R-universe search: reshape

hadley

reshape:Flexibly Reshape Data

Flexibly restructure and aggregate data using just two functions: melt and cast.

Maintained by Hadley Wickham. Last updated 3 years ago.

53.3 match 9.83 score 21k scripts 231 dependents

easystats

datawizard:Easy Data Wrangling and Statistical Transformations

A lightweight package to assist in key steps involved in any data analysis workflow: (1) wrangling the raw data to get it in the needed form, (2) applying preprocessing steps and statistical transformations, and (3) compute statistical summaries of data properties and distributions. It is also the data wrangling backend for packages in 'easystats' ecosystem. References: Patil et al. (2022) <doi:10.21105/joss.04684>.

Maintained by Etienne Bacher. Last updated 10 days ago.

data dplyr hacktoberfest janitor manipulation reshape tidyr wrangling

15.4 match 222 stars 14.71 score 436 scripts 119 dependents

trinker

textshape:Tools for Reshaping Text

Tools that can be used to reshape and restructure text data.

Maintained by Tyler Rinker. Last updated 12 months ago.

data-reshaping manipulation sentence-boundary-detection text-data text-formating tidy

13.4 match 50 stars 9.18 score 266 scripts 34 dependents

mrdwab

splitstackshape:Stack and Reshape Datasets After Splitting Concatenated Values

Online data collection tools like Google Forms often export multiple-response questions with data concatenated in cells. The concat.split (cSplit) family of functions splits such data into separate cells. The package also includes functions to stack groups of columns and to reshape wide data, even when the data are "unbalanced"---something which reshape (from base R) does not handle, and which melt and dcast from reshape2 do not easily handle.

Maintained by Ananda Mahto. Last updated 6 years ago.

10.2 match 59 stars 10.25 score 2.1k scripts 21 dependents

luckinet

tabshiftr:Reshape Disorganised Messy Data

Helps the user to build and register schema descriptions of disorganised (messy) tables. Disorganised tables are tables that are not in a topologically coherent form, where packages such as 'tidyr' could be used for reshaping. The schema description documents the arrangement of input tables and is used to reshape them into a standardised (tidy) output format.

Maintained by Steffen Ehrmann. Last updated 30 days ago.

data-management data-reshaping schemas

14.4 match 6 stars 7.18 score 62 scripts 1 dependents

kkholst

mets:Analysis of Multivariate Event Times

Implementation of various statistical models for multivariate event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>. Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray, Ghosh-Lin, Binomial regression) with fast computation of influence functions.

Maintained by Klaus K. Holst. Last updated 3 days ago.

multivariate-time-to-event survival-analysis time-to-event fortran openblas cpp

6.8 match 14 stars 13.47 score 236 scripts 42 dependents

hadley

reshape2:Flexibly Reshape Data: A Reboot of the Reshape Package

Flexibly restructure and aggregate data using just two functions: melt and 'dcast' (or 'acast').

Maintained by Hadley Wickham. Last updated 4 years ago.

cpp

5.0 match 210 stars 17.19 score 94k scripts 2.0k dependents

harrelfe

Hmisc:Harrell Miscellaneous

Contains many functions useful for data analysis, high-level graphics, utility operations, functions for computing sample size and power, simulation, importing and annotating datasets, imputing missing values, advanced table making, variable clustering, character string manipulation, conversion of R objects to LaTeX and html code, recoding variables, caching, simplified parallel computing, encrypting and decrypting data using a safe workflow, general moving window statistical estimation, and assistance in interpreting principal component analysis.

Maintained by Frank E Harrell Jr. Last updated 9 hours ago.

fortran

4.9 match 210 stars 17.61 score 17k scripts 750 dependents

rstudio

reticulate:Interface to 'Python'

Interface to 'Python' modules, classes, and functions. When calling into 'Python', R data types are automatically converted to their equivalent 'Python' types. When values are returned from 'Python' to R they are converted back to R types. Compatible with all versions of 'Python' >= 2.7.

Maintained by Tomasz Kalinowski. Last updated 2 days ago.

cpp

3.8 match 1.7k stars 21.07 score 18k scripts 427 dependents

rdatatable

data.table:Extension of `data.frame`

Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.

Maintained by Tyson Barrett. Last updated 2 days ago.

3.0 match 3.7k stars 23.53 score 230k scripts 4.6k dependents

hwborchers

pracma:Practical Numerical Math Functions

Provides a large number of functions from numerical analysis and linear algebra, numerical optimization, differential equations, time series, plus some well-known special mathematical functions. Uses 'MATLAB' function names where appropriate to simplify porting.

Maintained by Hans W. Borchers. Last updated 1 years ago.

5.3 match 29 stars 12.34 score 6.6k scripts 931 dependents

terminological

dtrackr:Track your Data Pipelines

Track and document 'dplyr' data pipelines. As you filter, mutate, and join your way through a data set, 'dtrackr' seamlessly keeps track of your data flow and makes publication ready documentation of a data pipeline simple.

Maintained by Robert Challen. Last updated 5 months ago.

7.2 match 69 stars 8.78 score 362 scripts 1 dependents

melff

memisc:Management of Survey Data and Presentation of Analysis Results

An infrastructure for the management of survey data including value labels, definable missing values, recoding of variables, production of code books, and import of (subsets of) 'SPSS' and 'Stata' files is provided. Further, the package allows to produce tables and data frames of arbitrary descriptive statistics and (almost) publication-ready tables of regression model estimates, which can be exported to 'LaTeX' and HTML.

Maintained by Martin Elff. Last updated 11 days ago.

survey-data

4.8 match 46 stars 12.34 score 1.2k scripts 13 dependents

cvxgrp

CVXR:Disciplined Convex Optimization

An object-oriented modeling language for disciplined convex programming (DCP) as described in Fu, Narasimhan, and Boyd (2020, <doi:10.18637/jss.v094.i14>). It allows the user to formulate convex optimization problems in a natural way following mathematical convention and DCP rules. The system analyzes the problem, verifies its convexity, converts it into a canonical form, and hands it off to an appropriate solver to obtain the solution. Interfaces to solvers on CRAN and elsewhere are provided, both commercial and open source.

Maintained by Anqi Fu. Last updated 4 months ago.

cpp

4.5 match 207 stars 12.89 score 768 scripts 51 dependents

mlr-org

mlr3torch:Deep Learning with 'mlr3'

Deep Learning library that extends the mlr3 framework by building upon the 'torch' package. It allows to conveniently build, train, and evaluate deep learning models without having to worry about low level details. Custom architectures can be created using the graph language defined in 'mlr3pipelines'.

Maintained by Sebastian Fischer. Last updated 1 months ago.

data-science deep-learning machine-learning mlr3 torch

7.5 match 42 stars 7.63 score 78 scripts

eagerai

fastai:Interface to 'fastai'

The 'fastai' <https://docs.fast.ai/index.html> library simplifies training fast and accurate neural networks using modern best practices. It is based on research in to deep learning best practices undertaken at 'fast.ai', including 'out of the box' support for vision, text, tabular, audio, time series, and collaborative filtering models.

Maintained by Turgut Abdullayev. Last updated 11 months ago.

audio collaborative-filtering darknet darknet-image-classification fastai medical object-detection tabular text vision

6.0 match 118 stars 9.40 score 76 scripts

marianschmidt

msSPChelpR:Helper Functions for Second Primary Cancer Analyses

A collection of helper functions for analyzing Second Primary Cancer data, including functions to reshape data, to calculate patient states and analyze cancer incidence.

Maintained by Marian Eberl. Last updated 1 years ago.

13.5 match 2 stars 4.18 score 15 scripts

mlverse

torch:Tensors and Neural Networks with 'GPU' Acceleration

Provides functionality to define and train neural networks similar to 'PyTorch' by Paszke et al (2019) <doi:10.48550/arXiv.1912.01703> but written entirely in R using the 'libtorch' library. Also supports low-level tensor operations and 'GPU' acceleration.

Maintained by Daniel Falbel. Last updated 6 days ago.

autograd deep-learning torch cpp

3.0 match 520 stars 16.52 score 1.4k scripts 38 dependents

hope-data-science

tidyfst:Tidy Verbs for Fast Data Manipulation

A toolkit of tidy data manipulation verbs with 'data.table' as the backend. Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table', 'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain. This package is an extension of 'data.table'. While enjoying a tidy syntax, it also wraps combinations of efficient functions to facilitate frequently-used data operations.

Maintained by Tian-Yuan Huang. Last updated 6 months ago.

4.8 match 98 stars 10.09 score 118 scripts 4 dependents

igraph

igraph:Network Analysis and Visualization

Routines for simple graphs and network analysis. It can handle large graphs very well and provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.

Maintained by Kirill Müller. Last updated 13 hours ago.

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

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

rpolars

polars:Lightning-Fast 'DataFrame' Library

Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.

Maintained by Soren Welling. Last updated 3 days ago.

arrow polars rust

3.8 match 499 stars 12.01 score 1.0k scripts 2 dependents

t-kalinowski

keras:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.

Maintained by Tomasz Kalinowski. Last updated 11 months ago.

3.8 match 10.82 score 10k scripts 54 dependents

frbcesab

forcis:An R Client to Access the FORCIS Database

Provides an interface to the FORCIS database (<https://zenodo.org/doi/10.5281/zenodo.7390791>) on global foraminifera distribution. This package allows to download and to handle FORCIS data. It is part of the FRB-CESAB working group FORCIS. <https://www.fondationbiodiversite.fr/en/the-frb-in-action/programs-and-projects/le-cesab/forcis/>.

Maintained by Nicolas Casajus. Last updated 11 days ago.

7.0 match 4 stars 5.76 score 5 scripts

djnavarro

lsr:Companion to "Learning Statistics with R"

A collection of tools intended to make introductory statistics easier to teach, including wrappers for common hypothesis tests and basic data manipulation. It accompanies Navarro, D. J. (2015). Learning Statistics with R: A Tutorial for Psychology Students and Other Beginners, Version 0.6.

Maintained by Danielle Navarro. Last updated 3 years ago.

4.0 match 12 stars 9.55 score 1.7k scripts 11 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.

2.5 match 456 stars 15.16 score 11k scripts 420 dependents

pachadotdev

cpp11armadillo:An 'Armadillo' Interface

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

Maintained by Mauricio Vargas Sepulveda. Last updated 26 days ago.

armadillo cpp cpp11 hacktoberfest linear-algebra

4.0 match 9 stars 9.14 score 1 scripts 16 dependents

konstantinryabov

dmtools:Tools for Clinical Data Management

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

Maintained by Konstantin Ryabov. Last updated 2 years ago.

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

8.3 match 1 stars 4.32 score 14 scripts

rstudio

tfprobability:Interface to 'TensorFlow Probability'

Interface to 'TensorFlow Probability', a 'Python' library built on 'TensorFlow' that makes it easy to combine probabilistic models and deep learning on modern hardware ('TPU', 'GPU'). 'TensorFlow Probability' includes a wide selection of probability distributions and bijectors, probabilistic layers, variational inference, Markov chain Monte Carlo, and optimizers such as Nelder-Mead, BFGS, and SGLD.

Maintained by Tomasz Kalinowski. Last updated 3 years ago.

