This package provides functions for phylogenetic analysis (Castiglione et al., 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
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>.
Optimizing methods for liquid chromatography coupled to mass spectrometry (LC-MS) poses a nontrivial challenge. The rawDiag package facilitates rational method optimization by generating MS operator-tailored diagnostic plots of scan-level metadata. The package is designed for use on the R shell or as a Shiny application on the Orbitrap instrument PC.
This package provides a simple and flexible way to generate Circos 2D track plot images. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics packages that comes with the base installation.
(guix-science-nonfree packages bioinformatics)This package provides helper functions to do pairwise comparisons of commonly covered CpG sites in single-cell DNA Methylation data.
Animate Shiny and R Markdown content when it comes into view using animate-css effects thanks to jQuery AniView'.
Create APA style text from analyses for use within R Markdown documents. Descriptive statistics, confidence intervals, and cell sizes are reported.
Client package for the AWS Key Management Service <https://aws.amazon.com/kms/>, a cloud service for managing encryption keys.
Use Newton's method, coordinate descent, and METIS clustering to solve the L1 regularized Gaussian MLE inverse covariance matrix estimation problem.
The CloudOS client library for R makes it easy to interact with CloudOS in the R environment for analysis.
It provides functions to bootstrap Credit Curves from market quotes (Credit Default Swap - CDS - spreads) and price Credit Default Swaps - CDS.
Design, conduct and analyze DCEs from a virtual interface in shiny. Reference: Perez-Troncoso, D. (2022) <https://github.com/danielpereztr/DCEtool>.
Data sets and sample analyses from Jay L. Devore (2008), "Probability and Statistics for Engineering and the Sciences (7th ed)", Thomson.
Shows you which rows have changed between two data frames with the same column structure. Useful for diffing slowly mutating data.
Offers robust tools to identify and manage incomplete responses in survey datasets, thereby enhancing the quality and reliability of research findings.
This package provides a collection of utility functions to download and manage data sets from the Internet or from other sources.
The FastRCS algorithm of Vakili and Schmitt (2014) for robust fit of the multivariable linear regression model and outliers detection.
It provides materials (i.e. serial axes objects, Andrew's plot, various glyphs for scatter plot) to visualize high dimensional data.
Generation of survival data with one (binary) time-dependent covariate. Generation of survival data arising from a progressive illness-death model.
Implementation of the two error variance estimation methods in high-dimensional linear models of Yu, Bien (2017) <arXiv:1712.02412>.
Th-U-Pb electron microprobe age dating of monazite, as originally described in <doi:10.1016/0009-2541(96)00024-1>.
Interface to NatureServe (<https://www.natureserve.org/>). Includes methods to get data, image metadata, search taxonomic names, and make maps.
Estimates corrected Procrustean correlation between matrices for removing overfitting effect. Coissac Eric and Gonindard-Melodelima Christelle (2019) <doi:10.1101/842070>.
Routines for flexible functional form estimation via basis regression, with model selection via the adaptive LASSO or SCAD to prevent overfitting.