Showing 116 of total 116 results (show query)
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.
8.1 match 517 stars 20.53 score 9.8k scripts 15k dependents
lmrodriguezr
enveomics.R:Various Utilities for Microbial Genomics and Metagenomics
A collection of functions for microbial ecology and other applications of genomics and metagenomics. Companion package for the Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016 <DOI:10.7287/peerj.preprints.1900v1>).
Maintained by Luis M. Rodriguez-R. Last updated 1 months ago.
72.4 match 2.17 score 26 scripts
skranz
RTutor:Interactive R problem sets with automatic testing of solutions and automatic hints
Interactive R problem sets with automatic testing of solutions and automatic hints
Maintained by Sebastian Kranz. Last updated 1 years ago.
economicslearn-to-codeproblem-setrstudiortutorshinyteaching
24.4 match 205 stars 5.83 score 111 scripts 1 dependents
arcadeantics
this.path:Get Executing Script's Path
Determine the path of the executing script. Compatible with several popular GUIs: 'Rgui', 'RStudio', 'Positron', 'VSCode', 'Jupyter', 'Emacs', and 'Rscript' (shell). Compatible with several functions and packages: 'source()', 'sys.source()', 'debugSource()' in 'RStudio', 'compiler::loadcmp()', 'utils::Sweave()', 'box::use()', 'knitr::knit()', 'plumber::plumb()', 'shiny::runApp()', 'package:targets', and 'testthat::source_file()'.
Maintained by Iris Simmons. Last updated 15 days ago.
16.0 match 49 stars 8.84 score 388 scripts 3 dependents
bcgov
bcdata:Search and Retrieve Data from the BC Data Catalogue
Search, query, and download tabular and 'geospatial' data from the British Columbia Data Catalogue (<https://catalogue.data.gov.bc.ca/>). Search catalogue data records based on keywords, data licence, sector, data format, and B.C. government organization. View metadata directly in R, download many data formats, and query 'geospatial' data available via the B.C. government Web Feature Service ('WFS') using 'dplyr' syntax.
Maintained by Andy Teucher. Last updated 1 months ago.
11.0 match 83 stars 10.29 score 186 scripts 4 dependentsbcgov
ssdtools:Species Sensitivity Distributions
Species sensitivity distributions are cumulative probability distributions which are fitted to toxicity concentrations for different species as described by Posthuma et al.(2001) <isbn:9781566705783>. The ssdtools package uses Maximum Likelihood to fit distributions such as the gamma, log-logistic, log-normal and log-normal log-normal mixture. Multiple distributions can be averaged using Akaike Information Criteria. Confidence intervals on hazard concentrations and proportions are produced by bootstrapping.
Maintained by Joe Thorley. Last updated 24 days ago.
ecotoxicologyenvspecies-sensitivity-distributioncpp
11.0 match 31 stars 10.23 score 111 scripts 4 dependents
danlwarren
ENMTools:Analysis of Niche Evolution using Niche and Distribution Models
Constructing niche models and analyzing patterns of niche evolution. Acts as an interface for many popular modeling algorithms, and allows users to conduct Monte Carlo tests to address basic questions in evolutionary ecology and biogeography. Warren, D.L., R.E. Glor, and M. Turelli (2008) <doi:10.1111/j.1558-5646.2008.00482.x> Glor, R.E., and D.L. Warren (2011) <doi:10.1111/j.1558-5646.2010.01177.x> Warren, D.L., R.E. Glor, and M. Turelli (2010) <doi:10.1111/j.1600-0587.2009.06142.x> Cardillo, M., and D.L. Warren (2016) <doi:10.1111/geb.12455> D.L. Warren, L.J. Beaumont, R. Dinnage, and J.B. Baumgartner (2019) <doi:10.1111/ecog.03900>.
Maintained by Dan Warren. Last updated 2 months ago.
15.1 match 105 stars 6.91 score 126 scripts
igraph
igraph:Network Analysis and Visualization
Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.
Maintained by Kirill Müller. Last updated 10 hours ago.
complex-networksgraph-algorithmsgraph-theorymathematicsnetwork-analysisnetwork-graphfortranlibxml2glpkopenblascpp
4.8 match 582 stars 21.11 score 31k scripts 1.9k dependentsbcgov
bcmaps:Map Layers and Spatial Utilities for British Columbia
Various layers of B.C., including administrative boundaries, natural resource management boundaries, census boundaries etc. All layers are available in BC Albers (<https://spatialreference.org/ref/epsg/3005/>) equal-area projection, which is the B.C. government standard. The layers are sourced from the British Columbia and Canadian government under open licenses, including B.C. Data Catalogue (<https://data.gov.bc.ca>), the Government of Canada Open Data Portal (<https://open.canada.ca/en/using-open-data>), and Statistics Canada (<https://www.statcan.gc.ca/en/reference/licence>).
Maintained by Andy Teucher. Last updated 3 months ago.
11.0 match 73 stars 8.65 score 254 scripts
cran
notebookutils:Dummy R APIs Used in 'Azure Synapse Analytics' for Local Developments
This is a pure dummy interfaces package which mirrors 'MsSparkUtils' APIs <https://learn.microsoft.com/en-us/azure/synapse-analytics/spark/microsoft-spark-utilities?pivots=programming-language-r> of 'Azure Synapse Analytics' <https://learn.microsoft.com/en-us/azure/synapse-analytics/> for R users, customer of Azure Synapse can download this package from CRAN for local development.
Maintained by runtimeexp. Last updated 11 months ago.
28.0 match 2.36 score 23 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.
immunooncologysequencingmicrobiomemetagenomicsclusteringclassificationmultiplecomparisongeneticvariability
3.5 match 597 stars 13.90 score 8.4k scripts 37 dependentsbioc
S4Vectors:Foundation of vector-like and list-like containers in Bioconductor
The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, Factor, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).
Maintained by Hervé Pagès. Last updated 1 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
3.0 match 18 stars 16.05 score 1.0k scripts 1.9k dependentsskranz
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.
7.7 match 16 stars 6.20 score 79 scripts 42 dependents
tdhock
directlabels:Direct Labels for Multicolor Plots
An extensible framework for automatically placing direct labels onto multicolor 'lattice' or 'ggplot2' plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method.
Maintained by Toby Dylan Hocking. Last updated 11 months ago.
4.5 match 83 stars 10.62 score 1.8k scripts 16 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.
