Showing 150 of total 150 results (show query)
cran
ForestElementsR:Data Structures and Functions for Working with Forest Data
Provides generic data structures and algorithms for use with forest mensuration data in a consistent framework. The functions and objects included are a collection of broadly applicable tools. More specialized applications should be implemented in separate packages that build on this foundation. Documentation about 'ForestElementsR' is provided by three vignettes included in this package. For an introduction to the field of forest mensuration, refer to the textbooks by Kershaw et al. (2017) <doi:10.1002/9781118902028>, and van Laar and Akca (2007) <doi:10.1007/978-1-4020-5991-9>.
Maintained by Peter Biber. Last updated 1 months ago.
39.7 match 3.48 scorecran
STAND:Statistical Analysis of Non-Detects
Provides functions for the analysis of occupational and environmental data with non-detects. Maximum likelihood (ML) methods for censored log-normal data and non-parametric methods based on the product limit estimate (PLE) for left censored data are used to calculate all of the statistics recommended by the American Industrial Hygiene Association (AIHA) for the complete data case. Functions for the analysis of complete samples using exact methods are also provided for the lognormal model. Revised from 2007-11-05 'survfit~1'.
Maintained by E. P. Adams. Last updated 9 years ago.
55.0 match 2.00 score
molina-valero
FORTLS:Automatic Processing of Terrestrial-Based Technologies Point Cloud Data for Forestry Purposes
Process automation of point cloud data derived from terrestrial-based technologies such as Terrestrial Laser Scanner (TLS) or Mobile Laser Scanner. 'FORTLS' enables (i) detection of trees and estimation of tree-level attributes (e.g. diameters and heights), (ii) estimation of stand-level variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories at stand-level, and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2022, <doi:10.1016/j.envsoft.2022.105337>).
Maintained by Juan Alberto Molina-Valero. Last updated 3 months ago.
forest-inventoryforest-monitoringlidar-point-cloudcpp
16.3 match 22 stars 6.16 score 11 scripts
statmanrobin
Stat2Data:Datasets for Stat2
Datasets for the textbook Stat2: Modeling with Regression and ANOVA (second edition). The package also includes data for the first edition, Stat2: Building Models for a World of Data and a few functions for plotting diagnostics.
Maintained by Robin Lock. Last updated 6 years ago.
18.4 match 5 stars 4.94 score 544 scripts
umr-amap
BIOMASS:Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests
Contains functions for estimating above-ground biomass/carbon and its uncertainty in tropical forests. These functions allow to (1) retrieve and correct taxonomy, (2) estimate wood density and its uncertainty, (3) build height-diameter models, (4) manage tree and plot coordinates, (5) estimate above-ground biomass/carbon at stand level with associated uncertainty. To cite ‘BIOMASS’, please use citation(‘BIOMASS’). For more information, see Réjou-Méchain et al. (2017) <doi:10.1111/2041-210X.12753>.
Maintained by Dominique Lamonica. Last updated 10 hours ago.
8.4 match 26 stars 9.90 score 68 scripts 1 dependents
billpetti
baseballr:Acquiring and Analyzing Baseball Data
Provides numerous utilities for acquiring and analyzing baseball data from online sources such as 'Baseball Reference' <https://www.baseball-reference.com/>, 'FanGraphs' <https://www.fangraphs.com/>, and the 'MLB Stats' API <https://www.mlb.com/>.
Maintained by Saiem Gilani. Last updated 4 months ago.
baseballpitchfxsabermetricsstatcast
7.8 match 380 stars 8.98 score 582 scripts
sportsdataverse
hoopR:Access Men's Basketball Play by Play Data
A utility to quickly obtain clean and tidy men's basketball play by play data. Provides functions to access live play by play and box score data from ESPN<https://www.espn.com> with shot locations when available. It is also a full NBA Stats API<https://www.nba.com/stats/> wrapper. It is also a scraping and aggregating interface for Ken Pomeroy's men's college basketball statistics website<https://kenpom.com>. It provides users with an active subscription the capability to scrape the website tables and analyze the data for themselves.
Maintained by Saiem Gilani. Last updated 1 years ago.
basketballcollege-basketballespnkenpomnbanba-analyticsnba-apinba-datanba-statisticsnba-statsnba-stats-apincaancaa-basketballncaa-bracketncaa-playersncaa-ratingsncaamsportsdataverse
8.8 match 91 stars 6.93 score 261 scripts
emf-creaf
medfateland:Mediterranean Landscape Simulation
Simulate forest hydrology, forest function and dynamics over landscapes [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>]. Parallelization is allowed in several simulation functions and simulations may be conducted including spatial processes such as lateral water transfer and seed dispersal.
Maintained by Miquel De Cáceres. Last updated 27 days ago.
8.8 match 5 stars 5.41 score 41 scriptsemf-creaf
medfate:Mediterranean Forest Simulation
Simulate Mediterranean forest functioning and dynamics using cohort-based description of vegetation [De Caceres et al. (2015) <doi:10.1016/j.agrformet.2015.06.012>; De Caceres et al. (2021) <doi:10.1016/j.agrformet.2020.108233>].
Maintained by Miquel De Cáceres. Last updated 11 days ago.
6.0 match 11 stars 7.49 score 183 scripts 1 dependents
blasbenito
distantia:Advanced Toolset for Efficient Time Series Dissimilarity Analysis
Fast C++ implementation of Dynamic Time Warping for time series dissimilarity analysis, with applications in environmental monitoring and sensor data analysis, climate science, signal processing and pattern recognition, and financial data analysis. Built upon the ideas presented in Benito and Birks (2020) <doi:10.1111/ecog.04895>, provides tools for analyzing time series of varying lengths and structures, including irregular multivariate time series. Key features include individual variable contribution analysis, restricted permutation tests for statistical significance, and imputation of missing data via GAMs. Additionally, the package provides an ample set of tools to prepare and manage time series data.
Maintained by Blas M. Benito. Last updated 27 days ago.
dissimilaritydynamic-time-warpinglock-steptime-seriescpp
7.0 match 23 stars 5.76 score 11 scripts
flavioleccese92
euroleaguer:Euroleague and Eurocup basketball API
Unofficial API wrapper for 'Euroleague' and 'Eurocup' basketball API (<https://www.euroleaguebasketball.net/en/euroleague/>), it allows to retrieve real-time and historical standard and advanced statistics about competitions, teams, players and games.
Maintained by Flavio Leccese. Last updated 3 months ago.
analyticsbasketballdatadata-sciencelibrary
9.3 match 7 stars 4.15 score 7 scripts
inasevmon
sitree:Single Tree Simulator
Framework to build an individual tree simulator.
Maintained by Ignacio Sevillano. Last updated 1 days ago.
13.4 match 2.78 score 1 dependents
nflverse
nflseedR:Functions to Efficiently Simulate and Evaluate NFL Seasons
A set of functions to simulate National Football League seasons including the sophisticated tie-breaking procedures.
Maintained by Sebastian Carl. Last updated 7 days ago.
football-simulationnflseason-simulations
5.8 match 23 stars 6.32 score 34 scripts 1 dependents
jozefhajnala
nhlapi:A Minimum-Dependency 'R' Interface to the 'NHL' API
Retrieves and processes the data exposed by the open 'NHL' API. This includes information on players, teams, games, tournaments, drafts, standings, schedules and other endpoints. A lower-level interface to access the data via URLs directly is also provided.
Maintained by Jozef Hajnala. Last updated 4 years ago.
6.0 match 29 stars 6.00 score 23 scripts
pschmidtwalter
LWFBrook90R:Simulate Evapotranspiration and Soil Moisture with the SVAT Model LWF-Brook90
Provides a flexible and easy-to use interface for the soil vegetation atmosphere transport (SVAT) model LWF-BROOK90, written in Fortran. The model simulates daily transpiration, interception, soil and snow evaporation, streamflow and soil water fluxes through a soil profile covered with vegetation, as described in Hammel & Kennel (2001, ISBN:978-3-933506-16-0) and Federer et al. (2003) <doi:10.1175/1525-7541(2003)004%3C1276:SOAETS%3E2.0.CO;2>. A set of high-level functions for model set up, execution and parallelization provides easy access to plot-level SVAT simulations, as well as multi-run and large-scale applications.
Maintained by Paul Schmidt-Walter. Last updated 5 months ago.
evapotranspirationmodelingwaterbalancewaterfluxfortran
5.1 match 11 stars 6.38 score 27 scriptssportsdataverse
wehoop:Access Women's Basketball Play by Play Data
A utility for working with women's basketball data. A scraping and aggregating interface for the WNBA Stats API <https://stats.wnba.com/> and ESPN's <https://www.espn.com> women's college basketball and WNBA statistics. It provides users with the capability to access the game play-by-plays, box scores, standings and results to analyze the data for themselves.
