Dichotomous and polytomous data analysis and their scoring using the unidimensional Item Response Theory model (Chalmers (2012) <doi:10.18637/jss.v048.i06>) with user-friendly graphic User Interface. Suitable for beginners who are learning item response theory.

This package provides a set of functions to calculate solar irradiance and insolation on Mars horizontal and inclined surfaces. Based on NASA Technical Memoranda 102299, 103623, 105216, 106321, and 106700, i.e. the canonical Mars solar radiation papers.

Maximum likelihood estimation for generalized linear mixed models via Monte Carlo EM. For a description of the algorithm see Brian S. Caffo, Wolfgang Jank and Galin L. Jones (2005) <DOI:10.1111/j.1467-9868.2005.00499.x>.

Interact seamlessly with Open Target GraphQL endpoint to query and retrieve tidy data tables, facilitating the analysis of gene, disease, drug, and genetic data. For more information about the Open Target API (<https://platform.opentargets.org/api>).

An extension to the Regression Modeling Strategies package that facilitates plotting ordinal regression model predictions together with confidence intervals for each dependent variable level. It also adds a functionality to plot the model summary as a modifiable object.

An open-access tool/framework to download, validate, visualize, and analyze multi-source precipitation data. More information and an example of implementation can be found in Vargas Godoy and Markonis (2023, <doi:10.1016/j.envsoft.2023.105711>).

Automate formation and evaluation of polynomial regression models. The motivation for this package is described in Polynomial Regression As an Alternative to Neural Nets by Xi Cheng, Bohdan Khomtchouk, Norman Matloff, and Pete Mohanty (<arXiv:1806.06850>).

An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) <doi:10.1101/2021.02.01.429207> for more details.

This package provides functions to speed up work flow for hydrological analysis. Focused on Australian climate data (SILO climate data), hydrological models (eWater Source) and in particular South Australia (<https://water.data.sa.gov.au> hydrological data).

The systemPipeShiny (SPS) framework comes with many useful utility functions. However, installing the whole framework is heavy and takes some time. If you like only a few useful utility functions from SPS, install this package is enough.

This package provides a client for running SPARQL queries directly from R. SPARQL (short for SPARQL Protocol and RDF Query Language) is a query language used to retrieve and manipulate data stored in RDF (Resource Description Framework) format.

This package provides a wrapper for the TexTra API <https://mt-auto-minhon-mlt.ucri.jgn-x.jp/>, a web service for translating texts between different languages. TexTra API account is required to use the service.

Draws tornado plots for model sensitivity to univariate changes. Implements methods for many modeling methods including linear models, generalized linear models, survival regression models, and arbitrary machine learning models in the caret package. Also draws variable importance plots.

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

Search, composite, and download Google Earth Engine imagery with reticulate bindings for the Python module geedim by Dugal Harris. Read the geedim documentation here: <https://geedim.readthedocs.io/>. Wrapper functions are provided to make it more convenient to use geedim to download images larger than the Google Earth Engine size limit <https://developers.google.com/earth-engine/apidocs/ee-image-getdownloadurl>. By default the "High Volume" API endpoint <https://developers.google.com/earth-engine/cloud/highvolume> is used to download data and this URL can be customized during initialization of the package.

User-friendly interface utilities for MCMC models via Just Another Gibbs Sampler (JAGS), facilitating the use of parallel (or distributed) processors for multiple chains, automated control of convergence and sample length diagnostics, and evaluation of the performance of a model using drop-k validation or against simulated data. Template model specifications can be generated using a standard lme4-style formula interface to assist users less familiar with the BUGS syntax. A JAGS extension module provides additional distributions including the Pareto family of distributions, the DuMouchel prior and the half-Cauchy prior.

This package provides an integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. Currently only Affymetrix oligonucleotide analysis is supported.

This package provides functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.

This package implements transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

PSIplot is an R package for generating plots of percent spliced-in (PSI) values of alternatively-spliced exons that were computed by vast-tools, an RNA-Seq pipeline for alternative splicing analysis. The plots are generated using ggplot2.

The lattice package provides a powerful and elegant high-level data visualization system inspired by Trellis graphics, with an emphasis on multivariate data. Lattice is sufficient for typical graphics needs, and is also flexible enough to handle most nonstandard requirements.

This package provides a collection of functions to compute the standardized effect sizes for experiments (Cohen d, Hedges g, Cliff delta, Vargha-Delaney A). The computation algorithms have been optimized to allow efficient computation even with very large data sets.

This package enables you to estimate the p-values for predictors x against target variable y in Lasso regression, using the regularization strength when each predictor enters the active set of regularization path for the first time as the statistic.

Webshot makes it easy to take screenshots of web pages from within R. It can also run Shiny applications locally and take screenshots of the application; and it can render and screenshot static as well as interactive R Markdown documents.