R-universe search: pipe

tidyverse

magrittr:A Forward-Pipe Operator for R

Provides a mechanism for chaining commands with a new forward-pipe operator, %>%. This operator will forward a value, or the result of an expression, into the next function call/expression. There is flexible support for the type of right-hand side expressions. For more information, see package vignette. To quote Rene Magritte, "Ceci n'est pas un pipe."

Maintained by Lionel Henry. Last updated 2 years ago.

pipe

34.7 match 961 stars 21.06 score 82k scripts 14k dependents

omega1x

pipenostics:Diagnostics, Reliability and Predictive Maintenance of Pipeline Systems

Functions that represent some useful empirical and data-driven models for heat loss, corrosion diagnostics, and predictive maintenance of pipeline systems. The package is designed for engineers who are involved in exploratory or routine calculations. Methods are described in Timashev et al. (2016) <doi:10.1007/978-3-319-25307-7>, A.C.Reddy (2017) <doi:10.1016/j.matpr.2017.07.081>, Minenergo (2008) <https://docs.cntd.ru/document/902148459>, Minenergo (2005) <https://docs.cntd.ru/document/1200035568>, Xing LU. (2014) <doi:10.1080/23744731.2016.1258371>.

Maintained by Yuri Possokhov. Last updated 10 months ago.

district-heating heat-losses inline-inspection remaining-useful-life

58.3 match 2 stars 4.73 score 108 scripts

r-lib

lintr:A 'Linter' for R Code

Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with 'RStudio IDE', 'Emacs', 'Vim', 'Sublime Text', 'Atom' and 'Visual Studio Code'.

Maintained by Michael Chirico. Last updated 8 days ago.

linter

9.6 match 1.2k stars 17.00 score 916 scripts 33 dependents

winvector

wrapr:Wrap R Tools for Debugging and Parametric Programming

Tools for writing and debugging R code. Provides: '%.>%' dot-pipe (an 'S3' configurable pipe), unpack/to (R style multiple assignment/return), 'build_frame()'/'draw_frame()' ('data.frame' example tools), 'qc()' (quoting concatenate), ':=' (named map builder), 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools::strmacro()' and 'base::bquote()'), and more.

Maintained by John Mount. Last updated 2 years ago.

13.2 match 137 stars 11.11 score 390 scripts 12 dependents

thomasgstewart

tangram.pipe:Row-by-Row Table Building

Builds tables with customizable rows. Users can specify the type of data to use for each row, as well as how to handle missing data and the types of comparison tests to run on the table columns.

Maintained by Andrew Guide. Last updated 3 years ago.

40.5 match 1 stars 3.60 score 1 scripts

gdemin

maditr:Fast Data Aggregation, Modification, and Filtering with Pipes and 'data.table'

Provides pipe-style interface for 'data.table'. Package preserves all 'data.table' features without significant impact on performance. 'let' and 'take' functions are simplified interfaces for most common data manipulation tasks. For example, you can write 'take(mtcars, mean(mpg), by = am)' for aggregation or 'let(mtcars, hp_wt = hp/wt, hp_wt_mpg = hp_wt/mpg)' for modification. Use 'take_if/let_if' for conditional aggregation/modification. Additionally there are some conveniences such as automatic 'data.frame' conversion to 'data.table'.

Maintained by Gregory Demin. Last updated 4 months ago.

data-table magrittr pipes

15.1 match 61 stars 8.98 score 248 scripts 7 dependents

miferreiro

bdpar:Big Data Preprocessing Architecture

Provide a tool to easily build customized data flows to pre-process large volumes of information from different sources. To this end, 'bdpar' allows to (i) easily use and create new functionalities and (ii) develop new data source extractors according to the user needs. Additionally, the package provides by default a predefined data flow to extract and pre-process the most relevant information (tokens, dates, ... ) from some textual sources (SMS, Email, YouTube comments).

Maintained by Miguel Ferreiro-Díaz. Last updated 1 years ago.

custom-flow custom-pipes preprocessing r6

25.5 match 8 stars 5.23 score 14 scripts

huizezhang-sherry

ferrn:Facilitate Exploration of touRR optimisatioN

Diagnostic plots for optimisation, with a focus on projection pursuit. These show paths the optimiser takes in the high-dimensional space in multiple ways: by reducing the dimension using principal component analysis, and also using the tour to show the path on the high-dimensional space. Several botanical colour palettes are included, reflecting the name of the package. A paper describing the methodology can be found at <https://journal.r-project.org/archive/2021/RJ-2021-105/index.html>.

Maintained by H. Sherry Zhang. Last updated 10 days ago.

25.2 match 6 stars 5.16 score 20 scripts

mikesweeting

pipe.design:Dual-Agent Dose Escalation for Phase I Trials using the PIPE Design

Implements the Product of Independent beta Probabilities dose Escalation (PIPE) design for dual-agent Phase I trials as described in Mander AP, Sweeting MJ (2015) <DOI:10.1002/sim.6434>.

Maintained by Michael Sweeting. Last updated 4 years ago.

46.5 match 2.70 score 3 scripts

daranzolin

ViewPipeSteps:Create View Tabs of Pipe Chains

Debugging pipe chains often consists of viewing the output after each step. This package adds RStudio addins and two functions that allow outputing each or select steps in a convenient way.

Maintained by David Ranzolin. Last updated 3 years ago.

magrittr pipes rstudio-addin

20.5 match 246 stars 5.49 score 25 scripts

bioc

tidybulk:Brings transcriptomics to the tidyverse

This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.

Maintained by Stefano Mangiola. Last updated 5 months ago.

assaydomain infrastructure rnaseq differentialexpression geneexpression normalization clustering qualitycontrol sequencing transcription transcriptomics bioconductor bulk-transcriptional-analyses deseq2 differential-expression edger ensembl-ids entrez gene-symbols gsea mds-dimensions pca pipe redundancy tibble tidy tidy-data tidyverse transcripts tsne

11.5 match 168 stars 9.48 score 172 scripts 1 dependents

edm44

hydraulics:Basic Pipe and Open Channel Hydraulics

Functions for basic hydraulic calculations related to water flow in circular pipes both flowing full (under pressure), and partially full (gravity flow), and trapezoidal open channels. For pressure flow this includes friction loss calculations by solving the Darcy-Weisbach equation for head loss, flow or diameter, plotting a Moody diagram, matching a pump characteristic curve to a system curve, and solving for flows in a pipe network using the Hardy-Cross method. The Darcy-Weisbach friction factor is calculated using the Colebrook (or Colebrook-White equation), the basis of the Moody diagram, the original citation being Colebrook (1939) <doi:10.1680/ijoti.1939.13150>. For gravity flow, the Manning equation is used, again solving for missing parameters. The derivation of and solutions using the Darcy-Weisbach equation and the Manning equation are outlined in many fluid mechanics texts such as Finnemore and Maurer (2024, ISBN:978-1-264-78729-6). Some gradually- and rapidly-varied flow functions are included. For the Manning equation solutions, this package uses modifications of original code from the 'iemisc' package by Irucka Embry.

Maintained by Ed Maurer. Last updated 4 months ago.

15.6 match 9 stars 5.13 score 8 scripts

stemangiola

tidygate:Interactively Gate Points

Interactively gate points on a scatter plot. Interactively drawn gates are recorded and can be applied programmatically to reproduce results exactly. Programmatic gating is based on the package gatepoints by Wajid Jawaid (who is also an author of this package).

Maintained by Stefano Mangiola. Last updated 6 months ago.

assaydomain infrastructure clustering datavis dataviz dplyr drawing facs gate ggplot2 interactive pipe programmatic seurat single-cell single-cell-rna-seq tibble tidy-data tidyverse

11.0 match 23 stars 6.89 score 14 scripts 1 dependents

bioc

ELMER:Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Maintained by Tiago Chedraoui Silva. Last updated 5 months ago.

dnamethylation geneexpression motifannotation software generegulation transcription network

9.7 match 7.42 score 176 scripts

renkun-ken

pipeR:Multi-Paradigm Pipeline Implementation

Provides various styles of function chaining methods: Pipe operator, Pipe object, and pipeline function, each representing a distinct pipeline model yet sharing almost a common set of features: A value can be piped to the first unnamed argument of a function and to dot symbol in an enclosed expression. The syntax is designed to make the pipeline more readable and friendly to a wide range of operations.

Maintained by Kun Ren. Last updated 9 years ago.

7.9 match 169 stars 8.83 score 616 scripts 9 dependents

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 2 months ago.

7.8 match 6 stars 8.58 score 177 scripts 1 dependents

haozhu233

kableExtra:Construct Complex Table with 'kable' and Pipe Syntax

Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr' and the piping syntax from 'magrittr'. Function 'kable()' is a light weight table generator coming from 'knitr'. This package simplifies the way to manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows users to construct complex tables and customize styles using a readable syntax.

Maintained by Hao Zhu. Last updated 10 days ago.

html kable kableextra knitr latex rmarkdown

3.4 match 702 stars 19.35 score 55k scripts 163 dependents

yihui

formatR:Format R Code Automatically

Provides a function tidy_source() to format R source code. Spaces and indent will be added to the code automatically, and comments will be preserved under certain conditions, so that R code will be more human-readable and tidy. There is also a Shiny app as a user interface in this package (see tidy_app()).

Maintained by Yihui Xie. Last updated 1 years ago.

code-formatter

4.4 match 259 stars 15.07 score 1.4k scripts 1.2k dependents

scheidan

WaMaSim:Simulate Rehabilitation Strategies for Water Distribution Systems

The outcome of various rehabilitation strategies for water distribution systems can be modeled with the Water Management Simulator (WaMaSim). Pipe breaks and the corresponding damage and rehabilitation costs are simulated. It is mainly intended to be used as educational tool for the Water Infrastructure Experimental and Computer Laboratory at ETH Zurich, Switzerland.

Maintained by Christian Foerster. Last updated 5 years ago.

20.2 match 1 stars 3.00 score 4 scripts

rstudio

promises:Abstractions for Promise-Based Asynchronous Programming

Provides fundamental abstractions for doing asynchronous programming in R using promises. Asynchronous programming is useful for allowing a single R process to orchestrate multiple tasks in the background while also attending to something else. Semantics are similar to 'JavaScript' promises, but with a syntax that is idiomatic R.

Maintained by Joe Cheng. Last updated 1 months ago.

cpp

3.5 match 204 stars 17.10 score 688 scripts 2.6k dependents

rossellhayes

incase:Pipe-Friendly Vector Replacement with Case Statements

Offers a pipe-friendly alternative to the 'dplyr' functions case_when() and if_else(), as well as a number of user-friendly simplifications for common use cases. These functions accept a vector as an optional first argument, allowing conditional statements to be built using the 'magrittr' dot operator. The functions also coerce all outputs to the same type, meaning you no longer have to worry about using specific typed variants of NA or explicitly declaring integer outputs, and evaluate outputs somewhat lazily, so you don't waste time on long operations that won't be used.

Maintained by Alexander Rossell Hayes. Last updated 8 months ago.

magrittr magrittr-pipes recode-values tidyverse

14.8 match 7 stars 3.85 score 9 scripts

uchidamizuki

navigatr:Navigation Menu for Pipe-Friendly Data Processing

Provides a navigation menu to enable pipe-friendly data processing for hierarchical data structures. By activating the menu items, you can perform operations on each item while maintaining the overall structure in attributes.

Maintained by Mizuki Uchida. Last updated 9 months ago.

pipe

14.4 match 5 stars 3.88 score 5 scripts 1 dependents

guillaumepressiat

stringfix:Strings manipulations in a piping way of coding

Some infix operators and other utility functions to make syntax more and more left to right. In a manner of coding, I just want to say %>% nothing.

Maintained by Guillaume Pressiat. Last updated 3 years ago.

19.0 match 13 stars 2.89 score 12 scripts

dipterix

dipsaus:A Dipping Sauce for Data Analysis and Visualizations

Works as an "add-on" to packages like 'shiny', 'future', as well as 'rlang', and provides utility functions. Just like dipping sauce adding flavors to potato chips or pita bread, 'dipsaus' for data analysis and visualizations adds handy functions and enhancements to popular packages. The goal is to provide simple solutions that are frequently asked for online, such as how to synchronize 'shiny' inputs without freezing the app, or how to get memory size on 'Linux' or 'MacOS' system. The enhancements roughly fall into these four categories: 1. 'shiny' input widgets; 2. high-performance computing using the 'future' package; 3. modify R calls and convert among numbers, strings, and other objects. 4. utility functions to get system information such like CPU chip-set, memory limit, etc.

