R-universe search: hierarchies

ropensci

taxize:Taxonomic Information from Around the Web

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

Maintained by Zachary Foster. Last updated 12 days ago.

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

15.4 match 274 stars 13.63 score 1.6k scripts 23 dependents

timelyportfolio

d3r:'d3.js' Utilities for R

Provides a suite of functions to help ease the use of 'd3.js' in R. These helpers include 'htmltools::htmlDependency' functions, hierarchy builders, and conversion tools for 'partykit', 'igraph,' 'table', and 'data.frame' R objects into the 'JSON' that 'd3.js' expects.

Maintained by Kent Russell. Last updated 1 years ago.

d3 hierarchies hierarchy igraph javascript json

24.1 match 155 stars 8.00 score 174 scripts 5 dependents

kurthornik

clue:Cluster Ensembles

CLUster Ensembles.

Maintained by Kurt Hornik. Last updated 4 months ago.

19.0 match 2 stars 9.85 score 496 scripts 401 dependents

bernhard-da

sdcHierarchies:Create and (Interactively) Modify Nested Hierarchies

Provides functionality to generate, (interactively) modify (by adding, removing and renaming nodes) and convert nested hierarchies between different formats. These tree like structures can be used to define for example complex hierarchical tables used for statistical disclosure control.

Maintained by Bernhard Meindl. Last updated 1 years ago.

cpp

31.9 match 2 stars 5.70 score 28 scripts 3 dependents

grunwaldlab

metacoder:Tools for Parsing, Manipulating, and Graphing Taxonomic Abundance Data

Reads, plots, and manipulates large taxonomic data sets, like those generated from modern high-throughput sequencing, such as metabarcoding (i.e. amplification metagenomics, 16S metagenomics, etc). It provides a tree-based visualization called "heat trees" used to depict statistics for every taxon in a taxonomy using color and size. It also provides various functions to do common tasks in microbiome bioinformatics on data in the 'taxmap' format defined by the 'taxa' package. The 'metacoder' package is described in the publication by Foster et al. (2017) <doi:10.1371/journal.pcbi.1005404>.

Maintained by Zachary Foster. Last updated 1 months ago.

community-diversity hierarchical metabarcoding pcr taxonomy trees cpp

18.0 match 140 stars 9.64 score 328 scripts

statisticsnorway

SSBtools:Algorithms and Tools for Tabular Statistics and Hierarchical Computations

Includes general data manipulation functions, algorithms for statistical disclosure control (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6> and functions for hierarchical computations by sparse model matrices (Langsrud, 2023) <doi:10.32614/RJ-2023-088>.

Maintained by Øyvind Langsrud. Last updated 3 days ago.

statistics

16.5 match 7 stars 7.62 score 68 scripts 7 dependents

peterreichert

utility:Construct, Evaluate and Plot Value and Utility Functions

Construct and plot objective hierarchies and associated value and utility functions. Evaluate the values and utilities and visualize the results as colored objective hierarchies or tables. Visualize uncertainty by plotting median and quantile intervals within the nodes of objective hierarchies. Get numerical results of the evaluations in standard R data types for further processing.

Maintained by Peter Reichert. Last updated 2 years ago.

31.8 match 3.35 score 82 scripts 1 dependents

idsia

bayesRecon:Probabilistic Reconciliation via Conditioning

Provides methods for probabilistic reconciliation of hierarchical forecasts of time series. The available methods include analytical Gaussian reconciliation (Corani et al., 2021) <doi:10.1007/978-3-030-67664-3_13>, MCMC reconciliation of count time series (Corani et al., 2024) <doi:10.1016/j.ijforecast.2023.04.003>, Bottom-Up Importance Sampling (Zambon et al., 2024) <doi:10.1007/s11222-023-10343-y>, methods for the reconciliation of mixed hierarchies (Mix-Cond and TD-cond) (Zambon et al., 2024. The 40th Conference on Uncertainty in Artificial Intelligence, accepted).

Maintained by Dario Azzimonti. Last updated 2 months ago.

reconciliation timeseries

12.4 match 7 stars 7.13 score 40 scripts

mrc-ide

naomi:Naomi Model for Subnational HIV Estimates

This package implements the Naomi model for subnational HIV estimates.

Maintained by Jeff Eaton. Last updated 6 days ago.

cpp

10.9 match 9 stars 7.74 score 54 scripts 2 dependents

mhahsler

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

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

Maintained by Michael Hahsler. Last updated 2 months ago.

clustering dbscan density-based-clustering hdbscan lof optics cpp

5.3 match 321 stars 15.62 score 1.6k scripts 84 dependents

vlarmet

cppRouting:Algorithms for Routing and Solving the Traffic Assignment Problem

Calculation of distances, shortest paths and isochrones on weighted graphs using several variants of Dijkstra algorithm. Proposed algorithms are unidirectional Dijkstra (Dijkstra, E. W. (1959) <doi:10.1007/BF01386390>), bidirectional Dijkstra (Goldberg, Andrew & Fonseca F. Werneck, Renato (2005) <https://archive.siam.org/meetings/alenex05/papers/03agoldberg.pdf>), A* search (P. E. Hart, N. J. Nilsson et B. Raphael (1968) <doi:10.1109/TSSC.1968.300136>), new bidirectional A* (Pijls & Post (2009) <https://repub.eur.nl/pub/16100/ei2009-10.pdf>), Contraction hierarchies (R. Geisberger, P. Sanders, D. Schultes and D. Delling (2008) <doi:10.1007/978-3-540-68552-4_24>), PHAST (D. Delling, A.Goldberg, A. Nowatzyk, R. Werneck (2011) <doi:10.1016/j.jpdc.2012.02.007>). Algorithms for solving the traffic assignment problem are All-or-Nothing assignment, Method of Successive Averages, Frank-Wolfe algorithm (M. Fukushima (1984) <doi:10.1016/0191-2615(84)90029-8>), Conjugate and Bi-Conjugate Frank-Wolfe algorithms (M. Mitradjieva, P. O. Lindberg (2012) <doi:10.1287/trsc.1120.0409>), Algorithm-B (R. B. Dial (2006) <doi:10.1016/j.trb.2006.02.008>).

Maintained by Vincent Larmet. Last updated 9 months ago.

algorithm algorithm-b bidirectional-a-star-algorithm c-plus-plus contraction-hierarchies dijkstra-algorithm distance frank-wolfe isochrones parallel-computing rcpp shortest-paths traffic-assignment cpp

10.0 match 112 stars 7.42 score 39 scripts 4 dependents

frankiecho

ahpsurvey:Analytic Hierarchy Process for Survey Data

The Analytic Hierarchy Process is a versatile multi-criteria decision-making tool introduced by Saaty (1987) <doi:10.1016/0270-0255(87)90473-8> that allows decision-makers to weigh attributes and evaluate alternatives presented to them. This package provides a consistent methodology for researchers to reformat data and run analytic hierarchy process in R on data that are formatted using the survey data entry mode. It is optimized for performing the analytic hierarchy process with many decision-makers, and provides tools and options for researchers to aggregate individual preferences and test multiple options. It also allows researchers to quantify, visualize and correct for inconsistency in the decision-maker's comparisons.

Maintained by Frankie Cho. Last updated 4 years ago.

analytic-hierarchy-process operations-research questionnaire survey-data

13.5 match 14 stars 5.28 score 27 scripts

ropensci

taxa:Classes for Storing and Manipulating Taxonomic Data

Provides classes for storing and manipulating taxonomic data. Most of the classes can be treated like base R vectors (e.g. can be used in tables as columns and can be named). Vectorized classes can store taxon names and authorities, taxon IDs from databases, taxon ranks, and other types of information. More complex classes are provided to store taxonomic trees and user-defined data associated with them.

Maintained by Zachary Foster. Last updated 1 years ago.

taxonomy biology hierarchy data-cleaning taxon

10.0 match 48 stars 6.80 score 217 scripts

gobbios

EloRating:Animal Dominance Hierarchies by Elo Rating

Provides functions to quantify animal dominance hierarchies. The major focus is on Elo rating and its ability to deal with temporal dynamics in dominance interaction sequences. For static data, David's score and de Vries' I&SI are also implemented. In addition, the package provides functions to assess transitivity, linearity and stability of dominance networks. See Neumann et al (2011) <doi:10.1016/j.anbehav.2011.07.016> for an introduction.

Maintained by Christof Neumann. Last updated 8 months ago.

cpp

9.6 match 4 stars 6.86 score 61 scripts 1 dependents

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 13 hours ago.

complex-networks graph-algorithms graph-theory mathematics network-analysis network-graph fortran libxml2 glpk openblas cpp

3.0 match 582 stars 21.11 score 31k scripts 1.9k dependents

thomasp85

ggraph:An Implementation of Grammar of Graphics for Graphs and Networks

The grammar of graphics as implemented in ggplot2 is a poor fit for graph and network visualizations due to its reliance on tabular data input. ggraph is an extension of the ggplot2 API tailored to graph visualizations and provides the same flexible approach to building up plots layer by layer.

Maintained by Thomas Lin Pedersen. Last updated 1 years ago.

ggplot-extension ggplot2 graph-visualization network-visualization visualization cpp

3.6 match 1.1k stars 16.96 score 9.2k scripts 111 dependents

r-lib

rprojroot:Finding Files in Project Subdirectories

Robust, reliable and flexible paths to files below a project root. The 'root' of a project is defined as a directory that matches a certain criterion, e.g., it contains a certain regular file.

Maintained by Kirill Müller. Last updated 1 months ago.

3.6 match 150 stars 16.70 score 1.4k scripts 1.4k dependents

henrikbengtsson

R.oo:R Object-Oriented Programming with or without References

Methods and classes for object-oriented programming in R with or without references. Large effort has been made on making definition of methods as simple as possible with a minimum of maintenance for package developers. The package has been developed since 2001 and is now considered very stable. This is a cross-platform package implemented in pure R that defines standard S3 classes without any tricks.

Maintained by Henrik Bengtsson. Last updated 5 months ago.

5.3 match 20 stars 11.49 score 329 scripts 828 dependents

stochastictree

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

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

Maintained by Drew Herren. Last updated 18 days ago.

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

6.5 match 20 stars 8.52 score 40 scripts

yonicd

d3Tree:Create Interactive Collapsible Trees with the JavaScript 'D3' Library

Create and customize interactive collapsible 'D3' trees using the 'D3' JavaScript library and the 'htmlwidgets' package. These trees can be used directly from the R console, from 'RStudio', in Shiny apps and R Markdown documents. When in Shiny the tree layout is observed by the server and can be used as a reactive filter of structured data.

Maintained by Jonathan Sidi. Last updated 1 years ago.

d3js hierarchy htmlwidgets query shiny

10.0 match 87 stars 5.46 score 33 scripts

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 12 days ago.

data-cleaning validation

4.3 match 418 stars 12.50 score 448 scripts 9 dependents

bioc

cola:A Framework for Consensus Partitioning

Subgroup classification is a basic task in genomic data analysis, especially for gene expression and DNA methylation data analysis. It can also be used to test the agreement to known clinical annotations, or to test whether there exist significant batch effects. The cola package provides a general framework for subgroup classification by consensus partitioning. It has the following features: 1. It modularizes the consensus partitioning processes that various methods can be easily integrated. 2. It provides rich visualizations for interpreting the results. 3. It allows running multiple methods at the same time and provides functionalities to straightforward compare results. 4. It provides a new method to extract features which are more efficient to separate subgroups. 5. It automatically generates detailed reports for the complete analysis. 6. It allows applying consensus partitioning in a hierarchical manner.

Maintained by Zuguang Gu. Last updated 1 months ago.

clustering geneexpression classification software consensus-clustering cpp

6.5 match 61 stars 7.49 score 112 scripts

mlr-org

mlr3pipelines:Preprocessing Operators and Pipelines for 'mlr3'

Dataflow programming toolkit that enriches 'mlr3' with a diverse set of pipelining operators ('PipeOps') that can be composed into graphs. Operations exist for data preprocessing, model fitting, and ensemble learning. Graphs can themselves be treated as 'mlr3' 'Learners' and can therefore be resampled, benchmarked, and tuned.

