statistics.qmd

---
title: "Research Statistics"
format: html
execute:
  warning: false
  message: false
---

```{r}
#| label: setup
#| echo: false

library(cranlogs)
library(scholar)
library(plotly)
library(dplyr)
library(htmltools)

# ---- Cohesive color palette (warm academic tones) ----
col_dark    <- "#1b2a4a"
col_blue    <- "#3a6ea5"
col_teal    <- "#28a99e"
col_orange  <- "#e8843c"
col_rose    <- "#c74b7a"
col_gray    <- "#5a6d7e"
col_purple  <- "#7b5ea7"

# Chart colors
chart_colors <- c(col_dark, col_teal, col_orange, col_blue, col_rose, col_gray, col_purple)

# ---- Google Scholar data (with local cache) ----
scholar_id <- "Qu66YZQAAAAJ"
cache_file <- "scholar_cache.json"

profile <- tryCatch({
  p <- get_profile(scholar_id)
  if (is.list(p) && "total_cites" %in% names(p)) p else stop("invalid")
}, error = function(e) NULL)

cite_history <- tryCatch({
  ch <- get_citation_history(scholar_id)
  if (is.data.frame(ch) && nrow(ch) > 0) ch else stop("invalid")
}, error = function(e) NULL)

# If Scholar API succeeded, save cache for CI use
if (!is.null(profile) && !is.null(cite_history)) {
  jsonlite::write_json(
    list(profile = profile, cite_history = cite_history),
    cache_file, auto_unbox = TRUE, pretty = TRUE
  )
}

# If Scholar API failed, load from cache
if (is.null(profile) || is.null(cite_history)) {
  if (file.exists(cache_file)) {
    cache <- jsonlite::read_json(cache_file, simplifyVector = TRUE)
    if (is.null(profile)) profile <- cache$profile
    if (is.null(cite_history)) cite_history <- as.data.frame(cache$cite_history)
  }
}
```

## Google Scholar Metrics

```{r}
#| label: scholar-metrics
#| echo: false

if (!is.null(profile)) {
  total_cites <- profile$total_cites
  h_index <- profile$h_index
  i10_index <- profile$i10_index
} else {
  total_cites <- "N/A"
  h_index <- "N/A"
  i10_index <- "N/A"
}

make_card <- function(value, label, bg_color) {
  div(
    style = paste0(
      "background:", bg_color, ";padding:1.5rem 2.5rem;",
      "border-radius:12px;text-align:center;min-width:180px;",
      "box-shadow:0 4px 12px rgba(0,0,0,0.15);"
    ),
    h1(style = "margin:0;font-size:2.5rem;font-weight:700;color:#ffffff;", value),
    tags$hr(style = "border:0;border-top:1px solid rgba(255,255,255,0.3);margin:0.5rem 1rem;"),
    p(style = "margin:0;color:rgba(255,255,255,0.9);font-size:0.95rem;", label)
  )
}

div(
  style = "display:flex;justify-content:center;gap:2rem;flex-wrap:wrap;margin:1.5rem 0;",
  make_card(format(total_cites, big.mark = ","), "Total Citations", col_dark),
  make_card(h_index, "H-Index", col_blue),
  make_card(i10_index, "i10-Index", col_teal)
)
```

### Citations per Year

```{r}
#| label: citations-per-year
#| echo: false

if (!is.null(cite_history)) {
  plot_ly(cite_history, x = ~year, y = ~cites, type = "bar",
          marker = list(color = col_teal),
          hovertemplate = "Year: %{x}<br>Citations: %{y:,}<extra></extra>") |>
    layout(
      xaxis = list(title = "Year", dtick = 1),
      yaxis = list(title = "Citations"),
      plot_bgcolor = "rgba(0,0,0,0)",
      paper_bgcolor = "rgba(0,0,0,0)",
      margin = list(t = 10, l = 60, r = 20, b = 50)
    )
} else {
  cat("Citation history currently unavailable.")
}
```

### Cumulative Citations

```{r}
#| label: cumulative-citations
#| echo: false

if (!is.null(cite_history)) {
  cite_history$cumulative <- cumsum(cite_history$cites)

  plot_ly(cite_history, x = ~year, y = ~cumulative, type = "scatter", mode = "lines+markers",
          line = list(color = col_dark, width = 3),
          marker = list(color = col_dark, size = 7),
          hovertemplate = "Year: %{x}<br>Cumulative: %{y:,}<extra></extra>") |>
    layout(
      xaxis = list(title = "Year", dtick = 2),
      yaxis = list(title = "Cumulative Citations"),
      plot_bgcolor = "rgba(0,0,0,0)",
      paper_bgcolor = "rgba(0,0,0,0)",
      margin = list(t = 10, l = 60, r = 20, b = 50)
    )
} else {
  cat("Citation history currently unavailable.")
}
```

---

## CRAN Package Downloads

```{r}
#| label: cran-downloads
#| echo: false

my_packages <- c("bibliometrix", "openalexR", "dimensionsR", "pubmedR", "e2tree", "contentanalysis", "tall")

totals <- lapply(my_packages, function(pkg) {
  tryCatch({
    dl <- cran_downloads(pkg, from = "2015-01-01", to = Sys.Date())
    data.frame(package = pkg, total = sum(dl$count, na.rm = TRUE))
  }, error = function(e) {
    data.frame(package = pkg, total = 0)
  })
})
totals_df <- bind_rows(totals) |> arrange(desc(total))
```