4.0 match 54 stars 8.63 score 221 scripts 3 dependents

cran

CornerstoneR:Collection of Scripts for Interface Between 'Cornerstone' and 'R'

Collection of generic 'R' scripts which enable you to use existing 'R' routines in 'Cornerstone'. . The desktop application 'Cornerstone' (<https://www.camline.com/en/products/cornerstone/cornerstone-core.html>) is a data analysis software provided by 'camLine' that empowers engineering teams to find solutions even faster. The engineers incorporate intensified hands-on statistics into their projects. They benefit from an intuitive and uniquely designed graphical Workmap concept: you design experiments (DoE) and explore data, analyze dependencies, and find answers you can act upon, immediately, interactively, and without any programming. . While 'Cornerstone's' interface to the statistical programming language 'R' has been available since version 6.0, the latest interface with 'R' is even much more efficient. 'Cornerstone' release 7.1.1 allows you to integrate user defined 'R' packages directly into the standard 'Cornerstone' GUI. Your engineering team stays in 'Cornerstone's' graphical working environment and can apply 'R' routines, immediately and without the need to deal with programming code. Additionally, your 'R' programming team develops corresponding 'R' packages detached from 'Cornerstone' in their favorite 'R' environment. . Learn how to use 'R' packages in 'Cornerstone' 7.1.1 on 'camLineTV' YouTube channel (<https://www.youtube.com/watch?v=HEQHwq_laXU>) (available in German).

Maintained by Gerrith Djaja. Last updated 5 years ago.

9.3 match 3.54 score

sebkrantz

collapse:Advanced and Fast Data Transformation

A C/C++ based package for advanced data transformation and statistical computing in R that is extremely fast, class-agnostic, robust and programmer friendly. Core functionality includes a rich set of S3 generic grouped and weighted statistical functions for vectors, matrices and data frames, which provide efficient low-level vectorizations, OpenMP multithreading, and skip missing values by default. These are integrated with fast grouping and ordering algorithms (also callable from C), and efficient data manipulation functions. The package also provides a flexible and rigorous approach to time series and panel data in R. It further includes fast functions for common statistical procedures, detailed (grouped, weighted) summary statistics, powerful tools to work with nested data, fast data object conversions, functions for memory efficient R programming, and helpers to effectively deal with variable labels, attributes, and missing data. It is well integrated with base R classes, 'dplyr'/'tibble', 'data.table', 'sf', 'units', 'plm' (panel-series and data frames), and 'xts'/'zoo'.

Maintained by Sebastian Krantz. Last updated 6 days ago.

data-aggregation data-analysis data-manipulation data-processing data-science data-transformation econometrics high-performance panel-data scientific-computing statistics time-series weighted weights cpp openmp

1.9 match 672 stars 16.63 score 708 scripts 97 dependents

mikeblazanin

gcplyr:Wrangle and Analyze Growth Curve Data

Easy wrangling and model-free analysis of microbial growth curve data, as commonly output by plate readers. Tools for reshaping common plate reader outputs into 'tidy' formats and merging them with design information, making data easy to work with using 'gcplyr' and other packages. Also streamlines common growth curve processing steps, like smoothing and calculating derivatives, and facilitates model-free characterization and analysis of growth data. See methods at <https://mikeblazanin.github.io/gcplyr/>.

Maintained by Mike Blazanin. Last updated 2 months ago.

dplyr ggplot2 tidyverse

3.8 match 30 stars 7.90 score 75 scripts

bioc

MultiAssayExperiment:Software for the integration of multi-omics experiments in Bioconductor

Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames. Facilities are provided for reshaping data into wide and long formats for adaptability to graphing and downstream analysis.

Maintained by Marcel Ramos. Last updated 2 months ago.

infrastructure datarepresentation bioconductor bioconductor-package genomics nci-itcr tcga u24ca289073

2.0 match 71 stars 14.95 score 670 scripts 127 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

3.8 match 50 stars 7.89 score 256 scripts 1 dependents

ethanbass

chromatographR:Chromatographic Data Analysis Toolset

Tools for high-throughput analysis of HPLC-DAD/UV chromatograms (or similar data). Includes functions for preprocessing, alignment, peak-finding and fitting, peak-table construction, data-visualization, etc. Preprocessing and peak-table construction follow the rough formula laid out in 'alsace' (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C., 2015. <doi:10.1093/bioinformatics/btv299>. Alignment of chromatograms is available using parametric time warping (as implemented in the 'ptw' package) (Wehrens, R., Bloemberg, T.G., and Eilers P.H.C. 2015. <doi:10.1093/bioinformatics/btv299>) or variable penalty dynamic time warping (as implemented in 'VPdtw') (Clifford, D., & Stone, G. 2012. <doi:10.18637/jss.v047.i08>). Peak-finding uses the algorithm by Tom O'Haver <https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm>. Peaks are then fitted to a gaussian or exponential-gaussian hybrid peak shape using non-linear least squares (Lan, K. & Jorgenson, J. W. 2001. <doi:10.1016/S0021-9673(01)00594-5>). See the vignette for more details and suggested workflow.

Maintained by Ethan Bass. Last updated 9 days ago.

bioinformatics cheminformatics chromatography gc-fid hplc hplc-dad hplc-pda hplv-uv metabolomics open-data open-science reproducibility reproducible-research

4.6 match 18 stars 6.33 score 8 scripts 1 dependents

easystats

bayestestR:Understand and Describe Bayesian Models and Posterior Distributions

Provides utilities to describe posterior distributions and Bayesian models. It includes point-estimates such as Maximum A Posteriori (MAP), measures of dispersion (Highest Density Interval - HDI; Kruschke, 2015 <doi:10.1016/C2012-0-00477-2>) and indices used for null-hypothesis testing (such as ROPE percentage, pd and Bayes factors). References: Makowski et al. (2021) <doi:10.21105/joss.01541>.

Maintained by Dominique Makowski. Last updated 10 hours ago.

bayes-factors bayesfactor bayesian bayesian-framework credible-interval easystats hacktoberfest hdi map posterior-distributions rope

1.7 match 579 stars 16.84 score 2.2k scripts 82 dependents

andrisignorell

DescTools:Tools for Descriptive Statistics

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

Maintained by Andri Signorell. Last updated 9 hours ago.

fortran cpp

1.7 match 87 stars 16.70 score 7.7k scripts 99 dependents

kasperwelbers

rsyntax:Extract Semantic Relations from Text by Querying and Reshaping Syntax

Various functions for querying and reshaping dependency trees, as for instance created with the 'spacyr' or 'udpipe' packages. This enables the automatic extraction of useful semantic relations from texts, such as quotes (who said what) and clauses (who did what). Method proposed in Van Atteveldt et al. (2017) <doi:10.1017/pan.2016.12>.

Maintained by Kasper Welbers. Last updated 3 years ago.

8.5 match 3.37 score 19 scripts 4 dependents

t-kalinowski

listarrays:A Toolbox for Working with R Arrays in a Functional Programming Style

A toolbox for R arrays. Flexibly split, bind, reshape, modify, subset and name arrays.

Maintained by Tomasz Kalinowski. Last updated 11 months ago.

6.2 match 15 stars 4.54 score 23 scripts

easystats

parameters:Processing of Model Parameters

Utilities for processing the parameters of various statistical models. Beyond computing p values, CIs, and other indices for a wide variety of models (see list of supported models using the function 'insight::supported_models()'), this package implements features like bootstrapping or simulating of parameters and models, feature reduction (feature extraction and variable selection) as well as functions to describe data and variable characteristics (e.g. skewness, kurtosis, smoothness or distribution).

Maintained by Daniel Lüdecke. Last updated 2 days ago.

beta bootstrap ci confidence-intervals data-reduction easystats fa feature-extraction feature-reduction hacktoberfest parameters pca pvalues regression-models robust-statistics standardize standardized-estimates statistical-models

1.8 match 453 stars 15.65 score 1.8k scripts 56 dependents

njtierney

naniar:Data Structures, Summaries, and Visualisations for Missing Data

Missing values are ubiquitous in data and need to be explored and handled in the initial stages of analysis. 'naniar' provides data structures and functions that facilitate the plotting of missing values and examination of imputations. This allows missing data dependencies to be explored with minimal deviation from the common work patterns of 'ggplot2' and tidy data. The work is fully discussed at Tierney & Cook (2023) <doi:10.18637/jss.v105.i07>.

Maintained by Nicholas Tierney. Last updated 4 days ago.

data-visualisation ggplot2 missing-data missingness tidy-data

1.8 match 657 stars 15.63 score 5.1k scripts 9 dependents

winvector

cdata:Fluid Data Transformations

Supplies higher-order coordinatized data specification and fluid transform operators that include pivot and anti-pivot as special cases. The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <https://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , <DOI:10.5281/zenodo.1173299> . This package introduces the idea of explicit control table specification of data transforms. Works on in-memory data or on remote data using 'rquery' and 'SQL' database interfaces.

Maintained by John Mount. Last updated 6 months ago.

3.5 match 46 stars 7.82 score 71 scripts 1 dependents

usaid-oha-si

tameDP:Import targets and PLHIV data from COP Target Setting Tool (formerly Data Pack)

Import PSNUxIM targets and PLHIV data from COP Data Pack. The purpose is to make the data tidy and more usable than their current structure in the Excel data packs.

Maintained by Aaron Chafetz. Last updated 1 years ago.

5.3 match 1 stars 4.92 score 46 scripts

jacob-long

panelr:Regression Models and Utilities for Repeated Measures and Panel Data

Provides an object type and associated tools for storing and wrangling panel data. Implements several methods for creating regression models that take advantage of the unique aspects of panel data. Among other capabilities, automates the "within-between" (also known as "between-within" and "hybrid") panel regression specification that combines the desirable aspects of both fixed effects and random effects econometric models and fits them as multilevel models (Allison, 2009 <doi:10.4135/9781412993869.d33>; Bell & Jones, 2015 <doi:10.1017/psrm.2014.7>). These models can also be estimated via generalized estimating equations (GEE; McNeish, 2019 <doi:10.1080/00273171.2019.1602504>) and Bayesian estimation is (optionally) supported via 'Stan'. Supports estimation of asymmetric effects models via first differences (Allison, 2019 <doi:10.1177/2378023119826441>) as well as a generalized linear model extension thereof using GEE.

Maintained by Jacob A. Long. Last updated 1 years ago.

social-science statistics

3.0 match 101 stars 8.76 score 181 scripts 1 dependents

brentkaplan

beezdiscounting:Behavioral Economic Easy Discounting

Facilitates some of the analyses performed in studies of behavioral economic discounting. The package supports scoring of the 27-Item Monetary Choice Questionnaire (see Kaplan et al., 2016; <doi:10.1007/s40614-016-0070-9>), calculating k values (Mazur's simple hyperbolic and exponential) using nonlinear regression, calculating various Area Under the Curve (AUC) measures, plotting regression curves for both fit-to-group and two-stage approaches, checking for unsystematic discounting (Johnson & Bickel, 2008; <doi:10.1037/1064-1297.16.3.264>) and scoring of the minute discounting task (see Koffarnus & Bickel, 2014; <doi:10.1037/a0035973>) using the Qualtrics 5-trial discounting template (see the Qualtrics Minute Discounting User Guide; <doi:10.13140/RG.2.2.26495.79527>), which is also available as a .qsf file in this package.

Maintained by Brent A. Kaplan. Last updated 2 months ago.

