Showing 31 of total 31 results (show query)
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 2 days ago.
geospatialrasterspatialvectoronetbbprojgdalgeoscpp
559 stars 17.64 score 17k scripts 855 dependentsrspatial
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 This package has been superseded by the "terra" package 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 14 hours ago.
163 stars 17.23 score 58k scripts 562 dependents
bioc
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 Hervรฉ Pagรจs. Last updated 2 months ago.
infrastructuredatarepresentationbioconductor-packagecore-package
18 stars 16.05 score 1.0k scripts 1.9k dependents
mhahsler
arules:Mining Association Rules and Frequent Itemsets
Provides the infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). Also provides C implementations of the association mining algorithms Apriori and Eclat. Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.
Maintained by Michael Hahsler. Last updated 2 months ago.
arulesassociation-rulesfrequent-itemsets
194 stars 13.99 score 3.3k scripts 28 dependents
data-cleaning
validate:Data Validation Infrastructure
Declare data validation rules and data quality indicators; confront data with them and analyze or visualize the results. The package supports rules that are per-field, in-record, cross-record or cross-dataset. Rules can be automatically analyzed for rule type and connectivity. Supports checks implied by an SDMX DSD file as well. See also Van der Loo and De Jonge (2018) <doi:10.1002/9781118897126>, Chapter 6 and the JSS paper (2021) <doi:10.18637/jss.v097.i10>.
Maintained by Mark van der Loo. Last updated 24 days ago.
419 stars 12.39 score 448 scripts 8 dependents
bioc
Cardinal:A mass spectrometry imaging toolbox for statistical analysis
Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.
Maintained by Kylie Ariel Bemis. Last updated 3 months ago.
softwareinfrastructureproteomicslipidomicsmassspectrometryimagingmassspectrometryimmunooncologynormalizationclusteringclassificationregression
48 stars 10.32 score 200 scriptsbioc
SpatialFeatureExperiment:Integrating SpatialExperiment with Simple Features in sf
A new S4 class integrating Simple Features with the R package sf to bring geospatial data analysis methods based on vector data to spatial transcriptomics. Also implements management of spatial neighborhood graphs and geometric operations. This pakage builds upon SpatialExperiment and SingleCellExperiment, hence methods for these parent classes can still be used.
Maintained by Lambda Moses. Last updated 2 months ago.
datarepresentationtranscriptomicsspatial
49 stars 9.40 score 322 scripts 1 dependents
pecanproject
PEcAnAssimSequential: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 Mike Dietze. Last updated 2 days ago.
bayesiancyberinfrastructuredata-assimilationdata-scienceecosystem-modelecosystem-scienceforecastingmeta-analysisnational-science-foundationpecanplantsjagscpp
216 stars 8.12 score 35 scripts
r-hyperspec
hyperSpec:Work with Hyperspectral Data, i.e. Spectra + Meta Information (Spatial, Time, Concentration, ...)
Comfortable ways to work with hyperspectral data sets, i.e. spatially or time-resolved spectra, or spectra with any other kind of information associated with each of the spectra. The spectra can be data as obtained in XRF, UV/VIS, Fluorescence, AES, NIR, IR, Raman, NMR, MS, etc. More generally, any data that is recorded over a discretized variable, e.g. absorbance = f(wavelength), stored as a vector of absorbance values for discrete wavelengths is suitable.
Maintained by Claudia Beleites. Last updated 10 months ago.
data-wranglinghyperspectralimaginginfrarednmrramanspectroscopyuv-visxrf
16 stars 8.10 score 233 scripts 2 dependents
polmine
polmineR:Verbs and Nouns for Corpus Analysis
Package for corpus analysis using the Corpus Workbench ('CWB', <https://cwb.sourceforge.io>) as an efficient back end for indexing and querying large corpora. The package offers functionality to flexibly create subcorpora and to carry out basic statistical operations (count, co-occurrences etc.). The original full text of documents can be reconstructed and inspected at any time. Beyond that, the package is intended to serve as an interface to packages implementing advanced statistical procedures. Respective data structures (document-term matrices, term-co-occurrence matrices etc.) can be created based on the indexed corpora.
Maintained by Andreas Blaette. Last updated 1 years ago.
49 stars 7.96 score 311 scripts
cran
timeSeries:Financial Time Series Objects (Rmetrics)
'S4' classes and various tools for financial time series: Basic functions such as scaling and sorting, subsetting, mathematical operations and statistical functions.
Maintained by Georgi N. Boshnakov. Last updated 6 months ago.
