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r-lib

testthat:Unit Testing for R

Software testing is important, but, in part because it is frustrating and boring, many of us avoid it. 'testthat' is a testing framework for R that is easy to learn and use, and integrates with your existing 'workflow'.

Maintained by Hadley Wickham. Last updated 30 days ago.

unit-testingcpp

900 stars 20.99 score 74k scripts 471 dependents

norskregnesentral

shapr:Prediction Explanation with Dependence-Aware Shapley Values

Complex machine learning models are often hard to interpret. However, in many situations it is crucial to understand and explain why a model made a specific prediction. Shapley values is the only method for such prediction explanation framework with a solid theoretical foundation. Previously known methods for estimating the Shapley values do, however, assume feature independence. This package implements methods which accounts for any feature dependence, and thereby produces more accurate estimates of the true Shapley values. An accompanying 'Python' wrapper ('shaprpy') is available through the GitHub repository.

Maintained by Martin Jullum. Last updated 3 days ago.

explainable-aiexplainable-mlrcpprcpparmadilloshapleyopenblascppopenmp

154 stars 10.59 score 175 scripts 1 dependents

mlverse

luz:Higher Level 'API' for 'torch'

A high level interface for 'torch' providing utilities to reduce the the amount of code needed for common tasks, abstract away torch details and make the same code work on both the 'CPU' and 'GPU'. It's flexible enough to support expressing a large range of models. It's heavily inspired by 'fastai' by Howard et al. (2020) <arXiv:2002.04688>, 'Keras' by Chollet et al. (2015) and 'PyTorch Lightning' by Falcon et al. (2019) <doi:10.5281/zenodo.3828935>.

Maintained by Daniel Falbel. Last updated 6 months ago.

89 stars 9.86 score 318 scripts 4 dependents

predictiveecology

Require:Installing and Loading R Packages for Reproducible Workflows

A single key function, 'Require' that makes rerun-tolerant versions of 'install.packages' and `require` for CRAN packages, packages no longer on CRAN (i.e., archived), specific versions of packages, and GitHub packages. This approach is developed to create reproducible workflows that are flexible and fast enough to use while in development stages, while able to build snapshots once a stable package collection is found. As with other functions in a reproducible workflow, this package emphasizes functions that return the same result whether it is the first or subsequent times running the function, with subsequent times being sufficiently fast that they can be run every time without undue waiting burden on the user or developer.

Maintained by Eliot J B McIntire. Last updated 29 days ago.

22 stars 9.42 score 144 scripts 13 dependents

masurp

specr:Conducting and Visualizing Specification Curve Analyses

Provides utilities for conducting specification curve analyses (Simonsohn, Simmons & Nelson (2020, <doi: 10.1038/s41562-020-0912-z>) or multiverse analyses (Steegen, Tuerlinckx, Gelman & Vanpaemel, 2016, <doi: 10.1177/1745691616658637>) including functions to setup, run, evaluate, and plot all specifications.

Maintained by Philipp K. Masur. Last updated 10 months ago.

multiversespecification-curve

68 stars 7.89 score 85 scripts

blue-matter

MSEtool:Management Strategy Evaluation Toolkit

Development, simulation testing, and implementation of management procedures for fisheries (see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).

Maintained by Adrian Hordyk. Last updated 5 days ago.

cpp

8 stars 7.71 score 163 scripts 3 dependents

jakobbossek

ecr:Evolutionary Computation in R

Framework for building evolutionary algorithms for both single- and multi-objective continuous or discrete optimization problems. A set of predefined evolutionary building blocks and operators is included. Moreover, the user can easily set up custom objective functions, operators, building blocks and representations sticking to few conventions. The package allows both a black-box approach for standard tasks (plug-and-play style) and a much more flexible white-box approach where the evolutionary cycle is written by hand.