Maintained by Martin Binder. Last updated 9 days ago.

bagging data-science dataflow-programming ensemble-learning machine-learning mlr3 pipelines preprocessing stacking

3.8 match 141 stars 12.36 score 448 scripts 7 dependents

ncss-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-group ncss-tech soil soil-survey soil-taxonomy subgroup suborder usda

8.0 match 15 stars 5.65 score

bioc

flowWorkspace:Infrastructure for representing and interacting with gated and ungated cytometry data sets.

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

Maintained by Greg Finak. Last updated 10 days ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation zlib openblas cpp

5.7 match 7.89 score 576 scripts 10 dependents

mountainmath

cancensus:Access, Retrieve, and Work with Canadian Census Data and Geography

Integrated, convenient, and uniform access to Canadian Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready tidy data frames and spatial data in multiple formats, as well as convenience functions for working with Census variables, variable hierarchies, and region selection. API keys are freely available with free registration at <https://censusmapper.ca/api>. Census data and boundary geometries are reproduced and distributed on an "as is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006; 2011; 2016; 2021).

Maintained by Dmitry Shkolnik. Last updated 1 years ago.

5.0 match 82 stars 8.80 score 414 scripts

usaid-oha-si

grabr:OHA/SI APIs Package

Provides a series of base functions useful to the GH OHA SI team. These function extend the utility functions in glamr, focusing primarily on API utility functions.

Maintained by Aaron Chafetz. Last updated 6 months ago.

8.6 match 1 stars 5.14 score 69 scripts

usaid-oha-si

Wavelength:Wavelength

USAID OHA Office. Munging of mission weekly HFR data.

Maintained by Aaron Chafetz. Last updated 2 years ago.

12.8 match 3 stars 3.39 score 55 scripts

bioc

clusterExperiment:Compare Clusterings for Single-Cell Sequencing

Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets.

Maintained by Elizabeth Purdom. Last updated 5 months ago.

clustering rnaseq sequencing software singlecell cpp

4.5 match 39 stars 9.63 score 192 scripts 1 dependents

danigiro

FoReco:Forecast Reconciliation

Classical (bottom-up and top-down), optimal combination and heuristic point (Di Fonzo and Girolimetto, 2023 <doi:10.1016/j.ijforecast.2021.08.004>) and probabilistic (Girolimetto et al. 2023 <doi:10.1016/j.ijforecast.2023.10.003>) forecast reconciliation procedures for linearly constrained time series (e.g., hierarchical or grouped time series) in cross-sectional, temporal, or cross-temporal frameworks.

Maintained by Daniele Girolimetto. Last updated 2 months ago.

forecasting reconciliation time-series

6.9 match 33 stars 6.19 score 104 scripts

klmr

box:Write Reusable, Composable and Modular R Code

A modern module system for R. Organise code into hierarchical, composable, reusable modules, and use it effortlessly across projects via a flexible, declarative dependency loading syntax.

Maintained by Konrad Rudolph. Last updated 13 days ago.

modules packages

3.3 match 888 stars 12.39 score 47 scripts 4 dependents

bioc

ShortRead:FASTQ input and manipulation

This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

dataimport sequencing qualitycontrol bioconductor-package core-package zlib cpp

3.4 match 8 stars 12.08 score 1.8k scripts 49 dependents

dalekube

hR:Better Data Engineering in Human Resources

Methods for data engineering in the human resources (HR) corporate domain. Designed for HR analytics practitioners and workforce-oriented data sets.

Maintained by Dale Kube. Last updated 8 hours ago.

analytics data data-engineering data-science human-resources

8.0 match 21 stars 5.02 score 8 scripts

augustinewigle

poth:Precision of Treatment Hierarchy (POTH)

Calculate POTH for treatment hierarchies from frequentist and Bayesian network meta-analysis. POTH quantifies the certainty in a treatment hierarchy. Subset POTH, POTH residuals, and cumulative POTH can also be calculated to improve interpretation of treatment hierarchies.

Maintained by Augustine Wigle. Last updated 5 months ago.

11.0 match 1 stars 3.65 score

songw01

MEGENA:Multiscale Clustering of Geometrical Network

Co-Expression Network Analysis by adopting network embedding technique. Song W.-M., Zhang B. (2015) Multiscale Embedded Gene Co-expression Network Analysis. PLoS Comput Biol 11(11): e1004574. <doi: 10.1371/journal.pcbi.1004574>.

Maintained by Won-Min Song. Last updated 1 years ago.

cpp

5.7 match 49 stars 6.82 score 45 scripts 1 dependents

johnjsl7

daewr:Design and Analysis of Experiments with R

Contains Data frames and functions used in the book "Design and Analysis of Experiments with R", Lawson(2015) ISBN-13:978-1-4398-6813-3.

Maintained by John Lawson. Last updated 2 years ago.

10.1 match 3 stars 3.83 score 217 scripts 3 dependents

bioc

rhdf5:R Interface to HDF5

This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.

Maintained by Mike Smith. Last updated 2 months ago.

infrastructure dataimport hdf5 rhdf5 openssl curl zlib cpp

2.4 match 62 stars 15.93 score 4.2k scripts 232 dependents

adafede

cascade:Contextualizing untargeted Annotation with Semi-quantitative Charged Aerosol Detection for pertinent characterization of natural Extracts

This package provides the infrastructure to perform Automated Composition Assessment of Natural Extracts.

Maintained by Adriano Rutz. Last updated 11 days ago.

metabolite annotation charged aerosol detector semi-quantitative natural products computational metabolomics specialized metabolome

6.5 match 2 stars 5.74 score 40 scripts 1 dependents

ubod

apcluster:Affinity Propagation Clustering

Implements Affinity Propagation clustering introduced by Frey and Dueck (2007) <DOI:10.1126/science.1136800>. The algorithms are largely analogous to the 'Matlab' code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.

Maintained by Ulrich Bodenhofer. Last updated 11 months ago.

cpp

3.8 match 10 stars 9.82 score 270 scripts 25 dependents

bioc

flowGraph:Identifying differential cell populations in flow cytometry data accounting for marker frequency

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

Maintained by Alice Yue. Last updated 5 months ago.

flowcytometry statisticalmethod immunooncology software cellbasedassays visualization

8.9 match 4.00 score 10 scripts

r-dbi

DBI:R Database Interface

A database interface definition for communication between R and relational database management systems. All classes in this package are virtual and need to be extended by the various R/DBMS implementations.

Maintained by Kirill Müller. Last updated 3 months ago.

database interface

1.7 match 302 stars 20.88 score 19k scripts 2.9k dependents

ddsjoberg

gtsummary:Presentation-Ready Data Summary and Analytic Result Tables

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

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

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

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

gavinsimpson

permute:Functions for Generating Restricted Permutations of Data

A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.

Maintained by Gavin L. Simpson. Last updated 7 months ago.

permutation restricted-permutations

2.5 match 23 stars 13.28 score 538 scripts 488 dependents

cran

sna:Tools for Social Network Analysis

A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.

Maintained by Carter T. Butts. Last updated 6 months ago.

4.9 match 8 stars 6.78 score 94 dependents

chgigot

epiphy:Analysis of Plant Disease Epidemics

A toolbox to make it easy to analyze plant disease epidemics. It provides a common framework for plant disease intensity data recorded over time and/or space. Implemented statistical methods are currently mainly focused on spatial pattern analysis (e.g., aggregation indices, Taylor and binary power laws, distribution fitting, SADIE and 'mapcomp' methods). See Laurence V. Madden, Gareth Hughes, Franck van den Bosch (2007) <doi:10.1094/9780890545058> for further information on these methods. Several data sets that were mainly published in plant disease epidemiology literature are also included in this package.

Maintained by Christophe Gigot. Last updated 1 years ago.

cpp

5.4 match 15 stars 6.05 score 37 scripts

mplex

multiplex:Algebraic Tools for the Analysis of Multiple Social Networks

Algebraic procedures for analyses of multiple social networks are delivered with this package as described in Ostoic (2020) <DOI:10.18637/jss.v092.i11>. 'multiplex' makes possible, among other things, to create and manipulate multiplex, multimode, and multilevel network data with different formats. Effective ways are available to treat multiple networks with routines that combine algebraic systems like the partially ordered semigroup with decomposition procedures or semiring structures with the relational bundles occurring in different types of multivariate networks. 'multiplex' provides also an algebraic approach for affiliation networks through Galois derivations between families of the pairs of subsets in the two domains of the network with visualization options.

Maintained by Antonio Rivero Ostoic. Last updated 2 months ago.

algebra network-analysis semigroup semiring

4.0 match 23 stars 8.12 score 69 scripts 2 dependents

bioc

sincell:R package for the statistical assessment of cell state hierarchies from single-cell RNA-seq data

Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.

Maintained by Miguel Julia. Last updated 5 months ago.

immunooncology sequencing rnaseq clustering graphandnetwork visualization geneexpression genesetenrichment biomedicalinformatics cellbiology functionalgenomics systemsbiology cpp

10.4 match 3.00 score 6 scripts

bioc

scTreeViz:R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters.

Maintained by Jayaram Kancherla. Last updated 5 months ago.

visualization infrastructure gui singlecell

7.7 match 4.00 score 3 scripts

trnnick

tsutils:Time Series Exploration, Modelling and Forecasting

Includes: (i) tests and visualisations that can help the modeller explore time series components and perform decomposition; (ii) modelling shortcuts, such as functions to construct lagmatrices and seasonal dummy variables of various forms; (iii) an implementation of the Theta method; (iv) tools to facilitate the design of the forecasting process, such as ABC-XYZ analyses; and (v) "quality of life" functions, such as treating time series for trailing and leading values.

Maintained by Nikolaos Kourentzes. Last updated 1 years ago.

3.9 match 12 stars 7.78 score 472 scripts 18 dependents

r-dbi

odbc:Connect to ODBC Compatible Databases (using the DBI Interface)

A DBI-compatible interface to ODBC databases.

Maintained by Hadley Wickham. Last updated 13 days ago.

database odbc unixodbc cpp

1.8 match 396 stars 16.22 score 2.9k scripts 22 dependents

microsoft

finnts:Microsoft Finance Time Series Forecasting Framework

Automated time series forecasting developed by Microsoft Finance. The Microsoft Finance Time Series Forecasting Framework, aka Finn, can be used to forecast any component of the income statement, balance sheet, or any other area of interest by finance. Any numerical quantity over time, Finn can be used to forecast it. While it can be applied outside of the finance domain, Finn was built to meet the needs of financial analysts to better forecast their businesses within a company, and has a lot of built in features that are specific to the needs of financial forecasters. Happy forecasting!

Maintained by Mike Tokic. Last updated 25 days ago.

business data-science feature-selection finance finnts forecasting machine-learning microsoft time-series

3.0 match 193 stars 9.45 score 39 scripts

florianjansen

vegdata:Access Vegetation Databases and Treat Taxonomy

Handling of vegetation data from different sources ( Turboveg 2.0 <https://www.synbiosys.alterra.nl/turboveg/>; the German national repository <https://www.vegetweb.de> and others. Taxonomic harmonization (given appropriate taxonomic lists, e.g. the German taxonomic standard list "GermanSL", <https://germansl.infinitenature.org>).

Maintained by Florian Jansen. Last updated 1 years ago.

7.3 match 2 stars 3.84 score 38 scripts 3 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 1 months ago.

arules association-rules frequent-itemsets

2.0 match 194 stars 13.99 score 3.3k scripts 28 dependents

cran

aniDom:Inferring Dominance Hierarchies and Estimating Uncertainty

Provides: (1) Tools to infer dominance hierarchies based on calculating Elo scores, but with custom functions to improve estimates in animals with relatively stable dominance ranks. (2) Tools to plot the shape of the dominance hierarchy and estimate the uncertainty of a given data set.

Maintained by Damien R. Farine. Last updated 4 years ago.

10.8 match 1 stars 2.46 score 24 scripts 1 dependents

mbq

vistla:Detecting Influence Paths with Information Theory

Traces information spread through interactions between features, utilising information theory measures and a higher-order generalisation of the concept of widest paths in graphs. In particular, 'vistla' can be used to better understand the results of high-throughput biomedical experiments, by organising the effects of the investigated intervention in a tree-like hierarchy from direct to indirect ones, following the plausible information relay circuits. Due to its higher-order nature, 'vistla' can handle multi-modality and assign multiple roles to a single feature.

Maintained by Miron B. Kursa. Last updated 25 days ago.

openmp

5.3 match 4.78 score 3 scripts

chavent

ClustOfVar:Clustering of Variables

Cluster analysis of a set of variables. Variables can be quantitative, qualitative or a mixture of both.

