:Downloading Supplementary Data from Published Manuscripts
Downloads data supplementary materials from manuscripts, using papers' DOIs as references. Facilitates open, reproducible research workflows: scientists re-analyzing published datasets can work with them as easily as if they were stored on their own computer, and others can track their analysis workflow painlessly. The main function suppdata() returns a (temporary) location on the user's computer where the file is stored, making it simple to use suppdata() with standard functions like read.csv().
Maintained by William D. Pearse. Last updated 1 years ago.
1.9 match 34 stars 4.83 score 9 scriptsparklab
Nozzle.R1:Nozzle Reports
The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.
Maintained by Nils Gehlenborg. Last updated 10 years ago.
gehlenborglabhtml-reportreproducible-research
1.7 match 67 stars 5.30 score 10 scripts 2 dependentsdaya6489
SmartEDA:Summarize and Explore the Data
Exploratory analysis on any input data describing the structure and the relationships present in the data. The package automatically select the variable and does related descriptive statistics. Analyzing information value, weight of evidence, custom tables, summary statistics, graphical techniques will be performed for both numeric and categorical predictors.
Maintained by Dayanand Ubrangala. Last updated 12 months ago.
analysisexploratory-data-analysis
1.2 match 42 stars 7.13 score 214 scriptsfelixfan
PubMedWordcloud:'Pubmed' Word Clouds
Create a word cloud using the abstract of publications from 'Pubmed'.
Maintained by Felix Yanhui Fan. Last updated 6 years ago.
1.8 match 22 stars 4.79 score 28 scriptsmlampros
ClusterR:Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids and Affinity Propagation Clustering
Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Maintained by Lampros Mouselimis. Last updated 7 months ago.
affinity-propagationcpp11gmmkmeanskmedoids-clusteringmini-batch-kmeansrcpparmadilloopenblascppopenmp
0.8 match 84 stars 10.90 score 632 scripts 24 dependentsdfsp-spirit
fsbrain:Managing and Visualizing Brain Surface Data
Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.
Maintained by Tim Schäfer. Last updated 2 months ago.
3dbraindtifreesurfermeshmrineuroimagingresearchsurfacevisualizationvoxel
1.2 match 65 stars 6.64 score 15 scriptsjianhong
colorBlindness:Safe Color Set for Color Blindness
Provide the safe color set for color blindness, the simulator of protanopia, deuteranopia. The color sets are collected from: Wong, B. (2011) <doi:10.1038/nmeth.1618>, and <http://mkweb.bcgsc.ca/biovis2012/>. The simulations of the appearance of the colors to color-deficient viewers were based on algorithms in Vienot, F., Brettel, H. and Mollon, J.D. (1999) <doi:10.1002/(SICI)1520-6378(199908)24:4%3C243::AID-COL5%3E3.0.CO;2-3>. The cvdPlot() function to generate 'ggplot' grobs of simulations were modified from <https://github.com/clauswilke/colorblindr>.
Maintained by Jianhong Ou. Last updated 4 years ago.
1.8 match 4.32 score 315 scriptsbhaskarvk
tilegramsR:R Spatial Data for Tilegrams
R spatial objects for Tilegrams. Tilegrams are tiled maps where the region size is proportional to the certain characteristics of the dataset.
Maintained by Bhaskar Karambelkar. Last updated 3 years ago.
1.3 match 52 stars 6.03 score 41 scriptstverbeke
SDaA:Sampling: Design and Analysis
Functions and Datasets from Lohr, S. (1999), Sampling: Design and Analysis, Duxbury.
Maintained by Tobias Verbeke. Last updated 3 years ago.
3.5 match 2.15 score 14 scriptssandrinepavoine
adiv:Analysis of Diversity
Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Maintained by Sandrine Pavoine. Last updated 11 months ago.
3.3 match 1 stars 2.27 score 62 scriptsshahlafaisal
JCRImpactFactor:Journal Citation Reports ('JCR') Impact Factor by 'Clarivate' 'Analytics'
The Impact Factor of a journal reported by Journal Citation Reports ('JCR') of 'Clarivate' 'Analytics' is provided. The impact factor is available for those journals only that were included Journal Citation Reports 'JCR'.
Maintained by Shahla Faisal. Last updated 4 years ago.
7.3 match 1.00 score 3 scriptscorybrunson
ggalluvial:Alluvial Plots in 'ggplot2'
Alluvial plots use variable-width ribbons and stacked bar plots to represent multi-dimensional or repeated-measures data with categorical or ordinal variables; see Riehmann, Hanfler, and Froehlich (2005) <doi:10.1109/INFVIS.2005.1532152> and Rosvall and Bergstrom (2010) <doi:10.1371/journal.pone.0008694>. Alluvial plots are statistical graphics in the sense of Wilkinson (2006) <doi:10.1007/0-387-28695-0>; they share elements with Sankey diagrams and parallel sets plots but are uniquely determined from the data and a small set of parameters. This package extends Wickham's (2010) <doi:10.1198/jcgs.2009.07098> layered grammar of graphics to generate alluvial plots from tidy data.
Maintained by Jason Cory Brunson. Last updated 5 months ago.
alluvial-diagramsalluvial-plotscategorical-data-visualizationggplot2repeated-measures-data
0.5 match 504 stars 13.93 score 3.0k scripts 19 dependentsgagolews
CITAN:CITation ANalysis Toolpack
Supports quantitative research in scientometrics and bibliometrics. Provides various tools for preprocessing bibliographic data retrieved, e.g., from Elsevier's SciVerse Scopus, computing bibliometric impact of individuals, or modelling phenomena encountered in the social sciences. This package is deprecated, see 'agop' instead.
Maintained by Marek Gagolewski. Last updated 3 years ago.
1.7 match 6 stars 3.82 score 22 scriptsocbe-uio
BayesMallows:Bayesian Preference Learning with the Mallows Rank Model
An implementation of the Bayesian version of the Mallows rank model (Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>; Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>; Sorensen et al., R Journal, 2020 <doi:10.32614/RJ-2020-026>; Stein, PhD Thesis, 2023 <https://eprints.lancs.ac.uk/id/eprint/195759>). Both Metropolis-Hastings and sequential Monte Carlo algorithms for estimating the models are available. Cayley, footrule, Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the posterior distributions of parameters are provided. The package also provides functions for estimating the partition function (normalizing constant) of the Mallows rank model, both with the importance sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm (Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Maintained by Oystein Sorensen. Last updated 7 days ago.
mallows-modelopenblascppopenmp
0.8 match 21 stars 8.09 score 36 scripts 1 dependentsmatthutchinson1
paco:Procrustes Application to Cophylogenetic Analysis
Procrustes analyses to infer co-phylogenetic matching between pairs of phylogenetic trees.
Maintained by Matthew Hutchinson. Last updated 4 years ago.
1.5 match 3.98 score 32 scripts 1 dependentsjulierennes
denoiseR:Regularized Low Rank Matrix Estimation
Estimate a low rank matrix from noisy data using singular values thresholding and shrinking functions. Impute missing values with matrix completion. The method is described in <arXiv:1602.01206>.
Maintained by Julie Josse. Last updated 5 years ago.
3.6 match 1.70 score 50 scriptsfinlaycampbell
outbreaker2:Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data
Bayesian reconstruction of disease outbreaks using epidemiological and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F, Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Maintained by Finlay Campbell. Last updated 4 months ago.
0.8 match 7.66 score 100 scripts 1 dependentsropensci
stplanr:Sustainable Transport Planning
Tools for transport planning with an emphasis on spatial transport data and non-motorized modes. The package was originally developed to support the 'Propensity to Cycle Tool', a publicly available strategic cycle network planning tool (Lovelace et al. 2017) <doi:10.5198/jtlu.2016.862>, but has since been extended to support public transport routing and accessibility analysis (Moreno-Monroy et al. 2017) <doi:10.1016/j.jtrangeo.2017.08.012> and routing with locally hosted routing engines such as 'OSRM' (Lowans et al. 2023) <doi:10.1016/j.enconman.2023.117337>. The main functions are for creating and manipulating geographic "desire lines" from origin-destination (OD) data (building on the 'od' package); calculating routes on the transport network locally and via interfaces to routing services such as <https://cyclestreets.net/> (Desjardins et al. 2021) <doi:10.1007/s11116-021-10197-1>; and calculating route segment attributes such as bearing. The package implements the 'travel flow aggregration' method described in Morgan and Lovelace (2020) <doi:10.1177/2399808320942779> and the 'OD jittering' method described in Lovelace et al. (2022) <doi:10.32866/001c.33873>. Further information on the package's aim and scope can be found in the vignettes and in a paper in the R Journal (Lovelace and Ellison 2018) <doi:10.32614/RJ-2018-053>, and in a paper outlining the landscape of open source software for geographic methods in transport planning (Lovelace, 2021) <doi:10.1007/s10109-020-00342-2>.
