### COMMON FUNCTIONS ####

# LOAD FUNCTIONS -----
formatDB <- function(obj) {
  ext <- sub(".*\\.", "", obj[1])
  switch(ext,
    txt = {
      format <- "plaintext"
    },
    csv = {
      format <- "csv"
    },
    bib = {
      format <- "bibtex"
    },
    ciw = {
      format <- "endnote"
    },
    xlsx = {
      format <- "excel"
    }
  )
  return(format)
}

## smart_load function ----
smart_load <- function(file) {
  var <- load(file)
  n <- length(var)
  if (!"M" %in% var) {
    if (n == 1) {
      eval(parse(text = paste0("M <- ", var)))
    } else {
      stop("I could not find bibliometrixDB object in your data file: ", file)
    }
  }
  rm(list = var[var != "M"])
  if (("M" %in% ls()) & inherits(M, "bibliometrixDB")) {
    return(M)
  } else {
    stop("Please make sure your RData/Rda file contains a bibliometrixDB object (M).")
  }
}


## merge collections ----
merge_files <- function(files) {
  ## load xlsx or rdata bibliometrix files
  if ("datapath" %in% names(files)) {
    file <- files$datapath
    ext <- unlist(lapply(file, getFileNameExtension))
  }

  Mfile <- list()
  n <- 0
  for (i in 1:length(file)) {
    extF <- ext[i]
    filename <- file[i]

    switch(tolower(extF),
      xlsx = {
        Mfile[[i]] <- readxl::read_excel(filename, col_types = "text") %>% as.data.frame()
        Mfile[[i]]$PY <- as.numeric(Mfile[[i]]$PY)
        Mfile[[i]]$TC <- as.numeric(Mfile[[i]]$TC)
      },
      rdata = {
        Mfile[[i]] <- smart_load(filename)
      }
    )
    n <- n + nrow(Mfile[[i]])
  }

  # merge bibliometrix files
  M <- mergeDbSources(Mfile, remove.duplicated = T)

  # save original size as attribute
  attr(M, "nMerge") <- n

  return(M)
}


# DATA TABLE FORMAT ----
DTformat <- function(df, nrow = 10, filename = "Table", pagelength = TRUE, left = NULL, right = NULL, numeric = NULL, dom = TRUE, size = "85%", filter = "top",
                     columnShort = NULL, columnSmall = NULL, round = 2, title = "", button = FALSE, escape = FALSE, selection = FALSE, scrollX = FALSE, scrollY = FALSE) {
  if ("text" %in% names(df)) {
    df <- df %>%
      mutate(text = gsub("<|>", "", text))
  }

  if (length(columnShort) > 0) {
    columnDefs <- list(
      list(
        className = "dt-center", targets = 0:(length(names(df)) - 1)
      ),
      list(
        targets = columnShort - 1,
        render = JS(
          "function(data, type, row, meta) {",
          "return type === 'display' && data.length > 500 ?",
          "'<span title=\"' + data + '\">' + data.substr(0, 500) + '...</span>' : data;",
          "}"
        )
      )
    )
  } else {
    columnDefs <- list(list(
      className = "dt-center", targets = 0:(length(names(df)) - 1)
    ))
  }
  if (isTRUE(button)) {
    if (isTRUE(pagelength)) {
      buttons <- list(
        list(extend = "pageLength"),
        list(
          extend = "excel",
          filename = paste0(filename, "_bibliometrix_", Sys.Date()),
          title = " ",
          header = TRUE,
          exportOptions = list(
            modifier = list(page = "all")
          )
        )
      )
    } else {
      buttons <- list(
        list(
          extend = "excel",
          filename = paste0(filename, "_bibliometrix_", Sys.Date()),
          title = " ",
          header = TRUE,
          exportOptions = list(
            modifier = list(page = "all")
          )
        )
      )
    }
  } else {
    buttons <- list(list(extend = "pageLength"))
  }

  if (isTRUE(dom)) {
    dom <- "Brtip"
  } else if (dom == FALSE) {
    dom <- "Bftp"
  } else {
    dom <- "t"
  }

  if (nchar(title) > 0) {
    caption <- htmltools::tags$caption(style = "caption-side: top; text-align: center; color:black;  font-size:140% ;", title)
  } else {
    caption <- htmltools::tags$caption(style = "caption-side: top; text-align: center; color:black;  font-size:140% ;", "")
  }

  if (isTRUE(selection)) {
    extensions <- c("Buttons", "Select", "ColReorder", "FixedHeader")
    buttons <- c(buttons, c("selectAll", "selectNone"))
    select <- list(style = "multiple", items = "row", selected = 1:nrow(df))
    # selection = list(mode = 'multiple', selected = 1:nrow(df), target = 'row')
  } else {
    extensions <- c("Buttons", "ColReorder", "FixedHeader")
    select <- NULL
    # selection = "none"
  }

  tab <- DT::datatable(df,
    escape = escape, rownames = FALSE,
    caption = caption,
    selection = "none",
    extensions = extensions,
    filter = filter,
    options = list(
      headerCallback = DT::JS(
        "function(thead) {",
        "  $(thead).css('font-size', '1em');",
        "}"
      ),
      colReorder = TRUE,
      fixedHeader = TRUE,
      pageLength = nrow,
      autoWidth = TRUE, scrollX = scrollX, scrollY = scrollY,
      dom = dom,
      buttons = buttons,
      select = select,
      lengthMenu = list(
        c(10, 25, 50, -1),
        c("10 rows", "25 rows", "50 rows", "Show all")
      ),
      columnDefs = columnDefs
    ),
    class = "cell-border compact stripe"
  ) %>%
    DT::formatStyle(
      names(df),
      backgroundColor = "white",
      textAlign = "center",
      fontSize = size
    )