Maintained by Marie Chavent. Last updated 5 years ago.

3.9 match 7 stars 6.47 score 142 scripts 2 dependents

davidsjoberg

hablar:Non-Astonishing Results in R

Simple tools for converting columns to new data types. Intuitive functions for columns with missing values.

Maintained by David Sjoberg. Last updated 2 years ago.

3.0 match 59 stars 8.30 score 468 scripts

ropensci

chopin:Computation of Spatial Data by Hierarchical and Objective Partitioning of Inputs for Parallel Processing

Geospatial data computation is parallelized by grid, hierarchy, or raster files. Based on future and mirai parallel backends, terra and sf functions as well as convenience functions in the package can be distributed over multiple threads. The simplest way of parallelizing generic geospatial computation is to start from `par_pad_*` functions to `par_grid`, `par_hierarchy`, or `par_multirasters` functions. Virtually any functions accepting classes in terra or sf packages can be used in the three parallelization functions. A common raster-vector overlay operation is provided as a function `extract_at`, which uses exactextractr, with options for kernel weights for summarizing raster values at vector geometries. Other convenience functions for vector-vector operations including simple areal interpolation (`summarize_aw`) and summation of exponentially decaying weights (`summarize_sedc`) are also provided.

Maintained by Insang Song. Last updated 15 days ago.

4.0 match 16 stars 6.11 score 23 scripts

straussed

DynaRankR:Inferring Longitudinal Dominance Hierarchies

Provides functions for inferring longitudinal dominance hierarchies, which describe dominance relationships and their dynamics in a single latent hierarchy over time. Strauss & Holekamp (in press).

Maintained by Eli D. Strauss. Last updated 5 years ago.

7.7 match 2 stars 3.04 score 11 scripts

bioc

mia:Microbiome analysis

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

Maintained by Tuomas Borman. Last updated 2 days ago.

microbiome software dataimport analysis bioconductor

2.0 match 52 stars 11.50 score 316 scripts 5 dependents

beckerbenj

eatGADS:Data Management of Large Hierarchical Data

Import 'SPSS' data, handle and change 'SPSS' meta data, store and access large hierarchical data in 'SQLite' data bases.

Maintained by Benjamin Becker. Last updated 23 days ago.

3.1 match 1 stars 7.36 score 34 scripts 1 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 6 days ago.

3.5 match 6.53 score 138 scripts 18 dependents

hanmingwu1103

dataSDA:Data Sets for Symbolic Data Analysis

Collects a diverse range of symbolic data and offers a comprehensive set of functions that facilitate the conversion of traditional data into the symbolic data format.

Maintained by Han-Ming Wu. Last updated 2 years ago.

8.3 match 2.70 score 2 scripts

cran

Rdiagnosislist:Manipulate SNOMED CT Diagnosis Lists

Functions and methods for manipulating 'SNOMED CT' concepts. The package contains functions for loading the 'SNOMED CT' release into a convenient R environment, selecting 'SNOMED CT' concepts using regular expressions, and navigating the 'SNOMED CT' ontology. It provides the 'SNOMEDconcept' S3 class for a vector of 'SNOMED CT' concepts (stored as 64-bit integers) and the 'SNOMEDcodelist' S3 class for a table of concepts IDs with descriptions. The package can be used to construct sets of 'SNOMED CT' concepts for research (<doi:10.1093/jamia/ocac158>). For more information about 'SNOMED CT' visit <https://www.snomed.org/>.

Maintained by Anoop D. Shah. Last updated 2 months ago.

6.1 match 1 stars 3.60 score

mlverse

tabnet:Fit 'TabNet' Models for Classification and Regression

Implements the 'TabNet' model by Sercan O. Arik et al. (2019) <doi:10.48550/arXiv.1908.07442> with 'Coherent Hierarchical Multi-label Classification Networks' by Giunchiglia et al. <doi:10.48550/arXiv.2010.10151> and provides a consistent interface for fitting and creating predictions. It's also fully compatible with the 'tidymodels' ecosystem.

Maintained by Christophe Regouby. Last updated 6 months ago.

tabnet

2.4 match 109 stars 9.00 score 65 scripts

thibautjombart

adegenet:Exploratory Analysis of Genetic and Genomic Data

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

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

1.7 match 182 stars 12.60 score 1.9k scripts 29 dependents

ropensci

geonames:Interface to the "Geonames" Spatial Query Web Service

The web service at <https://www.geonames.org/> provides a number of spatial data queries, including administrative area hierarchies, city locations and some country postal code queries. A (free) username is required and rate limits exist.

Maintained by Barry Rowlingson. Last updated 6 years ago.

2.5 match 37 stars 8.45 score 165 scripts 21 dependents

tpapak

nmarank:Complex Hierarchy Questions in Network Meta-Analysis

Derives the most frequent hierarchies along with their probability of occurrence. One can also define complex hierarchy criteria and calculate their probability. Methodology based on Papakonstantinou et al. (2021) <DOI:10.21203/rs.3.rs-858140/v1>.

Maintained by Theodoros Papakonstantinou. Last updated 8 months ago.

7.7 match 2.70 score 1 scripts

ddalthorp

GenEst:Generalized Mortality Estimator

Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.

Maintained by Daniel Dalthorp. Last updated 2 years ago.

cpp

2.7 match 7 stars 7.81 score 55 scripts 2 dependents

amarnathbose

AHPtools:Consistency in the Analytic Hierarchy Process

A Swiss Army knife of utility functions for users of the Analytic Hierarchy Process (AHP) which will help you to assess the consistency of a PCM as well as to improve its consistency ratio, to compute the sensitivity of a PCM, create a logical, not a random PCM, from the preferences you provide for the alternatives, and a function that helps evaluate the actual consistency of a PCM based on objective, fair bench marking. The various functions in the toolkit additionally provide the flexibility to users to specify only the upper triangular comparison ratios of the PCM in order to performs its assigned task.

Maintained by Amarnath Bose. Last updated 2 years ago.

6.9 match 3.00 score 3 scripts

alexanderrobitzsch

CDM:Cognitive Diagnosis Modeling

Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. This package enables the estimation of the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>), the multiple group (polytomous) GDINA model (de la Torre, 2011, <doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009, <doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008, <doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992, <doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis (Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>). See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02> or Robitzsch and George (2019, <doi:10.1007/978-3-030-05584-4_26>) for further details on estimation and the package structure. For tutorials on how to use the CDM package see George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as Ravand and Robitzsch (2015).

Maintained by Alexander Robitzsch. Last updated 9 months ago.

cognitive-diagnostic-models item-response-theory cpp

2.3 match 22 stars 8.76 score 138 scripts 28 dependents

bioc

ReactomeGraph4R:Interface for the Reactome Graph Database

Pathways, reactions, and biological entities in Reactome knowledge are systematically represented as an ordered network. Instances are represented as nodes and relationships between instances as edges; they are all stored in the Reactome Graph Database. This package serves as an interface to query the interconnected data from a local Neo4j database, with the aim of minimizing the usage of Neo4j Cypher queries.

Maintained by Chi-Lam Poon. Last updated 5 months ago.

dataimport pathways reactome network graphandnetwork

3.8 match 6 stars 5.26 score 6 scripts

briencj

asremlPlus:Augments 'ASReml-R' in Fitting Mixed Models and Packages Generally in Exploring Prediction Differences

Assists in automating the selection of terms to include in mixed models when 'asreml' is used to fit the models. Procedures are available for choosing models that conform to the hierarchy or marginality principle, for fitting and choosing between two-dimensional spatial models using correlation, natural cubic smoothing spline and P-spline models. A history of the fitting of a sequence of models is kept in a data frame. Also used to compute functions and contrasts of, to investigate differences between and to plot predictions obtained using any model fitting function. The content falls into the following natural groupings: (i) Data, (ii) Model modification functions, (iii) Model selection and description functions, (iv) Model diagnostics and simulation functions, (v) Prediction production and presentation functions, (vi) Response transformation functions, (vii) Object manipulation functions, and (viii) Miscellaneous functions (for further details see 'asremlPlus-package' in help). The 'asreml' package provides a computationally efficient algorithm for fitting a wide range of linear mixed models using Residual Maximum Likelihood. It is a commercial package and a license for it can be purchased from 'VSNi' <https://vsni.co.uk/> as 'asreml-R', who will supply a zip file for local installation/updating (see <https://asreml.kb.vsni.co.uk/>). It is not needed for functions that are methods for 'alldiffs' and 'data.frame' objects. The package 'asremPlus' can also be installed from <http://chris.brien.name/rpackages/>.

Maintained by Chris Brien. Last updated 28 days ago.

asreml mixed-models

2.1 match 19 stars 9.34 score 200 scripts

eeethb

edgedata:Datasets that Support the EDGE Server DIY Logic

Datasets from most recent Center for Consumer Information and Insurance Oversight (CCIIO) DIY entry in a tidy format. These support the Centers for Medicare and Medicaid Services' (CMS) risk adjustment Do-It-Yourself (DIY) process, which allows health insurance issuers to calculate member risk profiles under the Health and Human Services-Hierarchical Condition Categories (HHS-HCC) regression model. This regression model is used to calculate risk adjustment transfers. Risk adjustment is a selection mitigation program implemented under the Patient Protection and Affordable Care Act (ACA or Obamacare) in the USA. Under the ACA, health insurance issuers submit claims data to CMS in order for CMS to calculate a risk score under the HHS-HCC regression model. However, CMS does not inform issuers of their average risk score until after the data submission deadline. These data sets can be used by issuers to calculate their average risk score mid-year. More information about risk adjustment and the HHS-HCC model can be found here: <https://www.cms.gov/mmrr/Articles/A2014/MMRR2014_004_03_a03.html>.

Maintained by Ethan Brockmann. Last updated 3 years ago.

7.2 match 1 stars 2.70 score 1 scripts

bioc

treekoR:Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end points. These associations are aimed to recapitulate the nested proportions prevalent in workflows inovlving manual gating, which are often overlooked in workflows using automatic clustering to identify cell populations. We developed treekoR to: Derive a hierarchical tree structure of cell clusters; quantify a cell types as a proportion relative to all cells in a sample (%total), and, as the proportion relative to a parent population (%parent); perform significance testing using the calculated proportions; and provide an interactive html visualisation to help highlight key results.

Maintained by Adam Chan. Last updated 5 months ago.

clustering differentialexpression flowcytometry immunooncology massspectrometry singlecell software statisticalmethod visualization

4.3 match 4.56 score 12 scripts 1 dependents

bioc

iSEE:Interactive SummarizedExperiment Explorer

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.

Maintained by Kevin Rue-Albrecht. Last updated 11 days ago.

cellbasedassays clustering dimensionreduction featureextraction geneexpression gui immunooncology shinyapps singlecell transcription transcriptomics visualization dimension-reduction feature-extraction gene-expression hacktoberfest human-cell-atlas shiny single-cell

1.5 match 225 stars 12.86 score 380 scripts 9 dependents

bioc

LOBSTAHS:Lipid and Oxylipin Biomarker Screening through Adduct Hierarchy Sequences

LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.

Maintained by Henry Holm. Last updated 5 months ago.

immunooncology massspectrometry metabolomics lipidomics dataimport adduct algae bioconductor hplc-esi-ms lipid mass-spectrometry oxidative-stress-biomarkers oxidized-lipids oxylipins plankton

2.9 match 8 stars 6.56 score 9 scripts

r-lib

ymlthis:Write 'YAML' for 'R Markdown', 'bookdown', 'blogdown', and More

Write 'YAML' front matter for R Markdown and related documents. Work with 'YAML' objects more naturally and write the resulting 'YAML' to your clipboard or to 'YAML' files related to your project.

Maintained by Malcolm Barrett. Last updated 3 years ago.

1.9 match 165 stars 9.91 score 196 scripts 14 dependents

merliseclyde

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

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

Maintained by Merlise Clyde. Last updated 4 months ago.

