R-universe search: pointers

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.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

8.8 match 173 stars 9.65 score 203 scripts 2 dependents

jsugarelli

pointr:Working Comfortably with Pointers and Shortcuts to R Objects

R has no built-in pointer functionality. The 'pointr' package fills this gap and lets you create pointers to R objects, including subsets of dataframes. This makes your R code more readable and maintainable.

Maintained by Joachim Zuckarelli. Last updated 4 years ago.

pointers r-lang r-language

16.0 match 8 stars 4.31 score 17 scripts 1 dependents

cran

pointRes:Analyzing Pointer Years and Components of Resilience

Functions to calculate and plot event and pointer years as well as resilience indices. Designed for dendroecological applications, but also suitable to analyze patterns in other ecological time series.

Maintained by Marieke van der Maaten-Theunissen. Last updated 2 years ago.

24.9 match 1 stars 2.53 score 17 scripts

tiledb-inc

tiledb:Modern Database Engine for Complex Data Based on Multi-Dimensional Arrays

The modern database 'TileDB' introduces a powerful on-disk format for storing and accessing any complex data based on multi-dimensional arrays. It supports dense and sparse arrays, dataframes and key-values stores, cloud storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression, encryption and checksum filters, uses a fully multi-threaded implementation, supports parallel I/O, data versioning ('time travel'), metadata and groups. It is implemented as an embeddable cross-platform C++ library with APIs from several languages, and integrations. This package provides the R support.

Maintained by Isaiah Norton. Last updated 3 days ago.

array hdfs s3 storage-manager tiledb cpp

5.1 match 107 stars 11.96 score 306 scripts 4 dependents

nlmixr2

rxode2:Facilities for Simulating from ODE-Based Models

Facilities for running simulations from ordinary differential equation ('ODE') models, such as pharmacometrics and other compartmental models. A compilation manager translates the ODE model into C, compiles it, and dynamically loads the object code into R for improved computational efficiency. An event table object facilitates the specification of complex dosing regimens (optional) and sampling schedules. NB: The use of this package requires both C and Fortran compilers, for details on their use with R please see Section 6.3, Appendix A, and Appendix D in the "R Administration and Installation" manual. Also the code is mostly released under GPL. The 'VODE' and 'LSODA' are in the public domain. The information is available in the inst/COPYRIGHTS.

Maintained by Matthew L. Fidler. Last updated 29 days ago.

fortran openblas cpp openmp

5.4 match 39 stars 11.16 score 220 scripts 13 dependents

opendendro

dplR:Dendrochronology Program Library in R

Perform tree-ring analyses such as detrending, chronology building, and cross dating. Read and write standard file formats used in dendrochronology.

Maintained by Andy Bunn. Last updated 18 days ago.

fortran

5.0 match 39 stars 11.71 score 546 scripts 26 dependents

bioc

matter:Out-of-core statistical computing and signal processing

Toolbox for larger-than-memory scientific computing and visualization, providing efficient out-of-core data structures using files or shared memory, for dense and sparse vectors, matrices, and arrays, with applications to nonuniformly sampled signals and images.

Maintained by Kylie A. Bemis. Last updated 3 months ago.

infrastructure datarepresentation dataimport dimensionreduction preprocessing cpp

6.0 match 57 stars 9.52 score 64 scripts 2 dependents

pachadotdev

cpp11armadillo:An 'Armadillo' Interface

Provides function declarations and inline function definitions that facilitate communication between R and the 'Armadillo' 'C++' library for linear algebra and scientific computing. This implementation is detailed in Vargas Sepulveda and Schneider Malamud (2024) <doi:10.48550/arXiv.2408.11074>.

Maintained by Mauricio Vargas Sepulveda. Last updated 25 days ago.

armadillo cpp cpp11 hacktoberfest linear-algebra

6.0 match 9 stars 9.14 score 1 scripts 16 dependents

sgsokol

rmumps:Wrapper for MUMPS Library

Some basic features of 'MUMPS' (Multifrontal Massively Parallel sparse direct Solver) are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving. Third part ordering libraries are included and can be used: 'PORD', 'METIS', 'SCOTCH'. 'MUMPS' method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194> and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.