3.3 match 63 stars 13.74 score 5.7k scripts 814 dependents
gaborcsardi
dotenv:Load Environment Variables from '.env'
Load configuration from a '.env' file, that is in the current working directory, into environment variables.
Maintained by Gábor Csárdi. Last updated 2 years ago.
5.3 match 93 stars 8.55 score 884 scripts 2 dependentsbioc
IRanges:Foundation of integer range manipulation in Bioconductor
Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.
Maintained by Hervé Pagès. Last updated 1 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
3.0 match 22 stars 15.09 score 2.1k scripts 1.8k dependents
r-gregmisc
gdata:Various R Programming Tools for Data Manipulation
Various R programming tools for data manipulation, including medical unit conversions, combining objects, character vector operations, factor manipulation, obtaining information about R objects, generating fixed-width format files, extracting components of date & time objects, operations on columns of data frames, matrix operations, operations on vectors, operations on data frames, value of last evaluated expression, and a resample() wrapper for sample() that ensures consistent behavior for both scalar and vector arguments.
Maintained by Arni Magnusson. Last updated 2 months ago.
3.3 match 9 stars 13.62 score 4.5k scripts 124 dependentsbioc
LEA:LEA: an R package for Landscape and Ecological Association Studies
LEA is an R package dedicated to population genomics, landscape genomics and genotype-environment association tests. LEA can run analyses of population structure and genome-wide tests for local adaptation, and also performs imputation of missing genotypes. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm2). In addition, LEA computes values of genetic offset statistics based on new or predicted environments (genetic.gap, genetic.offset). LEA is mainly based on optimized programs that can scale with the dimensions of large data sets.
Maintained by Olivier Francois. Last updated 6 days ago.
softwarestatistical methodclusteringregressionopenblas
6.4 match 6.63 score 534 scripts
markbravington
mvbutils:General utilities, workspace organization, code and docu editing, live package maintenance, etc
Hierarchical workspace tree, code editing and backup, easy package prep, editing of packages while loaded, per-object lazy-loading, easy documentation, macro functions, and miscellaneous utilities. Needed by debug package.
Maintained by Mark V. Bravington. Last updated 6 days ago.
6.0 match 6.53 score 138 scripts 18 dependents
femiguez
apsimx:Inspect, Read, Edit and Run 'APSIM' "Next Generation" and 'APSIM' Classic
The functions in this package inspect, read, edit and run files for 'APSIM' "Next Generation" ('JSON') and 'APSIM' "Classic" ('XML'). The files with an 'apsim' extension correspond to 'APSIM' Classic (7.x) - Windows only - and the ones with an 'apsimx' extension correspond to 'APSIM' "Next Generation". For more information about 'APSIM' see (<https://www.apsim.info/>) and for 'APSIM' next generation (<https://apsimnextgeneration.netlify.app/>).
Maintained by Fernando Miguez. Last updated 2 days ago.
4.0 match 59 stars 9.71 score 68 scripts 2 dependents
r-spatial
RSAGA:SAGA Geoprocessing and Terrain Analysis
Provides access to geocomputing and terrain analysis functions of the geographical information system (GIS) 'SAGA' (System for Automated Geoscientific Analyses) from within R by running the command line version of SAGA. This package furthermore provides several R functions for handling ASCII grids, including a flexible framework for applying local functions (including predict methods of fitted models) and focal functions to multiple grids. SAGA GIS is available under GPL-2 / LGPL-2 licences from <https://sourceforge.net/projects/saga-gis/>.
Maintained by Alexander Brenning. Last updated 1 months ago.
4.3 match 23 stars 8.72 score 275 scripts
tidyverse
dplyr:A Grammar of Data Manipulation
A fast, consistent tool for working with data frame like objects, both in memory and out of memory.
Maintained by Hadley Wickham. Last updated 13 days ago.
1.3 match 4.8k stars 24.68 score 659k scripts 7.8k dependents
paulojus
geoR:Analysis of Geostatistical Data
Geostatistical analysis including variogram-based, likelihood-based and Bayesian methods. Software companion for Diggle and Ribeiro (2007) <doi:10.1007/978-0-387-48536-2>.
Maintained by Paulo Justiniano Ribeiro Jr. Last updated 1 years ago.
4.0 match 10 stars 7.57 score 1.8k scripts 12 dependents
decisionpatterns
formula.tools:Programmatic Utilities for Manipulating Formulas, Expressions, Calls, Assignments and Other R Objects
These utilities facilitate the programmatic manipulations of formulas, expressions, calls, assignments and other R language objects. These objects all share the same structure: a left-hand side, operator and right-hand side. This packages provides methods for accessing and modifying this structures as well as extracting and replacing names and symbols from these objects.
Maintained by Christopher Brown. Last updated 7 years ago.
3.3 match 17 stars 8.89 score 236 scripts 79 dependents
jeromeecoac
seewave:Sound Analysis and Synthesis
Functions for analysing, manipulating, displaying, editing and synthesizing time waves (particularly sound). This package processes time analysis (oscillograms and envelopes), spectral content, resonance quality factor, entropy, cross correlation and autocorrelation, zero-crossing, dominant frequency, analytic signal, frequency coherence, 2D and 3D spectrograms and many other analyses. See Sueur et al. (2008) <doi:10.1080/09524622.2008.9753600> and Sueur (2018) <doi:10.1007/978-3-319-77647-7>.
Maintained by Jerome Sueur. Last updated 1 years ago.
3.3 match 18 stars 8.88 score 880 scripts 23 dependents
shixiangwang
sigminer:Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
Maintained by Shixiang Wang. Last updated 5 months ago.
bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualizationcpp
3.0 match 150 stars 9.48 score 123 scripts 2 dependents
rapporter
pander:An R 'Pandoc' Writer
Contains some functions catching all messages, 'stdout' and other useful information while evaluating R code and other helpers to return user specified text elements (like: header, paragraph, table, image, lists etc.) in 'pandoc' markdown or several type of R objects similarly automatically transformed to markdown format. Also capable of exporting/converting (the resulting) complex 'pandoc' documents to e.g. HTML, 'PDF', 'docx' or 'odt'. This latter reporting feature is supported in brew syntax or with a custom reference class with a smarty caching 'backend'.