5-trial-discounting delay-discounting monetary-choice-questionnaire

6.8 match 2 stars 3.78 score 4 scripts

dgerbing

lessR:Less Code, More Results

Each function replaces multiple standard R functions. For example, two function calls, Read() and CountAll(), generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for summary statistics via pivot tables, a comprehensive regression analysis, ANOVA and t-test, visualizations including the Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, time series with aggregation and forecasting, color themes, and Trellis (facet) graphics. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, generation and rendering of regression instructions for interpretative output, and interactive visualizations.

Maintained by David W. Gerbing. Last updated 1 months ago.

3.4 match 6 stars 7.47 score 394 scripts 3 dependents

freguglia

mrf2d:Markov Random Field Models for Image Analysis

Model fitting, sampling and visualization for the (Hidden) Markov Random Field model with pairwise interactions and general interaction structure from Freguglia, Garcia & Bicas (2020) <doi:10.1002/env.2613>, which has many popular models used in 2-dimensional lattices as particular cases, like the Ising Model and Potts Model. A complete manuscript describing the package is available in Freguglia & Garcia (2022) <doi:10.18637/jss.v101.i08>.

Maintained by Victor Freguglia. Last updated 2 years ago.

gibbs-energy hidden-markov-model hidden-markov-models markov-random-field mrf mrf-models neighborhood cpp

5.0 match 9 stars 4.95 score 10 scripts

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

3.1 match 10 stars 7.95 score 92 scripts 2 dependents

cran

gaston:Genetic Data Handling (QC, GRM, LD, PCA) & Linear Mixed Models

Manipulation of genetic data (SNPs). Computation of GRM and dominance matrix, LD, heritability with efficient algorithms for linear mixed model (AIREML). Dandine et al <doi:10.1159/000488519>.

Maintained by Hervé Perdry. Last updated 1 years ago.

zlib cpp

4.1 match 5 stars 6.02 score 12 dependents

tom-wolff

ideanet:Integrating Data Exchange and Analysis for Networks ('ideanet')

A suite of convenient tools for social network analysis geared toward students, entry-level users, and non-expert practitioners. ‘ideanet’ features unique functions for the processing and measurement of sociocentric and egocentric network data. These functions automatically generate node- and system-level measures commonly used in the analysis of these types of networks. Outputs from these functions maximize the ability of novice users to employ network measurements in further analyses while making all users less prone to common data analytic errors. Additionally, ‘ideanet’ features an R Shiny graphic user interface that allows novices to explore network data with minimal need for coding.

Maintained by Tom Wolff. Last updated 3 days ago.

3.6 match 6 stars 6.80 score 10 scripts

rstudio

keras3:R Interface to 'Keras'

Interface to 'Keras' <https://keras.io>, a high-level neural networks API. 'Keras' was developed with a focus on enabling fast experimentation, supports both convolution based networks and recurrent networks (as well as combinations of the two), and runs seamlessly on both CPU and GPU devices.

Maintained by Tomasz Kalinowski. Last updated 4 days ago.

1.8 match 845 stars 13.57 score 264 scripts 2 dependents

henrikbengtsson

R.utils:Various Programming Utilities

Utility functions useful when programming and developing R packages.

Maintained by Henrik Bengtsson. Last updated 1 years ago.

1.8 match 63 stars 13.74 score 5.7k scripts 814 dependents

john-d-fox

RcmdrMisc:R Commander Miscellaneous Functions

Various statistical, graphics, and data-management functions used by the Rcmdr package in the R Commander GUI for R.

Maintained by John Fox. Last updated 1 years ago.

3.4 match 1 stars 7.00 score 432 scripts 42 dependents

tdhock

nc:Named Capture to Data Tables

User-friendly functions for extracting a data table (row for each match, column for each group) from non-tabular text data using regular expressions, and for melting columns that match a regular expression. Patterns are defined using a readable syntax that makes it easy to build complex patterns in terms of simpler, re-usable sub-patterns. Named R arguments are translated to column names in the output; capture groups without names are used internally in order to provide a standard interface to three regular expression 'C' libraries ('PCRE', 'RE2', 'ICU'). Output can also include numeric columns via user-specified type conversion functions.

Maintained by Toby Hocking. Last updated 2 months ago.

3.5 match 16 stars 6.85 score 46 scripts

emf-creaf

vegclust:Fuzzy Clustering of Vegetation Data

A set of functions to: (1) perform fuzzy clustering of vegetation data (De Caceres et al, 2010) <doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess ecological community similarity on the basis of structure and composition (De Caceres et al, 2013) <doi:10.1111/2041-210X.12116>.

Maintained by Miquel De Cáceres. Last updated 8 months ago.

3.8 match 2 stars 6.28 score 52 scripts 6 dependents

jienagu

dataMojo:Reshape Data Table

A grammar of data manipulation with 'data.table', providing a consistent a series of utility functions that help you solve the most common data manipulation challenges.

Maintained by Jiena McLellan. Last updated 2 years ago.

8.1 match 2.88 score 15 scripts

bioc

HDF5Array:HDF5 datasets as array-like objects in R

The HDF5Array package is an HDF5 backend for DelayedArray objects. It implements the HDF5Array, H5SparseMatrix, H5ADMatrix, and TENxMatrix classes, 4 convenient and memory-efficient array-like containers for representing and manipulating either: (1) a conventional (a.k.a. dense) HDF5 dataset, (2) an HDF5 sparse matrix (stored in CSR/CSC/Yale format), (3) the central matrix of an h5ad file (or any matrix in the /layers group), or (4) a 10x Genomics sparse matrix. All these containers are DelayedArray extensions and thus support all operations (delayed or block-processed) supported by DelayedArray objects.

Maintained by Hervé Pagès. Last updated 26 days ago.

infrastructure datarepresentation dataimport sequencing rnaseq coverage annotation genomeannotation singlecell immunooncology bioconductor-package core-package u24ca289073

1.8 match 12 stars 13.19 score 844 scripts 123 dependents

inventionate

TimeSpaceAnalysis:Statistical tools for time-space analysis

Use Geometric Data Analysis approaches (e.g. MCA or MFA), time pattern analysis (see "time sequence clustering") and places chronologies (see "time geography") analysis.

Maintained by Fabian Mundt. Last updated 7 days ago.

9.3 match 2.48 score 2 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

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

jamesramsay5

fda:Functional Data Analysis

These functions were developed to support functional data analysis as described in Ramsay, J. O. and Silverman, B. W. (2005) Functional Data Analysis. New York: Springer and in Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009). Functional Data Analysis with R and Matlab (Springer). The package includes data sets and script files working many examples including all but one of the 76 figures in this latter book. Matlab versions are available by ftp from <https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.

Maintained by James Ramsay. Last updated 4 months ago.

1.8 match 3 stars 12.29 score 2.0k scripts 143 dependents

jienagu

forestry:Reshape Data Tree

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

Maintained by Jiena McLellan. Last updated 5 years ago.

3.9 match 21 stars 5.66 score 44 scripts

rmheiberger

HH:Statistical Analysis and Data Display: Heiberger and Holland

Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.

Maintained by Richard M. Heiberger. Last updated 1 months ago.

3.3 match 3 stars 6.42 score 752 scripts 5 dependents

cran

matlab:'MATLAB' Emulation Package

Emulate 'MATLAB' code using 'R'.

Maintained by P. Roebuck. Last updated 9 months ago.

5.0 match 4.09 score 19 dependents

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

1.9 match 150 stars 10.61 score 496 scripts 4 dependents

bioc

synergyfinder:Calculate and Visualize Synergy Scores for Drug Combinations

Efficient implementations for analyzing pre-clinical multiple drug combination datasets. It provides efficient implementations for 1.the popular synergy scoring models, including HSA, Loewe, Bliss, and ZIP to quantify the degree of drug combination synergy; 2. higher order drug combination data analysis and synergy landscape visualization for unlimited number of drugs in a combination; 3. statistical analysis of drug combination synergy and sensitivity with confidence intervals and p-values; 4. synergy barometer for harmonizing multiple synergy scoring methods to provide a consensus metric of synergy; 5. evaluation of synergy and sensitivity simultaneously to provide an unbiased interpretation of the clinical potential of the drug combinations. Based on this package, we also provide a web application (http://www.synergyfinder.org) for users who prefer graphical user interface.

Maintained by Shuyu Zheng. Last updated 5 months ago.

software statisticalmethod

3.7 match 5.42 score 44 scripts

biometry

bipartite:Visualising Bipartite Networks and Calculating Some (Ecological) Indices

Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.

Maintained by Carsten F. Dormann. Last updated 7 days ago.

cpp

1.8 match 37 stars 10.93 score 592 scripts 15 dependents

psychmeta

psychmeta:Psychometric Meta-Analysis Toolkit

Tools for computing bare-bones and psychometric meta-analyses and for generating psychometric data for use in meta-analysis simulations. Supports bare-bones, individual-correction, and artifact-distribution methods for meta-analyzing correlations and d values. Includes tools for converting effect sizes, computing sporadic artifact corrections, reshaping meta-analytic databases, computing multivariate corrections for range variation, and more. Bugs can be reported to <https://github.com/psychmeta/psychmeta/issues> or <issues@psychmeta.com>.

Maintained by Jeffrey A. Dahlke. Last updated 9 months ago.

hacktoberfest meta-analysis psychology psychometric psychometrics

2.3 match 57 stars 8.25 score 151 scripts

flavjack

inti:Tools and Statistical Procedures in Plant Science

The 'inti' package is part of the 'inkaverse' project for developing different procedures and tools used in plant science and experimental designs. The mean aim of the package is to support researchers during the planning of experiments and data collection (tarpuy()), data analysis and graphics (yupana()) , and technical writing. Learn more about the 'inkaverse' project at <https://inkaverse.com/>.

Maintained by Flavio Lozano-Isla. Last updated 2 days ago.

agriculture apps inkaverse lmm plant-breeding plant-science shiny

2.3 match 5 stars 8.27 score 193 scripts

ocbe-uio

matlab2r:Translation Layer from MATLAB to R

Allows users familiar with MATLAB to use MATLAB-named functions in R. Several basic MATLAB functions are written in this package to mimic the behavior of their original counterparts, with more to come as this package grows.

Maintained by Waldir Leoncio. Last updated 2 years ago.

matlab

5.3 match 2 stars 3.48 score 1 dependents

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 25 days ago.

3.5 match 4.85 score

john-d-fox

Rcmdr:R Commander

A platform-independent basic-statistics GUI (graphical user interface) for R, based on the tcltk package.

Maintained by John Fox. Last updated 5 months ago.

1.8 match 4 stars 9.49 score 636 scripts 38 dependents

eltebioinformatics

mulea:Enrichment Analysis Using Multiple Ontologies and False Discovery Rate

Background - Traditional gene set enrichment analyses are typically limited to a few ontologies and do not account for the interdependence of gene sets or terms, resulting in overcorrected p-values. To address these challenges, we introduce mulea, an R package offering comprehensive overrepresentation and functional enrichment analysis. Results - mulea employs a progressive empirical false discovery rate (eFDR) method, specifically designed for interconnected biological data, to accurately identify significant terms within diverse ontologies. mulea expands beyond traditional tools by incorporating a wide range of ontologies, encompassing Gene Ontology, pathways, regulatory elements, genomic locations, and protein domains. This flexibility enables researchers to tailor enrichment analysis to their specific questions, such as identifying enriched transcriptional regulators in gene expression data or overrepresented protein domains in protein sets. To facilitate seamless analysis, mulea provides gene sets (in standardised GMT format) for 27 model organisms, covering 22 ontology types from 16 databases and various identifiers resulting in almost 900 files. Additionally, the muleaData ExperimentData Bioconductor package simplifies access to these pre-defined ontologies. Finally, mulea's architecture allows for easy integration of user-defined ontologies, or GMT files from external sources (e.g., MSigDB or Enrichr), expanding its applicability across diverse research areas. Conclusions - mulea is distributed as a CRAN R package. It offers researchers a powerful and flexible toolkit for functional enrichment analysis, addressing limitations of traditional tools with its progressive eFDR and by supporting a variety of ontologies. Overall, mulea fosters the exploration of diverse biological questions across various model organisms.

