Showing 88 of total 88 results (show query)
nutriverse
mwana:An Efficient Workflow for Plausibility Checks and Prevalence Analysis of Wasting in R
A simple and streamlined workflow for plausibility checks and prevalence analysis of wasting based on the Standardized Monitoring and Assessment of Relief and Transition (SMART) Methodology <https://smartmethodology.org/>, with application in R.
Maintained by Tomás Zaba. Last updated 1 months ago.
acute-malnutritionanthropometrymuacnutritionsmartsurveywasting
24.9 match 2 stars 4.23 score 6 scripts
nanxstats
hdnom:Benchmarking and Visualization Toolkit for Penalized Cox Models
Creates nomogram visualizations for penalized Cox regression models, with the support of reproducible survival model building, validation, calibration, and comparison for high-dimensional data.
Maintained by Nan Xiao. Last updated 6 months ago.
benchmarkhigh-dimensional-datalinear-regressionnomogram-visualizationpenalized-cox-modelssurvival-analysisopenblas
7.5 match 43 stars 8.07 score 68 scripts 1 dependents
jonathansmart
AquaticLifeHistory:Life History Analysis Tools
Estimate aquatic species life history using robust techniques. This package supports users undertaking two types of analysis: 1) Growth from length-at-age data, and 2) maturity analyses for length and/or age data. Maturity analyses are performed using generalised linear model approaches incorporating either a binomial or quasibinomial distribution. Growth modelling is performed using the multimodel approach presented by Smart et al. (2016) "Multimodel approaches in shark and ray growth studies: strengths, weaknesses and the future" <doi:10.1111/faf.12154>.
Maintained by Jonathan Smart. Last updated 1 years ago.
9.6 match 8 stars 5.42 score 11 scripts 1 dependents
diystat
NBPSeq:Negative Binomial Models for RNA-Sequencing Data
Negative Binomial (NB) models for two-group comparisons and regression inferences from RNA-Sequencing Data.
Maintained by Yanming Di. Last updated 11 years ago.
10.5 match 1 stars 4.88 score 17 scripts 3 dependents
tdhock
directlabels:Direct Labels for Multicolor Plots
An extensible framework for automatically placing direct labels onto multicolor 'lattice' or 'ggplot2' plots. Label positions are described using Positioning Methods which can be re-used across several different plots. There are heuristics for examining "trellis" and "ggplot" objects and inferring an appropriate Positioning Method.
Maintained by Toby Dylan Hocking. Last updated 11 months ago.
4.5 match 83 stars 10.62 score 1.8k scripts 16 dependents
kkholst
mets:Analysis of Multivariate Event Times
Implementation of various statistical models for multivariate event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>. Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray, Ghosh-Lin, Binomial regression) with fast computation of influence functions.
Maintained by Klaus K. Holst. Last updated 3 days ago.
multivariate-time-to-eventsurvival-analysistime-to-eventfortranopenblascpp
3.5 match 14 stars 13.47 score 236 scripts 42 dependentsjonathansmart
BayesGrowth:Estimate Fish Growth Using MCMC Analysis
Estimate fish length-at-age models using MCMC analysis with 'rstan' models. This package allows a multimodel approach to growth fitting to be applied to length-at-age data and is supported by further analyses to determine model selection and result presentation. The core methods of this package are presented in Smart and Grammer (2021) "Modernising fish and shark growth curves with Bayesian length-at-age models". PLOS ONE 16(2): e0246734 <doi:10.1371/journal.pone.0246734>.
Maintained by Jonathan Smart. Last updated 1 years ago.
9.6 match 11 stars 4.74 score 8 scripts
simon-smart88
shinyscholar:A Template for Creating Reproducible 'shiny' Applications
Create a skeleton 'shiny' application with create_template() that is reproducible, can be saved and meets academic standards for attribution. Forked from 'wallace'. Code is split into modules that are loaded and linked together automatically and each call one function. Guidance pages explain modules to users and flexible logging informs them of any errors. Options enable asynchronous operations, viewing of source code, interactive maps and data tables. Use to create complex analytical applications, following best practices in open science and software development. Includes functions for automating repetitive development tasks and an example application at run_shinyscholar() that requires install.packages("shinyscholar", dependencies = TRUE). A guide to developing applications can be found on the package website.
Maintained by Simon E. H. Smart. Last updated 1 months ago.
7.8 match 20 stars 5.36 score 5 scripts
quanteda
stopwords:Multilingual Stopword Lists
Provides multiple sources of stopwords, for use in text analysis and natural language processing.
Maintained by Kenneth Benoit. Last updated 3 years ago.
3.8 match 114 stars 10.54 score 1.1k scripts 65 dependents
christianhuber
smartsnp:Fast Multivariate Analyses of Big Genomic Data
Fast computation of multivariate analyses of small (10s to 100s markers) to big (1000s to 100000s) genotype data. Runs Principal Component Analysis allowing for centering, z-score standardization and scaling for genetic drift, projection of ancient samples to modern genetic space and multivariate tests for differences in group location (Permutation-Based Multivariate Analysis of Variance) and dispersion (Permutation-Based Multivariate Analysis of Dispersion).
Maintained by Christian Huber. Last updated 1 years ago.
