index.qmd

# Preface {.unnumbered}

```{r}
#| echo: false
#| cache: false

source("_common.R")
```

```{r setup}
#| include: false
#| cache: false

## get citation style
if (!file.exists("citations/ecology-letters.csl")) {
  dir.create("citations", showWarnings = FALSE)
  download.file("https://www.zotero.org/styles/ecology-letters?source=1", destfile = "citations/ecology-letters.csl")
}

## prevents GitHub from rendering book using Jekyll
# if (!file.exists("docs/.nojekyll")) {
#   file.create("docs/.nojekyll")
# }

if (!file.exists(".nojekyll")) {
  file.create(".nojekyll")
}

options(bookdown.post.latex = function(x) {
  # substitute nonbreaking spaces in \texttt{} with normal spaces
  m = gregexpr('\\\\texttt\\{[^}]+}', x)
  regmatches(x, m) = lapply(regmatches(x, m), function(z) {
    gsub('\\\\ ', ' ', z)
  })
  # only build a skeleton for the online version
  if (Sys.getenv('BOOKDOWN_FULL_PDF', '') == 'false') return(bookdown:::strip_latex_body(
    x, '\nThis PDF is only a skeleton. Please either read the free online HTML version, or purchase a hard-copy of this book.\n'
    ))
  # fix syntax highlighting:
  # \FunctionTok{tufte:}\AttributeTok{:tufte_html: default} ->
  # \FunctionTok{tufte::tufte_html:}\AttributeTok{ default}
  x = gsub('(\\\\AttributeTok\\{[^:]+:)(})(\\\\FunctionTok\\{)(:[^:]+:)', '\\1\\4\\2\\3', x)
  if (length(i <- grep('^\\\\begin\\{longtable\\}', x)) == 0) return(x)
  i1 = bookdown:::next_nearest(i, which(x == '\\toprule'))
  i2 = bookdown:::next_nearest(i, which(x == '\\endfirsthead'))
  x[i1 - 1] = paste0(x[i1 - 1], '\n\\begin{tabular}{', gsub('[^lcr]', '', gsub('.*\\[]', '', x[i])), '}')
  x[i] = '\\begin{table}'
  x[x == '\\end{longtable}'] = '\\end{tabular}\n\\end{table}'
  x[x == '\\endhead'] = ''
  x = x[-unlist(mapply(seq, i1, i2, SIMPLIFY = FALSE))]
  x
})
```

``` {r zenodoBadgePrep}
#| echo: false
#| eval: true
#| cache: false

## try to automatically get the commit URL and the path to the badge image
dir.create("figures", showWarnings = FALSE)
if (!file.exists("figures/zenodoBadge.svg")) {
  download.file(url = "https://zenodo.org/badge/112410440.svg",
                destfile = "figures/zenodoBadge.svg",
                mode = 'wb')
}
badgeURL <- "https://zenodo.org/badge/latestdoi/112410440"

## read in svg image
badgePath <- "figures/zenodoBadge.svg"
rsvgImage <- rsvg::rsvg(badgePath)

## change to png:
badgePath <- "figures/zenodoBadge.png"  
png::writePNG(rsvgImage, badgePath, dpi = 144)
```

``` {r zenodoBadge}
#| echo: false
#| cache: false
#| results: asis

## make string of markdown code to be executed as-is
cat(paste0("[![zenodoBadge](", badgePath, ")](", badgeURL, ")"))
```

```{r refs}
#| include: FALSE

knitr::write_bib(c(
  .packages(), "quarto", "knitr", "rmarkdown", "htmlwidgets", "webshot", "DT",
  "miniUI", "tufte", "servr", "citr", "rticles",
  "SpaDES", "SpaDES.core", "SpaDES.experiment", "reproducible", "Require", "SpaDES.install"
), "citations/packages.bib")
```

This guide will take you through how to make and link your own modules using `SpaDES` in two examples. Both examples draw on basic uses of statistical models in ecology, notably the relationships between environmental variables and species abundance and presence. 

[Chapter 1](Part1_DummyModel.qmd) is very minimal, and uses only dummy data. It is meant to introduce you to the different components of a `SpaDES` module.

[Chapter 2](Part2_SDMs.qmd) uses real and freely available data, and provides a deeper look into several useful aspects of `SpaDES`, notably caching and spatial data processing.

Full R scripts to execute SpaDES workflow examples can be found in the Appendices section.

To install `SpaDES`, please have a look at [SpaDES installation](https://github.com/PredictiveEcology/SpaDES/wiki/Installation), or follow steps at the start of [Chapter 2](Part2_SDMs.qmd).