Maintained by Tamas Stirling. Last updated 3 months ago.

annotation differentialexpression geneexpression genesetenrichment go graphandnetwork multiplecomparison pathways reactome software transcription visualization enrichment enrichment-analysis functional-enrichment-analysis gene-set-enrichment ontologies transcriptomics cpp

2.3 match 28 stars 7.36 score 34 scripts

skgithub14

sdtmval:Validate SDTM Domains

Provides a set of tools to assist statistical programmers in validating Study Data Tabulation Model (SDTM) domain data sets. Statistical programmers are required to validate that a SDTM data set domain has been programmed correctly, per the SDTM Implementation Guide (SDTMIG) by 'CDISC' (<https://www.cdisc.org/standards/foundational/sdtmig>), study specification, and study protocol using a process called double programming. Double programming involves two different programmers independently converting the raw electronic data cut (EDC) data into a SDTM domain data table and comparing their results to ensure accurate standardization of the data. One of these attempts is termed 'production' and the other 'validation'. Generally, production runs are the official programs for submittals and these are written in 'SAS'. Validation runs can be programmed in another language, in this case 'R'.

Maintained by Stephen Knapp. Last updated 1 years ago.

3.7 match 6 stars 4.48 score 4 scripts

msperlin

BatchGetSymbols:Downloads and Organizes Financial Data for Multiple Tickers

Makes it easy to download financial data from Yahoo Finance <https://finance.yahoo.com/>.

Maintained by Marcelo Perlin. Last updated 3 years ago.

financial-data individual-stocks tickers yahoo-finance

2.3 match 18 stars 7.21 score 393 scripts

dcousin3

superb:Summary Plots with Adjusted Error Bars

Computes standard error and confidence interval of various descriptive statistics under various designs and sampling schemes. The main function, superb(), return a plot. It can also be used to obtain a dataframe with the statistics and their precision intervals so that other plotting environments (e.g., Excel) can be used. See Cousineau and colleagues (2021) <doi:10.1177/25152459211035109> or Cousineau (2017) <doi:10.5709/acp-0214-z> for a review as well as Cousineau (2005) <doi:10.20982/tqmp.01.1.p042>, Morey (2008) <doi:10.20982/tqmp.04.2.p061>, Baguley (2012) <doi:10.3758/s13428-011-0123-7>, Cousineau & Laurencelle (2016) <doi:10.1037/met0000055>, Cousineau & O'Brien (2014) <doi:10.3758/s13428-013-0441-z>, Calderini & Harding <doi:10.20982/tqmp.15.1.p001> for specific references.

Maintained by Denis Cousineau. Last updated 2 months ago.

error-bars plotting statistics summary-plots summary-statistics visualization

1.7 match 19 stars 9.55 score 155 scripts 2 dependents

lindbrook

cholera:Amend, Augment and Aid Analysis of John Snow's Cholera Map

Amends errors, augments data and aids analysis of John Snow's map of the 1854 London cholera outbreak.

Maintained by lindbrook. Last updated 1 days ago.

cholera data-visualization datasets epidemiology john-snow public-health triangulation-delaunay voronoi voronoi-polygons

1.7 match 136 stars 9.33 score 95 scripts

tony2015116

mintyr:Streamlined Data Processing Tools for Genomic Selection

A toolkit for genomic selection in animal breeding with emphasis on multi-breed and multi-trait nested grouping operations. Streamlines iterative analysis workflows when working with 'ASReml-R' package. Includes utility functions for phenotypic data processing commonly used by animal breeders.

Maintained by Guo Meng. Last updated 3 months ago.

asreml-r genomic-selection

3.4 match 4.48 score 2 scripts

broadinstitute

gsalib:Utility Functions for 'GATK'

Provides utility functions used by the Genome Analysis Toolkit ('GATK') to load tables and plot data. The 'GATK' is a toolkit for variant discovery in high-throughput sequencing data.

Maintained by Louis Bergelson. Last updated 1 years ago.

3.9 match 6 stars 3.88 score 25 scripts

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

teos-10

gsw:Gibbs Sea Water Functions

Provides an interface to the Gibbs 'SeaWater' ('TEOS-10') C library, version 3.06-16-0 (commit '657216dd4f5ea079b5f0e021a4163e2d26893371', dated 2022-10-11, available at <https://github.com/TEOS-10/GSW-C>, which stems from 'Matlab' and other code written by members of Working Group 127 of 'SCOR'/'IAPSO' (Scientific Committee on Oceanic Research / International Association for the Physical Sciences of the Oceans).

Maintained by Dan Kelley. Last updated 8 days ago.

gibbs oceanography seawater teos-10

1.8 match 8 stars 8.53 score 286 scripts 19 dependents

dipterix

threeBrain:Your Advanced 3D Brain Visualization

A fast, interactive cross-platform, and easy to share 'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or 'AFNI/SUMA' surfaces. The viewer widget can be either standalone or embedded into 'R-shiny' applications. The standalone version only require a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox', 'Safari'), and can be inserted into any websites. The 'R-shiny' support allows the 3D viewer to be dynamically generated from reactive user inputs. Please check the publication by Wang, Magnotti, Zhang, and Beauchamp (2023, <doi:10.1523/ENEURO.0328-23.2023>) for electrode localization. This viewer has been fully adopted by 'RAVE' <https://rave.wiki>, an interactive toolbox to analyze 'iEEG' data by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>). Please check citation("threeBrain") for details.

Maintained by Zhengjia Wang. Last updated 2 days ago.

brain ecog electroencephalography ieeg localization mri-brain neuroimaging template-brains

1.8 match 44 stars 8.24 score 38 scripts 1 dependents

jsta

wql:Exploring Water Quality Monitoring Data

Functions to assist in the processing and exploration of data from environmental monitoring programs. The package name stands for "water quality" and reflects the original focus on time series data for physical and chemical properties of water, as well as the biota. Intended for programs that sample approximately monthly, quarterly or annually at discrete stations, a feature of many legacy data sets. Most of the functions should be useful for analysis of similar-frequency time series regardless of the subject matter.

Maintained by Jemma Stachelek. Last updated 2 months ago.

water-quality

2.0 match 12 stars 7.34 score 204 scripts 3 dependents

usaid-oha-si

gophr:Utility functions related to working with the MER Structured Dataset

This packages contains a number of functions for working with the PEPFAR MSD.

Maintained by Aaron Chafetz. Last updated 4 months ago.

2.3 match 1 stars 6.21 score 182 scripts 1 dependents

ibot-geoecology

myClim:Microclimatic Data Processing

Handling the microclimatic data in R. The 'myClim' workflow begins at the reading data primary from microclimatic dataloggers, but can be also reading of meteorological station data from files. Cleaning time step, time zone settings and metadata collecting is the next step of the work flow. With 'myClim' tools one can crop, join, downscale, and convert microclimatic data formats, sort them into localities, request descriptive characteristics and compute microclimatic variables. Handy plotting functions are provided with smart defaults.

Maintained by Vojtěch Kalčík. Last updated 13 days ago.

2.0 match 7 stars 6.97 score 30 scripts

cran

DCEmgmt:DCE Data Reshaping and Processing

Prepare the results of a DCE to be analysed through choice models.'DCEmgmt' reshapes DCE data from wide to long format considering the special characteristics of a DCE. 'DCEmgmt' includes the function 'DCEestm' which estimates choice models once the database has been reshaped with 'DCEmgmt'.

Maintained by Daniel Perez-Troncoso. Last updated 3 years ago.

6.9 match 2.00 score

aalfons

cvTools:Cross-validation tools for regression models

Tools that allow developers to write functions for cross-validation with minimal programming effort and assist users with model selection.

Maintained by Andreas Alfons. Last updated 13 years ago.

1.9 match 8 stars 7.26 score 460 scripts 18 dependents

yrhwang90

Ymisc:Miscellaneous Functions

The Author's personal R Package that contains miscellaneous functions. The current version of package contains miscellaneous functions for brain data to compute Asymmetry Index (AI) and bilateral (L+R) measures and reshape the data.

Maintained by Yoo Ri Hwang. Last updated 1 years ago.

5.0 match 2.70 score 7 scripts

onofriandreapg

drcSeedGerm:Utilities for Data Analyses in Seed Germination/Emergence Assays

Utility functions to be used to analyse datasets obtained from seed germination/emergence assays. Fits several types of seed germination/emergence models, including those reported in Onofri et al. (2018) "Hydrothermal-time-to-event models for seed germination", European Journal of Agronomy, 101, 129-139 <doi:10.1016/j.eja.2018.08.011>. Contains several datasets for practicing.

Maintained by Andrea Onofri. Last updated 2 months ago.

nonlinear-regression seed-germination-assays time-to-event

3.4 match 5 stars 3.97 score 37 scripts

rrprf

tablesgg:Presentation-Quality Tables, Displayed Using 'ggplot2'

Presentation-quality tables are displayed as plots on an R graphics device. Although there are other packages that format tables for display, this package is unique in combining two features: (a) It is aware of the logical structure of the table being presented, and makes use of that for automatic layout and styling of the table. This avoids the need for most manual adjustments to achieve an attractive result. (b) It displays tables using 'ggplot2' graphics. Therefore a table can be presented anywhere a graph could be, with no more effort. External software such as LaTeX or HTML or their viewers is not required. The package provides a full set of tools to control the style and appearance of tables, including titles, footnotes and reference marks, horizontal and vertical rules, and spacing of rows and columns. Methods are included to display matrices; data frames; tables created by R's ftable(), table(), and xtabs() functions; and tables created by the 'tables' and 'xtable' packages. Methods can be added to display other table-like objects. A vignette is included that illustrates usage and options available in the package.

Maintained by Richard Raubertas. Last updated 4 years ago.

3.6 match 3.70 score 5 scripts

shabbychef

madness:Automatic Differentiation of Multivariate Operations

An object that supports automatic differentiation of matrix- and multidimensional-valued functions with respect to multidimensional independent variables. Automatic differentiation is via 'forward accumulation'.

Maintained by Steven E. Pav. Last updated 4 years ago.

2.0 match 31 stars 6.59 score 28 scripts 3 dependents

egenn

rtemis:Machine Learning and Visualization

Advanced Machine Learning and Visualization. Unsupervised Learning (Clustering, Decomposition), Supervised Learning (Classification, Regression), Cross-Decomposition, Bagging, Boosting, Meta-models. Static and interactive graphics.

Maintained by E.D. Gennatas. Last updated 1 months ago.

data-science data-visualization machine-learning machine-learning-library visualization

1.8 match 145 stars 7.09 score 50 scripts 2 dependents

bioc

isobar:Analysis and quantitation of isobarically tagged MSMS proteomics data

isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.

