R-universe search: global

mapme-initiative

mapme.biodiversity:Efficient Monitoring of Global Biodiversity Portfolios

Biodiversity areas, especially primary forest, serve a multitude of functions for local economy, regional functionality of the ecosystems as well as the global health of our planet. Recently, adverse changes in human land use practices and climatic responses to increased greenhouse gas emissions, put these biodiversity areas under a variety of different threats. The present package helps to analyse a number of biodiversity indicators based on freely available geographical datasets. It supports computational efficient routines that allow the analysis of potentially global biodiversity portfolios. The primary use case of the package is to support evidence based reporting of an organization's effort to protect biodiversity areas under threat and to identify regions were intervention is most duly needed.

Maintained by Darius A. Görgen. Last updated 3 months ago.

environment eo gis mapme spatial sustainability

30.6 match 35 stars 9.24 score 287 scripts

myllym

GET:Global Envelopes

Implementation of global envelopes for a set of general d-dimensional vectors T in various applications. A 100(1-alpha)% global envelope is a band bounded by two vectors such that the probability that T falls outside this envelope in any of the d points is equal to alpha. Global means that the probability is controlled simultaneously for all the d elements of the vectors. The global envelopes can be used for graphical Monte Carlo and permutation tests where the test statistic is a multivariate vector or function (e.g. goodness-of-fit testing for point patterns and random sets, functional analysis of variance, functional general linear model, n-sample test of correspondence of distribution functions), for central regions of functional or multivariate data (e.g. outlier detection, functional boxplot) and for global confidence and prediction bands (e.g. confidence band in polynomial regression, Bayesian posterior prediction). See Myllymäki and Mrkvička (2024) <doi:10.18637/jss.v111.i03>, Myllymäki et al. (2017) <doi:10.1111/rssb.12172>, Mrkvička and Myllymäki (2023) <doi:10.1007/s11222-023-10275-7>, Mrkvička et al. (2016) <doi:10.1016/j.spasta.2016.04.005>, Mrkvička et al. (2017) <doi:10.1007/s11222-016-9683-9>, Mrkvička et al. (2020) <doi:10.14736/kyb-2020-3-0432>, Mrkvička et al. (2021) <doi:10.1007/s11009-019-09756-y>, Myllymäki et al. (2021) <doi:10.1016/j.spasta.2020.100436>, Mrkvička et al. (2022) <doi:10.1002/sim.9236>, Dai et al. (2022) <doi:10.5772/intechopen.100124>, Dvořák and Mrkvička (2022) <doi:10.1007/s00180-021-01134-y>, Mrkvička et al. (2023) <doi:10.48550/arXiv.2309.04746>, and Konstantinou et al. (2024) <doi: 10.1007/s00180-024-01569-z>.

Maintained by Mari Myllymäki. Last updated 4 months ago.

28.3 match 11 stars 9.33 score 46 scripts 5 dependents

ggseg

ggsegSchaefer:Schaefer datasets for the ggseg-plotting tool

This is a support package for the ggseg, and ggseg3d packages. It contains the Schaefer atlases to plot using functions from those two packages.

Maintained by Athanasia Mo Mowinckel. Last updated 3 years ago.

74.3 match 12 stars 3.49 score 51 scripts

rstudio

keras3:R Interface to 'Keras'

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

Maintained by Tomasz Kalinowski. Last updated 4 days ago.

17.2 match 845 stars 13.57 score 264 scripts 2 dependents

snoweye

pbdMPI:R Interface to MPI for HPC Clusters (Programming with Big Data Project)

A simplified, efficient, interface to MPI for HPC clusters. It is a derivation and rethinking of the Rmpi package. pbdMPI embraces the prevalent parallel programming style on HPC clusters. Beyond the interface, a collection of functions for global work with distributed data and resource-independent RNG reproducibility is included. It is based on S4 classes and methods.

Maintained by Wei-Chen Chen. Last updated 6 months ago.

openmpi

32.3 match 2 stars 7.11 score 179 scripts 3 dependents

andysouth

rworldmap:Mapping Global Data

Enables mapping of country level and gridded user datasets.

Maintained by Andy South. Last updated 2 years ago.

18.4 match 30 stars 11.83 score 3.2k scripts 14 dependents

radicalcommecol

cxr:A Toolbox for Modelling Species Coexistence in R

Recent developments in modern coexistence theory have advanced our understanding on how species are able to persist and co-occur with other species at varying abundances. However, applying this mathematical framework to empirical data is still challenging, precluding a larger adoption of the theoretical tools developed by empiricists. This package provides a complete toolbox for modelling interaction effects between species, and calculate fitness and niche differences. The functions are flexible, may accept covariates, and different fitting algorithms can be used. A full description of the underlying methods is available in García-Callejas, D., Godoy, O., and Bartomeus, I. (2020) <doi:10.1111/2041-210X.13443>. Furthermore, the package provides a series of functions to calculate dynamics for stage-structured populations across sites.

Maintained by David Garcia-Callejas. Last updated 1 months ago.

33.1 match 10 stars 6.51 score 27 scripts

r-spatial

spdep:Spatial Dependence: Weighting Schemes, Statistics

A collection of functions to create spatial weights matrix objects from polygon 'contiguities', from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree; a collection of tests for spatial 'autocorrelation', including global 'Morans I' and 'Gearys C' proposed by 'Cliff' and 'Ord' (1973, ISBN: 0850860369) and (1981, ISBN: 0850860814), 'Hubert/Mantel' general cross product statistic, Empirical Bayes estimates and 'Assunção/Reis' (1999) <doi:10.1002/(SICI)1097-0258(19990830)18:16%3C2147::AID-SIM179%3E3.0.CO;2-I> Index, 'Getis/Ord' G ('Getis' and 'Ord' 1992) <doi:10.1111/j.1538-4632.1992.tb00261.x> and multicoloured join count statistics, 'APLE' ('Li 'et al.' ) <doi:10.1111/j.1538-4632.2007.00708.x>, local 'Moran's I', 'Gearys C' ('Anselin' 1995) <doi:10.1111/j.1538-4632.1995.tb00338.x> and 'Getis/Ord' G ('Ord' and 'Getis' 1995) <doi:10.1111/j.1538-4632.1995.tb00912.x>, 'saddlepoint' approximations ('Tiefelsdorf' 2002) <doi:10.1111/j.1538-4632.2002.tb01084.x> and exact tests for global and local 'Moran's I' ('Bivand et al.' 2009) <doi:10.1016/j.csda.2008.07.021> and 'LOSH' local indicators of spatial heteroscedasticity ('Ord' and 'Getis') <doi:10.1007/s00168-011-0492-y>. The implementation of most of these measures is described in 'Bivand' and 'Wong' (2018) <doi:10.1007/s11749-018-0599-x>, with further extensions in 'Bivand' (2022) <doi:10.1111/gean.12319>. 'Lagrange' multiplier tests for spatial dependence in linear models are provided ('Anselin et al'. 1996) <doi:10.1016/0166-0462(95)02111-6>, as are 'Rao' score tests for hypothesised spatial 'Durbin' models based on linear models ('Koley' and 'Bera' 2023) <doi:10.1080/17421772.2023.2256810>. A local indicators for categorical data (LICD) implementation based on 'Carrer et al.' (2021) <doi:10.1016/j.jas.2020.105306> and 'Bivand et al.' (2017) <doi:10.1016/j.spasta.2017.03.003> was added in 1.3-7. From 'spdep' and 'spatialreg' versions >= 1.2-1, the model fitting functions previously present in this package are defunct in 'spdep' and may be found in 'spatialreg'.

Maintained by Roger Bivand. Last updated 18 days ago.

spatial-autocorrelation spatial-dependence spatial-weights

10.0 match 131 stars 16.62 score 6.0k scripts 107 dependents

r-barnes

dggridR:Discrete Global Grids

Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.

Maintained by Sebastian Krantz. Last updated 6 months ago.

discrete-global-grids geospatial spatial-analysis cpp

17.3 match 168 stars 9.37 score 388 scripts 1 dependents

ropensci

GSODR:Global Surface Summary of the Day ('GSOD') Weather Data Client

Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI'). Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity ('RH') are calculated from the original data using the improved August-Roche-Magnus approximation (Alduchov & Eskridge 1996) and included in the final data set. The resulting metadata include station identification information, country, state, latitude, longitude, elevation, weather observations and associated flags. For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, <https://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.

Maintained by Adam H. Sparks. Last updated 11 days ago.

us-ncei meteorological-data global-weather weather weather-data meteorology station-data surface-weather data-access us-ncdc daily-data daily-weather global-data gsod historical-data historical-weather ncdc ncei weather-information weather-stations

18.3 match 94 stars 8.70 score 116 scripts

ropensci

taxize:Taxonomic Information from Around the Web

Interacts with a suite of web application programming interfaces (API) for taxonomic tasks, such as getting database specific taxonomic identifiers, verifying species names, getting taxonomic hierarchies, fetching downstream and upstream taxonomic names, getting taxonomic synonyms, converting scientific to common names and vice versa, and more. Some of the services supported include 'NCBI E-utilities' (<https://www.ncbi.nlm.nih.gov/books/NBK25501/>), 'Encyclopedia of Life' (<https://eol.org/docs/what-is-eol/data-services>), 'Global Biodiversity Information Facility' (<https://techdocs.gbif.org/en/openapi/>), and many more. Links to the API documentation for other supported services are available in the documentation for their respective functions in this package.

Maintained by Zachary Foster. Last updated 12 days ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper biodiversity darwincore data taxize

10.9 match 274 stars 13.63 score 1.6k scripts 23 dependents

josiahparry

sfdep:Spatial Dependence for Simple Features

An interface to 'spdep' to integrate with 'sf' objects and the 'tidyverse'.

Maintained by Dexter Locke. Last updated 6 months ago.

r-spatial spatial

19.5 match 130 stars 7.01 score 130 scripts

bioc

nipalsMCIA:Multiple Co-Inertia Analysis via the NIPALS Method

Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.

Maintained by Maximilian Mattessich. Last updated 27 days ago.

software clustering classification multiplecomparison normalization preprocessing singlecell

20.4 match 6 stars 6.60 score 10 scripts

ardiad

DEoptim:Global Optimization by Differential Evolution

Implements the Differential Evolution algorithm for global optimization of a real-valued function of a real-valued parameter vector as described in Mullen et al. (2011) <doi:10.18637/jss.v040.i06>.

Maintained by Katharine Mullen. Last updated 2 years ago.

differential-evolution evolutionary-algorithm global-optimization optimization

11.1 match 29 stars 11.42 score 680 scripts 124 dependents

ropensci

CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections

Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.

Maintained by Alexander Zizka. Last updated 1 years ago.

11.5 match 82 stars 10.93 score 306 scripts 3 dependents

r-lib

rlang:Functions for Base Types and Core R and 'Tidyverse' Features

A toolbox for working with base types, core R features like the condition system, and core 'Tidyverse' features like tidy evaluation.

Maintained by Lionel Henry. Last updated 19 days ago.

5.9 match 517 stars 20.53 score 9.8k scripts 15k dependents

ropensci

nasapower:NASA POWER API Client

An API client for NASA POWER global meteorology, surface solar energy and climatology data API. POWER (Prediction Of Worldwide Energy Resources) data are freely available for download with varying spatial resolutions dependent on the original data and with several temporal resolutions depending on the POWER parameter and community. This work is funded through the NASA Earth Science Directorate Applied Science Program. For more on the data themselves, the methodologies used in creating, a web- based data viewer and web access, please see <https://power.larc.nasa.gov/>.

Maintained by Adam H. Sparks. Last updated 11 days ago.

nasa meteorological-data weather global weather-data meteorology nasa-power agroclimatology earth-science data-access climate-data agroclimatology-data weather-variables

11.5 match 101 stars 9.98 score 137 scripts 3 dependents

t-kalinowski

keras:R Interface to 'Keras'

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

Maintained by Tomasz Kalinowski. Last updated 11 months ago.

10.5 match 10.82 score 10k scripts 54 dependents

cloudyr

googleComputeEngineR:R Interface with Google Compute Engine

Interact with the 'Google Compute Engine' API in R. Lets you create, start and stop instances in the 'Google Cloud'. Support for preconfigured instances, with templates for common R needs.

Maintained by Mark Edmondson. Last updated 1 days ago.

api cloud-computing cloudyr google-cloud googleauthr launching-virtual-machines

11.1 match 152 stars 9.73 score 235 scripts

dsstoffer

astsa:Applied Statistical Time Series Analysis

Contains data sets and scripts for analyzing time series in both the frequency and time domains including state space modeling as well as supporting the texts Time Series Analysis and Its Applications: With R Examples (5th ed), by R.H. Shumway and D.S. Stoffer. Springer Texts in Statistics, 2025, <https://link.springer.com/book/9783031705830>, and Time Series: A Data Analysis Approach Using R. Chapman-Hall, 2019, <DOI:10.1201/9780429273285>.

Maintained by David Stoffer. Last updated 2 months ago.

13.7 match 7 stars 7.88 score 2.2k scripts 8 dependents

rpolars

polars:Lightning-Fast 'DataFrame' Library

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

Maintained by Soren Welling. Last updated 3 days ago.

arrow polars rust

9.0 match 499 stars 12.01 score 1.0k scripts 2 dependents

bioc

globaltest:Testing Groups of Covariates/Features for Association with a Response Variable, with Applications to Gene Set Testing

The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.