7.2 match 7 stars 5.32 score 6 scripts
cjvanlissa
tidySEM:Tidy Structural Equation Modeling
A tidy workflow for generating, estimating, reporting, and plotting structural equation models using 'lavaan', 'OpenMx', or 'Mplus'. Throughout this workflow, elements of syntax, results, and graphs are represented as 'tidy' data, making them easy to customize. Includes functionality to estimate latent class analyses, and to plot 'dagitty' and 'igraph' objects.
Maintained by Caspar J. van Lissa. Last updated 8 days ago.
3.3 match 58 stars 10.69 score 330 scripts 1 dependents
bioc
sparrow:Take command of set enrichment analyses through a unified interface
Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.
Maintained by Steve Lianoglou. Last updated 3 months ago.
genesetenrichmentpathwaysbioinformaticsgsea
5.4 match 21 stars 6.58 score 13 scriptsjonathansmart
SharkDemography:Shark Demographic Analyses Using Leslie Matrix Models
Run Leslie Matrix models using Monte Carlo simulations for any specified shark species. This package was developed during the publication of Smart, JJ, White, WT, Baje, L, et al. (2020) "Can multi-species shark longline fisheries be managed sustainably using size limits? Theoretically, yes. Realistically, no".J Appl Ecol. 2020; 57; 1847–1860. <doi:10.1111/1365-2664.13659>.
Maintained by Jonathan Smart. Last updated 1 years ago.
9.6 match 3 stars 3.18 score
mayoverse
arsenal:An Arsenal of 'R' Functions for Large-Scale Statistical Summaries
An Arsenal of 'R' functions for large-scale statistical summaries, which are streamlined to work within the latest reporting tools in 'R' and 'RStudio' and which use formulas and versatile summary statistics for summary tables and models. The primary functions include tableby(), a Table-1-like summary of multiple variable types 'by' the levels of one or more categorical variables; paired(), a Table-1-like summary of multiple variable types paired across two time points; modelsum(), which performs simple model fits on one or more endpoints for many variables (univariate or adjusted for covariates); freqlist(), a powerful frequency table across many categorical variables; comparedf(), a function for comparing data.frames; and write2(), a function to output tables to a document.
Maintained by Ethan Heinzen. Last updated 7 months ago.
baseline-characteristicsdescriptive-statisticsmodelingpaired-comparisonsreportingstatisticstableone
2.3 match 225 stars 13.45 score 1.2k scripts 16 dependents
rinterface
shinyMobile:Mobile Ready 'shiny' Apps with Standalone Capabilities
Develop outstanding 'shiny' apps for 'iOS' and 'Android' as well as beautiful 'shiny' gadgets. 'shinyMobile' is built on top of the latest 'Framework7' template <https://framework7.io>. Discover 14 new input widgets (sliders, vertical sliders, stepper, grouped action buttons, toggles, picker, smart select, ...), 2 themes (light and dark), 12 new widgets (expandable cards, badges, chips, timelines, gauges, progress bars, ...) combined with the power of server-side notifications such as alerts, modals, toasts, action sheets, sheets (and more) as well as 3 layouts (single, tabs and split).
Maintained by David Granjon. Last updated 2 months ago.
androidhacktoberfest2022pwashinyshinyappstemplate
2.5 match 409 stars 11.91 score 1.1k scripts 2 dependents
r-forge
tm:Text Mining Package
A framework for text mining applications within R.
Maintained by Kurt Hornik. Last updated 26 days ago.
2.3 match 12.96 score 14k scripts 101 dependentsnutriverse
nipnTK:National Information Platforms for Nutrition Anthropometric Data Toolkit
An implementation of the National Information Platforms for Nutrition or NiPN's analytic methods for assessing quality of anthropometric datasets that include measurements of weight, height or length, middle upper arm circumference, sex and age. The focus is on anthropometric status but many of the presented methods could be applied to other variables.
Maintained by Ernest Guevarra. Last updated 5 months ago.
anthropometrydata-qualitynipnnutrition
4.9 match 5 stars 5.92 score 28 scripts 1 dependentsnutriverse
zscorer:Child Anthropometry z-Score Calculator
A tool for calculating z-scores and centiles for weight-for-age, length/height-for-age, weight-for-length/height, BMI-for-age, head circumference-for-age, age circumference-for-age, subscapular skinfold-for-age, triceps skinfold-for-age based on the WHO Child Growth Standards.
Maintained by Ernest Guevarra. Last updated 4 years ago.
anthropometric-indicesanthropometrygrowth-chartsgrowth-standardsheight-for-agenutritionweight-for-ageweight-for-heightz-score
3.5 match 14 stars 7.30 score 47 scripts 1 dependents
banboo-data
RSmartlyIO:Loading Facebook and Instagram Advertising Data from 'Smartly.io'
Aims at loading Facebook and Instagram advertising data from 'Smartly.io' into R. 'Smartly.io' is an online advertising service that enables advertisers to display commercial ads on social media networks (see <http://www.smartly.io/> for more information). The package offers an interface to query the 'Smartly.io' API and loads data directly into R for further data processing and data analysis.
Maintained by Johannes Burkhardt. Last updated 6 years ago.
7.5 match 3 stars 3.18 score 1 scripts
adamspannbauer
lexRankr:Extractive Summarization of Text with the LexRank Algorithm
An R implementation of the LexRank algorithm described by G. Erkan and D. R. Radev (2004) <DOI:10.1613/jair.1523>.
