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tidyverse

hms:Pretty Time of Day

Implements an S3 class for storing and formatting time-of-day values, based on the 'difftime' class.

Maintained by Kirill Müller. Last updated 12 hours ago.

hmstime

85.7 match 141 stars 16.59 score 1.3k scripts 3.2k dependents

poissonconsulting

hmstimer:'hms' Based Timer

Tracks elapsed clock time using a `hms::hms()` scalar. It was was originally developed to time Bayesian model runs. It should not be used to estimate how long extremely fast code takes to execute as the package code adds a small time cost.

Maintained by Joe Thorley. Last updated 2 months ago.

hmstimer

47.0 match 2 stars 5.35 score 4 scripts 1 dependents

hms-dbmi

UpSetR:A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets

Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks (Conway 2017) <doi:10.1093/bioinformatics/btx364>.

Maintained by Jake Conway. Last updated 4 years ago.

gehlenborglabggplot2upsetupsetrvisualization

15.0 match 781 stars 15.33 score 4.8k scripts 42 dependents

wojtacht

hmsr:Multipopulation Evolutionary Strategy HMS

The HMS (Hierarchic Memetic Strategy) is a composite global optimization strategy consisting of a multi-population evolutionary strategy and some auxiliary methods. The HMS makes use of a dynamically-evolving data structure that provides an organization among the component populations. It is a tree with a fixed maximal height and variable internal node degree. Each component population is governed by a particular evolutionary engine. This package provides a simple R implementation with examples of using different genetic algorithms as the population engines. References: J. Sawicki, M. Łoś, M. Smołka, J. Alvarez-Aramberri (2022) <doi:10.1007/s11047-020-09836-w>.

Maintained by Wojciech Achtelik. Last updated 1 years ago.

39.8 match 3 stars 3.18 score 5 scripts

hms-dbmi

EHRtemporalVariability:Delineating Temporal Dataset Shifts in Electronic Health Records

Functions to delineate temporal dataset shifts in Electronic Health Records through the projection and visualization of dissimilarities among data temporal batches. This is done through the estimation of data statistical distributions over time and their projection in non-parametric statistical manifolds, uncovering the patterns of the data latent temporal variability. 'EHRtemporalVariability' is particularly suitable for multi-modal data and categorical variables with a high number of values, common features of biomedical data where traditional statistical process control or time-series methods may not be appropriate. 'EHRtemporalVariability' allows you to explore and identify dataset shifts through visual analytics formats such as Data Temporal heatmaps and Information Geometric Temporal (IGT) plots. An additional 'EHRtemporalVariability' Shiny app can be used to load and explore the package results and even to allow the use of these functions to those users non-experienced in R coding. (Sáez et al. 2020) <doi:10.1093/gigascience/giaa079>.

Maintained by Carlos Sáez. Last updated 11 months ago.

biomedical-data-sciencebiomedical-informaticsdata-qualitydata-quality-monitoringdataset-shiftselectronic-health-recordstimevariabilityvisualization

15.0 match 17 stars 5.27 score 22 scripts

tidyverse

lubridate:Make Dealing with Dates a Little Easier

Functions to work with date-times and time-spans: fast and user friendly parsing of date-time data, extraction and updating of components of a date-time (years, months, days, hours, minutes, and seconds), algebraic manipulation on date-time and time-span objects. The 'lubridate' package has a consistent and memorable syntax that makes working with dates easy and fun.

Maintained by Vitalie Spinu. Last updated 4 months ago.

datedate-time

3.3 match 757 stars 20.95 score 135k scripts 1.9k dependents

aljensen89

CommKern:Network-Based Communities and Kernel Machine Methods

Analysis of network community objects with applications to neuroimaging data. There are two main components to this package. The first is the hierarchical multimodal spinglass (HMS) algorithm, which is a novel community detection algorithm specifically tailored to the unique issues within brain connectivity. The other is a suite of semiparametric kernel machine methods that allow for statistical inference to be performed to test for potential associations between these community structures and an outcome of interest (binary or continuous).

Maintained by Alexandria Jensen. Last updated 3 years ago.

12.1 match 4.11 score 26 scripts

poissonconsulting

dttr2:Manipulate Date, POSIXct and hms Vectors

Manipulates date ('Date'), date time ('POSIXct') and time ('hms') vectors. Date/times are considered discrete and are floored whenever encountered. Times are wrapped and time zones are maintained unless explicitly altered by the user.

Maintained by Ayla Pearson. Last updated 2 months ago.