Maintained by Florian P Breitwieser. Last updated 5 months ago.

immunooncology proteomics massspectrometry bioinformatics multiplecomparisons qualitycontrol

1.8 match 10 stars 6.96 score 19 scripts

julienmoeys

soiltexture:Functions for Soil Texture Plot, Classification and Transformation

"The Soil Texture Wizard" is a set of R functions designed to produce texture triangles (also called texture plots, texture diagrams, texture ternary plots), classify and transform soil textures data. These functions virtually allows to plot any soil texture triangle (classification) into any triangle geometry (isosceles, right-angled triangles, etc.). This set of function is expected to be useful to people using soil textures data from different soil texture classification or different particle size systems. Many (> 15) texture triangles from all around the world are predefined in the package. A simple text based graphical user interface is provided: soiltexture_gui().

Maintained by Julien Moeys. Last updated 1 years ago.

1.8 match 28 stars 7.11 score 136 scripts 1 dependents

bioc

multiGSEA:Combining GSEA-based pathway enrichment with multi omics data integration

Extracted features from pathways derived from 8 different databases (KEGG, Reactome, Biocarta, etc.) can be used on transcriptomic, proteomic, and/or metabolomic level to calculate a combined GSEA-based enrichment score.

Maintained by Sebastian Canzler. Last updated 2 months ago.

genesetenrichment pathways reactome biocarta

1.8 match 18 stars 7.06 score 32 scripts

bieneschwarze

MicSim:Performing Continuous-Time Microsimulation

This toolkit allows performing continuous-time microsimulation for a wide range of life science (demography, social sciences, epidemiology) applications. Individual life-courses are specified by a continuous-time multi-state model.

Maintained by Sabine Zinn. Last updated 2 years ago.

3.6 match 2 stars 3.41 score 13 scripts

zerokgkg1368

KOFM:Test the Kronecker Product Structure in Tensor Factor Models

To test if a tensor time series following a Tucker-decomposition factor model has a Kronecker product structure. Supplementary functions for tensor reshape and its reversal are also included.

Maintained by Zetai Cen. Last updated 2 months ago.

6.1 match 2.00 score

bioc

h5mread:A fast HDF5 reader

The main function in the h5mread package is h5mread(), which allows reading arbitrary data from an HDF5 dataset into R, similarly to what the h5read() function from the rhdf5 package does. In the case of h5mread(), the implementation has been optimized to make it as fast and memory-efficient as possible.

Maintained by Hervé Pagès. Last updated 2 months ago.

infrastructure datarepresentation dataimport openssl curl zlib

1.8 match 1 stars 6.96 score 4 scripts 121 dependents

mschubert

narray:Subset- And Name-Aware Array Utility Functions

Stacking arrays according to dimension names, subset-aware splitting and mapping of functions, intersecting along arbitrary dimensions, converting to and from data.frames, and many other helper functions.

Maintained by Michael Schubert. Last updated 2 months ago.

array utility cpp

1.7 match 27 stars 6.91 score 10 scripts 10 dependents

dtacled

acledR:Manipulate ACLED Data

Tools working with data from ACLED (Armed Conflict Location and Event Data). Functions include simplified access to ACLED's API (<https://apidocs.acleddata.com/>), methods for keeping local versions of ACLED data up-to-date, and functions for common ACLED data transformations.

Maintained by Trey Billing. Last updated 18 days ago.

external

2.3 match 1 stars 5.13 score 6 scripts

pascalkieslich

mousetrap:Process and Analyze Mouse-Tracking Data

Mouse-tracking, the analysis of mouse movements in computerized experiments, is a method that is becoming increasingly popular in the cognitive sciences. The mousetrap package offers functions for importing, preprocessing, analyzing, aggregating, and visualizing mouse-tracking data. An introduction into mouse-tracking analyses using mousetrap can be found in Wulff, Kieslich, Henninger, Haslbeck, & Schulte-Mecklenbeck (2023) <doi:10.31234/osf.io/v685r> (preprint: <https://osf.io/preprints/psyarxiv/v685r>).

Maintained by Pascal J. Kieslich. Last updated 1 years ago.

analysis clustering mouse-tracking visualization cpp

1.7 match 46 stars 6.68 score 124 scripts

ethanbass

mzinspectr:Read and Analyze Mass Spectrometry Alignment Files

A few functions for analyzing MS-DIAL alignments in R. Includes functions for feature normalization, subtraction of blanks, and mass library (msp) search.

Maintained by Ethan Bass. Last updated 5 months ago.

cheminformatics gc-ms lc-ms metabolomics

4.0 match 3 stars 2.78 score

beckerbenj

eatGADS:Data Management of Large Hierarchical Data

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

Maintained by Benjamin Becker. Last updated 23 days ago.

1.5 match 1 stars 7.36 score 34 scripts 1 dependents

bioc

artMS:Analytical R tools for Mass Spectrometry

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Maintained by David Jimenez-Morales. Last updated 5 months ago.

proteomics differentialexpression biomedicalinformatics systemsbiology massspectrometry annotation qualitycontrol genesetenrichment clustering normalization immunooncology multiplecomparison analysis analytical ap-ms bioconductor bioinformatics mass-spectrometry phosphoproteomics post-translational-modification quantitative-analysis

1.7 match 14 stars 6.41 score 13 scripts

nano-optics

terms:T-matrix for Electromagnetic Radiation with Multiple Scatterers

A set of Fortran modules/routines for T-matrix-based calculations of light scattering by clusters of individual scatterers.

Maintained by Baptiste Auguié. Last updated 7 months ago.

light scattering

1.7 match 7 stars 6.46 score 828 scripts

dfsp-spirit

fsbrain:Managing and Visualizing Brain Surface Data

Provides high-level access to neuroimaging data from standard software packages like 'FreeSurfer' <http://freesurfer.net/> on the level of subjects and groups. Load morphometry data, surfaces and brain parcellations based on atlases. Mask data using labels, load data for specific atlas regions only, and visualize data and statistical results directly in 'R'.

Maintained by Tim Schäfer. Last updated 4 months ago.

3d brain dti freesurfer mesh mri neuroimaging research surface visualization voxel

1.7 match 66 stars 6.47 score 15 scripts

osofr

simcausal:Simulating Longitudinal Data with Causal Inference Applications

A flexible tool for simulating complex longitudinal data using structural equations, with emphasis on problems in causal inference. Specify interventions and simulate from intervened data generating distributions. Define and evaluate treatment-specific means, the average treatment effects and coefficients from working marginal structural models. User interface designed to facilitate the conduct of transparent and reproducible simulation studies, and allows concise expression of complex functional dependencies for a large number of time-varying nodes. See the package vignette for more information, documentation and examples.

Maintained by Oleg Sofrygin. Last updated 8 months ago.

counterfactual-data sem simulated-network simulating-data structural-equations

1.7 match 67 stars 6.06 score 170 scripts

florianstijven

Surrogate:Evaluation of Surrogate Endpoints in Clinical Trials

In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a (bio)marker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's Seventh Framework Programme for research, technological development and demonstration (Grant Agreement no 602552), the Special Research Fund (BOF) of Hasselt University (BOF-number: BOF2OCPO3), GlaxoSmithKline Biologicals, Baekeland Mandaat (HBC.2022.0145), and Johnson & Johnson Innovative Medicine.

Maintained by Wim Van Der Elst. Last updated 18 days ago.

1.6 match 1 stars 6.42 score 133 scripts

jansteinfeld

PP:Person Parameter Estimation

The PP package includes estimation of (MLE, WLE, MAP, EAP, ROBUST) person parameters for the 1,2,3,4-PL model and the GPCM (generalized partial credit model). The parameters are estimated under the assumption that the item parameters are known and fixed. The package is useful e.g. in the case that items from an item pool / item bank with known item parameters are administered to a new population of test-takers and an ability estimation for every test-taker is needed.

Maintained by Jan Steinfeld. Last updated 2 years ago.

irt person-parameter personfit cpp

1.5 match 1 stars 6.76 score 43 scripts 1 dependents

cran

wavethresh:Wavelets Statistics and Transforms

Performs 1, 2 and 3D real and complex-valued wavelet transforms, nondecimated transforms, wavelet packet transforms, nondecimated wavelet packet transforms, multiple wavelet transforms, complex-valued wavelet transforms, wavelet shrinkage for various kinds of data, locally stationary wavelet time series, nonstationary multiscale transfer function modeling, density estimation.

Maintained by Guy Nason. Last updated 7 months ago.

1.7 match 5.89 score 41 dependents

revelle

psychTools:Tools to Accompany the 'psych' Package for Psychological Research

Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as four vignettes. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.

Maintained by William Revelle. Last updated 12 months ago.

1.7 match 5.89 score 178 scripts 5 dependents

bioc

MultiRNAflow:An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions

Our R package MultiRNAflow provides an easy to use unified framework allowing to automatically make both unsupervised and supervised (DE) analysis for datasets with an arbitrary number of biological conditions and time points. In particular, our code makes a deep downstream analysis of DE information, e.g. identifying temporal patterns across biological conditions and DE genes which are specific to a biological condition for each time.

Maintained by Rodolphe Loubaton. Last updated 5 months ago.

sequencing rnaseq geneexpression transcription timecourse preprocessing visualization normalization principalcomponent clustering differentialexpression genesetenrichment pathways

1.9 match 6 stars 5.26 score 4 scripts

epiverse-trace

simulist:Simulate Disease Outbreak Line List and Contacts Data

Tools to simulate realistic raw case data for an epidemic in the form of line lists and contacts using a branching process. Simulated outbreaks are parameterised with epidemiological parameters and can have age-structured populations, age-stratified hospitalisation and death risk and time-varying case fatality risk.

Maintained by Joshua W. Lambert. Last updated 3 days ago.

epidemiology epiverse linelist outbreaks

1.3 match 9 stars 7.86 score 27 scripts

weirichs

eatTools:Miscellaneous Functions for the Analysis of Educational Assessments

Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep', 'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN'). The function for defining (weighted) contrasts in weighted effect coding refers to te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>. Functions for weighted statistics refer to Wolter (2007) <doi:10.1007/978-0-387-35099-8>.

Maintained by Sebastian Weirich. Last updated 3 months ago.

1.7 match 2 stars 5.38 score 11 scripts 2 dependents

schw4b

DGM:Dynamic Graphical Models

Dynamic graphical models for multivariate time series data to estimate directed dynamic networks in functional magnetic resonance imaging (fMRI), see Schwab et al. (2017) <doi:10.1016/j.neuroimage.2018.03.074>.

Maintained by Simon Schwab. Last updated 3 years ago.

dynamic-graphical-models functional-connectivity time-varying-connectivity openblas cpp openmp

1.7 match 25 stars 5.49 score 25 scripts

tjebo

eye:Analysis of Eye Data

There is no ophthalmic researcher who has not had headaches from the handling of visual acuity entries. Different notations, untidy entries. This shall now be a matter of the past. Eye makes it as easy as pie to work with VA data - easy cleaning, easy conversion between Snellen, logMAR, ETDRS letters, and qualitative visual acuity shall never pester you again. The eye package automates the pesky task to count number of patients and eyes, and can help to clean data with easy re-coding for right and left eyes. It also contains functions to help reshaping eye side specific variables between wide and long format. Visual acuity conversion is based on Schulze-Bonsel et al. (2006) <doi:10.1167/iovs.05-0981>, Gregori et al. (2010) <doi:10.1097/iae.0b013e3181d87e04>, Beck et al. (2003) <doi:10.1016/s0002-9394(02)01825-1> and Bach (2007) <http:michaelbach.de/sci/acuity.html>.

