Replication of David Schoch's blog post 'Six degrees of Hadley Wickham: The CRAN co-authorship network'
Source:vignettes/articles/six-degrees-replication.Rmd
six-degrees-replication.RmdThis article aims to replicate David Schoch’s analysis in his blog
post “Six
degrees of Hadley Wickham: The CRAN co-authorship network” using the
authoritative package.
library(authoritative)
library(tidyverse)
#> ── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
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#> ✔ ggplot2 3.5.2 ✔ tibble 3.3.0
#> ✔ lubridate 1.9.4 ✔ tidyr 1.3.1
#> ✔ purrr 1.0.4
#> ── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
#> ✖ dplyr::filter() masks stats::filter()
#> ✖ dplyr::lag() masks stats::lag()
#> ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors
library(igraph)
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#> Attaching package: 'igraph'
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#> %--%, union
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#> The following objects are masked from 'package:dplyr':
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#> as_data_frame, groups, union
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#> The following objects are masked from 'package:purrr':
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#> compose, simplify
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#> The following object is masked from 'package:tidyr':
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#> crossing
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#> The following object is masked from 'package:tibble':
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#> as_data_frame
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#> The following objects are masked from 'package:stats':
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#> union
library(netUtils)
db <- tools::CRAN_package_db()
author_pkg_cran <- db |>
dplyr::transmute(
Package = Package,
parsed_authors_r = purrr::map(authoritative::parse_authors_r(`Authors@R`), format, include = c("given", "family")),
parsed_authors = authoritative::parse_authors(Author)
) |>
dplyr::mutate(
authorsR = coalesce(parsed_authors_r, parsed_authors),
authorsR = map(authorsR, stringi::stri_trans_general, "ASCII"),
authorsR = map(authorsR, stringr::str_replace_all, "[[:punct:]]", " "),
authorsR = map(authorsR, stringr::str_replace_all, "[[:space:]]+", " "),
authorsR = map(authorsR, trimws),
.keep = "unused"
) |>
tidyr::unnest_longer(authorsR) |>
dplyr::mutate(authorsR = authoritative::expand_names(authorsR, authorsR)) |>
# Standardize capitalization
dplyr::mutate(
authorsR = stringr::str_to_title(authorsR)
)
# FIXME: these signal an problem in the parsing. So this should be fixed instead of dropping the values
author_pkg_cran <- author_pkg_cran |>
filter(!authorsR %in% Package)
author_pkg_cran_net <- netUtils::bipartite_from_data_frame(author_pkg_cran, "authorsR", "Package")
A <- as_biadjacency_matrix(author_pkg_cran_net, sparse = TRUE)
A <- as(A, "sparseMatrix")
B <- Matrix::t(A) %*% A
auth_auth_net <- graph_from_adjacency_matrix(B, "undirected", diag = FALSE, weighted = TRUE)
auth_auth_net
#> IGRAPH 8cde193 UNW- 28775 159521 --
#> + attr: name (v/c), weight (e/n)
#> + edges from 8cde193 (vertex names):
#> [1] Martin Bladt --Christian Furrer Martin Bladt --Alexander J Mcneil
#> [3] Martin Bladt --Jorge Yslas Martin Bladt --Alaric Muller
#> [5] Paul R Rosenbaum--Dylan Small Paul R Rosenbaum--Ruth Heller
#> [7] Paul R Rosenbaum--Marieke Stolte Paul R Rosenbaum--Luke Miratrix
#> [9] Paul R Rosenbaum--Luke Keele Paul R Rosenbaum--Sam Pimentel
#> [11] Sigbert Klinke --Jaroslav Myslivec Sigbert Klinke --Robert King
#> [13] Sigbert Klinke --Benjamin Dean Sigbert Klinke --Paul Van Staden
#> [15] Sigbert Klinke --Jekaterina Zukovska
#> + ... omitted several edges
comps_cran <- components(auth_auth_net)
comps_cran$no
#> [1] 4278
auth_auth_net_largest <- largest_component(auth_auth_net)
auth_auth_net_largest
#> IGRAPH 43018bb UNW- 17881 143849 --
#> + attr: name (v/c), weight (e/n)
#> + edges from 43018bb (vertex names):
#> [1] Martin Bladt --Christian Furrer Martin Bladt --Alexander J Mcneil
#> [3] Martin Bladt --Jorge Yslas Martin Bladt --Alaric Muller
#> [5] Paul R Rosenbaum--Dylan Small Paul R Rosenbaum--Ruth Heller
#> [7] Paul R Rosenbaum--Marieke Stolte Paul R Rosenbaum--Luke Miratrix
#> [9] Paul R Rosenbaum--Luke Keele Paul R Rosenbaum--Sam Pimentel
#> [11] Sigbert Klinke --Jaroslav Myslivec Sigbert Klinke --Robert King
#> [13] Sigbert Klinke --Benjamin Dean Sigbert Klinke --Paul Van Staden
#> [15] Sigbert Klinke --Jekaterina Zukovska
#> + ... omitted several edgesFrom the 28,775 recorded package authors, 17,881 (62.14%) are part of the largest connected component. All subsequent analyses will be done with this network.
emax_who <- ends(auth_auth_net_largest, E(auth_auth_net_largest)[which.max(E(auth_auth_net_largest)$weight)])[1, ]
emax <- max(E(auth_auth_net_largest)$weight)On average, every developer in the largest component has 16.09 co-authors. The median is 7. The two individuals who coauthored the most packages together (66), are Posit Software Pbc and Hadley Wickham. The person with the most co-authors (876) is Hadley Wickham. What a great transition for the next section.
hadley_idx <- which(V(auth_auth_net_largest)$name == "Hadley Wickham")
author_tbl <- tibble(
name = V(auth_auth_net_largest)$name,
dist2HW = distances(auth_auth_net_largest, to = hadley_idx, weights = NA),
cc = (1 / closeness(auth_auth_net_largest, weights = NA)) * 1 / vcount(auth_auth_net_largest)
)
author_tbl |>
count(dist2HW) |>
ggplot(aes(x = dist2HW, y = n)) +
geom_col(color = "white", fill = "black") +
theme_minimal() +
theme(
panel.grid.major.x = element_blank(),
panel.grid.minor.x = element_blank(),
) +
scale_x_continuous(breaks = seq(0, 10), name = "Hadley Number")
author_tbl |>
select(name, centrality = cc) |>
dplyr::top_n(10, -centrality) |>
dplyr::arrange(centrality) |>
knitr::kable()| name | centrality |
|---|---|
| Hadley Wickham | 2.955931 |
| Dirk Eddelbuettel | 3.066663 |
| Ben Bolker | 3.095464 |
| Posit Software Pbc | 3.105363 |
| Jim Hester | 3.138359 |
| Martin Maechler | 3.156647 |
| Kevin Ushey | 3.157318 |
| Romain Francois | 3.159555 |
| Brian D Ripley | 3.195067 |
| R Core Team | 3.210894 |