Maintained by Adam Spannbauer. Last updated 2 years ago.
lexranklexrank-algorithmnlprstatcpp
4.0 match 21 stars 5.81 score 61 scripts
rairizarry
rafalib:Convenience Functions for Routine Data Exploration
A series of shortcuts for routine tasks originally developed by Rafael A. Irizarry to facilitate data exploration.
Maintained by Rafael A. Irizarry. Last updated 10 years ago.
4.5 match 4.96 score 1.2k scripts 3 dependents
hongooi73
SAR:Smart Adaptive Recommendations
'Smart Adaptive Recommendations' (SAR) is the name of a fast, scalable, adaptive algorithm for personalized recommendations based on user transactions and item descriptions. It produces easily explainable/interpretable recommendations and handles "cold item" and "semi-cold user" scenarios. This package provides two implementations of 'SAR': a standalone implementation, and an interface to a web service in Microsoft's 'Azure' cloud: <https://github.com/Microsoft/Product-Recommendations/blob/master/doc/sar.md>. The former allows fast and easy experimentation, and the latter provides robust scalability and extra features for production use.
Maintained by Hong Ooi. Last updated 4 years ago.
3.8 match 21 stars 5.32 score 20 scripts
ychen178
DTRlearn2:Statistical Learning Methods for Optimizing Dynamic Treatment Regimes
We provide a comprehensive software to estimate general K-stage DTRs from SMARTs with Q-learning and a variety of outcome-weighted learning methods. Penalizations are allowed for variable selection and model regularization. With the outcome-weighted learning scheme, different loss functions - SVM hinge loss, SVM ramp loss, binomial deviance loss, and L2 loss - are adopted to solve the weighted classification problem at each stage; augmentation in the outcomes is allowed to improve efficiency. The estimated DTR can be easily applied to a new sample for individualized treatment recommendations or DTR evaluation.
Maintained by Yuan Chen. Last updated 3 years ago.
5.7 match 7 stars 3.54 score 7 scripts
wilart
smartsizer:Power Analysis for a SMART Design
A set of tools for determining the necessary sample size in order to identify the optimal dynamic treatment regime in a sequential, multiple assignment, randomized trial (SMART). Utilizes multiple comparisons with the best methodology to adjust for multiple comparisons. Designed for an arbitrary SMART design. Please see Artman (2018) <doi:10.1093/biostatistics/kxy064> for more details.
Maintained by William Artman. Last updated 4 years ago.
9.6 match 2.00 score 6 scriptsbioc
ChemmineR:Cheminformatics Toolkit for R
ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicscpp
2.0 match 14 stars 9.42 score 253 scripts 12 dependents
trangdata
treeheatr:Heatmap-Integrated Decision Tree Visualizations
Creates interpretable decision tree visualizations with the data represented as a heatmap at the tree's leaf nodes. 'treeheatr' utilizes the customizable 'ggparty' package for drawing decision trees.
Maintained by Trang Le. Last updated 2 years ago.
datavizdecision-treesggplotheatmapvisualization
3.2 match 57 stars 5.71 score 18 scripts
henrifnk
FACT:Feature Attributions for ClusTering
We present 'FACT' (Feature Attributions for ClusTering), a framework for unsupervised interpretation methods that can be used with an arbitrary clustering algorithm. The package is capable of re-assigning instances to clusters (algorithm agnostic), preserves the integrity of the data and does not introduce additional models. 'FACT' is inspired by the principles of model-agnostic interpretation in supervised learning. Therefore, some of the methods presented are based on 'iml', a R Package for Interpretable Machine Learning by Christoph Molnar, Giuseppe Casalicchio, and Bernd Bischl (2018) <doi:10.21105/joss.00786>.
Maintained by Henri Funk. Last updated 12 months ago.
5.2 match 6 stars 3.48 score 4 scriptsbioc
ChemmineOB:R interface to a subset of OpenBabel functionalities
ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.
Maintained by Thomas Girke. Last updated 5 months ago.
cheminformaticsbiomedicalinformaticspharmacogeneticspharmacogenomicsmicrotitreplateassaycellbasedassaysvisualizationinfrastructuredataimportclusteringproteomicsmetabolomicsopenbabelcpp
2.3 match 10 stars 7.87 score 77 scripts 1 dependents
brry
berryFunctions:Function Collection Related to Plotting and Hydrology
Draw horizontal histograms, color scattered points by 3rd dimension, enhance date- and log-axis plots, zoom in X11 graphics, trace errors and warnings, use the unit hydrograph in a linear storage cascade, convert lists to data.frames and arrays, fit multiple functions.
Maintained by Berry Boessenkool. Last updated 1 months ago.
1.9 match 13 stars 9.43 score 350 scripts 16 dependents
laresbernardo
lares:Analytics & Machine Learning Sidekick
Auxiliary package for better/faster analytics, visualization, data mining, and machine learning tasks. With a wide variety of family functions, like Machine Learning, Data Wrangling, Marketing Mix Modeling (Robyn), Exploratory, API, and Scrapper, it helps the analyst or data scientist to get quick and robust results, without the need of repetitive coding or advanced R programming skills.
Maintained by Bernardo Lares. Last updated 25 days ago.
analyticsapiautomationautomldata-sciencedescriptive-statisticsh2omachine-learningmarketingmmmpredictive-modelingpuzzlerlanguagerobynvisualization
1.8 match 233 stars 9.84 score 185 scripts 1 dependentsbioc
DEGreport:Report of DEG analysis
Creation of ready-to-share figures of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.