Maintained by Zhengjia Wang. Last updated 5 days ago.

cpp

6.8 match 13 stars 7.90 score 85 scripts 3 dependents

kassambara

rstatix:Pipe-Friendly Framework for Basic Statistical Tests

Provides a simple and intuitive pipe-friendly framework, coherent with the 'tidyverse' design philosophy, for performing basic statistical tests, including t-test, Wilcoxon test, ANOVA, Kruskal-Wallis and correlation analyses. The output of each test is automatically transformed into a tidy data frame to facilitate visualization. Additional functions are available for reshaping, reordering, manipulating and visualizing correlation matrix. Functions are also included to facilitate the analysis of factorial experiments, including purely 'within-Ss' designs (repeated measures), purely 'between-Ss' designs, and mixed 'within-and-between-Ss' designs. It's also possible to compute several effect size metrics, including "eta squared" for ANOVA, "Cohen's d" for t-test and 'Cramer V' for the association between categorical variables. The package contains helper functions for identifying univariate and multivariate outliers, assessing normality and homogeneity of variances.

Maintained by Alboukadel Kassambara. Last updated 2 years ago.

3.4 match 456 stars 15.16 score 11k scripts 420 dependents

tidymodels

infer:Tidy Statistical Inference

The objective of this package is to perform inference using an expressive statistical grammar that coheres with the tidy design framework.

Maintained by Simon Couch. Last updated 6 months ago.

3.3 match 734 stars 15.69 score 3.5k scripts 17 dependents

tidyverse

modelr:Modelling Functions that Work with the Pipe

Functions for modelling that help you seamlessly integrate modelling into a pipeline of data manipulation and visualisation.

Maintained by Hadley Wickham. Last updated 1 years ago.

modelling

3.1 match 401 stars 16.44 score 6.9k scripts 1.0k dependents

great-northern-diver

loon.ggplot:A Grammar of Interactive Graphics

Provides a bridge between the 'loon' and 'ggplot2' packages. Extends the grammar of ggplot to add clauses to create interactive 'loon' plots. Existing ggplot(s) can be turned into interactive 'loon' plots and 'loon' plots into static ggplot(s); the function 'loon.ggplot()' is the bridge from one plot structure to the other.

Maintained by Zehao Xu. Last updated 10 months ago.

data-analysis ggplot ggplot-features graphics interactive-plots loon visualizations

7.0 match 24 stars 7.11 score 9 scripts 3 dependents

tidyverse

dplyr:A Grammar of Data Manipulation

A fast, consistent tool for working with data frame like objects, both in memory and out of memory.

Maintained by Hadley Wickham. Last updated 12 days ago.

data-manipulation grammar cpp

2.0 match 4.8k stars 24.68 score 659k scripts 7.8k 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 2 days ago.

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

2.3 match 581 stars 21.10 score 31k scripts 1.9k dependents

sfcheung

semptools:Customizing Structural Equation Modelling Plots

Most function focus on specific ways to customize a graph. They use a 'qgraph' output as the first argument, and return a modified 'qgraph' object. This allows the functions to be chained by a pipe operator.

Maintained by Shu Fai Cheung. Last updated 2 months ago.

diagram graph lavaan plot sem structural-equation-modeling

6.3 match 7 stars 7.12 score 87 scripts

tidyverse

purrr:Functional Programming Tools

A complete and consistent functional programming toolkit for R.

Maintained by Hadley Wickham. Last updated 1 months ago.

functional-programming

2.0 match 1.3k stars 22.12 score 59k scripts 6.9k dependents

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.

7.8 match 5.32 score 1 scripts 2 dependents

nlmixr2

rxode2:Facilities for Simulating from ODE-Based Models

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

Maintained by Matthew L. Fidler. Last updated 30 days ago.

fortran openblas cpp openmp

3.7 match 39 stars 11.16 score 220 scripts 13 dependents

shikokuchuo

nanonext:NNG (Nanomsg Next Gen) Lightweight Messaging Library

R binding for NNG (Nanomsg Next Gen), a successor to ZeroMQ. NNG is a socket library for reliable, high-performance messaging over in-process, IPC, TCP, WebSocket and secure TLS transports. Implements 'Scalability Protocols', a standard for common communications patterns including publish/subscribe, request/reply and service discovery. As its own threaded concurrency framework, provides a toolkit for asynchronous programming and distributed computing. Intuitive 'aio' objects resolve automatically when asynchronous operations complete, and synchronisation primitives allow R to wait upon events signalled by concurrent threads.

Maintained by Charlie Gao. Last updated 1 days ago.

concurrency https ipc-message messaging-library nng rpc socket-communication synchronization-primitives tcp-protocol websocket mbedtls

4.1 match 60 stars 9.81 score 28 scripts 9 dependents

torfason

zfit:Fit Models in a Pipe

Improve the usage of model fitting functions within a piped work flow.

Maintained by Magnus Thor Torfason. Last updated 2 years ago.

14.8 match 1 stars 2.70 score 3 scripts

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 24 days ago.

7.8 match 4.98 score

thomaschln

opticskxi:OPTICS K-Xi Density-Based Clustering

Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates the k-Xi cluster extraction method. Finally, the models comparison framework is described and experimented on 2 genetic datasets to identify groups and their discriminating features. The k-Xi algorithm is a novel OPTICS cluster extraction method that specifies directly the number of clusters and does not require fine-tuning of the steepness parameter as the OPTICS Xi method. Combined with a framework that compares models with varying parameters, the OPTICS k-Xi method can identify groups in noisy datasets with unknown number of clusters. Results on summarized genetic data of 1,200 patients are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>. A short video tutorial can be found at <https://www.youtube.com/watch?v=P2XAjqI5Lc4/>.

Maintained by Thomas Charlon. Last updated 6 days ago.

7.8 match 4.90 score 1 scripts

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 24 days ago.

7.8 match 4.85 score

dtkaplan

LSTbook:Data and Software for "Lessons in Statistical Thinking"

"Lessons in Statistical Thinking" D.T. Kaplan (2014) <https://dtkaplan.github.io/Lessons-in-statistical-thinking/> is a textbook for a first or second course in statistics that embraces data wrangling, causal reasoning, modeling, statistical adjustment, and simulation. 'LSTbook' supports the student-centered, tidy, pipeline-oriented computing style featured in the book.

Maintained by Daniel Kaplan. Last updated 14 hours ago.

5.8 match 4 stars 6.29 score 27 scripts

thomaschln

snplinkage:Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a second correlation heatmap. The SNPs correlations are computed on Genotype Data objects from the 'GWASTools' package using the 'SNPRelate' package, and the plots are customizable 'ggplot2' and 'gtable' objects and are annotated using the 'biomaRt' package. Usage is detailed in the vignette with example data and results from up to 500 SNPs of 1,200 scans are in Charlon T. (2019) <doi:10.13097/archive-ouverte/unige:161795>.

Maintained by Thomas Charlon. Last updated 4 months ago.

geneticvariability microarray snp

7.8 match 4.62 score 14 scripts

thinkr-open

arpr:Advanced R Pipes

Provides convenience functions for programming with 'magrittr' pipes. Conditional pipes, a string prefixer and a function to pipe the given object into a specific argument given by character name are currently supported. It is named after the dadaist Hans Arp, a friend of Rene Magritte.

Maintained by Sébastien Rochette. Last updated 4 years ago.

8.2 match 7 stars 4.32 score 5 scripts 2 dependents

symbolixau

mapdeck:Interactive Maps Using 'Mapbox GL JS' and 'Deck.gl'

Provides a mechanism to plot an interactive map using 'Mapbox GL' (<https://docs.mapbox.com/mapbox-gl-js/api/>), a javascript library for interactive maps, and 'Deck.gl' (<https://deck.gl/>), a javascript library which uses 'WebGL' for visualising large data sets.

Maintained by David Cooley. Last updated 3 months ago.

deckgl geospatial mapbox mapbox-gl mapbox-gl-js maps cpp

3.3 match 363 stars 10.30 score 368 scripts 1 dependents

bwiernik

pipebind:Flexible Binding for Complex Function Evaluation with the Base R |> Pipe

Provides a simple function to bind a piped object to a placeholder symbol to enable complex function evaluation with the base R |> pipe.

Maintained by Brenton M. Wiernik. Last updated 2 years ago.

7.4 match 50 stars 4.54 score 14 scripts

bioc

gemini:GEMINI: Variational inference approach to infer genetic interactions from pairwise CRISPR screens

GEMINI uses log-fold changes to model sample-dependent and independent effects, and uses a variational Bayes approach to infer these effects. The inferred effects are used to score and identify genetic interactions, such as lethality and recovery. More details can be found in Zamanighomi et al. 2019 (in press).

Maintained by Sidharth Jain. Last updated 5 months ago.

software crispr bayesian dataimport computational-biology genetic-interactions

5.6 match 15 stars 6.02 score 9 scripts

r-lib

usethis:Automate Package and Project Setup

Automate package and project setup tasks that are otherwise performed manually. This includes setting up unit testing, test coverage, continuous integration, Git, 'GitHub', licenses, 'Rcpp', 'RStudio' projects, and more.

Maintained by Jennifer Bryan. Last updated 11 days ago.

github setup

1.9 match 869 stars 17.54 score 5.6k scripts 336 dependents

yihui

xfun:Supporting Functions for Packages Maintained by 'Yihui Xie'

Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.

Maintained by Yihui Xie. Last updated 3 days ago.

1.8 match 145 stars 18.18 score 916 scripts 4.4k dependents

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

8.4 match 3.86 score 12 scripts 2 dependents

symbolixau

googleway:Accesses Google Maps APIs to Retrieve Data and Plot Maps

Provides a mechanism to plot a 'Google Map' from 'R' and overlay it with shapes and markers. Also provides access to 'Google Maps' APIs, including places, directions, roads, distances, geocoding, elevation and timezone.

Maintained by David Cooley. Last updated 6 months ago.

google-map google-maps google-maps-api google-maps-javascript-api spatial spatial-analysis

3.3 match 236 stars 9.67 score 536 scripts 2 dependents

jmsigner

amt:Animal Movement Tools

Manage and analyze animal movement data. The functionality of 'amt' includes methods to calculate home ranges, track statistics (e.g. step lengths, speed, or turning angles), prepare data for fitting habitat selection analyses, and simulation of space-use from fitted step-selection functions.

Maintained by Johannes Signer. Last updated 4 months ago.

3.0 match 41 stars 10.54 score 418 scripts

pharmaverse

admiral:ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).

Maintained by Ben Straub. Last updated 4 days ago.

cdisc clinical-trials open-source

2.3 match 236 stars 13.89 score 486 scripts 4 dependents

jeroen

curl:A Modern and Flexible Web Client for R

Bindings to 'libcurl' <https://curl.se/libcurl/> for performing fully configurable HTTP/FTP requests where responses can be processed in memory, on disk, or streaming via the callback or connection interfaces. Some knowledge of 'libcurl' is recommended; for a more-user-friendly web client see the 'httr2' package which builds on this package with http specific tools and logic.

Maintained by Jeroen Ooms. Last updated 22 days ago.

curl

1.5 match 225 stars 19.95 score 4.0k scripts 5.8k dependents

data-edu

tidyLPA:Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software

Easily carry out latent profile analysis ("LPA"), determine the correct number of classes based on best practices, and tabulate and plot the results. Provides functionality to estimate commonly-specified models with free means, variances, and covariances for each profile. Follows a tidy approach, in that output is in the form of a data frame that can subsequently be computed on. Models can be estimated using the free open source 'R' packages 'Mclust' and 'OpenMx', or using the commercial program 'MPlus', via the 'MplusAutomation' package.

Maintained by Joshua M Rosenberg. Last updated 1 years ago.