Maintained by Serguei Sokol. Last updated 8 months ago.

fortran openblas cpp

7.8 match 10 stars 5.18 score 17 scripts 2 dependents

paulnorthrop

rust:Ratio-of-Uniforms Simulation with Transformation

Uses the generalized ratio-of-uniforms (RU) method to simulate from univariate and (low-dimensional) multivariate continuous distributions. The user specifies the log-density, up to an additive constant. The RU algorithm is applied after relocation of mode of the density to zero, and the user can choose a tuning parameter r. For details see Wakefield, Gelfand and Smith (1991) <DOI:10.1007/BF01889987>, Efficient generation of random variates via the ratio-of-uniforms method, Statistics and Computing (1991) 1, 129-133. A Box-Cox variable transformation can be used to make the input density suitable for the RU method and to improve efficiency. In the multivariate case rotation of axes can also be used to improve efficiency. From version 1.2.0 the 'Rcpp' package <https://cran.r-project.org/package=Rcpp> can be used to improve efficiency.

Maintained by Paul J. Northrop. Last updated 7 months ago.

1977 bayesian-inference kinderman monahan of posterior-samples ratio ratio-of-uniforms ratio-of-uniforms-method rcpp simulation transformation uniforms openblas cpp

5.3 match 7.13 score 36 scripts 7 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.

Maintained by Andri Signorell. Last updated 9 days ago.

fortran cpp

2.0 match 87 stars 16.68 score 7.7k scripts 99 dependents

mikejohnson51

climateR:climateR

Find, subset, and retrive geospatial data by AOI.

Maintained by Mike Johnson. Last updated 3 months ago.

aoi climate dataset geospatial gridded-climate-data weather

3.6 match 187 stars 8.74 score 156 scripts 1 dependents

coolbutuseless

callme:Easily Compile and Call Inline 'C' Functions

Compile inline 'C' code and easily call with automatically generated wrapper functions. By allowing user-defined headers and compilation flags (preprocessor, compiler and linking flags) the user can configure optimization options and linking to third party libraries. Multiple functions may be defined in a single block of code - which may be defined in a string or a path to a source file.

Maintained by Mike Cheng. Last updated 27 days ago.

c

4.3 match 20 stars 6.95 score 21 scripts

ecor

geotopbricks:An R Plug-in for the Distributed Hydrological Model GEOtop

It analyzes raster maps and other information as input/output files from the Hydrological Distributed Model GEOtop. It contains functions and methods to import maps and other keywords from geotop.inpts file. Some examples with simulation cases of GEOtop 2.x/3.x are presented in the package. Any information about the GEOtop Distributed Hydrological Model source code is available on www.geotop.org. Technical details about the model are available in Endrizzi et al (2014) <https://gmd.copernicus.org/articles/7/2831/2014/gmd-7-2831-2014.html>.

Maintained by Emanuele Cordano. Last updated 2 months ago.

5.6 match 4 stars 4.83 score 112 scripts

paulnorthrop

itp:The Interpolate, Truncate, Project (ITP) Root-Finding Algorithm

Implements the Interpolate, Truncate, Project (ITP) root-finding algorithm developed by Oliveira and Takahashi (2021) <doi:10.1145/3423597>. The user provides the function, from the real numbers to the real numbers, and an interval with the property that the values of the function at its endpoints have different signs. If the function is continuous over this interval then the ITP method estimates the value at which the function is equal to zero. If the function is discontinuous then a point of discontinuity at which the function changes sign may be found. The function can be supplied using either an R function or an external pointer to a C++ function. Tuning parameters of the ITP algorithm can be set by the user. Default values are set based on arguments in Oliveira and Takahashi (2021).

Maintained by Paul J. Northrop. Last updated 9 months ago.

algorithm bracketing itp itp-method root-finding cpp

5.2 match 12 stars 5.08 score 8 scripts

johncoene

echarts4r:Create Interactive Graphs with 'Echarts JavaScript' Version 5

Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes 36 chart types, themes, 'Shiny' proxies and animations.

Maintained by David Munoz Tord. Last updated 2 days ago.

echarts hacktoberfest htmlwidget htmlwidgets visualization

2.3 match 603 stars 11.45 score 1.3k scripts 11 dependents

mrc-ide

dust:Iterate Multiple Realisations of Stochastic Models

An Engine for simulation of stochastic models. Includes support for running stochastic models in parallel, either with shared or varying parameters. Simulations are run efficiently in compiled code and can be run with a fraction of simulated states returned to R, allowing control over memory usage. Support is provided for building bootstrap particle filter for performing Sequential Monte Carlo (e.g., Gordon et al. 1993 <doi:10.1049/ip-f-2.1993.0015>). The core of the simulation engine is the 'xoshiro256**' algorithm (Blackman and Vigna <arXiv:1805.01407>), and the package is further described in FitzJohn et al 2021 <doi:10.12688/wellcomeopenres.16466.2>.