Maintained by Robin Lovelace. Last updated 5 months ago.
cyclecyclingdesire-linesorigin-destinationpeer-reviewedpubic-transportroute-networkroutesroutingspatialtransporttransport-planningtransportationwalking
0.5 match 424 stars 11.98 score 676 scripts 2 dependentseco-hydro
phenofit:Extract Remote Sensing Vegetation Phenology
The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and growing season dividing method and a practical snow elimination method based on Whittaker were proposed. 7 curve fitting methods and 4 phenology extraction methods were provided. Parameters boundary are considered for every curve fitting methods according to their ecological meaning. And 'optimx' is used to select best optimization method for different curve fitting methods. Reference: Kong, D., (2020). R package: A state-of-the-art Vegetation Phenology extraction package, phenofit version 0.3.1, <doi:10.5281/zenodo.5150204>; Kong, D., Zhang, Y., Wang, D., Chen, J., & Gu, X. (2020). Photoperiod Explains the Asynchronization Between Vegetation Carbon Phenology and Vegetation Greenness Phenology. Journal of Geophysical Research: Biogeosciences, 125(8), e2020JG005636. <doi:10.1029/2020JG005636>; Kong, D., Zhang, Y., Gu, X., & Wang, D. (2019). A robust method for reconstructing global MODIS EVI time series on the Google Earth Engine. ISPRS Journal of Photogrammetry and Remote Sensing, 155, 13–24; Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013). Agric. For. Meteorol. 248, 408–417. <doi:10.1016/j.agrformet.2017.10.026>.
Maintained by Dongdong Kong. Last updated 3 months ago.
phenologyremote-sensingopenblascppopenmp
0.8 match 76 stars 7.70 score 332 scriptsbenjaminrich
table1:Tables of Descriptive Statistics in HTML
Create HTML tables of descriptive statistics, as one would expect to see as the first table (i.e. "Table 1") in a medical/epidemiological journal article.
Maintained by Benjamin Rich. Last updated 2 years ago.
0.5 match 81 stars 10.84 score 1.5k scripts 5 dependentsropensci
roadoi:Find Free Versions of Scholarly Publications via Unpaywall
This web client interfaces Unpaywall <https://unpaywall.org/products/api>, formerly oaDOI, a service finding free full-texts of academic papers by linking DOIs with open access journals and repositories. It provides unified access to various data sources for open access full-text links including Crossref and the Directory of Open Access Journals (DOAJ). API usage is free and no registration is required.
Maintained by Najko Jahn. Last updated 4 months ago.
altmetricscode4liboadoiopen-accesspeer-reviewedunpaywallwebclient
0.8 match 65 stars 7.28 score 73 scriptsbioc
broadSeq:broadSeq : for streamlined exploration of RNA-seq data
This package helps user to do easily RNA-seq data analysis with multiple methods (usually which needs many different input formats). Here the user will provid the expression data as a SummarizedExperiment object and will get results from different methods. It will help user to quickly evaluate different methods.
Maintained by Rishi Das Roy. Last updated 3 months ago.
geneexpressiondifferentialexpressionrnaseqtranscriptomicssequencingcoveragegenesetenrichmentgo
1.1 match 2 stars 4.95 score 7 scriptsfdzul
dendata:the dendata package provides the dengue spatial databases (areal data) available and published in scientific journals
the dendata package provides the dengue spatial databases (areal data) available and published in scientific journals.
Maintained by The package maintainer. Last updated 6 months ago.
3.2 match 1.70 score 1 scriptsrudeboybert
fivethirtyeight:Data and Code Behind the Stories and Interactives at 'FiveThirtyEight'
Datasets and code published by the data journalism website 'FiveThirtyEight' available at <https://github.com/fivethirtyeight/data>. Note that while we received guidance from editors at 'FiveThirtyEight', this package is not officially published by 'FiveThirtyEight'.
Maintained by Albert Y. Kim. Last updated 2 years ago.
data-sciencedatajournalismfivethirtyeightstatistics
0.5 match 455 stars 10.41 score 1.7k scriptsrwparsons
circacompare:Analyses of Circadian Data
Uses non-linear regression to statistically compare two circadian rhythms. Groups are only compared if both are rhythmic (amplitude is non-zero). Performs analyses regarding mesor, phase, and amplitude, reporting on estimates and statistical differences, for each, between groups. Details can be found in Parsons et al (2020) <doi:10.1093/bioinformatics/btz730>.
Maintained by Rex Parsons. Last updated 1 years ago.
1.1 match 7 stars 4.92 score 12 scriptsbips-hb
innsight:Get the Insights of Your Neural Network
Interpretation methods for analyzing the behavior and individual predictions of modern neural networks in a three-step procedure: Converting the model, running the interpretation method, and visualizing the results. Implemented methods are, e.g., 'Connection Weights' described by Olden et al. (2004) <doi:10.1016/j.ecolmodel.2004.03.013>, layer-wise relevance propagation ('LRP') described by Bach et al. (2015) <doi:10.1371/journal.pone.0130140>, deep learning important features ('DeepLIFT') described by Shrikumar et al. (2017) <doi:10.48550/arXiv.1704.02685> and gradient-based methods like 'SmoothGrad' described by Smilkov et al. (2017) <doi:10.48550/arXiv.1706.03825>, 'Gradient x Input' or 'Vanilla Gradient'. Details can be found in the accompanying scientific paper: Koenen & Wright (2024, Journal of Statistical Software, <doi:10.18637/jss.v111.i08>).
Maintained by Niklas Koenen. Last updated 2 months ago.
0.8 match 27 stars 6.95 score 55 scriptsalexchristensen
NetworkToolbox:Methods and Measures for Brain, Cognitive, and Psychometric Network Analysis
Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershgoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Maintained by Alexander Christensen. Last updated 2 years ago.
0.8 match 23 stars 6.90 score 102 scripts 3 dependentsrichardli
SUMMER:Small-Area-Estimation Unit/Area Models and Methods for Estimation in R
Provides methods for spatial and spatio-temporal smoothing of demographic and health indicators using survey data, with particular focus on estimating and projecting under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>, Li et al. (2019) <doi:10.1371/journal.pone.0210645>, Wu et al. (DHS Spatial Analysis Reports No. 21, 2021), and Li et al. (2023) <doi:10.48550/arXiv.2007.05117>.
Maintained by Zehang R Li. Last updated 14 days ago.
bayesian-inferencesmall-area-estimationspace-time
0.5 match 23 stars 10.30 score 134 scripts 2 dependentsagrdatasci
gdistance:Distances and Routes on Geographical Grids
Provides classes and functions to calculate various distance measures and routes in heterogeneous geographic spaces represented as grids. The package implements measures to model dispersal histories first presented by van Etten and Hijmans (2010) <doi:10.1371/journal.pone.0012060>. Least-cost distances as well as more complex distances based on (constrained) random walks can be calculated. The distances implemented in the package are used in geographical genetics, accessibility indicators, and may also have applications in other fields of geospatial analysis.
Maintained by Andrew Marx. Last updated 1 years ago.
0.5 match 16 stars 10.24 score 478 scripts 23 dependentsropensci
tabulapdf:Extract Tables from PDF Documents
Bindings for the 'Tabula' <https://tabula.technology/> 'Java' library, which can extract tables from PDF files. This tool can reduce time and effort in data extraction processes in fields like investigative journalism. It allows for automatic and manual table extraction, the latter facilitated through a 'Shiny' interface, enabling manual areas selection\ with a computer mouse for data retrieval.
Maintained by Mauricio Vargas Sepulveda. Last updated 18 days ago.
javapdfpdf-documentpeer-reviewedropenscitabulatabular-dataopenjdk
0.5 match 550 stars 10.07 score 159 scripts 1 dependentskjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 9 months ago.
2.3 match 2.28 score 38 scriptsepiforecasts
socialmixr:Social Mixing Matrices for Infectious Disease Modelling
Provides methods for sampling contact matrices from diary data for use in infectious disease modelling, as discussed in Mossong et al. (2008) <doi:10.1371/journal.pmed.0050074>.
Maintained by Sebastian Funk. Last updated 3 months ago.
0.5 match 38 stars 9.80 score 231 scripts 1 dependentsrvlenth
rsm:Response-Surface Analysis
Provides functions to generate response-surface designs, fit first- and second-order response-surface models, make surface plots, obtain the path of steepest ascent, and do canonical analysis. A good reference on these methods is Chapter 10 of Wu, C-F J and Hamada, M (2009) "Experiments: Planning, Analysis, and Parameter Design Optimization" ISBN 978-0-471-69946-0. An early version of the package is documented in Journal of Statistical Software <doi:10.18637/jss.v032.i07>.
Maintained by Russell Lenth. Last updated 8 months ago.