Maintained by Saiem Gilani. Last updated 8 months ago.
college-basketballespnespn-statsncaancaa-basketballprofessional-basketball-datasportsdataversewnbawnba-playerswnba-statswomens-basketball
5.9 match 28 stars 5.36 score 54 scripts
r-forge
RobAStBase:Robust Asymptotic Statistics
Base S4-classes and functions for robust asymptotic statistics.
Maintained by Matthias Kohl. Last updated 2 months ago.
6.3 match 4.96 score 64 scripts 4 dependents
rhartmano
labelr:Label Data Frames, Variables, and Values
Create and use data frame labels for data frame objects (frame labels), their columns (name labels), and individual values of a column (value labels). Value labels include one-to-one and many-to-one labels for nominal and ordinal variables, as well as numerical range-based value labels for continuous variables. Convert value-labeled variables so each value is replaced by its corresponding value label. Add values-converted-to-labels columns to a value-labeled data frame while preserving parent columns. Filter and subset a value-labeled data frame using labels, while returning results in terms of values. Overlay labels in place of values in common R commands to increase interpretability. Generate tables of value frequencies, with categories expressed as raw values or as labels. Access data frames that show value-to-label mappings for easy reference.
Maintained by Robert Hartman. Last updated 7 months ago.
5.6 match 3 stars 5.56 score 10 scriptsstatmanrobin
Lock5Data:Datasets for "Statistics: UnLocking the Power of Data"
Datasets for the third edition of "Statistics: Unlocking the Power of Data" by Lock^5 Includes version of datasets from earlier editions.
Maintained by Robin Lock. Last updated 4 years ago.
10.5 match 2.90 score 322 scripts
daroczig
logger:A Lightweight, Modern and Flexible Logging Utility
Inspired by the the 'futile.logger' R package and 'logging' Python module, this utility provides a flexible and extensible way of formatting and delivering log messages with low overhead.
Maintained by Gergely Daróczi. Last updated 2 months ago.
1.8 match 298 stars 16.88 score 1.5k scripts 98 dependents
fvafrcu
treePlotArea:Correction Factors for Tree Plot Areas Intersected by Stand Boundaries
The German national forest inventory uses angle count sampling, a sampling method first published as `Bitterlich, W.: Die Winkelzählmessung. Allgemeine Forst- und Holzwirtschaftliche Zeitung, 58. Jahrg., Folge 11/12 vom Juni 1947` and extended by Grosenbaugh (<https://academic.oup.com/jof/article-abstract/50/1/32/4684174>) as probability proportional to size sampling. When plots are located near stand boundaries, their sizes and hence their probabilities need to be corrected.
Maintained by Andreas Dominik Cullmann. Last updated 12 months ago.
6.7 match 4.00 score
thomas-neitmann
ggcharts:Get You to Your Desired Plot Faster
Streamlines the creation of common charts by taking care of a lot of data preprocessing and plot customization for the user. Provides a high-level interface for creating plots using 'ggplot2'.
Maintained by Thomas Neitmann. Last updated 3 years ago.
data-visualizationggplot2plots
3.1 match 291 stars 8.49 score 119 scripts 1 dependents
euctrl-pru
HexAeroR:A package to determine used airports, runways, taxiways and stands based on available flight coordinates.
HexAeroR is a EUROCONTROL R package designed for aviation professionals and data analysts. It allows for the determination of used airports, runways, taxiways, and stands based on available (ADS-B) flight trajectory coordinates. This tool aims to enhance aviation data analysis, facilitating the extraction of milestones for performance analysis.
Maintained by Quinten Goens. Last updated 1 years ago.
adepadesaircraftairportaprondetectioneurocontrolh3hexaerohexaerorrunwaystandstaxiwaystrajectoryuber
13.2 match 2.00 score 2 scripts
laurimeh
lmfor:Functions for Forest Biometrics
Functions for different purposes related to forest biometrics, including illustrative graphics, numerical computation, modeling height-diameter relationships, prediction of tree volumes, modelling of diameter distributions and estimation off stand density using ITD. Several empirical datasets are also included.
Maintained by Lauri Mehtatalo. Last updated 3 years ago.
10.7 match 3 stars 2.42 score 29 scripts 1 dependentscran
rsatscan:Tools, Classes, and Methods for Interfacing with 'SaTScan' Stand-Alone Software
'SaTScan'(TM) <https://www.satscan.org> is software for finding regions in Time, Space, or Time-Space that have excess risk, based on scan statistics, and uses Monte Carlo hypothesis testing to generate P-values for these regions. The 'rsatscan' package provides functions for writing R data frames in 'SaTScan'-readable formats, for setting 'SaTScan' parameters, for running 'SaTScan' in the OS, and for reading the files that 'SaTScan' creates.
Maintained by Scott Hostovich. Last updated 9 months ago.
4.5 match 8 stars 5.45 score 35 scripts
xavi-rp
LPDynR:Land Productivity Dynamics Indicator
It uses 'phenological' and productivity-related variables derived from time series of vegetation indexes, such as the Normalized Difference Vegetation Index, to assess ecosystem dynamics and change, which eventually might drive to land degradation. The final result of the Land Productivity Dynamics indicator is a categorical map with 5 classes of land productivity dynamics, ranging from declining to increasing productivity. See www.sciencedirect.com/science/article/pii/S1470160X21010517/ for a description of the methods used in the package to calculate the indicator.
Maintained by Xavier Rotllan-Puig. Last updated 6 months ago.
copernicus-global-land-serviceearth-observationland-degradationland-productivityvegetation
4.5 match 8 stars 4.90 score 5 scripts
elliottsmeds
lacunr:Fast 3D Lacunarity for Voxel Data
Calculates 3D lacunarity from voxel data. It is designed for use with point clouds generated from Light Detection And Ranging (LiDAR) scans in order to measure the spatial heterogeneity of 3-dimensional structures such as forest stands. It provides fast 'C++' functions to efficiently bin point cloud data into voxels and calculate lacunarity using different variants of the gliding-box algorithm originated by Allain & Cloitre (1991) <doi:10.1103/PhysRevA.44.3552>.
Maintained by Elliott Smeds. Last updated 9 months ago.
3.9 match 4 stars 5.56 score 7 scripts
jimmyday12
fitzRoy:Easily Scrape and Process AFL Data
An easy package for scraping and processing Australia Rules Football (AFL) data. 'fitzRoy' provides a range of functions for accessing publicly available data from 'AFL Tables' <https://afltables.com/afl/afl_index.html>, 'Footy Wire' <https://www.footywire.com> and 'The Squiggle' <https://squiggle.com.au>. Further functions allow for easy processing, cleaning and transformation of this data into formats that can be used for analysis.
Maintained by James Day. Last updated 2 months ago.
2.0 match 134 stars 10.74 score 324 scripts
predictiveecology
LandR:Landscape Ecosystem Modelling in R
Utilities for 'LandR' suite of landscape simulation models. These models simulate forest vegetation dynamics based on LANDIS-II, and incorporate fire and insect disturbance, as well as other important ecological processes. Models are implemented as 'SpaDES' modules.
Maintained by Eliot J B McIntire. Last updated 6 days ago.
ecological-modellinglandscape-ecosystem-modellingspades
3.5 match 17 stars 6.07 score 12 scripts 4 dependents
traitecoevo
plant:A Package for Modelling Forest Trait Ecology and Evolution
Solves trait, size and patch structured model from (Falster et al. 2016) using either method of characteristics or as stochastic, finite-sized population.
Maintained by Daniel Falster. Last updated 9 days ago.
c-plus-plusdemographydynamicecologyevolutionforestsplant-physiologyscience-researchsimulationtraitcpp
3.5 match 53 stars 5.87 score
neuhausi
canvasXpress:Visualization Package for CanvasXpress in R
Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.
Maintained by Connie Brett. Last updated 21 hours ago.
analyticsbioinformaticschartchartingdashdashboarddata-analyticsdata-sciencedata-visualizationgenomicsgraphsjavascriptnetworknetwork-visualizationpythonreproducible-researchshinyvisualization
1.8 match 295 stars 11.35 score 145 scripts
wadpac
GGIR:Raw Accelerometer Data Analysis
A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://activinsights.com/>, binary (.gt3x) and .csv-export data from 'Actigraph' <https://theactigraph.com> devices, and binary (.cwa) and .csv-export data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format. Also the package allows for external function embedding.