Maintained by Rich FitzJohn. Last updated 6 months ago.

cpp openmp

3.3 match 18 stars 7.84 score 60 scripts 3 dependents

snoweye

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

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

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

openmpi

3.5 match 2 stars 7.11 score 179 scripts 3 dependents

carlos-alberto-silva

ICESat2VegR:NASA's Ice, Cloud, and Elevation Satellite (ICESat-2) Data Analysis for Land and Vegetation Applications

Set of tools for downloading, reading, visualizing, processing and exporting NASA's ICESat-2 ATL03 (Global Geolocated Photon Data) and ATL08 (Land and Vegetation Height) products for Land and Vegetation Applications.

Maintained by Caio Hamamura. Last updated 6 months ago.

gdal proj cpp

5.3 match 11 stars 4.57 score 21 scripts

braunm

sparseHessianFD:Numerical Estimation of Sparse Hessians

Estimates Hessian of a scalar-valued function, and returns it in a sparse Matrix format. The sparsity pattern must be known in advance. The algorithm is especially efficient for hierarchical models with a large number of heterogeneous units. See Braun, M. (2017) <doi:10.18637/jss.v082.i10>.

Maintained by Michael Braun. Last updated 2 years ago.

cpp

6.2 match 3.70 score 3 scripts

apache

adbcdrivermanager:'Arrow' Database Connectivity ('ADBC') Driver Manager

Provides a developer-facing interface to 'Arrow' Database Connectivity ('ADBC') for the purposes of driver development, driver testing, and building high-level database interfaces for users. 'ADBC' <https://arrow.apache.org/adbc/> is an API standard for database access libraries that uses 'Arrow' for result sets and query parameters.

Maintained by Dewey Dunnington. Last updated 1 days ago.

cpp

1.9 match 417 stars 11.44 score 73 scripts 6 dependents

apache

nanoarrow:Interface to the 'nanoarrow' 'C' Library

Provides an 'R' interface to the 'nanoarrow' 'C' library and the 'Apache Arrow' application binary interface. Functions to import and export 'ArrowArray', 'ArrowSchema', and 'ArrowArrayStream' 'C' structures to and from 'R' objects are provided alongside helpers to facilitate zero-copy data transfer among 'R' bindings to libraries implementing the 'Arrow' 'C' data interface.

Maintained by Dewey Dunnington. Last updated 23 hours ago.

cpp

1.8 match 183 stars 11.79 score 37 scripts 27 dependents

konrad1991

ast2ast:Translates an R Function to a C++ Function

Enable translation of a tiny subset of R to C++. The user has to define a R function which gets translated. For a full list of possible functions check the documentation. After translation an R function is returned which is a shallow wrapper around the C++ code. Alternatively an external pointer to the C++ function is returned to the user. The intention of the package is to generate fast functions which can be used as ode-system or during optimization.

Maintained by Krämer Konrad. Last updated 3 months ago.

abstract-syntax-tree c c-plus-plus expression-template matrix rcpp transpiler vector cpp

2.8 match 34 stars 6.91 score 11 scripts 2 dependents

jhorzek

lessSEM:Non-Smooth Regularization for Structural Equation Models

Provides regularized structural equation modeling (regularized SEM) with non-smooth penalty functions (e.g., lasso) building on 'lavaan'. The package is heavily inspired by the ['regsem'](<https://github.com/Rjacobucci/regsem>) and ['lslx'](<https://github.com/psyphh/lslx>) packages.

Maintained by Jannik H. Orzek. Last updated 1 years ago.

lasso psychometrics regularization regularized-structural-equation-model sem structural-equation-modeling openblas cpp openmp

2.4 match 7 stars 7.19 score 223 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 1 days ago.

1.9 match 137 stars 8.63 score 20 scripts

nlmixr2

lbfgsb3c:Limited Memory BFGS Minimizer with Bounds on Parameters with optim() 'C' Interface

Interfacing to Nocedal et al. L-BFGS-B.3.0 (See <http://users.iems.northwestern.edu/~nocedal/lbfgsb.html>) limited memory BFGS minimizer with bounds on parameters. This is a fork of 'lbfgsb3'. This registers a 'R' compatible 'C' interface to L-BFGS-B.3.0 that uses the same function types and optimization as the optim() function (see writing 'R' extensions and source for details). This package also adds more stopping criteria as well as allowing the adjustment of more tolerances.