0.5 match 18 stars 9.94 score 192 scripts 8 dependentsevalclass
precrec:Calculate Accurate Precision-Recall and ROC (Receiver Operator Characteristics) Curves
Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves. Saito and Rehmsmeier (2015) <doi:10.1371/journal.pone.0118432>.
Maintained by Takaya Saito. Last updated 1 years ago.
0.5 match 45 stars 9.52 score 486 scripts 5 dependentsms609
TreeTools:Create, Modify and Analyse Phylogenetic Trees
Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) <doi:10.1371/journal.pone.0212942>; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>, and of tree balance (Mir et al. 2013, Lemant et al. 2022) <doi:10.1016/j.mbs.2012.10.005>, <doi:10.1093/sysbio/syac027>; artificial extinction (Asher & Smith, 2022) <doi:10.1093/sysbio/syab072>; import and export of trees from Newick, Nexus (Maddison et al. 1997) <doi:10.1093/sysbio/46.4.590>, and TNT <https://www.lillo.org.ar/phylogeny/tnt/> formats; and analysis of splits and cladistic information.
Maintained by Martin R. Smith. Last updated 8 days ago.
evolutionary-biologyphylogenetic-treesphylogeneticscpp
0.5 match 20 stars 9.67 score 124 scripts 10 dependentsshixiangwang
sigminer:Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Maintained by Shixiang Wang. Last updated 3 months ago.
bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualizationcpp
0.5 match 150 stars 9.59 score 123 scripts 2 dependentsbioc
recount:Explore and download data from the recount project
Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.
Maintained by Leonardo Collado-Torres. Last updated 1 months ago.
coveragedifferentialexpressiongeneexpressionrnaseqsequencingsoftwaredataimportimmunooncologyannotation-agnosticbioconductorcountderfinderdeseq2exongenehumanilluminajunctionrecount
0.5 match 40 stars 9.55 score 498 scripts 3 dependentscarloscinelli
sensemakr:Sensitivity Analysis Tools for Regression Models
Implements a suite of sensitivity analysis tools that extends the traditional omitted variable bias framework and makes it easier to understand the impact of omitted variables in regression models, as discussed in Cinelli, C. and Hazlett, C. (2020), "Making Sense of Sensitivity: Extending Omitted Variable Bias." Journal of the Royal Statistical Society, Series B (Statistical Methodology) <doi:10.1111/rssb.12348>.
Maintained by Carlos Cinelli. Last updated 2 months ago.
0.5 match 90 stars 9.40 score 132 scripts 2 dependentshuizezhang-sherry
cubble:A Vector Spatio-Temporal Data Structure for Data Analysis
A spatiotemperal data object in a relational data structure to separate the recording of time variant/ invariant variables. See the Journal of Statistical Software reference: <doi:10.18637/jss.v110.i07>.
Maintained by H. Sherry Zhang. Last updated 4 months ago.
0.5 match 56 stars 9.07 score 83 scriptsgorelab
waves:Vis-NIR Spectral Analysis Wrapper
Originally designed application in the context of resource-limited plant research and breeding programs, 'waves' provides an open-source solution to spectral data processing and model development by bringing useful packages together into a streamlined pipeline. This package is wrapper for functions related to the analysis of point visible and near-infrared reflectance measurements. It includes visualization, filtering, aggregation, preprocessing, cross-validation set formation, model training, and prediction functions to enable open-source association of spectral and reference data. This package is documented in a peer-reviewed manuscript in the Plant Phenome Journal <doi:10.1002/ppj2.20012>. Specialized cross-validation schemes are described in detail in Jarquín et al. (2017) <doi:10.3835/plantgenome2016.12.0130>. Example data is from Ikeogu et al. (2017) <doi:10.1371/journal.pone.0188918>.
Maintained by Jenna Hershberger. Last updated 9 months ago.
0.8 match 6 stars 6.16 score 40 scriptssebastien-plutniak
archeofrag:Spatial Analysis in Archaeology from Refitting Fragments
Methods to analyse spatial units in archaeology from the relationships between refitting fragmented objects scattered in these units (e.g. stratigraphic layers). Graphs are used to model archaeological observations. The package is mainly based on the 'igraph' package for graph analysis. Functions can: 1) create, manipulate, and simulate fragmentation graphs, 2) measure the cohesion and admixture of archaeological spatial units, and 3) characterise the topology of a specific set of refitting relationships. Empirical datasets are provided as examples. Documentation about 'archeofrag' is provided by the vignette included in this package, by the accompanying scientific papers: Plutniak (2021, Journal of Archaeological Science, <doi:10.1016/j.jas.2021.105501>) and Plutniak (2022, Journal of Open Source Software, <doi:10.21105/joss.04335>). This package is complemented by a companion GUI application available at <https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/>.
Maintained by Sebastien Plutniak. Last updated 3 days ago.
archaeological-objectsarchaeological-sciencearchaeologyfragmentationnetwork-analysis
0.8 match 19 stars 6.15 score 10 scripts 1 dependentsropensci
stats19:Work with Open Road Traffic Casualty Data from Great Britain
Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The datasets are provided as 'CSV' files with detailed road safety information about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979 to present. Tables are available on 'colissions' with the circumstances (e.g. speed limit of road), information about 'vehicles' involved (e.g. type of vehicle), and 'casualties' (e.g. age). The statistics relate only to events on public roads that were reported to the police, and subsequently recorded, using the 'STATS19' collision reporting form. See the Department for Transport website <https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data> for more information on these datasets. The package is described in a paper in the Journal of Open Source Software (Lovelace et al. 2019) <doi:10.21105/joss.01181>. See Gilardi et al. (2022) <doi:10.1111/rssa.12823>, Vidal-Tortosa et al. (2021) <doi:10.1016/j.jth.2021.101291>, and Tait et al. (2023) <doi:10.1016/j.aap.2022.106895> for examples of how the data can be used for methodological and empirical road safety research.
Maintained by Robin Lovelace. Last updated 7 days ago.
stats19road-safetytransportcar-crashesropenscidata
0.5 match 64 stars 9.34 score 187 scriptsss3sim
ss3sim:Fisheries Stock Assessment Simulation Testing with Stock Synthesis
A framework for fisheries stock assessment simulation testing with Stock Synthesis (SS3) as described in Anderson et al. (2014) <doi:10.1371/journal.pone.0092725>.
Maintained by Kelli F. Johnson. Last updated 3 months ago.
fisheriessimulationstock-synthesis
0.5 match 39 stars 8.87 score 140 scriptscran
rehh:Searching for Footprints of Selection using 'Extended Haplotype Homozygosity' Based Tests
Population genetic data such as 'Single Nucleotide Polymorphisms' (SNPs) is often used to identify genomic regions that have been under recent natural or artificial selection and might provide clues about the molecular mechanisms of adaptation. One approach, the concept of an 'Extended Haplotype Homozygosity' (EHH), introduced by (Sabeti 2002) <doi:10.1038/nature01140>, has given rise to several statistics designed for whole genome scans. The package provides functions to compute three of these, namely: 'iHS' (Voight 2006) <doi:10.1371/journal.pbio.0040072> for detecting positive or 'Darwinian' selection within a single population as well as 'Rsb' (Tang 2007) <doi:10.1371/journal.pbio.0050171> and 'XP-EHH' (Sabeti 2007) <doi:10.1038/nature06250>, targeted at differential selection between two populations. Various plotting functions are included to facilitate visualization and interpretation of these statistics.
Maintained by Alexander Klassmann. Last updated 3 years ago.
0.8 match 8 stars 6.06 score 241 scripts 1 dependentsanimint
animint2:Animated Interactive Grammar of Graphics
Functions are provided for defining animated, interactive data visualizations in R code, and rendering on a web page. The 2018 Journal of Computational and Graphical Statistics paper, <doi:10.1080/10618600.2018.1513367> describes the concepts implemented.
Maintained by Toby Hocking. Last updated 5 hours ago.
0.5 match 63 stars 8.91 score 192 scriptsanhoej
qicharts2:Quality Improvement Charts
Functions for making run charts, Shewhart control charts and Pareto charts for continuous quality improvement. Included control charts are: I, MR, Xbar, S, T, C, U, U', P, P', and G charts. Non-random variation in the form of minor to moderate persistent shifts in data over time is identified by the Anhoej rules for unusually long runs and unusually few crossing [Anhoej, Olesen (2014) <doi:10.1371/journal.pone.0113825>]. Non-random variation in the form of larger, possibly transient, shifts is identified by Shewhart's 3-sigma rule [Mohammed, Worthington, Woodall (2008) <doi:10.1136/qshc.2004.012047>].
Maintained by Jacob Anhoej. Last updated 8 days ago.