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

1.7 match 44 stars 10.81 score 420 scripts 3 dependents

josempozo

zoolog:Zooarchaeological Analysis with Log-Ratios

Includes functions and reference data to generate and manipulate log-ratios (also known as log size index (LSI) values) from measurements obtained on zooarchaeological material. Log ratios are used to compare the relative (rather than the absolute) dimensions of animals from archaeological contexts (Meadow 1999, ISBN: 9783896463883). zoolog is also able to seamlessly integrate data and references with heterogeneous nomenclature, which is internally managed by a zoolog thesaurus. A preliminary version of the zoolog methods was first used by Trentacoste, Nieto-Espinet, and Valenzuela-Lamas (2018) <doi:10.1371/journal.pone.0208109>.

Maintained by Jose M Pozo. Last updated 3 years ago.

4.0 match 6 stars 4.48 score 4 scripts

davidchall

bignum:Arbitrary-Precision Integer and Floating-Point Mathematics

Classes for storing and manipulating arbitrary-precision integer vectors and high-precision floating-point vectors. These extend the range and precision of the 'integer' and 'double' data types found in R. This package utilizes the 'Boost.Multiprecision' C++ library. It is specifically designed to work well with the 'tidyverse' collection of R packages.

Maintained by David Hall. Last updated 2 years ago.

arbitrary-precision bignum vctrs cpp

3.3 match 16 stars 5.32 score 13 scripts

mhahsler

stream:Infrastructure for Data Stream Mining

A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893, NSF CMMI 1728612, and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.

Maintained by Michael Hahsler. Last updated 4 days ago.

data-stream-clustering datastream stream-mining cpp

1.8 match 39 stars 10.05 score 132 scripts 3 dependents

anttonalberdi

hilldiv:Integral Analysis of Diversity Based on Hill Numbers

Tools for analysing, comparing, visualising and partitioning diversity based on Hill numbers. 'hilldiv' is an R package that provides a set of functions to assist analysis of diversity for diet reconstruction, microbial community profiling or more general ecosystem characterisation analyses based on Hill numbers, using OTU/ASV tables and associated phylogenetic trees as inputs. The package includes functions for (phylo)diversity measurement, (phylo)diversity profile plotting, (phylo)diversity comparison between samples and groups, (phylo)diversity partitioning and (dis)similarity measurement. All of these grounded in abundance-based and incidence-based Hill numbers. The statistical framework developed around Hill numbers encompasses many of the most broadly employed diversity (e.g. richness, Shannon index, Simpson index), phylogenetic diversity (e.g. Faith's PD, Allen's H, Rao's quadratic entropy) and dissimilarity (e.g. Sorensen index, Unifrac distances) metrics. This enables the most common analyses of diversity to be performed while grounded in a single statistical framework. The methods are described in Jost et al. (2007) <DOI:10.1890/06-1736.1>, Chao et al. (2010) <DOI:10.1098/rstb.2010.0272> and Chiu et al. (2014) <DOI:10.1890/12-0960.1>; and reviewed in the framework of molecularly characterised biological systems in Alberdi & Gilbert (2019) <DOI:10.1111/1755-0998.13014>.

Maintained by Antton Alberdi. Last updated 4 years ago.

4.0 match 11 stars 4.35 score 41 scripts

s-fleck

lgr:A Fully Featured Logging Framework

A flexible, feature-rich yet light-weight logging framework based on 'R6' classes. It supports hierarchical loggers, custom log levels, arbitrary data fields in log events, logging to plaintext, 'JSON', (rotating) files, memory buffers. For extra appenders that support logging to databases, email and push notifications see the the package lgr.app.

Maintained by Stefan Fleck. Last updated 4 months ago.

log4j logging r6

1.5 match 81 stars 11.29 score 120 scripts 93 dependents

r-spatialecology

belg:Boltzmann Entropy of a Landscape Gradient

Calculates the Boltzmann entropy of a landscape gradient. This package uses the analytical method created by Gao, P., Zhang, H. and Li, Z., 2018 (<doi:10.1111/tgis.12315>) and by Gao, P. and Li, Z., 2019 (<doi:10.1007/s10980-019-00854-3>). It also extend the original ideas by allowing calculations on data with missing values.

Maintained by Jakub Nowosad. Last updated 2 years ago.

entropy landscape raster spatial cpp

2.9 match 19 stars 5.80 score 11 scripts 1 dependents

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 4 days ago.

array hdfs s3 storage-manager tiledb cpp

1.3 match 107 stars 11.96 score 306 scripts 4 dependents

bioc

QFeatures:Quantitative features for mass spectrometry data

The QFeatures infrastructure enables the management and processing of quantitative features for high-throughput mass spectrometry assays. It provides a familiar Bioconductor user experience to manages quantitative data across different assay levels (such as peptide spectrum matches, peptides and proteins) in a coherent and tractable format.

Maintained by Laurent Gatto. Last updated 13 days ago.

infrastructure massspectrometry proteomics metabolomics bioconductor mass-spectrometry

1.3 match 27 stars 11.87 score 278 scripts 49 dependents

bioc

biocViews:Categorized views of R package repositories

Infrastructure to support 'views' used to classify Bioconductor packages. 'biocViews' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to 'software', 'annotation', and 'experiment data' packages.

Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.

infrastructure bioconductor-package core-package

1.6 match 4 stars 9.71 score 30 scripts 14 dependents

rdinnager

phyf:Phylogenetic Flow Objects for Easy Manipulation and Modelling of Data on Phylogenetic Trees and Graphs

The {phyf} package implements a tibble and vctrs based object for storing phylogenetic trees along with data. It is fast and flexible and directly produces data structures useful for phylogenetic modelling in the {fibre} package.

Maintained by Russell Dinnage. Last updated 7 months ago.

3.8 match 1 stars 4.20 score 53 scripts 1 dependents

jongheepark

MCMCpack:Markov Chain Monte Carlo (MCMC) Package

Contains functions to perform Bayesian inference using posterior simulation for a number of statistical models. Most simulation is done in compiled C++ written in the Scythe Statistical Library Version 1.0.3. All models return 'coda' mcmc objects that can then be summarized using the 'coda' package. Some useful utility functions such as density functions, pseudo-random number generators for statistical distributions, a general purpose Metropolis sampling algorithm, and tools for visualization are provided.

Maintained by Jong Hee Park. Last updated 7 months ago.

cpp

1.7 match 13 stars 9.40 score 2.6k scripts 150 dependents

ropensci

ritis:Integrated Taxonomic Information System Client

An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).

Maintained by Julia Blum. Last updated 1 months ago.

taxonomy biology nomenclature json api web api-client identifiers species names api-wrapper itis taxize

2.0 match 16 stars 7.72 score 64 scripts 24 dependents

ropensci

EML:Read and Write Ecological Metadata Language Files

Work with Ecological Metadata Language ('EML') files. 'EML' is a widely used metadata standard in the ecological and environmental sciences, described in Jones et al. (2006), <doi:10.1146/annurev.ecolsys.37.091305.110031>.

Maintained by Carl Boettiger. Last updated 3 years ago.

eml eml-metadata metadata-standard

1.3 match 97 stars 11.19 score 378 scripts 7 dependents

pharmar

riskmetric:Risk Metrics to Evaluating R Packages

Facilities for assessing R packages against a number of metrics to help quantify their robustness.

Maintained by Eli Miller. Last updated 9 days ago.

1.7 match 167 stars 8.89 score 43 scripts

ramiromagno

gwasrapidd:'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

'GWAS' R 'API' Data Download. This package provides easy access to the 'NHGRI'-'EBI' 'GWAS' Catalog data by accessing the 'REST' 'API' <https://www.ebi.ac.uk/gwas/rest/docs/api/>.

Maintained by Ramiro Magno. Last updated 1 years ago.

thirdpartyclient biomedicalinformatics genomewideassociation snp association-studies gwas-catalog human rest-client trait trait-ontology

1.8 match 95 stars 8.10 score 49 scripts 1 dependents

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

moosa-r

rbioapi:User-Friendly R Interface to Biologic Web Services' API

Currently fully supports Enrichr, JASPAR, miEAA, PANTHER, Reactome, STRING, and UniProt! The goal of rbioapi is to provide a user-friendly and consistent interface to biological databases and services. In a way that insulates the user from the technicalities of using web services API and creates a unified and easy-to-use interface to biological and medical web services. This is an ongoing project; New databases and services will be added periodically. Feel free to suggest any databases or services you often use.

Maintained by Moosa Rezwani. Last updated 1 months ago.

api-client bioinformatics biology enrichment enrichment-analysis enrichr jaspar mieaa over-representation-analysis panther reactome string uniprot

1.8 match 20 stars 7.60 score 55 scripts

bioc

gdsfmt:R Interface to CoreArray Genomic Data Structure (GDS) Files

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

Maintained by Xiuwen Zheng. Last updated 2 days ago.

infrastructure dataimport bioinformatics gds-format genomics cpp

1.2 match 18 stars 11.34 score 920 scripts 29 dependents

bioc

PhyloProfile:PhyloProfile

PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles, presence/absence patterns of genes over a set of species, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence/structure similarity, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R-Shiny, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification.

Maintained by Vinh Tran. Last updated 7 days ago.

software visualization datarepresentation multiplecomparison functionalprediction dimensionreduction bioinformatics heatmap interactive-visualizations orthologs phylogenetic-profile shiny

1.8 match 33 stars 7.77 score 10 scripts

garthtarr

edgebundleR:Circle Plot with Bundled Edges

Generates interactive circle plots with the nodes around the circumference and linkages between the connected nodes using hierarchical edge bundling via the D3 JavaScript library. See <http://d3js.org/> for more information on D3.

Maintained by Garth Tarr. Last updated 2 years ago.

1.9 match 68 stars 7.23 score 55 scripts

marconotaro

HEMDAG:Hierarchical Ensemble Methods for Directed Acyclic Graphs

An implementation of several Hierarchical Ensemble Methods (HEMs) for Directed Acyclic Graphs (DAGs). 'HEMDAG' package: 1) reconciles flat predictions with the topology of the ontology; 2) can enhance the predictions of virtually any flat learning methods by taking into account the hierarchical relationships between ontology classes; 3) provides biologically meaningful predictions that always obey the true-path-rule, the biological and logical rule that governs the internal coherence of biomedical ontologies; 4) is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but can be safely applied to tree-structured taxonomies as well (as FunCat), since trees are DAGs; 5) scales nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples; 6) provides several utility functions to process and analyze graphs; 7) provides several performance metrics to evaluate HEMs algorithms. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>).

Maintained by Marco Notaro. Last updated 4 months ago.

cpp

4.1 match 3.20 score 32 scripts

ludvigolsen

rearrr:Rearranging Data

Arrange data by a set of methods. Use rearrangers to reorder data points and mutators to change their values. From basic utilities, to centering the greatest value, to swirling in 3-dimensional space, 'rearrr' enables creativity when plotting and experimenting with data.

Maintained by Ludvig Renbo Olsen. Last updated 10 days ago.

arrange cluster expand forming generate ggplot2 order plotting-in-r roll rotate shaping swirl transformations

1.8 match 24 stars 7.26 score 128 scripts 8 dependents

cran

socialh:Rank and Social Hierarchy for Gregarious Animals

Tools developed to facilitate the establishment of the rank and social hierarchy for gregarious animals by the Si method developed by Kondo & Hurnik (1990)<doi:10.1016/0168-1591(90)90125-W>. It is also possible to determine the number of agonistic interactions between two individuals, sociometric and dyadics matrix from dataset obtained through electronic bins. In addition, it is possible plotting the results using a bar plot, box plot, and sociogram.

Maintained by Julia de Paula Soares Valente. Last updated 2 years ago.

6.5 match 2.00 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.

9.4 match 1.38 score 24 scripts

bioc

openCyto:Hierarchical Gating Pipeline for flow cytometry data

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

Maintained by Mike Jiang. Last updated 5 months ago.

immunooncology flowcytometry dataimport preprocessing datarepresentation cpp

1.7 match 7.62 score 404 scripts 1 dependents

sidharthmacherla

conjurer:A Parametric Method for Generating Synthetic Data

Generates synthetic data distributions to enable testing various modelling techniques in ways that real data does not allow. Noise can be added in a controlled manner such that the data seems real. This methodology is generic and therefore benefits both the academic and industrial research.

Maintained by Sidharth Macherla. Last updated 9 months ago.

dummy-data-generator synthetic-data synthetic-data-generation synthetic-dataset-generation synthetic-tabular-data

2.6 match 9 stars 4.95 score 3 scripts

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.

classification icd-10

2.0 match 22 stars 6.31 score 23 scripts

sgsokol

kvh:Read/Write Files in Key-Value-Hierarchy Format

The format KVH is a lightweight format that can be read/written both by humans and machines. It can be useful in situations where XML or alike formats seem to be an overkill. We provide an ability to parse KVH files in R pretty fast due to 'Rcpp' use.

