Numbering figures of plot(glm) in rmarkdown

Question

I created a Rmarkdown document and want to number my figures. What I am struggling with is if a plot gives me several output like plot("glm Object")?

Here is a minimal example:

---
documentclass: article
output: pdf_document
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(fig.path = 'figures/', fig.pos = 'htb!', echo = TRUE)
```

```{r, fig.cap = "Test"}
data(warpbreaks)
daten <- as.data.frame(warpbreaks)
test <- glm(breaks ~ tension + wool , family = "poisson", data = daten)
plot(test)
```

Answer 1

You can use a lesser-known feature of Rmarkdown and add captions to subfigures: https://stackoverflow.com/a/49086985/7347699

For your example:

---
documentclass: article
output: pdf_document
header-includes:
   - \usepackage{subfig}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(fig.path = 'figures/', fig.pos = 'htb!', echo = TRUE)
```

```{r, fig.cap = "Test",  fig.subcap=c('sub 1', 'sub 2', 'sub 3', 'sub 4'), out.width='.49\\linewidth', fig.asp=1, fig.ncol = 2}
data(warpbreaks)
daten <- as.data.frame(warpbreaks)
test <- glm(breaks ~ tension + wool , family = "poisson", data = daten)
plot(test)
```

Alternative Approach

A potentially easier way plotting multiple R plots is to use the par function before plotting. The benefit of this is its simplicity, and that you do not need to load addition LaTeX packages in the header. However, it is not possible to add a sub-caption to each plot.

---
documentclass: article
output: pdf_document
---

```{r, fig.cap = "Test", fig.asp = 1}
data(warpbreaks)
daten <- as.data.frame(warpbreaks)
test <- glm(breaks ~ tension + wool , family = "poisson", data = daten)

par(mfrow = c(2, 2))
plot(test)
```