0.5 match 39 stars 9.06 score 117 scripts 2 dependentsbisaloo
contactdata:Social Contact Matrices for 177 Countries
Data package for the supplementary data in Prem et al. (2017) <doi:10.1371/journal.pcbi.1005697> and Prem et al. <doi:10.1371/journal.pcbi.1009098>. Provides easy access to contact data for 177 countries, for use in epidemiological, demographic or social sciences research.
Maintained by Hugo Gruson. Last updated 2 months ago.
demographicsepidemiologysocial-sciences
0.8 match 9 stars 5.65 score 11 scriptsdoubleml
DoubleML:Double Machine Learning in R
Implementation of the double/debiased machine learning framework of Chernozhukov et al. (2018) <doi:10.1111/ectj.12097> for partially linear regression models, partially linear instrumental variable regression models, interactive regression models and interactive instrumental variable regression models. 'DoubleML' allows estimation of the nuisance parts in these models by machine learning methods and computation of the Neyman orthogonal score functions. 'DoubleML' is built on top of 'mlr3' and the 'mlr3' ecosystem. The object-oriented implementation of 'DoubleML' based on the 'R6' package is very flexible. More information available in the publication in the Journal of Statistical Software: <doi:10.18637/jss.v108.i03>.
Maintained by Philipp Bach. Last updated 2 months ago.
causal-inferencedata-sciencedouble-machine-learningeconometricsmachine-learningmlr3statistics
0.5 match 136 stars 8.78 score 247 scriptsbsaul
geex:An API for M-Estimation
Provides a general, flexible framework for estimating parameters and empirical sandwich variance estimator from a set of unbiased estimating equations (i.e., M-estimation in the vein of Stefanski & Boos (2002) <doi:10.1198/000313002753631330>). All examples from Stefanski & Boos (2002) are published in the corresponding Journal of Statistical Software paper "The Calculus of M-Estimation in R with geex" by Saul & Hudgens (2020) <doi:10.18637/jss.v092.i02>. Also provides an API to compute finite-sample variance corrections.
Maintained by Bradley Saul. Last updated 9 months ago.
asymptoticscovariance-estimatescovariance-estimationestimate-parametersestimating-equationsestimationinferencem-estimationrobustsandwich
0.5 match 8 stars 8.65 score 131 scripts 2 dependentsrapidsurveys
bbw:Blocked Weighted Bootstrap
The blocked weighted bootstrap (BBW) is an estimation technique for use with data from two-stage cluster sampled surveys in which either prior weighting (e.g. population-proportional sampling or PPS as used in Standardized Monitoring and Assessment of Relief and Transitions or SMART surveys) or posterior weighting (e.g. as used in rapid assessment method or RAM and simple spatial sampling method or S3M surveys) is implemented. See Cameron et al (2008) <doi:10.1162/rest.90.3.414> for application of bootstrap to cluster samples. See Aaron et al (2016) <doi:10.1371/journal.pone.0163176> and Aaron et al (2016) <doi:10.1371/journal.pone.0162462> for application of the blocked weighted bootstrap to estimate indicators from two-stage cluster sampled surveys.
Maintained by Ernest Guevarra. Last updated 5 days ago.
bootstrapping-statisticsramsurveys
0.8 match 3 stars 5.72 score 13 scripts 1 dependentscran
SiFINeT:Single Cell Feature Identification with Network Topology
Cluster-independent method based on topology structure of gene co-expression network for identifying feature gene sets, extracting cellular subpopulations, and elucidating intrinsic relationships among these subpopulations. Without prior cell clustering, SifiNet circumvents potential inaccuracies in clustering that may influence subsequent analyses. This method is introduced in Qi Gao, Zhicheng Ji, Liuyang Wang, Kouros Owzar, Qi-Jing Li, Cliburn Chan, Jichun Xie "SifiNet: a robust and accurate method to identify feature gene sets and annotate cells" (2024) <doi:10.1093/nar/gkae307>.
Maintained by Qi Gao. Last updated 5 days ago.
1.5 match 2.85 score 14 scriptsrobeltakele
AquaBEHER:Estimation and Prediction of Wet Season Calendar and Soil Water Balance for Agriculture
Computes and integrates daily potential evapotranspiration (PET) and a soil water balance model. It allows users to estimate and predict the wet season calendar, including onset, cessation, and duration, based on an agroclimatic approach for a specified period. This functionality helps in managing agricultural water resources more effectively. For detailed methodologies, users can refer to Allen et al. (1998, ISBN:92-5-104219-5); Allen (2005, ISBN:9780784408056); Doorenbos and Pruitt (1975, ISBN:9251002797); Guo et al. (2016) <doi:10.1016/j.envsoft.2015.12.019>; Hargreaves and Samani (1985) <doi:10.13031/2013.26773>; Priestley and Taylor (1972) <https://journals.ametsoc.org/view/journals/apme/18/7/1520-0450_1979_018_0898_tptema_2_0_co_2.xml>.
Maintained by Robel Takele. Last updated 4 months ago.
growing-seasonseasonal-calendarsoil-moisturesoil-water-balance
0.8 match 10 stars 5.70 score 6 scriptscomputationalstylistics
stylo:Stylometric Multivariate Analyses
Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html>. You are also encouraged to visit the Computational Stylistics Group's website <https://computationalstylistics.github.io/>, where a reasonable amount of information about the package and related projects are provided.
Maintained by Maciej Eder. Last updated 19 days ago.
0.5 match 180 stars 8.56 score 462 scriptsepiverse-trace
cfr:Estimate Disease Severity and Case Ascertainment
Estimate the severity of a disease and ascertainment of cases, as discussed in Nishiura et al. (2009) <doi:10.1371/journal.pone.0006852>.
Maintained by Adam Kucharski. Last updated 1 months ago.
case-fatality-rateepidemic-modellingepidemiologyepiversehealth-outcomesoutbreak-analysissdg-3
0.5 match 13 stars 8.18 score 35 scriptsuclahs-cds
BoutrosLab.plotting.general:Functions to Create Publication-Quality Plots
Contains several plotting functions such as barplots, scatterplots, heatmaps, as well as functions to combine plots and assist in the creation of these plots. These functions will give users great ease of use and customization options in broad use for biomedical applications, as well as general purpose plotting. Each of the functions also provides valid default settings to make plotting data more efficient and producing high quality plots with standard colour schemes simpler. All functions within this package are capable of producing plots that are of the quality to be presented in scientific publications and journals. P'ng et al.; BPG: Seamless, automated and interactive visualization of scientific data; BMC Bioinformatics 2019 <doi:10.1186/s12859-019-2610-2>.
Maintained by Paul Boutros. Last updated 4 months ago.
0.5 match 12 stars 8.48 score 414 scripts 6 dependentsmikejareds
hermiter:Efficient Sequential and Batch Estimation of Univariate and Bivariate Probability Density Functions and Cumulative Distribution Functions along with Quantiles (Univariate) and Nonparametric Correlation (Bivariate)
Facilitates estimation of full univariate and bivariate probability density functions and cumulative distribution functions along with full quantile functions (univariate) and nonparametric correlation (bivariate) using Hermite series based estimators. These estimators are particularly useful in the sequential setting (both stationary and non-stationary) and one-pass batch estimation setting for large data sets. Based on: Stephanou, Michael, Varughese, Melvin and Macdonald, Iain. "Sequential quantiles via Hermite series density estimation." Electronic Journal of Statistics 11.1 (2017): 570-607 <doi:10.1214/17-EJS1245>, Stephanou, Michael and Varughese, Melvin. "On the properties of Hermite series based distribution function estimators." Metrika (2020) <doi:10.1007/s00184-020-00785-z> and Stephanou, Michael and Varughese, Melvin. "Sequential estimation of Spearman rank correlation using Hermite series estimators." Journal of Multivariate Analysis (2021) <doi:10.1016/j.jmva.2021.104783>.
Maintained by Michael Stephanou. Last updated 5 months ago.
cumulative-distribution-functionkendall-correlation-coefficientonline-algorithmsprobability-density-functionquantilespearman-correlation-coefficientstatisticsstreaming-algorithmsstreaming-datacpp
0.8 match 15 stars 5.58 score 17 scriptsellessenne
rsimsum:Analysis of Simulation Studies Including Monte Carlo Error
Summarise results from simulation studies and compute Monte Carlo standard errors of commonly used summary statistics. This package is modelled on the 'simsum' user-written command in 'Stata' (White I.R., 2010 <https://www.stata-journal.com/article.html?article=st0200>), further extending it with additional performance measures and functionality.
Maintained by Alessandro Gasparini. Last updated 8 months ago.
biostatisticsmonte-carlo-errorsimulationsimulation-studysimulationsstatistics
0.5 match 27 stars 8.28 score 146 scriptsbioc
POMA:Tools for Omics Data Analysis
The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.