3.3 match 57 stars 8.71 score 121 scripts

erictleung

hp:Pipe a function into help()

After using autocomplete on a function, instead of scrolling to the front of the function to use the question mark to access the help page, this package allows you to pipe the function into a wrapper help function for easier access.

Maintained by Eric Leung. Last updated 4 years ago.

documentation help magrittr pipe rstudio

16.6 match 1.70 score 7 scripts

inlabru-org

inlabru:Bayesian Latent Gaussian Modelling using INLA and Extensions

Facilitates spatial and general latent Gaussian modeling using integrated nested Laplace approximation via the INLA package (<https://www.r-inla.org>). Additionally, extends the GAM-like model class to more general nonlinear predictor expressions, and implements a log Gaussian Cox process likelihood for modeling univariate and spatial point processes based on ecological survey data. Model components are specified with general inputs and mapping methods to the latent variables, and the predictors are specified via general R expressions, with separate expressions for each observation likelihood model in multi-likelihood models. A prediction method based on fast Monte Carlo sampling allows posterior prediction of general expressions of the latent variables. Ecology-focused introduction in Bachl, Lindgren, Borchers, and Illian (2019) <doi:10.1111/2041-210X.13168>.

Maintained by Finn Lindgren. Last updated 3 days ago.

2.2 match 96 stars 12.62 score 832 scripts 6 dependents

mrjoh3

c3:'C3.js' Chart Library

Create interactive charts with the 'C3.js' <http://c3js.org/> charting library. All plot types in 'C3.js' are available and include line, bar, scatter, and mixed geometry plots. Plot annotations, labels and axis are highly adjustable. Interactive web based charts can be embedded in R Markdown documents or Shiny web applications.

Maintained by Matt Johnson. Last updated 4 years ago.

chart htmlwidget plots

4.3 match 39 stars 6.45 score 72 scripts

sollano

forestmangr:Forest Mensuration and Management

Processing forest inventory data with methods such as simple random sampling, stratified random sampling and systematic sampling. There are also functions for yield and growth predictions and model fitting, linear and nonlinear grouped data fitting, and statistical tests. References: Kershaw Jr., Ducey, Beers and Husch (2016). <doi:10.1002/9781118902028>.

Maintained by Sollano Rabelo Braga. Last updated 3 months ago.

3.3 match 17 stars 7.97 score 378 scripts

r-tmap

tmaptools:Thematic Map Tools

Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.

Maintained by Martijn Tennekes. Last updated 2 months ago.

2.3 match 42 stars 11.67 score 1.8k scripts 26 dependents

ropensci

magick:Advanced Graphics and Image-Processing in R

Bindings to 'ImageMagick': the most comprehensive open-source image processing library available. Supports many common formats (png, jpeg, tiff, pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc). All operations are vectorized via the Magick++ STL meaning they operate either on a single frame or a series of frames for working with layers, collages, or animation. In RStudio images are automatically previewed when printed to the console, resulting in an interactive editing environment. The latest version of the package includes a native graphics device for creating in-memory graphics or drawing onto images using pixel coordinates.

Maintained by Jeroen Ooms. Last updated 20 days ago.

image-manipulation image-processing imagemagick cpp

1.5 match 468 stars 17.31 score 9.0k scripts 256 dependents

tidyverse

tidyverse:Easily Install and Load the 'Tidyverse'

The 'tidyverse' is a set of packages that work in harmony because they share common data representations and 'API' design. This package is designed to make it easy to install and load multiple 'tidyverse' packages in a single step. Learn more about the 'tidyverse' at <https://www.tidyverse.org>.

Maintained by Hadley Wickham. Last updated 5 months ago.

data-science tidyverse

1.3 match 1.7k stars 20.26 score 664k scripts 125 dependents

jonesor

Rcompadre:Utilities for using the 'COM(P)ADRE' Matrix Model Database

Utility functions for interacting with the 'COMPADRE' and 'COMADRE' databases of matrix population models. Described in Jones et al. (2021) <doi:10.1101/2021.04.26.441330>.

Maintained by Owen Jones. Last updated 5 months ago.

3.0 match 11 stars 7.74 score 55 scripts 2 dependents

rstudio

blastula:Easily Send HTML Email Messages

Compose and send out responsive HTML email messages that render perfectly across a range of email clients and device sizes. Helper functions let the user insert embedded images, web link buttons, and 'ggplot2' plot objects into the message body. Messages can be sent through an 'SMTP' server, through the 'Posit Connect' service, or through the 'Mailgun' API service <https://www.mailgun.com/>.

Maintained by Richard Iannone. Last updated 8 months ago.

easy-to-use email html markdown responsive-email smtp

2.3 match 552 stars 10.27 score 348 scripts 5 dependents

emf-creaf

meteoland:Landscape Meteorology Tools

Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].

Maintained by Miquel De Cáceres. Last updated 2 months ago.

cpp

2.8 match 10 stars 7.95 score 92 scripts 2 dependents

paws-r

paws:Amazon Web Services Software Development Kit

Interface to Amazon Web Services <https://aws.amazon.com>, including storage, database, and compute services, such as 'Simple Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda' functions-as-a-service.

Maintained by Dyfan Jones. Last updated 3 days ago.

aws aws-sdk

2.0 match 332 stars 11.25 score 177 scripts 12 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

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 23 days ago.

analytics api automation automl data-science descriptive-statistics h2o machine-learning marketing mmm predictive-modeling puzzle rlanguage robyn visualization

2.3 match 233 stars 9.84 score 185 scripts 1 dependents

uupharmacometrics

xpose:Diagnostics for Pharmacometric Models

Diagnostics for non-linear mixed-effects (population) models from 'NONMEM' <https://www.iconplc.com/solutions/technologies/nonmem/>. 'xpose' facilitates data import, creation of numerical run summary and provide 'ggplot2'-based graphics for data exploration and model diagnostics.

Maintained by Benjamin Guiastrennec. Last updated 2 months ago.

diagnostics ggplot2 nonmem pharmacometrics xpose

2.0 match 62 stars 11.02 score 183 scripts 6 dependents

dmurdoch

rgl:3D Visualization Using OpenGL

Provides medium to high level functions for 3D interactive graphics, including functions modelled on base graphics (plot3d(), etc.) as well as functions for constructing representations of geometric objects (cube3d(), etc.). Output may be on screen using OpenGL, or to various standard 3D file formats including WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.

Maintained by Duncan Murdoch. Last updated 2 months ago.

graphics opengl rgl webgl libglu libglvnd libpng libx11 freetype cpp

1.3 match 91 stars 17.49 score 7.3k scripts 300 dependents

nathaneastwood

poorman:A Poor Man's Dependency Free Recreation of 'dplyr'

A replication of key functionality from 'dplyr' and the wider 'tidyverse' using only 'base'.

Maintained by Nathan Eastwood. Last updated 1 years ago.

base-r data-manipulation grammar

2.0 match 341 stars 10.79 score 156 scripts 27 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

1.8 match 107 stars 11.96 score 306 scripts 4 dependents

ropensci

osfr:Interface to the 'Open Science Framework' ('OSF')

An interface for interacting with 'OSF' (<https://osf.io>). 'osfr' enables you to access open research materials and data, or create and manage your own private or public projects.

Maintained by Aaron Wolen. Last updated 8 months ago.

open-science osf reproducible-research

2.0 match 145 stars 10.18 score 588 scripts 3 dependents

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-characteristics descriptive-statistics modeling paired-comparisons reporting statistics tableone

1.5 match 225 stars 13.45 score 1.2k scripts 16 dependents

jakobbossek

grapherator:A Modular Multi-Step Graph Generator

Set of functions for step-wise generation of (weighted) graphs. Aimed for research in the field of single- and multi-objective combinatorial optimization. Graphs are generated adding nodes, edges and weights. Each step may be repeated multiple times with different predefined and custom generators resulting in high flexibility regarding the graph topology and structure of edge weights.

Maintained by Jakob Bossek. Last updated 3 years ago.

combinatorial-optimization graph-generator minimum-spanning-tree multi-objective-optimization optimization

3.3 match 9 stars 6.04 score 27 scripts 1 dependents

lyzander

tableHTML:A Tool to Create HTML Tables

A tool to create and style HTML tables with CSS. These can be exported and used in any application that accepts HTML (e.g. 'shiny', 'rmarkdown', 'PowerPoint'). It also provides functions to create CSS files (which also work with shiny).

Maintained by Theo Boutaris. Last updated 2 years ago.

2.3 match 22 stars 8.80 score 280 scripts 1 dependents

kwb-r

kwb.epanet:R Package for Interfacing EPANET

Functions enabling the reading and writing of EPANET (http://www.epa.gov/nrmrl/wswrd/dw/epanet.html) input files and reading of output files.

Maintained by Hauke Sonnenberg. Last updated 3 years ago.

epanet modelling pipe-network project-optiwells2

11.5 match 1.70 score 1 scripts

tidymodels

tidypredict:Run Predictions Inside the Database

It parses a fitted 'R' model object, and returns a formula in 'Tidy Eval' code that calculates the predictions. It works with several databases back-ends because it leverages 'dplyr' and 'dbplyr' for the final 'SQL' translation of the algorithm. It currently supports lm(), glm(), randomForest(), ranger(), earth(), xgb.Booster.complete(), cubist(), and ctree() models.

Maintained by Emil Hvitfeldt. Last updated 3 months ago.

dbplyr dplyr purrr rlang

1.8 match 261 stars 11.03 score 241 scripts 2 dependents

ropensci

robotstxt:A 'robots.txt' Parser and 'Webbot'/'Spider'/'Crawler' Permissions Checker

Provides functions to download and parse 'robots.txt' files. Ultimately the package makes it easy to check if bots (spiders, crawler, scrapers, ...) are allowed to access specific resources on a domain.

Maintained by Jordan Bradford. Last updated 4 months ago.

crawler peer-reviewed robotstxt scraper spider webscraping

1.8 match 68 stars 10.43 score 414 scripts 7 dependents

yonicd

slickR:Create Interactive Carousels with the 'JavaScript' 'Slick' Library

Create and customize interactive carousels using the 'Slick' 'JavaScript' library and the 'htmlwidgets' package. The carousels can contain plots produced in R, images, 'iframes', videos and other 'htmlwidgets'. These carousels can be created directly from the R console, and viewed in the 'RStudio' internal viewer, in 'Shiny' apps and R Markdown documents.

Maintained by Jonathan Sidi. Last updated 1 years ago.

htmlwidgets javascript slick

2.0 match 160 stars 9.37 score 199 scripts 1 dependents

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

2.3 match 95 stars 8.10 score 49 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.

3.5 match 30 stars 5.18 score 3 scripts

ffverse

ffscrapr:API Client for Fantasy Football League Platforms

Helps access various Fantasy Football APIs by handling authentication and rate-limiting, forming appropriate calls, and returning tidy dataframes which can be easily connected to other data sources.

Maintained by Tan Ho. Last updated 5 months ago.

api-client fantasy-football fantasy-football-api

2.3 match 84 stars 8.07 score 178 scripts 1 dependents

paws-r

paws.application.integration:'Amazon Web Services' Application Integration Services

Interface to 'Amazon Web Services' application integration services, including 'Simple Queue Service' ('SQS') message queue, 'Simple Notification Service' ('SNS') publish/subscribe messaging, and more <https://aws.amazon.com/>.

Maintained by Dyfan Jones. Last updated 3 days ago.

aws aws-sdk

2.0 match 332 stars 9.06 score 14 dependents

bradleyjeck

epanet2toolkit:Call 'EPANET' Functions to Simulate Pipe Networks

Enables simulation of water piping networks using 'EPANET'. The package provides functions from the 'EPANET' programmer's toolkit as R functions so that basic or customized simulations can be carried out from R. The package uses 'EPANET' version 2.2 from Open Water Analytics <https://github.com/OpenWaterAnalytics/EPANET/releases/tag/v2.2>.

Maintained by Bradley Eck. Last updated 3 months ago.

epanet epanet-api simulation water water-distribution-networks

3.4 match 15 stars 5.17 score 66 scripts

rapidsurveys

oldr:An Implementation of Rapid Assessment Method for Older People

An implementation of the Rapid Assessment Method for Older People or RAM-OP <https://www.helpage.org/resource/rapid-assessment-method-for-older-people-ramop-manual/>. It provides various functions that allow the user to design and plan the assessment and analyse the collected data. RAM-OP provides accurate and reliable estimates of the needs of older people.