2 stars 7.89 score 146 dependents
adamlilith
fasterRaster:Faster Raster and Spatial Vector Processing Using 'GRASS GIS'
Processing of large-in-memory/large-on disk rasters and spatial vectors using 'GRASS GIS' <https://grass.osgeo.org/>. Most functions in the 'terra' package are recreated. Processing of medium-sized and smaller spatial objects will nearly always be faster using 'terra' or 'sf', but for large-in-memory/large-on-disk objects, 'fasterRaster' may be faster. To use most of the functions, you must have the stand-alone version (not the 'OSGeoW4' installer version) of 'GRASS GIS' 8.0 or higher.
Maintained by Adam B. Smith. Last updated 2 days ago.
aspectdistancefragmentationfragmentation-indicesgisgrassgrass-gisrasterraster-projectionrasterizeslopetopographyvectorization
57 stars 7.68 score 8 scripts
poissonconsulting
nlist:Lists of Numeric Atomic Objects
Create and manipulate numeric list ('nlist') objects. An 'nlist' is an S3 list of uniquely named numeric objects. An numeric object is an integer or double vector, matrix or array. An 'nlists' object is a S3 class list of 'nlist' objects with the same names, dimensionalities and typeofs. Numeric list objects are of interest because they are the raw data inputs for analytic engines such as 'JAGS', 'STAN' and 'TMB'. Numeric lists objects, which are useful for storing multiple realizations of of simulated data sets, can be converted to coda::mcmc and coda::mcmc.list objects.
Maintained by Joe Thorley. Last updated 2 months ago.
6 stars 7.23 score 13 scripts 12 dependents
cytomining
cytominer:Methods for Image-Based Cell Profiling
`cytominer` is a suite of common functions used to process high-dimensional readouts from image-based cell profiling experiments.
Maintained by Shantanu Singh. Last updated 2 years ago.
50 stars 6.89 score 44 scriptsbioc
CoreGx:Classes and Functions to Serve as the Basis for Other 'Gx' Packages
A collection of functions and classes which serve as the foundation for our lab's suite of R packages, such as 'PharmacoGx' and 'RadioGx'. This package was created to abstract shared functionality from other lab package releases to increase ease of maintainability and reduce code repetition in current and future 'Gx' suite programs. Major features include a 'CoreSet' class, from which 'RadioSet' and 'PharmacoSet' are derived, along with get and set methods for each respective slot. Additional functions related to fitting and plotting dose response curves, quantifying statistical correlation and calculating area under the curve (AUC) or survival fraction (SF) are included. For more details please see the included documentation, as well as: Smirnov, P., Safikhani, Z., El-Hachem, N., Wang, D., She, A., Olsen, C., Freeman, M., Selby, H., Gendoo, D., Grossman, P., Beck, A., Aerts, H., Lupien, M., Goldenberg, A. (2015) <doi:10.1093/bioinformatics/btv723>. Manem, V., Labie, M., Smirnov, P., Kofia, V., Freeman, M., Koritzinksy, M., Abazeed, M., Haibe-Kains, B., Bratman, S. (2018) <doi:10.1101/449793>.
Maintained by Benjamin Haibe-Kains. Last updated 5 months ago.
softwarepharmacogenomicsclassificationsurvival
6.53 score 63 scripts 6 dependents
victor-navarro
calmr:Canonical Associative Learning Models and their Representations
Implementations of canonical associative learning models, with tools to run experiment simulations, estimate model parameters, and compare model representations. Experiments and results are represented using S4 classes and methods.
Maintained by Victor Navarro. Last updated 10 months ago.
3 stars 6.40 score 17 scriptsbioc
RNAmodR:Detection of post-transcriptional modifications in high throughput sequencing data
RNAmodR provides classes and workflows for loading/aggregation data from high througput sequencing aimed at detecting post-transcriptional modifications through analysis of specific patterns. In addition, utilities are provided to validate and visualize the results. The RNAmodR package provides a core functionality from which specific analysis strategies can be easily implemented as a seperate package.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
softwareinfrastructureworkflowstepvisualizationsequencingalkanilineseqbioconductormodificationsribomethseqrnarnamodr
3 stars 6.39 score 9 scripts 3 dependentsbioc
HiContacts:Analysing cool files in R with HiContacts
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
Maintained by Jacques Serizay. Last updated 10 days ago.
12 stars 6.07 score 49 scriptsbioc
tidyCoverage:Extract and aggregate genomic coverage over features of interest
`tidyCoverage` framework enables tidy manipulation of collections of genomic tracks and features using `tidySummarizedExperiment` methods. It facilitates the extraction, aggregation and visualization of genomic coverage over individual or thousands of genomic loci, relying on `CoverageExperiment` and `AggregatedCoverage` classes. This accelerates the integration of genomic track data in genomic analysis workflows.
Maintained by Jacques Serizay. Last updated 5 months ago.
21 stars 5.80 score 6 scripts
rjdverse
rjd3toolkit:Utility Functions around 'JDemetra+ 3.0'
R Interface to 'JDemetra+ 3.x' (<https://github.com/jdemetra>) time series analysis software. It provides functions allowing to model time series (create outlier regressors, user-defined calendar regressors, UCARIMA models...), to test the presence of trading days or seasonal effects and also to set specifications in pre-adjustment and benchmarking when using rjd3x13 or rjd3tramoseats.
