Functions for phylocom integration, community analyses, null-models, traits and evolution. Implements numerous ecophylogenetic approaches including measures of community phylogenetic and trait diversity, phylogenetic signal, estimation of trait values for unobserved taxa, null models for community and phylogeny randomizations, and utility functions for data input/output and phylogeny plotting. A full description of package functionality and methods are provided by Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.

Fast regularization paths for sparse Gaussian, binomial, Poisson,
    square-root-lasso, and multinomial models with lasso, smoothly clipped
    absolute deviation, or minimax concave penalties. Computation uses
    pathwise coordinate optimization, active-set updates, warm starts,
    screening rules, Proximal Newton iterations, quadratic majorization, and
    adaptive local linear approximation where appropriate. Core solvers are
    implemented in C++, and coefficient paths are returned as
    Matrix-compatible objects.

Contains functions to fit proportional hazards (PH) model to partly interval-censored (PIC) data (Pan et al. (2020) <doi:10.1177/0962280220921552>), PH model with spatial frailty to spatially dependent PIC data (Pan and Cai (2021) <doi:10.1080/03610918.2020.1839497>), and mixed effects PH model to clustered PIC data. Each random intercept/random effect can follow both a normal prior and a Dirichlet process mixture prior. It also includes the corresponding functions for general interval-censored data.

Provides a 'Shiny' input widget, pasteBoxInput, 
    that allows users to paste images directly into a 'Shiny' 
    application. The pasted images are captured as Base64 
    encoded strings and can be used within the application 
    for various purposes, such as display or further processing. 
    This package is particularly useful for applications that 
    require easy and quick image uploads without the need for 
    traditional file selection dialog boxes.