Maintained by Lorena Pantano. Last updated 5 months ago.
differentialexpressionvisualizationrnaseqreportwritinggeneexpressionimmunooncologybioconductordifferential-expressionqcreportrna-seqsmallrna
1.8 match 24 stars 9.42 score 354 scripts 1 dependentswilart
SMARTbayesR:Bayesian Set of Best Dynamic Treatment Regimes and Sample Size in SMARTs for Binary Outcomes
Permits determination of a set of optimal dynamic treatment regimes and sample size for a SMART design in the Bayesian setting with binary outcomes. Please see Artman (2020) <arXiv:2008.02341>.
Maintained by William Artman. Last updated 3 years ago.
8.3 match 2.00 score 2 scripts
ppbds
tutorial.helpers:Helper Functions for Creating Tutorials
Helper functions for creating, editing, and testing tutorials created with the 'learnr' package. Provides a simple method for allowing students to download their answers to tutorial questions. For examples of its use, see the 'r4ds.tutorials' package.
Maintained by David Kane. Last updated 5 days ago.
1.9 match 5 stars 8.48 score 152 scripts 1 dependentsbioc
Dune:Improving replicability in single-cell RNA-Seq cell type discovery
Given a set of clustering labels, Dune merges pairs of clusters to increase mean ARI between labels, improving replicability.
Maintained by Hector Roux de Bezieux. Last updated 5 months ago.
clusteringgeneexpressionrnaseqsoftwaresinglecelltranscriptomicsvisualization
3.4 match 4.61 score 41 scripts
radiant-rstats
radiant.data:Data Menu for Radiant: Business Analytics using R and Shiny
The Radiant Data menu includes interfaces for loading, saving, viewing, visualizing, summarizing, transforming, and combining data. It also contains functionality to generate reproducible reports of the analyses conducted in the application.
Maintained by Vincent Nijs. Last updated 5 months ago.
1.9 match 54 stars 8.30 score 146 scripts 6 dependents
hopfkons
SmartMeterAnalytics:Methods for Smart Meter Data Analysis
Methods for analysis of energy consumption data (electricity, gas, water) at different data measurement intervals. The package provides feature extraction methods and algorithms to prepare data for data mining and machine learning applications. Deatiled descriptions of the methods and their application can be found in Hopf (2019, ISBN:978-3-86309-669-4) "Predictive Analytics for Energy Efficiency and Energy Retailing" <doi:10.20378/irbo-54833> and Hopf et al. (2016) <doi:10.1007/s12525-018-0290-9> "Enhancing energy efficiency in the residential sector with smart meter data analytics".
Maintained by Konstantin Hopf. Last updated 5 years ago.
15.3 match 1.00 scorebioc
KCsmart:Multi sample aCGH analysis package using kernel convolution
Multi sample aCGH analysis package using kernel convolution
Maintained by Jorma de Ronde. Last updated 5 months ago.
copynumbervariationvisualizationacghmicroarray
4.0 match 3.60 score 1 scripts
mabafaba
lifx:Control "LIFX" Smart Light Bulbs
Allows you to read and change the state of "LIFX" smart light bulbs Covers most "LIFX" API endpoints, including changing light color and brightness, selecting lights by ID, group or location as well as activating effects.
Maintained by Martin Barner. Last updated 5 years ago.
5.3 match 2.70 score 1 scripts
csids
cstidy:Helpful Functions for Cleaning Surveillance Data
Helpful functions for the cleaning and manipulation of surveillance data, especially with regards to the creation and validation of panel data from individual level surveillance data.
Maintained by Richard Aubrey White. Last updated 9 months ago.
3.0 match 4.65 score 1 dependents
ropensci
beautier:'BEAUti' from R
'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.
Maintained by Richèl J.C. Bilderbeek. Last updated 23 days ago.
bayesianbeastbeast2beautiphylogenetic-inferencephylogenetics
1.5 match 13 stars 8.76 score 198 scripts 5 dependentsbioc
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.
softwarevisualizationdatarepresentationmultiplecomparisonfunctionalpredictiondimensionreductionbioinformaticsheatmapinteractive-visualizationsorthologsphylogenetic-profileshiny
1.7 match 33 stars 7.77 score 10 scripts
s-fleck
smartmap:Smartly Create Maps from R Objects
Preview spatial data as 'leaflet' maps with minimal effort. smartmap is optimized for interactive use and distinguishes itself from similar packages because it does not need real spatial ('sp' or 'sf') objects an input; instead, it tries to automatically coerce everything that looks like spatial data to sf objects or leaflet maps. It - for example - supports direct mapping of: a vector containing a single coordinate pair, a two column matrix, a data.frame with longitude and latitude columns, or the path or URL to a (possibly compressed) 'shapefile'.
Maintained by Stefan Fleck. Last updated 4 years ago.
4.7 match 2.70 score 5 scripts
gadenbuie
metathis:HTML Metadata Tags for 'R Markdown' and 'Shiny'
Create meta tags for 'R Markdown' HTML documents and 'Shiny' apps for customized social media cards, for accessibility, and quality search engine indexing. 'metathis' currently supports HTML documents created with 'rmarkdown', 'shiny', 'xaringan', 'pagedown', 'bookdown', and 'flexdashboard'.
Maintained by Garrick Aden-Buie. Last updated 1 years ago.