Maintained by Jakob Bossek. Last updated 2 years ago.

combinatorial-optimizationevolutionary-algorithmevolutionary-algorithmsevolutionary-strategygenetic-algorithm-frameworkmetaheuristicsmulti-objective-optimizationoptimizationoptimization-frameworkcpp

43 stars 7.36 score 89 scripts 2 dependents

ropensci

phylotaR:Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.

Maintained by Shixiang Wang. Last updated 8 months ago.

blastngenbankpeer-reviewedphylogeneticssequence-alignment

23 stars 5.86 score 156 scripts

amrrs

coinmarketcapr:Get 'Cryptocurrencies' Market Cap Prices from Coin Market Cap

Extract and monitor price and market cap of 'Cryptocurrencies' from 'Coin Market Cap' <https://coinmarketcap.com/api/>.

Maintained by AbdulMajedRaja RS. Last updated 3 years ago.

cryptocurrency

81 stars 5.84 score 43 scripts

tgve

tgver:Turing Geovisualization Engine R package

Turing Geovisualization Engine R package for geospatial visualization and analysis.

Maintained by Layik Hama. Last updated 2 years ago.

geospatial-analysisgeospatial-visualization

5 stars 5.48 score 3 scripts

sahilseth

funr:Simple Utility Providing Terminal Access to all R Functions

A small utility which wraps Rscript and provides access to all R functions from the shell.

Maintained by Sahil Seth. Last updated 4 years ago.

34 stars 5.25 score 104 scripts

anthonypileggi

casino:Play Casino Games

Play casino games in the R console, including poker, blackjack, and a slot machine. Try to build your fortune before you succumb to the gambler's ruin!

Maintained by Anthony Pileggi. Last updated 6 years ago.

10 stars 4.81 score 13 scripts

eddelbuettel

spdl:Easier Use of 'RcppSpdlog' Functions via Wrapper

Logging functions in 'RcppSpdlog' provide access to the logging functionality from the 'spdlog' 'C++' library. This package offers shorter convenience wrappers for the 'R' functions which match the 'C++' functions, namely via, say, 'spdl::debug()' at the debug level. The actual formatting is done by the 'fmt::format()' function from the 'fmtlib' library (that is also 'std::format()' in 'C++20' or later).

Maintained by Dirk Eddelbuettel. Last updated 10 months ago.

2 stars 4.78 score 1 scripts 6 dependents

henrikbengtsson

aroma.core:Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.

Maintained by Henrik Bengtsson. Last updated 2 years ago.

microarrayonechanneltwochannelmultichanneldataimportdatarepresentationguivisualizationpreprocessingqualitycontrolacghcopynumbervariants

1 stars 4.30 score 16 scripts 6 dependents

swihart

repeated:Non-Normal Repeated Measurements Models

Various functions to fit models for non-normal repeated measurements, such as Binary Random Effects Models with Two Levels of Nesting, Bivariate Beta-binomial Regression Models, Marginal Bivariate Binomial Regression Models, Cormack capture-recapture models, Continuous-time Hidden Markov Chain Models, Discrete-time Hidden Markov Chain Models, Changepoint Location Models using a Continuous-time Two-state Hidden Markov Chain, generalized nonlinear autoregression models, multivariate Gaussian copula models, generalized non-linear mixed models with one random effect, generalized non-linear mixed models using h-likelihood for one random effect, Repeated Measurements Models for Counts with Frailty or Serial Dependence, Repeated Measurements Models for Continuous Variables with Frailty or Serial Dependence, Ordinal Random Effects Models with Dropouts, marginal homogeneity models for square contingency tables, correlated negative binomial models with Kalman update. References include Lindsey's text books, JK Lindsey (2001) <isbn:10-0198508123> and JK Lindsey (1999) <isbn:10-0198505590>.