Maintained by Ernest Guevarra. Last updated 1 months ago.

assessment data-analysis odk ram-op rapid-assessment

3.5 match 2 stars 5.00 score 4 scripts

b-rodrigues

chronicler:Add Logging To Functions

Decorate functions to make them return enhanced output. The enhanced output consists in an object of type 'chronicle' containing the result of the function applied to its arguments, as well as a log detailing when the function was run, what were its inputs, what were the errors (if the function failed to run) and other useful information. Tools to handle decorated functions are included, such as a forward pipe operator that makes chaining decorated functions possible.

Maintained by Bruno Rodrigues. Last updated 11 months ago.

2.3 match 51 stars 7.51 score 35 scripts

r-box

boxr:Interface for the 'Box.com API'

An R interface for the remote file hosting service 'Box' (<https://www.box.com/>). In addition to uploading and downloading files, this package includes functions which mirror base R operations for local files, (e.g. box_load(), box_save(), box_read(), box_setwd(), etc.), as well as 'git' style functions for entire directories (e.g. box_fetch(), box_push()).

Maintained by Ian Lyttle. Last updated 11 months ago.

2.0 match 63 stars 8.65 score 238 scripts

r-spatial

qgisprocess:Use 'QGIS' Processing Algorithms

Provides seamless access to the 'QGIS' (<https://qgis.org>) processing toolbox using the standalone 'qgis_process' command-line utility. Both native and third-party (plugin) processing providers are supported. Beside referring data sources from file, also common objects from 'sf', 'terra' and 'stars' are supported. The native processing algorithms are documented by QGIS.org (2024) <https://docs.qgis.org/latest/en/docs/user_manual/processing_algs/>.

Maintained by Floris Vanderhaeghe. Last updated 5 months ago.

1.7 match 210 stars 10.09 score 175 scripts

bioc

MOFA2:Multi-Omics Factor Analysis v2

The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.

Maintained by Ricard Argelaguet. Last updated 5 months ago.

dimensionreduction bayesian visualization factor-analysis mofa multi-omics

1.7 match 319 stars 10.02 score 502 scripts

pik-piam

quitte:Bits and pieces of code to use with quitte-style data frames

A collection of functions for easily dealing with quitte-style data frames, doing multi-model comparisons and plots.

Maintained by Michaja Pehl. Last updated 2 days ago.

2.0 match 8.22 score 184 scripts 35 dependents

cynkra

constructive:Display Idiomatic Code to Construct Most R Objects

Prints code that can be used to recreate R objects. In a sense it is similar to 'base::dput()' or 'base::deparse()' but 'constructive' strives to use idiomatic constructors.

Maintained by Antoine Fabri. Last updated 1 days ago.

1.9 match 137 stars 8.63 score 20 scripts

flyaflya

causact:Fast, Easy, and Visual Bayesian Inference

Accelerate Bayesian analytics workflows in 'R' through interactive modelling, visualization, and inference. Define probabilistic graphical models using directed acyclic graphs (DAGs) as a unifying language for business stakeholders, statisticians, and programmers. This package relies on interfacing with the 'numpyro' python package.

Maintained by Adam Fleischhacker. Last updated 2 months ago.

bayesian-inference dags posterior-probability probabilistic-graphical-models probabilistic-programming

2.3 match 45 stars 7.15 score 52 scripts

nceas

rt:Interface to the 'Request Tracker' API

Provides a programmatic interface to the 'Request Tracker' (RT) HTTP API <https://rt-wiki.bestpractical.com/wiki/REST>. 'RT' is a popular ticket tracking system.

Maintained by Bryce Mecum. Last updated 4 years ago.

api request-tracker

2.0 match 6 stars 7.98 score 664 scripts

richierocks

rebus.base:Core Functionality for the 'rebus' Package

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

Maintained by Richard Cotton. Last updated 8 years ago.

3.3 match 2 stars 4.81 score 31 scripts 7 dependents

pbiecek

archivist:Tools for Storing, Restoring and Searching for R Objects

Data exploration and modelling is a process in which a lot of data artifacts are produced. Artifacts like: subsets, data aggregates, plots, statistical models, different versions of data sets and different versions of results. The more projects we work with the more artifacts are produced and the harder it is to manage these artifacts. Archivist helps to store and manage artifacts created in R. Archivist allows you to store selected artifacts as a binary files together with their metadata and relations. Archivist allows to share artifacts with others, either through shared folder or github. Archivist allows to look for already created artifacts by using it's class, name, date of the creation or other properties. Makes it easy to restore such artifacts. Archivist allows to check if new artifact is the exact copy that was produced some time ago. That might be useful either for testing or caching.

Maintained by Przemyslaw Biecek. Last updated 7 months ago.

1.8 match 74 stars 8.81 score 105 scripts 2 dependents

hadley

ggvis:Interactive Grammar of Graphics

An implementation of an interactive grammar of graphics, taking the best parts of 'ggplot2', combining them with the reactive framework of 'shiny' and drawing web graphics using 'vega'.

Maintained by Hadley Wickham. Last updated 1 years ago.

2.3 match 1 stars 7.02 score 2.3k scripts 11 dependents

tysonstanley

furniture:Furniture for Quantitative Scientists

Contains four main functions (i.e., four pieces of furniture): table1() which produces a well-formatted table of descriptive statistics common as Table 1 in research articles, tableC() which produces a well-formatted table of correlations, tableF() which provides frequency counts, and washer() which is helpful in cleaning up the data. These furniture-themed functions are designed to simplify common tasks in quantitative analysis. Other data summary and cleaning tools are also available.

Maintained by Tyson S. Barrett. Last updated 1 years ago.

descriptive-statistics exploratory-data-analysis health table-one table1 tables tidy tidyverse

2.0 match 50 stars 7.89 score 256 scripts 1 dependents

cran

tidytidbits:A Collection of Tools and Helpers Extending the Tidyverse

A selection of various tools to extend a data analysis workflow based on the 'tidyverse' packages. This includes high-level data frame editing methods (in the style of 'mutate'/'mutate_at'), some methods in the style of 'purrr' and 'forcats', 'lookup' methods for dict-like lists, a generic method for lumping a data frame by a given count, various low-level methods for special treatment of 'NA' values, 'python'-style tuple-assignment and 'truthy'/'falsy' checks, saving to PDF and PNG from a pipe and various small utilities.

Maintained by Marcel Wiesweg. Last updated 3 years ago.

6.3 match 2.48 score 2 dependents

k5cents

gluedown:Wrap Vectors in Markdown Formatting

Ease the transition between R vectors and markdown text. With 'gluedown' and 'rmarkdown', users can create traditional vectors in R, glue those strings together with the markdown syntax, and print those formatted vectors directly to the document. This package primarily uses GitHub Flavored Markdown (GFM), an offshoot of the unambiguous CommonMark specification by John MacFarlane (2019) <https://spec.commonmark.org/>.

Maintained by Kiernan Nicholls. Last updated 1 years ago.

markdown

2.0 match 115 stars 7.59 score 57 scripts

neuhausi

canvasXpress:Visualization Package for CanvasXpress in R

Enables creation of visualizations using the CanvasXpress framework in R. CanvasXpress is a standalone JavaScript library for reproducible research with complete tracking of data and end-user modifications stored in a single PNG image that can be played back. See <https://www.canvasxpress.org> for more information.

Maintained by Connie Brett. Last updated 3 days ago.

analytics bioinformatics chart charting dash dashboard data-analytics data-science data-visualization genomics graphs javascript network network-visualization python reproducible-research shiny visualization

1.3 match 295 stars 11.39 score 145 scripts

bluegreen-labs

ecmwfr:Interface to 'ECMWF' and 'CDS' Data Web Services

Programmatic interface to the European Centre for Medium-Range Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>) and Copernicus's Data Stores. Allows for easy downloads of weather forecasts and climate reanalysis data in R. Data stores covered include the Climate Data Store (CDS; <https://cds.climate.copernicus.eu>), Atmosphere Data Store (ADS; <https://ads.atmosphere.copernicus.eu>) and Early Warning Data Store (CEMS; <https://ewds.climate.copernicus.eu>).

Maintained by Koen Hufkens. Last updated 1 months ago.

cds climate-data copernicus ecmwf-api ecmwf-services

1.5 match 111 stars 10.08 score 156 scripts 3 dependents

nutterb

pixiedust:Tables so Beautifully Fine-Tuned You Will Believe It's Magic

The introduction of the 'broom' package has made converting model objects into data frames as simple as a single function. While the 'broom' package focuses on providing tidy data frames that can be used in advanced analysis, it deliberately stops short of providing functionality for reporting models in publication-ready tables. 'pixiedust' provides this functionality with a programming interface intended to be similar to 'ggplot2's system of layers with fine tuned control over each cell of the table. Options for output include printing to the console and to the common markdown formats (markdown, HTML, and LaTeX). With a little 'pixiedust' (and happy thoughts) tables can really fly.

Maintained by Benjamin Nutter. Last updated 1 years ago.

1.9 match 180 stars 8.01 score 94 scripts

mayer79

MetricsWeighted:Weighted Metrics and Performance Measures for Machine Learning

Provides weighted versions of several metrics and performance measures used in machine learning, including average unit deviances of the Bernoulli, Tweedie, Poisson, and Gamma distributions, see Jorgensen B. (1997, ISBN: 978-0412997112). The package also contains a weighted version of generalized R-squared, see e.g. Cohen, J. et al. (2002, ISBN: 978-0805822236). Furthermore, 'dplyr' chains are supported.

Maintained by Michael Mayer. Last updated 8 months ago.

machine-learning metrics performance statistics

2.2 match 11 stars 6.79 score 75 scripts 5 dependents

tbep-tech

tbeploads:Calculate Loading Data to Tampa Bay

Loading data from major sources to Tampa Bay are calculated on a monthly or annual basis. Major sources include domestic point source (reuse, end of pipe), industrial point source, material losses, non-point sources (MS4), atmospheric deposition, and groundwater.

Maintained by Marcus Beck. Last updated 7 months ago.

data-analysis loads tampa-bay tbep tbnmc water-quality

3.9 match 3.81 score 3 scripts

felixthestudent

cellpypes:Cell Type Pipes for Single-Cell RNA Sequencing Data

Annotate single-cell RNA sequencing data manually based on marker gene thresholds. Find cell type rules (gene+threshold) through exploration, use the popular piping operator '%>%' to reconstruct complex cell type hierarchies. 'cellpypes' models technical noise to find positive and negative cells for a given expression threshold and returns cell type labels or pseudobulks. Cite this package as Frauhammer (2022) <doi:10.5281/zenodo.6555728> and visit <https://github.com/FelixTheStudent/cellpypes> for tutorials and newest features.

Maintained by Felix Frauhammer. Last updated 1 years ago.

celltype-annotation classification-algorithm scrnaseq single-cell-rna-seq

3.3 match 51 stars 4.41 score 8 scripts

opengeos

whitebox:'WhiteboxTools' R Frontend

An R frontend for the 'WhiteboxTools' library, which is an advanced geospatial data analysis platform developed by Prof. John Lindsay at the University of Guelph's Geomorphometry and Hydrogeomatics Research Group. 'WhiteboxTools' can be used to perform common geographical information systems (GIS) analysis operations, such as cost-distance analysis, distance buffering, and raster reclassification. Remote sensing and image processing tasks include image enhancement (e.g. panchromatic sharpening, contrast adjustments), image mosaicing, numerous filtering operations, simple classification (k-means), and common image transformations. 'WhiteboxTools' also contains advanced tooling for spatial hydrological analysis (e.g. flow-accumulation, watershed delineation, stream network analysis, sink removal), terrain analysis (e.g. common terrain indices such as slope, curvatures, wetness index, hillshading; hypsometric analysis; multi-scale topographic position analysis), and LiDAR data processing. Suggested citation: Lindsay (2016) <doi:10.1016/j.cageo.2016.07.003>.