8.8 match 10 stars 5.65 score 5 scripts 6 dependents

hms-dbmi

picker:Pick Data Points from a Deck.gl Scatterplot

Performant interactive scatterplot for ~ 1 million points. Zoom, pan, and pick points. Includes tooltips, labels, a grid overlay, legend, and coupled interactions across multiple plots.

Maintained by Alex Pickering. Last updated 3 years ago.

15.0 match 3 stars 3.22 score 11 scripts

r-lib

scales:Scale Functions for Visualization

Graphical scales map data to aesthetics, and provide methods for automatically determining breaks and labels for axes and legends.

Maintained by Thomas Lin Pedersen. Last updated 5 months ago.

ggplot2

1.9 match 418 stars 19.90 score 88k scripts 8.0k dependents

krlmlr

kimisc:Kirill's Miscellaneous Functions

A collection of useful functions not found anywhere else, mainly for programming: Pretty intervals, generalized lagged differences, checking containment in an interval, and an alternative interface to assign().

Maintained by Kirill Müller. Last updated 4 months ago.

4.5 match 18 stars 6.47 score 76 scripts 3 dependents

tingtingzhan

ThomasJeffersonUniv:Handy Tools for TJU/TJUH Employees

Functions for admin needs of employees of Thomas Jefferson University and Thomas Jefferson University Hospital, Philadelphia, PA.

Maintained by Tingting Zhan. Last updated 21 days ago.

7.8 match 3.45 score

ijlyttle

vembedr:Embed Video in HTML

A set of functions for generating HTML to embed hosted video in your R Markdown documents or Shiny applications.

Maintained by Ian Lyttle. Last updated 3 years ago.

boxembed-videosrmarkdownshinyvimeoyoutube

3.3 match 58 stars 7.88 score 520 scripts

janmarvin

openxlsx2:Read, Write and Edit 'xlsx' Files

Simplifies the creation of 'xlsx' files by providing a high level interface to writing, styling and editing worksheets.

Maintained by Jan Marvin Garbuszus. Last updated 1 days ago.

xlsxcpp

1.7 match 139 stars 13.62 score 194 scripts 11 dependents

richierocks

rebus:Build Regular Expressions in a Human Readable Way

Build regular expressions piece by piece using human readable code. This package is designed for interactive use. For package development, use the rebus.* dependencies.

Maintained by Richard Cotton. Last updated 8 years ago.

3.3 match 33 stars 6.73 score 364 scripts 3 dependents

asgr

celestial:Collection of Common Astronomical Conversion Routines and Functions

Contains a number of common astronomy utility functions for cosmology and angular coordinates.

Maintained by Aaron Robotham. Last updated 1 years ago.

cpp

3.7 match 9 stars 5.22 score 68 scripts 9 dependents

spkaluzny

splusTimeDate:Times and Dates from 'S-PLUS'

A collection of classes and methods for working with times and dates. The code was originally available in 'S-PLUS'.

Maintained by Stephen Kaluzny. Last updated 2 months ago.

datetime

3.3 match 4.94 score 58 scripts 2 dependents

solarization

solaR2:Radiation and Photovoltaic Systems

Provides tools for calculating solar geometry, solar radiation on horizontal and inclined planes, and simulating the performance of various photovoltaic (PV) systems. Supports daily and intradaily irradiation data, enabling detailed analysis of grid-connected and water-pumping PV systems, including shading effects and solar angle calculations.

Maintained by Francisco Delgado-López. Last updated 1 months ago.

3.3 match 1 stars 4.08 score 5 scripts

celehs

MAP:Multimodal Automated Phenotyping

Electronic health records (EHR) linked with biorepositories are a powerful platform for translational studies. A major bottleneck exists in the ability to phenotype patients accurately and efficiently. Towards that end, we developed an automated high-throughput phenotyping method integrating International Classification of Diseases (ICD) codes and narrative data extracted using natural language processing (NLP). Specifically, our proposed method, called MAP (Map Automated Phenotyping algorithm), fits an ensemble of latent mixture models on aggregated ICD and NLP counts along with healthcare utilization. The MAP algorithm yields a predicted probability of phenotype for each patient and a threshold for classifying subjects with phenotype yes/no (See Katherine P. Liao, et al. (2019) <doi:10.1093/jamia/ocz066>.).

Maintained by Thomas Charlon. Last updated 3 months ago.

1.5 match 6 stars 8.58 score 177 scripts 1 dependents

bioc

apComplex:Estimate protein complex membership using AP-MS protein data

Functions to estimate a bipartite graph of protein complex membership using AP-MS data.