### Total CRAN Downloads

```{r}
#| label: download-cards
#| echo: false

card_colors <- c(col_dark, col_blue, col_teal, col_orange, col_rose, col_gray, col_purple)

make_dl_card <- function(value, label, bg_color) {
  div(
    style = paste0(
      "background:", bg_color, ";padding:0.8rem 1rem;",
      "border-radius:10px;text-align:center;",
      "box-shadow:0 4px 12px rgba(0,0,0,0.15);"
    ),
    h3(style = "margin:0;font-weight:700;color:#ffffff;font-size:1.3rem;", value),
    tags$hr(style = "border:0;border-top:1px solid rgba(255,255,255,0.3);margin:0.4rem 0.8rem;"),
    p(style = "margin:0;color:rgba(255,255,255,0.9);font-size:0.8rem;", label)
  )
}

cards <- lapply(seq_len(nrow(totals_df)), function(i) {
  bg <- card_colors[((i - 1) %% length(card_colors)) + 1]
  make_dl_card(format(totals_df$total[i], big.mark = ","), totals_df$package[i], bg)
})

div(
  style = "max-width:850px;margin:1.5rem auto;",
  div(
    style = "display:grid;grid-template-columns:repeat(4,1fr);gap:1rem;margin-bottom:1rem;",
    tagList(cards[1:min(4, length(cards))])
  ),
  div(
    style = "display:grid;grid-template-columns:repeat(3,1fr);gap:1rem;max-width:637px;margin:0 auto;",
    tagList(cards[5:length(cards)])
  )
)
```

### Cumulative Downloads Over Time

```{r}
#| label: cumulative-downloads
#| echo: false

monthly_data <- lapply(seq_along(my_packages), function(i) {
  pkg <- my_packages[i]
  tryCatch({
    dl <- cran_downloads(pkg, from = "2015-01-01", to = Sys.Date())
    dl$month <- format(dl$date, "%Y-%m")
    monthly <- dl |> group_by(month) |> summarise(downloads = sum(count), .groups = "drop")
    monthly$cumulative <- cumsum(monthly$downloads)
    monthly$package <- pkg
    monthly$date <- as.Date(paste0(monthly$month, "-01"))
    monthly
  }, error = function(e) NULL)
})

monthly_all <- bind_rows(monthly_data)

if (nrow(monthly_all) > 0) {
  p <- plot_ly()
  for (i in seq_along(unique(monthly_all$package))) {
    pkg <- unique(monthly_all$package)[i]
    d <- monthly_all |> filter(package == pkg)
    col <- chart_colors[((i - 1) %% length(chart_colors)) + 1]
    p <- p |> add_trace(data = d, x = ~date, y = ~cumulative,
                        type = "scatter", mode = "lines",
                        name = pkg,
                        line = list(width = 2.5, color = col),
                        hovertemplate = paste0(pkg, "<br>%{x|%b %Y}<br>Cumulative: %{y:,}<extra></extra>"))
  }
  p |> layout(
    xaxis = list(title = "Date"),
    yaxis = list(title = "Cumulative Downloads"),
    legend = list(orientation = "h", x = 0.5, xanchor = "center", y = -0.15),
    plot_bgcolor = "rgba(0,0,0,0)",
    paper_bgcolor = "rgba(0,0,0,0)",
    margin = list(t = 10, l = 60, r = 20, b = 70)
  )
}
```

### Monthly Downloads (Last 12 Months)

```{r}
#| label: monthly-downloads-recent
#| echo: false

recent_data <- lapply(seq_along(my_packages), function(i) {
  pkg <- my_packages[i]
  tryCatch({
    dl <- cran_downloads(pkg, from = Sys.Date() - 365, to = Sys.Date())
    dl$month <- format(dl$date, "%Y-%m")
    monthly <- dl |> group_by(month) |> summarise(downloads = sum(count), .groups = "drop")
    monthly$package <- pkg
    monthly$date <- as.Date(paste0(monthly$month, "-01"))
    monthly
  }, error = function(e) NULL)
})

recent_all <- bind_rows(recent_data)

if (nrow(recent_all) > 0) {
  p <- plot_ly()
  for (i in seq_along(my_packages)) {
    pkg <- my_packages[i]
    d <- recent_all |> filter(package == pkg)
    col <- chart_colors[((i - 1) %% length(chart_colors)) + 1]
    p <- p |> add_trace(data = d, x = ~date, y = ~downloads,
                        type = "bar", name = pkg,
                        marker = list(color = col),
                        hovertemplate = paste0(pkg, "<br>%{x|%b %Y}<br>Downloads: %{y:,}<extra></extra>"))
  }
  p |> layout(
    barmode = "group",
    xaxis = list(title = "Month"),
    yaxis = list(title = "Downloads"),
    legend = list(orientation = "h", x = 0.5, xanchor = "center", y = -0.15),
    plot_bgcolor = "rgba(0,0,0,0)",
    paper_bgcolor = "rgba(0,0,0,0)",
    margin = list(t = 10, l = 60, r = 20, b = 70)
  )
}
```

---

<p style="text-align: center; color: #8899a6; font-size: 0.85rem; margin-top: 2rem;">
Data updated automatically each time the site is rendered.<br>
Citations source: Google Scholar. Downloads source: CRAN logs.
</p>