Maintained by Andrew Brown. Last updated 5 months ago.

geomorphometry geoprocessing geospatial gis hydrology remote-sensing rstudio

1.5 match 173 stars 9.65 score 203 scripts 2 dependents

andrmenezes

unitquantreg:Parametric Quantile Regression Models for Bounded Data

A collection of parametric quantile regression models for bounded data. At present, the package provides 13 parametric quantile regression models. It can specify regression structure for any quantile and shape parameters. It also provides several S3 methods to extract information from fitted model, such as residual analysis, prediction, plotting, and model comparison. For more computation efficient the [dpqr]'s, likelihood, score and hessian functions are written in C++. For further details see Mazucheli et. al (2022) <doi:10.1016/j.cmpb.2022.106816>.

Maintained by André F. B. Menezes. Last updated 2 years ago.

cpp

3.5 match 1 stars 4.00 score 7 scripts

ekstroem

MESS:Miscellaneous Esoteric Statistical Scripts

A mixed collection of useful and semi-useful diverse statistical functions, some of which may even be referenced in The R Primer book. See Ekstrøm, C. T. (2016). The R Primer. 2nd edition. Chapman & Hall.

Maintained by Claus Thorn Ekstrøm. Last updated 29 days ago.

biostatistics power-analysis statistical-analysis statistical-methods statistical-models openblas cpp

1.8 match 4 stars 7.76 score 328 scripts 13 dependents

ropensci

stats19:Work with Open Road Traffic Casualty Data from Great Britain

Tools to help download, process and analyse the UK road collision data collected using the 'STATS19' form. The datasets are provided as 'CSV' files with detailed road safety information about the circumstances of car crashes and other incidents on the roads resulting in casualties in Great Britain from 1979 to present. Tables are available on 'colissions' with the circumstances (e.g. speed limit of road), information about 'vehicles' involved (e.g. type of vehicle), and 'casualties' (e.g. age). The statistics relate only to events on public roads that were reported to the police, and subsequently recorded, using the 'STATS19' collision reporting form. See the Department for Transport website <https://www.data.gov.uk/dataset/cb7ae6f0-4be6-4935-9277-47e5ce24a11f/road-accidents-safety-data> for more information on these datasets. The package is described in a paper in the Journal of Open Source Software (Lovelace et al. 2019) <doi:10.21105/joss.01181>. See Gilardi et al. (2022) <doi:10.1111/rssa.12823>, Vidal-Tortosa et al. (2021) <doi:10.1016/j.jth.2021.101291>, and Tait et al. (2023) <doi:10.1016/j.aap.2022.106895> for examples of how the data can be used for methodological and empirical road safety research.

Maintained by Robin Lovelace. Last updated 2 months ago.

stats19 road-safety transport car-crashes ropensci data

1.5 match 64 stars 9.20 score 193 scripts

robinhankin

mvp:Fast Symbolic Multivariate Polynomials

Fast manipulation of symbolic multivariate polynomials using the 'Map' class of the Standard Template Library. The package uses print and coercion methods from the 'mpoly' package but offers speed improvements. It is comparable in speed to the 'spray' package for sparse arrays, but retains the symbolic benefits of 'mpoly'. To cite the package in publications, use Hankin 2022 <doi:10.48550/ARXIV.2210.15991>. Uses 'disordR' discipline.

Maintained by Robin K. S. Hankin. Last updated 3 days ago.

cpp

2.0 match 9 stars 6.83 score 36 scripts 2 dependents

jonclayden

imbibe:A Pipe-Friendly Image Calculator

Provides a set of fast, chainable image-processing operations which are applicable to images of two, three or four dimensions, particularly medical images.

Maintained by Jon Clayden. Last updated 4 years ago.

3.1 match 14 stars 4.32 score 3 scripts

harrison4192

presenter:Present Data with Style

Consists of custom wrapper functions using packages 'openxlsx', 'flextable', and 'officer' to create highly formatted MS office friendly output of your data frames. These viewer friendly outputs are intended to match expectations of professional looking presentations in business and consulting scenarios. The functions are opinionated in the sense that they expect the input data frame to have certain properties in order to take advantage of the automated formatting.

Maintained by Harrison Tietze. Last updated 2 years ago.

excel powerpoint

2.0 match 11 stars 6.69 score 15 scripts 4 dependents

nepem-ufsc

pliman:Tools for Plant Image Analysis

Tools for both single and batch image manipulation and analysis (Olivoto, 2022 <doi:10.1111/2041-210X.13803>) and phytopathometry (Olivoto et al., 2022 <doi:10.1007/S40858-021-00487-5>). The tools can be used for the quantification of leaf area, object counting, extraction of image indexes, shape measurement, object landmark identification, and Elliptical Fourier Analysis of object outlines (Claude (2008) <doi:10.1007/978-0-387-77789-4>). The package also provides a comprehensive pipeline for generating shapefiles with complex layouts and supports high-throughput phenotyping of RGB, multispectral, and hyperspectral orthomosaics. This functionality facilitates field phenotyping using UAV- or satellite-based imagery.

Maintained by Tiago Olivoto. Last updated 2 days ago.

openblas fftw3 cpp openmp

2.0 match 10 stars 6.68 score 476 scripts

ewenharrison

finalfit:Quickly Create Elegant Regression Results Tables and Plots when Modelling

Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.

Maintained by Ewen Harrison. Last updated 7 months ago.

1.2 match 270 stars 11.43 score 1.0k scripts

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.

3.4 match 3 stars 3.83 score 217 scripts 3 dependents

sapfluxnet

sapfluxnetr:Working with 'Sapfluxnet' Project Data

Access, modify, aggregate and plot data from the 'Sapfluxnet' project (<http://sapfluxnet.creaf.cat>), the first global database of sap flow measurements.

Maintained by Victor Granda. Last updated 2 years ago.

2.0 match 25 stars 6.57 score 49 scripts

ropensci

CoordinateCleaner:Automated Cleaning of Occurrence Records from Biological Collections

Automated flagging of common spatial and temporal errors in biological and paleontological collection data, for the use in conservation, ecology and paleontology. Includes automated tests to easily flag (and exclude) records assigned to country or province centroid, the open ocean, the headquarters of the Global Biodiversity Information Facility, urban areas or the location of biodiversity institutions (museums, zoos, botanical gardens, universities). Furthermore identifies per species outlier coordinates, zero coordinates, identical latitude/longitude and invalid coordinates. Also implements an algorithm to identify data sets with a significant proportion of rounded coordinates. Especially suited for large data sets. The reference for the methodology is: Zizka et al. (2019) <doi:10.1111/2041-210X.13152>.

Maintained by Alexander Zizka. Last updated 1 years ago.

1.2 match 82 stars 10.93 score 306 scripts 3 dependents

bioc

CellBench:Construct Benchmarks for Single Cell Analysis Methods

This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.

Maintained by Shian Su. Last updated 5 months ago.

software infrastructure singlecell benchmark bioinformatics

1.5 match 30 stars 8.71 score 98 scripts

dhaine

episensr:Basic Sensitivity Analysis of Epidemiological Results

Basic sensitivity analysis of the observed relative risks adjusting for unmeasured confounding and misclassification of the exposure/outcome, or both. It follows the bias analysis methods and examples from the book by Lash T.L, Fox M.P, and Fink A.K. "Applying Quantitative Bias Analysis to Epidemiologic Data", ('Springer', 2021).

Maintained by Denis Haine. Last updated 1 years ago.

bias epidemiology sensitivity-analysis statistics

2.0 match 13 stars 6.48 score 39 scripts 1 dependents

till-tietz

parsel:Parallel Dynamic Web-Scraping Using 'RSelenium'

A system to increase the efficiency of dynamic web-scraping with 'RSelenium' by leveraging parallel processing. You provide a function wrapper for your 'RSelenium' scraping routine with a set of inputs, and 'parsel' runs it in several browser instances. Chunked input processing as well as error catching and logging ensures seamless execution and minimal data loss, even when unforeseen 'RSelenium' errors occur. You can additionally build safe scraping functions with minimal coding by utilizing constructor functions that act as wrappers around 'RSelenium' methods.

Maintained by Till Tietz. Last updated 1 years ago.

parallel rselenium web-scraping

3.3 match 15 stars 3.88 score 8 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

1.3 match 39 stars 9.63 score 192 scripts 1 dependents

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.

3.3 match 2 stars 3.89 score 77 scripts

cran

multipanelfigure:Infrastructure to Assemble Multi-Panel Figures (from Grobs)

Tools to create a layout for figures made of multiple panels, and to fill the panels with base, 'lattice', 'ggplot2' and 'ComplexHeatmap' plots, grobs, as well as content from all image formats supported by 'ImageMagick' (accessed through 'magick').

Maintained by Johannes Graumann. Last updated 11 months ago.

3.7 match 3 stars 3.48 score

ropensci

lingtypology:Linguistic Typology and Mapping

Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.

Maintained by George Moroz. Last updated 5 months ago.

abvd afbo atlas autotype bivaltyp clld glottolog-database linguistic-maps linguistics phoible sails typology wals

1.3 match 51 stars 9.58 score 694 scripts

ropensci

tsbox:Class-Agnostic Time Series

Time series toolkit with identical behavior for all time series classes: 'ts','xts', 'data.frame', 'data.table', 'tibble', 'zoo', 'timeSeries', 'tsibble', 'tis' or 'irts'. Also converts reliably between these classes.

Maintained by Christoph Sax. Last updated 5 months ago.

graphics time-series

1.2 match 150 stars 10.61 score 496 scripts 4 dependents

tylermorganwall

skpr:Design of Experiments Suite: Generate and Evaluate Optimal Designs

Generates and evaluates D, I, A, Alias, E, T, and G optimal designs. Supports generation and evaluation of blocked and split/split-split/.../N-split plot designs. Includes parametric and Monte Carlo power evaluation functions, and supports calculating power for censored responses. Provides a framework to evaluate power using functions provided in other packages or written by the user. Includes a Shiny graphical user interface that displays the underlying code used to create and evaluate the design to improve ease-of-use and make analyses more reproducible. For details, see Morgan-Wall et al. (2021) <doi:10.18637/jss.v099.i01>.

Maintained by Tyler Morgan-Wall. Last updated 8 days ago.

design-of-experiments linear-models linear-regression monte-carlo optimal-designs power split-plot-designs survival-analysis cpp

1.8 match 118 stars 6.89 score 35 scripts

mayer79

outForest:Multivariate Outlier Detection and Replacement

Provides a random forest based implementation of the method described in Chapter 7.1.2 (Regression model based anomaly detection) of Chandola et al. (2009) <doi:10.1145/1541880.1541882>. It works as follows: Each numeric variable is regressed onto all other variables by a random forest. If the scaled absolute difference between observed value and out-of-bag prediction of the corresponding random forest is suspiciously large, then a value is considered an outlier. The package offers different options to replace such outliers, e.g. by realistic values found via predictive mean matching. Once the method is trained on a reference data, it can be applied to new data.

Maintained by Michael Mayer. Last updated 8 months ago.

machine-learning outlier outlier-analysis outlier-detection random-forest

2.2 match 13 stars 5.39 score 19 scripts

abjur

abjutils:Useful Tools for Jurimetrical Analysis Used by the Brazilian Jurimetrics Association

The Brazilian Jurimetrics Association (ABJ in Portuguese, see <https://abj.org.br/> for more information) is a non-profit organization which aims to investigate and promote the use of statistics and probability in the study of Law and its institutions. This package implements general purpose tools used by ABJ, such as functions for sampling and basic manipulation of Brazilian lawsuits identification number. It also implements functions for text cleaning, such as accentuation removal.

Maintained by Caio Lente. Last updated 1 years ago.

jurimetrics toolkit

1.8 match 55 stars 6.76 score 78 scripts 1 dependents

rikenbit

WormTensor:A Clustering Method for Time-Series Whole-Brain Activity Data of 'C. elegans'

A toolkit to detect clusters from distance matrices. The distance matrices are assumed to be calculated between the cells of multiple animals ('Caenorhabditis elegans') from input time-series matrices. Some functions for generating distance matrices, performing clustering, evaluating the clustering, and visualizing the results of clustering and evaluation are available. We're also providing the download function to retrieve the calculated distance matrices from 'figshare' <https://figshare.com>.

Maintained by Kentaro Yamamoto. Last updated 8 months ago.

