Description: Calculates and plots the SiZer map for scatterplot data.
A SiZer map is a way of examining when the p-th derivative of a
scatterplot-smoother is significantly negative, possibly zero
or significantly positive across a range of smoothing

Authors@R: person("Derek", "Sonderegger", email="derek.sonderegger@gmail.com", role=c('aut','cre'))
Description: Calculates and plots the SiZer map for scatterplot data.  A
SiZer map is a way of examining when the p-th derivative of a
scatterplot-smoother is significantly negative, possibly zero or
significantly positive across a range of smoothing bandwidths.

Imports: stats, graphics, splines, boot, ggplot2, dplyr, tidyr, rlang

Title: Nonparametric Estimation by the Method of Sieves
Description: Performs multivariate nonparametric regression/classification by the method of sieves (or using orthogonal series). The method is suitable for continuous/binary problems with multivariate or moderate high-dimensional features (dimension < 100). The main estimator in this package, penalized sieve estimator, is adaptive to the feature dimension with provable theoretical guarantees. Moreover, such a method is computationally tractable in the sense it typically has a polynomial dependence (rather than an exponential one) on the feature dimension and an almost linear dependence on the sample size. Details of the methods and model assumptions can be found in: Tianyu Zhang, and Noah Simon (2022) <arXiv:2206.02994>.
Imports: Rcpp (>= 1.0.7), combinat, glmnet, methods

Description: Interfaces with the 'SigOpt' API. More info at <https://sigopt.com>.

Title: Identify and Visualize Significantly Responsive Branches in a
Author: John R. Stevens and Todd R. Jones
Maintainer: John R. Stevens <john.r.stevens@usu.edu>
Description: Takes a phylogenetic tree (of class phylo) and a data frame (or matrix) of corresponding tip labels and p-values, and determines the significance of the branches (families of p-values) and plots the tree with colored branches (corresponding to families) according to their levels of significance.  Also produces a CSV file with the p-values of all of the branches as well as which tips belong to which branches.  Finally, it exports a file that can be opened in FigTree that produces a colored plot (colored branches according to their significance of corresponding groups of p-values) with p-value annotations.
Imports: ape, phylobase, phyext2, RColorBrewer, phyloseq, graphics,