Maintained by Matthew L Fidler. Last updated 6 months ago.

fortran cpp

2.0 match 7.30 score 17 scripts 16 dependents

marshalllab

MGDrivE:Mosquito Gene Drive Explorer

Provides a model designed to be a reliable testbed where various gene drive interventions for mosquito-borne diseases control. It is being developed to accommodate the use of various mosquito-specific gene drive systems within a population dynamics framework that allows migration of individuals between patches in landscape. Previous work developing the population dynamics can be found in Deredec et al. (2001) <doi:10.1073/pnas.1110717108> and Hancock & Godfray (2007) <doi:10.1186/1475-2875-6-98>, and extensions to accommodate CRISPR homing dynamics in Marshall et al. (2017) <doi:10.1038/s41598-017-02744-7>.

Maintained by Héctor Manuel Sánchez Castellanos. Last updated 4 years ago.

cpp

2.0 match 6 stars 7.06 score 61 scripts

davidchall

ipaddress:Data Analysis for IP Addresses and Networks

Classes and functions for working with IP (Internet Protocol) addresses and networks, inspired by the Python 'ipaddress' module. Offers full support for both IPv4 and IPv6 (Internet Protocol versions 4 and 6) address spaces. It is specifically designed to work well with the 'tidyverse'.

Maintained by David Hall. Last updated 1 years ago.

cyber data-analysis ip-address ipv4 ipv6 vctrs cpp

2.0 match 32 stars 7.02 score 27 scripts 2 dependents

paulnorthrop

revdbayes:Ratio-of-Uniforms Sampling for Bayesian Extreme Value Analysis

Provides functions for the Bayesian analysis of extreme value models. The 'rust' package <https://cran.r-project.org/package=rust> is used to simulate a random sample from the required posterior distribution. The functionality of 'revdbayes' is similar to the 'evdbayes' package <https://cran.r-project.org/package=evdbayes>, which uses Markov Chain Monte Carlo ('MCMC') methods for posterior simulation. In addition, there are functions for making inferences about the extremal index, using the models for threshold inter-exceedance times of Suveges and Davison (2010) <doi:10.1214/09-AOAS292> and Holesovsky and Fusek (2020) <doi:10.1007/s10687-020-00374-3>. Also provided are d,p,q,r functions for the Generalised Extreme Value ('GEV') and Generalised Pareto ('GP') distributions that deal appropriately with cases where the shape parameter is very close to zero.

Maintained by Paul J. Northrop. Last updated 7 months ago.

analysis bayesian extreme extreme-value-statistics extremes generalized-pareto-distribution gev inference nhpp point-process posterior predictive rcpp value openblas cpp

1.8 match 4 stars 7.62 score 58 scripts 4 dependents

zhanxw

seqminer:Efficiently Read Sequence Data (VCF Format, BCF Format, METAL Format and BGEN Format) into R

Integrate sequencing data (Variant call format, e.g. VCF or BCF) or meta-analysis results in R. This package can help you (1) read VCF/BCF/BGEN files by chromosomal ranges (e.g. 1:100-200); (2) read RareMETAL summary statistics files; (3) read tables from a tabix-indexed files; (4) annotate VCF/BCF files; (5) create customized workflow based on Makefile.

Maintained by Xiaowei Zhan. Last updated 6 months ago.

annotation bcf bgen meta-analysis next-generation-sequencing plink sequencing tabix vcf workflow zlib bzip2 libzstd sqlite3 cpp

1.5 match 30 stars 8.29 score 111 scripts 6 dependents

uscbiostats

aphylo:Statistical Inference and Prediction of Annotations in Phylogenetic Trees

Implements a parsimonious evolutionary model to analyze and predict gene-functional annotations in phylogenetic trees as described in Vega Yon et al. (2021) <doi:10.1371/journal.pcbi.1007948>. Focusing on computational efficiency, 'aphylo' makes it possible to estimate pooled phylogenetic models, including thousands (hundreds) of annotations (trees) in the same run. The package also provides the tools for visualization of annotated phylogenies, calculation of posterior probabilities (prediction) and goodness-of-fit assessment featured in Vega Yon et al. (2021).

