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quanteda

quanteda:Quantitative Analysis of Textual Data

A fast, flexible, and comprehensive framework for quantitative text analysis in R. Provides functionality for corpus management, creating and manipulating tokens and n-grams, exploring keywords in context, forming and manipulating sparse matrices of documents by features and feature co-occurrences, analyzing keywords, computing feature similarities and distances, applying content dictionaries, applying supervised and unsupervised machine learning, visually representing text and text analyses, and more.

Maintained by Kenneth Benoit. Last updated 3 months ago.

corpusnatural-language-processingquantedatext-analyticsonetbbcpp

851 stars 16.65 score 5.4k scripts 52 dependents

r-forge

zoo:S3 Infrastructure for Regular and Irregular Time Series (Z's Ordered Observations)

An S3 class with methods for totally ordered indexed observations. It is particularly aimed at irregular time series of numeric vectors/matrices and factors. zoo's key design goals are independence of a particular index/date/time class and consistency with ts and base R by providing methods to extend standard generics.

Maintained by Achim Zeileis. Last updated 26 days ago.

16.23 score 33k scripts 2.2k dependents

bioc

Rsamtools:Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.

Maintained by Bioconductor Package Maintainer. Last updated 4 months ago.

dataimportsequencingcoveragealignmentqualitycontrolbioconductor-packagecore-packagecurlbzip2xz-utilszlibcpp

28 stars 15.34 score 3.2k scripts 569 dependents

tidyverts

tsibble:Tidy Temporal Data Frames and Tools

Provides a 'tbl_ts' class (the 'tsibble') for temporal data in an data- and model-oriented format. The 'tsibble' provides tools to easily manipulate and analyse temporal data, such as filling in time gaps and aggregating over calendar periods.

Maintained by Earo Wang. Last updated 2 months ago.

538 stars 14.47 score 4.4k scripts 42 dependents

r-lidar

lidR:Airborne LiDAR Data Manipulation and Visualization for Forestry Applications

Airborne LiDAR (Light Detection and Ranging) interface for data manipulation and visualization. Read/write 'las' and 'laz' files, computation of metrics in area based approach, point filtering, artificial point reduction, classification from geographic data, normalization, individual tree segmentation and other manipulations.

Maintained by Jean-Romain Roussel. Last updated 2 months ago.

alsforestrylaslazlidarpoint-cloudremote-sensingopenblascppopenmp

623 stars 14.47 score 844 scripts 8 dependents

bioc

xcms:LC-MS and GC-MS Data Analysis

Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.

Maintained by Steffen Neumann. Last updated 15 days ago.

immunooncologymassspectrometrymetabolomicsbioconductorfeature-detectionmass-spectrometrypeak-detectioncpp

196 stars 14.31 score 984 scripts 11 dependents

edzer

spacetime:Classes and Methods for Spatio-Temporal Data

Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.

Maintained by Edzer Pebesma. Last updated 2 months ago.

74 stars 13.29 score 628 scripts 72 dependents

kkholst

lava:Latent Variable Models

A general implementation of Structural Equation Models with latent variables (MLE, 2SLS, and composite likelihood estimators) with both continuous, censored, and ordinal outcomes (Holst and Budtz-Joergensen (2013) <doi:10.1007/s00180-012-0344-y>). Mixture latent variable models and non-linear latent variable models (Holst and Budtz-Joergensen (2020) <doi:10.1093/biostatistics/kxy082>). The package also provides methods for graph exploration (d-separation, back-door criterion), simulation of general non-linear latent variable models, and estimation of influence functions for a broad range of statistical models.

Maintained by Klaus K. Holst. Last updated 3 months ago.

latent-variable-modelssimulationstatisticsstructural-equation-models

33 stars 12.87 score 610 scripts 478 dependents

ycroissant

plm:Linear Models for Panel Data

A set of estimators for models and (robust) covariance matrices, and tests for panel data econometrics, including within/fixed effects, random effects, between, first-difference, nested random effects as well as instrumental-variable (IV) and Hausman-Taylor-style models, panel generalized method of moments (GMM) and general FGLS models, mean groups (MG), demeaned MG, and common correlated effects (CCEMG) and pooled (CCEP) estimators with common factors, variable coefficients and limited dependent variables models. Test functions include model specification, serial correlation, cross-sectional dependence, panel unit root and panel Granger (non-)causality. Typical references are general econometrics text books such as Baltagi (2021), Econometric Analysis of Panel Data (<doi:10.1007/978-3-030-53953-5>), Hsiao (2014), Analysis of Panel Data (<doi:10.1017/CBO9781139839327>), and Croissant and Millo (2018), Panel Data Econometrics with R (<doi:10.1002/9781119504641>).