Maintained by Vincent T van Hees. Last updated 4 days ago.
accelerometeractivity-recognitioncircadian-rhythmmovement-sensorsleep
1.5 match 109 stars 13.20 score 342 scripts 3 dependents
cynkra
dm:Relational Data Models
Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.
Maintained by Kirill Müller. Last updated 3 months ago.
data-modeldata-warehousingdatawarehousingdbidbplyrrelational-databases
1.3 match 511 stars 14.81 score 410 scripts 8 dependents
floschuberth
cSEM:Composite-Based Structural Equation Modeling
Estimate, assess, test, and study linear, nonlinear, hierarchical and multigroup structural equation models using composite-based approaches and procedures, including estimation techniques such as partial least squares path modeling (PLS-PM) and its derivatives (PLSc, ordPLSc, robustPLSc), generalized structured component analysis (GSCA), generalized structured component analysis with uniqueness terms (GSCAm), generalized canonical correlation analysis (GCCA), principal component analysis (PCA), factor score regression (FSR) using sum score, regression or Bartlett scores (including bias correction using Croon’s approach), as well as several tests and typical postestimation procedures (e.g., verify admissibility of the estimates, assess the model fit, test the model fit etc.).
Maintained by Florian Schuberth. Last updated 10 hours ago.
2.0 match 28 stars 9.22 score 56 scripts 2 dependents
ffverse
ffscrapr:API Client for Fantasy Football League Platforms
Helps access various Fantasy Football APIs by handling authentication and rate-limiting, forming appropriate calls, and returning tidy dataframes which can be easily connected to other data sources.
Maintained by Tan Ho. Last updated 5 months ago.
api-clientfantasy-footballfantasy-football-api
2.3 match 84 stars 8.07 score 178 scripts 1 dependents
scasanova
f1dataR:Access Formula 1 Data
Obtain Formula 1 data via the 'Jolpica API' <https://jolpi.ca> and the unofficial API <https://www.formula1.com/en/timing/f1-live> via the 'fastf1' 'Python' library <https://docs.fastf1.dev/>.
Maintained by Santiago Casanova. Last updated 17 days ago.
2.3 match 58 stars 7.96 score 26 scripts
winvector
rquery:Relational Query Generator for Data Manipulation at Scale
A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.
Maintained by John Mount. Last updated 2 years ago.
1.9 match 110 stars 9.53 score 126 scripts 3 dependentsnflverse
nflfastR:Functions to Efficiently Access NFL Play by Play Data
A set of functions to access National Football League play-by-play data from <https://www.nfl.com/>.
Maintained by Ben Baldwin. Last updated 2 months ago.
american-footballfootball-datanflnflstatsnflversesports-analytics
1.7 match 442 stars 10.40 score 596 scripts 3 dependents
maximeherve
RVAideMemoire:Testing and Plotting Procedures for Biostatistics
Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Maintained by Maxime HERVE. Last updated 1 years ago.
3.3 match 8 stars 5.31 score 632 scripts
remkoduursma
Maeswrap:Wrapper functions for MAESTRA/MAESPA
A bundle of functions for modifying MAESTRA/MAESPA input files, reading output files, and visualizing the stand in 3D. Handy for running sensitivity analyses, scenario analyses, etc.
Maintained by Remko Duursma. Last updated 5 years ago.
4.3 match 3 stars 3.92 score 28 scripts
pecanproject
PEcAn.allometry:PEcAn Allometry Functions
Synthesize allometric equations or fit allometries to data.
Maintained by Mike Dietze. Last updated 4 hours ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplants
1.5 match 216 stars 9.09 score 34 scripts
kjhealy
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 11 months ago.
5.9 match 2.28 score 38 scripts
atfutures
calendar:Create, Read, Write, and Work with 'iCalendar' Files, Calendars and Scheduling Data
Provides function to create, read, write, and work with 'iCalendar' files (which typically have '.ics' or '.ical' extensions), and the scheduling data, calendars and timelines of people, organisations and other entities that they represent. 'iCalendar' is an open standard for exchanging calendar and scheduling information between users and computers, described at <https://icalendar.org/>.
Maintained by Robin Lovelace. Last updated 7 months ago.
1.6 match 42 stars 8.39 score 113 scripts 1 dependents
muvisu
biplotEZ:EZ-to-Use Biplots
Provides users with an EZ-to-use platform for representing data with biplots. Currently principal component analysis (PCA), canonical variate analysis (CVA) and simple correspondence analysis (CA) biplots are included. This is accompanied by various formatting options for the samples and axes. Alpha-bags and concentration ellipses are included for visual enhancements and interpretation. For an extensive discussion on the topic, see Gower, J.C., Lubbe, S. and le Roux, N.J. (2011, ISBN: 978-0-470-01255-0) Understanding Biplots. Wiley: Chichester.
Maintained by Sugnet Lubbe. Last updated 8 days ago.
1.5 match 7 stars 8.39 score 30 scripts 1 dependents
bioc
LiquidAssociation:LiquidAssociation
The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data.
Maintained by Yen-Yi Ho. Last updated 5 months ago.
pathwaysgeneexpressioncellbiologygeneticsnetworktimecourse
3.3 match 3.78 score 3 scripts 1 dependents
ropensci
arkdb:Archive and Unarchive Databases Using Flat Files
Flat text files provide a robust, compressible, and portable way to store tables from databases. This package provides convenient functions for exporting tables from relational database connections into compressed text files and streaming those text files back into a database without requiring the whole table to fit in working memory.
Maintained by Carl Boettiger. Last updated 1 years ago.
archivingdatabasedbipeer-reviewed
1.8 match 79 stars 6.86 score 37 scripts
kkbrum
natstrat:Obtain Unweighted Natural Strata that Balance Many Covariates
Natural strata can be used in observational studies to balance the distributions of many covariates across any number of treatment groups and any number of comparisons. These strata have proportional amounts of units within each stratum across the treatments, allowing for simple interpretation and aggregation across strata. Within each stratum, the units are chosen using randomized rounding of a linear program that balances many covariates. To solve the linear program, the 'Gurobi' commercial optimization software is recommended, but not required. The 'gurobi' R package can be installed following the instructions at <https://www.gurobi.com/documentation/9.1/refman/ins_the_r_package.html>.
Maintained by Katherine Brumberg. Last updated 3 years ago.
3.3 match 3.70 score 3 scripts
pierreroudier
clhs:Conditioned Latin Hypercube Sampling
Conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006) <DOI:10.1016/j.cageo.2005.12.009>. This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012, <DOI:10.1201/b12728>).
Maintained by Pierre Roudier. Last updated 3 years ago.
1.6 match 12 stars 7.54 score 115 scripts 2 dependents
dcousin3
superb:Summary Plots with Adjusted Error Bars
Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.
Maintained by Denis Cousineau. Last updated 2 months ago.
error-barsplottingstatisticssummary-plotssummary-statisticsvisualization
1.2 match 19 stars 9.55 score 155 scripts 2 dependents
koki25ando
NBAloveR:Help Basketball Data Analysis
Provides interface to the online basketball data resources such as Basketball reference API <https://www.basketball-reference.com/> and helps R users analyze basketball data.
Maintained by Koki Ando. Last updated 3 years ago.
2.3 match 8 stars 4.60 score 5 scripts
mjnueda
lpda:Linear Programming Discriminant Analysis
Classification method obtained through linear programming. It is advantageous with respect to the classical developments when the distribution of the variables involved is unknown or when the number of variables is much greater than the number of individuals. LPDA method is published in Nueda, et al. (2022) "LPDA: A new classification method based on linear programming". <doi:10.1371/journal.pone.0270403>.
Maintained by Maria Jose Nueda. Last updated 2 years ago.
5.1 match 2.00 score 2 scripts
maarten14c
rbacon:Age-Depth Modelling using Bayesian Statistics
An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information on accumulation rates and their variability. See Blaauw & Christen (2011).
Maintained by Maarten Blaauw. Last updated 28 days ago.
age-depth-modelbayesianholocenelakesocean-sedimentspeatradiocarbon-calibrationcpp
1.5 match 7 stars 6.75 score 57 scripts 1 dependents
christophsax
seasonalview:Graphical User Interface for Seasonal Adjustment
A graphical user interface to the 'seasonal' package and 'X-13ARIMA-SEATS', the U.S. Census Bureau's seasonal adjustment software.
Maintained by Christoph Sax. Last updated 5 months ago.
seasonal-adjustmentshinytime-series
1.8 match 22 stars 5.59 score 105 scripts
evanodell
mnis:Easy Downloading Capabilities for the Members' Name Information Service
An API package for the Members' Name Information Service operated by the UK parliament. Documentation for the API itself can be found here: <http://data.parliament.uk/membersdataplatform/default.aspx>.