Maintained by George Vega Yon. Last updated 1 years ago.

annotations inference phylogenetics rcpparmadillo cpp

2.3 match 6 stars 5.49 score 104 scripts

crowding

memo:In-Memory Caching of Repeated Computations (Memoization)

A simple in-memory, LRU cache that can be wrapped around any function to memoize it. The cache is keyed on a hash of the input data (using 'digest') or on pointer equivalence.

Maintained by Peter Meilstrup. Last updated 1 years ago.

2.3 match 13 stars 5.26 score 28 scripts

jonasfoe

isnullptr:Check if an 'externalptr' is a Null Pointer

Check if an 'externalptr' is a null pointer. R does currently not have a native function for that purpose. This package contains a C function that returns TRUE in case of a null pointer.

Maintained by Jonas Förster. Last updated 8 months ago.

5.8 match 2.00 score 2 scripts

eddelbuettel

naarma:Connect nanoarrow with (Rcpp)Armadillo

The nanoarrow package offers C-level functionality to work with Arrow object, along with a small amount of C++ integration. This package uses it to interact with Armadillo objects. Some auxiliary testing facility from the nanoarrow package is included here as well.

Maintained by Dirk Eddelbuettel. Last updated 3 months ago.

armadillo arrow cpp mlpack cpp

5.8 match 2.00 score 4 scripts

polar-fhir

fhircrackr:Handling HL7 FHIR® Resources in R

Useful tools for conveniently downloading FHIR resources in xml format and converting them to R data.frames. The package uses FHIR-search to download bundles from a FHIR server, provides functions to save and read xml-files containing such bundles and allows flattening the bundles to data.frames using XPath expressions. FHIR® is the registered trademark of HL7 and is used with the permission of HL7. Use of the FHIR trademark does not constitute endorsement of this product by HL7.

Maintained by Julia Palm. Last updated 11 days ago.

fhir fhir-client

1.5 match 33 stars 7.63 score 46 scripts

brodieg

vetr:Trust, but Verify

Declarative template-based framework for verifying that objects meet structural requirements, and auto-composing error messages when they do not.

Maintained by Brodie Gaslam. Last updated 9 months ago.

argument-checks input-validation

1.5 match 79 stars 7.50 score 67 scripts 1 dependents

nlmixr2

dparser:Port of 'Dparser' Package

A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita (1987) algorithm. (Paper can be found at <https://aclanthology.org/P84-1073.pdf>). The original 'dparser' package documentation can be found at <https://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like rxode2's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use #include <dparser.h>. This also provides a R-based port of the make_dparser <https://dparser.sourceforge.net/d/make_dparser.cat> command called mkdparser(). Additionally you can parse an arbitrary grammar within R using the dparse() function, which works on most OSes and is mainly for grammar testing. The fastest parsing, of course, occurs at the C level, and is suggested.

Maintained by Matthew Fidler. Last updated 5 months ago.

1.9 match 4 stars 5.27 score 5 scripts 14 dependents

r-spatial

leafem:'leaflet' Extensions for 'mapview'

Provides extensions for packages 'leaflet' & 'mapdeck', many of which are used by package 'mapview'. Focus is on functionality readily available in Geographic Information Systems such as 'Quantum GIS'. Includes functions to display coordinates of mouse pointer position, query image values via mouse pointer and zoom-to-layer buttons. Additionally, provides a feature type agnostic function to add points, lines, polygons to a map.

Maintained by Tim Appelhans. Last updated 17 days ago.

0.8 match 108 stars 12.36 score 704 scripts 53 dependents

forestry-labs

Rforestry:Random Forests, Linear Trees, and Gradient Boosting for Inference and Interpretability

Provides fast implementations of Honest Random Forests, Gradient Boosting, and Linear Random Forests, with an emphasis on inference and interpretability. Additionally contains methods for variable importance, out-of-bag prediction, regression monotonicity, and several methods for missing data imputation.

Maintained by Theo Saarinen. Last updated 4 days ago.

openblas cpp

1.7 match 5.57 score 82 scripts 1 dependents

nlmixr2

n1qn1:Port of the 'Scilab' 'n1qn1' Module for Unconstrained BFGS Optimization

Provides 'Scilab' 'n1qn1'. This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian. If the Hessian is near enough the truth in optimization it can speed up the optimization problem. The algorithm is described in the 'Scilab' optimization documentation located at <https://www.scilab.org/sites/default/files/optimization_in_scilab.pdf>. This version uses manually modified code from 'f2c' to make this a C only binary.