Maintained by Serguei Sokol. Last updated 9 months ago.

cpp

4.6 match 2.70 score 5 scripts

connor-reid-tiffany

omu:A Metabolomics Analysis Tool for Intuitive Figures and Convenient Metadata Collection

Facilitates the creation of intuitive figures to describe metabolomics data by utilizing Kyoto Encyclopedia of Genes and Genomes (KEGG) hierarchy data, and gathers functional orthology and gene data from the KEGG-REST API.

Maintained by Connor Tiffany. Last updated 1 years ago.

2.5 match 3 stars 4.89 score 52 scripts

gobbios

EloSteepness:Bayesian Dominance Hierarchy Steepness via Elo Rating and David's Scores

Obtain Bayesian posterior distributions of dominance hierarchy steepness (Neumann and Fischer (2023) <doi:10.1111/2041-210X.14021>). Steepness estimation is based on Bayesian implementations of either Elo-rating or David's scores.

Maintained by Christof Neumann. Last updated 1 years ago.

cpp

3.3 match 3.70 score 5 scripts

ropensci

natserv:'NatureServe' Interface

Interface to 'NatureServe' (<https://www.natureserve.org/>). Includes methods to get data, image metadata, search taxonomic names, and make maps.

Maintained by Christopher Tracey. Last updated 1 months ago.

taxonomy species api web-services natureserve metadata maps taxize

1.7 match 11 stars 7.06 score 18 scripts 24 dependents

stocnet

manynet:Many Ways to Make, Modify, Map, Mark, and Measure Myriad Networks

Many tools for making, modifying, mapping, marking, measuring, and motifs and memberships of many different types of networks. All functions operate with matrices, edge lists, and 'igraph', 'network', and 'tidygraph' objects, and on one-mode, two-mode (bipartite), and sometimes three-mode networks. The package includes functions for importing and exporting, creating and generating networks, modifying networks and node and tie attributes, and describing and visualizing networks with sensible defaults.

Maintained by James Hollway. Last updated 3 months ago.

diffusion-models graphs network-analysis

1.9 match 13 stars 6.41 score 35 scripts 1 dependents

rivolli

utiml:Utilities for Multi-Label Learning

Multi-label learning strategies and others procedures to support multi- label classification in R. The package provides a set of multi-label procedures such as sampling methods, transformation strategies, threshold functions, pre-processing techniques and evaluation metrics. A complete overview of the matter can be seen in Zhang, M. and Zhou, Z. (2014) <doi:10.1109/TKDE.2013.39> and Gibaja, E. and Ventura, S. (2015) A Tutorial on Multi-label Learning.

Maintained by Adriano Rivolli. Last updated 4 years ago.

1.9 match 28 stars 6.39 score 87 scripts

bioc

GlobalAncova:Global test for groups of variables via model comparisons

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

Maintained by Manuela Hummel. Last updated 5 months ago.

microarray onechannel differentialexpression pathways regression

2.3 match 5.32 score 9 scripts 1 dependents

canmod

macpan2:Fast and Flexible Compartmental Modelling

Fast and flexible compartmental modelling with Template Model Builder.

Maintained by Steve Walker. Last updated 2 days ago.

compartmental-models epidemiology forecasting mixed-effects model-fitting optimization simulation simulation-modeling cpp

1.3 match 4 stars 8.89 score 246 scripts 1 dependents

vusaverse

vvtableau:R Interface for 'Tableau' Services

Provides an R interface for interacting with the 'Tableau' Server. It allows users to perform various operations such as publishing workbooks, refreshing data extracts, and managing users using the 'Tableau' REST API (see <https://help.tableau.com/current/api/rest_api/en-us/REST/rest_api_ref.htm> for details). Additionally, it includes functions to perform manipulations on local 'Tableau' workbooks.

Maintained by Tomer Iwan. Last updated 7 months ago.

rest-api tableau tableau-dashboards tableau-desktop tableau-rest-api tableau-server

1.9 match 7 stars 6.25 score 16 scripts

tidyverse

tidyr:Tidy Messy Data

Tools to help to create tidy data, where each column is a variable, each row is an observation, and each cell contains a single value. 'tidyr' contains tools for changing the shape (pivoting) and hierarchy (nesting and 'unnesting') of a dataset, turning deeply nested lists into rectangular data frames ('rectangling'), and extracting values out of string columns. It also includes tools for working with missing values (both implicit and explicit).

Maintained by Hadley Wickham. Last updated 13 days ago.

tidy-data cpp

0.5 match 1.4k stars 22.88 score 168k scripts 5.5k dependents

zmeers

flourishcharts:'Flourish' for 'R' and 'Python'

Interactive data visualization for data practitioners. 'flourishcharts' allows users to visualize their data using 'Flourish' graphs that are grounded in data storytelling principles. Users can create racing bar & line charts, as well as other interactive elements commonly found in 'D3' graphics, easily in 'R' and 'Python'. The package relies on an enterprise API provided by 'Flourish', a data visualization platform <https://developers.flourish.studio/api/introduction/>.

Maintained by Zoe Meers. Last updated 5 months ago.

3.9 match 3.00 score 5 scripts

christophergandrud

d3Network:The Old Package for Creating D3 JavaScript Network, Tree, Dendrogram, and Sankey Graphs

!!! NOTE: Active development has moved to the networkD3 package. !!!

Maintained by Christopher Gandrud. Last updated 10 years ago.

1.8 match 172 stars 6.63 score 82 scripts

csids

csdata:Structural Data for Norway

Datasets relating to population in municipalities, municipality/county matching, and how different municipalities have merged/redistricted over time from 2006 to 2024.

Maintained by Richard Aubrey White. Last updated 6 months ago.

csverse

2.0 match 5.78 score 6 scripts 2 dependents

amarnathbose

createLogicalPCM:Create Logical Pairwise Comparison Matrix for the Analytic Hierarchy Process

Create Pairwise Comparison Matrices for use in the Analytic Hierarchy Process. The Pairwise Comparison Matrix created will be a logical matrix, which unlike a random comparison matrix, is similar to what a rational decision maker would create on the basis of a preference vector for the alternatives considered.

Maintained by Amarnath Bose. Last updated 2 years ago.

5.0 match 2.30 score 3 scripts

ropensci

taxadb:A High-Performance Local Taxonomic Database Interface

Creates a local database of many commonly used taxonomic authorities and provides functions that can quickly query this data.

Maintained by Carl Boettiger. Last updated 11 months ago.

1.5 match 43 stars 7.68 score 53 scripts 1 dependents

cran

codelist:Working with Code Lists

Functions for working with code lists and vectors with codes. These are an alternative for factor that keep track of both the codes and labels. Methods allow for transforming between codes and labels. Also supports hierarchical code lists.

Maintained by Jan van der Laan. Last updated 24 days ago.

3.8 match 3.02 score 21 scripts

cpfaff

rtematres:Exploit vocabularies on tematres server.

Exploit vocabularies on tematres server and annotate data frames in R.

Maintained by Claas-Thido Pfaff. Last updated 10 years ago.

4.3 match 1 stars 2.70 score 3 scripts

canmod

iidda.analysis:Tools for Analyzing IIDDA Datasets

This package contains tools for working with data obtained from the International Infectious Disease Data Archive.

Maintained by Steven Walker. Last updated 4 months ago.

2.0 match 5.65 score 23 scripts

ptaranti

coppeCosenzaR:COPPE-Cosenza Fuzzy Hierarchy Model

The program implements the COPPE-Cosenza Fuzzy Hierarchy Model. The model was based on the evaluation of local alternatives, representing regional potentialities, so as to fulfill demands of economic projects. After defining demand profiles in terms of their technological coefficients, the degree of importance of factors is defined so as to represent the productive activity. The method can detect a surplus of supply without the restriction of the distance of classical algebra, defining a hierarchy of location alternatives. In COPPE-Cosenza Model, the distance between factors is measured in terms of the difference between grades of memberships of the same factors belonging to two or more sets under comparison. The required factors are classified under the following linguistic variables: Critical (CR); Conditioning (C); Little Conditioning (LC); and Irrelevant (I). And the alternatives can assume the following linguistic variables: Excellent (Ex), Good (G), Regular (R), Weak (W), Empty (Em), Zero (Z) and Inexistent (In). The model also provides flexibility, allowing different aggregation rules to be performed and defined by the Decision Maker. Such feature is considered in this package, allowing the user to define other aggregation matrices, since it considers the same linguistic variables mentioned.

Maintained by Pier Taranti. Last updated 5 years ago.

coppe-cosenza

3.8 match 3.00 score 20 scripts

selesnow

rgoogleads:Loading Data from 'Google Ads API'

Interface for loading data from 'Google Ads API', see <https://developers.google.com/google-ads/api/docs/start>. Package provide function for authorization and loading reports.

Maintained by Alexey Seleznev. Last updated 2 months ago.

1.8 match 14 stars 6.40 score 15 scripts 1 dependents

dleivaur79

steepness:Testing Steepness of Dominance Hierarchies

The steepness package computes steepness as a property of dominance hierarchies. Steepness is defined as the absolute slope of the straight line fitted to the normalized David's scores. The normalized David's scores can be obtained on the basis of dyadic dominance indices corrected for chance or by means of proportions of wins. Given an observed sociomatrix, it computes hierarchy's steepness and estimates statistical significance by means of a randomization test.

Maintained by David Leiva. Last updated 3 years ago.

9.3 match 1 stars 1.18 score 15 scripts

paterijk

MCDA:Support for the Multicriteria Decision Aiding Process

Support for the analyst in a Multicriteria Decision Aiding (MCDA) process with algorithms, preference elicitation and data visualisation functions. Sébastien Bigaret, Richard Hodgett, Patrick Meyer, Tatyana Mironova, Alexandru Olteanu (2017) Supporting the multi-criteria decision aiding process : R and the MCDA package, Euro Journal On Decision Processes, Volume 5, Issue 1 - 4, pages 169 - 194 <doi:10.1007/s40070-017-0064-1>.

Maintained by Patrick Meyer. Last updated 2 years ago.

1.8 match 30 stars 6.04 score 182 scripts

inbo

n2khab:Providing Preprocessed Reference Data for Flemish Natura 2000 Habitat Analyses

The n2khab package is an R package with preprocessing functions and standard reference data, useful for analyses regarding Flemish Natura 2000 habitats and regionally important biotopes (RIBs).

Maintained by Floris Vanderhaeghe. Last updated 2 months ago.

habitat natura2000 preprocessing-functions reproducibility

1.7 match 2 stars 6.32 score 139 scripts 1 dependents

flujoo

gm:Create Music with Ease

Provides a simple and intuitive high-level language for music representation. Generates and embeds music scores and audio files in 'RStudio', 'R Markdown' documents, and R 'Jupyter Notebooks'. Internally, uses 'MusicXML' <https://github.com/w3c/musicxml> to represent music, and 'MuseScore' <https://musescore.org/> to convert 'MusicXML'.

Maintained by Renfei Mao. Last updated 8 months ago.

algorithmic-composition music-programming musicxml

1.3 match 207 stars 8.06 score 35 scripts

ddediu

AdhereR:Adherence to Medications

Computation of adherence to medications from Electronic Health care Data and visualization of individual medication histories and adherence patterns. The package implements a set of S3 classes and functions consistent with current adherence guidelines and definitions. It allows the computation of different measures of adherence (as defined in the literature, but also several original ones), their publication-quality plotting, the estimation of event duration and time to initiation, the interactive exploration of patient medication history and the real-time estimation of adherence given various parameter settings. It scales from very small datasets stored in flat CSV files to very large databases and from single-thread processing on mid-range consumer laptops to parallel processing on large heterogeneous computing clusters. It exposes a standardized interface allowing it to be used from other programming languages and platforms, such as Python.

Maintained by Dan Dediu. Last updated 1 years ago.

adherence-to-medications electronic-healthcare-data hadoop medical-databases medication-histories python sql visualisation

1.5 match 28 stars 7.07 score 47 scripts 1 dependents

ropensci

taxizedb:Tools for Working with 'Taxonomic' Databases

Tools for working with 'taxonomic' databases, including utilities for downloading databases, loading them into various 'SQL' databases, cleaning up files, and providing a 'SQL' connection that can be used to do 'SQL' queries directly or used in 'dplyr'.