1.8 match 67 stars 6.29 score 584 scripts
ekstroem
dataReporter:Reproducible Data Screening Checks and Report of Possible Errors
Data screening is an important first step of any statistical analysis. 'dataReporter' auto generates a customizable data report with a thorough summary of the checks and the results that a human can use to identify possible errors. It provides an extendable suite of test for common potential errors in a dataset. See Petersen AH, Ekstrøm CT (2019). "dataMaid: Your Assistant for Documenting Supervised Data Quality Screening in R." _Journal of Statistical Software_, *90*(6), 1-38 <doi:10.18637/jss.v090.i06> for more information.
Maintained by Claus Thorn Ekstrøm. Last updated 2 years ago.
1.8 match 86 stars 6.16 score 34 scripts
crew102
slowraker:A Slow Version of the Rapid Automatic Keyword Extraction (RAKE) Algorithm
A mostly pure-R implementation of the RAKE algorithm (Rose, S., Engel, D., Cramer, N. and Cowley, W. (2010) <doi:10.1002/9780470689646.ch1>), which can be used to extract keywords from documents without any training data.
Maintained by Christopher Baker. Last updated 7 months ago.
2.0 match 6 stars 5.37 score 13 scripts 1 dependents
swarm-lab
magicLamp:'WeMo Switch' Smart Plug Utilities
Set of utility functions to interact with 'WeMo Switch', a smart plug that can be remotely controlled via wifi. The provided functions make it possible to turn one or more 'WeMo Switch' plugs on and off in a scriptable fashion. More information about 'WeMo Switch' can be found at <http://www.belkin.com/us/p/P-F7C027/>.
Maintained by Simon Garnier. Last updated 5 years ago.
3.5 match 2 stars 3.00 score 4 scripts
davidhodge931
ggblanket:Simplify 'ggplot2' Visualisation
Simplify 'ggplot2' visualisation with 'ggblanket' wrapper functions.
Maintained by David Hodge. Last updated 6 days ago.
data-visualisationdata-visualizationggplotggplot-extensionggplot2ggplot2-enhancementsvisualisationvisualization
1.1 match 170 stars 8.43 score 45 scripts
wa-department-of-agriculture
WaCSE:Washington Climate Smart Estimator
The Washington Climate Smart Estimator (WaCSE) is a shiny application to explore greenhouse gas mitigation potential from different agricultural conservation practices across Washington's diverse counties.
Maintained by Jadey Ryan. Last updated 3 days ago.
3.6 match 8 stars 2.60 scorebioc
KnowSeq:KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline
KnowSeq proposes a novel methodology that comprises the most relevant steps in the Transcriptomic gene expression analysis. KnowSeq expects to serve as an integrative tool that allows to process and extract relevant biomarkers, as well as to assess them through a Machine Learning approaches. Finally, the last objective of KnowSeq is the biological knowledge extraction from the biomarkers (Gene Ontology enrichment, Pathway listing and Visualization and Evidences related to the addressed disease). Although the package allows analyzing all the data manually, the main strenght of KnowSeq is the possibilty of carrying out an automatic and intelligent HTML report that collect all the involved steps in one document. It is important to highligh that the pipeline is totally modular and flexible, hence it can be started from whichever of the different steps. KnowSeq expects to serve as a novel tool to help to the experts in the field to acquire robust knowledge and conclusions for the data and diseases to study.
Maintained by Daniel Castillo-Secilla. Last updated 5 months ago.
geneexpressiondifferentialexpressiongenesetenrichmentdataimportclassificationfeatureextractionsequencingrnaseqbatcheffectnormalizationpreprocessingqualitycontrolgeneticstranscriptomicsmicroarrayalignmentpathwayssystemsbiologygoimmunooncology
2.9 match 3.30 score 5 scripts
sinnweja
smartDesign:Sequential Multiple Assignment Randomized Trial Design
SMART trial design, as described by He, J., McClish, D., Sabo, R. (2021) <doi:10.1080/19466315.2021.1883472>, includes multiple stages of randomization, where participants are randomized to an initial treatment in the first stage and then subsequently re-randomized between treatments in the following stage.
Maintained by Jason Sinnwell. Last updated 1 years ago.
3.0 match 3.00 score 1 scripts
bcable
Rsgf:SGF (Smart Game File) File Format Import
Import SGF (Smart Game File) into R.
Maintained by Brad Cable. Last updated 4 years ago.
5.1 match 1 stars 1.70 score 3 scripts
biooss
mistral:Methods in Structural Reliability
Various reliability analysis methods for rare event inference (computing failure probability and quantile from model/function outputs).
Maintained by Bertrand Iooss. Last updated 1 years ago.
3.3 match 1 stars 2.43 score 27 scripts
iqis
Q7:Types and Features for Object Oriented Programming
Construct message-passing style objects with types and features. Q7 types uses composition instead of inheritance in creating derived types, allowing definining any code segment as feature and associating any feature to any object. Compared to R6, Q7 is simpler, more flexible, and more friendly.
Maintained by Siqi Zhang. Last updated 3 years ago.
1.5 match 5 stars 5.10 score 10 scriptsbioc
raer:RNA editing tools in R
Toolkit for identification and statistical testing of RNA editing signals from within R. Provides support for identifying sites from bulk-RNA and single cell RNA-seq datasets, and general methods for extraction of allelic read counts from alignment files. Facilitates annotation and exploratory analysis of editing signals using Bioconductor packages and resources.