Maintained by Matthew Fidler. Last updated 7 months ago.

openblas cpp

1.8 match 1 stars 4.26 score 4 scripts 10 dependents

talgalili

heatmaply:Interactive Cluster Heat Maps Using 'plotly' and 'ggplot2'

Create interactive cluster 'heatmaps' that can be saved as a stand- alone HTML file, embedded in 'R Markdown' documents or in a 'Shiny' app, and available in the 'RStudio' viewer pane. Hover the mouse pointer over a cell to show details or drag a rectangle to zoom. A 'heatmap' is a popular graphical method for visualizing high-dimensional data, in which a table of numbers are encoded as a grid of colored cells. The rows and columns of the matrix are ordered to highlight patterns and are often accompanied by 'dendrograms'. 'Heatmaps' are used in many fields for visualizing observations, correlations, missing values patterns, and more. Interactive 'heatmaps' allow the inspection of specific value by hovering the mouse over a cell, as well as zooming into a region of the 'heatmap' by dragging a rectangle around the relevant area. This work is based on the 'ggplot2' and 'plotly.js' engine. It produces similar 'heatmaps' to 'heatmap.2' with the advantage of speed ('plotly.js' is able to handle larger size matrix), the ability to zoom from the 'dendrogram' panes, and the placing of factor variables in the sides of the 'heatmap'.

Maintained by Tal Galili. Last updated 8 months ago.

d3-heatmap dendextend dendrogram ggplot2 heatmap plotly

0.5 match 386 stars 14.21 score 2.0k scripts 45 dependents

boennecd

mdgc:Missing Data Imputation Using Gaussian Copulas

Provides functions to impute missing values using Gaussian copulas for mixed data types as described by Christoffersen et al. (2021) <arXiv:2102.02642>. The method is related to Hoff (2007) <doi:10.1214/07-AOAS107> and Zhao and Udell (2019) <arXiv:1910.12845> but differs by making a direct approximation of the log marginal likelihood using an extended version of the Fortran code created by Genz and Bretz (2002) <doi:10.1198/106186002394> in addition to also support multinomial variables.

Maintained by Benjamin Christoffersen. Last updated 2 years ago.

binary gaussian-copula imputation multinomial-variables ordinal semi-parametric fortran openblas cpp openmp

1.7 match 10 stars 3.78 score 12 scripts

bioc

XVector:Foundation of external vector representation and manipulation in Bioconductor

Provides memory efficient S4 classes for storing sequences "externally" (e.g. behind an R external pointer, or on disk).

Maintained by Hervé Pagès. Last updated 2 months ago.

infrastructure datarepresentation bioconductor-package core-package zlib

0.5 match 2 stars 11.36 score 67 scripts 1.7k dependents

aidenlab

strawr:Fast Implementation of Reading/Dump for .hic Files

API for fast data extraction for .hic files that provides programmatic access to the matrices. It doesn't store the pointer data for all the matrices, only the one queried, and currently we are only supporting matrices (not vectors).

Maintained by Neva Cherniavsky Durand. Last updated 12 months ago.

curl zlib cpp

0.5 match 67 stars 8.23 score 49 scripts 11 dependents

r-prof

procmaps:Portable Address Space Mapping

Portable '/proc/self/maps' as a data frame. Determine which library or other region is mapped to a specific address of a process. -- R packages can contain native code, compiled to shared libraries at build or installation time. When loaded, each shared library occupies a portion of the address space of the main process. When only a machine instruction pointer is available (e.g. from a backtrace during error inspection or profiling), the address space map determines which library this instruction pointer corresponds to.

Maintained by Kirill Müller. Last updated 2 months ago.

system-utility cpp

0.8 match 3 stars 5.18 score 3 scripts 1 dependents

sahirbhatnagar

manhattanly:Interactive Q-Q and Manhattan Plots Using 'plotly.js'

