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Generalized Kernel Regularized Least Squares
Kernel regularized least squares, also known as kernel ridge regression,
is a flexible machine learning method. This package implements this method by
providing a smooth term for use with 'mgcv' and uses random sketching to
facilitate scalable estimation on large datasets. It provides additional
functions for calculating marginal effects after estimation and for use with
ensembles ('SuperLearning'), double/debiased machine learning ('DoubleML'),
and robust/clustered standard errors ('sandwich'). Chang and Goplerud (2024)
Distributional Stochastic Frontier Analysis
Framework to fit distributional stochastic frontier models. Casts the stochastic frontier model into the flexible framework of distributional regression or otherwise known as General Additive Models of Location, Scale and Shape (GAMLSS). Allows for linear, non-linear, random and spatial effects on all the parameters of the distribution of the output, e.g. effects on the production or cost function, heterogeneity of the noise and inefficiency. Available distributions are the normal-halfnormal and normal-exponential distribution. Estimation via the fast and reliable routines of the 'mgcv' package. For more details see
Create Elegant Data Visualisations Using the Grammar of Graphics
A system for 'declaratively' creating graphics, based on "The Grammar of Graphics". You provide the data, tell 'ggplot2' how to map variables to aesthetics, what graphical primitives to use, and it takes care of the details.
Predict and Visualize Population-Level Changes in Allele Frequencies in Response to Climate Change
Methods (
Meta-Analysis of Generalized Additive Models
Meta-analysis of generalized additive
models and generalized additive mixed models. A typical use case is
when data cannot be shared across locations, and an overall meta-analytic
fit is sought. 'metagam' provides functionality for removing individual
participant data from models computed using the 'mgcv' and 'gamm4' packages such
that the model objects can be shared without exposing individual data.
Furthermore, methods for meta-analysing these fits are provided. The implemented
methods are described in Sorensen et al. (2020),
Transformation Models with Mixed Effects
Likelihood-based estimation of mixed-effects transformation models
using the Template Model Builder ('TMB', Kristensen et al., 2016)
Generalized Additive Models with Flexible Response Functions
Standard generalized additive models assume a response function,
which induces an assumption on the shape of the distribution of the
response. However, miss-specifying the response function results in biased
estimates. Therefore in Spiegel et al. (2017)
Easy Graphs for Data Visualisation and Linear Models for ANOVA
Easily explore data by plotting graphs with a few lines of code. Use these ggplot() wrappers to quickly draw graphs of scatter/dots with box-whiskers, violins or SD error bars, data distributions, before-after graphs, factorial ANOVA and more. Customise graphs in many ways, for example, by choosing from colour blind-friendly palettes (12 discreet, 3 continuous and 2 divergent palettes). Use the simple code for ANOVA as ordinary (lm()) or mixed-effects linear models (lmer()), including randomised-block or repeated-measures designs, and fit non-linear outcomes as a generalised additive model (gam) using mgcv(). Obtain estimated marginal means and perform post-hoc comparisons on fitted models (via emmeans()). Also includes small datasets for practising code and teaching basics before users move on to more complex designs. See vignettes for details on usage < https://grafify.shenoylab.com/>. Citation:
Community Ecology Package
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Companion to Applied Regression
Functions to Accompany J. Fox and S. Weisberg, An R Companion to Applied Regression, Third Edition, Sage, 2019.