2.8 match 4.18 score 3 scripts

mindthegap-erc

StratPal:Stratigraphic Paleobiology Modeling Pipelines

The fossil record is a joint expression of ecological, taphonomic, evolutionary, and stratigraphic processes (Holland and Patzkowsky, 2012, ISBN:978-0226649382). This package allowing to simulate biological processes in the time domain (e.g., trait evolution, fossil abundance), and examine how their expression in the rock record (stratigraphic domain) is influenced based on age-depth models, ecological niche models, and taphonomic effects. Functions simulating common processes used in modeling trait evolution or event type data such as first/last occurrences are provided and can be used standalone or as part of a pipeline. The package comes with example data sets and tutorials in several vignettes, which can be used as a template to set up one's own simulation.

Maintained by Niklas Hohmann. Last updated 24 days ago.

palaeobiology palaeontology paleobiology paleontology stratigraphic-paleobiology stratigraphy

2.0 match 1 stars 5.88 score 18 scripts

mariusbarth

tinylabels:Lightweight Variable Labels

Assign, extract, or remove variable labels from R vectors. Lightweight and dependency-free.

Maintained by Marius Barth. Last updated 27 days ago.

1.9 match 3 stars 6.26 score 24 scripts 2 dependents

aariq

holodeck:A Tidy Interface for Simulating Multivariate Data

Provides pipe-friendly (%>%) wrapper functions for MASS::mvrnorm() to create simulated multivariate data sets with groups of variables with different degrees of variance, covariance, and effect size.

Maintained by Eric Scott. Last updated 2 years ago.

multivariate-data simulated-data simulating-multivariate-data tidy-interface

2.3 match 11 stars 5.14 score 25 scripts

skranz

RTutor:Interactive R problem sets with automatic testing of solutions and automatic hints

Interactive R problem sets with automatic testing of solutions and automatic hints

Maintained by Sebastian Kranz. Last updated 1 years ago.

economics learn-to-code problem-set rstudio rtutor shiny teaching

2.0 match 205 stars 5.83 score 111 scripts 1 dependents

ndphillips

FFTrees:Generate, Visualise, and Evaluate Fast-and-Frugal Decision Trees

Create, visualize, and test fast-and-frugal decision trees (FFTs) using the algorithms and methods described by Phillips, Neth, Woike & Gaissmaier (2017), <doi:10.1017/S1930297500006239>. FFTs are simple and transparent decision trees for solving binary classification problems. FFTs can be preferable to more complex algorithms because they require very little information, are easy to understand and communicate, and are robust against overfitting.

Maintained by Hansjoerg Neth. Last updated 5 months ago.

1.2 match 135 stars 9.58 score 144 scripts

cole-brokamp

automagic:Automagically Document and Install Packages Necessary to Run R Code

Parse R code in a given directory for R packages and attempt to install them from CRAN or GitHub. Optionally use a dependencies file for tighter control over which package versions to install.

Maintained by Cole Brokamp. Last updated 4 years ago.

2.0 match 57 stars 5.61 score 12 scripts 2 dependents

thomaschln

linevis:Interactive Time Series Visualizations

Create interactive time series visualizations. 'linevis' includes an extensive API to manipulate time series after creation, and supports getting data out of the visualization. Based on the 'timevis' package and the 'vis.js' Timeline 'JavaScript' library <https://visjs.github.io/vis-timeline/docs/graph2d/>.

Maintained by Thomas Charlon. Last updated 24 days ago.

2.5 match 4.40 score

bioc

HIPPO:Heterogeneity-Induced Pre-Processing tOol

For scRNA-seq data, it selects features and clusters the cells simultaneously for single-cell UMI data. It has a novel feature selection method using the zero inflation instead of gene variance, and computationally faster than other existing methods since it only relies on PCA+Kmeans rather than graph-clustering or consensus clustering.

Maintained by Tae Kim. Last updated 5 months ago.

sequencing singlecell geneexpression differentialexpression clustering

1.8 match 18 stars 6.16 score 4 scripts

bioc

plotGrouper:Shiny app GUI wrapper for ggplot with built-in statistical analysis

A shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed).

Maintained by John D. Gagnon. Last updated 5 months ago.

immunooncology flowcytometry graphandnetwork statisticalmethod dataimport gui multiplecomparison bioconductor ggplot2 plotting shiny

2.3 match 6 stars 4.78 score 10 scripts

skgrange

rmweather:Tools to Conduct Meteorological Normalisation and Counterfactual Modelling for Air Quality Data

An integrated set of tools to allow data users to conduct meteorological normalisation and counterfactual modelling for air quality data. The meteorological normalisation technique uses predictive random forest models to remove variation of pollutant concentrations so trends and interventions can be explored in a robust way. For examples, see Grange et al. (2018) <doi:10.5194/acp-18-6223-2018> and Grange and Carslaw (2019) <doi:10.1016/j.scitotenv.2018.10.344>. The random forest models can also be used for counterfactual or business as usual (BAU) modelling by using the models to predict, from the model's perspective, the future. For an example, see Grange et al. (2021) <doi:10.5194/acp-2020-1171>.

Maintained by Stuart K. Grange. Last updated 23 days ago.

1.7 match 49 stars 6.24 score 239 scripts

jrosell

jrrosell:Personal R package for Jordi Rosell

Useful functions for personal usage.

Maintained by Jordi Rosell. Last updated 3 months ago.

3.5 match 2 stars 3.08 score 7 scripts

koalaverse

KraljicMatrix:A Quantified Implementation of the Kraljic Matrix

Implements a quantified approach to the Kraljic Matrix (Kraljic, 1983, <https://hbr.org/1983/09/purchasing-must-become-supply-management>) for strategically analyzing a firm’s purchasing portfolio. It combines multi-objective decision analysis to measure purchasing characteristics and uses this information to place products and services within the Kraljic Matrix.

Maintained by Bradley Boehmke. Last updated 7 years ago.

decision-support kraljic-matrix managerial-preferences

2.3 match 3 stars 4.73 score 18 scripts

wahani

saeSim:Simulation Tools for Small Area Estimation

Tools for the simulation of data in the context of small area estimation. Combine all steps of your simulation - from data generation over drawing samples to model fitting - in one object. This enables easy modification and combination of different scenarios. You can store your results in a folder or start the simulation in parallel.

Maintained by Sebastian Warnholz. Last updated 3 years ago.

2.3 match 3 stars 4.72 score 35 scripts

crp2a

gamma:Dose Rate Estimation from in-Situ Gamma-Ray Spectrometry Measurements

Process in-situ Gamma-Ray Spectrometry for Luminescence Dating. This package allows to import, inspect and correct the energy shifts of gamma-ray spectra. It provides methods for estimating the gamma dose rate by the use of a calibration curve as described in Mercier and Falguères (2007). The package only supports Canberra CNF and TKA and Kromek SPE files.

Maintained by Archéosciences Bordeaux. Last updated 6 months ago.

archaeometry gamma-spectrometry geochronology luminescence-dating

1.5 match 6 stars 6.99 score 11 scripts 1 dependents

sfcheung

semhelpinghands:Helper Functions for Structural Equation Modeling

An assortment of helper functions for doing structural equation modeling, mainly by 'lavaan' for now. Most of them are time-saving functions for common tasks in doing structural equation modeling and reading the output. This package is not for functions that implement advanced statistical procedures. It is a light-weight package for simple functions that do simple tasks conveniently, with as few dependencies as possible.

Maintained by Shu Fai Cheung. Last updated 4 months ago.

bootstrapping lavaan structural-equation-modeling

2.0 match 5.13 score 27 scripts

mucollective

multiverse:Create 'multiverse analysis' in R

Implement 'multiverse' style analyses (Steegen S., Tuerlinckx F, Gelman A., Vanpaemal, W., 2016) <doi:10.1177/1745691616658637> to show the robustness of statistical inference. 'Multiverse analysis' is a philosophy of statistical reporting where paper authors report the outcomes of many different statistical analyses in order to show how fragile or robust their findings are. The 'multiverse' package (Sarma A., Kale A., Moon M., Taback N., Chevalier F., Hullman J., Kay M., 2021) <doi:10.31219/osf.io/yfbwm> allows users to concisely and flexibly implement 'multiverse-style' analysis, which involve declaring alternate ways of performing an analysis step, in R and R Notebooks.

Maintained by Abhraneel Sarma. Last updated 4 months ago.

1.2 match 62 stars 8.37 score 42 scripts

sfirke

janitor:Simple Tools for Examining and Cleaning Dirty Data

The main janitor functions can: perfectly format data.frame column names; provide quick counts of variable combinations (i.e., frequency tables and crosstabs); and explore duplicate records. Other janitor functions nicely format the tabulation results. These tabulate-and-report functions approximate popular features of SPSS and Microsoft Excel. This package follows the principles of the "tidyverse" and works well with the pipe function %>%. janitor was built with beginning-to-intermediate R users in mind and is optimized for user-friendliness.

Maintained by Sam Firke. Last updated 3 months ago.

data-analysis data-cleaning data-science dirty-data excel pivot-tables spss tabulations tidyverse

0.5 match 1.4k stars 19.15 score 35k scripts 231 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 6 days ago.

1.7 match 1 stars 5.84 score 12 scripts

rohanalexander

heapsofpapers:Easily Download Heaps of PDF and CSV Files

Makes it easy to download a large number of files such as PDF files and CSV files, while automatically slowing down requests, letting you know where it is up to, and adjusting for files that have already been downloaded.

Maintained by Rohan Alexander. Last updated 4 years ago.

2.0 match 2 stars 4.78 score 12 scripts

lchansson

rKolada:Access Data from the 'Kolada' Database

Methods for downloading and processing data and metadata from 'Kolada', the official Swedish regions and municipalities database <https://www.kolada.se/>.

Maintained by Love Hansson. Last updated 10 months ago.

1.8 match 4 stars 5.30 score 5 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

1.3 match 28 stars 7.07 score 47 scripts 1 dependents

bmsasilva

soundClass:Sound Classification Using Convolutional Neural Networks

Provides an all-in-one solution for automatic classification of sound events using convolutional neural networks (CNN). The main purpose is to provide a sound classification workflow, from annotating sound events in recordings to training and automating model usage in real-life situations. Using the package requires a pre-compiled collection of recordings with sound events of interest and it can be employed for: 1) Annotation: create a database of annotated recordings, 2) Training: prepare training data from annotated recordings and fit CNN models, 3) Classification: automate the use of the fitted model for classifying new recordings. By using automatic feature selection and a user-friendly GUI for managing data and training/deploying models, this package is intended to be used by a broad audience as it does not require specific expertise in statistics, programming or sound analysis. Please refer to the vignette for further information. Gibb, R., et al. (2019) <doi:10.1111/2041-210X.13101> Mac Aodha, O., et al. (2018) <doi:10.1371/journal.pcbi.1005995> Stowell, D., et al. (2019) <doi:10.1111/2041-210X.13103> LeCun, Y., et al. (2012) <doi:10.1007/978-3-642-35289-8_3>.

Maintained by Bruno Silva. Last updated 2 years ago.

2.3 match 3 stars 4.18 score 2 scripts

nelson-gon

manymodelr:Build and Tune Several Models

Frequently one needs a convenient way to build and tune several models in one go.The goal is to provide a number of machine learning convenience functions. It provides the ability to build, tune and obtain predictions of several models in one function. The models are built using functions from 'caret' with easier to read syntax. Kuhn(2014) <arXiv:1405.6974>.

Maintained by Nelson Gonzabato. Last updated 18 hours ago.

analysis-of-variance anova correlation correlation-coefficient generalized-linear-models gradient-boosting-decision-trees knn-classification linear-models linear-regression machine-learning missing-values models r-programming random-forest-algorithm regression-models

1.7 match 2 stars 5.60 score 50 scripts

sahilseth

pipefittr:Convert Nested Functions to Pipes

To take nested function calls and convert them to a more readable form using pipes from package 'magrittr'.

Maintained by Sahil Seth. Last updated 9 years ago.

5.5 match 1.70 score 3 scripts

r-lib

httr2:Perform HTTP Requests and Process the Responses

Tools for creating and modifying HTTP requests, then performing them and processing the results. 'httr2' is a modern re-imagining of 'httr' that uses a pipe-based interface and solves more of the problems that API wrapping packages face.