Maintained by Evan Odell. Last updated 4 years ago.
parliamentary-monitoringpolitical-sciencepoliticianspoliticscpp
1.9 match 4 stars 5.13 score 67 scripts
phytoclass
phytoclass:Estimate Chla Concentrations of Phytoplankton Groups
Determine the chlorophyll a (Chl a) concentrations of different phytoplankton groups based on their pigment biomarkers. The method uses non-negative matrix factorisation and simulated annealing to minimise error between the observed and estimated values of pigment concentrations (Hayward et al. (2023) <doi:10.1002/lom3.10541>). The approach is similar to the widely used 'CHEMTAX' program (Mackey et al. 1996) <doi:10.3354/meps144265>, but is more straightforward, accurate, and not reliant on initial guesses for the pigment to Chl a ratios for phytoplankton groups.
Maintained by Alexander Hayward. Last updated 12 days ago.
1.6 match 2 stars 5.88 score 9 scripts
garthtarr
edgebundleR:Circle Plot with Bundled Edges
Generates interactive circle plots with the nodes around the circumference and linkages between the connected nodes using hierarchical edge bundling via the D3 JavaScript library. See <http://d3js.org/> for more information on D3.
Maintained by Garth Tarr. Last updated 2 years ago.
1.3 match 68 stars 7.23 score 55 scriptsemf-creaf
vegclust:Fuzzy Clustering of Vegetation Data
A set of functions to: (1) perform fuzzy clustering of vegetation data (De Caceres et al, 2010) <doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess ecological community similarity on the basis of structure and composition (De Caceres et al, 2013) <doi:10.1111/2041-210X.12116>.
Maintained by Miquel De Cáceres. Last updated 8 months ago.
1.3 match 2 stars 6.28 score 52 scripts 6 dependents
aplantin
MiRKAT:Microbiome Regression-Based Kernel Association Tests
Test for overall association between microbiome composition data and phenotypes via phylogenetic kernels. The phenotype can be univariate continuous or binary (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>), survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>), multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>). The package can also use robust regression (unpublished work) and integrated quantile regression (Wang et al. (2021) <doi:10.1093/bioinformatics/btab668>). In each case, the microbiome community effect is modeled nonparametrically through a kernel function, which can incorporate phylogenetic tree information.
Maintained by Anna Plantinga. Last updated 2 years ago.
1.6 match 3 stars 4.74 score 183 scriptspredictiveecology
fireSenseUtils:Utilities for Working With the 'fireSense' Group of 'SpaDES' Modules
Utilities for working with the 'fireSense' group of 'SpaDES' modules.
Maintained by Eliot J B McIntire. Last updated 1 months ago.
1.7 match 1 stars 4.51 score 2 scripts
dipterix
ravedash:Dashboard System for Reproducible Visualization of 'iEEG'
Dashboard system to display the analysis results produced by 'RAVE' (Magnotti J.F., Wang Z., Beauchamp M.S. (2020), Reproducible analysis and visualizations of 'iEEG' <doi:10.1016/j.neuroimage.2020.117341>). Provides infrastructure to integrate customized analysis pipelines into dashboard modules, including file structures, front-end widgets, and event handlers.
Maintained by Zhengjia Wang. Last updated 5 months ago.
1.7 match 1 stars 4.35 score 45 scripts
talgalili
heatmaply:Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'
Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' to 'heatmap.2' with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.
Maintained by Tal Galili. Last updated 8 months ago.
d3-heatmapdendextenddendrogramggplot2heatmapplotly
0.5 match 386 stars 14.21 score 2.0k scripts 45 dependents
nano-optics
planar:Multilayer Optics
Solves the electromagnetic problem of reflection and transmission at a planar multilayer interface. Also computed are the decay rates and emission profile for a dipolar emitter.
Maintained by Baptiste Auguié. Last updated 3 years ago.
1.1 match 7 stars 5.83 score 65 scripts
zongzheng
forestHES:Forest Health Evaluation System at the Forest Stand Level
Assessing forest ecosystem health is an effective way for forest resource management.The national forest health evaluation system at the forest stand level using analytic hierarchy process, has a high application value and practical significance. The package can effectively and easily realize the total assessment process, and help foresters to further assess and management forest resources.
Maintained by Zongzheng Chai. Last updated 5 months ago.
5.1 match 1 stars 1.11 score 13 scripts
lightbridge-ks
thaipdf:R Markdown to PDF in Thai Language
Provide R Markdown templates and LaTeX preamble which are necessary for creating PDF from R Markdown documents in Thai language.
Maintained by Kittipos Sirivongrungson. Last updated 3 years ago.
latex-templatepdf-documentrmarkdownthaithai-language
1.2 match 5 stars 4.40 score 1 scripts
cols4all
cols4all:Colors for all
Color palettes for all people, including those with color vision deficiency. Popular color palette series have been organized by type and have been scored on several properties such as color-blind-friendliness and fairness (i.e. do colors stand out equally?). Own palettes can also be loaded and analysed. Besides the common palette types (categorical, sequential, and diverging) it also includes cyclic and bivariate color palettes. Furthermore, a color for missing values is assigned to each palette.
Maintained by Martijn Tennekes. Last updated 2 months ago.
0.5 match 343 stars 9.98 score 26 dependents
michaelsimmler
triact:Analyzing the Lying Behavior of Cows from Accelerometer Data
Assists in analyzing the lying behavior of cows from raw data recorded with a triaxial accelerometer attached to the hind leg of a cow. Allows the determination of common measures for lying behavior including total lying duration, the number of lying bouts, and the mean duration of lying bouts. Further capabilities are the description of lying laterality and the calculation of proxies for the level of physical activity of the cow. Reference: Simmler M., Brouwers S. P. (2023) <https://gitlab.com/AgroSimi/triact_manuscript>.
Maintained by Michael Simmler. Last updated 2 years ago.
2.5 match 2.00 score 2 scripts
fmichonneau
foghorn:Summarize CRAN Check Results in the Terminal
The CRAN check results and where your package stands in the CRAN submission queue in your R terminal.
Maintained by Francois Michonneau. Last updated 9 months ago.
0.6 match 58 stars 8.76 score 21 scripts
osgeo
rgrass:Interface Between 'GRASS' Geographical Information System and 'R'
An interface between the 'GRASS' geographical information system ('GIS') and 'R', based on starting 'R' from within the 'GRASS' 'GIS' environment, or running a free-standing 'R' session in a temporary 'GRASS' location; the package provides facilities for using all 'GRASS' commands from the 'R' command line. The original interface package for 'GRASS 5' (2000-2010) is described in Bivand (2000) <doi:10.1016/S0098-3004(00)00057-1> and Bivand (2001) <https://www.r-project.org/conferences/DSC-2001/Proceedings/Bivand.pdf>. This was succeeded by 'spgrass6' for 'GRASS 6' (2006-2016) and 'rgrass7' for 'GRASS 7' (2015-present). The 'rgrass' package modernizes the interface for 'GRASS 8' while still permitting the use of 'GRASS 7'.
Maintained by Steven Pawley. Last updated 25 days ago.
0.5 match 28 stars 9.23 score 91 scripts 2 dependents
matloff
qeML:Quick and Easy Machine Learning Tools
The letters 'qe' in the package title stand for "quick and easy," alluding to the convenience goal of the package. We bring together a variety of machine learning (ML) tools from standard R packages, providing wrappers with a simple, convenient, and uniform interface.
Maintained by Norm Matloff. Last updated 28 days ago.
0.5 match 41 stars 8.41 score 48 scripts 1 dependents
cost-fp1304-profound
ProfoundData:Downloading and Exploring Data from the PROFOUND Database
Provides an R interface for the PROFOUND database <doi:10.5880/PIK.2019.008>. The PROFOUND database contains a wide range of data to evaluate vegetation models and simulate climate impacts at the forest stand scale. It includes 9 forest sites across Europe, and provides for them a site description as well as soil, climate, CO2, Nitrogen deposition, tree-level, forest stand-level and remote sensing data. Moreover, for a subset of 5 sites, also time series of carbon fluxes, energy balances and soil water are available.
Maintained by Florian Hartig. Last updated 5 years ago.
0.8 match 9 stars 5.58 score 14 scripts
adamlilith
fasterRaster:Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
Processing of large-in-memory/large-on disk rasters and spatial vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in the 'terra' package are recreated. Processing of medium-sized and smaller spatial objects will nearly always be faster using 'terra' or 'sf', but for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster. To use most of the functions, you must have the stand-alone version (not the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.