Maintained by Gergely Daróczi. Last updated 16 days ago.
literate-programmingmarkdownpandocpandoc-markdownreproducible-researchrmarkdowncpp
1.7 match 297 stars 16.60 score 7.6k scripts 108 dependents
ncss-tech
aqp:Algorithms for Quantitative Pedology
The Algorithms for Quantitative Pedology (AQP) project was started in 2009 to organize a loosely-related set of concepts and source code on the topic of soil profile visualization, aggregation, and classification into this package (aqp). Over the past 8 years, the project has grown into a suite of related R packages that enhance and simplify the quantitative analysis of soil profile data. Central to the AQP project is a new vocabulary of specialized functions and data structures that can accommodate the inherent complexity of soil profile information; freeing the scientist to focus on ideas rather than boilerplate data processing tasks <doi:10.1016/j.cageo.2012.10.020>. These functions and data structures have been extensively tested and documented, applied to projects involving hundreds of thousands of soil profiles, and deeply integrated into widely used tools such as SoilWeb <https://casoilresource.lawr.ucdavis.edu/soilweb-apps>. Components of the AQP project (aqp, soilDB, sharpshootR, soilReports packages) serve an important role in routine data analysis within the USDA-NRCS Soil Science Division. The AQP suite of R packages offer a convenient platform for bridging the gap between pedometric theory and practice.
Maintained by Dylan Beaudette. Last updated 29 days ago.
digital-soil-mappingncss-technrcspedologypedometricssoilsoil-surveyusda
2.3 match 55 stars 11.77 score 1.2k scripts 2 dependents
dkahle
TITAN2:Threshold Indicator Taxa Analysis
Uses indicator species scores across binary partitions of a sample set to detect congruence in taxon-specific changes of abundance and occurrence frequency along an environmental gradient as evidence of an ecological community threshold. Relevant references include Baker and King (2010) <doi:10.1111/j.2041-210X.2009.00007.x>, King and Baker (2010) <doi:10.1899/09-144.1>, and Baker and King (2013) <doi:10.1899/12-142.1>.
Maintained by David Kahle. Last updated 1 years ago.
4.0 match 13 stars 6.59 score 30 scripts
cynkra
constructive:Display Idiomatic Code to Construct Most R Objects
Prints code that can be used to recreate R objects. In a sense it is similar to 'base::dput()' or 'base::deparse()' but 'constructive' strives to use idiomatic constructors.
Maintained by Antoine Fabri. Last updated 2 days ago.
3.0 match 137 stars 8.63 score 20 scriptsncss-tech
soilDB:Soil Database Interface
A collection of functions for reading soil data from U.S. Department of Agriculture Natural Resources Conservation Service (USDA-NRCS) and National Cooperative Soil Survey (NCSS) databases.
Maintained by Andrew Brown. Last updated 7 days ago.
ksslnasisnrcssoilsoil-data-accesssoil-surveysoilwebsqlusda
2.3 match 87 stars 11.34 score 1.0k scripts 1 dependents
michaelgruenstaeudl
PACVr:Plastome Assembly Coverage Visualization
Visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes. For more information, please see Gruenstaeudl and Jenke (2020) <doi:10.1186/s12859-020-3475-0>.
Maintained by Michael Gruenstaeudl. Last updated 4 months ago.
4.0 match 3 stars 5.69 score 5 scriptsr-lib
tidyselect:Select from a Set of Strings
A backend for the selecting functions of the 'tidyverse'. It makes it easy to implement select-like functions in your own packages in a way that is consistent with other 'tidyverse' interfaces for selection.
Maintained by Lionel Henry. Last updated 4 months ago.
1.3 match 130 stars 18.31 score 1.9k scripts 8.2k dependents
opengeos
whitebox:'WhiteboxTools' R Frontend
An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.
Maintained by Andrew Brown. Last updated 5 months ago.
geomorphometrygeoprocessinggeospatialgishydrologyremote-sensingrstudio
2.3 match 173 stars 9.65 score 203 scripts 2 dependents
mrkaye97
slackr:Send Messages, Images, R Objects and Files to 'Slack' Channels/Users
'Slack' <https://slack.com/> provides a service for teams to collaborate by sharing messages, images, links, files and more. Functions are provided that make it possible to interact with the 'Slack' platform 'API'. When you need to share information or data from R, rather than resort to copy/ paste in e-mails or other services like 'Skype' <https://www.skype.com/en/>, you can use this package to send well-formatted output from multiple R objects and expressions to all teammates at the same time with little effort. You can also send images from the current graphics device, R objects, and upload files.
Maintained by Matt Kaye. Last updated 5 months ago.
1.8 match 306 stars 11.66 score 179 scripts
metrumresearchgroup
mrgsolve:Simulate from ODE-Based Models
Fast simulation from ordinary differential equation (ODE) based models typically employed in quantitative pharmacology and systems biology.
Maintained by Kyle T Baron. Last updated 1 months ago.
1.8 match 138 stars 10.90 score 1.2k scripts 3 dependents
jonathanlees
RSEIS:Seismic Time Series Analysis Tools
Multiple interactive codes to view and analyze seismic data, via spectrum analysis, wavelet transforms, particle motion, hodograms. Includes general time-series tools, plotting, filtering, interactive display.
Maintained by Jonathan M. Lees. Last updated 6 months ago.
4.5 match 3 stars 4.27 score 262 scripts 4 dependentsfemiguez
nlraa:Nonlinear Regression for Agricultural Applications
Additional nonlinear regression functions using self-start (SS) algorithms. One of the functions is the Beta growth function proposed by Yin et al. (2003) <doi:10.1093/aob/mcg029>. There are several other functions with breakpoints (e.g. linear-plateau, plateau-linear, exponential-plateau, plateau-exponential, quadratic-plateau, plateau-quadratic and bilinear), a non-rectangular hyperbola and a bell-shaped curve. Twenty eight (28) new self-start (SS) functions in total. This package also supports the publication 'Nonlinear regression Models and applications in agricultural research' by Archontoulis and Miguez (2015) <doi:10.2134/agronj2012.0506>, a book chapter with similar material <doi:10.2134/appliedstatistics.2016.0003.c15> and a publication by Oddi et. al. (2019) in Ecology and Evolution <doi:10.1002/ece3.5543>. The function 'nlsLMList' uses 'nlsLM' for fitting, but it is otherwise almost identical to 'nlme::nlsList'.In addition, this release of the package provides functions for conducting simulations for 'nlme' and 'gnls' objects as well as bootstrapping. These functions are intended to work with the modeling framework of the 'nlme' package. It also provides four vignettes with extended examples.