Maintained by Jelle Goeman. Last updated 5 months ago.

microarray onechannel bioinformatics differentialexpression go pathways

15.4 match 6.96 score 79 scripts 7 dependents

ropensci

rsi:Efficiently Retrieve and Process Satellite Imagery

Downloads spatial data from spatiotemporal asset catalogs ('STAC'), computes standard spectral indices from the Awesome Spectral Indices project (Montero et al. (2023) <doi:10.1038/s41597-023-02096-0>) against raster data, and glues the outputs together into predictor bricks. Methods focus on interoperability with the broader spatial ecosystem; function arguments and outputs use classes from 'sf' and 'terra', and data downloading functions support complex 'CQL2' queries using 'rstac'.

Maintained by Michael Mahoney. Last updated 2 months ago.

14.9 match 49 stars 7.20 score 38 scripts

rspatial

terra:Spatial Data Analysis

Methods for spatial data analysis with vector (points, lines, polygons) and raster (grid) data. Methods for vector data include geometric operations such as intersect and buffer. Raster methods include local, focal, global, zonal and geometric operations. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/> to get started. 'terra' replaces the 'raster' package ('terra' can do more, and it is faster and easier to use).

Maintained by Robert J. Hijmans. Last updated 22 hours ago.

geospatial raster spatial vector onetbb proj gdal geos cpp

6.1 match 559 stars 17.64 score 17k scripts 851 dependents

dankelley

oce:Analysis of Oceanographic Data

Supports the analysis of Oceanographic data, including 'ADCP' measurements, measurements made with 'argo' floats, 'CTD' measurements, sectional data, sea-level time series, coastline and topographic data, etc. Provides specialized functions for calculating seawater properties such as potential temperature in either the 'UNESCO' or 'TEOS-10' equation of state. Produces graphical displays that conform to the conventions of the Oceanographic literature. This package is discussed extensively by Kelley (2018) "Oceanographic Analysis with R" <doi:10.1007/978-1-4939-8844-0>.

Maintained by Dan Kelley. Last updated 1 days ago.

oceanography fortran cpp

6.9 match 146 stars 15.42 score 4.2k scripts 18 dependents

predictiveecology

SpaDES.core:Core Utilities for Developing and Running Spatially Explicit Discrete Event Models

Provides the core framework for a discrete event system to implement a complete data-to-decisions, reproducible workflow. The core components facilitate the development of modular pieces, and enable the user to include additional functionality by running user-built modules. Includes conditional scheduling, restart after interruption, packaging of reusable modules, tools for developing arbitrary automated workflows, automated interweaving of modules of different temporal resolution, and tools for visualizing and understanding the within-project dependencies. The suggested package 'NLMR' can be installed from the repository (<https://PredictiveEcology.r-universe.dev>).

Maintained by Eliot J B McIntire. Last updated 19 days ago.

discrete-events-simulations simulation-framework simulation-modeling

9.1 match 10 stars 10.61 score 142 scripts 6 dependents

jokergoo

GlobalOptions:Generate Functions to Get or Set Global Options

It provides more configurations on the option values such as validation and filtering on the values, making options invisible or private.

Maintained by Zuguang Gu. Last updated 9 months ago.

9.7 match 9 stars 9.48 score 40 scripts 217 dependents

dboslab

expowo:An R package for mining global plant diversity and distribution data

Produces diversity estimates and species lists with associated global distribution for any vascular plant family and genus from 'Plants of the World Online' database <https://powo.science.kew.org/>, by interacting with the source code of each plant taxon page. It also creates global maps of species richness, graphics of species discoveries and nomenclatural changes over time. For more details

Maintained by Debora Zuanny. Last updated 5 months ago.

data-mining extractor

11.7 match 8 stars 7.36 score 64 scripts

r-lib

withr:Run Code 'With' Temporarily Modified Global State

A set of functions to run code 'with' safely and temporarily modified global state. Many of these functions were originally a part of the 'devtools' package, this provides a simple package with limited dependencies to provide access to these functions.

Maintained by Lionel Henry. Last updated 19 days ago.

4.6 match 176 stars 17.92 score 1.2k scripts 12k dependents

pik-piam

mrremind:MadRat REMIND Input Data Package

The mrremind packages contains data preprocessing for the REMIND model.

Maintained by Lavinia Baumstark. Last updated 3 days ago.

13.2 match 4 stars 6.25 score 15 scripts 1 dependents

cbergmeir

Rlgt:Bayesian Exponential Smoothing Models with Trend Modifications

An implementation of a number of Global Trend models for time series forecasting that are Bayesian generalizations and extensions of some Exponential Smoothing models. The main differences/additions include 1) nonlinear global trend, 2) Student-t error distribution, and 3) a function for the error size, so heteroscedasticity. The methods are particularly useful for short time series. When tested on the well-known M3 dataset, they are able to outperform all classical time series algorithms. The models are fitted with MCMC using the 'rstan' package.

Maintained by Christoph Bergmeir. Last updated 8 months ago.

cpp

11.6 match 20 stars 7.05 score 31 scripts

rich-iannone

DiagrammeR:Graph/Network Visualization

Build graph/network structures using functions for stepwise addition and deletion of nodes and edges. Work with data available in tables for bulk addition of nodes, edges, and associated metadata. Use graph selections and traversals to apply changes to specific nodes or edges. A wide selection of graph algorithms allow for the analysis of graphs. Visualize the graphs and take advantage of any aesthetic properties assigned to nodes and edges.

Maintained by Richard Iannone. Last updated 2 months ago.

graph graph-functions network-graph property-graph visualization

5.3 match 1.7k stars 15.18 score 3.8k scripts 87 dependents

sbgraves237

Ecdat:Data Sets for Econometrics

Data sets for econometrics, including political science.

Maintained by Spencer Graves. Last updated 4 months ago.

10.9 match 2 stars 7.25 score 740 scripts 3 dependents

tobiste

tectonicr:Analyzing the Orientation of Maximum Horizontal Stress

Models the direction of the maximum horizontal stress using relative plate motion parameters. Statistical algorithms to evaluate the modeling results compared with the observed data. Provides plots to visualize the results. Methods described in Stephan et al. (2023) <doi:10.1038/s41598-023-42433-2> and Wdowinski (1998) <doi:10.1016/S0079-1946(98)00091-3>.

Maintained by Tobias Stephan. Last updated 14 days ago.

geology structural-geology tectonics

10.6 match 7 stars 7.26 score 33 scripts

bioc

InPAS:Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.

Maintained by Jianhong Ou. Last updated 2 months ago.

alternative polyadenylation differential polyadenylation site usage rna-seq gene regulation transcription

17.9 match 4.30 score 1 scripts

vegandevs

vegan:Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Maintained by Jari Oksanen. Last updated 16 days ago.

ecological-modelling ecology ordination fortran openblas

3.9 match 472 stars 19.41 score 15k scripts 440 dependents

fgazzelloni

hmsidwR:Health Metrics and the Spread of Infectious Diseases

A collection of datasets and supporting functions accompanying Health Metrics and the Spread of Infectious Diseases by Federica Gazzelloni (2024). This package provides data for health metrics calculations, including Disability-Adjusted Life Years (DALYs), Years of Life Lost (YLLs), and Years Lived with Disability (YLDs), as well as additional tools for analyzing and visualizing health data. Federica Gazzelloni (2024) <doi:10.5281/zenodo.10818338>.

Maintained by Federica Gazzelloni. Last updated 2 months ago.

deaths health-data infectious-diseases lifeexpectancy

13.5 match 4 stars 5.48 score 6 scripts

emmanuelparadis

ape:Analyses of Phylogenetics and Evolution

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.

Maintained by Emmanuel Paradis. Last updated 12 hours ago.

openblas cpp

4.1 match 64 stars 17.22 score 13k scripts 599 dependents

rich-iannone

stationaRy:Detailed Meteorological Data from Stations All Over the World

Acquire hourly meteorological data from stations located all over the world. There is a wealth of data available, with historic weather data accessible from nearly 30,000 stations. The available data is automatically downloaded from a data repository and processed into a 'tibble' for the exact range of years requested. A relative humidity approximation is provided using the 'August-Roche-Magnus' formula, which was adapted from Alduchov and Eskridge (1996) <doi:10.1175%2F1520-0450%281996%29035%3C0601%3AIMFAOS%3E2.0.CO%3B2>.

Maintained by Richard Iannone. Last updated 5 years ago.

dataset global met-data

11.0 match 250 stars 6.44 score 74 scripts

dnychka

fields:Tools for Spatial Data

For curve, surface and function fitting with an emphasis on splines, spatial data, geostatistics, and spatial statistics. The major methods include cubic, and thin plate splines, Kriging, and compactly supported covariance functions for large data sets. The splines and Kriging methods are supported by functions that can determine the smoothing parameter (nugget and sill variance) and other covariance function parameters by cross validation and also by restricted maximum likelihood. For Kriging there is an easy to use function that also estimates the correlation scale (range parameter). A major feature is that any covariance function implemented in R and following a simple format can be used for spatial prediction. There are also many useful functions for plotting and working with spatial data as images. This package also contains an implementation of sparse matrix methods for large spatial data sets and currently requires the sparse matrix (spam) package. Use help(fields) to get started and for an overview. The fields source code is deliberately commented and provides useful explanations of numerical details as a companion to the manual pages. The commented source code can be viewed by expanding the source code version and looking in the R subdirectory. The reference for fields can be generated by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development of this package was supported in part by the National Science Foundation Grant 1417857, the National Center for Atmospheric Research, and Colorado School of Mines. See the Fields URL for a vignette on using this package and some background on spatial statistics.

Maintained by Douglas Nychka. Last updated 9 months ago.

fortran

5.6 match 15 stars 12.60 score 7.7k scripts 295 dependents

bioc

MEIGOR:MEIGOR - MEtaheuristics for bIoinformatics Global Optimization

MEIGOR provides a comprehensive environment for performing global optimization tasks in bioinformatics and systems biology. It leverages advanced metaheuristic algorithms to efficiently search the solution space and is specifically tailored to handle the complexity and high-dimensionality of biological datasets. This package supports various optimization routines and is integrated with Bioconductor's infrastructure for a seamless analysis workflow.

Maintained by Jose A. Egea. Last updated 5 months ago.

systemsbiology optimization software

16.5 match 4.25 score 44 scripts

modeloriented

survex:Explainable Machine Learning in Survival Analysis

Survival analysis models are commonly used in medicine and other areas. Many of them are too complex to be interpreted by human. Exploration and explanation is needed, but standard methods do not give a broad enough picture. 'survex' provides easy-to-apply methods for explaining survival models, both complex black-boxes and simpler statistical models. They include methods specific to survival analysis such as SurvSHAP(t) introduced in Krzyzinski et al., (2023) <doi:10.1016/j.knosys.2022.110234>, SurvLIME described in Kovalev et al., (2020) <doi:10.1016/j.knosys.2020.106164> as well as extensions of existing ones described in Biecek et al., (2021) <doi:10.1201/9780429027192>.

Maintained by Mikołaj Spytek. Last updated 9 months ago.

biostatistics brier-scores censored-data cox-model cox-regression explainable-ai explainable-machine-learning explainable-ml explanatory-model-analysis interpretable-machine-learning interpretable-ml machine-learning probabilistic-machine-learning shap survival-analysis time-to-event variable-importance xai

8.3 match 110 stars 8.40 score 114 scripts

gadget-framework

gadget3:Globally-Applicable Area Disaggregated General Ecosystem Toolbox V3

A framework to assist creation of marine ecosystem models, generating either 'R' or 'C++' code which can then be optimised using the 'TMB' package and standard 'R' tools. Principally designed to reproduce gadget2 models in 'TMB', but can be extended beyond gadget2's capabilities. Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug, Bradley M. Bell (2016) <doi:10.18637/jss.v070.i05> "TMB: Automatic Differentiation and Laplace Approximation.". Begley, J., & Howell, D. (2004) <https://core.ac.uk/download/pdf/225936648.pdf> "An overview of Gadget, the globally applicable area-disaggregated general ecosystem toolbox. ICES.".

Maintained by Jamie Lentin. Last updated 30 days ago.

8.0 match 8 stars 8.66 score 170 scripts

ropensci

rgbif:Interface to the Global Biodiversity Information Facility API

A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility (GBIF; <https://www.gbif.org/developer/summary>). GBIF is a database of species occurrence records from sources all over the globe. rgbif includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the GBIF tile map service to make rasters summarizing huge amounts of data.

Maintained by John Waller. Last updated 3 days ago.

gbif specimens api web-services occurrences species taxonomy biodiversity data lifewatch oscibio spocc

5.2 match 161 stars 13.26 score 2.1k scripts 20 dependents

bioc

ComplexHeatmap:Make Complex Heatmaps

Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various annotation graphics.

Maintained by Zuguang Gu. Last updated 5 months ago.

software visualization sequencing clustering complex-heatmaps heatmap

4.0 match 1.3k stars 16.93 score 16k scripts 151 dependents

apache

arrow:Integration to 'Apache' 'Arrow'

'Apache' 'Arrow' <https://arrow.apache.org/> is a cross-language development platform for in-memory data. It specifies a standardized language-independent columnar memory format for flat and hierarchical data, organized for efficient analytic operations on modern hardware. This package provides an interface to the 'Arrow C++' library.

Maintained by Jonathan Keane. Last updated 1 months ago.

arrow curl openssl cpp

3.5 match 15k stars 19.22 score 10k scripts 81 dependents

mboeck11

BGVAR:Bayesian Global Vector Autoregressions

Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available. The package has a companion paper: Boeck, M., Feldkircher, M. and F. Huber (2022) "BGVAR: Bayesian Global Vector Autoregressions with Shrinkage Priors in R", Journal of Statistical Software, Vol. 104(9), pp. 1-28 <doi:10.18637/jss.v104.i09>.