Maintained by Bruce Swihart. Last updated 6 months ago.

fortran

3.97 score 31 scripts

aalfons

simFrame:Simulation Framework

A general framework for statistical simulation, which allows researchers to make use of a wide range of simulation designs with minimal programming effort. The package provides functionality for drawing samples from a distribution or a finite population, for adding outliers and missing values, as well as for visualization of the simulation results. It follows a clear object-oriented design and supports parallel computing to increase computational performance.

Maintained by Andreas Alfons. Last updated 3 years ago.

cpp

2 stars 3.90 score 80 scripts

mobreza

genesysr:Genesys PGR Client

Access data on plant genetic resources from genebanks around the world published on Genesys (<https://www.genesys-pgr.org>). Your use of data is subject to terms and conditions available at <https://www.genesys-pgr.org/content/legal/terms>.

Maintained by Matija Obreza. Last updated 1 years ago.

3.00 score 6 scripts

daniellemccool

topdowntimeratio:Top-Down Time Ratio Segmentation for Coordinate Trajectories

Data collected on movement behavior is often in the form of time- stamped latitude/longitude coordinates sampled from the underlying movement behavior. These data can be compressed into a set of segments via the Top- Down Time Ratio Segmentation method described in Meratnia and de By (2004) <doi:10.1007/978-3-540-24741-8_44> which, with some loss of information, can both reduce the size of the data as well as provide corrective smoothing mechanisms to help reduce the impact of measurement error. This is an improvement on the well-known Douglas-Peucker algorithm for segmentation that operates not on the basis of perpendicular distances. Top-Down Time Ratio segmentation allows for disparate sampling time intervals by calculating the distance between locations and segments with respect to time. Provided a trajectory with timestamps, tdtr() returns a set of straight- line segments that can represent the full trajectory. McCool, Lugtig, and Schouten (2022) <doi:10.1007/s11116-022-10328-2> describe this method as implemented here in more detail.

Maintained by Danielle McCool. Last updated 3 years ago.

2.70 score 4 scripts

pik-piam

rOpenscmRunner:Run different simple climate models from R using a unified interface

Using openscm-runner, you can run different simple climate models using a unified API. It supports emissions-driven runs only. rOpenscmRunner is a wrapper to easily use openscm-runner from R.

Maintained by Mika Pflüger. Last updated 1 years ago.

1 stars 2.70 score

obreschkow

nbody:Gravitational N-Body Simulation

Run simple direct gravitational N-body simulations. The package can access different external N-body simulators (e.g. GADGET-4 by Springel et al. (2021) <doi:10.48550/arXiv.2010.03567>), but also has a simple built-in simulator. This default simulator uses a variable block time step and lets the user choose between a range of integrators, including 4th and 6th order integrators for high-accuracy simulations. Basic top-hat smoothing is available as an option. The code also allows the definition of background particles that are fixed or in uniform motion, not subject to acceleration by other particles.

Maintained by Danail Obreschkow. Last updated 6 months ago.

cpp

2.48 score 1 scripts

nomahi

NMA:Network Meta-Analysis Based on Multivariate Meta-Analysis Models

Network meta-analysis tools based on contrast-based approach using the multivariate meta-analysis and meta-regression models (Noma et al. (2023) <Forthcoming>). Standard analysis tools for network meta-analysis and meta-regression (e.g., synthesis analysis, ranking analysis, and creating league table) are available by simple commands. For inconsistency analyses, the local and global inconsistency tests based on the Higgins' design-by-treatment interaction model can be applied. Also, the side-splitting and the Jackson's random inconsistency model are available. Standard graphical tools for network meta-analysis (e.g., network plot, ranked forest plot, and transitivity analysis) can also be utilized. For the synthesis analyses, the Noma-Hamura's improved REML (restricted maximum likelihood)-based methods (Noma et al. (2023) <doi:10.1002/jrsm.1652> <doi:10.1002/jrsm.1651>) are adopted as the default methods.

Maintained by Hisashi Noma. Last updated 11 months ago.

1.00 score 6 scripts

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