Maintained by Fernando Miguez. Last updated 10 months ago.
agriculturalecologynonlinear-mixed-modelsnonlinear-regression
2.3 match 23 stars 8.19 score 112 scripts 2 dependents
project-gen3sis
gen3sis:General Engine for Eco-Evolutionary Simulations
Contains an engine for spatially-explicit eco-evolutionary mechanistic models with a modular implementation and several support functions. It allows exploring the consequences of ecological and macroevolutionary processes across realistic or theoretical spatio-temporal landscapes on biodiversity patterns as a general term. Reference: Oskar Hagen, Benjamin Flueck, Fabian Fopp, Juliano S. Cabral, Florian Hartig, Mikael Pontarp, Thiago F. Rangel, Loic Pellissier (2021) "gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity" <doi:10.1371/journal.pbio.3001340>.
Maintained by Oskar Hagen. Last updated 1 years ago.
biodiversityecologyevolutionmechanisticmodelmodelingsimulationcpp
2.2 match 29 stars 7.56 score 69 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.
1.9 match 8 stars 8.66 score 170 scripts
hzhanghenry
RCircos:Circos 2D Track Plot
A simple and flexible way to generate Circos 2D track plot images for genomic data visualization is implemented in this package. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation.
Maintained by Hongen Zhang. Last updated 3 years ago.
2.3 match 6 stars 7.21 score 298 scripts 3 dependents
dkaschek
dMod:Dynamic Modeling and Parameter Estimation in ODE Models
The framework provides functions to generate ODEs of reaction networks, parameter transformations, observation functions, residual functions, etc. The framework follows the paradigm that derivative information should be used for optimization whenever possible. Therefore, all major functions produce and can handle expressions for symbolic derivatives.
Maintained by Daniel Kaschek. Last updated 10 days ago.
1.9 match 20 stars 8.35 score 251 scriptsbioc
isobar:Analysis and quantitation of isobarically tagged MSMS proteomics data
isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.
Maintained by Florian P Breitwieser. Last updated 5 months ago.
immunooncologyproteomicsmassspectrometrybioinformaticsmultiplecomparisonsqualitycontrol
2.3 match 10 stars 6.96 score 19 scripts
sagiegurari
scriptexec:Execute Native Scripts
Run complex native scripts with a single command, similar to system commands.
Maintained by Sagie Gur-Ari. Last updated 4 years ago.
bash-scriptscriptingshell-script
3.4 match 3 stars 4.50 score 21 scriptsbioc
widgetTools:Creates an interactive tcltk widget
This packages contains tools to support the construction of tcltk widgets
Maintained by Jianhua Zhang. Last updated 5 months ago.
3.0 match 5.04 score 11 scripts 8 dependentsbioc
sevenbridges:Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R
R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.
Maintained by Phil Webster. Last updated 5 months ago.
softwaredataimportthirdpartyclientapi-clientbioconductorbioinformaticscloudcommon-workflow-languagesevenbridges
2.0 match 35 stars 7.40 score 24 scripts
cmann3
eList:List Comprehension and Tools
Create list comprehensions (and other types of comprehension) similar to those in 'python', 'haskell', and other languages. List comprehension in 'R' converts a regular for() loop into a vectorized lapply() function. Support for looping with multiple variables, parallelization, and across non-standard objects included. Package also contains a variety of functions to help with list comprehension.
Maintained by Chris Mann. Last updated 4 years ago.
3.3 match 2 stars 4.48 score 9 scripts 1 dependents
mlr-org
mlr3spatiotempcv:Spatiotemporal Resampling Methods for 'mlr3'
Extends the mlr3 machine learning framework with spatio-temporal resampling methods to account for the presence of spatiotemporal autocorrelation (STAC) in predictor variables. STAC may cause highly biased performance estimates in cross-validation if ignored. A JSS article is available at <doi:10.18637/jss.v111.i07>.
Maintained by Patrick Schratz. Last updated 4 months ago.
cross-validationmlr3resamplingresampling-methodsspatialtemporal
1.8 match 50 stars 8.09 score 123 scripts
gjwgit
rattle:Graphical User Interface for Data Science in R
The R Analytic Tool To Learn Easily (Rattle) provides a collection of utilities functions for the data scientist. A Gnome (RGtk2) based graphical interface is included with the aim to provide a simple and intuitive introduction to R for data science, allowing a user to quickly load data from a CSV file (or via ODBC), transform and explore the data, build and evaluate models, and export models as PMML (predictive modelling markup language) or as scores. A key aspect of the GUI is that all R commands are logged and commented through the log tab. This can be saved as a standalone R script file and as an aid for the user to learn R or to copy-and-paste directly into R itself. Note that RGtk2 and cairoDevice have been archived on CRAN. See <https://rattle.togaware.com> for installation instructions.
Maintained by Graham Williams. Last updated 3 years ago.
1.7 match 16 stars 8.48 score 3.0k scripts 3 dependents
modeloriented
DALEXtra:Extension for 'DALEX' Package
Provides wrapper of various machine learning models. In applied machine learning, there is a strong belief that we need to strike a balance between interpretability and accuracy. However, in field of the interpretable machine learning, there are more and more new ideas for explaining black-box models, that are implemented in 'R'. 'DALEXtra' creates 'DALEX' Biecek (2018) <arXiv:1806.08915> explainer for many type of models including those created using 'python' 'scikit-learn' and 'keras' libraries, and 'java' 'h2o' library. Important part of the package is Champion-Challenger analysis and innovative approach to model performance across subsets of test data presented in Funnel Plot.
Maintained by Szymon Maksymiuk. Last updated 2 years ago.
1.8 match 67 stars 7.71 score 400 scripts 1 dependentsskranz
repgame:Solve discounted repeated games with monetary transfers
Solve discounted repeated games with monetary transfers using the fast Algorithms develeoped by Goldluecke and Kranz (JET, 2013)
Maintained by Sebastian Kranz. Last updated 7 years ago.
