Author

George Roff

Published

March 18, 2025

Publication list dynamically generated via scholar, bibtex, kbl)

Code 
library(tidyverse)
library(scholar)
library(DT)
library(magrittr)
library(RColorBrewer)

scholar_id <- "g_m1R7IAAAAJ"

scholar_output <- scholar::get_publications(id = scholar_id) %>%
  rowwise() %>%
  mutate(
    author = case_when(
    str_ends(author, "\\.\\.\\.") ~ get_complete_authors(id = scholar_id, pubid = pubid),
    TRUE ~ author
    )
  ) %>%
ungroup()

scholar_output_prepped <- scholar_output %>%
  ungroup() %>%
  arrange(desc(year), cites) %>%
  mutate(
    n = seq(1:nrow(.)),
    author = gsub("(G Roff)", "<b>\\1</b>", author, ignore.case = TRUE),  # Use HTML for bold formatting
    cites = as.numeric(cites)  # Ensure cites is numeric
  ) %>%
  select(n, author, year, title, journal, number, cites) %>%
  rename(
    "Year" = "year",
    "Authors" = "author",
    "Journal" = "journal",
    "Issue/Number" = "number",
    "Citations" = "cites"
  )

profile <- scholar::get_profile(scholar_id)
                                
citation_history <- scholar::get_citation_history(id = scholar_id)


npapers <- scholar_output$title |> unique() |> length()
ncites <- scholar_output$cites |> sum()
hindex <- profile$h_index
i10 <- profile$i10_index
affiliation <- profile$affiliation

datatable(
  data.frame(
    a = c("Author", "Affiliation", "Total Citations", "i-10 index", "h-index", paste0("Publications (", min(scholar_output_prepped$Year, na.rm=T), "-present)")),
    b = c("George Roff", affiliation, ncites, hindex, i10, npapers)
  ) |> t(),
  colnames = NULL,
  options = list(
    dom = 't',  # show only the table body
    paging = FALSE,
    ordering = FALSE
  ),
  rownames = FALSE
) %>%
  formatStyle(columns = c(1, 2, 3, 4, 5, 6, 7), fontSize = '80%')
Code 
## All publications to bib
# Convert to BibTeX format
scholar_bib <- scholar_output %>%
  mutate(
    bibtex_entry = paste0(
      "@article{", pubid, ",\n",
      "  title = {", title, "},\n",
      "  author = {", author, "},\n",
      "  journal = {", journal, "},\n",
      "  year = {", year, "},\n",
      "  volume = {", sub(" \\(.*", "", number), "},\n", # Extract volume before '('
      "  number = {", sub(".*\\((.*)\\).*", "\\1", number), "},\n", # Extract issue inside '()'
      "  pages = {", cites, "},\n",
      "  cid = {", cid, "},\n",
      "  pubid = {", pubid, "}\n",
      "}"
    )
  ) %>%
  pull(bibtex_entry)

#writeLines(scholar_bib, "scholar_output.bib")

## select publications to bib
search_terms <- c("Global disparity", "sharks on coral reefs", "evolutionary history", "seascapes", "decline of branching", "decoupled in Holocene")

scholar_bib <- scholar_output %>%
  filter(sapply(title, function(x) any(grepl(paste(search_terms, collapse = "|"), x, ignore.case = TRUE)))) |> 
  mutate(
    bibtex_entry = paste0(
      "@article{", pubid, ",\n",
      "  title = {", title, "},\n",
      "  author = {", author, "},\n",
      "  journal = {", journal, "},\n",
      "  year = {", year, "},\n",
      "  volume = {", sub(" \\(.*", "", number), "},\n", # Extract volume before '('
      "  number = {", sub(".*\\((.*)\\).*", "\\1", number), "},\n", # Extract issue inside '()'
      "  pages = {", cites, "},\n",
      "  cid = {", cid, "},\n",
      "  pubid = {", pubid, "}\n",
      "}"
    )
  ) %>%
  pull(bibtex_entry)

writeLines(scholar_bib, "select_scholar_output.bib")