Maintained by Maximilian Boeck. Last updated 3 months ago.

openblas cpp

8.8 match 27 stars 7.58 score 156 scripts

r-lib

usethis:Automate Package and Project Setup

Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

Maintained by Jennifer Bryan. Last updated 11 days ago.

github setup

3.8 match 869 stars 17.54 score 5.6k scripts 336 dependents

stochastictree

stochtree:Stochastic Tree Ensembles (XBART and BART) for Supervised Learning and Causal Inference

Flexible stochastic tree ensemble software. Robust implementations of Bayesian Additive Regression Trees (BART) Chipman, George, McCulloch (2010) <doi:10.1214/09-AOAS285> for supervised learning and Bayesian Causal Forests (BCF) Hahn, Murray, Carvalho (2020) <doi:10.1214/19-BA1195> for causal inference. Enables model serialization and parallel sampling and provides a low-level interface for custom stochastic forest samplers.

Maintained by Drew Herren. Last updated 18 days ago.

bart bayesian-machine-learning bayesian-methods decision-trees gradient-boosted-trees machine-learning probabilistic-models tree-ensembles cpp

7.7 match 20 stars 8.52 score 40 scripts

astamm

nloptr:R Interface to NLopt

Solve optimization problems using an R interface to NLopt. NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. See <https://nlopt.readthedocs.io/en/latest/NLopt_Algorithms/> for more information on the available algorithms. Building from included sources requires 'CMake'. On Linux and 'macOS', if a suitable system build of NLopt (2.7.0 or later) is found, it is used; otherwise, it is built from included sources via 'CMake'. On Windows, NLopt is obtained through 'rwinlib' for 'R <= 4.1.x' or grabbed from the appropriate toolchain for 'R >= 4.2.0'.

Maintained by Aymeric Stamm. Last updated 10 hours ago.

cpp

3.8 match 108 stars 17.13 score 1.1k scripts 1.8k dependents

yihui

xfun:Supporting Functions for Packages Maintained by 'Yihui Xie'

Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.

Maintained by Yihui Xie. Last updated 3 days ago.

3.5 match 145 stars 18.18 score 916 scripts 4.4k dependents

bioc

safe:Significance Analysis of Function and Expression

SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.

Maintained by Ludwig Geistlinger. Last updated 5 months ago.

differentialexpression pathways genesetenrichment statisticalmethod software

11.3 match 5.60 score 32 scripts 5 dependents

r-tmap

tmap:Thematic Maps

Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.

Maintained by Martijn Tennekes. Last updated 5 days ago.

choropleth-maps maps spatial thematic-maps visualisation

3.6 match 880 stars 16.73 score 13k scripts 24 dependents

sofia-taf

fishstat:Global Fishery and Aquaculture Statistics

The Food and Agriculture Organization of the United Nations (FAO) FishStat database is the leading source of global fishery and aquaculture statistics and provides unique information for sector analysis and monitoring. This package provides the global production data from all fisheries and aquaculture in R format, ready for analysis.

Maintained by Arni Magnusson. Last updated 20 days ago.

17.5 match 3.40 score

mpio-be

rangeMapper:A Platform for the Study of Macro-Ecology of Life History Traits

Tools for generation of (life-history) traits and diversity maps on hexagonal or square grids. Valcu et al.(2012) <doi:10.1111/j.1466-8238.2011.00739.x>.

Maintained by Mihai Valcu. Last updated 2 years ago.

assemblage-level ecology global life-history-traits raster-cell species

11.0 match 8 stars 5.38 score 30 scripts

stscl

geocn:Loads Spatial Data Sets of China

Providing various commonly used spatial data related to Chinese regions in the R programming environment.

Maintained by Wenbo Lv. Last updated 3 months ago.

china china-region geospatial-visualization maps

11.9 match 17 stars 4.93 score 10 scripts

lightbluetitan

timeSeriesDataSets:Time Series Data Sets

Provides a diverse collection of time series datasets spanning various fields such as economics, finance, energy, healthcare, and more. Designed to support time series analysis in R by offering datasets from multiple disciplines, making it a valuable resource for researchers and analysts.

Maintained by Renzo Caceres Rossi. Last updated 6 months ago.

10.2 match 10 stars 5.71 score 103 scripts

bioc

GlobalAncova:Global test for groups of variables via model comparisons

The association between a variable of interest (e.g. two groups) and the global pattern of a group of variables (e.g. a gene set) is tested via a global F-test. We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. The framework is generalized to groups of categorical variables or even mixed data by a likelihood ratio approach. Closed and hierarchical testing procedures are supported. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.

Maintained by Manuela Hummel. Last updated 5 months ago.

microarray onechannel differentialexpression pathways regression

10.7 match 5.32 score 9 scripts 1 dependents

databio

simpleCache:Simply Caching R Objects

Provides intuitive functions for caching R objects, encouraging reproducible, restartable, and distributed R analysis. The user selects a location to store caches, and then provides nothing more than a cache name and instructions (R code) for how to produce the R object. Also provides some advanced options like environment assignments, recreating or reloading caches, and cluster compute bindings (using the 'batchtools' package) making it flexible enough for use in large-scale data analysis projects.

Maintained by Nathan Sheffield. Last updated 4 years ago.

7.6 match 34 stars 7.51 score 70 scripts 1 dependents

adeverse

ade4:Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.

Maintained by Aurélie Siberchicot. Last updated 12 days ago.

openblas cpp

3.8 match 39 stars 14.96 score 2.2k scripts 256 dependents

nowosad

motif:Local Pattern Analysis

Describes spatial patterns of categorical raster data for any defined regular and irregular areas. Patterns are described quantitatively using built-in signatures based on co-occurrence matrices but also allows for any user-defined functions. It enables spatial analysis such as search, change detection, and clustering to be performed on spatial patterns (Nowosad (2021) <doi:10.1007/s10980-020-01135-0>).

Maintained by Jakub Nowosad. Last updated 7 months ago.

categorical-raster global-ecology landscape-ecology spatial cpp

7.5 match 63 stars 7.48 score 48 scripts

obrl-soil

h3jsr:Access Uber's H3 Library

Provides access to Uber's H3 library for geospatial indexing via its JavaScript transpile 'h3-js' <https://github.com/uber/h3-js> and 'V8' <https://github.com/jeroen/v8>.

Maintained by Lauren OBrien. Last updated 1 years ago.

discrete-global-grids h3 spatial-indexing

6.7 match 67 stars 8.39 score 205 scripts 4 dependents

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.

24.5 match 2.28 score 38 scripts

cwatson

brainGraph:Graph Theory Analysis of Brain MRI Data

A set of tools for performing graph theory analysis of brain MRI data. It works with data from a Freesurfer analysis (cortical thickness, volumes, local gyrification index, surface area), diffusion tensor tractography data (e.g., from FSL) and resting-state fMRI data (e.g., from DPABI). It contains a graphical user interface for graph visualization and data exploration, along with several functions for generating useful figures.

Maintained by Christopher G. Watson. Last updated 1 years ago.

brain-connectivity brain-imaging complex-networks connectome connectomics fmri graph-theory mri network-analysis neuroimaging neuroscience statistics tractography

7.1 match 188 stars 7.86 score 107 scripts 3 dependents

singmann

afex:Analysis of Factorial Experiments

Convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), automatically aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger or Satterthwaite approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex_plot() provides a high-level interface for interaction or one-way plots using ggplot2, combining raw data and model estimates. afex uses type 3 sums of squares as default (imitating commercial statistical software).

Maintained by Henrik Singmann. Last updated 7 months ago.

3.8 match 123 stars 14.50 score 1.4k scripts 15 dependents

mhahsler

dbscan:Density-Based Spatial Clustering of Applications with Noise (DBSCAN) and Related Algorithms

A fast reimplementation of several density-based algorithms of the DBSCAN family. Includes the clustering algorithms DBSCAN (density-based spatial clustering of applications with noise) and HDBSCAN (hierarchical DBSCAN), the ordering algorithm OPTICS (ordering points to identify the clustering structure), shared nearest neighbor clustering, and the outlier detection algorithms LOF (local outlier factor) and GLOSH (global-local outlier score from hierarchies). The implementations use the kd-tree data structure (from library ANN) for faster k-nearest neighbor search. An R interface to fast kNN and fixed-radius NN search is also provided. Hahsler, Piekenbrock and Doran (2019) <doi:10.18637/jss.v091.i01>.

Maintained by Michael Hahsler. Last updated 2 months ago.

clustering dbscan density-based-clustering hdbscan lof optics cpp

3.5 match 321 stars 15.62 score 1.6k scripts 84 dependents

bioc

MSstatsPTM:Statistical Characterization of Post-translational Modifications

MSstatsPTM provides general statistical methods for quantitative characterization of post-translational modifications (PTMs). Supports DDA, DIA, SRM, and tandem mass tag (TMT) labeling. Typically, the analysis involves the quantification of PTM sites (i.e., modified residues) and their corresponding proteins, as well as the integration of the quantification results. MSstatsPTM provides functions for summarization, estimation of PTM site abundance, and detection of changes in PTMs across experimental conditions.

Maintained by Devon Kohler. Last updated 4 months ago.

immunooncology massspectrometry proteomics software differentialexpression onechannel twochannel normalization qualitycontrol post-translational-modification cpp

6.8 match 10 stars 7.98 score 36 scripts 2 dependents

thibautjombart

adegenet:Exploratory Analysis of Genetic and Genomic Data

Toolset for the exploration of genetic and genomic data. Adegenet provides formal (S4) classes for storing and handling various genetic data, including genetic markers with varying ploidy and hierarchical population structure ('genind' class), alleles counts by populations ('genpop'), and genome-wide SNP data ('genlight'). It also implements original multivariate methods (DAPC, sPCA), graphics, statistical tests, simulation tools, distance and similarity measures, and several spatial methods. A range of both empirical and simulated datasets is also provided to illustrate various methods.

Maintained by Zhian N. Kamvar. Last updated 1 months ago.

4.3 match 182 stars 12.60 score 1.9k scripts 29 dependents

talgalili

dendextend:Extending 'dendrogram' Functionality in R

Offers a set of functions for extending 'dendrogram' objects in R, letting you visualize and compare trees of 'hierarchical clusterings'. You can (1) Adjust a tree's graphical parameters - the color, size, type, etc of its branches, nodes and labels. (2) Visually and statistically compare different 'dendrograms' to one another.

Maintained by Tal Galili. Last updated 2 months ago.

3.1 match 154 stars 17.02 score 6.0k scripts 164 dependents

moondog1969

streamDAG:Analytical Methods for Stream DAGs

Provides indices and tools for directed acyclic graphs (DAGs), particularly DAG representations of intermittent streams. A detailed introduction to the package can be found in the publication: "Non-perennial stream networks as directed acyclic graphs: The R-package streamDAG" (Aho et al., 2023) <doi:10.1016/j.envsoft.2023.105775>, and in the introductory package vignette.

Maintained by Ken Aho. Last updated 5 months ago.

12.7 match 1 stars 4.18 score 4 scripts

rladies

meetupr:Meetup R API

Provides access to data from <https:www.meetup.com> (see <https:www.meetup.com/meetup_api/> for more information).

Maintained by Athanasia Mo Mowinckel. Last updated 2 years ago.

api api-wrapper meetup r-ladies rladies rladies-global

7.5 match 77 stars 7.03 score 92 scripts

r-forge

Sleuth3:Data Sets from Ramsey and Schafer's "Statistical Sleuth (3rd Ed)"

Data sets from Ramsey, F.L. and Schafer, D.W. (2013), "The Statistical Sleuth: A Course in Methods of Data Analysis (3rd ed)", Cengage Learning.

Maintained by Berwin A Turlach. Last updated 1 years ago.

8.3 match 6.38 score 522 scripts

daqana

dqrng:Fast Pseudo Random Number Generators

Several fast random number generators are provided as C++ header only libraries: The PCG family by O'Neill (2014 <https://www.cs.hmc.edu/tr/hmc-cs-2014-0905.pdf>) as well as the Xoroshiro / Xoshiro family by Blackman and Vigna (2021 <doi:10.1145/3460772>). In addition fast functions for generating random numbers according to a uniform, normal and exponential distribution are included. The latter two use the Ziggurat algorithm originally proposed by Marsaglia and Tsang (2000, <doi:10.18637/jss.v005.i08>). The fast sampling methods support unweighted sampling both with and without replacement. These functions are exported to R and as a C++ interface and are enabled for use with the default 64 bit generator from the PCG family, Xoroshiro128+/++/** and Xoshiro256+/++/** as well as the 64 bit version of the 20 rounds Threefry engine (Salmon et al., 2011, <doi:10.1145/2063384.2063405>) as provided by the package 'sitmo'.

Maintained by Ralf Stubner. Last updated 6 months ago.

random random-distributions random-generation random-sampling rng cpp

4.0 match 42 stars 13.12 score 188 scripts 183 dependents

dwarton

ecostats:Code and Data Accompanying the Eco-Stats Text (Warton 2022)

Functions and data supporting the Eco-Stats text (Warton, 2022, Springer), and solutions to exercises. Functions include tools for using simulation envelopes in diagnostic plots, and a function for diagnostic plots of multivariate linear models. Datasets mentioned in the package are included here (where not available elsewhere) and there is a vignette for each chapter of the text with solutions to exercises.

Maintained by David Warton. Last updated 1 years ago.

8.0 match 8 stars 6.58 score 53 scripts

modeloriented

vivo:Variable Importance via Oscillations

Provides an easy to calculate local variable importance measure based on Ceteris Paribus profile and global variable importance measure based on Partial Dependence Profiles.

