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")
fig05_png <- file.path (here, "vignettes", "figures", "_fig05.png")

datafile <- file.path (here, "data-raw", "pkgstats-results.Rds")
x <- load_pkgstats_data (datafile, raw = TRUE, latest = FALSE) |>
        group_by (package) |>
        mutate (seq = seq_along (package))
x$loc_R [which (is.na (x$loc_R))] <- 0L
x$loc_src [which (is.na (x$loc_src))] <- 0L
x$loc_inst [which (is.na (x$loc_inst))] <- 0L
x$loc_total <- x$loc_R + x$loc_src + x$loc_inst
x$doclines_per_fn_exp_mn [which (!is.finite (x$doclines_per_fn_exp_mn))] <- NA

x_rel <- x |>
    group_by (seq) |>
    summarise (
       loc = logmean (loc_total),
       loc_R = logmean (loc_R, na.rm = TRUE),
       loc_src = logmean (loc_src, na.rm = TRUE),
       loc_inst = logmean (loc_inst, na.rm = TRUE),
       n_fns_r_exported = logmean (n_fns_r_exported, na.rm = TRUE),
       n_fns_r_not_exported = logmean (n_fns_r_not_exported, na.rm = TRUE),
       n_fns_src = logmean (n_fns_src, na.rm = TRUE),
       n_fns_per_file_r = logmean (n_fns_per_file_r, na.rm = TRUE),
       n_fns_per_file_src = logmean (n_fns_per_file_src, na.rm = TRUE),
       npars_exported_mn = logmean (npars_exported_mn, na.rm = TRUE),
       npars_exported_md = logmean (npars_exported_md, na.rm = TRUE),
       loc_per_fn_r_mn = logmean (loc_per_fn_r_mn, na.rm = TRUE),
       loc_per_fn_r_md = logmean (loc_per_fn_r_md, na.rm = TRUE),
       loc_per_fn_r_exp_mn = logmean (loc_per_fn_r_exp_mn, na.rm = TRUE),
       loc_per_fn_r_exp_md = logmean (loc_per_fn_r_exp_md, na.rm = TRUE),
       loc_per_fn_r_not_exp_mn = logmean (loc_per_fn_r_not_exp_mn, na.rm = TRUE),
       loc_per_fn_r_not_exp_md = logmean (loc_per_fn_r_not_exp_md, na.rm = TRUE),
       loc_per_fn_src_mn = logmean (loc_per_fn_src_mn, na.rm = TRUE),
       loc_per_fn_src_md = logmean (loc_per_fn_src_md, na.rm = TRUE),
       doclines_per_fn_exp_mn = logmean (doclines_per_fn_exp_mn, na.rm = TRUE),
       doclines_per_fn_exp_md = logmean (doclines_per_fn_exp_md, na.rm = TRUE),
       doclines_per_fn_not_exp_mn = logmean (doclines_per_fn_not_exp_mn, na.rm = TRUE),
       doclines_per_fn_not_exp_md = logmean (doclines_per_fn_not_exp_md, na.rm = TRUE),
       docchars_per_par_exp_mn = logmean (docchars_per_par_exp_mn, na.rm = TRUE),
       docchars_per_par_exp_md = logmean (docchars_per_par_exp_md, na.rm = TRUE))

x_rel |>
    select (c (seq, loc, loc_R, loc_src, loc_inst)) |>
    rename (total = loc,
            R = loc_R,
            src = loc_src,
            inst = loc_inst) |>
    filter (seq <= 100) |>
    pivot_longer (c (total, R, src, inst)) |>
    rename (type = name, number = value) |>
    ggplot (aes (x = seq, y = number, colour = type)) +
        geom_line () +
        #geom_smooth (method = "loess", formula = "y ~ x", se = FALSE, lwd = 1) +
        theme (legend.title = element_blank(),
               legend.position = c (0.25, 0.85),
               legend.background = element_rect(fill='transparent', colour='transparent')) +
        ylab ("Lines of Code") +
        guides (color = guide_legend (ncol = 2)) +
        ggtitle ("A: Lines of Code") -> p1

x_rel |>
    select (c (seq, loc_per_fn_r_exp_mn, loc_per_fn_r_not_exp_mn,
               loc_per_fn_src_mn)) |>
    rename (R_exp = loc_per_fn_r_exp_mn,
            R_non = loc_per_fn_r_not_exp_mn,
            src = loc_per_fn_src_mn) |>
    filter (seq <= 100) |>
    pivot_longer (c (R_exp, R_non, src)) |>
    rename (type = name, number = value) |>
    ggplot (aes (x = seq, y = number, colour = type)) +
        geom_line () +
        #geom_smooth (method = "loess", formula = "y ~ x", se = FALSE) +
        theme (legend.title = element_blank(),
               legend.position = c (0.25, 0.85),
               legend.background = element_rect(fill='transparent', colour='transparent')) +
        ylab ("Lines of Code") +
        guides (color = guide_legend (ncol = 2)) +
        ggtitle ("B: LoC per fn") -> p2

x_rel |>
    select (c (seq, n_fns_r_exported, n_fns_r_not_exported, n_fns_src)) |>
    rename (r_exp = n_fns_r_exported,
            r_non = n_fns_r_not_exported,
            src = n_fns_src) |>
    filter (seq <= 100) |>
    pivot_longer (c (r_exp, r_non, src)) |>
    rename (type = name, number = value) |>
    ggplot (aes (x = seq, y = number, colour = type)) +
        geom_line () +
        #geom_smooth (method = "loess", formula = "y ~ x", se = FALSE) +
        theme (legend.title = element_blank(),
               legend.position = c (0.3, 0.85),
               legend.background = element_rect(fill='transparent', colour='transparent')) +
        ylab ("Numbers of functions") +
        guides (color = guide_legend (ncol = 2)) +
        ggtitle ("C: Total functions") -> p3

x_rel |>
    select (c (seq, n_fns_per_file_r, n_fns_per_file_src)) |>
    rename (R = n_fns_per_file_r,
            src = n_fns_per_file_src) |>
    filter (seq <= 100) |>
    pivot_longer (c (R, src)) |>
    rename (type = name, number = value) |>
    ggplot (aes (x = seq, y = number, colour = type)) +
        geom_line () +
        #geom_smooth (method = "loess", formula = "y ~ x", se = FALSE) +
        theme (legend.title = element_blank(),
               legend.position = c (0.5, 0.85),
               legend.background = element_rect(fill='transparent', colour='transparent')) +
        ylab ("Numbers of functions") +
        guides (color = guide_legend (ncol = 2)) +
        ggtitle ("D: Functions per file") -> p4

png (fig05_png, width = 7, height = 7, units = "in", res = 300)
(p1 + p2) / (p3 + p4)
graphics.off ()

knitr::include_graphics (fig05_png)

x2 <- x_rel |>
    filter (seq > 50 & seq <= 100) |>
    select (seq, loc_per_fn_r_exp_mn, loc_per_fn_r_not_exp_mn, loc_per_fn_src_mn)
s_r_exp <- lm (loc_per_fn_r_exp_mn ~ seq, data = x2)$coefficients [2]
s_r_non <- lm (loc_per_fn_r_not_exp_mn ~ seq, data = x2)$coefficients [2]
s_src <- lm (loc_per_fn_src_mn ~ seq, data = x2)$coefficients [2]
#c (1 / s_r_exp, 1 / s_r_non, 1 / s_src)