Maintained by Tamás Stirling. Last updated 1 months ago.

itis taxize taxonomic-databases taxonomy

1.8 match 31 stars 5.86 score 86 scripts 1 dependents

lucianea

AHPWR:Compute Analytic Hierarchy Process

Compute a tree level hierarchy, judgment matrix, consistency index and ratio, priority vectors, hierarchic synthesis and rank. Based on the book entitled "Models, Methods, Concepts and Applications of the Analytic Hierarchy Process" by Saaty and Vargas (2012, ISBN 978-1-4614-3597-6).

Maintained by Luciane Ferreira Alcoforado. Last updated 2 years ago.

openjdk

5.3 match 2.00 score 3 scripts

danforthcenter

pcvr:Plant Phenotyping and Bayesian Statistics

Analyse common types of plant phenotyping data, provide a simplified interface to longitudinal growth modeling and select Bayesian statistics, and streamline use of 'PlantCV' output. Several Bayesian methods and reporting guidelines for Bayesian methods are described in Kruschke (2018) <doi:10.1177/2515245918771304>, Kruschke (2013) <doi:10.1037/a0029146>, and Kruschke (2021) <doi:10.1038/s41562-021-01177-7>.

Maintained by Josh Sumner. Last updated 5 days ago.

1.5 match 4 stars 6.99 score 39 scripts

nifu-no

saros.base:Base Tools for Semi-Automatic Reporting of Ordinary Surveys

Scaffold an entire web-based report using template chunks, based on a small chapter overview and a dataset. Highly adaptable with prefixes, suffixes, translations, etc. Also contains tools for password-protecting, e.g. for each organization's report on a website. Developed for the common case of a survey across multiple organizations/sites where each organization wants to obtain results for their organization compared with everyone else. See 'saros' (<https://CRAN.R-project.org/package=saros>) for tools used for authors in the drafted reports.

Maintained by Stephan Daus. Last updated 1 months ago.

1.8 match 1 stars 5.98 score 7 scripts

phuse-org

sendigR:Enable Cross-Study Analysis of 'CDISC' 'SEND' Datasets

A system enables cross study Analysis by extracting and filtering study data for control animals from 'CDISC' 'SEND' Study Repository. These data types are supported: Body Weights, Laboratory test results and Microscopic findings. These database types are supported: 'SQLite' and 'Oracle'.

Maintained by Wenxian Wang. Last updated 10 days ago.

1.6 match 12 stars 6.28 score 6 scripts

bioc

BERT:High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT)

Provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Maintained by Yannis Schumann. Last updated 2 months ago.

batcheffect preprocessing experimentaldesign qualitycontrol batch-effect bioconductor-package bioinformatics data-integration data-science

1.9 match 2 stars 5.40 score 18 scripts

ropensci

mregions2:Access Data from Marineregions.org: Gazetteer & Data Products

Explore and retrieve marine geospatial data from the Marine Regions Gazetteer <https://marineregions.org/gazetteer.php?p=webservices> and the Marine Regions Data Products <https://marineregions.org/webservices.php>.

Maintained by Salvador Jesús Fernández Bejarano. Last updated 2 days ago.

1.7 match 9 stars 5.97 score 40 scripts

bioc

bioCancer:Interactive Multi-Omics Cancers Data Visualization and Analysis

This package is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.

Maintained by Karim Mezhoud. Last updated 5 months ago.

gui datarepresentation network multiplecomparison pathways reactome visualization geneexpression genetarget analysis biocancer-interface cancer cancer-studies rmarkdown

1.6 match 20 stars 5.95 score 7 scripts

rstudio

rscontract:Generic implementation of the 'RStudio' connections contract

Provides a generic implementation of the 'RStudio' connection contract to make it easier for database connections, and other type of connections, opened via R packages integrate with the connections pane inside the 'RStudio' interactive development environment (IDE).

Maintained by Nathan Stephens. Last updated 4 years ago.

connections-pane rstudio

1.9 match 22 stars 5.12 score 4 scripts 2 dependents

uclouvain-cbio

scpdata:Single-Cell Proteomics Data Package

The package disseminates mass spectrometry (MS)-based single-cell proteomics (SCP) datasets. The data were collected from published work and formatted using the `scp` data structure. The data sets contain quantitative information at spectrum, peptide and/or protein level for single cells or minute sample amounts.

Maintained by Christophe Vanderaa. Last updated 10 days ago.

experimentdata expressiondata experimenthub reproducibleresearch massspectrometrydata proteome singlecelldata packagetypedata

1.7 match 6 stars 5.58 score 16 scripts

astamm

fdacluster:Joint Clustering and Alignment of Functional Data

Implementations of the k-means, hierarchical agglomerative and DBSCAN clustering methods for functional data which allows for jointly aligning and clustering curves. It supports functional data defined on one-dimensional domains but possibly evaluating in multivariate codomains. It supports functional data defined in arrays but also via the 'fd' and 'funData' classes for functional data defined in the 'fda' and 'funData' packages respectively. It currently supports shift, dilation and affine warping functions for functional data defined on the real line and uses the SRVF framework to handle boundary-preserving warping for functional data defined on a specific interval. Main reference for the k-means algorithm: Sangalli L.M., Secchi P., Vantini S., Vitelli V. (2010) "k-mean alignment for curve clustering" <doi:10.1016/j.csda.2009.12.008>. Main reference for the SRVF framework: Tucker, J. D., Wu, W., & Srivastava, A. (2013) "Generative models for functional data using phase and amplitude separation" <doi:10.1016/j.csda.2012.12.001>.

Maintained by Aymeric Stamm. Last updated 2 months ago.

openblas cpp openmp

1.5 match 5 stars 6.14 score 31 scripts 1 dependents

b-cubed-eu

gcube:Simulating Biodiversity Data Cubes

This R package provides a simulation framework for biodiversity data cubes. This can start from simulating multiple species distributed in a landscape over a temporal scope. In a second phase, the simulation of a variety of observation processes and effort can generate actual occurrence datasets. Based on their (simulated) spatial uncertainty, occurrences can then be designated to a grid to form a data cube.

Maintained by Ward Langeraert. Last updated 1 months ago.

biodiversity-informatics data-cubes simulations

2.0 match 6 stars 4.60 score 9 scripts

michael626

glinternet:Learning Interactions via Hierarchical Group-Lasso Regularization

Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.

Maintained by Michael Lim. Last updated 4 years ago.

openmp

2.1 match 12 stars 4.26 score 42 scripts 2 dependents

braverock

FinancialInstrument:Financial Instrument Model Infrastructure for R

Infrastructure for defining meta-data and relationships for financial instruments.

Maintained by Ross Bennett. Last updated 7 years ago.

1.8 match 19 stars 4.99 score 102 scripts

r-forge

Matrix:Sparse and Dense Matrix Classes and Methods

A rich hierarchy of sparse and dense matrix classes, including general, symmetric, triangular, and diagonal matrices with numeric, logical, or pattern entries. Efficient methods for operating on such matrices, often wrapping the 'BLAS', 'LAPACK', and 'SuiteSparse' libraries.

Maintained by Martin Maechler. Last updated 7 days ago.

openblas

0.5 match 1 stars 17.23 score 33k scripts 12k dependents

comeetie

greed:Clustering and Model Selection with the Integrated Classification Likelihood

An ensemble of algorithms that enable the clustering of networks and data matrices (such as counts, categorical or continuous) with different type of generative models. Model selection and clustering is performed in combination by optimizing the Integrated Classification Likelihood (which is equivalent to minimizing the description length). Several models are available such as: Stochastic Block Model, degree corrected Stochastic Block Model, Mixtures of Multinomial, Latent Block Model. The optimization is performed thanks to a combination of greedy local search and a genetic algorithm (see <arXiv:2002:11577> for more details).

Maintained by Etienne Côme. Last updated 2 years ago.

openblas cpp openmp

1.5 match 14 stars 5.94 score 41 scripts

sfcheung

lmhelprs:Helper Functions for Linear Model Analysis

A collection of helper functions for multiple regression models fitted by lm(). Most of them are simple functions for simple tasks which can be done with coding, but may not be easy for occasional users of R. Most of the tasks addressed are those sometimes needed when using the 'manymome' package (Cheung and Cheung, 2023, <doi:10.3758/s13428-023-02224-z>) and 'stdmod' package (Cheung, Cheung, Lau, Hui, and Vong, 2022, <doi:10.1037/hea0001188>). However, they can also be used in other scenarios.

Maintained by Shu Fai Cheung. Last updated 26 days ago.

regression-models

2.0 match 4.45 score 14 scripts

bcjaeger

table.glue:Make and Apply Customized Rounding Specifications for Tables

Translate double and integer valued data into character values formatted for tabulation in manuscripts or other types of academic reports.

Maintained by Byron Jaeger. Last updated 4 months ago.

1.5 match 7 stars 5.92 score 60 scripts

bioc

rhdf5client:Access HDF5 content from HDF Scalable Data Service

This package provides functionality for reading data from HDF Scalable Data Service from within R. The HSDSArray function bridges from HSDS to the user via the DelayedArray interface. Bioconductor manages an open HSDS instance graciously provided by John Readey of the HDF Group.

Maintained by Vincent Carey. Last updated 5 months ago.

dataimport software infrastructure

1.8 match 4.82 score 37 scripts 2 dependents

chaoliu-cl

textAnnotatoR:Interactive Text Annotation Tool with 'shiny' GUI

A comprehensive text annotation tool built with 'shiny'. Provides an interactive graphical user interface for coding text documents, managing code hierarchies, creating memos, and analyzing coding patterns. Features include code co-occurrence analysis, visualization of coding patterns, comparison of multiple coding sets, and export capabilities. Supports collaborative qualitative research through standardized annotation formats and analysis tools.

Maintained by Chao Liu. Last updated 4 months ago.

2.0 match 4.30 score 5 scripts

tevrenoglou

mtrank:Ranking using Probabilistic Models and Treatment Choice Criteria

Implementation of a novel frequentist approach to produce clinically relevant treatment hierarchies in network meta-analysis. The method is based on treatment choice criteria (TCC) and probabilistic ranking models, as described by Evrenoglou et al. (2024) <DOI:10.48550/arXiv.2406.10612>. The TCC are defined using a rule based on the minimal clinically important difference. Using the defined TCC, the study-level data (i.e., treatment effects and standard errors) are first transformed into a preference format, indicating either a treatment preference (e.g., treatment A > treatment B) or a tie (treatment A = treatment B). The preference data are then synthesized using a probabilistic ranking model, which estimates the latent ability parameter of each treatment and produces the final treatment hierarchy. This parameter represents each treatment’s ability to outperform all the other competing treatments in the network. Consequently, larger ability estimates indicate higher positions in the ranking list.

Maintained by Theodoros Evrenoglou. Last updated 18 days ago.

2.4 match 1 stars 3.54 score 2 scripts

statisticsnorway

GaussSuppression:Tabular Data Suppression using Gaussian Elimination

A statistical disclosure control tool to protect tables by suppression using the Gaussian elimination secondary suppression algorithm (Langsrud, 2024) <doi:10.1007/978-3-031-69651-0_6>. A suggestion is to start by working with functions SuppressSmallCounts() and SuppressDominantCells(). These functions use primary suppression functions for the minimum frequency rule and the dominance rule, respectively. Novel functionality for suppression of disclosive cells is also included. General primary suppression functions can be supplied as input to the general working horse function, GaussSuppressionFromData(). Suppressed frequencies can be replaced by synthetic decimal numbers as described in Langsrud (2019) <doi:10.1007/s11222-018-9848-9>.

Maintained by Øyvind Langsrud. Last updated 3 days ago.

1.3 match 2 stars 6.61 score 50 scripts

philboileau

neatmaps:Heatmaps for Multiple Network Data

Simplify the exploratory data analysis process for multiple network data sets with the help of hierarchical clustering, consensus clustering and heatmaps. Multiple network data consists of multiple disjoint networks that have common variables (e.g. ego networks). This package contains the necessary tools for exploring such data, from the data pre-processing stage to the creation of dynamic visualizations.

Maintained by Philippe Boileau. Last updated 3 years ago.