Maintained by Denise Scholtens. Last updated 5 months ago.

immunooncologynetworkinferencemassspectrometrygraphandnetwork

4.8 match 2.60 score 8 scripts

richierocks

rebus.datetimes:Date and Time Extensions for the 'rebus' Package

Build regular expressions piece by piece using human readable code. This package contains date and time functionality, and is primarily intended to be used by package developers.

Maintained by Richard Cotton. Last updated 2 years ago.

3.3 match 1 stars 3.78 score 4 scripts 4 dependents

armcn

quickcheck:Property Based Testing

Property based testing, inspired by the original 'QuickCheck'. This package builds on the property based testing framework provided by 'hedgehog' and is designed to seamlessly integrate with 'testthat'.

Maintained by Andrew McNeil. Last updated 1 years ago.

functional-programmingproperty-based-testing

2.3 match 25 stars 4.94 score 70 scripts

cran

tis:Time Indexes and Time Indexed Series

Functions and S3 classes for time indexes and time indexed series, which are compatible with FAME frequencies.

Maintained by Brian Salzer. Last updated 4 years ago.

3.3 match 3.35 score 6 dependents

agdamsbo

REDCapCAST:REDCap Metadata Casting and Castellated Data Handling

Casting metadata for REDCap database creation and handling of castellated data using repeated instruments and longitudinal projects in 'REDCap'. Keeps a focused data export approach, by allowing to only export required data from the database. Also for casting new REDCap databases based on datasets from other sources. Originally forked from the R part of 'REDCapRITS' by Paul Egeler. See <https://github.com/pegeler/REDCapRITS>. 'REDCap' (Research Electronic Data Capture) is a secure, web-based software platform designed to support data capture for research studies, providing 1) an intuitive interface for validated data capture; 2) audit trails for tracking data manipulation and export procedures; 3) automated export procedures for seamless data downloads to common statistical packages; and 4) procedures for data integration and interoperability with external sources (Harris et al (2009) <doi:10.1016/j.jbi.2008.08.010>; Harris et al (2019) <doi:10.1016/j.jbi.2019.103208>).

Maintained by Andreas Gammelgaard Damsbo. Last updated 22 days ago.

1.8 match 1 stars 5.84 score 12 scripts

parklab

Nozzle.R1:Nozzle Reports

The Nozzle package provides an API to generate HTML reports with dynamic user interface elements based on JavaScript and CSS (Cascading Style Sheets). Nozzle was designed to facilitate summarization and rapid browsing of complex results in data analysis pipelines where multiple analyses are performed frequently on big data sets. The package can be applied to any project where user-friendly reports need to be created.

Maintained by Nils Gehlenborg. Last updated 10 years ago.

gehlenborglabhtml-reportreproducible-research

1.8 match 68 stars 5.31 score 10 scripts 2 dependents

oscarperpinan

solaR:Radiation and Photovoltaic Systems

Calculation methods of solar radiation and performance of photovoltaic systems from daily and intradaily irradiation data sources.

Maintained by Oscar Perpiñán Lamigueiro. Last updated 3 years ago.

3.3 match 1 stars 2.74 score 55 scripts

nsaph-software

GPCERF:Gaussian Processes for Estimating Causal Exposure Response Curves

Provides a non-parametric Bayesian framework based on Gaussian process priors for estimating causal effects of a continuous exposure and detecting change points in the causal exposure response curves using observational data. Ren, B., Wu, X., Braun, D., Pillai, N., & Dominici, F.(2021). "Bayesian modeling for exposure response curve via gaussian processes: Causal effects of exposure to air pollution on health outcomes." arXiv preprint <doi:10.48550/arXiv.2105.03454>.

Maintained by Boyu Ren. Last updated 11 months ago.

cpp

1.5 match 9 stars 5.86 score 16 scripts

lcbc-uio

questionnaires:Package with functions to calculate components and sums for LCBC questionnaires

Creates summaries and factorials of answers to questionnaires.

Maintained by Athanasia Mo Mowinckel. Last updated 2 years ago.

1.8 match 3 stars 4.63 score 13 scripts

thomaschln

sgraph:Network Visualization Using 'sigma.js'

Interactive visualizations of graphs created with the 'igraph' package using a 'htmlwidgets' wrapper for the 'sigma.js' network visualization v2.4.0 <https://www.sigmajs.org/>, enabling to display several thousands of nodes. While several 'R' packages have been developed to interface 'sigma.js', all were developed for v1.x.x and none have migrated to v2.4.0 nor are they planning to. This package builds upon the 'sigmaNet' package, and users familiar with it will recognize the similar design approach. Two extensions have been added to the classic 'sigma.js' visualizations by overriding the underlying 'JavaScript' code, enabling to draw a frame around node labels, and to display labels on multiple lines by parsing line breaks. Other additional functionalities that did not require overriding 'sigma.js' code include toggling node visibility when clicked using a node attribute and highlighting specific edges. 'sigma.js' is currently preparing a stable release v3.0.0, and this package plans to update to it when it is available.