Maintained by Hadley Wickham. Last updated 8 days ago.

http

0.5 match 246 stars 17.66 score 1.9k scripts 1.1k dependents

bioc

profileplyr:Visualization and annotation of read signal over genomic ranges with profileplyr

Quick and straightforward visualization of read signal over genomic intervals is key for generating hypotheses from sequencing data sets (e.g. ChIP-seq, ATAC-seq, bisulfite/methyl-seq). Many tools both inside and outside of R and Bioconductor are available to explore these types of data, and they typically start with a bigWig or BAM file and end with some representation of the signal (e.g. heatmap). profileplyr leverages many Bioconductor tools to allow for both flexibility and additional functionality in workflows that end with visualization of the read signal.

Maintained by Tom Carroll. Last updated 5 months ago.

chipseq dataimport sequencing chiponchip coverage

2.3 match 4.03 score 54 scripts

gisler

DTSg:A Class for Working with Time Series Data Based on 'data.table' and 'R6' with Largely Optional Reference Semantics

Basic time series functionalities such as listing of missing values, application of arbitrary aggregation as well as rolling (asymmetric) window functions and automatic detection of periodicity. As it is mainly based on 'data.table', it is fast and (in combination with the 'R6' package) offers reference semantics. In addition to its native R6 interface, it provides an S3 interface for those who prefer the latter. Finally yet importantly, its functional approach allows for incorporating functionalities from many other packages.

Maintained by Gerold Hepp. Last updated 22 hours ago.

class reference-semantics time-series-data

1.5 match 5 stars 5.98 score 24 scripts

epiverse-trace

cleanepi:Clean and Standardize Epidemiological Data

Cleaning and standardizing tabular data package, tailored specifically for curating epidemiological data. It streamlines various data cleaning tasks that are typically expected when working with datasets in epidemiology. It returns the processed data in the same format, and generates a comprehensive report detailing the outcomes of each cleaning task.

Maintained by Karim Mané. Last updated 2 days ago.

data-cleaning epidemiology epiverse

1.2 match 9 stars 7.44 score 19 scripts

alexioannides

pipeliner:Machine Learning Pipelines for R

A framework for defining 'pipelines' of functions for applying data transformations, model estimation and inverse-transformations, resulting in predicted value generation (or model-scoring) functions that automatically apply the entire pipeline of functions required to go from input to predicted output.

Maintained by Alex Ioannides. Last updated 8 years ago.

data-science machine-learning machine-learning-pipelines pipeline prediction statistics transform-functions workflow

1.5 match 67 stars 5.94 score 26 scripts

bioc

sevenbridges:Seven Bridges Platform API Client and Common Workflow Language Tool Builder in R

R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.

Maintained by Phil Webster. Last updated 5 months ago.

software dataimport thirdpartyclient api-client bioconductor bioinformatics cloud common-workflow-language sevenbridges

1.2 match 35 stars 7.40 score 24 scripts

josie-athens

pubh:A Toolbox for Public Health and Epidemiology

A toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand 'ggplot2' plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.

Maintained by Josie Athens. Last updated 5 months ago.

1.5 match 5 stars 5.73 score 72 scripts

ropensci

skimr:Compact and Flexible Summaries of Data

A simple to use summary function that can be used with pipes and displays nicely in the console. The default summary statistics may be modified by the user as can the default formatting. Support for data frames and vectors is included, and users can implement their own skim methods for specific object types as described in a vignette. Default summaries include support for inline spark graphs. Instructions for managing these on specific operating systems are given in the "Using skimr" vignette and the README.

Maintained by Elin Waring. Last updated 2 months ago.

peer-reviewed ropensci summary-statistics unconf unconf17

0.5 match 1.1k stars 16.80 score 18k scripts 14 dependents

swang87

fc:Function Composition in R

Provides a way to compose functions in R, and allows for chaining commands using the magrittr-esque forward-pipe operator, %>%.

Maintained by Xiaofei (Susan) Wang. Last updated 5 years ago.

2.3 match 3.74 score 11 scripts

mikejareds

hermiter:Efficient Sequential and Batch Estimation of Univariate and Bivariate Probability Density Functions and Cumulative Distribution Functions along with Quantiles (Univariate) and Nonparametric Correlation (Bivariate)

Facilitates estimation of full univariate and bivariate probability density functions and cumulative distribution functions along with full quantile functions (univariate) and nonparametric correlation (bivariate) using Hermite series based estimators. These estimators are particularly useful in the sequential setting (both stationary and non-stationary) and one-pass batch estimation setting for large data sets. Based on: Stephanou, Michael, Varughese, Melvin and Macdonald, Iain. "Sequential quantiles via Hermite series density estimation." Electronic Journal of Statistics 11.1 (2017): 570-607 <doi:10.1214/17-EJS1245>, Stephanou, Michael and Varughese, Melvin. "On the properties of Hermite series based distribution function estimators." Metrika (2020) <doi:10.1007/s00184-020-00785-z> and Stephanou, Michael and Varughese, Melvin. "Sequential estimation of Spearman rank correlation using Hermite series estimators." Journal of Multivariate Analysis (2021) <doi:10.1016/j.jmva.2021.104783>.

Maintained by Michael Stephanou. Last updated 7 months ago.

cumulative-distribution-function kendall-correlation-coefficient online-algorithms probability-density-function quantile spearman-correlation-coefficient statistics streaming-algorithms streaming-data cpp

1.5 match 15 stars 5.58 score 17 scripts

stla

polyhedralCubature:Multiple Integration over Convex Polyhedra

Evaluation of multiple integrals over convex polyhedra. This is useful when the bounds of the integrals are some linear combinations of the variables.

Maintained by Stéphane Laurent. Last updated 1 years ago.

integration multidimensional-integration

2.3 match 3.70 score 4 scripts

coolbutuseless

ctypesio:Read and Write Standard 'C' Types from Files, Connections and Raw Vectors

Interacting with binary files can be difficult because R's types are a subset of what is generally supported by 'C'. This package provides a suite of functions for reading and writing binary data (with files, connections, and raw vectors) using 'C' type descriptions. These functions convert data between 'C' types and R types while checking for values outside the type limits, 'NA' values, etc.

Maintained by Mike Cheng. Last updated 2 months ago.

1.3 match 5 stars 6.02 score 6 scripts 1 dependents

mwheymans

miceafter:Data and Statistical Analyses after Multiple Imputation

Statistical Analyses and Pooling after Multiple Imputation. A large variety of repeated statistical analysis can be performed and finally pooled. Statistical analysis that are available are, among others, Levene's test, Odds and Risk Ratios, One sample proportions, difference between proportions and linear and logistic regression models. Functions can also be used in combination with the Pipe operator. More and more statistical analyses and pooling functions will be added over time. Heymans (2007) <doi:10.1186/1471-2288-7-33>. Eekhout (2017) <doi:10.1186/s12874-017-0404-7>. Wiel (2009) <doi:10.1093/biostatistics/kxp011>. Marshall (2009) <doi:10.1186/1471-2288-9-57>. Sidi (2021) <doi:10.1080/00031305.2021.1898468>. Lott (2018) <doi:10.1080/00031305.2018.1473796>. Grund (2021) <doi:10.31234/osf.io/d459g>.

Maintained by Martijn Heymans. Last updated 2 years ago.

1.6 match 2 stars 4.84 score 23 scripts

jhelvy

cbcTools:Choice-Based Conjoint Experiment Design Generation and Power Evaluation in R

Design and evaluate choice-based conjoint survey experiments. Generate a variety of survey designs, including random designs, full factorial designs, orthogonal designs, D-optimal designs, and Bayesian D-efficient designs as well as designs with "no choice" options and "labeled" (also known as "alternative specific") designs. Conveniently inspect the design balance and overlap, and simulate choice data for a survey design either randomly or according to a multinomial or mixed logit utility model defined by user-provided prior parameters. Conduct a power analysis for a given survey design by estimating the same model on different subsets of the data to simulate different sample sizes. Full factorial and orthogonal designs are obtained using the 'DoE.base' package (Grömping, 2018) <doi:10.18637/jss.v085.i05>. D-optimal designs are obtained using the 'AlgDesign' package (Wheeler, 2022) <https://CRAN.R-project.org/package=AlgDesign>. Bayesian D-efficient designs are obtained using the 'idefix' package (Traets et al, 2020) <doi:10.18637/jss.v096.i03>. Choice simulation and model estimation in power analyses are handled using the 'logitr' package (Helveston, 2023) <doi:10.18637/jss.v105.i10>.

Maintained by John Helveston. Last updated 1 years ago.

cbc conjoint design discrete-choice sawtooth survey

1.5 match 6 stars 5.30 score 67 scripts

edpeyton

pkgdepR:Statically Determine Function Dependencies Between Packages

Statically determine and visualize the function dependencies within and across packages. This may be useful for managing function dependencies across a code base of multiple R packages.

Maintained by Ed Peyton. Last updated 3 months ago.

function-dependency visualization

1.8 match 11 stars 4.36 score 14 scripts

emeyers

NeuroDecodeR:Decode Information from Neural Activity

Neural decoding is method of analyzing neural data that uses a pattern classifiers to predict experimental conditions based on neural activity. 'NeuroDecodeR' is a system of objects that makes it easy to run neural decoding analyses. For more information on neural decoding see Meyers & Kreiman (2011) <doi:10.7551/mitpress/8404.003.0024>.

Maintained by Ethan Meyers. Last updated 1 years ago.

1.2 match 12 stars 6.49 score 17 scripts

cynkra

dm:Relational Data Models

Provides tools for working with multiple related tables, stored as data frames or in a relational database. Multiple tables (data and metadata) are stored in a compound object, which can then be manipulated with a pipe-friendly syntax.

Maintained by Kirill Müller. Last updated 2 months ago.

data-model data-warehousing datawarehousing dbi dbplyr relational-databases

0.5 match 511 stars 14.81 score 410 scripts 8 dependents

tysonstanley

MarginalMediation:Marginal Mediation

Provides the ability to perform "Marginal Mediation"--mediation wherein the indirect and direct effects are in terms of the average marginal effects (Bartus, 2005, <https://EconPapers.repec.org/RePEc:tsj:stataj:v:5:y:2005:i:3:p:309-329>). The style of the average marginal effects stems from Thomas Leeper's work on the "margins" package. This framework allows the use of categorical mediators and outcomes with little change in interpretation from the continuous mediators/outcomes. See <doi:10.13140/RG.2.2.18465.92001> for more details on the method.

Maintained by Tyson S Barrett. Last updated 3 years ago.

average-marginal-effects margins mediation mediation-analysis mediator partial-effects rstudio

1.8 match 3 stars 4.29 score 13 scripts

trelliscope

trelliscope:Create Interactive Multi-Panel Displays

Trelliscope enables interactive exploration of data frames of visualizations.

Maintained by Ryan Hafen. Last updated 7 months ago.

visualization

1.2 match 29 stars 6.43 score 117 scripts

beerda

rmake:Makefile Generator for R Analytical Projects

Creates and maintains a build process for complex analytic tasks in R. Package allows to easily generate Makefile for the (GNU) 'make' tool, which drives the build process by (in parallel) executing build commands in order to update results accordingly to given dependencies on changed data or updated source files.

Maintained by Michal Burda. Last updated 3 years ago.

makefile rmake

1.9 match 1 stars 4.11 score 26 scripts

oldlipe

Rwtss:Client for Web Time-Series Service

Allows remote access to satellite image time series provided by the web time series service (WTSS) available at servers such as <https://brazildatacube.dpi.inpe.br/wtss/>. The functions include listing the data sets available in WTSS servers, describing the contents of a data set, and retrieving a time series based on spatial location and temporal filters.

Maintained by Felipe Souza. Last updated 3 years ago.

3.3 match 2.28 score 19 scripts

petermeissner

crossword.r:Generating Crosswords from Word Lists

Generate crosswords from a list of words.

