by-parameter.Rmd

---
output: github_document
title: By parameter
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = FALSE)
library(yaml)
library(data.table)
source("functions.R")
```

```{r results='asis'}
menu_maker("")
```

INDEX

```{r listing-reading}
fns <- list.files("../data", full.names = TRUE) |> sort()
fns <- fns[!grepl("README[.]md$", fns)]
headers <- get_headers(fns)
```


```{r create-tables, results='asis'}
tab <- lapply(names(headers), \(h) {
  
  f        <- headers[[h]]
  
  title    <- f$`title-paper`
  software <- f$`software-package`
  doi      <- f$doi
  
  # Processing software tools
  software <- if (length(software)) {
    sprintf(
      "[%s (%s)](%s)",
      sapply(software, "[[", 2),
      sapply(software, "[[", 1),
      sapply(software, "[[", 3)
    ) |> paste(collapse = ", ")
  } else
    ""
  
  # Processing DOI
  doi <- if (length(doi)) {
    sprintf("[%s](https://doi.org/%s)", doi, doi)
  } else 
    ""
  
  # Processing parameters
  parameters <- f$parameters
  parameters <- if (length(parameters))
    paste0("`", parameters, "`", collapse = ", ")
  else
    ""
  
  # Putting all together
  data.table(
    title    = paste(
      null2empty(title),
      sprintf("[(**link**)](%s)", gsub("[.]{2}/data", "entries", h))
      ),
    software = software,
    doi      = null2empty(doi),
    parameters = parameters
  )
  
}) |> rbindlist(fill = TRUE)

tab$files <- names(headers)

tab[, parameters := tolower(parameters)]

# Building parameters entries
parameters <- strsplit(tab$parameters, split = "\\s*,\\s*") |>
  unlist(recursive = TRUE) |>
  sort()

# Extracting the first letter word (to make an index)
parameters <- data.table(
  parameters = parameters,
  first   = gsub("^`([[:alnum:]]).+", "\\1", parameters)
)

for (l in sort(unique(parameters$first))) {
  cat("**", toupper(l), "** ", sep = "")
  tmp <- parameters[first == l, c(parameters)] |>
    unique()
  
  linker(tmp, tmp) |>
    cat(sep = ", ")
  
  cat("\n\n")
}
```

# Details

```{r printer, results='asis'}
for (kw in sort(unique(parameters$parameters))) {
  
  cat("\n\n## ", gsub("`", "", kw), "\n\n")
  
  entries <- tab[grepl(kw, parameters)]
  
  cat(
    sprintf(
      "%i. %s %s",
      1:nrow(entries),
      entries$title,
      fifelse(entries$software == "", "", paste0("(*software*: ", entries$software, ")"))
      ),
    sep = "\n"
  )

}
```