Create interactive manhattan, Q-Q and volcano plots that are usable from the R console, in 'Dash' apps, in the 'RStudio' viewer pane, in 'R Markdown' documents, and in 'Shiny' apps. Hover the mouse pointer over a point to show details or drag a rectangle to zoom. A manhattan plot is a popular graphical method for visualizing results from high-dimensional data analysis such as a (epi)genome wide association study (GWAS or EWAS), in which p-values, Z-scores, test statistics are plotted on a scatter plot against their genomic position. Manhattan plots are used for visualizing potential regions of interest in the genome that are associated with a phenotype. Interactive manhattan plots allow the inspection of specific value (e.g. rs number or gene name) by hovering the mouse over a cell, as well as zooming into a region of the genome (e.g. a chromosome) by dragging a rectangle around the relevant area. This work is based on the 'qqman' package and the 'plotly.js' engine. It produces similar manhattan and Q-Q plots as the 'manhattan' and 'qq' functions in the 'qqman' package, with the advantage of including extra annotation information and interactive web-based visualizations directly from R. Once uploaded to a 'plotly' account, 'plotly' graphs (and the data behind them) can be viewed and modified in a web browser.

Maintained by Sahir Bhatnagar. Last updated 4 years ago.

0.5 match 60 stars 7.15 score 78 scripts

thk686

strider:Strided Iterator and Range

The strided iterator adapts multidimensional buffers to work with the C++ standard library and range-based for-loops. Given a pointer or iterator into a multidimensional data buffer, one can generate an iterator range using make_strided to construct strided versions of the standard library's begin and end. For constructing range-based for-loops, a strided_range class is provided. These help authors to avoid integer-based indexing, which in some cases can impede algorithm performance and introduce indexing errors. This library exists primarily to expose the header file to other R projects.

Maintained by Tim Keitt. Last updated 5 years ago.

cpp iterators cpp

0.5 match 4 stars 4.34 score 11 scripts

shikokuchuo

sakura:Extension to R Serialization

Extends the functionality of R serialization by augmenting the built-in reference hook system. This enhanced implementation allows an integrated single-pass operation that combines R serialization with third-party serialization methods. Facilitates the serialization of even complex R objects, which contain non-system reference objects, such as those accessed via external pointers, to enable their use in parallel and distributed computing.

Maintained by Charlie Gao. Last updated 12 days ago.

marshalling serialization

0.5 match 12 stars 4.26 score

hongyuanjia

rdyncall:Improved Foreign Function Interface and Dynamic Bindings to C Libraries

Provides a cross-platform framework for dynamic binding of C libraries using a flexible Foreign Function Interface ('FFI'). The FFI supports almost all fundamental C types, multiple calling conventions, symbolic access to foreign C 'struct'/'union' data types and wrapping of R functions as C callback function pointers. Dynamic bindings to shared C libraries are data-driven by cross-platform binding specification using a compact plain text format; an initial repository of bindings to a couple of common C libraries ('OpenGL', 'SDL2', 'Expat', 'glew', 'CUDA', 'OpenCL', 'ODE', 'R') comes with the package. The package includes a variety of technology demos and OS-specific notes for installation of shared libraries.

Maintained by Hongyuan Jia. Last updated 2 years ago.

0.5 match 6 stars 3.84 score 23 scripts

landroni

RcmdrPlugin.Export:Export R Output to LaTeX or HTML

Export Rcmdr output to LaTeX or HTML code. The plug-in was originally intended to facilitate exporting Rcmdr output to formats other than ASCII text and to provide R novices with an easy-to-use, easy-to-access reference on exporting R objects to formats suited for printed output. The package documentation contains several pointers on creating reports, either by using conventional word processors or LaTeX/LyX.

Maintained by Liviu Andronic. Last updated 9 years ago.

0.5 match 2.70 score 3 scripts

louissirugue

directotree:Creates an Interactive Tree Structure of a Directory

Represents the content of a directory as an interactive collapsible tree. Offers the possibility to assign a text (e.g., a 'Readme.txt') to each folder (represented as a clickable node), so that when the user hovers the pointer over a node, the corresponding text is displayed as a tooltip.

Maintained by Louis Sirugue. Last updated 6 years ago.

collapsible-tree data-visualization directotree tree

0.5 match 2 stars 2.30 score 1 scripts

cran

spectralGP:Approximate Gaussian Processes Using the Fourier Basis

Routines for creating, manipulating, and performing Bayesian inference about Gaussian processes in one and two dimensions using the Fourier basis approximation: simulation and plotting of processes, calculation of coefficient variances, calculation of process density, coefficient proposals (for use in MCMC). It uses R environments to store GP objects as references/pointers.

Maintained by Chris Paciorek. Last updated 10 years ago.

0.5 match 1 stars 1.65 score 45 scripts