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

library ("pkgstatsAnalyses")
here <- here::here ()
v_data_dir <- file.path (here, "vignettes", "data")
logmean <- function (x, ...) {
    10 ^ mean (log10 (x [which (x > 0)]), na.rm = TRUE)
}

n_files_file <- file.path (v_data_dir, "fig03-n-files-data.Rds")
n_files_exists <- file.exists (n_files_file)
datafile <- file.path (here, "data-raw", "pkgstats-results.Rds")

fig03_png <- file.path (here, "vignettes", "figures", "_fig03.png")
f_fig3_pkg_level <- file.path (v_data_dir, "fig03-pkg-n-files.Rds")
do_fig3_pkg_n_files <- !file.exists (f_fig3_pkg_level) & !file.exists (fig03_png)

# takes a few tens of seconds
x <- load_pkgstats_data (datafile, raw = TRUE, latest = FALSE)
nfiles_one_year <- function (x, year = 2015) {

    x1 <- x |>
        filter (year <= !!year) |>
        group_by (package) |>
        slice_max (date) |>
        summarise (R = logmean (files_R),
                   src = logmean (files_src),
                   inst = logmean (files_inst),
                   vignettes = logmean (files_vignettes),
                   tests = logmean (files_tests),
                   data = logmean (num_data_files))
    n_mean <- colMeans (x1 [, -1], na.rm = TRUE)

    c (year = year, n_mean)
}
dat <- vapply (sort (unique (x$year)), function (i)
               nfiles_one_year (x, i),
               numeric (7))
dat <- data.frame (t (dat))
dat$year <- lubridate::year (paste0 (dat$year, "-01-01"))

xy <- x |>
    group_by (year) |>
    summarise (R = logmean (files_R),
               src = logmean (files_src),
               inst = logmean (files_inst),
               vignettes = logmean (files_vignettes),
               tests = logmean (files_tests),
               data = logmean (num_data_files))

dat$what <- "cran_by_year"
xy$what <- "annual"

dat <- rbind (dat, xy)
dat$inst [!is.finite (dat$inst)] <- NA
dat$vignettes [!is.finite (dat$vignettes)] <- NA
dat$tests [!is.finite (dat$tests)] <- NA
dat$data [!is.finite (dat$data)] <- NA

saveRDS (dat, n_files_file)

x_per_pkg <- load_pkgstats_data (datafile, raw = TRUE, latest = FALSE) |>
    group_by (package) |>
    summarise (R = files_R,
               src = files_src,
               inst = files_inst,
               vignettes = files_vignettes,
               tests = files_tests,
               data = num_data_files,
               seq = seq_along (R),
               .groups = "keep") |>
    mutate_at(vars (R, src, inst, vignettes, tests, data),
              ~replace (., !is.finite (.), NA)) |>
    group_by (seq) |>
    summarise (R = mean (R, na.rm = TRUE),
               src = mean (src, na.rm = TRUE),
               inst = mean (inst, na.rm = TRUE),
               vignettes = mean (vignettes, na.rm = TRUE),
               tests = mean (tests, na.rm = TRUE),
               data = mean (data, na.rm = TRUE),
               .groups = "keep") |>
    filter (seq > 1) |>
    pivot_longer (cols = c (R, src, inst, vignettes, tests, data)) |>
    rename (dir = name)

saveRDS (x_per_pkg, f_fig3_pkg_level)

dat <- readRDS (n_files_file) |>
    mutate (inst = inst * max (src, na.rm = TRUE) / max (inst, na.rm = TRUE)) |>
    filter (what == "cran_by_year") |>
    pivot_longer (cols = c (R, src, inst, vignettes, tests, data)) |>
    rename (n_files = value, dir = name)
dat_ann <- readRDS (n_files_file) |>
    mutate (inst = inst * max (src, na.rm = TRUE) / max (inst, na.rm = TRUE)) |>
    filter (what == "annual") |>
    pivot_longer (cols = c (R, src, inst, vignettes, tests, data)) |>
    rename (n_files = value, dir = name)
p1 <- ggplot (dat, aes (x = year, y = n_files, color = dir)) +
    geom_line (lwd = 0.4, lty = 2) +
    geom_smooth (method = "loess", formula = "y ~ x", se = FALSE, lwd = 0.5) +
    #geom_line (data = dat_ann, lty = 2) +
    ggtitle ("A: Numbers of files per year") +
    ylab ("Num. files") +
    ylim (c (0, max (dat$n_files))) +
    theme (legend.position = "none")
# dat_ann are very similar but much noisier, so not shown

p2 <- readRDS (f_fig3_pkg_level) |>
    filter (seq <= 20) |>
    ggplot (aes (x = seq, y = value, colour = dir)) +
    geom_line (lwd = 0.4, lty = 2) +
    geom_smooth (method = "loess", formula = "y ~ x", se = FALSE, span = 0.7, lwd = 0.5) +
    xlab ("Release Sequence") +
    ylab ("Num. files") + 
    ggtitle ("B: Numbers of files per release") +
    guides (color = guide_legend (ncol = 2)) +
    theme (legend.title = element_blank(),
           legend.position = c (0.3, 0.85),
           legend.background = element_rect(fill='transparent', colour='transparent'))

png (fig03_png, width = 7, height = 3.5, units = "in", res = 300)
p1 + p2
graphics.off ()

knitr::include_graphics (fig03_png)

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