Maintained by Pol Castellano-Escuder. Last updated 2 months ago.
batcheffectclassificationclusteringdecisiontreedimensionreductionmultidimensionalscalingnormalizationpreprocessingprincipalcomponentregressionrnaseqsoftwarestatisticalmethodvisualizationbioconductorbioinformaticsdata-visualizationdimension-reductionexploratory-data-analysismachine-learningomics-data-integrationpipelinepre-processingstatistical-analysisuser-friendlyworkflow
0.5 match 11 stars 8.38 score 20 scripts 1 dependentsjgraux
PRROC:Precision-Recall and ROC Curves for Weighted and Unweighted Data
Computes the areas under the precision-recall (PR) and ROC curve for weighted (e.g., soft-labeled) and unweighted data. In contrast to other implementations, the interpolation between points of the PR curve is done by a non-linear piecewise function. In addition to the areas under the curves, the curves themselves can also be computed and plotted by a specific S3-method. References: Davis and Goadrich (2006) <doi:10.1145/1143844.1143874>; Keilwagen et al. (2014) <doi:10.1371/journal.pone.0092209>; Grau et al. (2015) <doi:10.1093/bioinformatics/btv153>.
Maintained by Jan Grau. Last updated 7 years ago.
0.5 match 8.25 score 1.2k scripts 50 dependentscmilando
WhiteLabRt:Novel Methods for Reproduction Number Estimation, Back-Calculation, and Forecasting
A collection of functions related to novel methods for estimating R(t), created by the lab of Professor Laura White. Currently implemented methods include two-step Bayesian back-calculation and now-casting for line-list data with missing reporting delays, adapted in 'STAN' from Li (2021) <doi:10.1371/journal.pcbi.1009210>, and calculation of time-varying reproduction number assuming a flux between various adjacent states, adapted into 'STAN' from Zhou (2021) <doi:10.1371/journal.pcbi.1010434>.
Maintained by Chad Milando. Last updated 5 months ago.
0.8 match 6 stars 5.38 score 4 scriptspcruniversum
MBmca:Nucleic Acid Melting Curve Analysis
Lightweight utilities for nucleic acid melting curve analysis are important in life sciences and diagnostics. This software can be used for the analysis and presentation of melting curve data from microbead-based assays (surface melting curve analysis) and reactions in solution (e.g., quantitative PCR (qPCR), real-time isothermal Amplification). Further information are described in detail in two publications in The R Journal [ <https://journal.r-project.org/archive/2013-2/roediger-bohm-schimke.pdf>; <https://journal.r-project.org/archive/2015-1/RJ-2015-1.pdf>].
Maintained by Stefan Roediger. Last updated 4 years ago.
0.9 match 4 stars 4.53 score 17 scriptsjaredsmurray
bcf:Causal Inference for a Binary Treatment and Continuous Outcome using Bayesian Causal Forests
Causal inference for a binary treatment and continuous outcome using Bayesian Causal Forests. See Hahn, Murray and Carvalho (2020) <https://projecteuclid.org/journals/bayesian-analysis/volume-15/issue-3/Bayesian-Regression-Tree-Models-for-Causal-Inference--Regularization-Confounding/10.1214/19-BA1195.full> for additional information. This implementation relies on code originally accompanying Pratola et. al. (2013) <arXiv:1309.1906>.
Maintained by Jared S. Murray. Last updated 1 years ago.
0.5 match 41 stars 8.11 score 45 scriptsahb108
rcarbon:Calibration and Analysis of Radiocarbon Dates
Enables the calibration and analysis of radiocarbon dates, often but not exclusively for the purposes of archaeological research. It includes functions not only for basic calibration, uncalibration, and plotting of one or more dates, but also a statistical framework for building demographic and related longitudinal inferences from aggregate radiocarbon date lists, including: Monte-Carlo simulation test (Timpson et al 2014 <doi:10.1016/j.jas.2014.08.011>), random mark permutation test (Crema et al 2016 <doi:10.1371/journal.pone.0154809>) and spatial permutation tests (Crema, Bevan, and Shennan 2017 <doi:10.1016/j.jas.2017.09.007>).
Maintained by Enrico Crema. Last updated 5 months ago.
0.5 match 33 stars 8.12 score 274 scripts 2 dependentsnsaph-software
CausalGPS:Matching on Generalized Propensity Scores with Continuous Exposures
Provides a framework for estimating causal effects of a continuous exposure using observational data, and implementing matching and weighting on the generalized propensity score. Wu, X., Mealli, F., Kioumourtzoglou, M.A., Dominici, F. and Braun, D., 2022. Matching on generalized propensity scores with continuous exposures. Journal of the American Statistical Association, pp.1-29.
Maintained by Naeem Khoshnevis. Last updated 7 months ago.
0.5 match 24 stars 7.67 score 39 scriptsusepa
spmodel:Spatial Statistical Modeling and Prediction
Fit, summarize, and predict for a variety of spatial statistical models applied to point-referenced and areal (lattice) data. Parameters are estimated using various methods. Additional modeling features include anisotropy, non-spatial random effects, partition factors, big data approaches, and more. Model-fit statistics are used to summarize, visualize, and compare models. Predictions at unobserved locations are readily obtainable. For additional details, see Dumelle et al. (2023) <doi:10.1371/journal.pone.0282524>.
Maintained by Michael Dumelle. Last updated 3 months ago.
0.5 match 15 stars 7.66 score 112 scripts 3 dependentsrhaunschild
BibPlots:Plot Functions for Use in Bibliometrics
Currently, the package provides several functions for plotting and analyzing bibliometric data (JIF, Journal Impact Factor, and paper percentile values), beamplots with citations and percentiles, and three plot functions to visualize the result of a reference publication year spectroscopy (RPYS) analysis performed in the free software 'CRExplorer' (see <http://crexplorer.net>). Further extension to more plot variants is planned.
Maintained by Robin Haunschild. Last updated 3 years ago.
3.9 match 1.00 score 3 scriptsproject-gen3sis
gen3sis:General Engine for Eco-Evolutionary Simulations
Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.
Maintained by Oskar Hagen. Last updated 1 years ago.
biodiversityecologyevolutionmechanisticmodelmodelingsimulationcpp
0.5 match 29 stars 7.56 score 70 scriptsandrewcparnell
simmr:A Stable Isotope Mixing Model
Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load() and simmr_mcmc(). The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Maintained by Emma Govan. Last updated 10 months ago.
0.5 match 28 stars 7.53 score 80 scriptsnrcan
PlotFTIR:Plot FTIR Spectra
The goal of 'PlotFTIR' is to easily and quickly kick-start the production of journal-quality Fourier Transform Infra-Red (FTIR) spectral plots in R using 'ggplot2'. The produced plots can be published directly or further modified by 'ggplot2' functions. L'objectif de 'PlotFTIR' est de démarrer facilement et rapidement la production des tracés spectraux de spectroscopie infrarouge à transformée de Fourier (IRTF) de qualité journal dans R à l'aide de 'ggplot2'. Les tracés produits peuvent être publiés directement ou modifiés davantage par les fonctions 'ggplot2'.
Maintained by Philip Bulsink. Last updated 2 months ago.
0.8 match 4.93 score 5 scriptsliamdbailey
climwin:Climate Window Analysis
Contains functions to detect and visualise periods of climate sensitivity (climate windows) for a given biological response. Please see van de Pol et al. (2016) <doi:10.1111/2041-210X.12590> and Bailey and van de Pol (2016) <doi:10.1371/journal.pone.0167980> for details.
Maintained by Liam D. Bailey. Last updated 5 years ago.
0.5 match 12 stars 7.39 score 129 scriptsrobingenuer
VSURF:Variable Selection Using Random Forests
Three steps variable selection procedure based on random forests. Initially developed to handle high dimensional data (for which number of variables largely exceeds number of observations), the package is very versatile and can treat most dimensions of data, for regression and supervised classification problems. First step is dedicated to eliminate irrelevant variables from the dataset. Second step aims to select all variables related to the response for interpretation purpose. Third step refines the selection by eliminating redundancy in the set of variables selected by the second step, for prediction purpose. Genuer, R. Poggi, J.-M. and Tuleau-Malot, C. (2015) <https://journal.r-project.org/archive/2015-2/genuer-poggi-tuleaumalot.pdf>.
Maintained by Robin Genuer. Last updated 6 months ago.
0.5 match 36 stars 7.49 score 192 scripts 1 dependentscran
MVN:Multivariate Normality Tests
Performs multivariate normality tests and graphical approaches and implements multivariate outlier detection and univariate normality of marginal distributions through plots and tests, and performs multivariate Box-Cox transformation (Korkmaz et al, (2014), <https://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf>).
Maintained by Selcuk Korkmaz. Last updated 4 years ago.