Maintained by Kevin Tappe. Last updated 13 days ago.

59 stars 12.06 score 39 dependents

crunch-io

crunch:Crunch.io Data Tools

The Crunch.io service <https://crunch.io/> provides a cloud-based data store and analytic engine, as well as an intuitive web interface. Using this package, analysts can interact with and manipulate Crunch datasets from within R. Importantly, this allows technical researchers to collaborate naturally with team members, managers, and clients who prefer a point-and-click interface.

Maintained by Greg Freedman Ellis. Last updated 7 days ago.

9 stars 10.47 score 200 scripts 2 dependents

ropensci

jqr:Client for 'jq', a 'JSON' Processor

Client for 'jq', a 'JSON' processor (<https://jqlang.github.io/jq/>), written in C. 'jq' allows the following with 'JSON' data: index into, parse, do calculations, cut up and filter, change key names and values, perform conditionals and comparisons, and more.

Maintained by Jeroen Ooms. Last updated 3 months ago.

jqjson

144 stars 10.04 score 95 scripts 28 dependents

huizezhang-sherry

cubble:A Vector Spatio-Temporal Data Structure for Data Analysis

A spatiotemperal data object in a relational data structure to separate the recording of time variant/ invariant variables. See the Journal of Statistical Software reference: <doi:10.18637/jss.v110.i07>.

Maintained by H. Sherry Zhang. Last updated 6 months ago.

57 stars 9.07 score 83 scripts

eguidotti

calculus:High Dimensional Numerical and Symbolic Calculus

Efficient C++ optimized functions for numerical and symbolic calculus as described in Guidotti (2022) <doi:10.18637/jss.v104.i05>. It includes basic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, high-order derivatives, ordinary differential equations, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.

Maintained by Emanuele Guidotti. Last updated 2 years ago.

calculuscoordinate-systemscurldivergenceeinsteinfinite-differencegradienthermitehessianjacobianlaplaciannumerical-derivationnumerical-derivativesnumerical-differentiationsymbolic-computationsymbolic-differentiationtaylorcpp

47 stars 8.98 score 66 scripts 7 dependents

flr

FLCore:Core Package of FLR, Fisheries Modelling in R

Core classes and methods for FLR, a framework for fisheries modelling and management strategy simulation in R. Developed by a team of fisheries scientists in various countries. More information can be found at <http://flr-project.org/>.

Maintained by Iago Mosqueira. Last updated 9 days ago.

fisheriesflrfisheries-modelling

16 stars 8.78 score 956 scripts 23 dependents

atorus-research

pharmaRTF:Enhanced RTF Wrapper for Use with Existing Table Packages

Enhanced RTF wrapper written in R for use with existing R tables packages such as 'Huxtable' or 'GT'. This package fills a gap where tables in certain packages can be written out to RTF, but cannot add certain metadata or features to the document that are required/expected in a report for a regulatory submission, such as multiple levels of titles and footnotes, making the document landscape, and controlling properties such as margins.

Maintained by Michael Stackhouse. Last updated 4 years ago.

34 stars 8.02 score 128 scripts 2 dependents

shikokuchuo

ichimoku:Visualization and Tools for Ichimoku Kinko Hyo Strategies

An implementation of 'Ichimoku Kinko Hyo', also commonly known as 'cloud charts'. Static and interactive visualizations with tools for creating, backtesting and development of quantitative 'ichimoku' strategies. As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement on candlestick charting, originating from Japan and now in widespread use in technical analysis worldwide. Translating as 'one-glance equilibrium chart', it allows the price action and market structure of financial securities to be determined 'at-a-glance'. Incorporates an interface with the OANDA fxTrade API <https://developer.oanda.com/> for retrieving historical and live streaming price data for major currencies, metals, commodities, government bonds and stock indices.