Maintained by Anna Kozak. Last updated 4 years ago.

explainable-ai explainable-artificial-intelligence explainable-ml iml interpretable-machine-learning variable-importance xai

9.6 match 14 stars 5.45 score 7 scripts

kwb-r

kwb.utils:General Utility Functions Developed at KWB

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

Maintained by Hauke Sonnenberg. Last updated 12 months ago.

7.1 match 8 stars 7.33 score 12 scripts 78 dependents

lrberge

dreamerr:Error Handling Made Easy

Set of tools to facilitate package development and make R a more user-friendly place. Mostly for developers (or anyone who writes/shares functions). Provides a simple, powerful and flexible way to check the arguments passed to functions. The developer can easily describe the type of argument needed. If the user provides a wrong argument, then an informative error message is prompted with the requested type and the problem clearly stated--saving the user a lot of time in debugging.

Maintained by Laurent Berge. Last updated 5 months ago.

5.5 match 27 stars 9.32 score 16 scripts 32 dependents

r-spatial

gstat:Spatial and Spatio-Temporal Geostatistical Modelling, Prediction and Simulation

Variogram modelling; simple, ordinary and universal point or block (co)kriging; spatio-temporal kriging; sequential Gaussian or indicator (co)simulation; variogram and variogram map plotting utility functions; supports sf and stars.

Maintained by Edzer Pebesma. Last updated 10 days ago.

openblas

3.5 match 197 stars 14.78 score 4.8k scripts 57 dependents

benmarwick

gsloid:Global Sea Level and Oxygen Isotope Data

Contains published data sets for global benthic d18O data for 0-5.3 Myr <doi:10.1029/2004PA001071> and global sea levels based on marine sediment core data for 0-800 ka <doi:10.5194/cp-12-1-2016>.

Maintained by Ben Marwick. Last updated 1 years ago.

10.3 match 5 stars 4.90 score 32 scripts

vpnsctl

mixpoissonreg:Mixed Poisson Regression for Overdispersed Count Data

Fits mixed Poisson regression models (Poisson-Inverse Gaussian or Negative-Binomial) on data sets with response variables being count data. The models can have varying precision parameter, where a linear regression structure (through a link function) is assumed to hold on the precision parameter. The Expectation-Maximization algorithm for both these models (Poisson Inverse Gaussian and Negative Binomial) is an important contribution of this package. Another important feature of this package is the set of functions to perform global and local influence analysis. See Barreto-Souza and Simas (2016) <doi:10.1007/s11222-015-9601-6> for further details.

Maintained by Alexandre B. Simas. Last updated 4 years ago.

count-data diagnostics influence-analysis local-influence negative-binomial-regression poisson-inverse-gaussian-regression

9.1 match 3 stars 5.44 score 23 scripts

lenarddome

psp:Parameter Space Partitioning MCMC for Global Model Evaluation

Implements an n-dimensional parameter space partitioning algorithm for evaluating the global behaviour of formal computational models as described by Pitt, Kim, Navarro and Myung (2006) <doi:10.1037/0033-295X.113.1.57>.

Maintained by Lenard Dome. Last updated 8 months ago.

cognitive-science computational-modelling global-analysis model-evaluation parameter-space-analysis psychology cpp

12.6 match 8 stars 3.90 score 6 scripts

dreamrs

fresh:Create Custom 'Bootstrap' Themes to Use in 'Shiny'

Customize 'Bootstrap' and 'Bootswatch' themes, like colors, fonts, grid layout, to use in 'Shiny' applications, 'rmarkdown' documents and 'flexdashboard'.

Maintained by Victor Perrier. Last updated 9 months ago.

bootstrap shiny shiny-applications shiny-themes

4.1 match 228 stars 11.99 score 546 scripts 47 dependents

nifu-no

saros:Semi-Automatic Reporting of Ordinary Surveys

Offers a systematic way for conditional reporting of figures and tables for many (and bivariate combinations of) variables, typically from survey data. Contains interactive 'ggiraph'-based (<https://CRAN.R-project.org/package=ggiraph>) plotting functions and data frame-based summary tables (bivariate significance tests, frequencies/proportions, unique open ended responses, etc) with many arguments for customization, and extensions possible. Uses a global options() system for neatly reducing redundant code. Also contains tools for immediate saving of objects and returning a hashed link to the object, useful for creating download links to high resolution images upon rendering in 'Quarto'. Suitable for highly customized reports, primarily intended for survey research.

Maintained by Stephan Daus. Last updated 1 months ago.

7.7 match 2 stars 6.32 score 20 scripts

trinker

qdap:Bridging the Gap Between Qualitative Data and Quantitative Analysis

Automates many of the tasks associated with quantitative discourse analysis of transcripts containing discourse including frequency counts of sentence types, words, sentences, turns of talk, syllables and other assorted analysis tasks. The package provides parsing tools for preparing transcript data. Many functions enable the user to aggregate data by any number of grouping variables, providing analysis and seamless integration with other R packages that undertake higher level analysis and visualization of text. This affords the user a more efficient and targeted analysis. 'qdap' is designed for transcript analysis, however, many functions are applicable to other areas of Text Mining/ Natural Language Processing.

Maintained by Tyler Rinker. Last updated 4 years ago.

qdap quantitative-discourse-analysis text-analysis text-mining text-plotting openjdk

5.0 match 176 stars 9.61 score 1.3k scripts 3 dependents

dcomtois

summarytools:Tools to Quickly and Neatly Summarize Data

Data frame summaries, cross-tabulations, weight-enabled frequency tables and common descriptive (univariate) statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.

Maintained by Dominic Comtois. Last updated 1 days ago.

descriptive-statistics frequency-table html-report markdown pander pandoc pandoc-markdown rmarkdown rstudio

3.3 match 526 stars 14.52 score 2.9k scripts 6 dependents

henrikbengtsson

R.utils:Various Programming Utilities

Utility functions useful when programming and developing R packages.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

3.5 match 63 stars 13.74 score 5.7k scripts 814 dependents

adeverse

adespatial:Multivariate Multiscale Spatial Analysis

Tools for the multiscale spatial analysis of multivariate data. Several methods are based on the use of a spatial weighting matrix and its eigenvector decomposition (Moran's Eigenvectors Maps, MEM). Several approaches are described in the review Dray et al (2012) <doi:10.1890/11-1183.1>.

Maintained by Aurélie Siberchicot. Last updated 12 days ago.

openblas

4.3 match 36 stars 11.06 score 398 scripts 2 dependents

thlytras

rspiro:Implementation of Spirometry Equations

Implementation of various spirometry equations in R, currently the GLI-2012 (Global Lung Initiative; Quanjer et al. 2012 <doi:10.1183/09031936.00080312>), the race-neutral GLI global 2022 (Global Lung Initiative; Bowerman et al. 2023 <doi:10.1164/rccm.202205-0963OC>), the NHANES3 (National Health and Nutrition Examination Survey; Hankinson et al. 1999 <doi:10.1164/ajrccm.159.1.9712108>) and the JRS 2014 (Japanese Respiratory Society; Kubota et al. 2014 <doi:10.1016/j.resinv.2014.03.003>) equations. Also the GLI-2017 diffusing capacity equations <doi:10.1183/13993003.00010-2017> are implemented. Contains user-friendly functions to calculate predicted and LLN (Lower Limit of Normal) values for different spirometric parameters such as FEV1 (Forced Expiratory Volume in 1 second), FVC (Forced Vital Capacity), etc, and to convert absolute spirometry measurements to percent (%) predicted and z-scores.

Maintained by Theodore Lytras. Last updated 9 months ago.

9.2 match 15 stars 5.10 score 28 scripts

jonathanlees

GEOmap:Topographic and Geologic Mapping

Set of routines for making map projections (forward and inverse), topographic maps, perspective plots, geological maps, geological map symbols, geological databases, interactive plotting and selection of focus regions.

Maintained by Jonathan M. Lees. Last updated 8 months ago.

13.8 match 3.38 score 162 scripts 3 dependents

lbau7

basksim:Simulation-Based Calculation of Basket Trial Operating Characteristics

Provides a unified syntax for the simulation-based comparison of different single-stage basket trial designs with a binary endpoint and equal sample sizes in all baskets. Methods include the designs by Baumann et al. (2024) <doi:10.48550/arXiv.2309.06988>, Fujikawa et al. (2020) <doi:10.1002/bimj.201800404>, Berry et al. (2020) <doi:10.1177/1740774513497539>, Neuenschwander et al. (2016) <doi:10.1002/pst.1730> and Psioda et al. (2021) <doi:10.1093/biostatistics/kxz014>. For the latter three designs, the functions are mostly wrappers for functions provided by the packages 'bhmbasket' and 'bmabasket'.

Maintained by Lukas Baumann. Last updated 11 months ago.

jags cpp

13.4 match 1 stars 3.45 score 19 scripts

sylvainschmitt

rcontroll:Individual-Based Forest Growth Simulator 'TROLL'

'TROLL' is coded in C++ and it typically simulates hundreds of thousands of individuals over hundreds of years. The 'rcontroll' R package is a wrapper of 'TROLL'. 'rcontroll' includes functions that generate inputs for simulations and run simulations. Finally, it is possible to analyse the 'TROLL' outputs through tables, figures, and maps taking advantage of other R visualisation packages. 'rcontroll' also offers the possibility to generate a virtual LiDAR point cloud that corresponds to a snapshot of the simulated forest.

Maintained by Sylvain Schmitt. Last updated 6 months ago.

gsl cpp

8.0 match 5 stars 5.76 score 19 scripts

ca4wa

adpss:Design and Analysis of Locally or Globally Efficient Adaptive Designs

Provides the functions for planning and conducting a clinical trial with adaptive sample size determination. Maximal statistical efficiency will be exploited even when dramatic or multiple adaptations are made. Such a trial consists of adaptive determination of sample size at an interim analysis and implementation of frequentist statistical test at the interim and final analysis with a prefixed significance level. The required assumptions for the stage-wise test statistics are independent and stationary increments and normality. Predetermination of adaptation rule is not required.

Maintained by Kosuke Kashiwabara. Last updated 2 years ago.

cpp

12.3 match 3.70 score 6 scripts

biooss

sensitivity:Global Sensitivity Analysis of Model Outputs and Importance Measures

A collection of functions for sensitivity analysis of model outputs (factor screening, global sensitivity analysis and robustness analysis), for variable importance measures of data, as well as for interpretability of machine learning models. Most of the functions have to be applied on scalar output, but several functions support multi-dimensional outputs.

Maintained by Bertrand Iooss. Last updated 7 months ago.

cpp

6.7 match 17 stars 6.74 score 472 scripts 8 dependents

francescobartolucci

LMest:Generalized Latent Markov Models

Latent Markov models for longitudinal continuous and categorical data. See Bartolucci, Pandolfi, Pennoni (2017)<doi:10.18637/jss.v081.i04>.

Maintained by Francesco Bartolucci. Last updated 2 months ago.

fortran openblas

9.9 match 3 stars 4.58 score 42 scripts

bioc

phyloseq:Handling and analysis of high-throughput microbiome census data

phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.

Maintained by Paul J. McMurdie. Last updated 5 months ago.

immunooncology sequencing microbiome metagenomics clustering classification multiplecomparison geneticvariability

3.3 match 597 stars 13.90 score 8.4k scripts 37 dependents

asardaes

dtwclust:Time Series Clustering Along with Optimizations for the Dynamic Time Warping Distance

Time series clustering along with optimized techniques related to the Dynamic Time Warping distance and its corresponding lower bounds. Implementations of partitional, hierarchical, fuzzy, k-Shape and TADPole clustering are available. Functionality can be easily extended with custom distance measures and centroid definitions. Implementations of DTW barycenter averaging, a distance based on global alignment kernels, and the soft-DTW distance and centroid routines are also provided. All included distance functions have custom loops optimized for the calculation of cross-distance matrices, including parallelization support. Several cluster validity indices are included.

Maintained by Alexis Sarda. Last updated 8 months ago.

clustering dtw time-series openblas cpp

3.6 match 261 stars 12.39 score 406 scripts 14 dependents

paulnorthrop

bang:Bayesian Analysis, No Gibbs

Provides functions for the Bayesian analysis of some simple commonly-used models, without using Markov Chain Monte Carlo (MCMC) methods such as Gibbs sampling. The 'rust' package <https://cran.r-project.org/package=rust> is used to simulate a random sample from the required posterior distribution, using the generalized ratio-of-uniforms method. See Wakefield, Gelfand and Smith (1991) <DOI:10.1007/BF01889987> for details. At the moment three conjugate hierarchical models are available: beta-binomial, gamma-Poisson and a 1-way analysis of variance (ANOVA).

Maintained by Paul J. Northrop. Last updated 1 months ago.

anova bayesian beta binomial gamma gibbs hierarchical poisson

8.0 match 3 stars 5.62 score 35 scripts

sebkrantz

collapse:Advanced and Fast Data Transformation

A C/C++ based package for advanced data transformation and statistical computing in R that is extremely fast, class-agnostic, robust and programmer friendly. Core functionality includes a rich set of S3 generic grouped and weighted statistical functions for vectors, matrices and data frames, which provide efficient low-level vectorizations, OpenMP multithreading, and skip missing values by default. These are integrated with fast grouping and ordering algorithms (also callable from C), and efficient data manipulation functions. The package also provides a flexible and rigorous approach to time series and panel data in R. It further includes fast functions for common statistical procedures, detailed (grouped, weighted) summary statistics, powerful tools to work with nested data, fast data object conversions, functions for memory efficient R programming, and helpers to effectively deal with variable labels, attributes, and missing data. It is well integrated with base R classes, 'dplyr'/'tibble', 'data.table', 'sf', 'units', 'plm' (panel-series and data frames), and 'xts'/'zoo'.