0.5 match 1 stars 7.38 score 604 scripts 4 dependentsyqzhong7
AIPW:Augmented Inverse Probability Weighting
The 'AIPW' package implements the augmented inverse probability weighting, a doubly robust estimator, for average causal effect estimation with user-defined stacked machine learning algorithms. To cite the 'AIPW' package, please use: "Yongqi Zhong, Edward H. Kennedy, Lisa M. Bodnar, Ashley I. Naimi (2021). AIPW: An R Package for Augmented Inverse Probability Weighted Estimation of Average Causal Effects. American Journal of Epidemiology. doi: 10.1093/aje/kwab207". Visit: <https://yqzhong7.github.io/AIPW/> for more information.
Maintained by Yongqi Zhong. Last updated 4 months ago.
causal-inferencemachine-learningrobust-estimators
0.5 match 24 stars 7.35 score 31 scripts 1 dependentswaldronlab
SingleCellMultiModal:Integrating Multi-modal Single Cell Experiment datasets
SingleCellMultiModal is an ExperimentHub package that serves multiple datasets obtained from GEO and other sources and represents them as MultiAssayExperiment objects. We provide several multi-modal datasets including scNMT, 10X Multiome, seqFISH, CITEseq, SCoPE2, and others. The scope of the package is is to provide data for benchmarking and analysis. To cite, use the 'citation' function and see <https://doi.org/10.1371/journal.pcbi.1011324>.
Maintained by Marcel Ramos. Last updated 2 months ago.
experimentdatasinglecelldatareproducibleresearchexperimenthubgeobioconductor-packageu24ca289073
0.5 match 17 stars 7.27 score 57 scriptseldarrak
FLightR:Reconstruct Animal Paths from Solar Geolocation Loggers Data
Spatio-temporal locations of an animal are computed from annotated data with a hidden Markov model via particle filter algorithm. The package is relatively robust to varying degrees of shading. The hidden Markov model is described in Movement Ecology - Rakhimberdiev et al. (2015) <doi:10.1186/s40462-015-0062-5>, general package description is in the Methods in Ecology and Evolution - Rakhimberdiev et al. (2017) <doi:10.1111/2041-210X.12765> and package accuracy assessed in the Journal of Avian Biology - Rakhimberdiev et al. (2016) <doi:10.1111/jav.00891>.
Maintained by Eldar Rakhimberdiev. Last updated 4 months ago.
movement-ecologysolar-geolocation-loggerssolar-geolocator
0.5 match 22 stars 7.27 score 113 scriptsjonathancornelissen
highfrequency:Tools for Highfrequency Data Analysis
Provide functionality to manage, clean and match highfrequency trades and quotes data, calculate various liquidity measures, estimate and forecast volatility, detect price jumps and investigate microstructure noise and intraday periodicity. A detailed vignette can be found in the paper "Analyzing Intraday Financial Data in R: The highfrequency Package" by Boudt, Kleen, and Sjoerup (2022, <doi:10.18637/jss.v104.i08>). The DOI in the CITATION is for a new Journal of Statistical Software publication that will be registered after publication on CRAN. A working paper version can be found on SSRN: <doi:10.2139/ssrn.3917548>.
Maintained by Kris Boudt. Last updated 2 years ago.
0.5 match 150 stars 7.27 score 286 scriptsfarhadpishgar
MatchThem:Matching and Weighting Multiply Imputed Datasets
Provides essential tools for the pre-processing techniques of matching and weighting multiply imputed datasets. The package includes functions for matching within and across multiply imputed datasets using various methods, estimating weights for units in the imputed datasets using multiple weighting methods, calculating causal effect estimates in each matched or weighted dataset using parametric or non-parametric statistical models, and pooling the resulting estimates according to Rubin's rules (please see <https://journal.r-project.org/archive/2021/RJ-2021-073/> for more details).
Maintained by Farhad Pishgar. Last updated 3 months ago.
0.5 match 14 stars 7.24 score 95 scriptszpneal
backbone:Extracts the Backbone from Graphs
An implementation of methods for extracting an unweighted unipartite graph (i.e. a backbone) from an unweighted unipartite graph, a weighted unipartite graph, the projection of an unweighted bipartite graph, or the projection of a weighted bipartite graph (Neal, 2022 <doi:10.1371/journal.pone.0269137>).
Maintained by Zachary Neal. Last updated 12 months ago.
0.5 match 41 stars 7.03 score 29 scripts 2 dependentsplfjohnson
adaptivetau:Tau-Leaping Stochastic Simulation
Implements adaptive tau leaping to approximate the trajectory of a continuous-time stochastic process as described by Cao et al. (2007) The Journal of Chemical Physics <doi:10.1063/1.2745299> (aka. the Gillespie stochastic simulation algorithm). This package is based upon work supported by NSF DBI-0906041 and NIH K99-GM104158 to Philip Johnson and NIH R01-AI049334 to Rustom Antia.
Maintained by Philip Johnson. Last updated 3 months ago.
0.5 match 7.09 score 138 scripts 2 dependentssmin95
smplot2:Create Standalone and Composite Plots in 'ggplot2' for Publications
Provides functions for creating and annotating a composite plot in 'ggplot2'. Offers background themes and shortcut plotting functions that produce figures that are appropriate for the format of scientific journals. Some methods are described in Min and Zhou (2021) <doi:10.3389/fgene.2021.802894>.
Maintained by Seung Hyun Min. Last updated 2 days ago.
easy-to-useggplot2scientific-visualizationvisualization
0.5 match 23 stars 7.00 score 288 scripts 1 dependentsszymonnowakowski
DMRnet:Delete or Merge Regressors Algorithms for Linear and Logistic Model Selection and High-Dimensional Data
Model selection algorithms for regression and classification, where the predictors can be continuous or categorical and the number of regressors may exceed the number of observations. The selected model consists of a subset of numerical regressors and partitions of levels of factors. Szymon Nowakowski, Piotr Pokarowski, Wojciech Rejchel and Agnieszka Sołtys, 2023. Improving Group Lasso for High-Dimensional Categorical Data. In: Computational Science – ICCS 2023. Lecture Notes in Computer Science, vol 14074, p. 455-470. Springer, Cham. <doi:10.1007/978-3-031-36021-3_47>. Aleksandra Maj-Kańska, Piotr Pokarowski and Agnieszka Prochenka, 2015. Delete or merge regressors for linear model selection. Electronic Journal of Statistics 9(2): 1749-1778. <doi:10.1214/15-EJS1050>. Piotr Pokarowski and Jan Mielniczuk, 2015. Combined l1 and greedy l0 penalized least squares for linear model selection. Journal of Machine Learning Research 16(29): 961-992. <https://www.jmlr.org/papers/volume16/pokarowski15a/pokarowski15a.pdf>. Piotr Pokarowski, Wojciech Rejchel, Agnieszka Sołtys, Michał Frej and Jan Mielniczuk, 2022. Improving Lasso for model selection and prediction. Scandinavian Journal of Statistics, 49(2): 831–863. <doi:10.1111/sjos.12546>.
Maintained by Szymon Nowakowski. Last updated 1 years ago.
group-lassolassopartitionpartition-selectionselectionvariable-selection
0.9 match 1 stars 4.04 score 22 scriptsloelschlaeger
fHMM:Fitting Hidden Markov Models to Financial Data
Fitting (hierarchical) hidden Markov models to financial data via maximum likelihood estimation. See Oelschläger, L. and Adam, T. "Detecting Bearish and Bullish Markets in Financial Time Series Using Hierarchical Hidden Markov Models" (2021, Statistical Modelling) <doi:10.1177/1471082X211034048> for a reference on the method. A user guide is provided by the accompanying software paper "fHMM: Hidden Markov Models for Financial Time Series in R", Oelschläger, L., Adam, T., and Michels, R. (2024, Journal of Statistical Software) <doi:10.18637/jss.v109.i09>.
Maintained by Lennart Oelschläger. Last updated 4 months ago.
financehidden-markov-modelscppopenmp
0.5 match 16 stars 7.06 score 5 scriptsswihart
stable:Probability Functions and Generalized Regression Models for Stable Distributions
Density, distribution, quantile and hazard functions of a stable variate; generalized regression models for the parameters of a stable distribution. See the README for how to make equivalent calls to those of 'stabledist' (i.e., Nolan's 0-parameterization and 1-parameterization as detailed in Nolan (2020)). See github for Lambert and Lindsey 1999 JRSS-C journal article, which details the parameterization of the Buck (1995) stable. See the Details section of the `?dstable` help file for context and references.
Maintained by Bruce Swihart. Last updated 3 years ago.
0.5 match 5 stars 6.97 score 30 scripts 49 dependentssongw01
MEGENA:Multiscale Clustering of Geometrical Network
Co-Expression Network Analysis by adopting network embedding technique. Song W.-M., Zhang B. (2015) Multiscale Embedded Gene Co-expression Network Analysis. PLoS Comput Biol 11(11): e1004574. <doi: 10.1371/journal.pcbi.1004574>.