Maintained by Charlie Gao. Last updated 14 days ago.

ichimokuichimoku-cloudoandaquantitative-finance

31 stars 7.73 score 34 scripts

snstatcomp

rtrim:Trends and Indices for Monitoring Data

The TRIM model is widely used for estimating growth and decline of animal populations based on (possibly sparsely available) count data. The current package is a reimplementation of the original TRIM software developed at Statistics Netherlands by Jeroen Pannekoek. See <https://www.cbs.nl/en-gb/society/nature-and-environment/indices-and-trends%2d%2dtrim%2d%2d> for more information about TRIM.

Maintained by Patrick Bogaart. Last updated 24 days ago.

10 stars 7.33 score 60 scripts 1 dependents

kvasilopoulos

exuber:Econometric Analysis of Explosive Time Series

Testing for and dating periods of explosive dynamics (exuberance) in time series using the univariate and panel recursive unit root tests proposed by Phillips et al. (2015) <doi:10.1111/iere.12132> and Pavlidis et al. (2016) <doi:10.1007/s11146-015-9531-2>.The recursive least-squares algorithm utilizes the matrix inversion lemma to avoid matrix inversion which results in significant speed improvements. Simulation of a variety of periodically-collapsing bubble processes. Details can be found in Vasilopoulos et al. (2022) <doi:10.18637/jss.v103.i10>.

Maintained by Kostas Vasilopoulos. Last updated 1 years ago.

dickey-fullerexplosive-dynamicssimulationtime-seriesopenblascpp

29 stars 6.83 score 77 scripts

robinhankin

spray:Sparse Arrays and Multivariate Polynomials

Sparse arrays interpreted as multivariate polynomials. Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/ARXIV.2210.03856>). To cite the package in publications please use Hankin (2022) <doi:10.48550/ARXIV.2210.10848>.

Maintained by Robin K. S. Hankin. Last updated 2 months ago.

cpp

2 stars 6.62 score 35 scripts 4 dependents

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 4 days ago.

6.57 score 138 scripts 18 dependents

ropensci

coder:Deterministic Categorization of Items Based on External Code Data

Fast categorization of items based on external code data identified by regular expressions. A typical use case considers patient with medically coded data, such as codes from the International Classification of Diseases ('ICD') or the Anatomic Therapeutic Chemical ('ATC') classification system. Functions of the package relies on a triad of objects: (1) case data with unit id:s and possible dates of interest; (2) external code data for corresponding units in (1) and with optional dates of interest and; (3) a classification scheme ('classcodes' object) with regular expressions to identify and categorize relevant codes from (2). It is easy to introduce new classification schemes ('classcodes' objects) or to use default schemes included in the package. Use cases includes patient categorization based on 'comorbidity indices' such as 'Charlson', 'Elixhauser', 'RxRisk V', or the 'comorbidity-polypharmacy' score (CPS), as well as adverse events after hip and knee replacement surgery.

Maintained by Erik Bulow. Last updated 2 years ago.

classificationicd-10

22 stars 6.31 score 23 scripts

spgarbet

tangram:The Grammar of Tables

Provides an extensible formula system to quickly and easily create production quality tables. The processing steps are a formula parser, statistical content generation from data as defined by formula, followed by rendering into a table. Each step of the processing is separate and user definable thus creating a set of composable building blocks for highly customizable table generation. A user is not limited by any of the choices of the package creator other than the formula grammar. For example, one could chose to add a different S3 rendering function and output a format not provided in the default package, or possibly one would rather have Gini coefficients for their statistical content in a resulting table. Routines to achieve New England Journal of Medicine style, Lancet style and Hmisc::summaryM() statistics are provided. The package contains rendering for HTML5, Rmarkdown and an indexing format for use in tracing and tracking are provided.

Maintained by Shawn Garbett. Last updated 2 years ago.

68 stars 5.93 score 62 scripts

bergsmat

tablet:Tabulate Descriptive Statistics in Multiple Formats

Creates a table of descriptive statistics for factor and numeric columns in a data frame. Displays these by groups, if any. Highly customizable, with support for 'html' and 'pdf' provided by 'kableExtra'. Respects original column order, column labels, and factor level order. See ?tablet.data.frame and vignettes.

Maintained by Tim Bergsma. Last updated 5 months ago.

3 stars 5.57 score 26 scripts

beanumber

tidychangepoint:A Tidy Framework for Changepoint Detection Analysis

Changepoint detection algorithms for R are widespread but have different interfaces and reporting conventions. This makes the comparative analysis of results difficult. We solve this problem by providing a tidy, unified interface for several different changepoint detection algorithms. We also provide consistent numerical and graphical reporting leveraging the 'broom' and 'ggplot2' packages.