# Function to lighten a vector of colors
lighten_colors <- function(colors, factor = 0.5) {
  if (factor < 0 || factor > 1) stop("Factor must be between 0 and 1")
  col2rgb(colors) %>%
    t() %>%
    apply(1, function(col) {
      rgb(
        red = col[1] + (255 - col[1]) * factor,
        green = col[2] + (255 - col[2]) * factor,
        blue = col[3] + (255 - col[3]) * factor,
        maxColorValue = 255
      )
    })
}


# Generate colors using RColorBrewer with adjusted alpha
num_colors <- nrow(scholar_output_prepped)
color_palette <- colorRampPalette(rev(brewer.pal(9, "RdYlBu")))(num_colors)
color_palette <- lighten_colors(color_palette, factor = 0.4)  # Set alpha to 0.7

# Map colors to the Citations column
scholar_output_prepped <- scholar_output_prepped %>%
  mutate(
    cite_color = color_palette[rank(Citations, ties.method = "first")]
  )

## kbl format
# scholar_output_prepped %>%
#   select(-cite_color) %>%
#   kbl(escape = FALSE) %>%  # Enable rendering of HTML
#   kable_styling(bootstrap_options = "striped", 
#                 font_size = 12, 
#                 fixed_thead = TRUE,
#                 position = "left") %>%
#   column_spec(7, color = "black", 
#               background = scholar_output_prepped$cite_color) %>%  # Use mapped colors
#   column_spec(2, width_max = "30em") %>%
#   column_spec(4, width_max = "60em") %>%
#   column_spec(5, width_max = "40em") 

# scholar_output |> 
#   group_by(year) |> 
#   summarise(TotalCitations = sum(cites)) |> 
#   mutate(TotalCitations = cumsum(TotalCitations)) |> 
# ggplot() + theme_bw() +
#   geom_point(aes(year, TotalCitations, fill=year), shape=21, show.legend=FALSE) + 
#   scale_fill_distiller(palette="Spectral") + ylab("Cumulative Citations")


datatable(
  scholar_output_prepped %>% select(-cite_color),
  escape = FALSE,
  options = list(
    search = list(regex = TRUE, caseInsensitive = FALSE),
    initComplete = JS(
      "function(settings, json) {",
      "$('body').css({'font-family': 'Arial', 'font-size': '60%'});",
      "}"
    ),
    autoWidth = FALSE,
    dom = 't<"bottom"ip>',
    pageLength = 100,
    columnDefs = list(
      list(className = 'dt-center', targets = "_all"),
      list(width = '10%', targets = 0),
      list(width = '30%', targets = 1),
      list(width = '10%', targets = 2),
      list(width = '30%', targets = 3),
      list(width = '10%', targets = 4),
      list(width = '10%', targets = 5),
      list(width = '10%', targets = 6)
    )
  ),
  rownames = FALSE,
  class = "cell-border stripe"
) %>% formatStyle(
  'Citations',
  backgroundColor = styleEqual(scholar_output_prepped$Citations, scholar_output_prepped$cite_color),
  color = "black"
) %>%
  formatStyle(columns = c(1, 2, 3, 4, 5, 6, 7), fontSize = '80%')
Code 
# JIF
# via https://www.google.com/url?sa=t&source=web&rct=j&opi=89978449&url=https://www.nie.re.kr/nie/cmmn/file/fileDown.do%3FatchFileId%3Deacd8968895c44c6a961680f3c0539d6%26fileSn%3D5&ved=2ahUKEwjK-uXPyYeLAxUVyDgGHVAsEeMQFnoECBYQAQ&usg=AOvVaw1_Y5_qHGFtehu4K4W6Uvas

# jif <- read.csv("2024_jif.csv")
# 
# #find.IF.JCR("Ecology", 2024, exact.match = TRUE)
# 
# scholar_output_prepped <- scholar_output_prepped %>%
#   mutate(
#     matched_jif_name = sapply(Journal, function(journal) {
#       # Perform partial matching with grep
#       match_idx <- grep(journal, jif$Name, ignore.case = TRUE)
#       if (length(match_idx) > 0) {
#         jif$Name[match_idx[1]]  # Use the first match if multiple matches exist
#       } else {
#         NA  # No match found
#       }
#     })
#   )