6.8 match 2 stars 2.00 score 3 scriptsncss-tech
SoilTaxonomy:A System of Soil Classification for Making and Interpreting Soil Surveys
Taxonomic dictionaries, formative element lists, and functions related to the maintenance, development and application of U.S. Soil Taxonomy. Data and functionality are based on official U.S. Department of Agriculture sources including the latest edition of the Keys to Soil Taxonomy. Descriptions and metadata are obtained from the National Soil Information System or Soil Survey Geographic databases. Other sources are referenced in the data documentation. Provides tools for understanding and interacting with concepts in the U.S. Soil Taxonomic System. Most of the current utilities are for working with taxonomic concepts at the "higher" taxonomic levels: Order, Suborder, Great Group, and Subgroup.
Maintained by Andrew Brown. Last updated 6 months ago.
great-groupncss-techsoilsoil-surveysoil-taxonomysubgroupsuborderusda
2.3 match 15 stars 5.65 score
richardjtelford
palaeoSig:Significance Tests for Palaeoenvironmental Reconstructions
Several tests of quantitative palaeoenvironmental reconstructions from microfossil assemblages, including the null model tests of the statistically significant of reconstructions developed by Telford and Birks (2011) <doi:10.1016/j.quascirev.2011.03.002>, and tests of the effect of spatial autocorrelation on transfer function model performance using methods from Telford and Birks (2009) <doi:10.1016/j.quascirev.2008.12.020> and Trachsel and Telford (2016) <doi:10.5194/cp-12-1215-2016>. Age-depth models with generalized mixed-effect regression from Heegaard et al (2005) <doi:10.1191/0959683605hl836rr> are also included.
Maintained by Richard Telford. Last updated 2 years ago.
2.3 match 3 stars 5.45 score 31 scriptsbioc
RCM:Fit row-column association models with the negative binomial distribution for the microbiome
Combine ideas of log-linear analysis of contingency table, flexible response function estimation and empirical Bayes dispersion estimation for explorative visualization of microbiome datasets. The package includes unconstrained as well as constrained analysis. In addition, diagnostic plot to detect lack of fit are available.
Maintained by Stijn Hawinkel. Last updated 5 months ago.
metagenomicsdimensionreductionmicrobiomevisualizationordinationphyloseqrcm
1.8 match 16 stars 6.90 score 25 scriptsbioc
makecdfenv:CDF Environment Maker
This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.
Maintained by James W. MacDonald. Last updated 2 months ago.
onechanneldataimportpreprocessingzlib
2.0 match 5.81 score 36 scripts 2 dependents
xiaolei-lab
simer:Data Simulation for Life Science and Breeding
Data simulator including genotype, phenotype, pedigree, selection and reproduction in R. It simulates most of reproduction process of animals or plants and provides data for GS (Genomic Selection), GWAS (Genome-Wide Association Study), and Breeding. For ADI model, please see Kao C and Zeng Z (2002) <doi:10.1093/genetics/160.3.1243>. For build.cov, please see B. D. Ripley (1987) <ISBN:9780470009604>.
Maintained by Xiaolei Liu. Last updated 18 days ago.
2.0 match 28 stars 5.80 score 2 scripts
ha-pu
globaltrends:Download and Measure Global Trends Through Google Search Volumes
Google offers public access to global search volumes from its search engine through the Google Trends portal. The package downloads these search volumes provided by Google Trends and uses them to measure and analyze the distribution of search scores across countries or within countries. The package allows researchers and analysts to use these search scores to investigate global trends based on patterns within these scores. This offers insights such as degree of internationalization of firms and organizations or dissemination of political, social, or technological trends across the globe or within single countries. An outline of the package's methodological foundations and potential applications is available as a working paper: <https://papers.ssrn.com/sol3/papers.cfm?abstract_id=3969013>.
Maintained by Harald Puhr. Last updated 2 years ago.
google-trendsinternationalization
2.3 match 18 stars 5.00 score 11 scripts
asa12138
pctax:Professional Comprehensive Omics Data Analysis
Provides a comprehensive suite of tools for analyzing omics data. It includes functionalities for alpha diversity analysis, beta diversity analysis, differential abundance analysis, community assembly analysis, visualization of phylogenetic tree, and functional enrichment analysis. With a progressive approach, the package offers a range of analysis methods to explore and understand the complex communities. It is designed to support researchers and practitioners in conducting in-depth and professional omics data analysis.
Maintained by Chen Peng. Last updated 4 months ago.
microbiomesoftwarevisualizationomics
1.9 match 14 stars 5.89 score 14 scripts
centerforstatistics-ugent
pim:Fit Probabilistic Index Models
Fit a probabilistic index model as described in Thas et al, 2012: <doi:10.1111/j.1467-9868.2011.01020.x>. The interface to the modeling function has changed in this new version. The old version is still available at R-Forge.
Maintained by Joris Meys. Last updated 2 months ago.
2.0 match 10 stars 5.33 score 43 scripts
alenxav
SoyNAM:Soybean Nested Association Mapping Dataset
Genomic and multi-environmental soybean data. Soybean Nested Association Mapping (SoyNAM) project dataset funded by the United Soybean Board (USB). BLUP function formats data for genome-wide prediction and association analysis.
Maintained by Alencar Xavier. Last updated 3 years ago.
3.3 match 1 stars 3.18 score 4 scripts
traitecoevo
plant:A Package for Modelling Forest Trait Ecology and Evolution
Solves trait, size and patch structured model from (Falster et al. 2016) using either method of characteristics or as stochastic, finite-sized population.
Maintained by Daniel Falster. Last updated 7 days ago.
c-plus-plusdemographydynamicecologyevolutionforestsplant-physiologyscience-researchsimulationtraitcpp
1.7 match 53 stars 5.87 score
jaak-s
rDEA:Robust Data Envelopment Analysis (DEA) for R
Data Envelopment Analysis for R, estimating robust DEA scores without and with environmental variables and doing returns-to-scale tests.
Maintained by Jaak Simm. Last updated 2 years ago.
2.0 match 24 stars 4.92 score 23 scripts
jcaledo
EnvNJ:Whole Genome Phylogenies Using Sequence Environments
Contains utilities for the analysis of protein sequences in a phylogenetic context. Allows the generation of phylogenetic trees base on protein sequences in an alignment-independent way. Two different methods have been implemented. One approach is based on the frequency analysis of n-grams, previously described in Stuart et al. (2002) <doi:10.1093/bioinformatics/18.1.100>. The other approach is based on the species-specific neighborhood preference around amino acids. Features include the conversion of a protein set into a vector reflecting these neighborhood preferences, pairwise distances (dissimilarity) between these vectors, and the generation of trees based on these distance matrices.