Maintained by Adam B. Smith. Last updated 21 days ago.
aspectdistancefragmentationfragmentation-indicesgisgrassgrass-gisrasterraster-projectionrasterizeslopetopographyvectorization
0.5 match 58 stars 7.69 score 8 scripts
ipeagit
gtfs2emis:Estimating Public Transport Emissions from General Transit Feed Specification (GTFS) Data
A bottom up model to estimate the emission levels of public transport systems based on General Transit Feed Specification (GTFS) data. The package requires two main inputs: i) Public transport data in the GTFS standard format; and ii) Some basic information on fleet characteristics such as fleet age, technology, fuel and Euro stage. As it stands, the package estimates several pollutants at high spatial and temporal resolutions. Pollution levels can be calculated for specific transport routes, trips, time of the day or for the transport system as a whole. The output with emission estimates can be extracted in different formats, supporting analysis on how emission levels vary across space, time and by fleet characteristics. A full description of the methods used in the 'gtfs2emis' model is presented in Vieira, J. P. B.; Pereira, R. H. M.; Andrade, P. R. (2022) <doi:10.31219/osf.io/8m2cy>.
Maintained by Joao Bazzo. Last updated 2 months ago.
emissionsenvironmental-modellinggtfspublic-transportrspatialtransport
0.5 match 28 stars 7.47 score 29 scripts
jsta
wql:Exploring Water Quality Monitoring Data
Functions to assist in the processing and exploration of data from environmental monitoring programs. The package name stands for "water quality" and reflects the original focus on time series data for physical and chemical properties of water, as well as the biota. Intended for programs that sample approximately monthly, quarterly or annually at discrete stations, a feature of many legacy data sets. Most of the functions should be useful for analysis of similar-frequency time series regardless of the subject matter.
Maintained by Jemma Stachelek. Last updated 2 months ago.
0.5 match 12 stars 7.34 score 204 scripts 3 dependents
lvulliard
BioCircos:Interactive Circular Visualization of Genomic Data using 'htmlwidgets' and 'BioCircos.js'
Implement in 'R' interactive Circos-like visualizations of genomic data, to map information such as genetic variants, genomic fusions and aberrations to a circular genome, as proposed by the 'JavaScript' library 'BioCircos.js', based on the 'JQuery' and 'D3' technologies. The output is by default displayed in stand-alone HTML documents or in the 'RStudio' viewer pane. Moreover it can be integrated in 'R Markdown' documents and 'Shiny' applications.
Maintained by Loan Vulliard. Last updated 6 years ago.
biocircosbioinformaticscircoscircos-graphshtmlwidgetsshiny
0.5 match 37 stars 6.98 score 58 scripts
pik-piam
mrwater:madrat based MAgPIE water Input Data Library
Provides functions for MAgPIE cellular input data generation and stand-alone water calculations.
Maintained by Felicitas Beier. Last updated 5 months ago.
0.5 match 6.45 score 4 scripts 3 dependentsbioc
RedeR:Interactive visualization and manipulation of nested networks
RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes can be configured using either graphical or command-line methods, following igraph syntax rules.
Maintained by Mauro Castro. Last updated 5 months ago.
guigraphandnetworknetworknetworkenrichmentnetworkinferencesoftwaresystemsbiology
0.5 match 6.65 score 107 scripts 7 dependents
mingzehuang
latentcor:Fast Computation of Latent Correlations for Mixed Data
The first stand-alone R package for computation of latent correlation that takes into account all variable types (continuous/binary/ordinal/zero-inflated), comes with an optimized memory footprint, and is computationally efficient, essentially making latent correlation estimation almost as fast as rank-based correlation estimation. The estimation is based on latent copula Gaussian models. For continuous/binary types, see Fan, J., Liu, H., Ning, Y., and Zou, H. (2017). For ternary type, see Quan X., Booth J.G. and Wells M.T. (2018) <arXiv:1809.06255>. For truncated type or zero-inflated type, see Yoon G., Carroll R.J. and Gaynanova I. (2020) <doi:10.1093/biomet/asaa007>. For approximation method of computation, see Yoon G., Müller C.L. and Gaynanova I. (2021) <doi:10.1080/10618600.2021.1882468>. The latter method uses multi-linear interpolation originally implemented in the R package <https://cran.r-project.org/package=chebpol>.
Maintained by Mingze Huang. Last updated 2 years ago.
data-analysisdata-miningdata-processingdata-sciencedata-structuresmachine-learningmixed-typesstatistics
0.5 match 16 stars 6.65 score 46 scripts 1 dependentsbioc
ViSEAGO:ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
The main objective of ViSEAGO package is to carry out a data mining of biological functions and establish links between genes involved in the study. We developed ViSEAGO in R to facilitate functional Gene Ontology (GO) analysis of complex experimental design with multiple comparisons of interest. It allows to study large-scale datasets together and visualize GO profiles to capture biological knowledge. The acronym stands for three major concepts of the analysis: Visualization, Semantic similarity and Enrichment Analysis of Gene Ontology. It provides access to the last current GO annotations, which are retrieved from one of NCBI EntrezGene, Ensembl or Uniprot databases for several species. Using available R packages and novel developments, ViSEAGO extends classical functional GO analysis to focus on functional coherence by aggregating closely related biological themes while studying multiple datasets at once. It provides both a synthetic and detailed view using interactive functionalities respecting the GO graph structure and ensuring functional coherence supplied by semantic similarity. ViSEAGO has been successfully applied on several datasets from different species with a variety of biological questions. Results can be easily shared between bioinformaticians and biologists, enhancing reporting capabilities while maintaining reproducibility.
Maintained by Aurelien Brionne. Last updated 2 months ago.
softwareannotationgogenesetenrichmentmultiplecomparisonclusteringvisualization
0.5 match 6.64 score 22 scripts
wilkelab
sicegar:Analysis of Single-Cell Viral Growth Curves
Aims to quantify time intensity data by using sigmoidal and double sigmoidal curves. It fits straight lines, sigmoidal, and double sigmoidal curves on to time vs intensity data. Then all the fits are used to make decision on which model best describes the data. This method was first developed in the context of single-cell viral growth analysis (for details, see Caglar et al. (2018) <doi:10.7717/peerj.4251>), and the package name stands for "SIngle CEll Growth Analysis in R".
Maintained by Claus O. Wilke. Last updated 4 years ago.
0.5 match 9 stars 6.57 score 41 scripts
larsot23
Benchmarking:Benchmark and Frontier Analysis Using DEA and SFA
Methods for frontier analysis, Data Envelopment Analysis (DEA), under different technology assumptions (fdh, vrs, drs, crs, irs, add/frh, and fdh+), and using different efficiency measures (input based, output based, hyperbolic graph, additive, super, and directional efficiency). Peers and slacks are available, partial price information can be included, and optimal cost, revenue and profit can be calculated. Evaluation of mergers is also supported. Methods for graphing the technology sets are also included. There is also support for comparative methods based on Stochastic Frontier Analyses (SFA) and for convex nonparametric least squares of convex functions (STONED). In general, the methods can be used to solve not only standard models, but also many other model variants. It complements the book, Bogetoft and Otto, Benchmarking with DEA, SFA, and R, Springer-Verlag, 2011, but can of course also be used as a stand-alone package.
Maintained by Lars Otto. Last updated 28 days ago.
0.5 match 7 stars 6.17 score 192 scripts 7 dependents
bergsmat
latexpdf:Convert Tables to PDF or PNG
Converts table-like objects to stand-alone PDF or PNG. Can be used to embed tables and arbitrary content in PDF or Word documents. Provides a low-level R interface for creating 'LaTeX' code, e.g. command() and a high-level interface for creating PDF documents, e.g. as.pdf.data.frame(). Extensive customization is available via mid-level functions, e.g. as.tabular(). See also 'package?latexpdf'. Support for PNG is experimental; see 'as.png.data.frame'. Adapted from 'metrumrg' <https://r-forge.r-project.org/R/?group_id=1215>. Requires a compatible installation of 'pdflatex', e.g. <https://miktex.org/>.
Maintained by Tim Bergsma. Last updated 5 months ago.
0.5 match 1 stars 5.57 score 106 scripts 4 dependents
md-anderson-bioinformatics
NGCHM:Next Generation Clustered Heat Maps
Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) <doi:10.12688/f1000research.20590.2> for more details.
Maintained by Mary A Rohrdanz. Last updated 11 days ago.
0.5 match 9 stars 5.48 score 28 scripts
svmiller
peacesciencer:Tools and Data for Quantitative Peace Science Research
These are useful tools and data sets for the study of quantitative peace science. The goal for this package is to include tools and data sets for doing original research that mimics well what a user would have to previously get from a software package that may not be well-sourced or well-supported. Those software bundles were useful the extent to which they encourage replications of long-standing analyses by starting the data-generating process from scratch. However, a lot of the functionality can be done relatively quickly and more transparently in the R programming language.