Maintained by Thomas Charlon. Last updated 4 months ago.

1.6 match 5.02 score 1 scripts 1 dependents

thomaschln

nlpembeds:Natural Language Processing Embeddings

Provides efficient methods to compute co-occurrence matrices, pointwise mutual information (PMI) and singular value decomposition (SVD). In the biomedical and clinical settings, one challenge is the huge size of databases, e.g. when analyzing data of millions of patients over tens of years. To address this, this package provides functions to efficiently compute monthly co-occurrence matrices, which is the computational bottleneck of the analysis, by using the 'RcppAlgos' package and sparse matrices. Furthermore, the functions can be called on 'SQL' databases, enabling the computation of co-occurrence matrices of tens of gigabytes of data, representing millions of patients over tens of years. Partly based on Hong C. (2021) <doi:10.1038/s41746-021-00519-z>.

Maintained by Thomas Charlon. Last updated 1 months ago.

1.6 match 4.98 score

thomaschln

kgraph:Knowledge Graphs Constructions and Visualizations

Knowledge graphs enable to efficiently visualize and gain insights into large-scale data analysis results, as p-values from multiple studies or embedding data matrices. The usual workflow is a user providing a data frame of association studies results and specifying target nodes, e.g. phenotypes, to visualize. The knowledge graph then shows all the features which are significantly associated with the phenotype, with the edges being proportional to the association scores. As the user adds several target nodes and grouping information about the nodes such as biological pathways, the construction of such graphs soon becomes complex. The 'kgraph' package aims to enable users to easily build such knowledge graphs, and provides two main features: first, to enable building a knowledge graph based on a data frame of concepts relationships, be it p-values or cosine similarities; second, to enable determining an appropriate cut-off on cosine similarities from a complete embedding matrix, to enable the building of a knowledge graph directly from an embedding matrix. The 'kgraph' package provides several display, layout and cut-off options, and has already proven useful to researchers to enable them to visualize large sets of p-value associations with various phenotypes, and to quickly be able to visualize embedding results. Two example datasets are provided to demonstrate these behaviors, and several live 'shiny' applications are hosted by the CELEHS laboratory and Parse Health, as the KESER Mental Health application <https://keser-mental-health.parse-health.org/> based on Hong C. (2021) <doi:10.1038/s41746-021-00519-z>.

Maintained by Thomas Charlon. Last updated 6 days ago.

1.5 match 4.90 score

bioc

PANR:Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations

This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.

Maintained by Xin Wang. Last updated 5 months ago.

immunooncologynetworkinferencevisualizationgraphandnetworkclusteringcellbasedassays

1.8 match 3.30 score 2 scripts

jemus42

poddr:Collect Metadata for Selected Podcasts

Collecting all the data, but just for The Incomparable, Relay.fm and ATP.

Maintained by Lukas Burk. Last updated 30 days ago.

1.7 match 1 stars 2.48 score 6 scripts

bodkan

admixr:An Interface for Running 'ADMIXTOOLS' Analyses

An interface for performing all stages of 'ADMIXTOOLS' analyses (<https://reich.hms.harvard.edu/software>) entirely from R. Wrapper functions (D, f4, f3, etc.) completely automate the generation of intermediate configuration files, run 'ADMIXTOOLS' programs on the command-line, and parse output files to extract values of interest. This allows users to focus on the analysis itself instead of worrying about low-level technical details. A set of complementary functions for processing and filtering of data in the 'EIGENSTRAT' format is also provided.

Maintained by Martin Petr. Last updated 1 months ago.

bioinformaticspopgenpopulation-genetics

0.5 match 29 stars 7.42 score 91 scripts

poissonconsulting

readwritesqlite:Enhanced Reading and Writing for 'SQLite' Databases

Reads and writes data frames to 'SQLite' databases while preserving time zones (for POSIXct columns), projections (for 'sfc' columns), units (for 'units' columns), levels (for factors and ordered factors) and classes for logical, Date and 'hms' columns. It also logs changes to tables and provides more informative error messages.

Maintained by Joe Thorley. Last updated 3 months ago.

dbilogmetadataposixctreadsfcsqliteunitswrite

0.5 match 38 stars 6.42 score 11 scripts 1 dependents

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