Reprex.qmd

---
title: "Dynamic Table Captions"
author: "Jon Peake"
format: html
editor: visual
---

## Example 1: from a column value

If the information for our dynamic caption is contained within a column in the dataset (say, a single static column for the species or gear), we can extract the information from the columns of interest. Let's create a dataset with a constant species and gear.

```{r}
#| label: createdata_colval
# Create a dummy dataset
dat <- data.frame(species = rep('Mycteroperca microlepis', 10),
                  gear = rep(c('HL','LL','SP','UA'),5),
                  age = 1:20,
                  size = seq(1,100,5))

write.csv(dat, file = 'dat_colval.csv',row.names = F)
```

We can make a dynamic label in a few ways. If a caption with a similar format is going to be used multiple times throughout the document, it might be easiest to make this a function. Otherwise, we can just use a standard call to `paste`:

```{r}
# Make dynamic label
# read in the data file
library(tidyverse)
dat <- read.csv('dat_colval.csv') %>%
  mutate(gear = factor(gear),
         gear_name = factor(case_when(gear == 'HL' ~ 'hook and line',
                               gear == 'LL' ~ 'longline',
                               gear == 'SP' ~ 'spear',
                               gear == 'UA' ~ 'unassigned gear code')))
  

# extract the species name
spp <- unique(dat$species)

# extract the gear
gear <- levels(dat$gear)

gear_name <- levels(dat$gear_name)

gear_caption_string <- paste0(gear_name,' (',gear,')')

# paste together the caption
cap <- paste0('Age and length of ',
             spp,
             ' from ',
             paste(gear_caption_string[-length(gear_caption_string)],collapse = ', '),
             ', and ',
             gear_caption_string[length(gear_caption_string)],
             '.')
cap
```

We can assign the caption using the `#| tbl-cap` option in our table code chunk. To input an r variable, we use the following notation:

```         
#| tbl-cap: !expr cap
```

By using `!expr` we can insert an R variable or even a full expression into the caption. This example inserts the value of `cap` into the caption.

```{r}
#| label: tbl-colval
#| tbl-cap: !expr cap

# Make table using kable
library(knitr)
kable(dat)
```

## Example 2: from a column header

If instead our dynamic information is in a column header, we can use the `colnames` function to extract the appropriate information. This may be useful if the structure of the data is constant but a value column changes names across datasets.

```{r}
#| label: createdata_colname
# Create a dummy dataset
dat <- data.frame(species = rep('Mycteroperca microlepis', 10),
                  SL = 1:10,
                  FL = 1:10)

write.csv(dat, file = 'dat_colname.csv',row.names = F)
```

```{r}
# Make dynamic label
# read in the data file
dat <- read.csv('dat_colname.csv')

# extract the species name
spp <- unique(dat$species)

# extract the length types
param_1 <- colnames(dat)[2]

param_2 <- colnames(dat)[3]

# paste together the caption
cap <- paste(spp,
             param_1,
             'vs.',
             param_2
             )
cap
```

```{r}
#| label: fig-colname
#| fig-cap: !expr cap

# Make plot using ggplot
library(ggplot2)
ggplot(dat) + geom_point(aes(x = SL, y = FL))
```