Maintained by Juan Carlos Aledo. Last updated 3 years ago.
9.0 match 1.04 score 11 scripts
slequime
nosoi:A Forward Agent-Based Transmission Chain Simulator
The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. Methods in Ecology and Evolution 11:1002-1007). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.
Maintained by Sebastian Lequime. Last updated 2 months ago.
1.3 match 8 stars 7.26 score 30 scripts
nicholasjcooper
NCmisc:Miscellaneous Functions for Creating Adaptive Functions and Scripts
A set of handy functions. Includes a versatile one line progress bar, one line function timer with detailed output, time delay function, text histogram, object preview, CRAN package search, simpler package installer, Linux command install check, a flexible Mode function, top function, simulation of correlated data, and more.
Maintained by Nicholas Cooper. Last updated 2 years ago.
2.3 match 3.86 score 172 scripts 5 dependents
miracum
DIZutils:Utilities for 'DIZ' R Package Development
Utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Maintained by Jonathan M. Mang. Last updated 4 months ago.
1.7 match 3 stars 5.03 score 5 scripts 2 dependents
squ4reanalytics
D4TAlink.light:FAIR Data - Workflow Management
Tools, methods and processes for the management of analysis workflows. These lightweight solutions facilitate structuring R&D activities. These solutions were developed to comply with Good Documentation Practice (GDP), with FAIR principles as discussed by Jacobsen et al. (2017) <doi:10.1162/dint_r_00024>, and with ALCOA+ principles as proposed by the U.S. FDA.
Maintained by Gregoire Thomas. Last updated 4 months ago.
2.0 match 4.30 scorebioc
TransView:Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.
Maintained by Julius Muller. Last updated 2 months ago.
immunooncologydnamethylationgeneexpressiontranscriptionmicroarraysequencingchipseqrnaseqmethylseqdataimportvisualizationclusteringmultiplecomparisoncurlbzip2xz-utilszlib
3.3 match 2.60 scoreskranz
skUtils:Helper functions for repgames and dyngames
Helper functions needed by my package repgames and dyngames
Maintained by Sebastian Kranz. Last updated 4 years ago.
8.5 match 1.00 scoremiracum
DIZtools:Lightweight Utilities for 'DIZ' R Package Development
Lightweight utility functions used for the R package development infrastructure inside the data integration centers ('DIZ') to standardize and facilitate repetitive tasks such as setting up a database connection or issuing notification messages and to avoid redundancy.
Maintained by Jonathan M. Mang. Last updated 1 years ago.
1.8 match 3 stars 4.13 score 2 scripts 3 dependents
repboxr
repboxReg:Repbox module for analysing regressions
Repbox module for analysing regressions
Maintained by Sebastian Kranz. Last updated 30 days ago.
1.9 match 3.71 score 6 scripts 2 dependents
molevolepid
SEEPS:Sequence evolution and epidemiological process simulator
A modular, modern simulation suite and toolkit for simulating transmission networks, phylogenies, and evolutionary pairwise distance matrices under different models and assumptions for viral/sequence evolution. While intially developed for HIV, SEEPS offers modular utilities for custom workflows for extension beyond HIV.
Maintained by Michael Kupperman. Last updated 2 months ago.
biological-sequencesepidemiologyevolutionhivsimulation-framework
1.7 match 1 stars 3.95 score 6 scripts
rbgramacy
plgp:Particle Learning of Gaussian Processes
Sequential Monte Carlo (SMC) inference for fully Bayesian Gaussian process (GP) regression and classification models by particle learning (PL) following Gramacy & Polson (2011) <arXiv:0909.5262>. The sequential nature of inference and the active learning (AL) hooks provided facilitate thrifty sequential design (by entropy) and optimization (by improvement) for classification and regression models, respectively. This package essentially provides a generic PL interface, and functions (arguments to the interface) which implement the GP models and AL heuristics. Functions for a special, linked, regression/classification GP model and an integrated expected conditional improvement (IECI) statistic provide for optimization in the presence of unknown constraints. Separable and isotropic Gaussian, and single-index correlation functions are supported. See the examples section of ?plgp and demo(package="plgp") for an index of demos.
Maintained by Robert B. Gramacy. Last updated 2 years ago.
2.3 match 1 stars 2.96 score 102 scripts 3 dependentstdhock
inlinedocs:Convert Inline Comments to Documentation
Generates Rd files from R source code with comments. The main features of the default syntax are that (1) docs are defined in comments near the relevant code, (2) function argument names are not repeated in comments, and (3) examples are defined in R code, not comments. It is also easy to define a new syntax.
Maintained by Toby Dylan Hocking. Last updated 1 years ago.
2.0 match 2 stars 3.14 score 47 scripts
uribo
sudachir:R Interface to 'Sudachi'
Interface to 'Sudachi' <https://github.com/WorksApplications/sudachi.rs>, a Japanese morphological analyzer. This is a port of what is available in Python.
Maintained by Shinya Uryu. Last updated 2 years ago.
1.8 match 6 stars 3.48 score 6 scripts
fanhansen
creditmodel:Toolkit for Credit Modeling, Analysis and Visualization
Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization.Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster. The references including: 1 Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard: Development and Implementation Using SAS; 2 Bezdek, James C.FCM: The fuzzy c-means clustering algorithm. Computers & Geosciences (0098-3004),<DOI:10.1016/0098-3004(84)90020-7>.
Maintained by Dongping Fan. Last updated 3 years ago.
1.8 match 4 stars 3.48 score 15 scripts
benwiseman
sentiment.ai:Simple Sentiment Analysis Using Deep Learning
Sentiment Analysis via deep learning and gradient boosting models with a lot of the underlying hassle taken care of to make the process as simple as possible. In addition to out-performing traditional, lexicon-based sentiment analysis (see <https://benwiseman.github.io/sentiment.ai/#Benchmarks>), it also allows the user to create embedding vectors for text which can be used in other analyses. GPU acceleration is supported on Windows and Linux.
Maintained by Ben Wiseman. Last updated 3 years ago.