Maintained by Benjamin S. Baumer. Last updated 2 months ago.

2 stars 5.30 score 8 scripts

robinhankin

frab:How to Add Two R Tables

Methods to "add" two R tables; also an alternative interpretation of named vectors as generalized R tables, so that c(a=1,b=2,c=3) + c(b=3,a=-1) will return c(b=5,c=3). Uses 'disordR' discipline (Hankin, 2022, <doi:10.48550/arXiv.2210.03856>). Extraction and replacement methods are provided. The underlying mathematical structure is the Free Abelian group, hence the name. To cite in publications please use Hankin (2023) <doi:10.48550/arXiv.2307.13184>.

Maintained by Robin K. S. Hankin. Last updated 8 days ago.

cpp

1 stars 5.22 score 1 dependents

cfhammill

lenses:Elegant Data Manipulation with Lenses

Provides tools for creating and using lenses to simplify data manipulation. Lenses are composable getter/setter pairs for working with data in a purely functional way. Inspired by the 'Haskell' library 'lens' (Kmett, 2012) <https://hackage.haskell.org/package/lens>. For a fairly comprehensive (and highly technical) history of lenses please see the 'lens' wiki <https://github.com/ekmett/lens/wiki/History-of-Lenses>.

Maintained by Chris Hammill. Last updated 6 years ago.

functional-programming

27 stars 4.75 score 42 scripts

bioc

alabaster.files:Wrappers to Save Common File Formats

Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.

Maintained by Aaron Lun. Last updated 5 months ago.

datarepresentationdataimport

4.50 score 21 scripts

program--

hilbert:Coordinate Indexing on Hilbert Curves

Provides utilities for encoding and decoding coordinates to/from Hilbert curves based on the iterative encoding implementation described in Chen et al. (2006) <doi:10.1002/spe.793>.

Maintained by Justin Singh-Mohudpur. Last updated 3 years ago.

hilbert-curvespatialcpp

5 stars 4.40 score 5 scripts

bioc

ctsGE:Clustering of Time Series Gene Expression data

Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.

Maintained by Michal Sharabi-Schwager. Last updated 5 months ago.

immunooncologygeneexpressiontranscriptiondifferentialexpressiongenesetenrichmentgeneticsbayesianclusteringtimecoursesequencingrnaseq

1 stars 4.00 score 3 scripts

quantgen

LinkedMatrix:Column-Linked and Row-Linked Matrices

A class that links matrix-like objects (nodes) by rows or by columns while behaving similarly to a base R matrix. Very large matrices are supported if the nodes are file-backed matrices.

Maintained by Alexander Grueneberg. Last updated 5 years ago.

r-pkg

2 stars 3.92 score 14 scripts 2 dependents

oobianom

r2shortcode:Shorten Function Names of Functions in Another Package and Create an Index to Make Them Accessible

When creating a package, authors may sometimes struggle with coming up with easy and straightforward function names, and at the same time hoping that other packages do not already have the same function names. In trying to meet this goal, sometimes, function names are not descriptive enough and may confuse the potential users. The purpose of this package is to serve as a package function short form generator and also provide shorthand names for other functions. Having this package will entice authors to create long function names without the fear of users not wanting to use their packages because of the long names. In a way, everyone wins - the authors can use long descriptive function names, and the users can use this package to make short functions names while still using the package in question.

Maintained by Obinna Obianom. Last updated 12 months ago.

3.70 score

flr

AAP:Aarts and Poos Stock Assessment Model that Estimates Bycatch

FLR version of Aarts and Poos stock assessment model.

Maintained by Iago Mosqueira. Last updated 1 years ago.

2.70 score 5 scripts

btorobrob

cesr:Trend analysis of Constant Effort Site ringing data

Functions for reading EuroCES data in Euring format to produce annual indices of abundance, productivity and survival. Designed to primarily analyse data from schemes with 10-12 visits per year following methods used by the BTO. Use read.ces() to read in data, extract.data() and index() to do abundance/productivity trends and extract.ch() and mark.ces() to estimate survival probabilities.

Maintained by Rob Robinson. Last updated 4 days ago.

cpp

1 stars 2.16 score 29 scripts

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