Maintained by Tjebo Heeren. Last updated 3 years ago.

1.8 match 6 stars 4.92 score 14 scripts

inzightvit

iNZightTools:Tools for 'iNZight'

Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.

Maintained by Tom Elliott. Last updated 3 months ago.

1.8 match 1 stars 5.16 score 18 scripts 2 dependents

fberding

aifeducation:Artificial Intelligence for Education

In social and educational settings, the use of Artificial Intelligence (AI) is a challenging task. Relevant data is often only available in handwritten forms, or the use of data is restricted by privacy policies. This often leads to small data sets. Furthermore, in the educational and social sciences, data is often unbalanced in terms of frequencies. To support educators as well as educational and social researchers in using the potentials of AI for their work, this package provides a unified interface for neural nets in 'PyTorch' to deal with natural language problems. In addition, the package ships with a shiny app, providing a graphical user interface. This allows the usage of AI for people without skills in writing python/R scripts. The tools integrate existing mathematical and statistical methods for dealing with small data sets via pseudo-labeling (e.g. Cascante-Bonilla et al. (2020) <doi:10.48550/arXiv.2001.06001>) and imbalanced data via the creation of synthetic cases (e.g. Bunkhumpornpat et al. (2012) <doi:10.1007/s10489-011-0287-y>). Performance evaluation of AI is connected to measures from content analysis which educational and social researchers are generally more familiar with (e.g. Berding & Pargmann (2022) <doi:10.30819/5581>, Gwet (2014) <ISBN:978-0-9708062-8-4>, Krippendorff (2019) <doi:10.4135/9781071878781>). Estimation of energy consumption and CO2 emissions during model training is done with the 'python' library 'codecarbon'. Finally, all objects created with this package allow to share trained AI models with other people.

Maintained by Berding Florian. Last updated 1 months ago.

cpp

2.0 match 4.48 score 8 scripts

albgarre

biogrowth:Modelling of Population Growth

Modelling of population growth under static and dynamic environmental conditions. Includes functions for model fitting and making prediction under isothermal and dynamic conditions. The methods (algorithms & models) are based on predictive microbiology (See Perez-Rodriguez and Valero (2012, ISBN:978-1-4614-5519-6)).

Maintained by Alberto Garre. Last updated 2 days ago.

1.3 match 5 stars 6.71 score 44 scripts

bioc

spiky:Spike-in calibration for cell-free MeDIP

spiky implements methods and model generation for cfMeDIP (cell-free methylated DNA immunoprecipitation) with spike-in controls. CfMeDIP is an enrichment protocol which avoids destructive conversion of scarce template, making it ideal as a "liquid biopsy," but creating certain challenges in comparing results across specimens, subjects, and experiments. The use of synthetic spike-in standard oligos allows diagnostics performed with cfMeDIP to quantitatively compare samples across subjects, experiments, and time points in both relative and absolute terms.

Maintained by Tim Triche. Last updated 5 months ago.

differentialmethylation dnamethylation normalization preprocessing qualitycontrol sequencing

1.8 match 2 stars 4.90 score 3 scripts

cran

mand:Multivariate Analysis for Neuroimaging Data

Several functions can be used to analyze neuroimaging data using multivariate methods based on the 'msma' package. The functions used in the book entitled "Multivariate Analysis for Neuroimaging Data" (2021, ISBN-13: 978-0367255329) are contained.

Maintained by Atsushi Kawaguchi. Last updated 2 years ago.

3.0 match 2.85 score 10 scripts

eitsupi

neopolars:R Bindings for the 'polars' Rust Library

Lightning-fast 'DataFrame' library written in 'Rust'. Convert R data to 'Polars' data and vice versa. Perform fast, lazy, larger-than-memory and optimized data queries. 'Polars' is interoperable with the package 'arrow', as both are based on the 'Apache Arrow' Columnar Format.

Maintained by Tatsuya Shima. Last updated 1 days ago.

rust cargo

1.8 match 40 stars 4.86 score 1 scripts

aalfons

perry:Resampling-Based Prediction Error Estimation for Regression Models

Tools that allow developers to write functions for prediction error estimation with minimal programming effort and assist users with model selection in regression problems.

Maintained by Andreas Alfons. Last updated 3 years ago.

1.8 match 2 stars 4.84 score 20 scripts 10 dependents

ugroempi

DoE.base:Full Factorials, Orthogonal Arrays and Base Utilities for DoE Packages

Creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Provides diverse quality criteria. Provides utility functions for the class design, which is also used by other packages for designed experiments.

Maintained by Ulrike Groemping. Last updated 1 years ago.

1.9 match 1 stars 4.50 score 104 scripts 19 dependents

sccmckenzie

sift:Intelligently Peruse Data

Facilitate extraction of key information from common datasets.

Maintained by Scott McKenzie. Last updated 4 years ago.

cpp

1.9 match 4.30 score 4 scripts

ddisab01

quest:Prepare Questionnaire Data for Analysis

Offers a suite of functions to prepare questionnaire data for analysis (perhaps other types of data as well). By data preparation, I mean data analytic tasks to get your raw data ready for statistical modeling (e.g., regression). There are functions to investigate missing data, reshape data, validate responses, recode variables, score questionnaires, center variables, aggregate by groups, shift scores (i.e., leads or lags), etc. It provides functions for both single level and multilevel (i.e., grouped) data. With a few exceptions (e.g., ncases()), functions without an "s" at the end of their primary word (e.g., center_by()) act on atomic vectors, while functions with an "s" at the end of their primary word (e.g., centers_by()) act on multiple columns of a data.frame.

Maintained by David Disabato. Last updated 1 years ago.

4.1 match 1.98 score 12 scripts

pv71u98h1

m61r:Package About Data Manipulation in Pure Base R

Data manipulation in one package and in base R. Minimal. No dependencies. 'dplyr' and 'tidyr'-like in one place. Nothing else than base R to build the package.

Maintained by Jean-Marie Lepioufle. Last updated 5 months ago.

2.0 match 1 stars 4.00 score 5 scripts

aprilnguyen1

icdcomorbid:Mapping ICD Codes to Comorbidity

Provides tools for mapping International Classification of Diseases codes to comorbidity, enabling the identification and analysis of various medical conditions within healthcare data.

Maintained by April Nguyen. Last updated 7 months ago.

3.0 match 2.70 score

traitecoevo

austraits:Helpful functions to access the AusTraits database and wrangle data from other traits.build databases

`austraits` allow users to **access, explore and wrangle data** from traits.build relational databases. It is also an R interface to AusTraits, the Australian plant trait database. This package contains functions for joining data from various tables, filtering to specific records, combining multiple databases and visualising the distribution of the data. We expect this package will assist users in working with `traits.build` databases.

Maintained by Fonti Kar. Last updated 2 months ago.

australia database plants traits

1.3 match 22 stars 5.93 score 43 scripts 1 dependents

onofriandreapg

drcte:Statistical Approaches for Time-to-Event Data in Agriculture

A specific and comprehensive framework for the analyses of time-to-event data in agriculture. Fit non-parametric and parametric time-to-event models. Compare time-to-event curves for different experimental groups. Plots and other displays. It is particularly tailored to the analyses of data from germination and emergence assays. The methods are described in Onofri et al. (2022) "A unified framework for the analysis of germination, emergence, and other time-to-event data in weed science", Weed Science, 70, 259-271 <doi:10.1017/wsc.2022.8>.

Maintained by Andrea Onofri. Last updated 1 years ago.

non-linear-regression seed-germination time-to-event

1.9 match 4.07 score 39 scripts 2 dependents

herveabdi

DistatisR:DiSTATIS Three Way Metric Multidimensional Scaling

Implement DiSTATIS and CovSTATIS (three-way multidimensional scaling). DiSTATIS and CovSTATIS are used to analyze multiple distance/covariance matrices collected on the same set of observations. These methods are based on Abdi, H., Williams, L.J., Valentin, D., & Bennani-Dosse, M. (2012) <doi:10.1002/wics.198>.

Maintained by Herve Abdi. Last updated 1 years ago.

3-way-mds distatis metric-multidimensional-scaling

1.7 match 4 stars 4.42 score 44 scripts

jimlemon

prettyR:Pretty Descriptive Stats

Functions for conventionally formatting descriptive stats, reshaping data frames and formatting R output as HTML.

Maintained by Jim Lemon. Last updated 6 years ago.

2.3 match 3.13 score 207 scripts 1 dependents

pedropark99

figma:Web Client/Wrapper to the 'Figma API'

An easy-to-use web client/wrapper for the 'Figma API' <https://www.figma.com/developers/api>. It allows you to bring all data from a 'Figma' file to your 'R' session. This includes the data of all objects that you have drawn in this file, and their respective canvas/page metadata.

Maintained by Pedro Faria. Last updated 2 years ago.

api api-rest figma

1.3 match 4 stars 5.30 score 33 scripts

qcrates

psidread:Streamline Building Panel Data from Panel Study of Income Dynamics ('PSID') Raw Files

Streamline the management, creation, and formatting of panel data from the Panel Study of Income Dynamics ('PSID') <https://psidonline.isr.umich.edu> using this user-friendly tool. Simply define variable names and input code book details directly from the 'PSID' official website, and this toolbox will efficiently facilitate the data preparation process, transforming raw 'PSID' files into a well-organized format ready for further analysis.

Maintained by Shuyi Qiu. Last updated 1 years ago.

1.9 match 1 stars 3.70 score 5 scripts

desiquintans

novelqualcodes:Visualise the Path to a Stopping Point in Qualitative Interviews Based on Novel Codes

In semi-structured interviews that use the 'framework' method, it is not always clear how refinements to interview questions affect the decision of when to stop interviews. The trend of 'novel' and 'duplicate' interview codes (novel codes are information that other interviewees have not previously mentioned) provides insight into the richness of qualitative information. This package provides tools to visualise when refinements occur and how that affects the trends of novel and duplicate codes. These visualisations, when used progressively as new interviews are finished, can help the researcher to decide on a stopping point for their interviews.

Maintained by Desi Quintans. Last updated 1 years ago.

1.9 match 3.70 score 3 scripts

molaison

MantaID:A Machine-Learning Based Tool to Automate the Identification of Biological Database IDs

The number of biological databases is growing rapidly, but different databases use different IDs to refer to the same biological entity. The inconsistency in IDs impedes the integration of various types of biological data. To resolve the problem, we developed 'MantaID', a data-driven, machine-learning based approach that automates identifying IDs on a large scale. The 'MantaID' model's prediction accuracy was proven to be 99%, and it correctly and effectively predicted 100,000 ID entries within two minutes. 'MantaID' supports the discovery and exploitation of ID patterns from large quantities of databases. (e.g., up to 542 biological databases). An easy-to-use freely available open-source software R package, a user-friendly web application, and API were also developed for 'MantaID' to improve applicability. To our knowledge, 'MantaID' is the first tool that enables an automatic, quick, accurate, and comprehensive identification of large quantities of IDs, and can therefore be used as a starting point to facilitate the complex assimilation and aggregation of biological data across diverse databases.

Maintained by Zhengpeng Zeng. Last updated 6 months ago.