Maintained by Sebastian Krantz. Last updated 6 days ago.

data-aggregation data-analysis data-manipulation data-processing data-science data-transformation econometrics high-performance panel-data scientific-computing statistics time-series weighted weights cpp openmp

2.7 match 672 stars 16.63 score 708 scripts 97 dependents

yihui

knitr:A General-Purpose Package for Dynamic Report Generation in R

Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.

Maintained by Yihui Xie. Last updated 2 days ago.

dynamic-documents knitr literate-programming rmarkdown sweave

1.9 match 2.4k stars 23.62 score 116k scripts 4.2k dependents

cran

GPoM:Generalized Polynomial Modelling

Platform dedicated to the Global Modelling technique. Its aim is to obtain ordinary differential equations of polynomial form directly from time series. It can be applied to single or multiple time series under various conditions of noise, time series lengths, sampling, etc. This platform is developped at the Centre d'Etudes Spatiales de la Biosphere (CESBIO), UMR 5126 UPS/CNRS/CNES/IRD, 18 av. Edouard Belin, 31401 TOULOUSE, FRANCE. The developments were funded by the French program Les Enveloppes Fluides et l'Environnement (LEFE, MANU, projets GloMo, SpatioGloMo and MoMu). The French program Defi InFiNiTi (CNRS) and PNTS are also acknowledged (projects Crops'IChaos and Musc & SlowFast). The method is described in the article : Mangiarotti S. and Huc M. (2019) <doi:10.1063/1.5081448>.

Maintained by Mireille Huc. Last updated 2 years ago.

15.3 match 2.90 score

bioc

BASiCS:Bayesian Analysis of Single-Cell Sequencing data

Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.

Maintained by Catalina Vallejos. Last updated 5 months ago.

immunooncology normalization sequencing rnaseq software geneexpression transcriptomics singlecell differentialexpression bayesian cellbiology bioconductor-package gene-expression rcpp rcpparmadillo scrna-seq single-cell openblas cpp openmp

4.3 match 83 stars 10.26 score 368 scripts 1 dependents

gamlss-dev

gamlss:Generalized Additive Models for Location Scale and Shape

Functions for fitting the Generalized Additive Models for Location Scale and Shape introduced by Rigby and Stasinopoulos (2005), <doi:10.1111/j.1467-9876.2005.00510.x>. The models use a distributional regression approach where all the parameters of the conditional distribution of the response variable are modelled using explanatory variables.

Maintained by Mikis Stasinopoulos. Last updated 4 months ago.

3.9 match 16 stars 11.23 score 2.0k scripts 49 dependents

merliseclyde

BAS:Bayesian Variable Selection and Model Averaging using Bayesian Adaptive Sampling

Package for Bayesian Variable Selection and Model Averaging in linear models and generalized linear models using stochastic or deterministic sampling without replacement from posterior distributions. Prior distributions on coefficients are from Zellner's g-prior or mixtures of g-priors corresponding to the Zellner-Siow Cauchy Priors or the mixture of g-priors from Liang et al (2008) <DOI:10.1198/016214507000001337> for linear models or mixtures of g-priors from Li and Clyde (2019) <DOI:10.1080/01621459.2018.1469992> in generalized linear models. Other model selection criteria include AIC, BIC and Empirical Bayes estimates of g. Sampling probabilities may be updated based on the sampled models using sampling w/out replacement or an efficient MCMC algorithm which samples models using a tree structure of the model space as an efficient hash table. See Clyde, Ghosh and Littman (2010) <DOI:10.1198/jcgs.2010.09049> for details on the sampling algorithms. Uniform priors over all models or beta-binomial prior distributions on model size are allowed, and for large p truncated priors on the model space may be used to enforce sampling models that are full rank. The user may force variables to always be included in addition to imposing constraints that higher order interactions are included only if their parents are included in the model. This material is based upon work supported by the National Science Foundation under Division of Mathematical Sciences grant 1106891. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Maintained by Merlise Clyde. Last updated 4 months ago.

bayesian bayesian-inference generalized-linear-models linear-regression logistic-regression mcmc model-selection poisson-regression predictive-modeling regression variable-selection fortran openblas

4.0 match 44 stars 10.81 score 420 scripts 3 dependents

openintrostat

openintro:Datasets and Supplemental Functions from 'OpenIntro' Textbooks and Labs

Supplemental functions and data for 'OpenIntro' resources, which includes open-source textbooks and resources for introductory statistics (<https://www.openintro.org/>). The package contains datasets used in our open-source textbooks along with custom plotting functions for reproducing book figures. Note that many functions and examples include color transparency; some plotting elements may not show up properly (or at all) when run in some versions of Windows operating system.

Maintained by Mine Çetinkaya-Rundel. Last updated 3 months ago.

data openintro

3.8 match 240 stars 11.39 score 6.0k scripts

mikejohnson51

climateR:climateR

Find, subset, and retrive geospatial data by AOI.

Maintained by Mike Johnson. Last updated 3 months ago.

aoi climate dataset geospatial gridded-climate-data weather

4.9 match 187 stars 8.74 score 156 scripts 1 dependents

svmiller

stevedata:Steve's Toy Data for Teaching About a Variety of Methodological, Social, and Political Topics

This is a collection of various kinds of data with broad uses for teaching. My students, and academics like me who teach the same topics I teach, should find this useful if their teaching workflow is also built around the R programming language. The applications are multiple but mostly cluster on topics of statistical methodology, international relations, and political economy.

Maintained by Steve Miller. Last updated 4 days ago.

7.1 match 8 stars 5.97 score 178 scripts

jokergoo

GetoptLong:Parsing Command-Line Arguments and Simple Variable Interpolation

This is a command-line argument parser which wraps the powerful Perl module Getopt::Long and with some adaptations for easier use in R. It also provides a simple way for variable interpolation in R.

Maintained by Zuguang Gu. Last updated 2 years ago.

3.8 match 17 stars 10.98 score 478 scripts 155 dependents

cvxgrp

CVXR:Disciplined Convex Optimization

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

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

3.2 match 207 stars 12.89 score 768 scripts 51 dependents

bioc

iSEEu:iSEE Universe

iSEEu (the iSEE universe) contains diverse functionality to extend the usage of the iSEE package, including additional classes for the panels, or modes allowing easy configuration of iSEE applications.

Maintained by Kevin Rue-Albrecht. Last updated 5 months ago.

immunooncology visualization gui dimensionreduction featureextraction clustering transcription geneexpression transcriptomics singlecell cellbasedassays hacktoberfest

5.8 match 9 stars 7.15 score 35 scripts 1 dependents

rspatial

geodata:Download Geographic Data

Functions for downloading of geographic data for use in spatial analysis and mapping. The package facilitates access to climate, crops, elevation, land use, soil, species occurrence, accessibility, administrative boundaries and other data.

Maintained by Robert J. Hijmans. Last updated 1 months ago.

3.8 match 162 stars 10.75 score 1.5k scripts 7 dependents

rstudio

bslib:Custom 'Bootstrap' 'Sass' Themes for 'shiny' and 'rmarkdown'

Simplifies custom 'CSS' styling of both 'shiny' and 'rmarkdown' via 'Bootstrap' 'Sass'. Supports 'Bootstrap' 3, 4 and 5 as well as their various 'Bootswatch' themes. An interactive widget is also provided for previewing themes in real time.

Maintained by Carson Sievert. Last updated 11 days ago.

bootstrap htmltools rmarkdown sass shiny

2.3 match 511 stars 18.02 score 5.1k scripts 4.3k dependents

sdctools

sdcMicro:Statistical Disclosure Control Methods for Anonymization of Data and Risk Estimation

Data from statistical agencies and other institutions are mostly confidential. This package, introduced in Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>, can be used for the generation of anonymized (micro)data, i.e. for the creation of public- and scientific-use files. The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>. Various risk estimation and anonymization methods are included. Note that the package includes a graphical user interface published in Meindl and Templ (2019) <doi:10.3390/a12090191> that allows to use various methods of this package.

Maintained by Matthias Templ. Last updated 26 days ago.

cpp

4.0 match 83 stars 9.89 score 258 scripts

andybega

spduration:Split-Population Duration (Cure) Regression

An implementation of split-population duration regression models. Unlike regular duration models, split-population duration models are mixture models that accommodate the presence of a sub-population that is not at risk for failure, e.g. cancer patients who have been cured by treatment. This package implements Weibull and Loglogistic forms for the duration component, and focuses on data with time-varying covariates. These models were originally formulated in Boag (1949) and Berkson and Gage (1952), and extended in Schmidt and Witte (1989).

Maintained by Andreas Beger. Last updated 1 years ago.

mixture-model regression split-population survival-analysis cpp

7.3 match 4 stars 5.38 score 40 scripts

talgalili

installr:Using R to Install Stuff on Windows OS (Such As: R, 'Rtools', 'RStudio', 'Git', and More!)

R is great for installing software. Through the 'installr' package you can automate the updating of R (on Windows, using updateR()) and install new software. Software installation is initiated through a GUI (just run installr()), or through functions such as: install.Rtools(), install.pandoc(), install.git(), and many more. The updateR() command performs the following: finding the latest R version, downloading it, running the installer, deleting the installation file, copy and updating old packages to the new R installation.

Maintained by Tal Galili. Last updated 1 years ago.

3.9 match 273 stars 10.19 score 1.2k scripts

bsnatr

tswge:Time Series for Data Science

Accompanies the texts Time Series for Data Science with R by Woodward, Sadler and Robertson & Applied Time Series Analysis with R, 2nd edition by Woodward, Gray, and Elliott. It is helpful for data analysis and for time series instruction.

Maintained by Bivin Sadler. Last updated 2 years ago.

14.5 match 2.70 score 496 scripts

cloudyr

googleCloudStorageR:Interface with Google Cloud Storage API

Interact with Google Cloud Storage <https://cloud.google.com/storage/> API in R. Part of the 'cloudyr' <https://cloudyr.github.io/> project.

Maintained by Mark Edmondson. Last updated 4 days ago.

api api-client google-cloud-storage googleauthr

3.8 match 104 stars 10.28 score 548 scripts 1 dependents

mmollina

mappoly:Genetic Linkage Maps in Autopolyploids

Construction of genetic maps in autopolyploid full-sib populations. Uses pairwise recombination fraction estimation as the first source of information to sequentially position allelic variants in specific homologous chromosomes. For situations where pairwise analysis has limited power, the algorithm relies on the multilocus likelihood obtained through a hidden Markov model (HMM). For more detail, please see Mollinari and Garcia (2019) <doi:10.1534/g3.119.400378> and Mollinari et al. (2020) <doi:10.1534/g3.119.400620>.

Maintained by Marcelo Mollinari. Last updated 11 days ago.

polyploid polyploid-genetic-mapping polyploidy cpp

5.1 match 27 stars 7.56 score 111 scripts 1 dependents

cran

evtree:Evolutionary Learning of Globally Optimal Trees

Commonly used classification and regression tree methods like the CART algorithm are recursive partitioning methods that build the model in a forward stepwise search. Although this approach is known to be an efficient heuristic, the results of recursive tree methods are only locally optimal, as splits are chosen to maximize homogeneity at the next step only. An alternative way to search over the parameter space of trees is to use global optimization methods like evolutionary algorithms. The 'evtree' package implements an evolutionary algorithm for learning globally optimal classification and regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while the 'partykit' package is leveraged to represent the resulting trees in R, providing unified infrastructure for summaries, visualizations, and predictions.

Maintained by Thomas Grubinger. Last updated 6 years ago.

cpp

8.4 match 7 stars 4.54 score 2 dependents

bioc

mia:Microbiome analysis

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Maintained by Tuomas Borman. Last updated 2 days ago.

microbiome software dataimport analysis bioconductor

3.3 match 52 stars 11.50 score 316 scripts 5 dependents

hoehna

TESS:Diversification Rate Estimation and Fast Simulation of Reconstructed Phylogenetic Trees under Tree-Wide Time-Heterogeneous Birth-Death Processes Including Mass-Extinction Events

Simulation of reconstructed phylogenetic trees under tree-wide time-heterogeneous birth-death processes and estimation of diversification parameters under the same model. Speciation and extinction rates can be any function of time and mass-extinction events at specific times can be provided. Trees can be simulated either conditioned on the number of species, the time of the process, or both. Additionally, the likelihood equations are implemented for convenience and can be used for Maximum Likelihood (ML) estimation and Bayesian inference.

Maintained by Sebastian Hoehna. Last updated 3 years ago.

cpp

6.4 match 2 stars 5.93 score 95 scripts 1 dependents

markvanderloo

settings:Software Option Settings Manager for R

Provides option settings management that goes beyond R's default 'options' function. With this package, users can define their own option settings manager holding option names, default values and (if so desired) ranges or sets of allowed option values that will be automatically checked. Settings can then be retrieved, altered and reset to defaults with ease. For R programmers and package developers it offers cloning and merging functionality which allows for conveniently defining global and local options, possibly in a multilevel options hierarchy. See the package vignette for some examples concerning functions, S4 classes, and reference classes. There are convenience functions to reset par() and options() to their 'factory defaults'.

Maintained by Mark van der Loo. Last updated 9 months ago.

4.0 match 7 stars 9.32 score 1.0k scripts 36 dependents

tidyverse

ggplot2:Create Elegant Data Visualisations Using the Grammar of Graphics

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

Maintained by Thomas Lin Pedersen. Last updated 9 days ago.

data-visualisation visualisation

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

dreamrs

toastui:Interactive Tables, Calendars and Charts for the Web

Create interactive tables, calendars and charts with 'TOAST UI' <https://ui.toast.com/> libraries to integrate in 'shiny' applications or 'rmarkdown' 'HTML' documents.