Maintained by Kent Riemondy. Last updated 5 months ago.
multiplecomparisonrnaseqsinglecellsequencingcoverageepitranscriptomicsfeatureextractionannotationalignmentbioconductor-packagerna-seq-analysissingle-cell-analysissingle-cell-rna-seqcurlbzip2xz-utilszlib
1.2 match 8 stars 5.98 score 6 scripts
syksy
hamlet:Hierarchical Optimal Matching and Machine Learning Toolbox
Various functions and algorithms are provided here for solving optimal matching tasks in the context of preclinical cancer studies. Further, various helper and plotting functions are provided for unsupervised and supervised machine learning as well as longitudinal mixed-effects modeling of tumor growth response patterns.
Maintained by Teemu Daniel Laajala. Last updated 2 years ago.
1.7 match 4.18 score 25 scripts 2 dependents
timcdlucas
disaggregation:Disaggregation Modelling
Fits disaggregation regression models using 'TMB' ('Template Model Builder'). When the response data are aggregated to polygon level but the predictor variables are at a higher resolution, these models can be useful. Regression models with spatial random fields. The package is described in detail in Nandi et al. (2023) <doi:10.18637/jss.v106.i11>.
Maintained by Tim Lucas. Last updated 4 months ago.
1.5 match 2 stars 4.60 score 9 scripts
kwb-r
kwb.qmra:QMRA (quantitative microbial risk assessment)
QMRA for water supply systems.
Maintained by Michael Rustler. Last updated 4 years ago.
project-aquanesproject-demowareproject-smartcontrolqmraqmra-webapp-backend-engine
1.5 match 4 stars 4.53 score 21 scriptshopfkons
ResidentialEnergyConsumption:Residential Energy Consumption Data
Datasets with energy consumption data of different data measurement frequencies. The data stems from several publicly funded research projects of the Chair of Information Systems and Energy Efficient Systems at the University of Bamberg.
Maintained by Konstantin Hopf. Last updated 4 years ago.
6.9 match 1.00 score
cran
needmining:A Simple Needmining Implementation
Showcasing needmining (the semi-automatic extraction of customer needs from social media data) with Twitter data. It uses the handling of the Twitter API provided by the package 'rtweet' and the textmining algorithms provided by the package 'tm'. Niklas Kuehl (2016) <doi:10.1007/978-3-319-32689-4_14> wrote an introduction to the topic of needmining.
Maintained by Dorian Proksch. Last updated 6 years ago.
6.9 match 1.00 score 7 scripts
andyphilips
dynamac:Dynamic Simulation and Testing for Single-Equation ARDL Models
While autoregressive distributed lag (ARDL) models allow for extremely flexible dynamics, interpreting substantive significance of complex lag structures remains difficult. This package is designed to assist users in dynamically simulating and plotting the results of various ARDL models. It also contains post-estimation diagnostics, including a test for cointegration when estimating the error-correction variant of the autoregressive distributed lag model (Pesaran, Shin, and Smith 2001 <doi:10.1002/jae.616>).
Maintained by Soren Jordan. Last updated 4 years ago.
ardlstatatime-seriestime-series-analysis
1.2 match 7 stars 5.59 score 37 scripts 1 dependents
zhukovyuri
SUNGEO:Sub-National Geospatial Data Archive: Geoprocessing Toolkit
Tools for integrating spatially-misaligned GIS datasets. Part of the Sub-National Geospatial Data Archive System.
Maintained by Yuri M. Zhukov. Last updated 10 months ago.
1.9 match 5 stars 3.42 score 8 scriptsbioc
scRecover:scRecover for imputation of single-cell RNA-seq data
scRecover is an R package for imputation of single-cell RNA-seq (scRNA-seq) data. It will detect and impute dropout values in a scRNA-seq raw read counts matrix while keeping the real zeros unchanged, since there are both dropout zeros and real zeros in scRNA-seq data. By combination with scImpute, SAVER and MAGIC, scRecover not only detects dropout and real zeros at higher accuracy, but also improve the downstream clustering and visualization results.
Maintained by Zhun Miao. Last updated 5 months ago.
geneexpressionsinglecellrnaseqtranscriptomicssequencingpreprocessingsoftware
1.2 match 8 stars 5.20 score 9 scripts
syedhaider5
chicane:Capture Hi-C Analysis Engine
Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.
Maintained by Syed Haider. Last updated 3 years ago.
2.3 match 2.75 score 28 scripts
niccologalatioto
hydReng:Hydraulic Engineering Tools
The 'hydReng' package provides a set of functions for hydraulic engineering tasks and natural hazard assessments. It includes basic hydraulics (wetted area, wetted perimeter, flow, flow velocity, flow depth, and maximum flow) for open channels with arbitrary geometry under uniform flow conditions. For structures such as circular pipes, weirs, and gates, the package includes calculations for pressure flow, backwater depth, and overflow over a weir crest. Additionally, it provides formulas for calculating bedload transport. The formulas used can be found in standard literature on hydraulics, such as Bollrich (2019, ISBN:978-3-410-29169-5) or Hager (2011, ISBN:978-3-642-77430-0).
Maintained by Galatioto Niccolo. Last updated 2 months ago.
