---
title: "icesSAG Package Dependency Report"
output:
    rmarkdown::html_vignette:
        toc: true
vignette: >
    %\VignetteIndexEntry{icesSAG Package Dependency Report}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(
    echo = FALSE
    , warning=FALSE
    , out.width='100%'
)
pkgnet:::silence_logger()

pkg <- "icesSAG"
base <- TRUE

pkgs_all <- installed.packages()
pkgs_avail <- available.packages(repos = "https://cloud.r-project.org")
rm(reporter)

reporter <- pkgnet::DependencyReporter$new(installed = TRUE) # has to be true, as we need non-cran packages
reporter$set_package(pkg_name = pkg)
```

## Dependency Network

This section analyzes the recursive package dependencies of **`r reporter$pkg_name`**.

```{r echo = FALSE, error = TRUE}
reporter$calculate_default_measures()
```

### Visualization

Nodes are packages. Edges point in the direction of dependence.

```{r echo = FALSE, error = TRUE}

plotDTnodes <- data.table::copy(reporter$nodes) # Don't modify original
plotDTnodes[, id := node]
plotDTnodes[, label := id]

pkgs <- pkgs_all[plotDTnodes$node, ]
repo <- sapply(pkgs[, "Package"], function(x) packageDescription(x)$Repository %||% NA)
repo[pkgs[, "Priority"] == "base"] <- "Base"
repo[pkgs[, "Priority"] == "recommended"] <- "Recommended"

plotDTnodes[, Repo := repo]

# colour nodes based on package type
plotDTnodes[, color := "red"]
plotDTnodes[Repo == "CRAN", color := "orange"]
plotDTnodes[Repo == "Base", color := "lightgreen"]
plotDTnodes[Repo == "Recommended", color := "lightblue"]
plotDTnodes[node == pkg, color := "steelblue"]

# colour or outline in dotted lines, nodes based on whether package is on CRAN or not


# colour based on package build status?

# extend to analyse a icesSAG analysis project, showing dependencies between packages and scripts

plotDTedges <- data.table::copy(reporter$edges) # Don't modify original
plotDTedges[, from := SOURCE]
plotDTedges[, to := TARGET]
plotDTedges[, color := "#848484"]


# remove base packages
if (!base) {
  plotDTnodes <- plotDTnodes[Repo != "Base" | node == pkg]
  plotDTedges <- plotDTedges[
    SOURCE %in% plotDTnodes$node & TARGET %in% plotDTnodes$node
  ]
}


g <- visNetwork::visNetwork(
  nodes = plotDTnodes,
  edges = plotDTedges
) |>
  visNetwork::visIgraphLayout(
    layout = "layout_as_tree",
    smooth = TRUE,
    mode = "all",
    flip.y = FALSE,
    root = which(plotDTnodes$node == pkg)
  ) |>
  visNetwork::visEdges(arrows = "to") |>
  visNetwork::visOptions(
    highlightNearest = list(
      enabled = TRUE,
      degree = nrow(plotDTnodes), # guarantee full path
      algorithm = "hierarchical"
    ),
    collapse = FALSE,
    selectedBy = "Repo"
  )

g
```

### Table

```{r error = TRUE}
reporter$get_summary_view()
```

---

```{r results="asis"}
cat(sprintf("<sup>This report built with **pkgnet v%s**.</sup>", packageVersion('pkgnet')))
```

<sup>[**pkgnet**](https://uptakeopensource.github.io/pkgnet/) is an open-source R package, copyright &copy; 2017-2019 Uptake, made available under the 3-Clause BSD License.</sup>

```{r echo = FALSE}
pkgnet:::unsilence_logger()
```