Maintained by Victor Perrier. Last updated 16 days ago.

htmlwidgets

3.8 match 86 stars 10.03 score 144 scripts 8 dependents

dbosak01

logr:Creates Log Files

Contains functions to help create log files. The package aims to overcome the difficulty of the base R sink() command. The log_print() function will print to both the console and the file log, without interfering in other write operations.

Maintained by David Bosak. Last updated 1 months ago.

log logging logr tidylog

3.8 match 13 stars 10.03 score 265 scripts 3 dependents

cwolock

survML:Tools for Flexible Survival Analysis Using Machine Learning

Statistical tools for analyzing time-to-event data using machine learning. Implements survival stacking for conditional survival estimation, standardized survival function estimation for current status data, and methods for algorithm-agnostic variable importance. See Wolock CJ, Gilbert PB, Simon N, and Carone M (2024) <doi:10.1080/10618600.2024.2304070>.

Maintained by Charles Wolock. Last updated 2 months ago.

4.7 match 16 stars 8.06 score 73 scripts 1 dependents

bquast

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.

5.5 match 17 stars 6.78 score 118 scripts 1 dependents

r-lib

httr:Tools for Working with URLs and HTTP

Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).

Maintained by Hadley Wickham. Last updated 1 years ago.

api curl http

1.8 match 989 stars 20.56 score 29k scripts 4.3k dependents

venelin

PCMBase:Simulation and Likelihood Calculation of Phylogenetic Comparative Models

Phylogenetic comparative methods represent models of continuous trait data associated with the tips of a phylogenetic tree. Examples of such models are Gaussian continuous time branching stochastic processes such as Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the tips of the tree as an observed (final) state of a Markov process starting from an initial state at the root and evolving along the branches of the tree. The PCMBase R package provides a general framework for manipulating such models. This framework consists of an application programming interface for specifying data and model parameters, and efficient algorithms for simulating trait evolution under a model and calculating the likelihood of model parameters for an assumed model and trait data. The package implements a growing collection of models, which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed Gaussian models, in which different types of the above models can be associated with different branches of the tree. The PCMBase package is limited to trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic models. The PCMFit package provides functionality for inference of these models to tree and trait data. The package web-site <https://venelin.github.io/PCMBase/> provides access to the documentation and other resources.

Maintained by Venelin Mitov. Last updated 10 months ago.

4.9 match 6 stars 7.56 score 85 scripts 3 dependents

mlampros

IceSat2R:ICESat-2 Altimeter Data using R

Programmatic connection to the 'OpenAltimetry API' <https://openaltimetry.earthdatacloud.nasa.gov/data/openapi/swagger-ui/index.html/> to download and process 'ATL03' (Global Geolocated Photon Data), 'ATL06' (Land Ice Height), 'ATL07' (Sea Ice Height), 'ATL08' (Land and Vegetation Height), 'ATL10' (Sea Ice Freeboard), 'ATL12' (Ocean Surface Height) and 'ATL13' (Inland Water Surface Height) 'ICESat-2' Altimeter Data. The user has the option to download the data by selecting a bounding box from a 1- or 5-degree grid globally utilizing a shiny application. The 'ICESat-2' mission collects altimetry data of the Earth's surface. The sole instrument on 'ICESat-2' is the Advanced Topographic Laser Altimeter System (ATLAS) instrument that measures ice sheet elevation change and sea ice thickness, while also generating an estimate of global vegetation biomass. 'ICESat-2' continues the important observations of ice-sheet elevation change, sea-ice freeboard, and vegetation canopy height begun by 'ICESat' in 2003.

Maintained by Lampros Mouselimis. Last updated 1 months ago.

icesat-2 openaltimetry

5.6 match 12 stars 6.64 score 3 scripts

helske

KFAS:Kalman Filter and Smoother for Exponential Family State Space Models

State space modelling is an efficient and flexible framework for statistical inference of a broad class of time series and other data. KFAS includes computationally efficient functions for Kalman filtering, smoothing, forecasting, and simulation of multivariate exponential family state space models, with observations from Gaussian, Poisson, binomial, negative binomial, and gamma distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.

Maintained by Jouni Helske. Last updated 6 months ago.

dynamic-linear-model exponential-family fortran gaussian-models state-space time-series openblas

3.3 match 64 stars 10.97 score 242 scripts 16 dependents

zpneal

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 1 years ago.

cpp

5.2 match 41 stars 7.06 score 31 scripts 2 dependents

matthiasgomolka

simfinapi:Accessing 'SimFin' Data

Through simfinapi, you can intuitively access the 'SimFin' Web-API (<https://www.simfin.com/>) to make 'SimFin' data easily available in R. To obtain an 'SimFin' API key (and thus to use this package), you need to register at <https://app.simfin.com/login>.

Maintained by Matthias Gomolka. Last updated 11 months ago.

api simfin-data

6.2 match 19 stars 5.90 score 21 scripts

aleksandarsekulic

meteo:RFSI & STRK Interpolation for Meteo and Environmental Variables

Random Forest Spatial Interpolation (RFSI, Sekulić et al. (2020) <doi:10.3390/rs12101687>) and spatio-temporal geostatistical (spatio-temporal regression Kriging (STRK)) interpolation for meteorological (Kilibarda et al. (2014) <doi:10.1002/2013JD020803>, Sekulić et al. (2020) <doi:10.1007/s00704-019-03077-3>) and other environmental variables. Contains global spatio-temporal models calculated using publicly available data.

Maintained by Aleksandar Sekulić. Last updated 6 months ago.

7.2 match 18 stars 5.06 score 64 scripts

vitomuggeo

segmented:Regression Models with Break-Points / Change-Points Estimation (with Possibly Random Effects)

Fitting regression models where, in addition to possible linear terms, one or more covariates have segmented (i.e., broken-line or piece-wise linear) or stepmented (i.e. piece-wise constant) effects. Multiple breakpoints for the same variable are allowed. The estimation method is discussed in Muggeo (2003, <doi:10.1002/sim.1545>) and illustrated in Muggeo (2008, <https://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf>). An approach for hypothesis testing is presented in Muggeo (2016, <doi:10.1080/00949655.2016.1149855>), and interval estimation for the breakpoint is discussed in Muggeo (2017, <doi:10.1111/anzs.12200>). Segmented mixed models, i.e. random effects in the change point, are discussed in Muggeo (2014, <doi:10.1177/1471082X13504721>). Estimation of piecewise-constant relationships and changepoints (mean-shift models) is discussed in Fasola et al. (2018, <doi:10.1007/s00180-017-0740-4>).

Maintained by Vito M. R. Muggeo. Last updated 16 days ago.

3.6 match 9 stars 10.03 score 1.2k scripts 203 dependents

stewid

SimInf:A Framework for Data-Driven Stochastic Disease Spread Simulations

Provides an efficient and very flexible framework to conduct data-driven epidemiological modeling in realistic large scale disease spread simulations. The framework integrates infection dynamics in subpopulations as continuous-time Markov chains using the Gillespie stochastic simulation algorithm and incorporates available data such as births, deaths and movements as scheduled events at predefined time-points. Using C code for the numerical solvers and 'OpenMP' (if available) to divide work over multiple processors ensures high performance when simulating a sample outcome. One of our design goals was to make the package extendable and enable usage of the numerical solvers from other R extension packages in order to facilitate complex epidemiological research. The package contains template models and can be extended with user-defined models. For more details see the paper by Widgren, Bauer, Eriksson and Engblom (2019) <doi:10.18637/jss.v091.i12>. The package also provides functionality to fit models to time series data using the Approximate Bayesian Computation Sequential Monte Carlo ('ABC-SMC') algorithm of Toni and others (2009) <doi:10.1098/rsif.2008.0172>.

Maintained by Stefan Widgren. Last updated 5 days ago.

data-driven epidemiology high-performance-computing markov-chain mathematical-modelling gsl openmp

3.5 match 35 stars 10.09 score 227 scripts

spatstat

spatstat.explore:Exploratory Data Analysis for the 'spatstat' Family

Functionality for exploratory data analysis and nonparametric analysis of spatial data, mainly spatial point patterns, in the 'spatstat' family of packages. (Excludes analysis of spatial data on a linear network, which is covered by the separate package 'spatstat.linnet'.) Methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.

Maintained by Adrian Baddeley. Last updated 1 months ago.

cluster-detection confidence-intervals hypothesis-testing k-function roc-curves scan-statistics significance-testing simulation-envelopes spatial-analysis spatial-data-analysis spatial-sharpening spatial-smoothing spatial-statistics

3.5 match 1 stars 10.17 score 67 scripts 148 dependents

mayer79

flashlight:Shed Light on Black Box Machine Learning Models

Shed light on black box machine learning models by the help of model performance, variable importance, global surrogate models, ICE profiles, partial dependence (Friedman J. H. (2001) <doi:10.1214/aos/1013203451>), accumulated local effects (Apley D. W. (2016) <arXiv:1612.08468>), further effects plots, interaction strength, and variable contribution breakdown (Gosiewska and Biecek (2019) <arxiv:1903.11420>). All tools are implemented to work with case weights and allow for stratified analysis. Furthermore, multiple flashlights can be combined and analyzed together.

Maintained by Michael Mayer. Last updated 8 months ago.

interpretability interpretable-machine-learning machine-learning xai

5.7 match 22 stars 6.25 score 54 scripts 1 dependents

snoweye

pmclust:Parallel Model-Based Clustering using Expectation-Gathering-Maximization Algorithm for Finite Mixture Gaussian Model

Aims to utilize model-based clustering (unsupervised) for high dimensional and ultra large data, especially in a distributed manner. The code employs 'pbdMPI' to perform a expectation-gathering-maximization algorithm for finite mixture Gaussian models. The unstructured dispersion matrices are assumed in the Gaussian models. The implementation is default in the single program multiple data programming model. The code can be executed through 'pbdMPI' and MPI' implementations such as 'OpenMPI' and 'MPICH'. See the High Performance Statistical Computing website <https://snoweye.github.io/hpsc/> for more information, documents and examples.

Maintained by Wei-Chen Chen. Last updated 2 years ago.

9.6 match 5 stars 3.70 score 4 scripts

thinkr-open

checkhelper:Deal with Check Outputs

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

Maintained by Sebastien Rochette. Last updated 1 years ago.

5.3 match 34 stars 6.74 score 18 scripts

rstudio

renv:Project Environments

A dependency management toolkit for R. Using 'renv', you can create and manage project-local R libraries, save the state of these libraries to a 'lockfile', and later restore your library as required. Together, these tools can help make your projects more isolated, portable, and reproducible.

Maintained by Kevin Ushey. Last updated 3 days ago.

1.9 match 1.0k stars 18.55 score 1.5k scripts 113 dependents

evelinag

clusternomics:Integrative Clustering for Heterogeneous Biomedical Datasets

Integrative context-dependent clustering for heterogeneous biomedical datasets. Identifies local clustering structures in related datasets, and a global clusters that exist across the datasets.

Maintained by Evelina Gabasova. Last updated 8 years ago.

7.0 match 14 stars 4.92 score 12 scripts

mlizhangx

NAIR:Network Analysis of Immune Repertoire

Pipelines for studying the adaptive immune repertoire of T cells and B cells via network analysis based on receptor sequence similarity. Relate clinical outcomes to immune repertoires based on their network properties, or to particular clusters and clones within a repertoire. Yang et al. (2023) <doi:10.3389/fimmu.2023.1181825>.

Maintained by Brian Neal. Last updated 2 months ago.

cpp openmp

5.1 match 7 stars 6.83 score 27 scripts

davidgohel

flextable:Functions for Tabular Reporting

Use a grammar for creating and customizing pretty tables. The following formats are supported: 'HTML', 'PDF', 'RTF', 'Microsoft Word', 'Microsoft PowerPoint' and R 'Grid Graphics'. 'R Markdown', 'Quarto' and the package 'officer' can be used to produce the result files. The syntax is the same for the user regardless of the type of output to be produced. A set of functions allows the creation, definition of cell arrangement, addition of headers or footers, formatting and definition of cell content with text and or images. The package also offers a set of high-level functions that allow tabular reporting of statistical models and the creation of complex cross tabulations.

Maintained by David Gohel. Last updated 1 months ago.

docx html5 ms-office-documents rmarkdown table

2.0 match 583 stars 17.04 score 7.3k scripts 119 dependents

markdrisser

convoSPAT:Convolution-Based Nonstationary Spatial Modeling

Fits convolution-based nonstationary Gaussian process models to point-referenced spatial data. The nonstationary covariance function allows the user to specify the underlying correlation structure and which spatial dependence parameters should be allowed to vary over space: the anisotropy, nugget variance, and process variance. The parameters are estimated via maximum likelihood, using a local likelihood approach. Also provided are functions to fit stationary spatial models for comparison, calculate the Kriging predictor and standard errors, and create various plots to visualize nonstationarity.

Maintained by Mark D. Risser. Last updated 7 years ago.

12.6 match 2 stars 2.70 score 25 scripts

tidyverts

tsibbledata:Diverse Datasets for 'tsibble'

Provides diverse datasets in the 'tsibble' data structure. These datasets are useful for learning and demonstrating how tidy temporal data can tidied, visualised, and forecasted.

Maintained by Mitchell OHara-Wild. Last updated 4 months ago.

dataset tsibble

4.0 match 25 stars 8.44 score 740 scripts 2 dependents

bioc

motifStack:Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.

