cran.R
In crandep: Network Analysis of Dependencies of CRAN Packages

## ----invisible_setup, include = FALSE-----------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup, message = FALSE---------------------------------------------------
library(crandep)
library(dplyr)
library(ggplot2)
library(igraph)
library(visNetwork)

## ----cran_dependencies--------------------------------------------------------
data(cran_dependencies)
cran_dependencies
dplyr::count(cran_dependencies, type, reverse)

## ----get_dep_all_packages-----------------------------------------------------
df0.cran <- get_dep_all_packages()
head(df0.cran)
dplyr::count(df0.cran, type, reverse) # numbers in general larger than above

## ---- echo = FALSE------------------------------------------------------------
df1.cran <- df0.cran |> dplyr::count(from, type, reverse) |> dplyr::count(from)
v9.all <- dplyr::filter(df1.cran, n == 9L)$from
v0.all <- dplyr::filter(df1.cran, n == 10L)$from

## ----get_graph_all_packages---------------------------------------------------
g0.depends <- get_graph_all_packages(type = "depends")
g0.depends

## ----get_graph_all_packages_rev, eval = FALSE---------------------------------
#  # Not run
#  g0.rev_depends <- get_graph_all_packages(type = "depends", reverse = TRUE)
#  g0.rev_depends

## ----forward_equivalent-------------------------------------------------------
g1.depends <- df0.cran |>
  dplyr::filter(type == "depends" & !reverse) |>
  df_to_graph(nodelist = dplyr::rename(df0.cran, name = from))
g1.depends # same as g0.depends

## ----reverse_equivalent, eval = FALSE-----------------------------------------
#  # Not run
#  g1.rev_depends <- df0.cran |>
#    dplyr::filter(type == "depends" & reverse) |>
#    df_to_graph(nodelist = dplyr::rename(df0.cran, name = from))
#  g1.rev_depends # should be same as g0.rev_depends

## ----is_dag-------------------------------------------------------------------
igraph::is_dag(g0.depends)
igraph::is_dag(g1.depends)

## ----external_rev_defunct-----------------------------------------------------
df1.rev_depends <- df0.cran |>
  dplyr::filter(type == "depends" & reverse) |>
  df_to_graph(nodelist = NULL, gc = FALSE) |>
  igraph::as_data_frame() # to obtain the edge list
df1.depends <- df0.cran |>
  dplyr::filter(type == "depends" & !reverse) |>
  df_to_graph(nodelist = NULL, gc = FALSE) |>
  igraph::as_data_frame()
dfa.diff.depends <- dplyr::anti_join(
  df1.rev_depends,
  df1.depends,
  c("from" = "to", "to" = "from")
)
head(dfa.diff.depends)

## ----external_rev_defunct_again-----------------------------------------------
dfb.diff.depends <- dplyr::anti_join(
  df1.depends,
  df1.rev_depends,
  c("from" = "to", "to" = "from")
)
head(dfb.diff.depends)

## ----summary------------------------------------------------------------------
df0.summary <- dplyr::count(df0.cran, from, type, reverse)
head(df0.summary)

## ----tops---------------------------------------------------------------------
df0.summary |>
  dplyr::filter(reverse) |>
  dplyr::group_by(type) |>
  dplyr::top_n(1, n)

## ----summary_plot, out.width="660px", out.height="660px", fig.width=9, fig.height=9----
df1.summary <- df0.summary |>
  dplyr::count(type, reverse, n)
gg0.summary <- df1.summary |>
  dplyr::mutate(reverse = ifelse(reverse, "reverse", "forward")) |>
  ggplot2::ggplot() +
  ggplot2::geom_point(ggplot2::aes(n, nn)) +
  ggplot2::facet_grid(type ~ reverse) +
  ggplot2::scale_x_log10() +
  ggplot2::scale_y_log10() +
  ggplot2::labs(x = "Degree", y = "Number of packages") +
  ggplot2::theme_bw(20)
gg0.summary

## ----visualise----------------------------------------------------------------
prefix <- "http://CRAN.R-project.org/package=" # canonical form
degrees <- igraph::degree(g0.depends)
df0.nodes <- data.frame(id = names(degrees), value = degrees) |>
  dplyr::mutate(title = paste0('<a href=\"', prefix, id, '\">', id, '</a>'))
df0.edges <- igraph::as_data_frame(g0.depends, what = "edges")

## ----visNetwork---------------------------------------------------------------
set.seed(2345L)
vis0 <- visNetwork::visNetwork(df0.nodes, df0.edges, width = "100%", height = "720px") |>
  visNetwork::visOptions(highlightNearest = TRUE) |>
  visNetwork::visEdges(arrows = "to", color = list(opacity = 0.5)) |>
  visNetwork::visNodes(fixed = TRUE) |>
  visNetwork::visIgraphLayout(layout = "layout_with_drl")
vis0