3.0 match 1 stars 2.70 score 7 scripts

sammo3182

drhutools:Political Science Academic Research Gears

Using these tools to simplify the research process of political science and other social sciences. The current version can create folder system for academic project in political science, calculate psychological trait scores, visualize experimental and spatial data, and set up color-blind palette, functions used in academic research of political psychology or political science in general.

Maintained by Yue Hu. Last updated 3 months ago.

1.8 match 2 stars 4.45 score 3 scripts

josesamos

tab2xml:XML Generation from Tables

Converting structured data from tables into XML format using predefined templates ensures consistency and flexibility, making it ideal for data exchange, reporting, and automated workflows.

Maintained by Jose Samos. Last updated 18 days ago.

2.0 match 4.00 score 4 scripts

ctu-bern

kpitools:Tools for creating key performance indicator reports for clinical trial

Assessing performance of clinical trials can assist identify problems earlier in the trial than might be possible without it and help to improve trial quality. Tools for the creating performance indicator reports are however uncommon. 'kpitools' aims to provide tools to create such reports.

Maintained by Alan G. Haynes. Last updated 7 months ago.

key-performance-indicator kpi quality-control

2.0 match 2 stars 3.90 score 8 scripts

bioc

hierGWAS:Asessing statistical significance in predictive GWA studies

Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.

Maintained by Laura Buzdugan. Last updated 5 months ago.

snp linkagedisequilibrium clustering

2.3 match 3.30 score 1 scripts

jto888

FaultTree:Fault Trees for Risk and Reliability Analysis

Construction, calculation and display of fault trees. Methods derived from Clifton A. Ericson II (2005, ISBN: 9780471739425) <DOI:10.1002/0471739421>, Antoine Rauzy (1993) <DOI:10.1016/0951-8320(93)90060-C>, Tim Bedford and Roger Cooke (2012, ISBN: 9780511813597) <DOI:10.1017/CBO9780511813597>, Nikolaos Limnios, (2007, ISBN: 9780470612484) <DOI: 10.1002/9780470612484>.

Maintained by Jacob Ormerod. Last updated 2 years ago.

cpp

1.8 match 9 stars 4.10 score 14 scripts

psolymos

clickrup:Interacting with the ClickUp v2 API from R

Work with the ClickUp productivity app from R to manage tasks, goals, time tracking, and more.

Maintained by Peter Solymos. Last updated 1 years ago.

api clickup clickup-api project-management

2.3 match 18 stars 3.26 score 7 scripts

marcohlmann

metanetwork:Handling and Representing Trophic Networks in Space and Time

A toolbox to handle and represent trophic networks in space or time across aggregation levels. This package contains a layout algorithm specifically designed for trophic networks, using dimension reduction on a diffusion graph kernel and trophic levels. Importantly, this package provides a layout method applicable for large trophic networks. The package also implements network diversity indices at different aggregation levels and connectance computation.

Maintained by Marc Ohlmann. Last updated 2 years ago.

1.9 match 2 stars 3.89 score 77 scripts

r-forge

stops:Structure Optimized Proximity Scaling

Methods that use flexible variants of multidimensional scaling (MDS) which incorporate parametric nonlinear distance transformations and trade-off the goodness-of-fit fit with structure considerations to find optimal hyperparameters, also known as structure optimized proximity scaling (STOPS) (Rusch, Mair & Hornik, 2023,<doi:10.1007/s11222-022-10197-w>). The package contains various functions, wrappers, methods and classes for fitting, plotting and displaying different 1-way MDS models with ratio, interval, ordinal optimal scaling in a STOPS framework. These cover essentially the functionality of the package smacofx, including Torgerson (classical) scaling with power transformations of dissimilarities, SMACOF MDS with powers of dissimilarities, Sammon mapping with powers of dissimilarities, elastic scaling with powers of dissimilarities, spherical SMACOF with powers of dissimilarities, (ALSCAL) s-stress MDS with powers of dissimilarities, r-stress MDS, MDS with powers of dissimilarities and configuration distances, elastic scaling powers of dissimilarities and configuration distances, Sammon mapping powers of dissimilarities and configuration distances, power stress MDS (POST-MDS), approximate power stress, Box-Cox MDS, local MDS, Isomap, curvilinear component analysis (CLCA), curvilinear distance analysis (CLDA) and sparsified (power) multidimensional scaling and (power) multidimensional distance analysis (experimental models from smacofx influenced by CLCA). All of these models can also be fit by optimizing over hyperparameters based on goodness-of-fit fit only (i.e., no structure considerations). The package further contains functions for optimization, specifically the adaptive Luus-Jaakola algorithm and a wrapper for Bayesian optimization with treed Gaussian process with jumps to linear models, and functions for various c-structuredness indices.

Maintained by Thomas Rusch. Last updated 2 months ago.

openjdk

1.6 match 1 stars 4.48 score 23 scripts

bioc

lute:Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments

Provides a framework for adjustment on cell type size when performing bulk transcripomics deconvolution. The main framework function provides a means of reference normalization using cell size scale factors. It allows for marker selection and deconvolution using non-negative least squares (NNLS) by default. The framework is extensible for other marker selection and deconvolution algorithms, and users may reuse the generics, methods, and classes for these when developing new algorithms.

Maintained by Sean K Maden. Last updated 5 months ago.

rnaseq sequencing singlecell coverage transcriptomics normalization

1.3 match 2 stars 5.26 score 3 scripts

sciviews

svFlow:Data Analysis Work Flow and Pipeline Operator for 'SciViews::R'

Data work flow analysis using 'proto' objects and pipe operator that integrates non-standard evaluation and the 'lazyeval' mechanism.

Maintained by Philippe Grosjean. Last updated 11 months ago.

sciviews workflow

1.8 match 3.86 score 12 scripts 2 dependents

bioc

ExperimentSubset:Manages subsets of data with Bioconductor Experiment objects

Experiment objects such as the SummarizedExperiment or SingleCellExperiment are data containers for one or more matrix-like assays along with the associated row and column data. Often only a subset of the original data is needed for down-stream analysis. For example, filtering out poor quality samples will require excluding some columns before analysis. The ExperimentSubset object is a container to efficiently manage different subsets of the same data without having to make separate objects for each new subset.

Maintained by Irzam Sarfraz. Last updated 5 months ago.

infrastructure software dataimport datarepresentation

1.7 match 4.00 score 8 scripts

interstellar-consultation-services

covid19dbcand:Selected 'Drugbank' Drugs for COVID-19 Treatment Related Data in R Format

Provides different datasets parsed from 'Drugbank' <https://www.drugbank.ca/covid-19> database using 'dbparser' package. It is a smaller version from 'dbdataset' package. It contains only information about COVID-19 possible treatment.

Maintained by Mohammed Ali. Last updated 11 months ago.

dataset dbparser drugbank drugbank-database

1.5 match 3 stars 4.48 score 6 scripts

michaelhallquist

ggbrain:Create Images of Volumetric Brain Data in NIfTI Format Using 'ggplot2' Syntax

A 'ggplot2'-consistent approach to generating 2D displays of volumetric brain imaging data. Display data from multiple NIfTI images using standard 'ggplot2' conventions such scales, limits, and themes to control the appearance of displays. The resulting plots are returned as 'patchwork' objects, inheriting from 'ggplot', allowing for any standard modifications of display aesthetics supported by 'ggplot2'.

Maintained by Michael Hallquist. Last updated 25 days ago.

cpp

1.3 match 2 stars 5.03 score 18 scripts

bioc

flowMatch:Matching and meta-clustering in flow cytometry

Matching cell populations and building meta-clusters and templates from a collection of FC samples.

Maintained by Ariful Azad. Last updated 5 months ago.

immunooncology clustering flowcytometry cpp

1.7 match 3.90 score 1 scripts

edonnachie

ICD10gm:Metadata Processing for the German Modification of the ICD-10 Coding System

Provides convenient access to the German modification of the International Classification of Diagnoses, 10th revision (ICD-10-GM). It provides functionality to aid in the identification, specification and historisation of ICD-10 codes. Its intended use is the analysis of routinely collected data in the context of epidemiology, medical research and health services research. The underlying metadata are released by the German Institute for Medical Documentation and Information <https://www.dimdi.de>, and are redistributed in accordance with their license.

Maintained by Ewan Donnachie. Last updated 1 years ago.

bfarm charlson comorbidities diagnoses dimdi icd-10 metadata routinedaten versorgungsforschung

1.3 match 10 stars 5.30 score 20 scripts

desanou

mglasso:Multiscale Graphical Lasso

Inference of Multiscale graphical models with neighborhood selection approach. The method is based on solving a convex optimization problem combining a Lasso and fused-group Lasso penalties. This allows to infer simultaneously a conditional independence graph and a clustering partition. The optimization is based on the Continuation with Nesterov smoothing in a Shrinkage-Thresholding Algorithm solver (Hadj-Selem et al. 2018) <doi:10.1109/TMI.2018.2829802> implemented in python.

Maintained by Edmond Sanou. Last updated 2 years ago.

1.6 match 2 stars 4.11 score 13 scripts

konstantinryabov

dmtools:Tools for Clinical Data Management

For checking the dataset from EDC(Electronic Data Capture) in clinical trials. 'dmtools' reshape your dataset in a tidy view and check events. You can reshape the dataset and choose your target to check, for example, the laboratory reference range.

Maintained by Konstantin Ryabov. Last updated 2 years ago.

cdisc clinical-data-management laboratory-reference-range-validate

1.5 match 1 stars 4.32 score 14 scripts

clavellab

maldipickr:Dereplicate and Cherry-Pick Mass Spectrometry Spectra

Convenient wrapper functions for the analysis of matrix-assisted laser desorption/ionization-time-of-flight (MALDI-TOF) spectra data in order to select only representative spectra (also called cherry-pick). The package covers the preprocessing and dereplication steps (based on Strejcek, Smrhova, Junkova and Uhlik (2018) <doi:10.3389/fmicb.2018.01294>) needed to cluster MALDI-TOF spectra before the final cherry-picking step. It enables the easy exclusion of spectra and/or clusters to accommodate complex cherry-picking strategies. Alternatively, cherry-picking using taxonomic identification MALDI-TOF data is made easy with functions to import inconsistently formatted reports.

Maintained by Charlie Pauvert. Last updated 23 days ago.

cherry-pick dereplication maldi-tof-ms

1.2 match 2 stars 5.32 score 8 scripts

bodysbobb

HARplus:Enhanced R Package for 'GEMPACK' .har and .sl4 Files

Provides tools for processing and analyzing .har and .sl4 files, making it easier for 'GEMPACK' users and 'GTAP' researchers to handle large economic datasets. It simplifies the management of multiple experiment results, enabling faster and more efficient comparisons without complexity. Users can extract, restructure, and merge data seamlessly, ensuring compatibility across different tools. The processed data can be exported and used in 'R', 'Stata', 'Python', 'Julia', or any software that supports Text, CSV, or 'Excel' formats.

Maintained by Pattawee Puangchit. Last updated 15 hours ago.

gempack gtap har-files sl4-file

1.3 match 2 stars 4.70 score

statisticsnorway

SmallCountRounding:Small Count Rounding of Tabular Data

A statistical disclosure control tool to protect frequency tables in cases where small values are sensitive. The function PLSrounding() performs small count rounding of necessary inner cells so that all small frequencies of cross-classifications to be published (publishable cells) are rounded. This is equivalent to changing micro data since frequencies of unique combinations are changed. Thus, additivity and consistency are guaranteed. The methodology is described in Langsrud and Heldal (2018) <https://www.researchgate.net/publication/327768398_An_Algorithm_for_Small_Count_Rounding_of_Tabular_Data>.

Maintained by Øyvind Langsrud. Last updated 3 days ago.

statistics

1.2 match 3 stars 5.36 score 14 scripts

mrc-ide

naomi.utils:Utility Functions For Naomi Datasets

This package contains utility functions for creating and manipulating datasets for the Naomi model and related projects.

Maintained by Jeffrey Eaton. Last updated 12 months ago.

3.6 match 1 stars 1.64 score 11 scripts

marsdu1989

easyAHP:Analytic Hierarchy Process (AHP)

Given the scores from decision makers, the analytic hierarchy process can be conducted easily.

Maintained by Zhicheng Du. Last updated 7 years ago.