Maintained by Jianhong Ou. Last updated 2 months ago.

sequencematching visualization sequencing microarray alignment chipchip chipseq motifannotation dataimport

4.3 match 7.93 score 188 scripts 6 dependents

cjvanlissa

worcs:Workflow for Open Reproducible Code in Science

Create reproducible and transparent research projects in 'R'. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an 'RStudio' project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021). <doi:10.3233/DS-210031>.

Maintained by Caspar J. Van Lissa. Last updated 11 days ago.

3.6 match 83 stars 9.26 score 59 scripts

jeffreyevans

spatialEco:Spatial Analysis and Modelling Utilities

Utilities to support spatial data manipulation, query, sampling and modelling in ecological applications. Functions include models for species population density, spatial smoothing, multivariate separability, point process model for creating pseudo- absences and sub-sampling, Quadrant-based sampling and analysis, auto-logistic modeling, sampling models, cluster optimization, statistical exploratory tools and raster-based metrics.

Maintained by Jeffrey S. Evans. Last updated 13 days ago.

biodiversity conservation ecology r-spatial raster spatial vector

3.5 match 110 stars 9.55 score 736 scripts 2 dependents

skranz

restorepoint:Debugging with Restore Points

Debugging with restore points instead of break points. A restore point stores all local variables when called inside a function. The stored values can later be retrieved and evaluated in a modified R console that replicates the function's environment. To debug step by step, one can simply copy & paste the function body from the R script. Particularly convenient in combination with "RStudio". See the "Github" page inst/vignettes for a tutorial.

Maintained by Roman Zenka. Last updated 9 months ago.

debugging

5.4 match 16 stars 6.20 score 79 scripts 42 dependents

kassambara

ggpubr:'ggplot2' Based Publication Ready Plots

The 'ggplot2' package is excellent and flexible for elegant data visualization in R. However the default generated plots requires some formatting before we can send them for publication. Furthermore, to customize a 'ggplot', the syntax is opaque and this raises the level of difficulty for researchers with no advanced R programming skills. 'ggpubr' provides some easy-to-use functions for creating and customizing 'ggplot2'- based publication ready plots.

Maintained by Alboukadel Kassambara. Last updated 2 years ago.

2.0 match 1.2k stars 16.68 score 65k scripts 409 dependents

mayoverse

arsenal:An Arsenal of 'R' Functions for Large-Scale Statistical Summaries

An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of one or more categorical variables; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); freqlist(), a powerful frequency table across many categorical variables; comparedf(), a function for comparing data.frames; and write2(), a function to output tables to a document.

Maintained by Ethan Heinzen. Last updated 7 months ago.

baseline-characteristics descriptive-statistics modeling paired-comparisons reporting statistics tableone

2.5 match 225 stars 13.45 score 1.2k scripts 16 dependents

bioc

destiny:Creates diffusion maps

Create and plot diffusion maps.

Maintained by Philipp Angerer. Last updated 4 months ago.

cellbiology cellbasedassays clustering software visualization diffusion-maps dimensionality-reduction cpp

3.0 match 81 stars 10.94 score 792 scripts

otoliths

SP2000:Catalogue of Life Toolkit

A programmatic interface to <http://sp2000.org.cn>, re-written based on an accompanying 'Species 2000' API. Access tables describing catalogue of the Chinese known species of animals, plants, fungi, micro-organisms, and more. This package also supports access to catalogue of life global <http://catalogueoflife.org>, China animal scientific database <http://zoology.especies.cn> and catalogue of life Taiwan <https://taibnet.sinica.edu.tw/home_eng.php>. The development of 'SP2000' package were supported by Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China <2019HJ2096001006>,Yunnan University's "Double First Class" Project <C176240405> and Yunnan University's Research Innovation Fund for Graduate Students <2019227>.

Maintained by Liuyong Ding. Last updated 1 years ago.

animals biodiversity catalogue-of-life-china catalogue-of-life-global-checklist catalogue-of-life-taiwan-checklist china china-animal-scientific-database fungi microorganisms plants redlist-of-chinese-biodiversity species2000

8.6 match 13 stars 3.81 score 3 scripts

kentonwhite

ProjectTemplate:Automates the Creation of New Statistical Analysis Projects

Provides functions to automatically build a directory structure for a new R project. Using this structure, 'ProjectTemplate' automates data loading, preprocessing, library importing and unit testing.

Maintained by Kenton White. Last updated 14 days ago.

3.6 match 626 stars 8.99 score 612 scripts

projectmosaic

mosaicCalc:R-Language Based Calculus Operations for Teaching

Software to support the introductory *MOSAIC Calculus* textbook <https://www.mosaic-web.org/MOSAIC-Calculus/>), one of many data- and modeling-oriented educational resources developed by Project MOSAIC (<https://www.mosaic-web.org/>). Provides symbolic and numerical differentiation and integration, as well as support for applied linear algebra (for data science), and differential equations/dynamics. Includes grammar-of-graphics-based functions for drawing vector fields, trajectories, etc. The software is suitable for general use, but intended mainly for teaching calculus.

Maintained by Daniel Kaplan. Last updated 20 days ago.

3.8 match 13 stars 8.68 score 546 scripts

bioc

Biostrings:Efficient manipulation of biological strings

Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.

Maintained by Hervé Pagès. Last updated 24 days ago.

sequencematching alignment sequencing genetics dataimport datarepresentation infrastructure bioconductor-package core-package

1.8 match 61 stars 17.83 score 8.6k scripts 1.2k dependents

teos-10

gsw:Gibbs Sea Water Functions

Provides an interface to the Gibbs 'SeaWater' ('TEOS-10') C library, version 3.06-16-0 (commit '657216dd4f5ea079b5f0e021a4163e2d26893371', dated 2022-10-11, available at <https://github.com/TEOS-10/GSW-C>, which stems from 'Matlab' and other code written by members of Working Group 127 of 'SCOR'/'IAPSO' (Scientific Committee on Oceanic Research / International Association for the Physical Sciences of the Oceans).

Maintained by Dan Kelley. Last updated 8 days ago.

gibbs oceanography seawater teos-10

3.8 match 8 stars 8.53 score 286 scripts 19 dependents

rspatial

raster:Geographic Data Analysis and Modeling

Reading, writing, manipulating, analyzing and modeling of spatial data. This package has been superseded by the "terra" package <https://CRAN.R-project.org/package=terra>.

Maintained by Robert J. Hijmans. Last updated 2 months ago.

cpp

1.9 match 164 stars 17.05 score 58k scripts 555 dependents

ddsjoberg

gtsummary:Presentation-Ready Data Summary and Analytic Result Tables

Creates presentation-ready tables summarizing data sets, regression models, and more. The code to create the tables is concise and highly customizable. Data frames can be summarized with any function, e.g. mean(), median(), even user-written functions. Regression models are summarized and include the reference rows for categorical variables. Common regression models, such as logistic regression and Cox proportional hazards regression, are automatically identified and the tables are pre-filled with appropriate column headers.

Maintained by Daniel D. Sjoberg. Last updated 2 days ago.

easy-to-use gt html5 regression-models reproducibility reproducible-research statistics summary-statistics summary-tables table1 tableone

1.9 match 1.1k stars 17.00 score 8.2k scripts 15 dependents

ggpmxdevelopment

ggPMX:'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME Models

At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling activities in order to reduce the overall effort required for generating such plots. For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox, called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient for publication and submissions using few lines of code. This package focuses on plots recommended by ISoP <doi:10.1002/psp4.12161>. While not required, you can get/install the 'R' 'lixoftConnectors' package in the 'Monolix' installation, as described at the following url <https://monolix.lixoft.com/monolix-api/lixoftconnectors_installation/>. When 'lixoftConnectors' is available, 'R' can use 'Monolix' directly to create the required Chart Data instead of exporting it from the 'Monolix' gui.

Maintained by Matthew Fidler. Last updated 1 years ago.

pharmacometrics pmx reporting

4.4 match 39 stars 7.23 score 80 scripts

nspyrison

cheem:Interactively Explore Local Explanations with the Radial Tour

Given a non-linear model, calculate the local explanation. We purpose view the data space, explanation space, and model residuals as ensemble graphic interactive on a shiny application. After an observation of interest is identified, the normalized variable importance of the local explanation is used as a 1D projection basis. The support of the local explanation is then explored by changing the basis with the use of the radial tour <doi:10.32614/RJ-2020-027>; <doi:10.1080/10618600.1997.10474754>.

Maintained by Nicholas Spyrison. Last updated 1 years ago.

6.7 match 2 stars 4.73 score 54 scripts

bquast

gvc:Global Value Chains Tools

Several tools for Global Value Chain ('GVC') analysis are implemented.

Maintained by Bastiaan Quast. Last updated 3 years ago.

5.6 match 21 stars 5.67 score 45 scripts

jakobbossek

smoof:Single and Multi-Objective Optimization Test Functions

Provides generators for a high number of both single- and multi- objective test functions which are frequently used for the benchmarking of (numerical) optimization algorithms. Moreover, it offers a set of convenient functions to generate, plot and work with objective functions.

Maintained by Jakob Bossek. Last updated 1 years ago.

benchmark-functions multi-objective-optimization single-objective-optimization cpp

3.7 match 36 stars 8.54 score 261 scripts 9 dependents

biometrician

shrink:Global, Parameterwise and Joint Shrinkage Factor Estimation

The predictive value of a statistical model can often be improved by applying shrinkage methods. This can be achieved, e.g., by regularized regression or empirical Bayes approaches. Various types of shrinkage factors can also be estimated after a maximum likelihood. While global shrinkage modifies all regression coefficients by the same factor, parameterwise shrinkage factors differ between regression coefficients. With variables which are either highly correlated or associated with regard to contents, such as several columns of a design matrix describing a nonlinear effect, parameterwise shrinkage factors are not interpretable and a compromise between global and parameterwise shrinkage, termed 'joint shrinkage', is a useful extension. A computational shortcut to resampling-based shrinkage factor estimation based on DFBETA residuals can be applied. Global, parameterwise and joint shrinkage for models fitted by lm(), glm(), coxph(), or mfp() is available.

Maintained by Daniela Dunkler. Last updated 1 years ago.

7.3 match 2 stars 4.28 score 19 scripts

albgarre

biogrowth:Modelling of Population Growth

Modelling of population growth under static and dynamic environmental conditions. Includes functions for model fitting and making prediction under isothermal and dynamic conditions. The methods (algorithms & models) are based on predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).

Maintained by Alberto Garre. Last updated 2 days ago.

4.7 match 5 stars 6.71 score 44 scripts

bioc

omXplore:Vizualization tools for 'omics' datasets with R

This package contains a collection of functions (written as shiny modules) for the visualisation and the statistical analysis of omics data. These plots can be displayed individually or embedded in a global Shiny module. Additionaly, it is possible to integrate third party modules to the main interface of the package omXplore.

Maintained by Samuel Wieczorek. Last updated 12 days ago.

software shinyapps massspectrometry datarepresentation gui qualitycontrol prostar2

5.8 match 5.40 score 23 scripts

r-quantities

units:Measurement Units for R Vectors

Support for measurement units in R vectors, matrices and arrays: automatic propagation, conversion, derivation and simplification of units; raising errors in case of unit incompatibility. Compatible with the POSIXct, Date and difftime classes. Uses the UNIDATA udunits library and unit database for unit compatibility checking and conversion. Documentation about 'units' is provided in the paper by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>), included in this package as a vignette; see 'citation("units")' for details.

Maintained by Edzer Pebesma. Last updated 4 days ago.

udunits cpp

1.8 match 181 stars 17.28 score 3.3k scripts 1.2k dependents

anhoej

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 1 months ago.

3.4 match 39 stars 9.04 score 122 scripts 2 dependents

modeloriented

arenar:Arena for the Exploration and Comparison of any ML Models

Generates data for challenging machine learning models in 'Arena' <https://arena.drwhy.ai> - an interactive web application. You can start the server with XAI (Explainable Artificial Intelligence) plots to be generated on-demand or precalculate and auto-upload data file beside shareable 'Arena' URL.

Maintained by Piotr Piątyszek. Last updated 4 years ago.

axplainable-artificial-intelligence ema explainability explanatory-model-analysis iml interactive-xai interpretability xai

5.2 match 31 stars 5.94 score 14 scripts

eddelbuettel

RcppDE:Global Optimization by Differential Evolution in C++

An efficient C++ based implementation of the 'DEoptim' function which performs global optimization by differential evolution. Its creation was motivated by trying to see if the old approximation "easier, shorter, faster: pick any two" could in fact be extended to achieving all three goals while moving the code from plain old C to modern C++. The initial version did in fact do so, but a good part of the gain was due to an implicit code review which eliminated a few inefficiencies which have since been eliminated in 'DEoptim'.

Maintained by Dirk Eddelbuettel. Last updated 26 days ago.

cpp

3.5 match 14 stars 8.78 score 45 scripts 20 dependents

pecanproject

PEcAn.assim.batch:PEcAn Functions Used for Ecological Forecasts and Reanalysis

The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific workflow management tool that is designed to simplify the management of model parameterization, execution, and analysis. The goal of PECAn is to streamline the interaction between data and models, and to improve the efficacy of scientific investigation.

Maintained by Istem Fer. Last updated 2 days ago.

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

3.1 match 216 stars 9.94 score 20 scripts 2 dependents

avrodrigues

naturaList:Classify Occurrences by Confidence Levels in the Species ID

Classify occurrence records based on confidence levels of species identification. In addition, implement tools to filter occurrences inside grid cells and to manually check for possibles errors with an interactive shiny application.

Maintained by Arthur Vinicius Rodrigues. Last updated 1 years ago.