Maintained by Won-Min Song. Last updated 1 years ago.
0.5 match 49 stars 6.82 score 45 scripts 1 dependentslcrawlab
mvMAPIT:Multivariate Genome Wide Marginal Epistasis Test
Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants that are involved in epistasis, and nearly all of these approaches carry out this task by focusing on analyzing one trait at a time. Previous studies have shown that jointly modeling multiple phenotypes can often dramatically increase statistical power for association mapping. In this package, we present the 'multivariate MArginal ePIstasis Test' ('mvMAPIT') – a multi-outcome generalization of a recently proposed epistatic detection method which seeks to detect marginal epistasis or the combined pairwise interaction effects between a given variant and all other variants. By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact – thus, potentially alleviating much of the statistical and computational burden associated with conventional explicit search based methods. Our proposed 'mvMAPIT' builds upon this strategy by taking advantage of correlation structure between traits to improve the identification of variants involved in epistasis. We formulate 'mvMAPIT' as a multivariate linear mixed model and develop a multi-trait variance component estimation algorithm for efficient parameter inference and P-value computation. Together with reasonable model approximations, our proposed approach is scalable to moderately sized genome-wide association studies. Crawford et al. (2017) <doi:10.1371/journal.pgen.1006869>. Stamp et al. (2023) <doi:10.1093/g3journal/jkad118>.
Maintained by Julian Stamp. Last updated 3 months ago.
cppepistasisepistasis-analysisgwasgwas-toolslinear-mixed-modelsmapitmvmapitvariance-componentsopenblascppopenmp
0.5 match 11 stars 6.90 score 17 scripts 1 dependentsbquast
decompr:Global Value Chain Decomposition
Three global value chain (GVC) decompositions are implemented. The Leontief decomposition derives the value added origin of exports by country and industry as in Hummels, Ishii and Yi (2001). The Koopman, Wang and Wei (2014) decomposition splits country-level exports into 9 value added components, and the Wang, Wei and Zhu (2013) decomposition splits bilateral exports into 16 value added components. Various GVC indicators based on these decompositions are computed in the complimentary 'gvc' package. --- References: --- Hummels, D., Ishii, J., & Yi, K. M. (2001). The nature and growth of vertical specialization in world trade. Journal of international Economics, 54(1), 75-96. Koopman, R., Wang, Z., & Wei, S. J. (2014). Tracing value-added and double counting in gross exports. American Economic Review, 104(2), 459-94. Wang, Z., Wei, S. J., & Zhu, K. (2013). Quantifying international production sharing at the bilateral and sector levels (No. w19677). National Bureau of Economic Research.
Maintained by Bastiaan Quast. Last updated 1 years ago.
0.5 match 17 stars 6.78 score 118 scripts 1 dependentstejapi
Tejapi:API Wrapper for Taiwan Economic Journal Data Service
Functions for interacting directly with the Taiwan Economic Journal API to offer data in R. For more information go to <https://api.tej.com.tw>.
Maintained by Peter Young. Last updated 6 years ago.
3.4 match 1.00 score 3 scriptsmaliny12
sugarglider:Create Glyph-Maps of Spatiotemporal Data
Provides 'ggplot2' extensions to construct glyph-maps for visualizing seasonality in spatiotemporal data. See the Journal of Statistical Software reference: Zhang, H. S., Cook, D., Laa, U., Langrené, N., & Menéndez, P. (2024) <doi:10.18637/jss.v110.i07>. The manuscript for this package is currently under preparation and can be found on GitHub at <https://github.com/maliny12/paper-sugarglider>.
Maintained by Maliny Po. Last updated 12 days ago.
0.5 match 9 stars 6.60 score 7 scriptss3alfisc
fwildclusterboot:Fast Wild Cluster Bootstrap Inference for Linear Models
Implementation of fast algorithms for wild cluster bootstrap inference developed in 'Roodman et al' (2019, 'STATA' Journal, <doi:10.1177/1536867X19830877>) and 'MacKinnon et al' (2022), which makes it feasible to quickly calculate bootstrap test statistics based on a large number of bootstrap draws even for large samples. Multiple bootstrap types as described in 'MacKinnon, Nielsen & Webb' (2022) are supported. Further, 'multiway' clustering, regression weights, bootstrap weights, fixed effects and 'subcluster' bootstrapping are supported. Further, both restricted ('WCR') and unrestricted ('WCU') bootstrap are supported. Methods are provided for a variety of fitted models, including 'lm()', 'feols()' (from package 'fixest') and 'felm()' (from package 'lfe'). Additionally implements a 'heteroskedasticity-robust' ('HC1') wild bootstrap. Last, the package provides an R binding to 'WildBootTests.jl', which provides additional speed gains and functionality, including the 'WRE' bootstrap for instrumental variable models (based on models of type 'ivreg()' from package 'ivreg') and hypotheses with q > 1.
Maintained by Alexander Fischer. Last updated 1 years ago.
clustered-standard-errorslinear-regression-modelswild-bootstrapwild-cluster-bootstrapopenblascppopenmp
0.5 match 24 stars 6.68 score 111 scripts 2 dependentskbhoehn
dowser:B Cell Receptor Phylogenetics Toolkit
Provides a set of functions for inferring, visualizing, and analyzing B cell phylogenetic trees. Provides methods to 1) reconstruct unmutated ancestral sequences, 2) build B cell phylogenetic trees using multiple methods, 3) visualize trees with metadata at the tips, 4) reconstruct intermediate sequences, 5) detect biased ancestor-descendant relationships among metadata types Workflow examples available at documentation site (see URL). Citations: Hoehn et al (2022) <doi:10.1371/journal.pcbi.1009885>, Hoehn et al (2021) <doi:10.1101/2021.01.06.425648>.
Maintained by Kenneth Hoehn. Last updated 6 days ago.
0.5 match 6.64 score 57 scriptstidymodels
plsmod:Model Wrappers for Projection Methods
Bindings for additional regression models for use with the 'parsnip' package, including ordinary and spare partial least squares models for regression and classification (Rohart et al (2017) <doi:10.1371/journal.pcbi.1005752>).
Maintained by Max Kuhn. Last updated 3 months ago.
0.5 match 14 stars 6.47 score 58 scripts 1 dependentsanhoej
qicharts:Quality Improvement Charts
Functions for making run charts [Anhoej, Olesen (2014) <doi:10.1371/journal.pone.0113825>] and basic Shewhart control charts [Mohammed, Worthington, Woodall (2008) <doi:10.1136/qshc.2004.012047>] for measure and count data. The main function, qic(), creates run and control charts and has a simple interface with a rich set of options to control data analysis and plotting, including options for automatic data aggregation by subgroups, easy analysis of before-and-after data, exclusion of one or more data points from analysis, and splitting charts into sequential time periods. Missing values and empty subgroups are handled gracefully.
Maintained by Jacob Anhoej. Last updated 4 years ago.
0.5 match 4 stars 6.60 score 83 scripts 1 dependentsmhashemihsmw
MLMOI:Estimating Frequencies, Prevalence and Multiplicity of Infection
The implemented methods reach out to scientists that seek to estimate multiplicity of infection (MOI) and lineage (allele) frequencies and prevalences at molecular markers using the maximum-likelihood method described in Schneider (2018) <doi:10.1371/journal.pone.0194148>, and Schneider and Escalante (2014) <doi:10.1371/journal.pone.0097899>. Users can import data from Excel files in various formats, and perform maximum-likelihood estimation on the imported data by the package's moimle() function.
Maintained by Meraj Hashemi. Last updated 1 years ago.
datadata-visualizationdataanalysisdatapreprocessingdatawranglingstatistical-models
0.8 match 4.30 score 2 scriptssdanzige
ADAPTS:Automated Deconvolution Augmentation of Profiles for Tissue Specific Cells
Tools to construct (or add to) cell-type signature matrices using flow sorted or single cell samples and deconvolve bulk gene expression data. Useful for assessing the quality of single cell RNAseq experiments, estimating the accuracy of signature matrices, and determining cell-type spillover. Please cite: Danziger SA et al. (2019) ADAPTS: Automated Deconvolution Augmentation of Profiles for Tissue Specific cells <doi:10.1371/journal.pone.0224693>.
Maintained by Samuel A Danziger. Last updated 2 years ago.
0.5 match 2 stars 6.56 score 40 scripts 1 dependentsmottensmann
GCalignR:Simple Peak Alignment for Gas-Chromatography Data
Aligns peak based on peak retention times and matches homologous peaks across samples. The underlying alignment procedure comprises three sequential steps. (1) Full alignment of samples by linear transformation of retention times to maximise similarity among homologous peaks (2) Partial alignment of peaks within a user-defined retention time window to cluster homologous peaks (3) Merging rows that are likely representing homologous substances (i.e. no sample shows peaks in both rows and the rows have similar retention time means). The algorithm is described in detail in Ottensmann et al., 2018 <doi:10.1371/journal.pone.0198311>.
