overview_modelling_packages.Rmd

---
title: "Overview of R Modelling Packages"
author: "Daniel Lüdecke"
output: html_document
---

```{r setup, include=FALSE}
library(knitr)
library(docxtractr)

knitr::opts_chunk$set(echo = TRUE)

docx <- read_docx("Regressionspakete.docx")
tab <- docx_extract_tbl(docx)
colnames(tab) <- c("Nature of Response", "Example", "Type of Regression", "R package or function", "Example Webpage", "Bayesian with [`brms`](https://paul-buerkner.github.io/brms/reference/brmsfamily.html)")
```

This is an overview of R packages and functions for fitting different types of regression models. For each row, the upper cells in the last column (_packages and functions_) refer to "simple" models, while the lower cells refer to their mixed models counterpart (if available and known).

This overview raises no claims towards completeness of available modelling packages. Rather, it shows commonly or more often used packages, but there a plenty of other packages as well (that might even perform better in doing those mentioned tasks - if you're aware of such packages or think that an important package or function is missing, please [file an issue](https://github.com/strengejacke/mixed-models-snippets/issues)).

## Modelling Packages

```{r echo=FALSE}
kable(tab)
```

_Note that ratios or proportions from **count data**, like `cbind(successes, failures)`, are modelled as logistic regression with `glm(cbind(successes, failures), family=binomial())`, while ratios from **continuous data** (where the response ranges from 0 to 1) are modelled using beta-regression._

_Usually, zero-inflated models are used when 0 or 1 come from a separate process or category. However, when the 0/1 values are most consistent with censoring rather than with a separate category/process, the ordered beta regression is probably a better choice (i.e., 0 mean "below detection", not "something qualitatively different happened") (Source: https://twitter.com/bolkerb/status/1577755600808775680)_

## Included packages for non-mixed models:

  - Base R: `lm()`, `glm()`
  - [AER](https://CRAN.R-project.org/package=AER): `tobit()`
  - [aod](https://CRAN.R-project.org/package=aod): `betabin()`
  - [betareg](https://CRAN.R-project.org/package=betareg): `betareg()`
  - [brglm2](https://CRAN.R-project.org/package=brglm2): `bracl()`, `brmultinom()`
  - [censReg](https://CRAN.R-project.org/package=censReg): `censReg()`
  - [cplm](https://CRAN.R-project.org/package=cplm): `cpglm()`
  - [coxph](https://CRAN.R-project.org/package=survival): `coxph()`
  - [DirichletReg](https://CRAN.R-project.org/package=DirichletReg): `DirichReg()`
  - [HRQoL](https://CRAN.R-project.org/package=HRQoL): `BBreg()`
  - [MASS](https://CRAN.R-project.org/package=MASS): `glm.nb()`, `polr()`
  - [nnet](https://CRAN.R-project.org/package=nnet): `multinom()`
  - [ordbetareg](https://cran.r-project.org/package=ordbetareg): `ordbetareg()`
  - [ordinal](https://CRAN.R-project.org/package=ordinal): `clm()`, `clm2()`
  - [pscl](https://CRAN.R-project.org/package=pscl): `zeroinfl()`, `hurdle()`
  - [statmod](https://CRAN.R-project.org/package=statmod): `tweedie()`
  - [VGAM](https://CRAN.R-project.org/package=VGAM): `vglm()`

## Included packages for mixed models:

  - [cplm](https://CRAN.R-project.org/package=cplm): `cpglmm()`
  - [coxme](https://CRAN.R-project.org/package=coxme): `coxme()`
  - [glmmTMB](https://CRAN.R-project.org/package=glmmTMB): `glmmTMB()`
  - [lme4](https://CRAN.R-project.org/package=lme4): `lmer()`, `glmer()`, `glmer.nb()`
  - [MCMCglmm](https://CRAN.R-project.org/package=MCMCglmm): `MCMCglmm()`
  - [mixor](https://CRAN.R-project.org/package=mixor): `mixor()`
  - [ordbetareg](https://cran.r-project.org/package=ordbetareg): `ordbetareg()`
  - [ordinal](https://CRAN.R-project.org/package=ordinal): `clmm()`, `clmm2()`
  - [smicd](https://cran.r-project.org/package=smicd): `semLme()`
  
## Included packages for Bayesian models (mixed an non-mixed):

  - [brms](https://cran.r-project.org/package=brms): `brm()`

## Handout

There is a [handout](regression_pkgs_handout.pdf) in PDF-format.

![](by2-small.png)