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r-mertools
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public |
Provides methods for extracting results from mixed-effect model objects fit with the 'lme4' package. Allows construction of prediction intervals efficiently from large scale linear and generalized linear mixed-effects models.
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2025-09-24 |
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r-dagwood
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public |
DAGs With Omitted Objects Displayed (DAGWOOD) is a framework to help reveal key hidden assumptions in a causal DAG. This package provides an implementation of the DAGWOOD algorithm. Further description can be found in Haber et al (2022) <DOI:10.1016/j.annepidem.2022.01.001>.
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2025-09-24 |
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r-spiralize
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public |
It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>. It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high resolution. 2. It is efficient for time series data to reveal periodic patterns.
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2025-09-24 |
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r-tmle
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public |
Targeted maximum likelihood estimation of point treatment effects (Targeted Maximum Likelihood Learning, The International Journal of Biostatistics, 2(1), 2006. This version automatically estimates the additive treatment effect among the treated (ATT) and among the controls (ATC). The tmle() function calculates the adjusted marginal difference in mean outcome associated with a binary point treatment, for continuous or binary outcomes. Relative risk and odds ratio estimates are also reported for binary outcomes. Missingness in the outcome is allowed, but not in treatment assignment or baseline covariate values. The population mean is calculated when there is missingness, and no variation in the treatment assignment. The tmleMSM() function estimates the parameters of a marginal structural model for a binary point treatment effect. Effect estimation stratified by a binary mediating variable is also available. An ID argument can be used to identify repeated measures. Default settings call 'SuperLearner' to estimate the Q and g portions of the likelihood, unless values or a user-supplied regression function are passed in as arguments.
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2025-09-24 |
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r-autoplotly
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public |
Functionalities to automatically generate interactive visualizations for popular statistical results supported by 'ggfortify', such as time series, PCA, clustering and survival analysis, with 'plotly.js' <https://plot.ly/> and 'ggplot2' style. The generated visualizations can also be easily extended using 'ggplot2' and 'plotly' syntax while staying interactive.
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2025-09-24 |
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r-detectseparation
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public |
Provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in generalized linear models with categorical responses. The pre-fit methods apply on binomial-response generalized liner models such as logit, probit and cloglog regression, and can be directly supplied as fitting methods to the glm() function. They solve the linear programming problems for the detection of separation developed in Konis (2007, <https://ora.ox.ac.uk/objects/uuid:8f9ee0d0-d78e-4101-9ab4-f9cbceed2a2a>) using 'ROI' <https://cran.r-project.org/package=ROI> or 'lpSolveAPI' <https://cran.r-project.org/package=lpSolveAPI>. The post-fit methods apply to models with categorical responses, including binomial-response generalized linear models and multinomial-response models, such as baseline category logits and adjacent category logits models; for example, the models implemented in the 'brglm2' <https://cran.r-project.org/package=brglm2> package. The post-fit methods successively refit the model with increasing number of iteratively reweighted least squares iterations, and monitor the ratio of the estimated standard error for each parameter to what it has been in the first iteration. According to the results in Lesaffre & Albert (1989, <https://www.jstor.org/stable/2345845>), divergence of those ratios indicates data separation.
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2025-09-24 |
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r-snotelr
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public |
Programmatic interface to the 'SNOTEL' snow data (<https://www.nrcs.usda.gov/wps/portal/wcc/home>). Provides easy downloads of snow data into your R work space or a local directory. Additional post-processing routines to extract snow season indexes are provided.
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2025-09-24 |
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r-rcdk
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public |
Allows the user to access functionality in the 'CDK', a Java framework for chemoinformatics. This allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and so on. In addition, the 'CDK' API allows the user to view structures in 2D.
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2025-09-24 |
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r-enrichr
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public |
Provides an R interface to all 'Enrichr' databases. 'Enrichr' is a web-based tool for analysing gene sets and returns any enrichment of common annotated biological features. Quoting from their website 'Enrichment analysis is a computational method for inferring knowledge about an input gene set by comparing it to annotated gene sets representing prior biological knowledge.' See (<http://amp.pharm.mssm.edu/Enrichr/>) for further details.
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2025-09-24 |
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r-cleanrmd
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public |
A collection of clean 'R Markdown' HTML document templates using classy-looking classless CSS styles. These documents use a minimal set of dependencies but still look great, making them suitable for use a package vignettes or for sharing results via email.
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2025-09-24 |
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r-measurements
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public |
Collection of tools to make working with physical measurements easier. Convert between metric and imperial units, or calculate a dimension's unknown value from other dimensions' measurements.
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2025-09-24 |
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r-reportroc
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public |
Provides an easy way to report the results of ROC analysis, including: 1. an ROC curve. 2. the value of Cutoff, AUC (Area Under Curve), ACC (accuracy), SEN (sensitivity), SPE (specificity), PLR (positive likelihood ratio), NLR (negative likelihood ratio), PPV (positive predictive value), NPV (negative predictive value).
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2025-09-24 |
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nccmp
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public |
Comparison of NetCDF files
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2025-09-24 |
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partsegcore-compiled-backend
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public |
PartSeg is a GUI and a library for segmentation algorithms. This is PartSegCore, its compiled backend.
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2025-09-24 |
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r-downloadthis
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public |
Implement download buttons in HTML output from 'rmarkdown' without the need for 'runtime:shiny'.
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2025-09-24 |
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xarray-eopf
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public |
A backend implementation for xarray that allows for analysis-ready reading of ESA EOPF data products.
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2025-09-24 |
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r-thinkr
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public |
Some tools for cleaning up messy 'Excel' files to be suitable for R. People who have been working with 'Excel' for years built more or less complicated sheets with names, characters, formats that are not homogeneous. To be able to use them in R nowadays, we built a set of functions that will avoid the majority of importation problems and keep all the data at best.
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2025-09-24 |
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r-clusterrepro
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public |
This is a function for validating microarray clusters via reproducibility, based on the paper referenced below.
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2025-09-24 |
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r-ggpage
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public |
Facilitates the creation of page layout visualizations in which words are represented as rectangles with sizes relating to the length of the words. Which then is divided in lines and pages for easy overview of up to quite large texts.
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2025-09-24 |
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r-sever
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public |
Customise 'Shiny' disconnected screens as well as sanitize error messages to make them clearer and friendlier to the user.
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2025-09-24 |
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r-rolocisccnbs
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public |
A colour list and colour metric based on the ISCC-NBS System of Color Designation for use with the 'roloc' package for converting colour specifications to colour names.
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2025-09-24 |
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r-ggpointless
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public |
Add minimal emphasis to your plots. 'ggpointless' is a small extension of the 'ggplot2' library making it easy to highlight the first, or last observations, sample minimum and maximum. The goal is to provide additional context. Or just some visual sugar.
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2025-09-24 |
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r-castor
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public |
Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
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2025-09-24 |
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r-moonbook
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public |
Several analysis-related functions for the book entitled "R statistics and graph for medical articles" (written in Korean), version 1, by Keon-Woong Moon with Korean demographic data with several plot functions.
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2025-09-24 |
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r-kernsmoothirt
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public |
Fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools. The kernel smoothing is based on methods described in Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman & Hall, London.
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2025-09-24 |