Maintained by Peter Meissner. Last updated 6 years ago.

algorithm crossword

1.8 match 28 stars 4.15 score 8 scripts

bioc

pipeFrame:Pipeline framework for bioinformatics in R

pipeFrame is an R package for building a componentized bioinformatics pipeline. Each step in this pipeline is wrapped in the framework, so the connection among steps is created seamlessly and automatically. Users could focus more on fine-tuning arguments rather than spending a lot of time on transforming file format, passing task outputs to task inputs or installing the dependencies. Componentized step elements can be customized into other new pipelines flexibly as well. This pipeline can be split into several important functional steps, so it is much easier for users to understand the complex arguments from each step rather than parameter combination from the whole pipeline. At the same time, componentized pipeline can restart at the breakpoint and avoid rerunning the whole pipeline, which may save a lot of time for users on pipeline tuning or such issues as power off or process other interrupts.

Maintained by Zheng Wei. Last updated 5 months ago.

software infrastructure workflowstep

1.8 match 1 stars 4.08 score 2 scripts 1 dependents

johnmackintosh

runcharter:Automatically Plot, Analyse and Revises Limits of Multiple Run Charts

Plots multiple run charts, finds successive signals of improvement, and revises medians when each signal occurs. Finds runs above, below, or on both sides of the median, and returns a plot and a data.table summarising original medians and any revisions, for all groups within the supplied data.

Maintained by John MacKintosh. Last updated 3 years ago.

chart-analysis healthcare nhs nhs-r-community quality-control quality-improvement quality-improvement-efforts rdatatable

1.2 match 38 stars 6.11 score 17 scripts

gergness

srvyr:'dplyr'-Like Syntax for Summary Statistics of Survey Data

Use piping, verbs like 'group_by' and 'summarize', and other 'dplyr' inspired syntactic style when calculating summary statistics on survey data using functions from the 'survey' package.

Maintained by Greg Freedman Ellis. Last updated 1 months ago.

survey

0.5 match 215 stars 13.88 score 1.8k scripts 15 dependents

bioc

xcore:xcore expression regulators inference

xcore is an R package for transcription factor activity modeling based on known molecular signatures and user's gene expression data. Accompanying xcoredata package provides a collection of molecular signatures, constructed from publicly available ChiP-seq experiments. xcore use ridge regression to model changes in expression as a linear combination of molecular signatures and find their unknown activities. Obtained, estimates can be further tested for significance to select molecular signatures with the highest predicted effect on the observed expression changes.

Maintained by Maciej Migdał. Last updated 5 months ago.

geneexpression generegulation epigenetics regression sequencing

1.8 match 4.00 score 8 scripts

crew102

hippie:Hippie Code Completion in 'RStudio'

An 'RStudio' Addin for Hippie Expand (AKA Hippie Code Completion or Cyclic Expand Word). This type of completion searches for matching tokens within the user's current source editor file, regardless of file type. By searching only within the current source file, 'hippie' offers a fast way to identify and insert completions that appear around the user's cursor.

Maintained by Christopher Baker. Last updated 7 months ago.

autocompletion codecompletion completions productivity rstudio-addin shortcuts

1.8 match 20 stars 4.00 score 3 scripts

insightsengineering

rtables:Reporting Tables

Reporting tables often have structure that goes beyond simple rectangular data. The 'rtables' package provides a framework for declaring complex multi-level tabulations and then applying them to data. This framework models both tabulation and the resulting tables as hierarchical, tree-like objects which support sibling sub-tables, arbitrary splitting or grouping of data in row and column dimensions, cells containing multiple values, and the concept of contextual summary computations. A convenient pipe-able interface is provided for declaring table layouts and the corresponding computations, and then applying them to data.

Maintained by Joe Zhu. Last updated 2 months ago.

pharmaceuticals tables

0.5 match 232 stars 13.65 score 238 scripts 17 dependents

bergsmat

nonmemica:Create and Evaluate NONMEM Models in a Project Context

Systematically creates and modifies NONMEM(R) control streams. Harvests NONMEM output, builds run logs, creates derivative data, generates diagnostics. NONMEM (ICON Development Solutions <https://www.iconplc.com/>) is software for nonlinear mixed effects modeling. See 'package?nonmemica'.

Maintained by Tim Bergsma. Last updated 2 months ago.

1.5 match 4 stars 4.58 score 45 scripts

kwb-r

kwb.en13508.2:Read and Write CCTV Inspection Data According to Norm EN13508-2

functions to read and write CCTV inspections according to EN13508-2.

Maintained by Hauke Sonnenberg. Last updated 1 months ago.

cctv-inspection data-export data-import project-sema sewer-classification

1.9 match 3.43 score 1 scripts 9 dependents

kwb-r

kwbGompitz:Interface to GompitZ Tool for Modelling the Degradation of Sewer Pipelines

Functions enabling the writing of GompitZ input files, running of GompitZ Tools (gompcal.exe, gompred.exe) and reading of GompitZ output files.

Maintained by Hauke Sonnenberg. Last updated 3 years ago.

modelling project-sema sewer-classification cpp

3.8 match 1.70 score 1 scripts

skgrange

saqgetr:Import Air Quality Monitoring Data in a Fast and Easy Way

A collection of tools to access prepared air quality monitoring data files from web servers with ease and speed. Air quality data are sourced from open and publicly accessible repositories and can be found in these locations: <https://www.eea.europa.eu/data-and-maps/data/airbase-the-european-air-quality-database-8> and <https://discomap.eea.europa.eu/map/fme/AirQualityExport.htm>. The web server space has been provided by Ricardo Energy & Environment.

Maintained by Stuart K. Grange. Last updated 6 months ago.

1.7 match 9 stars 3.65 score 9 scripts

elipousson

cliExtras:A Collection of Helper Functions for the cli package

Extends the cli package with user response prompts and stopifnot equivalents.

Maintained by Eli Pousson. Last updated 12 months ago.

cli

1.8 match 3 stars 3.56 score 2 scripts 8 dependents

gogonzo

ox:Shorthand if-Else

Short hand if-else function to easily switch the values depending on a logical condition.

Maintained by Dawid Kałędkowski. Last updated 3 years ago.

1.3 match 4 stars 4.60 score 6 scripts

bluegreen-labs

skylight:A Simple Sky Illuminance Model

A tool to calculate sky illuminance values (in lux) for both sun and moon. The model is a verbatim translation of the code by Janiczek and DeYoung (1987) <https://archive.org/details/DTIC_ADA182110>.

Maintained by Koen Hufkens. Last updated 1 years ago.

ephemerides illuminance sky

1.3 match 4 stars 4.60 score 6 scripts

darwin-eu

CDMConnector:Connect to an OMOP Common Data Model

Provides tools for working with observational health data in the Observational Medical Outcomes Partnership (OMOP) Common Data Model format with a pipe friendly syntax. Common data model database table references are stored in a single compound object along with metadata.

Maintained by Adam Black. Last updated 18 days ago.

0.5 match 12 stars 11.39 score 502 scripts 12 dependents

cran

regexPipes:Wrappers Around 'base::grep()' for Use with Pipes

Provides wrappers around base::grep() where the first argument is standardized to take the data object. This makes it less of a pain to use regular expressions with 'magrittr' or other pipe operators.

Maintained by Billy Buchanan. Last updated 9 years ago.

3.4 match 1 stars 1.70 score

bioc

CausalR:Causal network analysis methods

Causal network analysis methods for regulator prediction and network reconstruction from genome scale data.

Maintained by Glyn Bradley. Last updated 5 months ago.

immunooncology systemsbiology network graphandnetwork network inference transcriptomics proteomics differentialexpression rnaseq microarray

1.6 match 3.60 score 7 scripts

indrajeetpatil

statsExpressions:Tidy Dataframes and Expressions with Statistical Details

Utilities for producing dataframes with rich details for the most common types of statistical approaches and tests: parametric, nonparametric, robust, and Bayesian t-test, one-way ANOVA, correlation analyses, contingency table analyses, and meta-analyses. The functions are pipe-friendly and provide a consistent syntax to work with tidy data. These dataframes additionally contain expressions with statistical details, and can be used in graphing packages. This package also forms the statistical processing backend for 'ggstatsplot'. References: Patil (2021) <doi:10.21105/joss.03236>.

Maintained by Indrajeet Patil. Last updated 19 days ago.

bayesian-inference bayesian-statistics contingency-table correlation effectsize meta-analysis parametric robust robust-statistics statistical-details statistical-tests tidy

0.5 match 312 stars 10.97 score 146 scripts 2 dependents

grantmcdermott

ritest:Randomisation Inference Testing

An experimental port of the `ritest` Stata routine by Simon Heß. Fast and user-friendly. Aims to support a variety of model classes once it is fully baked.

Maintained by . Last updated 3 years ago.

1.5 match 10 stars 3.70 score 7 scripts

ropensci

antanym:Antarctic Geographic Place Names

Antarctic geographic names from the Composite Gazetteer of Antarctica, and functions for working with those place names.

Maintained by Ben Raymond. Last updated 3 years ago.

antarctic southern ocean place names gazetteer peer-reviewed

1.3 match 7 stars 3.89 score 22 scripts

jthaman

ciTools:Confidence or Prediction Intervals, Quantiles, and Probabilities for Statistical Models

Functions to append confidence intervals, prediction intervals, and other quantities of interest to data frames. All appended quantities are for the response variable, after conditioning on the model and covariates. This package has a data frame first syntax that allows for easy piping. Currently supported models include (log-) linear, (log-) linear mixed, generalized linear models, generalized linear mixed models, and accelerated failure time models.

Maintained by John Haman. Last updated 1 years ago.

lme4 modeling tidyverse

0.5 match 107 stars 9.85 score 148 scripts 5 dependents

leslie-lu

createAddins:Create commonly used Addins in RStudio

Create commonly used Addins in RStudio, including '%<>%'.

Maintained by Zhen Lu. Last updated 10 months ago.

1.8 match 2.70 score 3 scripts

comp-cogneuro-lang

LexFindR:Find Related Items and Lexical Dimensions in a Lexicon

Implements code to identify lexical competitors in a given list of words. We include many of the standard competitor types used in spoken word recognition research, such as functions to find cohorts, neighbors, and rhymes, amongst many others. The package includes documentation for using a variety of lexicon files, including those with form codes made up of multiple letters (i.e., phoneme codes) and also basic orthographies. Importantly, the code makes use of multiple CPU cores and vectorization when possible, making it extremely fast and able to handle large lexicons. Additionally, the package contains documentation for users to easily write new functions, allowing researchers to examine other relationships within a lexicon. Preprint: <https://osf.io/preprints/psyarxiv/8dyru/>. Open access: <doi:10.3758/s13428-021-01667-6>. Citation: Li, Z., Crinnion, A.M. & Magnuson, J.S. (2021). <doi:10.3758/s13428-021-01667-6>.

Maintained by ZhaoBin Li. Last updated 9 months ago.

1.1 match 4 stars 4.30 score 5 scripts

winvector

rquery:Relational Query Generator for Data Manipulation at Scale

A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible table modeling step, plus explicit query reasoning and checking.

Maintained by John Mount. Last updated 2 years ago.

0.5 match 110 stars 9.53 score 126 scripts 3 dependents

merck

simtrial:Clinical Trial Simulation

Provides some basic routines for simulating a clinical trial. The primary intent is to provide some tools to generate trial simulations for trials with time to event outcomes. Piecewise exponential failure rates and piecewise constant enrollment rates are the underlying mechanism used to simulate a broad range of scenarios such as those presented in Lin et al. (2020) <doi:10.1080/19466315.2019.1697738>. However, the basic generation of data is done using pipes to allow maximum flexibility for users to meet different needs.

Maintained by Yujie Zhao. Last updated 2 days ago.

cpp

0.5 match 21 stars 9.16 score 52 scripts

markvanderloo

simputation:Simple Imputation

Easy to use interfaces to a number of imputation methods that fit in the not-a-pipe operator of the 'magrittr' package.

Maintained by Mark van der Loo. Last updated 8 months ago.

data-science imputation officialstatistics

0.5 match 92 stars 8.38 score 350 scripts

lcbc-uio

noasr:NOAS convenience functions

Functions created to work well with LCBC's Nephew of All Spreadsheet data.

Maintained by Athanasia Mo Mowinckel. Last updated 4 years ago.

1.5 match 3.00 score 4 scripts