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: .

Latent Variable Models Diagnostics

Diagnostics and visualization tools for latent variable models fitted with 'lavaan' (Rosseel, 2012 ). The package provides fast, parallel-safe factor-score prediction (lavPredict_parallel()), data augmentation with model predictions, residuals, delta-method standard errors and confidence intervals (augment()), and model-based latent grids for continuous, ordinal, or mixed indicators (prepare()). It offers item-level empirical versus model curve comparison using generalized additive models for both continuous and ordinal indicators (item_data(), item_plot()) via 'mgcv' (Wood, 2017, ISBN:9781498728331), residual diagnostics including residual correlation tables and plots (resid_cor(), resid_corrplot()) using 'corrplot' (Wei and Simko, 2021 < https://github.com/taiyun/corrplot>), and Q–Q checks of residual z-statistics (resid_qq()), optionally with non-overlapping labels from 'ggrepel' (Slowikowski, 2024 < https://CRAN.R-project.org/package=ggrepel>). Heavy computations are parallelized via 'future'/'furrr' (Bengtsson, 2021 ; Vaughan and Dancho, 2018 < https://CRAN.R-project.org/package=furrr>). Methods build on established literature and packages listed above.

Smooth Survival Models, Including Generalized Survival Models

R implementation of generalized survival models (GSMs), smooth accelerated failure time (AFT) models and Markov multi-state models. For the GSMs, g(S(t|x))=eta(t,x) for a link function g, survival S at time t with covariates x and a linear predictor eta(t,x). The main assumption is that the time effect(s) are smooth . For fully parametric models with natural splines, this re-implements Stata's 'stpm2' function, which are flexible parametric survival models developed by Royston and colleagues. We have extended the parametric models to include any smooth parametric smoothers for time. We have also extended the model to include any smooth penalized smoothers from the 'mgcv' package, using penalized likelihood. These models include left truncation, right censoring, interval censoring, gamma frailties and normal random effects , and copulas. For the smooth AFTs, S(t|x) = S_0(t*eta(t,x)), where the baseline survival function S_0(t)=exp(-exp(eta_0(t))) is modelled for natural splines for eta_0, and the time-dependent cumulative acceleration factor eta(t,x)=\int_0^t exp(eta_1(u,x)) du for log acceleration factor eta_1(u,x). The Markov multi-state models allow for a range of models with smooth transitions to predict transition probabilities, length of stay, utilities and costs, with differences, ratios and standardisation.

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.

Spatial and Spatiotemporal SPDE-Based GLMMs with 'TMB'

Implements spatial and spatiotemporal GLMMs (Generalized Linear Mixed Effect Models) using 'TMB', 'fmesher', and the SPDE (Stochastic Partial Differential Equation) Gaussian Markov random field approximation to Gaussian random fields. One common application is for spatially explicit species distribution models (SDMs). See Anderson et al. (2024) .

Extra Graphical Utilities Based on Lattice

Building on the infrastructure provided by the lattice package, this package provides several new high-level functions and methods, as well as additional utilities such as panel and axis annotation functions.

Vector Generalized Linear and Additive Models

An implementation of about 6 major classes of statistical regression models. The central algorithm is Fisher scoring and iterative reweighted least squares. At the heart of this package are the vector generalized linear and additive model (VGLM/VGAM) classes. VGLMs can be loosely thought of as multivariate GLMs. VGAMs are data-driven VGLMs that use smoothing. The book "Vector Generalized Linear and Additive Models: With an Implementation in R" (Yee, 2015) gives details of the statistical framework and the package. Currently only fixed-effects models are implemented. Many (100+) models and distributions are estimated by maximum likelihood estimation (MLE) or penalized MLE. The other classes are RR-VGLMs (reduced-rank VGLMs), quadratic RR-VGLMs, doubly constrained RR-VGLMs, quadratic RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction models)---these classes perform constrained and unconstrained quadratic ordination (CQO/UQO) models in ecology, as well as constrained additive ordination (CAO). Hauck-Donner effect detection is implemented. Note that these functions are subject to change; see the NEWS and ChangeLog files for latest changes.

Political Science Computational Laboratory

Bayesian analysis of item-response theory (IRT) models, roll call analysis; computing highest density regions; maximum likelihood estimation of zero-inflated and hurdle models for count data; goodness-of-fit measures for GLMs; data sets used in writing and teaching; seats-votes curves.

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.