Maintained by Tanguy Barthelemy. Last updated 5 months ago.
javajdemetraseasonal-adjustmenttime-seriestimeseriesopenjdk
6 stars 5.74 score 48 scripts 16 dependents
tesselle
nexus:Sourcing Archaeological Materials by Chemical Composition
Exploration and analysis of compositional data in the framework of Aitchison (1986, ISBN: 978-94-010-8324-9). This package provides tools for chemical fingerprinting and source tracking of ancient materials.
Maintained by Nicolas Frerebeau. Last updated 24 days ago.
archaeologyarchaeological-sciencearchaeometrycompositional-dataprovenance-studies
5.21 score 26 scripts 1 dependentsbioc
topdownr:Investigation of Fragmentation Conditions in Top-Down Proteomics
The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.
Maintained by Sebastian Gibb. Last updated 5 months ago.
immunooncologyinfrastructureproteomicsmassspectrometrycoveragemass-spectrometrytopdown
1 stars 5.08 score
mrc-ide
gonovax:Deterministic Compartmental Model of Gonorrhoea with Vaccination
Model for gonorrhoea vaccination, using odin.
Maintained by Lilith Whittles. Last updated 14 days ago.
3 stars 4.56 score
eurostat
hicp:Harmonised Index of Consumer Prices
The Harmonised Index of Consumer Prices (HICP) is the key economic figure to measure inflation in the euro area. The methodology underlying the HICP is documented in the HICP Methodological Manual (<https://ec.europa.eu/eurostat/web/products-manuals-and-guidelines/w/ks-gq-24-003>). Based on the manual, this package provides functions to access and work with HICP data from Eurostat's public database (<https://ec.europa.eu/eurostat/data/database>).
Maintained by Sebastian Weinand. Last updated 8 months ago.
consumer-price-indexinflationpricesstatistics
2 stars 4.48 score 6 scriptsbioc
RNAmodR.ML:Detecting patterns of post-transcriptional modifications using machine learning
RNAmodR.ML extend the functionality of the RNAmodR package and classical detection strategies towards detection through machine learning models. RNAmodR.ML provides classes, functions and an example workflow to establish a detection stratedy, which can be packaged.
Maintained by Felix G.M. Ernst. Last updated 5 months ago.
softwareinfrastructureworkflowstepvisualizationsequencing
1 stars 4.00 score 3 scripts
spkaluzny
splusTimeSeries:Time Series from 'S-PLUS'
A collection of classes and methods for working with indexed rectangular data. The index values can be calendar (timeSeries class) or numeric (signalSeries class). Methods are included for aggregation, alignment, merging, and summaries. The code was originally available in 'S-PLUS'.
Maintained by Stephen Kaluzny. Last updated 6 months ago.
3.95 score 20 scripts 1 dependents
aalfons
simFrame:Simulation Framework
A general framework for statistical simulation, which allows researchers to make use of a wide range of simulation designs with minimal programming effort. The package provides functionality for drawing samples from a distribution or a finite population, for adding outliers and missing values, as well as for visualization of the simulation results. It follows a clear object-oriented design and supports parallel computing to increase computational performance.
Maintained by Andreas Alfons. Last updated 3 years ago.
2 stars 3.90 score 80 scripts
lawremi
rsolr:R to Solr Interface
A comprehensive R API for querying Apache Solr databases. A Solr core is represented as a data frame or list that supports Solr-side filtering, sorting, transformation and aggregation, all through the familiar base R API. Queries are processed lazily, i.e., a query is only sent to the database when the data are required.
Maintained by Michael Lawrence. Last updated 3 years ago.
9 stars 3.65 score 6 scripts
adamkocsis
via:Virtual Arrays
The base class 'VirtualArray' is defined, which acts as a wrapper around lists allowing users to fold arbitrary sequential data into n-dimensional, R-style virtual arrays. The derived 'XArray' class is defined to be used for homogeneous lists that contain a single class of objects. The 'RasterArray' and 'SfArray' classes enable the use of stacked spatial data instead of lists.
Maintained by Adam T. Kocsis. Last updated 2 years ago.
3 stars 3.18 score 8 scripts
cb12991
expstudy:Tools for Actuarial Experience Studies
Experiences studies are an integral component of the actuarial control cycle. Regardless of the decrement or policyholder behavior of interest, the analyses conducted is often the same. Ultimately, this package aims to reduce time spent writing the same code used for different experience studies, therefore increasing the time for to uncover new insights inherit within the relevant experience.
Maintained by Cody Buehler. Last updated 9 months ago.
1 stars 2.70 score 7 scripts