1.8 match 3.40 scorekwb-r
kwb.heatsine:R Package for Calculating Hydraulic Travel Times Based on Sinus Temperature Fitting
Requires daily temperature times series in a surface water body and one groundwater observation well (in case of an production well this data needs to be cleaned in order to reduce temperature fluctuations due to the operation scheme!).
Maintained by Michael Rustler. Last updated 4 years ago.
1.6 match 3.65 score 4 scripts 1 dependentskwb-r
kwb.heatsine.opencpu:Wrapper for R Package kwb.heatsine for OpenCPU Usage
Contains higher level functions build on top of R package kwb.heatsine for connecting with OpenCPU.
Maintained by Michael Rustler. Last updated 4 years ago.
1.5 match 3.00 score 3 scriptsbioc
scPipe:Pipeline for single cell multi-omic data pre-processing
A preprocessing pipeline for single cell RNA-seq/ATAC-seq data that starts from the fastq files and produces a feature count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.
Maintained by Shian Su. Last updated 3 months ago.
immunooncologysoftwaresequencingrnaseqgeneexpressionsinglecellvisualizationsequencematchingpreprocessingqualitycontrolgenomeannotationdataimportcurlbzip2xz-utilszlibcpp
0.5 match 68 stars 9.02 score 84 scripts
kjhealy
gssrdoc:Document General Social Survey Variable
The General Social Survey (GSS) is a long-running, mostly annual survey of US households. It is administered by the National Opinion Research Center (NORC). This package contains the a tibble with information on the survey variables, together with every variable documented as an R help page. For more information on the GSS see \url{http://gss.norc.org}.
Maintained by Kieran Healy. Last updated 11 months ago.
1.8 match 2.28 score 38 scripts
msberends
cleaner:Fast and Easy Data Cleaning
Data cleaning functions for classes logical, factor, numeric, character, currency and Date to make data cleaning fast and easy. Relying on very few dependencies, it provides smart guessing, but with user options to override anything if needed.
Maintained by Matthijs S. Berends. Last updated 4 months ago.
0.5 match 32 stars 6.95 score 64 scripts 9 dependents
ibot-geoecology
myClim:Microclimatic Data Processing
Handling the microclimatic data in R. The 'myClim' workflow begins at the reading data primary from microclimatic dataloggers, but can be also reading of meteorological station data from files. Cleaning time step, time zone settings and metadata collecting is the next step of the work flow. With 'myClim' tools one can crop, join, downscale, and convert microclimatic data formats, sort them into localities, request descriptive characteristics and compute microclimatic variables. Handy plotting functions are provided with smart defaults.
Maintained by Vojtěch Kalčík. Last updated 14 days ago.
0.5 match 7 stars 6.97 score 30 scripts
alexpkeil1
metropolis:The Metropolis Algorithm
Learning and using the Metropolis algorithm for Bayesian fitting of a generalized linear model. The package vignette includes examples of hand-coding a logistic model using several variants of the Metropolis algorithm. The package also contains R functions for simulating posterior distributions of Bayesian generalized linear model parameters using guided, adaptive, guided-adaptive and random walk Metropolis algorithms. The random walk Metropolis algorithm was originally described in Metropolis et al (1953); <doi:10.1063/1.1699114>.
Maintained by Alexander Keil. Last updated 4 years ago.
1.2 match 2.70 score 5 scripts
clewerenz
ilabelled:Simple Handling of Labelled Data
Simple handling of survey data. Smart handling of meta-information like e.g. variable-labels value-labels and scale-levels. Easy access and validation of meta-information. Useage of value labels and values respectively for subsetting and recoding data.
Maintained by Christof Lewerenz. Last updated 2 months ago.
0.5 match 2 stars 6.02 score 13 scripts
rapidsurveys
bbw:Blocked Weighted Bootstrap
The blocked weighted bootstrap (BBW) is an estimation technique for use with data from two-stage cluster sampled surveys in which either prior weighting (e.g. population-proportional sampling or PPS as used in Standardized Monitoring and Assessment of Relief and Transitions or SMART surveys) or posterior weighting (e.g. as used in rapid assessment method or RAM and simple spatial sampling method or S3M surveys) is implemented. See Cameron et al (2008) <doi:10.1162/rest.90.3.414> for application of bootstrap to cluster samples. See Aaron et al (2016) <doi:10.1371/journal.pone.0163176> and Aaron et al (2016) <doi:10.1371/journal.pone.0162462> for application of the blocked weighted bootstrap to estimate indicators from two-stage cluster sampled surveys.
Maintained by Ernest Guevarra. Last updated 2 months ago.
bootstrapping-statisticsramsurveys
0.5 match 3 stars 5.61 score 9 scripts 1 dependentsbioc
CleanUpRNAseq:Detect and Correct Genomic DNA Contamination in RNA-seq Data
RNA-seq data generated by some library preparation methods, such as rRNA-depletion-based method and the SMART-seq method, might be contaminated by genomic DNA (gDNA), if DNase I disgestion is not performed properly during RNA preparation. CleanUpRNAseq is developed to check if RNA-seq data is suffered from gDNA contamination. If so, it can perform correction for gDNA contamination and reduce false discovery rate of differentially expressed genes.