5.5 match 1.00 score 1 scripts

jgx65

hierfstat:Estimation and Tests of Hierarchical F-Statistics

Estimates hierarchical F-statistics from haploid or diploid genetic data with any numbers of levels in the hierarchy, following the algorithm of Yang (Evolution(1998), 52:950). Tests via randomisations the significance of each F and variance components, using the likelihood-ratio statistics G (Goudet et al. (1996) <https://academic.oup.com/genetics/article/144/4/1933/6017091>). Estimates genetic diversity statistics for haploid and diploid genetic datasets in various formats, including inbreeding and coancestry coefficients, and population specific F-statistics following Weir and Goudet (2017) <https://academic.oup.com/genetics/article/206/4/2085/6072590>.

Maintained by Jerome Goudet. Last updated 4 months ago.

devtools fstatistics gwas hierfstat kinship population-genetics population-genomics quantitative-genetics simulations

0.5 match 25 stars 10.94 score 560 scripts 4 dependents

bernhard-da

sdcTable:Methods for Statistical Disclosure Control in Tabular Data

Methods for statistical disclosure control in tabular data such as primary and secondary cell suppression as described for example in Hundepol et al. (2012) <doi:10.1002/9781118348239> are covered in this package.

Maintained by Bernhard Meindl. Last updated 5 days ago.

glpk cpp

1.5 match 1 stars 3.32 score 25 scripts 2 dependents

smorenoa

ODMeans:OD-Means: k-Means for Origin-Destination

OD-means is a hierarchical adaptive k-means algorithm based on origin-destination pairs. In the first layer of the hierarchy, the clusters are separated automatically based on the variation of the within-cluster distance of each cluster until convergence. The second layer of the hierarchy corresponds to the sub clustering process of small clusters based on the distance between the origin and destination of each cluster.

Maintained by Sebastian Moreno. Last updated 12 months ago.

4.8 match 1.00 score

markvanderloo

settings:Software Option Settings Manager for R

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

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

0.5 match 7 stars 9.32 score 1.0k scripts 36 dependents

dmuellner

fastcluster:Fast Hierarchical Clustering Routines for R and 'Python'

This is a two-in-one package which provides interfaces to both R and 'Python'. It implements fast hierarchical, agglomerative clustering routines. Part of the functionality is designed as drop-in replacement for existing routines: linkage() in the 'SciPy' package 'scipy.cluster.hierarchy', hclust() in R's 'stats' package, and the 'flashClust' package. It provides the same functionality with the benefit of a much faster implementation. Moreover, there are memory-saving routines for clustering of vector data, which go beyond what the existing packages provide. For information on how to install the 'Python' files, see the file INSTALL in the source distribution. Based on the present package, Christoph Dalitz also wrote a pure 'C++' interface to 'fastcluster': <https://lionel.kr.hs-niederrhein.de/~dalitz/data/hclust/>.

Maintained by Daniel Müllner. Last updated 1 years ago.

cpp

0.5 match 10 stars 9.29 score 444 scripts 107 dependents

lsteinmeister

htsDegenerateR:Degenerate Hierarchical Time Series Reconciliation

Takes the MinT implementation of [hts: Hierarchical and Grouped Time Series]<https://cran.r-project.org/package=hts> and adapts it to allow degenerate hierarchical structures. Instead of the "nodes" argument, this function takes an S matrix which is more versatile in the structures it allows. For a demo, see [Degenerate Hierarchical Time Series Reconciliation With The Minimum Trace Algorithm in R]<doi:10.15488/17729>. The MinT algorithm is based on [Optimal Forecast Reconciliation for Hierarchical and Grouped Time Series Through Trace Minimization]<doi:10.1080/01621459.2018.1448825>.

Maintained by Louis Steinmeister. Last updated 3 months ago.

1.6 match 1 stars 3.00 score

nschuwirth

ecoval:Procedures for Ecological Assessment of Surface Waters

Functions for evaluating and visualizing ecological assessment procedures for surface waters containing physical, chemical and biological assessments in the form of value functions.

Maintained by Nele Schuwirth. Last updated 3 years ago.

3.5 match 1.34 score 22 scripts

cran

Rgff:R Utilities for GFF Files

R utilities for gff files, either general feature format (GFF3) or gene transfer format (GTF) formatted files. This package includes functions for producing summary stats, check for consistency and sorting errors, conversion from GTF to GFF3 format, file sorting, visualization and plotting of feature hierarchy, and exporting user defined feature subsets to SAF format. This tool was developed by the BioinfoGP core facility at CNB-CSIC.

Maintained by Juan Antonio Garcia-Martin. Last updated 2 years ago.

2.3 match 2.00 score

zdeneksulc

nomclust:Hierarchical Cluster Analysis of Nominal Data

Similarity measures for hierarchical clustering of objects characterized by nominal (categorical) variables. Evaluation criteria for nominal data clustering.

Maintained by Zdenek Sulc. Last updated 2 years ago.

cpp

1.8 match 4 stars 2.48 score 38 scripts

celehs

phecodemap:Visualization for Phecode Mapping with ICD-9 and ICD-10-cm Codes

Phecodemap builds a shiny app to visualize the hierarchy of Phecode Mapping with ICD. The same Phecode hierarchy is displayed in two ways: as a sunburst plot and as a tree.

Maintained by Parse Health. Last updated 1 years ago.

0.8 match 3 stars 5.07 score 13 scripts

ropengov

pxweb:R Interface to PXWEB APIs

Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis API is used by organizations such as Statistics Sweden and Statistics Finland to disseminate data. The R package can interact with all PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract metadata and extract and parse statistics to R data.frame format. PX-Web is a solution to disseminate PC-Axis data files in dynamic tables on the web. Since 2013 PX-Web contains an API to disseminate PC-Axis files.

Maintained by Mans Magnusson. Last updated 1 years ago.

ropengov

0.5 match 66 stars 7.67 score 2 dependents

gagolews

genieclust:Fast and Robust Hierarchical Clustering with Noise Points Detection

A retake on the Genie algorithm (Gagolewski, 2021 <DOI:10.1016/j.softx.2021.100722>), which is a robust hierarchical clustering method (Gagolewski, Bartoszuk, Cena, 2016 <DOI:10.1016/j.ins.2016.05.003>). It is now faster and more memory efficient; determining the whole cluster hierarchy for datasets of 10M points in low dimensional Euclidean spaces or 100K points in high-dimensional ones takes only a minute or so. Allows clustering with respect to mutual reachability distances so that it can act as a noise point detector or a robustified version of 'HDBSCAN*' (that is able to detect a predefined number of clusters and hence it does not dependent on the somewhat fragile 'eps' parameter). The package also features an implementation of inequality indices (e.g., Gini and Bonferroni), external cluster validity measures (e.g., the normalised clustering accuracy, the adjusted Rand index, the Fowlkes-Mallows index, and normalised mutual information), and internal cluster validity indices (e.g., the Calinski-Harabasz, Davies-Bouldin, Ball-Hall, Silhouette, and generalised Dunn indices). See also the 'Python' version of 'genieclust' available on 'PyPI', which supports sparse data, more metrics, and even larger datasets.

Maintained by Marek Gagolewski. Last updated 5 days ago.

cluster-analysis clustering clustering-algorithm data-analysis data-mining data-science genie hdbscan hierarchical-clustering hierarchical-clustering-algorithm machine-learning machine-learning-algorithms mlpack nmslib python python3 sparse cpp openmp

0.5 match 61 stars 7.29 score 13 scripts 5 dependents

bioc

scClassify:scClassify: single-cell Hierarchical Classification

scClassify is a multiscale classification framework for single-cell RNA-seq data based on ensemble learning and cell type hierarchies, enabling sample size estimation required for accurate cell type classification and joint classification of cells using multiple references.

Maintained by Yingxin Lin. Last updated 5 months ago.

singlecell geneexpression classification

0.5 match 23 stars 6.92 score 30 scripts

mmaechler

classGraph:Construct Graphs of S4 Class Hierarchies

Construct directed graphs of S4 class hierarchies and visualize them. In general, these graphs typically are DAGs (directed acyclic graphs), often simple trees in practice.

Maintained by Martin Maechler. Last updated 2 years ago.

3.5 match 1.00 score 1 scripts

cran

pmr:Probability Models for Ranking Data

Descriptive statistics (mean rank, pairwise frequencies, and marginal matrix), Analytic Hierarchy Process models (with Saaty's and Koczkodaj's inconsistencies), probability models (Luce models, distance-based models, and rank-ordered logit models) and visualization with multidimensional preference analysis for ranking data are provided. Current, only complete rankings are supported by this package.

Maintained by Paul H. Lee. Last updated 3 years ago.

2.4 match 1.48 score 1 dependents

bioc

epiregulon:Gene regulatory network inference from single cell epigenomic data

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

Maintained by Xiaosai Yao. Last updated 7 days ago.

singlecell generegulation networkinference network geneexpression transcription genetarget cpp

0.5 match 14 stars 6.67 score 17 scripts

distancedevelopment

readdst:Convert Distance for Windows projects to R analyses

Take projects built using Distance for Windows and create R scripts which duplicate the analysis. Optionally build a test suite that checks analysis results from Distance with the equivalent R results.

Maintained by David Miller. Last updated 3 years ago.

1.8 match 1 stars 1.78 score 12 scripts

eworx-org

labourR:Classify Multilingual Labour Market Free-Text to Standardized Hierarchical Occupations

Allows the user to map multilingual free-text of occupations to a broad range of standardized classifications. The package facilitates automatic occupation coding (see, e.g., Gweon et al. (2017) <doi:10.1515/jos-2017-0006> and Turrell et al. (2019) <doi:10.3386/w25837>), where the ISCO to ESCO mapping is exploited to extend the occupations hierarchy, Le Vrang et al. (2014) <doi:10.1109/mc.2014.283>. Document vectorization is performed using the multilingual ESCO corpus. A method based on the nearest neighbor search is used to suggest the closest ISCO occupation.

Maintained by Alexandros Kouretsis. Last updated 3 years ago.

0.5 match 28 stars 6.29 score 23 scripts 1 dependents

jienagu

forestry:Reshape Data Tree

'forestry' a series of utility functions to help with reshaping hierarchy of data tree, and reform the structure of data tree.

Maintained by Jiena McLellan. Last updated 5 years ago.

0.5 match 21 stars 5.66 score 44 scripts

bioc

famat:Functional analysis of metabolic and transcriptomic data

Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user's genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user's elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user's genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.

Maintained by Mathieu Charles. Last updated 5 months ago.

functionalprediction genesetenrichment pathways go reactome kegg compound gene-ontology genes shiny

0.8 match 1 stars 3.78 score 2 scripts

laijiangshan

rdacca.hp:Hierarchical Partitioning for Canonical Analysis

This function calculates the independent contribution of each explanatory variable to explained variation (R-squared) on RDA,CCA and db-RDA, applying the hierarchy algorithm of Chevan, A. and Sutherland, M. 1991 Hierarchical Partitioning.The American Statistician, 90-96 <DOI:10.1080/00031305.1991.10475776>.

Maintained by Jiangshan Lai. Last updated 23 days ago.

0.5 match 19 stars 5.22 score 29 scripts 1 dependents

jancaha

FuzzyAHP:(Fuzzy) AHP Calculation

Calculation of AHP (Analytic Hierarchy Process - <http://en.wikipedia.org/wiki/Analytic_hierarchy_process>) with classic and fuzzy weights based on Saaty's pairwise comparison method for determination of weights.

Maintained by Jan Caha. Last updated 5 years ago.

ahp fuzzy

0.5 match 3 stars 5.07 score 13 scripts 1 dependents

decisionpatterns

backpipe:Backward Pipe (Right-to-Left) Operator

Provides a backward-pipe operator for 'magrittr' (%<%) or 'pipeR' (%<<%) that allows for a performing operations from right-to-left. This allows writing more legible code where right-to-left ordering is natural. This is common with hierarchies and nested structures such as trees, directories or markup languages (e.g. HTML and XML). The package also includes a R-Studio add-in that can be bound to a keyboard shortcut.

Maintained by Christopher Brown. Last updated 7 years ago.

0.5 match 30 stars 5.18 score 3 scripts

uchidamizuki

timbr:Forest/Tree Data Frames

Provides data frames for forest or tree data structures. You can create forest data structures from data frames and process them based on their hierarchies.

Maintained by Mizuki Uchida. Last updated 5 months ago.

0.5 match 11 stars 4.93 score 31 scripts