6.6 match 4.66 score 23 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-service earth-observation land-degradation land-productivity vegetation

6.3 match 8 stars 4.90 score 5 scripts

statistics-in-portfolio-theory

DOSPortfolio:Dynamic Optimal Shrinkage Portfolio

Constructs dynamic optimal shrinkage estimators for the weights of the global minimum variance portfolio which are reconstructed at given reallocation points as derived in Bodnar, Parolya, and Thorsén (2021) (<arXiv:2106.02131>). Two dynamic shrinkage estimators are available in this package. One using overlapping samples while the other use nonoverlapping samples.

Maintained by Erik Thorsén. Last updated 4 years ago.

7.1 match 4 stars 4.30 score 4 scripts

jtlandis

ggside:Side Grammar Graphics

The grammar of graphics as shown in 'ggplot2' has provided an expressive API for users to build plots. 'ggside' extends 'ggplot2' by allowing users to add graphical information about one of the main panel's axis using a familiar 'ggplot2' style API with tidy data. This package is particularly useful for visualizing metadata on a discrete axis, or summary graphics on a continuous axis such as a boxplot or a density distribution.

Maintained by Justin Landis. Last updated 10 months ago.

3.0 match 346 stars 10.18 score 349 scripts 6 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 25 days ago.

5.3 match 23 stars 5.76 score 11 scripts

christopherkenny

geomander:Geographic Tools for Studying Gerrymandering

A compilation of tools to complete common tasks for studying gerrymandering. This focuses on the geographic tool side of common problems, such as linking different levels of spatial units or estimating how to break up units. Functions exist for creating redistricting-focused data for the US.

Maintained by Christopher T. Kenny. Last updated 18 days ago.

cpp

3.9 match 14 stars 7.81 score 191 scripts 1 dependents

huizezhang-sherry

tidyindex:A Tidy Data Pipeline to Construct, Compare, and Analyse Indexes

Construct and analyse indexes in a pipeline tidy workflow. 'tidyindex' contains modules for transforming variables, aggregating variables across time, reducing data dimension through weighting, and fitting distributions. A manuscript describing the methodology can be found at <https://github.com/huizezhang-sherry/paper-tidyindex>.

Maintained by H. Sherry Zhang. Last updated 7 months ago.

5.4 match 2 stars 5.56 score 13 scripts

cmusso86

recalibratiNN:Quantile Recalibration for Regression Models

Enables the diagnostics and enhancement of regression model calibration.It offers both global and local visualization tools for calibration diagnostics and provides one recalibration method: Torres R, Nott DJ, Sisson SA, Rodrigues T, Reis JG, Rodrigues GS (2024) <doi:10.48550/arXiv.2403.05756>. The method leverages on Probabilistic Integral Transform (PIT) values to both evaluate and perform the calibration of statistical models. For a more detailed description of the package, please refer to the bachelor's thesis available bellow.

Maintained by Carolina Musso. Last updated 2 months ago.

calibration gaussian-models neural-network probability recalibration regression-models

5.6 match 7 stars 5.39 score 8 scripts

bioc

chromPlot:Global visualization tool of genomic data

Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end.

Maintained by Karen Y. Orostica. Last updated 5 months ago.

datarepresentation functionalgenomics genetics sequencing annotation visualization

6.6 match 4.53 score 24 scripts

evolecolgroup

pastclim:Manipulate Time Series of Climate Reconstructions

Methods to easily extract and manipulate climate reconstructions for ecological and anthropological analyses, as described in Leonardi et al. (2023) <doi:10.1111/ecog.06481>. The package includes datasets of palaeoclimate reconstructions, present observations, and future projections from multiple climate models.

Maintained by Andrea Manica. Last updated 3 days ago.

climate-data paleoclimate species-distribution-modelling

3.7 match 38 stars 8.12 score 49 scripts

bioc

BiocParallel:Bioconductor facilities for parallel evaluation

This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.

Maintained by Martin Morgan. Last updated 26 days ago.

infrastructure bioconductor-package core-package u24ca289073 cpp

1.7 match 67 stars 17.40 score 7.3k scripts 1.1k dependents

andrewzm

FRK:Fixed Rank Kriging

A tool for spatial/spatio-temporal modelling and prediction with large datasets. The approach models the field, and hence the covariance function, using a set of basis functions. This fixed-rank basis-function representation facilitates the modelling of big data, and the method naturally allows for non-stationary, anisotropic covariance functions. Discretisation of the spatial domain into so-called basic areal units (BAUs) facilitates the use of observations with varying support (i.e., both point-referenced and areal supports, potentially simultaneously), and prediction over arbitrary user-specified regions. `FRK` also supports inference over various manifolds, including the 2D plane and 3D sphere, and it provides helper functions to model, fit, predict, and plot with relative ease. Version 2.0.0 and above also supports the modelling of non-Gaussian data (e.g., Poisson, binomial, negative-binomial, gamma, and inverse-Gaussian) by employing a generalised linear mixed model (GLMM) framework. Zammit-Mangion and Cressie <doi:10.18637/jss.v098.i04> describe `FRK` in a Gaussian setting, and detail its use of basis functions and BAUs, while Sainsbury-Dale, Zammit-Mangion, and Cressie <doi:10.18637/jss.v108.i10> describe `FRK` in a non-Gaussian setting; two vignettes are available that summarise these papers and provide additional examples.

Maintained by Andrew Zammit-Mangion. Last updated 6 months ago.

cpp

3.4 match 71 stars 8.70 score 188 scripts 1 dependents

bioc

EnrichDO:a Global Weighted Model for Disease Ontology Enrichment Analysis

To implement disease ontology (DO) enrichment analysis, this package is designed and presents a double weighted model based on the latest annotations of the human genome with DO terms, by integrating the DO graph topology on a global scale. This package exhibits high accuracy that it can identify more specific DO terms, which alleviates the over enriched problem. The package includes various statistical models and visualization schemes for discovering the associations between genes and diseases from biological big data.

Maintained by Hongyu Fu. Last updated 4 months ago.

annotation visualization genesetenrichment software

6.2 match 4.74 score 9 scripts

bnaras

distcomp:Computations over Distributed Data without Aggregation

Implementing algorithms and fitting models when sites (possibly remote) share computation summaries rather than actual data over HTTP with a master R process (using 'opencpu', for example). A stratified Cox model and a singular value decomposition are provided. The former makes direct use of code from the R 'survival' package. (That is, the underlying Cox model code is derived from that in the R 'survival' package.) Sites may provide data via several means: CSV files, Redcap API, etc. An extensible design allows for new methods to be added in the future and includes facilities for local prototyping and testing. Web applications are provided (via 'shiny') for the implemented methods to help in designing and deploying the computations.

Maintained by Balasubramanian Narasimhan. Last updated 9 months ago.

5.5 match 9 stars 5.33 score 47 scripts

bioc

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 5 months ago.

structuralprediction proteomics cellbiology

4.7 match 4 stars 6.16 score 20 scripts

tilltnet

egor:Import and Analyse Ego-Centered Network Data

Tools for importing, analyzing and visualizing ego-centered network data. Supports several data formats, including the export formats of 'EgoNet', 'EgoWeb 2.0' and 'openeddi'. An interactive (shiny) app for the intuitive visualization of ego-centered networks is provided. Also included are procedures for creating and visualizing Clustered Graphs (Lerner 2008 <DOI:10.1109/PACIFICVIS.2008.4475458>).

Maintained by Till Krenz. Last updated 13 days ago.

ego-centered egonet egor network-analysis sna

3.3 match 24 stars 8.64 score 76 scripts 2 dependents

danilofreire

prisonbrief:Downloads and Parses World Prison Brief Data

Download, parses and tidies information from the World Prison Brief project <http://www.prisonstudies.org/>.

Maintained by Danilo Freire. Last updated 4 years ago.

data prison world-prison-brief

7.3 match 18 stars 3.95 score 8 scripts

nixtla

nixtlar:A Software Development Kit for 'Nixtla''s 'TimeGPT'

A Software Development Kit for working with 'Nixtla''s 'TimeGPT', a foundation model for time series forecasting. 'API' is an acronym for 'application programming interface'; this package allows users to interact with 'TimeGPT' via the 'API'. You can set and validate 'API' keys and generate forecasts via 'API' calls. It is compatible with 'tsibble' and base R. For more details visit <https://docs.nixtla.io/>.

Maintained by Mariana Menchero. Last updated 28 days ago.

3.5 match 30 stars 8.16 score 38 scripts

yiluheihei

RevEcoR:Reverse Ecology Analysis on Microbiome

An implementation of the reverse ecology framework. Reverse ecology refers to the use of genomics to study ecology with no a priori assumptions about the organism(s) under consideration, linking organisms to their environment. It allows researchers to reconstruct the metabolic networks and study the ecology of poorly characterized microbial species from their genomic information, and has substantial potentials for microbial community ecological analysis.

Maintained by Yang Cao. Last updated 6 years ago.

4.9 match 6 stars 5.77 score 22 scripts 1 dependents

biocro

BioCro:Modular Crop Growth Simulations

A cross-platform representation of models as sets of equations that facilitates modularity in model building and allows users to harness modern techniques for numerical integration and data visualization. Documentation is provided by several vignettes included in this package; also see Lochocki et al. (2022) <doi:10.1093/insilicoplants/diac003>.

Maintained by Justin M. McGrath. Last updated 9 days ago.

cpp

3.5 match 45 stars 8.09 score 81 scripts

cran

forestinventory:Design-Based Global and Small-Area Estimations for Multiphase Forest Inventories

Extensive global and small-area estimation procedures for multiphase forest inventories under the design-based Monte-Carlo approach are provided. The implementation has been published in the Journal of Statistical Software (<doi:10.18637/jss.v097.i04>) and includes estimators for simple and cluster sampling published by Daniel Mandallaz in 2007 (<doi:10.1201/9781584889779>), 2013 (<doi:10.1139/cjfr-2012-0381>, <doi:10.1139/cjfr-2013-0181>, <doi:10.1139/cjfr-2013-0449>, <doi:10.3929/ethz-a-009990020>) and 2016 (<doi:10.3929/ethz-a-010579388>). It provides point estimates, their external- and design-based variances and confidence intervals, as well as a set of functions to analyze and visualize the produced estimates. The procedures have also been optimized for the use of remote sensing data as auxiliary information, as demonstrated in 2018 by Hill et al. (<doi:10.3390/rs10071052>).

Maintained by Andreas Hill. Last updated 4 years ago.

9.4 match 3.00 score 20 scripts

rdatatable

data.table:Extension of `data.frame`

Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.

Maintained by Tyson Barrett. Last updated 2 days ago.

1.2 match 3.7k stars 23.53 score 230k scripts 4.6k dependents

rdinnager

slimr:Create, Run and Post-Process 'SLiM' Population Genetics Forward Simulations

Lets you write 'SLiM' scripts (population genomics simulation) using your favourite R IDE, using a syntax as close as possible to the original 'SLiM' language. It offer many tools to manipulate those scripts, as well as run them in the 'SLiM' software from R, as well as capture and post-process their output, after or even during a simulation.

Maintained by Russell Dinnage. Last updated 4 months ago.

6.0 match 8 stars 4.70 score 42 scripts

lifebrain

gbhs:Lifebrain Global Brain Health Survey Data

Between June 2019 and August 2020, Lifebrain conducted the Global Brain Health Survey to collect data on people’s perceptions of brain health and willingness to take care of their brain by adopting new lifestyles. The survey was conducted online and translated into 14 languages to reach as many people as possible. In total, it collected 27,590 responses from people in 81 countries. This package contains code and data from this survey.

Maintained by Athanasia Mo Mowinckel. Last updated 2 years ago.

10.2 match 1 stars 2.78 score 12 scripts

guokai8

microbial:Do 16s Data Analysis and Generate Figures

Provides functions to enhance the available statistical analysis procedures in R by providing simple functions to analysis and visualize the 16S rRNA data.Here we present a tutorial with minimum working examples to demonstrate usage and dependencies.

Maintained by Kai Guo. Last updated 5 months ago.

software graphandnetwork microbiome microbiome-analysis

4.8 match 13 stars 5.81 score 25 scripts

bioc

globalSeq:Global Test for Counts

The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size. Useful for testing for association between RNA-Seq and high-dimensional data.

Maintained by Armin Rauschenberger. Last updated 5 months ago.

geneexpression exonarray differentialexpression genomewideassociation transcriptomics dimensionreduction regression sequencing wholegenome rnaseq exomeseq mirna multiplecomparison

5.2 match 1 stars 5.32 score 4 scripts

carpentries

sandpaper:Create and Curate Carpentries Lessons

We provide tools to build a Carpentries-themed lesson repository into an accessible standalone static website. These include local tools and those designed to be used in a continuous integration context so that all the lesson author needs to focus on is writing the content of the actual lesson.

Maintained by Robert Davey. Last updated 2 months ago.

carpentries carpentries-infrastructure carpentries-workbench lesson-template lessons markdown static-site-generator

3.6 match 44 stars 7.72 score 8 scripts

idem-lab

sdmtools:Utility tools for Species Distribution Modelling

What the package does (one paragraph).

Maintained by Gerry Ryan. Last updated 3 months ago.

4.5 match 9 stars 6.13 score 674 scripts

lbau7

baskexact:Analytical Calculation of Basket Trial Operating Characteristics

Analytically calculates the operating characteristics of single-stage and two-stage basket trials with equal sample sizes using the power prior design by Baumann et al. (2024) <doi:10.48550/arXiv.2309.06988> and the design by Fujikawa et al. (2020) <doi:10.1002/bimj.201800404>.

Maintained by Lukas Baumann. Last updated 7 months ago.

openblas cpp

5.3 match 2 stars 5.22 score 11 scripts