Maintained by Haibo Liu. Last updated 4 months ago.
qualitycontrolsequencinggeneexpression
0.5 match 5 stars 5.44 score 4 scripts
harrison4192
framecleaner:Clean Data Frames
Provides a friendly interface for modifying data frames with a sequence of piped commands built upon the 'tidyverse' Wickham et al., (2019) <doi:10.21105/joss.01686> . The majority of commands wrap 'dplyr' mutate statements in a convenient way to concisely solve common issues that arise when tidying small to medium data sets. Includes smart defaults and allows flexible selection of columns via 'tidyselect'.
Maintained by Harrison Tietze. Last updated 1 years ago.
0.5 match 2 stars 5.18 score 5 scripts 5 dependents
chingchuan-chen
RcppBlaze:'Rcpp' Integration for the 'Blaze' High-Performance 'C++' Math Library
Blaze is an open-source, high-performance 'C++' math library for dense and sparse arithmetic. With its state-of-the-art Smart Expression Template implementation Blaze combines the elegance and ease of use of a domain-specific language with HPC-grade performance, making it one of the most intuitive and fastest 'C++' math libraries available. The 'RcppBlaze' package includes the header files from the 'Blaze' library with disabling some functionalities related to link to the thread and system libraries which make 'RcppBlaze' be a header-only library. Therefore, users do not need to install 'Blaze'.
Maintained by Ching-Chuan Chen. Last updated 11 months ago.
0.5 match 16 stars 4.86 score 2 scripts 1 dependents
jmablog
tinieR:Shrink Image Filesizes with TinyPNG.com API
Shrink image filesizes with the TinyPNG API <https://tinypng.com>. From the TinyPNG website: "TinyPNG uses smart lossy compression techniques to reduce the file size of your files. By selectively decreasing the number of colors in the image, fewer bytes are required to store the data. The effect is nearly invisible but it makes a very large difference in file size!" TinieR works with .png and .jpg/.jpeg files, and can return the new image filepath to enable embedding in other image workflows/functions.
Maintained by James Adams. Last updated 3 years ago.
0.5 match 11 stars 4.22 score 4 scripts
trn000
norMmix:Direct MLE for Multivariate Normal Mixture Distributions
Multivariate Normal (i.e. Gaussian) Mixture Models (S3) Classes. Fitting models to data using 'MLE' (maximum likelihood estimation) for multivariate normal mixtures via smart parametrization using the 'LDL' (Cholesky) decomposition, see McLachlan and Peel (2000, ISBN:9780471006268), Celeux and Govaert (1995) <doi:10.1016/0031-3203(94)00125-6>.
Maintained by Nicolas Trutmann. Last updated 6 months ago.
gaussian-mixture-modelsmaximum-likelihood-estimationr-language
0.5 match 4.18 score 3 scripts
djbetancourt-gh
funGp:Gaussian Process Models for Scalar and Functional Inputs
Construction and smart selection of Gaussian process models for analysis of computer experiments with emphasis on treatment of functional inputs that are regularly sampled. This package offers: (i) flexible modeling of functional-input regression problems through the fairly general Gaussian process model; (ii) built-in dimension reduction for functional inputs; (iii) heuristic optimization of the structural parameters of the model (e.g., active inputs, kernel function, type of distance). An in-depth tutorial in the use of funGp is provided in Betancourt et al. (2024) <doi:10.18637/jss.v109.i05> and Metamodeling background is provided in Betancourt et al. (2020) <doi:10.1016/j.ress.2020.106870>. The algorithm for structural parameter optimization is described in <https://hal.science/hal-02532713>.
Maintained by Jose Betancourt. Last updated 10 months ago.
0.5 match 4 stars 3.78 score 2 scripts
denis-arnold
AcousticNDLCodeR:Coding Sound Files for Use with NDL
Make acoustic cues to use with the R packages 'ndl' or 'ndl2'. The package implements functions used in the PLoS ONE paper: Denis Arnold, Fabian Tomaschek, Konstantin Sering, Florence Lopez, and R. Harald Baayen (2017). Words from spontaneous conversational speech can be recognized with human-like accuracy by an error-driven learning algorithm that discriminates between meanings straight from smart acoustic features, bypassing the phoneme as recognition unit. PLoS ONE 12(4):e0174623 <doi:10.1371/journal.pone.0174623> More details can be found in the paper and the supplement. 'ndl' is available on CRAN. 'ndl2' is available by request from <konstantin.sering@uni-tuebingen.de>.
Maintained by Denis Arnold. Last updated 7 years ago.
0.5 match 3.00 score 8 scripts
theclue
sensibo.sky:Access to 'Sensibo Sky' API V2 for Air Conditioners Remote Control
Provides an interface to the 'Sensibo Sky' API which allows to remotely control non-smart air conditioning units. See <https://sensibo.com> for more informations.
Maintained by Gabriele Baldassarre. Last updated 6 years ago.
0.5 match 2.70 score
yili-hong
SPREDA:Statistical Package for Reliability Data Analysis
The Statistical Package for REliability Data Analysis (SPREDA) implements recently-developed statistical methods for the analysis of reliability data. Modern technological developments, such as sensors and smart chips, allow us to dynamically track product/system usage as well as other environmental variables, such as temperature and humidity. We refer to these variables as dynamic covariates. The package contains functions for the analysis of time-to-event data with dynamic covariates and degradation data with dynamic covariates. The package also contains functions that can be used for analyzing time-to-event data with right censoring, and with left truncation and right censoring. Financial support from NSF and DuPont are acknowledged.
Maintained by Yili Hong. Last updated 6 years ago.
0.5 match 1.43 score 27 scripts