2.3 match 2.70 score 7 scriptsbioc
annmap:Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl. The annmap database can be downloaded from: https://figshare.manchester.ac.uk/account/articles/16685071
Maintained by Chris Wirth. Last updated 5 months ago.
annotationmicroarrayonechannelreportwritingtranscriptionvisualization
2.0 match 3.00 score 2 scripts
obreschkow
nbody:Gravitational N-Body Simulation
Run simple direct gravitational N-body simulations. The package can access different external N-body simulators (e.g. GADGET-4 by Springel et al. (2021) <doi:10.48550/arXiv.2010.03567>), but also has a simple built-in simulator. This default simulator uses a variable block time step and lets the user choose between a range of integrators, including 4th and 6th order integrators for high-accuracy simulations. Basic top-hat smoothing is available as an option. The code also allows the definition of background particles that are fixed or in uniform motion, not subject to acceleration by other particles.
Maintained by Danail Obreschkow. Last updated 5 months ago.
2.3 match 2.48 score 1 scriptsrepboxr
repboxR:Repbox for R code files in code supplements
Repbox for R code files in code supplements
Maintained by Sebastian Kranz. Last updated 1 years ago.
2.3 match 2.48 score 2 dependentsbioc
ExiMiR:R functions for the normalization of Exiqon miRNA array data
This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.
Maintained by Sylvain Gubian. Last updated 5 months ago.
microarrayonechanneltwochannelpreprocessinggeneexpressiontranscription
2.0 match 2.78 score 3 scripts
the-mad-statter
wubik:Helpful R Functions for Databricks at WashU
This package provides helpful functions for using R on Databricks at WashU.
Maintained by Matthew Schuelke. Last updated 9 months ago.
3.0 match 1.70 score 1 scriptsrepboxr
repboxRfun:Repbox functions called by code injections into R scripts
Try to use as little special dependencies as reasonably possible
Maintained by Sebastian Kranz. Last updated 1 years ago.
2.0 match 2.18 score 1 dependents
piotrekjanus
aiRly:R Wrapper for 'Airly' API
Get information about air quality using 'Airly' <https://airly.eu/> API through R.
Maintained by Piotr Janus. Last updated 5 years ago.
1.6 match 2.70 score 2 scripts
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
1.7 match 2.28 score 38 scripts
andrewcparnell
simmr:A Stable Isotope Mixing Model
Fits Stable Isotope Mixing Models (SIMMs) and is meant as a longer term replacement to the previous widely-used package SIAR. SIMMs are used to infer dietary proportions of organisms consuming various food sources from observations on the stable isotope values taken from the organisms' tissue samples. However SIMMs can also be used in other scenarios, such as in sediment mixing or the composition of fatty acids. The main functions are simmr_load() and simmr_mcmc(). The two vignettes contain a quick start and a full listing of all the features. The methods used are detailed in the papers Parnell et al 2010 <doi:10.1371/journal.pone.0009672>, and Parnell et al 2013 <doi:10.1002/env.2221>.
Maintained by Emma Govan. Last updated 11 months ago.
0.5 match 31 stars 7.58 score 81 scripts
ecohealthalliance
ehallm:What the Package Does (Title Case)
More about what it does (maybe more than one line) Use four spaces when indenting paragraphs within the Description.
Maintained by The package maintainer. Last updated 4 months ago.
1.6 match 1 stars 2.18 score
cran
bio.infer:Predict Environmental Conditions from Biological Observations
Imports benthic count data, reformats this data, and computes environmental inferences from this data.
Maintained by Lester L. Yuan. Last updated 5 years ago.
2.3 match 1.38 score 24 scripts
ddemateis
dlim:Distributed Lag Interaction Model
Collection of functions for fitting and interpreting distributed lag interaction models (DLIM). A DLIM regresses a scalar outcome on repeated measures of exposure and allows for modification by a continuous variable. Includes a dlim() function for fitting, predict() function for inference, and plotting functions for visualization. Details on methodology are described in Demateis et al. (2024) <doi:10.1002/env.2843>.
Maintained by Danielle Demateis. Last updated 10 months ago.
0.5 match 4 stars 5.20 score 7 scripts
psolymos
detect:Analyzing Wildlife Data with Detection Error
Models for analyzing site occupancy and count data models with detection error, including single-visit based models (Lele et al. 2012 <doi:10.1093/jpe/rtr042>, Moreno et al. 2010 <doi:10.1890/09-1073.1>, Solymos et al. 2012 <doi:10.1002/env.1149>, Denes et al. 2016 <doi:10.1111/1365-2664.12818>), conditional distance sampling and time-removal models (Solymos et al. 2013 <doi:10.1111/2041-210X.12106>, Solymos et al. 2018 <doi:10.1650/CONDOR-18-32.1>). Package development was supported by the Alberta Biodiversity Monitoring Institute and the Boreal Avian Modelling Project.
Maintained by Peter Solymos. Last updated 10 months ago.
0.5 match 5 stars 5.27 score 123 scripts
lidiamandre
ReturnCurves:Estimation of Return Curves
Estimates the p-probability return curve proposed by Murphy-Barltrop et al. (2023) <doi:10.1002/env.2797>. Implements pointwise and smooth estimation of the angular dependence function introduced by Wadsworth and Tawn (2013) <doi:10.3150/12-BEJ471>.
Maintained by Lídia André. Last updated 1 months ago.
0.5 match 1 stars 5.06 score 19 scripts
freguglia
mrf2d:Markov Random Field Models for Image Analysis
Model fitting, sampling and visualization for the (Hidden) Markov Random Field model with pairwise interactions and general interaction structure from Freguglia, Garcia & Bicas (2020) <doi:10.1002/env.2613>, which has many popular models used in 2-dimensional lattices as particular cases, like the Ising Model and Potts Model. A complete manuscript describing the package is available in Freguglia & Garcia (2022) <doi:10.18637/jss.v101.i08>.
Maintained by Victor Freguglia. Last updated 2 years ago.
gibbs-energyhidden-markov-modelhidden-markov-modelsmarkov-random-fieldmrfmrf-modelsneighborhoodcpp
0.5 match 9 stars 4.95 score 10 scripts
paulnorthrop
lite:Likelihood-Based Inference for Time Series Extremes
Performs likelihood-based inference for stationary time series extremes. The general approach follows Fawcett and Walshaw (2012) <doi:10.1002/env.2133>. Marginal extreme value inferences are adjusted for cluster dependence in the data using the methodology in Chandler and Bate (2007) <doi:10.1093/biomet/asm015>, producing an adjusted log-likelihood for the model parameters. A log-likelihood for the extremal index is produced using the K-gaps model of Suveges and Davison (2010) <doi:10.1214/09-AOAS292>. These log-likelihoods are combined to make inferences about extreme values. Both maximum likelihood and Bayesian approaches are available.