Maintained by Steve Miller. Last updated 5 days ago.
0.5 match 29 stars 5.49 score 211 scripts
bayer-group
adepro:A 'shiny' Application for the (Audio-)Visualization of Adverse Event Profiles
Contains a 'shiny' application called AdEPro (Animation of Adverse Event Profiles) which (audio-)visualizes adverse events occurring in clinical trials. As this data is usually considered sensitive, this tool is provided as a stand-alone application that can be launched from any local machine on which the data is stored.
Maintained by Bodo Kirsch. Last updated 6 months ago.
0.5 match 3 stars 5.30 score 11 scripts
magichead99
bread:Analyze Big Files Without Loading Them in Memory
A simple set of wrapper functions for data.table::fread() that allows subsetting or filtering rows and selecting columns of table-formatted files too large for the available RAM. 'b stands for 'big files'. bread makes heavy use of Unix commands like 'grep', 'sed', 'wc', 'awk' and 'cut'. They are available by default in all Unix environments. For Windows, you need to install those commands externally in order to simulate a Unix environment and make sure that the executables are in the Windows PATH variable. To my knowledge, the simplest ways are to install 'RTools', 'Git' or 'Cygwin'. If they have been correctly installed (with the expected registry entries), they should be detected on loading the package and the correct directories will be added automatically to the PATH.
Maintained by Vincent Guegan. Last updated 2 years ago.
0.5 match 14 stars 5.37 score 56 scripts 2 dependents
dewittpe
REDCapExporter:Automated Construction of R Data Packages from REDCap Projects
Export all data, including metadata, from a REDCap (Research Electronic Data Capture) Project via the REDCap API <https://projectredcap.org/wp-content/resources/REDCapTechnicalOverview.pdf>. The exported (meta)data will be processed and formatted into a stand alone R data package which can be installed and shared between researchers. Several default reports are generated as vignettes in the resulting package.
Maintained by Peter DeWitt. Last updated 4 months ago.
apidata-exportredcapredcap-api
0.5 match 2 stars 5.28 score 21 scriptsropensci
handlr:Convert Among Citation Formats
Converts among many citation formats, including 'BibTeX', 'Citeproc', 'Codemeta', 'RDF XML', 'RIS', 'Schema.org', and 'Citation File Format'. A low level 'R6' class is provided, as well as stand-alone functions for each citation format for both read and write.
Maintained by Brenton M. Wiernik. Last updated 15 days ago.
doimetadatacitationbibtexcrossrefcrosscitecodemetarisciteprocrdfxmljsoncitationsdigital-object-identifier
0.5 match 38 stars 5.22 score 29 scriptsbioc
SiPSiC:Calculate Pathway Scores for Each Cell in scRNA-Seq Data
Infer biological pathway activity of cells from single-cell RNA-sequencing data by calculating a pathway score for each cell (pathway genes are specified by the user). It is recommended to have the data in Transcripts-Per-Million (TPM) or Counts-Per-Million (CPM) units for best results. Scores may change when adding cells to or removing cells off the data. SiPSiC stands for Single Pathway analysis in Single Cells.
Maintained by Daniel Davis. Last updated 5 months ago.
softwaredifferentialexpressiongenesetenrichmentbiomedicalinformaticscellbiologytranscriptomicsrnaseqsinglecelltranscriptionsequencingimmunooncologydataimport
0.5 match 7 stars 5.24 score 3 scripts
dzhakparov
GeneSelectR:Comprehensive Feature Selection Worfkflow for Bulk RNAseq Datasets
GeneSelectR is a versatile R package designed for efficient RNA sequencing data analysis. Its key innovation lies in the seamless integration of the Python sklearn machine learning framework with R-based bioinformatics tools. This integration enables GeneSelectR to perform robust ML-driven feature selection while simultaneously leveraging the power of Gene Ontology (GO) enrichment and semantic similarity analyses. By combining these diverse methodologies, GeneSelectR offers a comprehensive workflow that optimizes both the computational aspects of ML and the biological insights afforded by advanced bioinformatics analyses. Ideal for researchers in bioinformatics, GeneSelectR stands out as a unique tool for analyzing complex RNAseq datasets with enhanced precision and relevance.
Maintained by Damir Zhakparov. Last updated 10 months ago.
0.5 match 19 stars 5.28 score 7 scripts
moran79
folda:Forward Stepwise Discriminant Analysis with Pillai's Trace
A novel forward stepwise discriminant analysis framework that integrates Pillai's trace with Uncorrelated Linear Discriminant Analysis (ULDA), providing an improvement over traditional stepwise LDA methods that rely on Wilks' Lambda. A stand-alone ULDA implementation is also provided, offering a more general solution than the one available in the 'MASS' package. It automatically handles missing values and provides visualization tools. For more details, see Wang (2024) <doi:10.48550/arXiv.2409.03136>.
Maintained by Siyu Wang. Last updated 5 months ago.
0.5 match 2 stars 5.18 score 6 scripts 1 dependentsbioc
NuPoP:An R package for nucleosome positioning prediction
NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at https://github.com/jipingw. The Fortran codes have complete functonality as the R package. Note: NuPoP has two separate functions for prediction of nucleosome positioning, one for MNase-map trained models and the other for chemical map-trained models. The latter was implemented for four species including yeast, S.pombe, mouse and human, trained based on our recent publications. We noticed there is another package nuCpos by another group for prediction of nucleosome positioning trained with chemicals. A report to compare recent versions of NuPoP with nuCpos can be found at https://github.com/jiping/NuPoP_doc. Some more information can be found and will be posted at https://github.com/jipingw/NuPoP.
Maintained by Ji-Ping Wang. Last updated 5 months ago.
geneticsvisualizationclassificationnucleosomepositioninghiddenmarkovmodelfortran
0.5 match 5.04 score 11 scripts
gagolews
stringx:Replacements for Base String Functions Powered by 'stringi'
English is the native language for only 5% of the World population. Also, only 17% of us can understand this text. Moreover, the Latin alphabet is the main one for merely 36% of the total. The early computer era, now a very long time ago, was dominated by the US. Due to the proliferation of the internet, smartphones, social media, and other technologies and communication platforms, this is no longer the case. This package replaces base R string functions (such as grep(), tolower(), sprintf(), and strptime()) with ones that fully support the Unicode standards related to natural language and date-time processing. It also fixes some long-standing inconsistencies, and introduces some new, useful features. Thanks to 'ICU' (International Components for Unicode) and 'stringi', they are fast, reliable, and portable across different platforms.
Maintained by Marek Gagolewski. Last updated 2 months ago.
icuicu4cnatural-language-processingnlpregexregexpstring-manipulationstringitexttext-processingunicode
0.5 match 28 stars 4.75 score 1 scripts
cran
CUB:A Class of Mixture Models for Ordinal Data
For ordinal rating data, estimate and test models within the family of CUB models and their extensions (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions); Simulation routines, plotting facilities and fitting measures are also provided.
Maintained by Rosaria Simone. Last updated 1 years ago.
0.5 match 4.37 score 79 scripts 1 dependents
pbs-software
PBSadmb:ADMB for R Using Scripts or GUI
A collection of software provides R support for 'ADMB' (Automatic Differentiation Model Builder) and a 'GUI' interface facilitates the conversion of 'ADMB' template code to 'C code' followed by compilation to a binary executable. Stand-alone functions can also be run by users not interested in clicking a 'GUI'.
Maintained by Rowan Haigh. Last updated 11 months ago.
0.5 match 1 stars 4.31 score 41 scripts
cozygene
Unico:Unified Cross-Omics Deconvolution
UNIfied Cross-Omics deconvolution (Unico) deconvolves standard 2-dimensional bulk matrices of samples by features into a 3-dimensional tensors representing samples by features by cell types. Unico stands out as the first principled model-based deconvolution method that is theoretically justified for any heterogeneous genomic data. For more details see Chen and Rahmani et al. (2024) <doi:10.1101/2024.01.27.577588>.
Maintained by Zeyuan Chen. Last updated 1 years ago.
0.5 match 3 stars 4.18 score 5 scripts
hangangtrue
ONEST:Observers Needed to Evaluate Subjective Tests
This ONEST software implements the method of assessing the pathologist agreement in reading PD-L1 assays (Reisenbichler et al. (2020 <doi:10.1038/s41379-020-0544-x>)), to determine the minimum number of evaluators needed to estimate agreement involving a large number of raters. Input to the program should be binary(1/0) pathology data, where “0” may stand for negative and “1” for positive. Additional examples were given using the data from Rimm et al. (2017 <doi:10.1001/jamaoncol.2017.0013>).