Maintained by Meinolf Ottensmann. Last updated 4 months ago.
0.5 match 5 stars 6.57 score 41 scriptsbeirnaert
speaq:Tools for Nuclear Magnetic Resonance (NMR) Spectra Alignment, Peak Based Processing, Quantitative Analysis and Visualizations
Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More details can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
Maintained by Charlie Beirnaert. Last updated 3 years ago.
0.5 match 9 stars 6.55 score 26 scripts 1 dependentsthongphamthe
PAFit:Generative Mechanism Estimation in Temporal Complex Networks
Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>. Thong Pham et al. (2021) <doi:10.1093/comnet/cnab024>.
Maintained by Thong Pham. Last updated 10 months ago.
complex-networksfit-get-richergeneral-preferential-attachmentminorize-maximizationpreferential-attachmentrich-get-richerscale-freetemporal-networkscppopenmp
0.5 match 17 stars 6.47 score 70 scriptsremkoduursma
plantecophys:Modelling and Analysis of Leaf Gas Exchange Data
Coupled leaf gas exchange model, A-Ci curve simulation and fitting, Ball-Berry stomatal conductance models, leaf energy balance using Penman-Monteith, Cowan-Farquhar optimization, humidity unit conversions. See Duursma (2015) <doi:10.1371/journal.pone.0143346>.
Maintained by Remko Duursma. Last updated 4 years ago.
0.5 match 6.38 score 159 scriptsnucleic-acid
namedropR:Create Visual Citations for Presentations and Posters
Provides 'visual citations' containing the metadata of a scientific paper and a 'QR' code. A 'visual citation' is a banner containing title, authors, journal and year of a publication. This package can create such banners based on 'BibTeX' and 'BibLaTeX' references or call the reference metadata from 'Crossref'-API. The banners include a QR code pointing to the 'DOI'. The resulting HTML object or PNG image can be included in a presentation to point the audience to good resources for further reading. Styling is possible via predefined designs or via custom 'CSS'. This package is not intended as replacement for proper reference manager packages, but a tool to enrich scientific presentation slides and conference posters.
Maintained by Christian A. Gebhard. Last updated 2 years ago.
0.5 match 61 stars 6.44 score 8 scriptsfcampelo
MOEADr:Component-Wise MOEA/D Implementation
Modular implementation of Multiobjective Evolutionary Algorithms based on Decomposition (MOEA/D) [Zhang and Li (2007), <DOI:10.1109/TEVC.2007.892759>] for quick assembling and testing of new algorithmic components, as well as easy replication of published MOEA/D proposals. The full framework is documented in a paper published in the Journal of Statistical Software [<doi:10.18637/jss.v092.i06>].
Maintained by Felipe Campelo. Last updated 2 years ago.
moeadmultiobjective-optimization
0.5 match 20 stars 6.30 score 40 scriptspaulregular
SimSurvey:Test Surveys by Simulating Spatially-Correlated Populations
Simulate age-structured populations that vary in space and time and explore the efficacy of a range of built-in or user-defined sampling protocols to reproduce the population parameters of the known population. (See Regular et al. (2020) <doi:10.1371/journal.pone.0232822> for more details).
Maintained by Paul Regular. Last updated 1 years ago.
analysisfisheries-researchsimulation-testingsurvey-design
0.5 match 11 stars 6.24 score 106 scriptsastamm
roahd:Robust Analysis of High Dimensional Data
A collection of methods for the robust analysis of univariate and multivariate functional data, possibly in high-dimensional cases, and hence with attention to computational efficiency and simplicity of use. See the R Journal publication of Ieva et al. (2019) <doi:10.32614/RJ-2019-032> for an in-depth presentation of the 'roahd' package. See Aleman-Gomez et al. (2021) <arXiv:2103.08874> for details about the concept of depthgram.
Maintained by Aymeric Stamm. Last updated 3 years ago.
0.5 match 2 stars 6.29 score 164 scripts 2 dependentsgforge
Greg:Regression Helper Functions
Methods for manipulating regression models and for describing these in a style adapted for medical journals. Contains functions for generating an HTML table with crude and adjusted estimates, plotting hazard ratio, plotting model estimates and confidence intervals using forest plots, extending this to comparing multiple models in a single forest plots. In addition to the descriptive methods, there are functions for the robust covariance matrix provided by the 'sandwich' package, a function for adding non-linearities to a model, and a wrapper around the 'Epi' package's Lexis() functions for time-splitting a dataset when modeling non-proportional hazards in Cox regressions.
Maintained by Max Gordon. Last updated 12 months ago.
0.5 match 6 stars 6.21 score 67 scriptsstoreylab
popkin:Estimate Kinship and FST under Arbitrary Population Structure
Provides functions to estimate the kinship matrix of individuals from a large set of biallelic SNPs, and extract inbreeding coefficients and the generalized FST (Wright's fixation index). Method described in Ochoa and Storey (2021) <doi:10.1371/journal.pgen.1009241>.
Maintained by Alejandro Ochoa. Last updated 4 months ago.
0.5 match 19 stars 6.09 score 65 scriptsbioc
idpr:Profiling and Analyzing Intrinsically Disordered Proteins in R
‘idpr’ aims to integrate tools for the computational analysis of intrinsically disordered proteins (IDPs) within R. This package is used to identify known characteristics of IDPs for a sequence of interest with easily reported and dynamic results. Additionally, this package includes tools for IDP-based sequence analysis to be used in conjunction with other R packages. Described in McFadden WM & Yanowitz JL (2022). "idpr: A package for profiling and analyzing Intrinsically Disordered Proteins in R." PloS one, 17(4), e0266929. <https://doi.org/10.1371/journal.pone.0266929>.
Maintained by William M. McFadden. Last updated 3 months ago.
structuralpredictionproteomicscellbiology
0.5 match 4 stars 6.16 score 20 scriptsjto888
stosim:Stochastic Simulator for Reliability Modeling of Repairable Systems
A toolkit for Reliability Availability and Maintainability (RAM) modeling of industrial process systems.
Maintained by Jacob Ormerod. Last updated 1 years ago.
3.1 match 1.00 score 4 scriptsvaleriapolicastro
robin:ROBustness in Network
Assesses the robustness of the community structure of a network found by one or more community detection algorithm to give indications about their reliability. It detects if the community structure found by a set of algorithms is statistically significant and compares the different selected detection algorithms on the same network. robin helps to choose among different community detection algorithms the one that better fits the network of interest. Reference in Policastro V., Righelli D., Carissimo A., Cutillo L., De Feis I. (2021) <https://journal.r-project.org/archive/2021/RJ-2021-040/index.html>.
Maintained by Valeria Policastro. Last updated 8 days ago.
0.5 match 18 stars 6.10 score 8 scriptserblast
easyalluvial:Generate Alluvial Plots with a Single Line of Code
Alluvial plots are similar to sankey diagrams and visualise categorical data over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694> Their graphical grammar however is a bit more complex then that of a regular x/y plots. The 'ggalluvial' package made a great job of translating that grammar into 'ggplot2' syntax and gives you many options to tweak the appearance of an alluvial plot, however there still remains a multi-layered complexity that makes it difficult to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple interface to this package that allows you to produce a decent alluvial plot from any dataframe in either long or wide format from a single line of code while also handling continuous data. It is meant to allow a quick visualisation of entire dataframes with a focus on different colouring options that can make alluvial plots a great tool for data exploration.
Maintained by Bjoern Koneswarakantha. Last updated 1 years ago.
0.5 match 110 stars 6.13 score 81 scripts 1 dependentsmhahsler
streamMOA:Interface for MOA Stream Clustering Algorithms
Interface for data stream clustering algorithms implemented in the MOA (Massive Online Analysis) framework (Albert Bifet, Geoff Holmes, Richard Kirkby, Bernhard Pfahringer (2010). MOA: Massive Online Analysis, Journal of Machine Learning Research 11: 1601-1604).
Maintained by Michael Hahsler. Last updated 5 months ago.
clusteringdataminingdatastreamopenjdk
0.5 match 12 stars 5.95 score 37 scriptspaterijk
MCDA:Support for the Multicriteria Decision Aiding Process
Support for the analyst in a Multicriteria Decision Aiding (MCDA) process with algorithms, preference elicitation and data visualisation functions. Sébastien Bigaret, Richard Hodgett, Patrick Meyer, Tatyana Mironova, Alexandru Olteanu (2017) Supporting the multi-criteria decision aiding process : R and the MCDA package, Euro Journal On Decision Processes, Volume 5, Issue 1 - 4, pages 169 - 194 <doi:10.1007/s40070-017-0064-1>.
Maintained by Patrick Meyer. Last updated 2 years ago.
0.5 match 29 stars 6.02 score 181 scripts