In mpadge/pkgstats-analyses: Analyses of 'pkgstats' Results for all CRAN Packages

library ("pkgstatsAnalyses")
here <- here::here ()
datafile <- file.path (here, "data-raw", "pkgstats-results.Rds")
v_data_dir <- file.path (here, "vignettes", "data")
logmean <- function (x, ...) {
    index <- which (x > 0 & !is.nan (x) & is.finite (x))
    10 ^ mean (log10 (x [index]), na.rm = TRUE)
}

fig09_png <- file.path (here, "vignettes", "figures", "_fig09.png")

# graph metrics for inter-package dependency networks
xraw <- load_pkgstats_data (datafile, raw = TRUE, latest = FALSE)

x <- xraw |>
    group_by (package) |>
    mutate (nfns_total = n_fns_r + n_fns_src) |>
    mutate (seq = seq_along (package)) |>
    group_by (seq) |>
    summarise (
               #n_edges = mean (n_edges [which (!is.na (n_edges))]),
               #n_edges_r = mean (n_edges_r [which (!is.na (n_edges_r))]),
               #n_edges_src = mean (n_edges_src [which (!is.na (n_edges_src))]),
               #n_clusters = mean (n_clusters [which (!is.na (n_clusters))]),
               n_edges = logmean (n_edges / nfns_total, na.rm = TRUE),
               n_edges_r = logmean (n_edges_r / n_fns_r, na.rm = TRUE),
               n_edges_src = logmean (n_edges_src / n_fns_src, na.rm = TRUE),
               n_clusters = logmean (n_clusters, na.rm = TRUE),
               centr_dir_mn = logmean (centrality_dir_mn, na.rm = TRUE),
               centr_dir_md = logmean (centrality_dir_md, na.rm = TRUE),
               centr_dir_mn_no0 = logmean (centrality_dir_mn_no0, na.rm = TRUE),
               centr_dir_md_no0 = logmean (centrality_dir_md_no0, na.rm = TRUE),
               centr_undir_mn = logmean (centrality_undir_mn, na.rm = TRUE),
               centr_undir_md = logmean (centrality_undir_md, na.rm = TRUE),
               centr_undir_mn_no0 = logmean (centrality_undir_mn_no0, na.rm = TRUE),
                centr_undir_md_no0 = logmean (centrality_undir_md_no0, na.rm = TRUE),
                central_edges_dir = mean (num_terminal_edges_dir, na.rm = TRUE),
                term_edges = logmean (num_terminal_edges_undir, na.rm = TRUE),
                node_degree_mn = logmean (node_degree_mn, na.rm = TRUE),
                node_degree_md = logmean (node_degree_md, na.rm = TRUE),
                node_degree_max = logmean (node_degree_max, na.rm = TRUE))

x1 <- x |>
    select (seq, starts_with ("n_")) |>
    rename (total = n_edges, R = n_edges_r, src = n_edges_src) |>
    filter (seq <= 100)

coeff_fig09_p1 <- max (x1$n_clusters) / max (x1$total)
colours_fig09_p1 <- c ("total" = "red",
                       "R" = "green",
                       "src" = "blue",
                       "n_clusters" = "orange")

fig09_p1 <- x1 |>
    ggplot (aes (x = seq)) +
        geom_line (aes (y = total, col = "total")) +
        geom_line (aes (y = R, col = "R")) +
        geom_line (aes (y = src, col = "src")) +
        geom_line (aes (y = n_clusters / coeff_fig09_p1, col = "n_clusters")) +
        #scale_colour_manual (values = colours_fig09_p1) +
        ylab ("Ratio edges/vertices") +
        scale_y_continuous (
            sec.axis = sec_axis (~.*coeff_fig09_p1, name = "Num. clusters")) +
        ggtitle ("A: Pkg edges and clusters") +
        guides (color = guide_legend (ncol = 2)) +
        theme (legend.title = element_blank (),
               legend.position = c (0.3, 0.9),
               legend.background = element_rect(fill='transparent', colour='transparent'))

# slope:
s <- lm (total ~ seq, data = x1)$coefficients [2]

x2 <- x |>
    select (seq, centr_dir_mn, node_degree_mn, term_edges) |>
    rename (centr = centr_dir_mn,
            vert_degree = node_degree_mn)  |>
    mutate (vert_degree = vert_degree * 10) |>
    filter (seq < 100)

coeff_fig09_p2 <- max (x2$centr) / max (x2$term_edges)
colours_fig1e_p2 <- c ("centr" = "red",
                      "vert_degree" = "green",
                      "term_edges" = "blue")
fig09_p2 <- x2 |>
    ggplot (aes (x = seq)) +
        geom_line (aes (y = centr / coeff_fig09_p2, col = "centr")) +
        geom_line (aes (y = vert_degree, col = "vert_degree")) +
        geom_line (aes (y = term_edges, col = "term_edges")) +
        ggtitle ("D: pkg centrality metrics") +
        ylab ("Vert degree (x10) / Term edges") +
        scale_y_continuous (
            sec.axis = sec_axis (~.*coeff_fig09_p2, name = "Centrality")) +
        #guides (color = guide_legend (ncol = 2)) +
        theme (legend.title = element_blank (),
               legend.position = c (0.25, 0.87),
               legend.background = element_rect(fill='transparent', colour='transparent'))

png (fig09_png, width = 7, height = 3.5, units = "in", res = 300)
fig09_p1 + fig09_p2
graphics.off ()

knitr::include_graphics (fig09_png)

mpadge/pkgstats-analyses documentation built on Dec. 10, 2022, 4:20 a.m.