Maintained by Gang Han. Last updated 4 years ago.
0.5 match 3 stars 4.18 score 5 scripts
nutriverse
squeacr:Semi-Quantitative Evaluation of Access and Coverage (SQUEAC) Tools
In the recent past, measurement of coverage has been mainly through two-stage cluster sampled surveys either as part of a nutrition assessment or through a specific coverage survey known as Centric Systematic Area Sampling (CSAS). However, such methods are resource intensive and often only used for final programme evaluation meaning results arrive too late for programme adaptation. SQUEAC, which stands for Semi-Quantitative Evaluation of Access and Coverage, is a low resource method designed specifically to address this limitation and is used regularly for monitoring, planning and importantly, timely improvement to programme quality, both for agency and Ministry of Health (MoH) led programmes. This package provides functions for use in conducting a SQUEAC investigation.
Maintained by Ernest Guevarra. Last updated 3 months ago.
acute-malnutritioncmamcoveragesqueacsurveywasting
0.5 match 2 stars 4.18 score 6 scripts 1 dependents
cran
Fragman:Fragment Analysis in R
Performs fragment analysis using genetic data coming from capillary electrophoresis machines. These are files with FSA extension which stands for FASTA-type file, and .txt files from Beckman CEQ 8000 system, both contain DNA fragment intensities read by machinery. In addition to visualization, it performs automatic scoring of SSRs (Sample Sequence Repeats; a type of genetic marker very common across the genome) and other type of PCR markers (standing for Polymerase Chain Reaction) in biparental populations such as F1, F2, BC (backcross), and diversity panels (collection of genetic diversity).
Maintained by Giovanny Covarrubias-Pazaran. Last updated 7 years ago.
0.8 match 5 stars 2.65 score 1 dependents
krajnc
densitr:Analysing Density Profiles from Resistance Drilling of Trees
Provides various tools for analysing density profiles obtained by resistance drilling. It can load individual or multiple files and trim the starting and ending part of each density profile. Tools are also provided to trim profiles manually, to remove the trend from measurements using several methods, to plot the profiles and to detect tree rings automatically. Written with a focus on forestry use of resistance drilling in standing trees.
Maintained by Luka Krajnc. Last updated 3 years ago.
0.5 match 2 stars 3.90 score 9 scripts
rich-iannone
i18n:Internationalization Data from the 'Unicode CLDR' in Tabular Form
Up-to-date data from the 'Unicode CLDR Project' (where 'CLDR' stands for 'Common Locale Data Repository') are available here as a series of easy-to-parse datasets. Several functions are provided for extracting key elements from the tabular datasets.
Maintained by Richard Iannone. Last updated 9 months ago.
0.5 match 10 stars 3.70 score 9 scriptsbioc
pfamAnalyzeR:Identification of domain isotypes in pfam data
Protein domains is one of the most import annoation of proteins we have with the Pfam database/tool being (by far) the most used tool. This R package enables the user to read the pfam prediction from both webserver and stand-alone runs into R. We have recently shown most human protein domains exist as multiple distinct variants termed domain isotypes. Different domain isotypes are used in a cell, tissue, and disease-specific manner. Accordingly, we find that domain isotypes, compared to each other, modulate, or abolish the functionality of a protein domain. This R package enables the identification and classification of such domain isotypes from Pfam data.
Maintained by Kristoffer Vitting-Seerup. Last updated 5 months ago.
alternativesplicingtranscriptomevariantbiomedicalinformaticsfunctionalgenomicssystemsbiologyannotationfunctionalpredictiongenepredictiondataimport
0.5 match 1 stars 3.78 score 1 scripts 1 dependents
billvenables
bannerCommenter:Make Banner Comments with a Consistent Format
A convenience package for use while drafting code. It facilitates making stand-out comment lines decorated with bands of characters. The input text strings are converted into R comment lines, suitably formatted. These are then displayed in a console window and, if possible, automatically transferred to a clipboard ready for pasting into an R script. Designed to save time when drafting R scripts that will need to be navigated and maintained by other programmers.
Maintained by Bill Venables. Last updated 4 years ago.
0.5 match 1 stars 3.48 score 50 scripts 2 dependents
paulesantos
avesperu:Access to the List of Birds Species of Peru
Allows access to the data found in the species list featured in the renowned 'List of the Birds of Peru' Plenge, M. A. (2023) <https://sites.google.com/site/boletinunop/checklist>. This publication stands as one of Peru's most comprehensive reviews of bird diversity. The dataset incorporates detailed species accounts and has been meticulously structured for effortless utilization within the R environment.
Maintained by Paul E. Santos Andrade. Last updated 3 months ago.
0.5 match 1 stars 3.45 score 14 scriptsnutriverse
sleacr:Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage (SLEAC) Tools
In the recent past, measurement of coverage has been mainly through two-stage cluster sampled surveys either as part of a nutrition assessment or through a specific coverage survey known as Centric Systematic Area Sampling (CSAS). However, such methods are resource intensive and often only used for final programme evaluation meaning results arrive too late for programme adaptation. SLEAC, which stands for Simplified Lot Quality Assurance Sampling Evaluation of Access and Coverage, is a low resource method designed specifically to address this limitation and is used regularly for monitoring, planning and importantly, timely improvement to programme quality, both for agency and Ministry of Health (MoH) led programmes. SLEAC is designed to complement the Semi-quantitative Evaluation of Access and Coverage (SQUEAC) method. This package provides functions for use in conducting a SLEAC assessment.
Maintained by Ernest Guevarra. Last updated 1 months ago.
acute-malnutritioncmamcoveragenutritionsleacwasting
0.5 match 1 stars 3.48 score 5 scripts
forest-economics-goettingen
woodValuationDE:Wood Valuation Germany
Monetary valuation of wood in German forests (stumpage values), including estimations of harvest quantities, wood revenues, and harvest costs. The functions are sensitive to tree species, mean diameter of the harvested trees, stand quality, and logging method. The functions include estimations for the consequences of disturbances on revenues and costs. The underlying assortment tables are taken from Offer and Staupendahl (2018) with corresponding functions for salable and skidded volume derived in Fuchs et al. (2023). Wood revenue and harvest cost functions were taken from v. Bodelschwingh (2018). The consequences of disturbances refer to Dieter (2001), Moellmann and Moehring (2017), and Fuchs et al. (2022a, 2022b). For the full references see documentation of the functions, package README, and Fuchs et al. (2023). Apart from Dieter (2001) and Moellmann and Moehring (2017), all functions and factors are based on data from HessenForst, the forest administration of the Federal State of Hesse in Germany.
Maintained by Jasper M. Fuchs. Last updated 8 months ago.
0.5 match 2 stars 3.30 score 2 scripts
rozen-lab
cosmicsig:Mutational Signatures from COSMIC (Catalogue of Somatic Mutations in Cancer)
A data package with 2 main package variables: 'signature' and 'etiology'. The 'signature' variable contains the latest mutational signature profiles released on COSMIC <https://cancer.sanger.ac.uk/signatures/> for 3 mutation types: * Single base substitutions in the context of preceding and following bases, * Doublet base substitutions, and * Small insertions and deletions. The 'etiology' variable provides the known or hypothesized causes of signatures. 'cosmicsig' stands for COSMIC signatures. Please run ?'cosmicsig' for more information.
Maintained by Steven Rozen. Last updated 2 years ago.
0.5 match 1 stars 3.04 score 22 scriptsrozen-lab
mSigTools:Mutational Signature Analysis Tools
Utility functions for mutational signature analysis as described in Alexandrov, L. B. (2020) <doi:10.1038/s41586-020-1943-3>. This package provides two groups of functions. One is for dealing with mutational signature "exposures" (i.e. the counts of mutations in a sample that are due to each mutational signature). The other group of functions is for matching or comparing sets of mutational signatures. 'mSigTools' stands for mutational Signature analysis Tools.
Maintained by Steven Rozen. Last updated 2 years ago.
0.5 match 2 stars 3.00 score 9 scripts
zkamvar
repvar:Extract Samples to Represent All Variables
In population genetics, it's not uncommon to re-genotype sets of samples to use as positive controls in future studies or for diagnostic panels. To save cost, it's often desireable to have the minimum number of samples that represent all of the alleles in the data. This package provides a procedure that will select these samples with alternative options. The name 'repvar' stands for 'REPresent VARiables'.
Maintained by Zhian N. Kamvar. Last updated 2 months ago.
