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Taxonomix keys for Rmarkdown/bookdown

heibl 2y ago

Dear Yihui (and anybody else who is interested)

I've been following your work for quite some time. The power of these tools is so amazing! Thanks a lot!

Being originally a plant systematist, I have developed a LaTeX package (14 years ago and surely not perfect) that helped me to include taxonomic identification keys into LaTeX documents:

https://ctan.org/pkg/bracketkey?lang=de

Now with bookdown being such an inspiring tool, I felt that it would be great to have such a functionality ported to Rmarkdown. I am quite aware that something like this is only a niche product - compared to tables or figures. But, anyway, maybe you are interested and have the time to take a glimpse of the bracketkey package and offer your appraisal: would it be easy to accomplish or a waste of time or something in between? How would you go about it?

Best regards,
Christoph

1 Reply

yihui 2y ago

Hi Christoph, thanks for the information! I'm afraid that I don't have enough expertise to evaluate this LaTeX package after I read the documentation and example. If you have a proof-of-concept implementation in R, I can probably understand it better. Or perhaps other people can share their insights, which I'd love to hear.

heibl 2y ago

Dear Yihui,
thanks, your answer brought it right to my mind: it is possible to build dichotomous identification keys directly in R with kable. Only a small function key is needed. The input object x (attached as Poa.csv) is a tibble with columns Couplet, Lead, Description, and Result. Being a dichotomous key each couplet contains two leads.

key <- function(x){
  
  # darkred: #8b0000
  
  ## Which leads (rows) contain forward pointers
  x <- mutate(x, isPointer = str_detect(Result, pattern = "^[[:digit:]]*$"))
  
  ## Prepare backward pointers
  bp <- x %>% 
    group_by(Couplet) %>%
    mutate(allPointer = all(isPointer)) %>%
    ungroup() %>%
    filter(Lead == 2, allPointer) %>%
    select(Couplet, Result)
  
  ## Style for forward pointers and species names
  x <- mutate(x, Result = ifelse(
    isPointer, 
    paste0("[", Result, "]{style='float:right;font-weight:bold;color:#808080'}"), 
    paste0("[", Result, "]{style='float:right;font-weight:bold;font-style:italic'}")))
  
  ## Set backwards pointers (don't know how to do with pure dplyr)
  x <- mutate(x, bp = 0)
  for (i in 1:nrow(bp)){
    x$bp[x$Couplet == bp$Result[i] & x$Lead == 1] <- bp$Couplet[i]
  }
  x <- x %>% 
    mutate(Couplet = paste0("[", Couplet, c("", "*"), "]{style='font-weight:bold'}")) %>%
    mutate(Couplet = if_else(
      bp == 0, Couplet,
      paste0(Couplet, paste0("(", bp, ")"))))
  
  ### Prepare kable object       
  x %>% mutate(Description = paste(Description, Result)) %>%
    select(Couplet, Description) %>%
    kbl(col.names = NULL, align = "ll", escape = FALSE) %>%
    column_spec(1, color = "#808080", width_min = "8mm",
                extra_css = "vertical-align:top;") %>%
    column_spec(2, extra_css = "vertical-align:top;") %>%
    row_spec(seq.int(from = 2, to = nrow(x), by = 2), 
             extra_css = "border-bottom: 0.5px solid",
             hline_after = TRUE)
}

Then we can use it inside an Rmd-document to build an HTML-key:

---
title: "Identification keys for Rmarkdown"
output: 
  html_document
---

```{r setup, include=FALSE, message=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(readr)
library(stringr)
library(dplyr)
library(kableExtra)
source("key.R")
```

#### Key to meadow-grass (*Poa*) in the Bavarian Forest National Park

```{r key, message=FALSE, echo=FALSE}
x <- read_csv2("Poa.csv", locale = locale(decimal_mark = ","))
key(x)
```

As is easy as that. Of course, for longer keys, it would be nice to have forward and backward pointers cross-referenced, but I wasn't able to figure out that.

Poa.csv