1.8 match 3.78 score 2 scripts

rahmarid

stablespec:Stable Specification Search in Structural Equation Models

An exploratory and heuristic approach for specification search in Structural Equation Modeling. The basic idea is to subsample the original data and then search for optimal models on each subset. Optimality is defined through two objectives: model fit and parsimony. As these objectives are conflicting, we apply a multi-objective optimization methods, specifically NSGA-II, to obtain optimal models for the whole range of model complexities. From these optimal models, we consider only the relevant model specifications (structures), i.e., those that are both stable (occur frequently) and parsimonious and use those to infer a causal model.

Maintained by Ridho Rahmadi. Last updated 8 years ago.

2.0 match 5 stars 3.40 score 7 scripts

friendly

twoway:Analysis of Two-Way Tables

Carries out analyses of two-way tables with one observation per cell, together with graphical displays for an additive fit and a diagnostic plot for removable 'non-additivity' via a power transformation of the response. It implements Tukey's Exploratory Data Analysis (1973) <ISBN: 978-0201076165> methods, including a 1-degree-of-freedom test for row*column 'non-additivity', linear in the row and column effects.

Maintained by Michael Friendly. Last updated 5 months ago.

anova residuals transformations tukey

1.7 match 4 stars 3.94 score 22 scripts

alekrutkowski

eurodata:Fast and Easy Eurostat Data Import and Search

Interface to Eurostat’s API (SDMX 2.1) with fast data.table-based import of data, labels, and metadata. On top of the core functionality, data search and data description/comparison functions are also provided. Use <https://github.com/alekrutkowski/eurodata_codegen> — a point-and-click app for rapid and easy generation of richly-commented R code — to import a Eurostat dataset or its subset (based on the eurodata::importData() function).

Maintained by Aleksander Rutkowski. Last updated 4 months ago.

cpp

1.8 match 11 stars 3.74 score 7 scripts

scholaempirica

reschola:The Schola Empirica Package

A collection of utilies, themes and templates for data analysis at Schola Empirica.

Maintained by Jan Netík. Last updated 5 months ago.

1.3 match 4 stars 4.83 score 14 scripts

bodysbobb

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

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

Maintained by Pattawee Puangchit. Last updated 15 hours ago.

gempack gtap har-files sl4-file

1.3 match 2 stars 4.70 score

ingmbioinfo

combiroc:Selection and Ranking of Omics Biomarkers Combinations Made Easy

Provides functions and a workflow to easily and powerfully calculating specificity, sensitivity and ROC curves of biomarkers combinations. Allows to rank and select multi-markers signatures as well as to find the best performing sub-signatures, now also from single-cell RNA-seq datasets. The method used was first published as a Shiny app and described in Mazzara et al. (2017) <doi:10.1038/srep45477> and further described in Bombaci & Rossi (2019) <doi:10.1007/978-1-4939-9164-8_16>, and widely expanded as a package as presented in the bioRxiv pre print Ferrari et al. <doi:10.1101/2022.01.17.476603>.

Maintained by Riccardo L. Rossi. Last updated 9 months ago.

1.8 match 5 stars 3.48 score 12 scripts

usaid-oha-si

Wavelength:Wavelength

USAID OHA Office. Munging of mission weekly HFR data.

Maintained by Aaron Chafetz. Last updated 2 years ago.

1.8 match 3 stars 3.39 score 55 scripts

hvillalo

satin:Visualisation and Analysis of Ocean Data Derived from Satellites

With 'satin' functions, visualisation, data extraction and further analysis like producing climatologies from several images, and anomalies of satellite derived ocean data can be easily done. Reading functions can import a user defined geographical extent of data stored in netCDF files. Currently supported ocean data sources include NASA's Oceancolor web page <https://oceancolor.gsfc.nasa.gov/>, sensors VIIRS-SNPP; MODIS-Terra; MODIS-Aqua; and SeaWiFS. Available variables from this source includes chlorophyll concentration, sea surface temperature (SST), and several others. Data sources specific for SST that can be imported too includes Pathfinder AVHRR <https://www.ncei.noaa.gov/products/avhrr-pathfinder-sst> and GHRSST <https://www.ghrsst.org/>. In addition, ocean productivity data produced by Oregon State University <http://sites.science.oregonstate.edu/ocean.productivity/> can also be handled previous conversion from HDF4 to HDF5 format. Many other ocean variables can be processed by importing netCDF data files from two European Union's Copernicus Marine Service databases <https://marine.copernicus.eu/>, namely Global Ocean Physical Reanalysis and Global Ocean Biogeochemistry Hindcast.

Maintained by Héctor Villalobos. Last updated 10 months ago.

avhrr copernicus ghrsst modis

1.8 match 4 stars 3.30 score 9 scripts

schochastics

RFPNG:Very Fast PNG Image Reader/Writer for 24/32bpp Images

Wraps 'fpng', a very fast C++ .PNG image reader/writer for 24/32bpp images

Maintained by David Schoch. Last updated 1 years ago.

cpp

2.7 match 3 stars 2.18 score 2 scripts

janmarvin

nlsur:Estimating Nonlinear Least Squares for Equation Systems

"Estimation of Nonlinear Least Squares (NLS), Feasible Generalized NLS (FGNLS) and Iterative FGNLS (IFGNLS) for Equation Systems."

Maintained by Jan Marvin Garbuszus. Last updated 7 months ago.

equation-systems fgnls ifgnls nls seemingly-unrelated-regression openblas cpp

1.8 match 16 stars 3.20 score 8 scripts

fpaskali

LFApp:Shiny Apps for Lateral Flow Assays

Shiny apps for the quantitative analysis of images from lateral flow assays (LFAs). The images are segmented and background corrected and color intensities are extracted. The apps can be used to import and export intensity data and to calibrate LFAs by means of linear, loess, or gam models. The calibration models can further be saved and applied to intensity data from new images for determining concentrations.

Maintained by Filip Paskali. Last updated 10 months ago.

calibration image-processing medical-image-processing shiny

1.2 match 3 stars 4.78 score 2 scripts

weirichs

eatRep:Educational Assessment Tools for Replication Methods

Replication methods to compute some basic statistic operations (means, standard deviations, frequency tables, percentiles, mean comparisons using weighted effect coding, generalized linear models, and linear multilevel models) in complex survey designs comprising multiple imputed or nested imputed variables and/or a clustered sampling structure which both deserve special procedures at least in estimating standard errors. See the package documentation for a more detailed description along with references.

Maintained by Sebastian Weirich. Last updated 17 days ago.

1.1 match 1 stars 5.16 score 13 scripts

jmhewitt

telefit:Estimation and Prediction for Remote Effects Spatial Process Models

Implementation of the remote effects spatial process (RESP) model for teleconnection. The RESP model is a geostatistical model that allows a spatially-referenced variable (like average precipitation) to be influenced by covariates defined on a remote domain (like sea surface temperatures). The RESP model is introduced in Hewitt et al. (2018) <doi:10.1002/env.2523>. Sample code for working with the RESP model is available at <https://jmhewitt.github.io/research/resp_example>. This material is based upon work supported by the National Science Foundation under grant number AGS 1419558. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation.

Maintained by Joshua Hewitt. Last updated 5 years ago.

openblas cpp

1.8 match 1 stars 3.19 score 31 scripts

cran

GenderInfer:This is a Collection of Functions to Analyse Gender Differences

Implementation of functions, which combines binomial calculation and data visualisation, to analyse the differences in publishing authorship by gender described in Day et al. (2020) <doi:10.1039/C9SC04090K>. It should only be used when self-reported gender is unavailable.

Maintained by Rita Giordano. Last updated 3 years ago.

1.7 match 2.70 score

cjbarrie

academictwitteR:Access the Twitter Academic Research Product Track V2 API Endpoint

Package to query the Twitter Academic Research Product Track, providing access to full-archive search and other v2 API endpoints. Functions are written with academic research in mind. They provide flexibility in how the user wishes to store collected data, and encourage regular storage of data to mitigate loss when collecting large volumes of tweets. They also provide workarounds to manage and reshape the format in which data is provided on the client side.

Maintained by Christopher Barrie. Last updated 2 years ago.

twitter twitter-api

0.5 match 275 stars 8.94 score 177 scripts

svdpas

BayesSurvival:Bayesian Survival Analysis for Right Censored Data

Performs unadjusted Bayesian survival analysis for right censored time-to-event data. The main function, BayesSurv(), computes the posterior mean and a credible band for the survival function and for the cumulative hazard, as well as the posterior mean for the hazard, starting from a piecewise exponential (histogram) prior with Gamma distributed heights that are either independent, or have a Markovian dependence structure. A function, PlotBayesSurv(), is provided to easily create plots of the posterior means of the hazard, cumulative hazard and survival function, with a credible band accompanying the latter two. The priors and samplers are described in more detail in Castillo and Van der Pas (2020) "Multiscale Bayesian survival analysis" <arXiv:2005.02889>. In that paper it is also shown that the credible bands for the survival function and the cumulative hazard can be considered confidence bands (under mild conditions) and thus offer reliable uncertainty quantification.

Maintained by Stephanie van der Pas. Last updated 4 years ago.

1.7 match 2.70 score 4 scripts

ulthran

demic:Dynamic Estimator of Microbial Communities

Multi-sample algorithm based on contigs and coverage values, to infer the relative distances of contigs from the replication origin and to accurately compare bacterial growth rates between samples. Yuan Gao and Hongzhe Li (2018) <doi:10.1038/s41592-018-0182-0>.

Maintained by Charlie Bushman. Last updated 1 years ago.

1.7 match 2.70 score 3 scripts

bhaibeka

SIGN:Similarity Identification in Gene Expression

Provides a classification framework to use expression patterns of pathways as features to identify similarity between biological samples. It provides a new measure for quantifying similarity between expression patterns of pathways.

Maintained by Benjamin Haibe-Kains. Last updated 6 years ago.

geneexpression classification clustering survival

1.6 match 2.70 score 3 scripts

ralmond

Peanut:Parameterized Bayesian Networks, Abstract Classes

This provides support of learning conditional probability tables parameterized using CPTtools. This provides and object oriented layer on top of a CPTtools, to facilitate calculations with Parameterized models for Bayesian networks. Peanut is a collection of abstract classes and generic functions defining a protocol, with the intent that the protocol can be implemented with different Bayes net engines. The companion pacakge PNetica provides an implementation using Netica and RNetica.

Maintained by Russell Almond. Last updated 2 years ago.

bayesian-network knowledge-representation

1.7 match 1 stars 2.48 score 4 scripts 2 dependents

bioc

biobroom:Turn Bioconductor objects into tidy data frames

This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.

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

multiplecomparison differentialexpression regression geneexpression proteomics dataimport

0.5 match 49 stars 8.22 score 280 scripts 1 dependents

alexcannon

GEVcdn:GEV Conditional Density Estimation Network

Implements a flexible nonlinear modelling framework for nonstationary generalized extreme value analysis in hydroclimatology following Cannon (2010) <doi:10.1002/hyp.7506>.

Maintained by Alex J. Cannon. Last updated 5 years ago.

4.0 match 1 stars 1.00 score 5 scripts

cran

rNeighborQTL:Interval Mapping for Quantitative Trait Loci Underlying Neighbor Effects

To enable quantitative trait loci mapping of neighbor effects, this package extends a single-marker regression to interval mapping. The theoretical background of the method is described in Sato et al. (2021) <doi:10.1093/g3journal/jkab017>.

Maintained by Yasuhiro Sato. Last updated 4 years ago.

2.0 match 2.00 score 3 scripts

cran

pwrRasch:Statistical Power Simulation for Testing the Rasch Model

Statistical power simulation for testing the Rasch Model based on a three-way analysis of variance design with mixed classification.