0.5 match 2.70 score 1 scripts
torfason
qst:Store Tables in SQL Database
Provides functions for quickly writing (and reading back) a data.frame to file in 'SQLite' format. The name stands for *Store Tables using 'SQLite'*, or alternatively for *Quick Store Tables* (either way, it could be pronounced as *Quest*). For data.frames containing the supported data types it is intended to work as a drop-in replacement for the 'write_*()' and 'read_*()' functions provided by similar packages.
Maintained by Magnus Thor Torfason. Last updated 1 years ago.
0.5 match 2.70 score 1 scripts
biods
rrnni:Manipulate with RNNI Tree Space
Calculate RNNI distance between and manipulate with ranked trees. RNNI stands for Ranked Nearest Neighbour Interchange and is an extension of the classical NNI space (space of trees created by the NNI moves) to ranked trees, where internal nodes are ordered according to their heights (usually assumed to be times). The RNNI distance takes the tree topology into account, as standard NNI does, but also penalizes changes in the order of internal nodes, i.e. changes in the order of times of evolutionary events. For more information about the RNNI space see: Gavryushkin et al. (2018) <doi:10.1007/s00285-017-1167-9>, Collienne & Gavryushkin (2021) <doi:10.1007/s00285-021-01567-5>, Collienne et al. (2021) <doi:10.1007/s00285-021-01685-0>, and Collienne (2021) <http://hdl.handle.net/10523/12606>.
Maintained by Jiří C. Moravec. Last updated 2 years ago.
0.5 match 1 stars 2.70 score 1 scripts
yufeng031
bestridge:A Comprehensive R Package for Best Subset Selection
The bestridge package is designed to provide a one-stand service for users to successfully carry out best ridge regression in various complex situations via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2020) <doi:10.18637/jss.v094.i04>. This package allows users to perform the regression, classification, count regression and censored regression for (ultra) high dimensional data, and it also supports advanced usages like group variable selection and nuisance variable selection.
Maintained by Liyuan Hu. Last updated 3 years ago.
0.5 match 2.00 score 6 scripts
samuelemerson
UNCOVER:Utilising Normalisation Constant Optimisation via Edge Removal (UNCOVER)
Model data with a suspected clustering structure (either in co-variate space, regression space or both) using a Bayesian product model with a logistic regression likelihood. Observations are represented graphically and clusters are formed through various edge removals or additions. Cluster quality is assessed through the log Bayesian evidence of the overall model, which is estimated using either a Sequential Monte Carlo sampler or a suitable transformation of the Bayesian Information Criterion as a fast approximation of the former. The internal Iterated Batch Importance Sampling scheme (Chopin (2002 <doi:10.1093/biomet/89.3.539>)) is made available as a free standing function.
Maintained by Samuel Emerson. Last updated 2 years ago.
0.5 match 2.00 score 4 scripts
stefanedwards
microCRAN:Hosting an Independent CRAN Repository
Stand-alone HTTP capable R-package repository, that fully supports R's install.packages() and available.packages(). It also contains API endpoints for end-users to add/update packages. This package can supplement 'miniCRAN', which has functions for maintaining a local (partial) copy of 'CRAN'. Current version is bare-minimum without any access-control or much security.
Maintained by Stefan McKinnon Edwards. Last updated 1 years ago.
0.5 match 1.70 score 2 scripts
jwildfire
volcanoPlot:Volcano Plot for Clinical Trial Adverse Events
Interactive adverse event (AE) volcano plot for monitoring clinical trial safety. This tool allows users to view the overall distribution of AEs in a clinical trial using standard (e.g. MedDRA preferred term) or custom (e.g. Gender) categories using a volcano plot similar to proposal by Zink et al. (2013) <doi:10.1177/1740774513485311>. This tool provides a stand-along shiny application and flexible shiny modules allowing this tool to be used as a part of more robust safety monitoring framework like the Shiny app from the 'safetyGraphics' R package.
Maintained by Jeremy Wildfire. Last updated 2 years ago.
0.5 match 1.70 score 2 scriptscran
cg:Compare Groups, Analytically and Graphically
Comprehensive data analysis software, and the name "cg" stands for "compare groups." Its genesis and evolution are driven by common needs to compare administrations, conditions, etc. in medicine research and development. The current version provides comparisons of unpaired samples, i.e. a linear model with one factor of at least two levels. It also provides comparisons of two paired samples. Good data graphs, modern statistical methods, and useful displays of results are emphasized.
Maintained by Bill Pikounis. Last updated 9 years ago.
0.5 match 1.60 score
gertjanssenswillen
understandBPMN:Calculator of Understandability Metrics for BPMN
Calculate several understandability metrics of BPMN models. BPMN stands for business process modelling notation and is a language for expressing business processes into business process diagrams. Examples of these understandability metrics are: average connector degree, maximum connector degree, sequentiality, cyclicity, diameter, depth, token split, control flow complexity, connector mismatch, connector heterogeneity, separability, structuredness and cross connectivity. See R documentation and paper on metric implementation included in this package for more information concerning the metrics.
Maintained by Gert Janssenswillen. Last updated 5 years ago.
0.5 match 1.57 score 37 scriptszongzheng
forestSAS:Forest Spatial Structure Analysis Systems
Recent years have seen significant interest in neighborhood-based structural parameters that effectively represent the spatial characteristics of tree populations and forest communities, and possess strong applicability for guiding forestry practices. This package provides valuable information that enhances our understanding and analysis of the fine-scale spatial structure of tree populations and forest stands. Reference: Yan L, Tan W, Chai Z, et al (2019) <doi:10.13323/j.cnki.j.fafu(nat.sci.).2019.03.007>.
Maintained by Zongzheng Chai. Last updated 4 months ago.
0.5 match 1.38 score 24 scriptscran
MplusTrees:Decision Trees with Structural Equation Models Fit in 'Mplus'
Uses recursive partitioning to create homogeneous subgroups based on structural equation models fit in 'Mplus', a stand-alone program developed by Muthen and Muthen.
Maintained by Sarfaraz Serang. Last updated 2 years ago.
0.5 match 1.00 scorecran
FastCUB:Fast Estimation of CUB Models via Louis' Identity
For ordinal rating data, consider the accelerated EM algorithm to estimate and test models within the family of CUB models (where CUB stands for Combination of a discrete Uniform and a shifted Binomial distributions). The procedure is built upon Louis' identity for the observed information matrix. Best-subset variable selection is then implemented since it becomes more feasible from the computational point of view.
Maintained by Rosaria Simone. Last updated 1 years ago.
0.5 match 1 stars 1.00 score
yeasinstat
WaveletETS:Wavelet Based Error Trend Seasonality Model
ETS stands for Error, Trend, and Seasonality, and it is a popular time series forecasting method. Wavelet decomposition can be used for denoising, compression, and feature extraction of signals. By removing the high-frequency components, wavelet decomposition can remove noise from the data while preserving important features. A hybrid Wavelet ETS (Error Trend-Seasonality) model has been developed for time series forecasting using algorithm of Anjoy and Paul (2017) <DOI:10.1007/s00521-017-3289-9>.
Maintained by Dr. Md Yeasin. Last updated 2 years ago.
0.5 match 1.00 score
imiqbal
ImFoR:Non-Linear Height Diameter Models for Forestry
Tree height is an important dendrometric variable and forms the basis of vertical structure of a forest stand. This package will help to fit and validate various non-linear height diameter models for assessing the underlying relationship that exists between tree height and diameter at breast height in case of conifer trees. This package has been implemented on Naslund, Curtis, Michailoff, Meyer, Power, Michaelis-Menten and Wykoff non linear models using algorithm of Huang et al. (1992) <doi:10.1139/x92-172> and Zeide et al. (1993) <doi:10.1093/forestscience/39.3.594>.
Maintained by M. Iqbal Jeelani. Last updated 1 years ago.
0.5 match 1.00 score
mirrelijn
ecpc:Flexible Co-Data Learning for High-Dimensional Prediction
Fit linear, logistic and Cox survival regression models penalised with adaptive multi-group ridge penalties. The multi-group penalties correspond to groups of covariates defined by (multiple) co-data sources. Group hyperparameters are estimated with an empirical Bayes method of moments, penalised with an extra level of hyper shrinkage. Various types of hyper shrinkage may be used for various co-data. Co-data may be continuous or categorical. The method accommodates inclusion of unpenalised covariates, posterior selection of covariates and multiple data types. The model fit is used to predict for new samples. The name 'ecpc' stands for Empirical Bayes, Co-data learnt, Prediction and Covariate selection. See Van Nee et al. (2020) <arXiv:2005.04010>.
Maintained by Mirrelijn M. van Nee. Last updated 2 years ago.
0.5 match 1.00 score 9 scripts