manuscript anaylsis code and plots

_manuscript_scripts/01_commits.R

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+# 1. Package loading and functions ------------
+
+# Load required libraries
+library(gh)
+library(ggplot2)
+library(dplyr)
+library(tidyr)
+
+# Function to fetch commits for a repository
+get_commits <- function(repo) {
+  message("Fetching commits for: ", repo)
+  commits <- gh("/repos/{owner}/{repo}/commits", owner = owner, repo = repo, .limit = Inf)
+  data.frame(
+    repo = repo,
+    sha = sapply(commits, function(x) x$sha),
+    author = sapply(commits, function(x) ifelse(is.null(x$author$login), x$commit$committer$name, x$author$login)),
+    date = as.POSIXct(sapply(commits, function(x) x$commit$author$date), format = "%Y-%m-%dT%H:%M:%SZ", tz = "Africa/Nairobi"),
+    message = sapply(commits, function(x) x$commit$message),
+    stringsAsFactors = FALSE
+  )
+}
+
+## function to save fig
+fig_save <- function(name,
+                     fig,
+                     width = 6,
+                     height = 6,
+                     plot_dir = file.path(here::here(), "analysis/plots"),
+                     pdf_plot = TRUE,
+                     font_family = "Helvetica",
+                     res = 300,
+                     ...) {
+
+  if(!is.null(font_family)) {
+    fig <- fig + ggplot2::theme(text = ggplot2::element_text(family = font_family))
+  }
+
+  dir.create(plot_dir, showWarnings = FALSE)
+  fig_path <- function(name) {paste0(plot_dir, "/", name)}
+
+  ragg::agg_png(fig_path(paste0(name,".png")),
+                width = width,
+                height = height,
+                units = "in",
+                res = res,
+                ...)
+  print(fig)
+  dev.off()
+
+  if(pdf_plot) {
+    pdf(file = fig_path(paste0(name,".pdf")), width = width, height = height)
+    print(fig)
+    dev.off()
+  }
+
+}
+
+
+# 2. Sourcing Commit Data ------------
+
+# Organisation name
+owner <- "CEMA-MRC-Hackathon"
+
+# List of repositories
+repos <- c(
+  "animal-surveillance",
+  "malaria-vaccine",
+  "data-quality-validation",
+  "human-resources",
+  "cold-chain-capacity",
+  "measles-outbreaks-threshold"
+)
+
+
+# Loop through repositories and collect commits
+all_commits <- do.call(rbind, lapply(repos, get_commits))
+
+# correct where people some how made commits without usernames
+all_commits <- all_commits %>%
+  mutate(author = case_when(
+  author == "John Ojal" ~ "ojal",
+  author == "Evans Omondi" ~ "Komondi",
+  .default = as.character(author)
+))
+
+
+# 3. Plot 1: Cumulative commits over time by repository ---------
+
+plot1_data <- all_commits %>%
+  group_by(repo, date) %>%
+  summarise(commits = n(), .groups = "drop") %>%
+  arrange(repo, date) %>%
+  group_by(repo) %>%
+  mutate(cumulative_commits = cumsum(commits))
+
+gg1 <- plot1_data %>%
+  filter(date < "2025-01-25") %>%
+  ungroup() %>%
+  tidyr::complete(repo, date) %>%
+  arrange(repo, date) %>%
+  group_by(repo) %>%
+  fill(cumulative_commits, .direction = "downup") %>%
+ggplot(aes(x = date + lubridate::hours(3), y = cumulative_commits, colour = repo)) +
+  geom_line(size = 1) +
+  labs(
+    x = "Date",
+    y = "Cumulative Commits",
+    colour = "Repository"
+  ) +
+  theme_minimal(base_family = "Helvetica", base_size = 14) +
+  MetBrewer::scale_color_met_d("Klimt") +
+  scale_x_datetime(date_breaks = "1 day", limits = as.POSIXct(c("2025-01-20","2025-01-25")), date_labels = "%b %d") +
+  theme(axis.line = element_line(), panel.grid.major.x = element_line(colour = "darkgrey", linewidth = 0.5, linetype = "dashed")) +
+  scale_y_continuous(expand = expand_scale(mult = c(0, 0),
+                                           add = c(0, 1)),
+                     labels = scales::number_format(accuracy = 1))
+gg1
+
+# 4. Plot 2: Cumulative commits by user over time, coloured by repo ------
+
+plot2_data <- all_commits %>%
+  group_by(author, repo, date) %>%
+  summarise(commits = n(), .groups = "drop") %>%
+  arrange(author, date) %>%
+  group_by(author, repo) %>%
+  mutate(cumulative_commits = cumsum(commits))
+
+gg2 <- plot2_data %>%
+  filter(date < "2025-01-25") %>%
+  ungroup() %>%
+  tidyr::complete(author, date) %>%
+  arrange(author, date) %>%
+  group_by(author) %>%
+  fill(repo, .direction = "downup") %>%
+  fill(cumulative_commits, .direction = "down") %>%
+  mutate(cumulative_commits = replace_na(cumulative_commits, 0)) %>%
+ggplot(aes(x = date + lubridate::hours(3), y = cumulative_commits, colour = repo, group = interaction(author, repo))) +
+  geom_line(size = 1) +
+  labs(
+    x = "Date",
+    y = "Cumulative Commits by Participant",
+    colour = "Repository"
+  ) +
+  lemon::facet_rep_wrap(.~repo, scales = "free_y", ncol = 3)+
+  theme_minimal(base_family = "Helvetica", base_size = 14) +
+  MetBrewer::scale_color_met_d("Klimt") +
+  scale_x_datetime(date_breaks = "1 day", limits = as.POSIXct(c("2025-01-20","2025-01-25")), date_labels = "%b %d") +
+  theme(axis.line = element_line(), panel.grid.major.x = element_line(colour = "darkgrey", linewidth = 0.5, linetype = "dashed")) +
+  scale_y_continuous(expand = expand_scale(mult = c(0, 0),
+                                           add = c(0, 1)),
+                                           labels = scales::number_format(accuracy = 1))
+gg2
+
+# 5. Save figure to plots director
+commit_gg <- cowplot::plot_grid(
+    gg1 + theme(legend.position = c(0.25,0.85), legend.background = element_rect()),
+    gg2 + theme(legend.position = "none"),
+    ncol = 2,
+    rel_widths = c(0.4, 0.6), scale = 0.98, labels = "AUTO"
+  )
+
+fig_save("commits", commit_gg, width = 18, height = 7, res = 600, plot_dir = "_manuscript_scripts/plots")
+
+
+# 5. Save figure to plots director
+commit_gg2 <- cowplot::plot_grid(
+  gg1 + theme(legend.position = c(0.15,0.65), legend.background = element_rect()),
+  gg2 + theme(legend.position = "none", axis.text.x = element_text(size = 10)),
+  ncol = 1,
+  rel_heights = c(0.4, 0.6), scale = 0.98, labels = "AUTO"
+)
+
+fig_save("commits2", commit_gg2, width = 10, height = 9, res = 600, plot_dir = "_manuscript_scripts/plots")
+
+