Maintained by Takuya Yanagida. Last updated 9 years ago.

4.0 match 1 stars 1.00 score 9 scripts

alisonlanski

IPEDSuploadables:Transforms Institutional Data into Text Files for IPEDS Automated Import/Upload

Starting from user-supplied institutional data, these scripts transform, aggregate, and reshape the information to produce key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System) through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes. Final files are saved locally to a location of the user's choice. User-friendly readable files can also be produced for purposes of data review and validation.

Maintained by Alison Lanski. Last updated 3 months ago.

0.5 match 8 stars 7.05 score 39 scripts

sebkrantz

samadb:South Africa Macroeconomic Database API

An R API providing access to a relational database with macroeconomic time series data for South Africa, obtained from the South African Reserve Bank (SARB) and Statistics South Africa (STATSSA), and updated on a weekly basis via the EconData <https://www.econdata.co.za/> platform and automated scraping of the SARB and STATSSA websites. The database is maintained at the Department of Economics at Stellenbosch University.

Maintained by Sebastian Krantz. Last updated 10 months ago.

3.5 match 1.00 score 2 scripts

sebkrantz

ugatsdb:Uganda Time Series Database API

An R API providing easy access to a relational database with macroeconomic, financial and development related time series data for Uganda. Overall more than 5000 series at varying frequency (daily, monthly, quarterly, annual in fiscal or calendar years) can be accessed through the API. The data is provided by the Bank of Uganda, the Ugandan Ministry of Finance, Planning and Economic Development, the IMF and the World Bank. The database is being updated once a month.

Maintained by Sebastian Krantz. Last updated 2 years ago.

3.5 match 1.00 score 9 scripts

sebkrantz

africamonitor:Africa Macroeconomic Monitor Database API

An R API providing access to a relational database with macroeconomic data for Africa. The database contains >700 macroeconomic time series from mostly international sources, grouped into 50 macroeconomic and development-related topics. Series are carefully selected on the basis of data coverage for Africa, frequency, and relevance to the macro-development context. The project is part of the 'Kiel Institute Africa Initiative' <https://www.ifw-kiel.de/institute/initiatives/kiel-institute-africa-initiative/>, which, amongst other things, aims to develop a parsimonious database with highly relevant indicators to monitor macroeconomic developments in Africa, accessible through a fast API and a web-based platform at <https://africamonitor.ifw-kiel.de/>. The database is maintained at the Kiel Institute for the World Economy <https://www.ifw-kiel.de/>.

Maintained by Sebastian Krantz. Last updated 1 years ago.

3.5 match 1.00 score 2 scripts

j-mitchel

scITD:Single-Cell Interpretable Tensor Decomposition

Single-cell Interpretable Tensor Decomposition (scITD) employs the Tucker tensor decomposition to extract multicell-type gene expression patterns that vary across donors/individuals. This tool is geared for use with single-cell RNA-sequencing datasets consisting of many source donors. The method has a wide range of potential applications, including the study of inter-individual variation at the population-level, patient sub-grouping/stratification, and the analysis of sample-level batch effects. Each "multicellular process" that is extracted consists of (A) a multi cell type gene loadings matrix and (B) a corresponding donor scores vector indicating the level at which the corresponding loadings matrix is expressed in each donor. Additional methods are implemented to aid in selecting an appropriate number of factors and to evaluate stability of the decomposition. Additional tools are provided for downstream analysis, including integration of gene set enrichment analysis and ligand-receptor analysis. Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Maintained by Jonathan Mitchel. Last updated 2 years ago.

cpp

1.8 match 1.98 score 19 scripts

alexcannon

CaDENCE:Conditional Density Estimation Network Construction and Evaluation

Parameters of a user-specified probability distribution are modelled by a multi-layer perceptron artificial neural network. This framework can be used to implement probabilistic nonlinear models including mixture density networks, heteroscedastic regression models, zero-inflated models, etc. following Cannon (2012) <doi:10.1016/j.cageo.2011.08.023>.

Maintained by Alex J. Cannon. Last updated 7 years ago.

2.3 match 1.45 score 28 scripts

kwb-r

kwb.waterParcel:Lagrangian Sampling Interpretation

Conservative tracers within the water can be used to interpret the results of a sampling compaign following one water parcel (Lagrangian Sampling).

Maintained by Malte Zamzow. Last updated 2 years ago.

1.8 match 1.70 score

tjmahr

polypoly:Helper Functions for Orthogonal Polynomials

Tools for reshaping, plotting, and manipulating matrices of orthogonal polynomials.

Maintained by Tristan Mahr. Last updated 2 years ago.

data-science statistics

0.6 match 19 stars 5.12 score 14 scripts

csoireland

csodata:Download Data from the CSO 'PxStat' API

Imports 'PxStat' data in JSON-stat format and (optionally) reshapes it into wide format. The Central Statistics Office (CSO) is the national statistical institute of Ireland and 'PxStat' is the CSOs online database of Official Statistics. This database contains current and historical data series compiled from CSO statistical releases and is accessed at <http://data.cso.ie>. The CSO 'PxStat' Application Programming Interface (API), which is accessed in this package, provides access to 'PxStat' data in JSON-stat format at <http://data.cso.ie>. This dissemination tool allows developers machine to machine access to CSO 'PxStat' data.

Maintained by Conor Crowley. Last updated 10 months ago.

0.5 match 14 stars 5.77 score 14 scripts

maraab23

ggseqplot:Render Sequence Plots using 'ggplot2'

A set of wrapper functions that mainly re-produces most of the sequence plots rendered with TraMineR::seqplot(). Whereas 'TraMineR' uses base R to produce the plots this library draws on 'ggplot2'. The plots are produced on the basis of a sequence object defined with TraMineR::seqdef(). The package automates the reshaping and plotting of sequence data. Resulting plots are of class 'ggplot', i.e. components can be added and tweaked using '+' and regular 'ggplot2' functions.

Maintained by Marcel Raab. Last updated 4 months ago.

ggplot2 sequence-analysis traminer visualization

0.5 match 14 stars 5.70 score 18 scripts

rmendels

plotdap:Easily Visualize Data from 'ERDDAP' Servers via the 'rerddap' Package

Easily visualize and animate 'tabledap' and 'griddap' objects obtained via the 'rerddap' package in a simple one-line command, using either base graphics or 'ggplot2' graphics. 'plotdap' handles extracting and reshaping the data, map projections and continental outlines. Optionally the data can be animated through time using the 'gganmiate' package.

Maintained by Roy Mendelssohn. Last updated 1 years ago.

0.5 match 10 stars 5.05 score 37 scripts 1 dependents

wittenburg

hsrecombi:Estimation of Recombination Rate and Maternal LD in Half-Sibs

Paternal recombination rate and maternal linkage disequilibrium (LD) are estimated for pairs of biallelic markers such as single nucleotide polymorphisms (SNPs) from progeny genotypes and sire haplotypes. The implementation relies on paternal half-sib families. If maternal half-sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. For parameter estimation, at least one sire has to be double heterozygous at the investigated pairs of SNPs. Based on recombination rates, genetic distances between markers can be estimated. Markers with unusually large recombination rate to markers in close proximity (i.e. putatively misplaced markers) shall be discarded in this derivation. A workflow description is attached as vignette. *A pipeline is available at GitHub* <https://github.com/wittenburg/hsrecombi> Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of recombination rate and maternal linkage disequilibrium in half-sibs" <doi:10.3389/fgene.2018.00186>. Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium in half-sib families" <doi:10.1534/genetics.111.137521>.

Maintained by Dörte Wittenburg. Last updated 2 years ago.

cpp

1.2 match 2.00 score 7 scripts

ellakaye

BradleyTerryScalable:Fits the Bradley-Terry Model to Potentially Large and Sparse Networks of Comparison Data

Facilities are provided for fitting the simple, unstructured Bradley-Terry model to networks of binary comparisons. The implemented methods are designed to scale well to large, potentially sparse, networks. A fairly high degree of scalability is achieved through the use of EM and MM algorithms, which are relatively undemanding in terms of memory usage (relative to some other commonly used methods such as iterative weighted least squares, for example). Both maximum likelihood and Bayesian MAP estimation methods are implemented. The package provides various standard methods for a newly defined 'btfit' model class, such as the extraction and summarisation of model parameters and the simulation of new datasets from a fitted model. Tools are also provided for reshaping data into the newly defined "btdata" class, and for analysing the comparison network, prior to fitting the Bradley-Terry model. This package complements, rather than replaces, the existing 'BradleyTerry2' package. (BradleyTerry2 has rather different aims, which are mainly the specification and fitting of "structured" Bradley-Terry models in which the strength parameters depend on covariates.)

Maintained by Ella Kaye. Last updated 3 years ago.

openblas cpp openmp

0.5 match 25 stars 3.80 score 25 scripts

statkim7578

RMM:Revenue Management Modeling

The RMM fits Revenue Management Models using the RDE(Robust Demand Estimation) method introduced in the paper by <doi:10.2139/ssrn.3598259>, one of the customer choice-based Revenue Management Model. Furthermore, it is possible to select a multinomial model as well as a conditional logit model as a model of RDE.

Maintained by Chul Kim. Last updated 3 years ago.

cpp

1.9 match 1.00 score 4 scripts

njtierney

broomstick:Convert Decision Tree Objects into Tidy Data Frames

Convert Decision Tree objects into tidy data frames, by using the framework laid out by the package broom, this means that decision tree output can be easily reshaped, porocessed, and combined with tools like 'dplyr', 'tidyr' and 'ggplot2'. Like the package broom, broomstick provides three S3 generics: tidy, to summarise decision tree specific features - tidy returns the variable importance table; augment adds columns to the original data such as predictions and residuals; and glance, which provides a one-row summary of model-level statistics.

Maintained by Nicholas Tierney. Last updated 1 years ago.

broom decision-trees gbm machine-learning randomforest rpart statistical-learning

0.5 match 29 stars 3.59 score 27 scripts

sandipgarai

tsLSTMx:Predict Time Series Using LSTM Model Including Exogenous Variable to Denote Zero Values

It is a versatile tool for predicting time series data using Long Short-Term Memory (LSTM) models. It is specifically designed to handle time series with an exogenous variable, allowing users to denote whether data was available for a particular period or not. The package encompasses various functionalities, including hyperparameter tuning, custom loss function support, model evaluation, and one-step-ahead forecasting. With an emphasis on ease of use and flexibility, it empowers users to explore, evaluate, and deploy LSTM models for accurate time series predictions and forecasting in diverse applications. More details can be found in Garai and Paul (2023) <doi:10.1016/j.iswa.2023.200202>.

Maintained by Sandip Garai. Last updated 1 years ago.

1.8 match 1.00 score

iankopacka

eufmdis.adapt:Analyse 'EuFMDiS' Output Files via a Shiny App

Analyses 'EuFMDiS' output files in a Shiny App. The distributions of relevant output parameters are described in form of tables (quantiles) and plots. The App is called using eufmdis.adapt::run_adapt().

Maintained by Ian Kopacka. Last updated 2 years ago.

1.7 match 1.00 score

aazaff

velociraptr:Fossil Analysis

Functions for downloading, reshaping, culling, cleaning, and analyzing fossil data from the Paleobiology Database <https://paleobiodb.org>.

Maintained by Andrew A Zaffos. Last updated 6 years ago.

0.5 match 1 stars 2.04 score 22 scripts