Maintained by Paul J. Northrop. Last updated 8 months ago.
clusteredextremal-indexextreme-value-statisticsextremesfrequentistgeneralised-paretoinferencelikelihoodlog-likelihoodthresholdtime-series
0.5 match 3 stars 4.56 score 12 scripts
heplersa
multiocc:Fits Multivariate Spatio-Temporal Occupancy Model
Spatio-temporal multivariate occupancy models can handle multiple species in occupancy models. This method for fitting such models is described in Hepler and Erhardt (2021) "A spatiotemporal model for multivariate occupancy data" <https://onlinelibrary.wiley.com/doi/abs/10.1002/env.2657>.
Maintained by Staci Hepler. Last updated 2 years ago.
0.5 match 3.70 score 4 scripts
chabert-liddell
robber:Using Block Model to Estimate the Robustness of Ecological Network
Implementation of a variety of methods to compute the robustness of ecological interaction networks with binary interactions as described in <doi:10.1002/env.2709>. In particular, using the Stochastic Block Model and its bipartite counterpart, the Latent Block Model to put a parametric model on the network, allows the comparison of the robustness of networks differing in species richness and number of interactions. It also deals with networks that are partially sampled and/or with missing values.
Maintained by Saint-Clair Chabert-Liddell. Last updated 1 years ago.
ecological-networkrobberrobustness
0.5 match 1 stars 3.70 score 4 scripts
singator
autoharp:Semi-Automatic Grading of R and Rmd Scripts
A customisable set of tools for assessing and grading R or R-markdown scripts from students. It allows for checking correctness of code output, runtime statistics and static code analysis. The latter feature is made possible by representing R expressions using a tree structure.
Maintained by Vik Gopal. Last updated 3 years ago.
1.8 match 1 stars 1.00 score 8 scripts
envisim
BalancedSampling:Balanced and Spatially Balanced Sampling
Select balanced and spatially balanced probability samples in multi-dimensional spaces with any prescribed inclusion probabilities. It contains fast (C++ via Rcpp) implementations of the included sampling methods. The local pivotal method by Grafström, Lundström and Schelin (2012) <doi:10.1111/j.1541-0420.2011.01699.x> and spatially correlated Poisson sampling by Grafström (2012) <doi:10.1016/j.jspi.2011.07.003> are included. Also the cube method (for balanced sampling) and the local cube method (for doubly balanced sampling) are included, see Grafström and Tillé (2013) <doi:10.1002/env.2194>.
Maintained by Anton Grafström. Last updated 4 months ago.
0.5 match 1 stars 3.52 score 53 scripts 1 dependents
egpivo
SpatMCA:Regularized Spatial Maximum Covariance Analysis
Provide regularized maximum covariance analysis incorporating smoothness, sparseness and orthogonality of couple patterns by using the alternating direction method of multipliers algorithm. The method can be applied to either regularly or irregularly spaced data, including 1D, 2D, and 3D (Wang and Huang, 2018 <doi:10.1002/env.2481>).
Maintained by Wen-Ting Wang. Last updated 7 months ago.
admmccacross-covariancelassomatrix-factorizationrcpparmadillorcppparallelsplinesopenblascppopenmp
0.5 match 5 stars 3.40 score 4 scripts
jmhewitt
telefit:Estimation and Prediction for Remote Effects Spatial Process Models
Implementation of the remote effects spatial process (RESP) model for teleconnection. The RESP model is a geostatistical model that allows a spatially-referenced variable (like average precipitation) to be influenced by covariates defined on a remote domain (like sea surface temperatures). The RESP model is introduced in Hewitt et al. (2018) <doi:10.1002/env.2523>. Sample code for working with the RESP model is available at <https://jmhewitt.github.io/research/resp_example>. This material is based upon work supported by the National Science Foundation under grant number AGS 1419558. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.
Maintained by Joshua Hewitt. Last updated 5 years ago.
0.5 match 1 stars 3.19 score 31 scriptslmrodriguezr
Nonpareil:Metagenome Coverage Estimation and Projections for 'Nonpareil'
Plot, process, and analyze NPO files produced by 'Nonpareil' <http://enve-omics.ce.gatech.edu/nonpareil/>.
Maintained by Luis M. Rodriguez-R. Last updated 9 months ago.
0.5 match 2.56 score 36 scripts
angieshen6
BayesPPD:Bayesian Power Prior Design
Bayesian power/type I error calculation and model fitting using the power prior and the normalized power prior for generalized linear models. Detailed examples of applying the package are available at <doi:10.32614/RJ-2023-016>. Models for time-to-event outcomes are implemented in the R package 'BayesPPDSurv'. The Bayesian clinical trial design methodology is described in Chen et al. (2011) <doi:10.1111/j.1541-0420.2011.01561.x>, and Psioda and Ibrahim (2019) <doi:10.1093/biostatistics/kxy009>. The normalized power prior is described in Duan et al. (2006) <doi:10.1002/env.752> and Ibrahim et al. (2015) <doi:10.1002/sim.6728>.
Maintained by Yueqi Shen. Last updated 2 months ago.
0.5 match 2.48 score 7 scripts 1 dependents
hanzifei
NPP:Normalized Power Prior Bayesian Analysis
Posterior sampling in several commonly used distributions using normalized power prior as described in Duan, Ye and Smith (2006) <doi:10.1002/env.752> and Ibrahim et.al. (2015) <doi:10.1002/sim.6728>. Sampling of the power parameter is achieved via either independence Metropolis-Hastings or random walk Metropolis-Hastings based on transformation.
Maintained by Zifei Han. Last updated 1 years ago.
0.5 match 1.48 score 1 scriptscran
clespr:Composite Likelihood Estimation for Spatial Data
Composite likelihood approach is implemented to estimating statistical models for spatial ordinal and proportional data based on Feng et al. (2014) <doi:10.1002/env.2306>. Parameter estimates are identified by maximizing composite log-likelihood functions using the limited memory BFGS optimization algorithm with bounding constraints, while standard errors are obtained by estimating the Godambe information matrix.
Maintained by Ting Fung (Ralph) Ma. Last updated 7 years ago.
0.5 match 1.00 score