Rmd_functions

# Subchunkify
# Dynamically create chunks, which fixes the interactive plots
# not rendered in loops or functions

subchunkify <- function(g, chunkname, fig_height=6, fig_width=6) {
  g_deparsed <- paste0(deparse(function() {g}), collapse = '')
  sub_chunk <- paste0("`","``{r subchunk_", chunkname, ", fig.height=", fig_height,
                      ", fig.width=", fig_width, " , echo=FALSE}",
                      "\n(", g_deparsed, ")()", "\n`", "``")
  cat(knitr::knit(text = knitr::knit_expand(text = sub_chunk), quiet = TRUE))
}


# Linkify
# Convert a file path to a link when Rmd in rendered
linkify <- function(filepath) {
  cat(paste0('\n\n[', filepath, '](', filepath, ')\n\n'))
}


# Create log file with path to running R (and thus giving clues as to
# which conda environment was used if applicable), rmarkdown::render
# parameters, messages, warnings and errors.
# Add this chunk at the begining of the Rmd

```{r global_options, include=FALSE}
# sets up global options for rendering RMarkdown into HTML.
knitr::opts_chunk$set(
    warning=TRUE,
    message=TRUE,
    error=TRUE   # technically this means keep running after an error, but will now be caught by knitr::knit_hooks$set(error = ...)
)

# log file
log_fn <- paste0(knitr::current_input(), '.log')

# sets up the redirect of messages to log file
knitr::knit_hooks$set(
  message = function(x, options) {
    cat(x, file = log_fn, append = TRUE)
    return()
  },
  warning = function(x, options) {
    cat(x, file = log_fn, append = TRUE)
    return()
  },
  error = function(x, options) {
    cat(x, file = log_fn, append = TRUE)
    return(stop(x))
  }
)

# append current run metadata
message(paste0('\n', Sys.time()))
message(paste0('Environment: ', Sys.which("R")))
if (exists("params") & !exists("params", mode='function')) {
  message(paste0('rmarkdown::render params: ', paste0(params, collapse=';')))
}
```