  ## left aligning

  if (!is.null(left)) {
    tab <- tab %>%
      DT::formatStyle(
        names(df)[left],
        backgroundColor = "white",
        textAlign = "left",
        fontSize = size
      )
  }

  # right aligning
  if (!is.null(right)) {
    tab <- tab %>%
      DT::formatStyle(
        names(df)[right],
        backgroundColor = "white",
        textAlign = "right",
        fontSize = size
      )
  }

  # numeric round
  if (!is.null(numeric)) {
    tab <- tab %>%
      formatRound(names(df)[c(numeric)], digits = round)
  }

  tab
}


authorNameFormat <- function(M, format) {
  if (format == "AF" & "AF" %in% names(M)) {
    M <- M %>%
      rename(
        AU_IN = AU,
        AU = AF
      )
  }
  return(M)
}

split_text_numbers <- function(input_str, UT) {
  # Split the string into components based on "; "
  components <- unlist(strsplit(input_str, "; ", fixed = TRUE))

  # Initialize two vectors to store the separated parts
  texts <- character(length(components))
  numbers <- numeric(length(components))

  # Iterate through each component to separate text and numbers
  for (i in seq_along(components)) {
    # Extract the text using regex, matching everything up to " ("
    texts[i] <- gsub("\\s\\(.*$", "", components[i])

    # Extract the numbers using regex, matching digits inside parentheses
    numbers[i] <- as.numeric(gsub(".*\\((\\d+)\\).*", "\\1", components[i]))
  }

  # Return a list with texts and numbers separated
  data.frame(Texts = texts, Numbers = numbers, UT = UT)
}


AuthorNameMerge <- function(M) {
  df_list <- list()
  for (i in 1:nrow(M)) {
    if (nchar(M$AU[i]) > 0) {
      df_list[[i]] <- split_text_numbers(M$AU[i], M$UT[i])
    }
  }

  df <- do.call(rbind, df_list)

  AU <- df %>%
    group_by(Numbers, Texts) %>%
    count() %>%
    group_by(Numbers) %>%
    arrange(desc(n)) %>%
    mutate(AU = Texts[1]) %>%
    select(-"n", -"Texts") %>%
    ungroup() %>%
    distinct()

  df <- df %>%
    left_join(AU, by = "Numbers") %>%
    group_by(UT) %>%
    summarize(
      AU = paste0(AU, collapse = ";"),
      AU_ID = paste0(Numbers, collapse = ";")
    )

  M <- M %>%
    rename(AU_original = AU) %>%
    left_join(df, by = "UT")
  return(M)
}

getFileNameExtension <- function(fn) {
  # remove a path
  splitted <- strsplit(x = fn, split = "/")[[1]]
  # or use .Platform$file.sep in stead of '/'
  fn <- splitted[length(splitted)]
  ext <- ""
  splitted <- strsplit(x = fn, split = "\\.")[[1]]
  l <- length(splitted)
  if (l > 1 && sum(splitted[1:(l - 1)] != "")) ext <- splitted[l]
  # the extention must be the suffix of a non-empty name
  ext
}

# Initial to upper case
firstup <- function(x) {
  x <- tolower(x)
  substr(x, 1, 1) <- toupper(substr(x, 1, 1))
  x
}


# string preview (stopwords)
strPreview <- function(string, sep = ",") {
  str1 <- unlist(strsplit(string, sep))
  str1 <- str1[1:min(c(length(str1), 5))]
  str1 <- paste(str1, collapse = sep)
  HTML(paste("<pre>", "File Preview: ", str1, "</pre>", sep = "<br/>"))
}

# string preview (synonyms)
strSynPreview <- function(string) {
  string <- string[1]
  str1 <- unlist(strsplit(string, ";"))
  str1 <- str1[1:min(c(length(str1), 5))]
  str1 <- paste(paste(str1[1], " <- ", collapse = ""), paste(str1[-1], collapse = ";"), collapse = "")
  HTML(paste("<pre>", "File Preview: ", str1, "</pre>", sep = "<br/>"))
}

# from igraph to png file
igraph2PNG <- function(x, filename, width = 10, height = 7, dpi = 75) {
  V(x)$centr <- centr_betw(x)$res
  df <- data.frame(name = V(x)$label, cluster = V(x)$color, centr = V(x)$centr) %>%
    group_by(cluster) %>%
    slice_head(n = 3)
  V(x)$label[!(V(x)$label %in% df$name)] <- ""
  png(filename = filename, width = width, height = height, unit = "in", res = dpi)
  grid::grid.draw(plot(x))
  dev.off()
}

# from ggplot to plotly
plot.ly <- function(g, flip = FALSE, side = "r", aspectratio = 1, size = 0.15, data.type = 2, height = 0, customdata = NA) {
  g <- g + labs(title = NULL)

  gg <- ggplotly(g, tooltip = "text") %>%
    config(
      displaylogo = FALSE,
      modeBarButtonsToRemove = c(
        "toImage",
        "sendDataToCloud",
        "pan2d",
        "select2d",
        "lasso2d",
        "toggleSpikelines",
        "hoverClosestCartesian",
        "hoverCompareCartesian"
      )
    )

  return(gg)
}

freqPlot <- function(xx, x, y, textLaby, textLabx, title, values, string.max = 70) {
  xl <- c(max(xx[, x]) - 0.02 - diff(range(xx[, x])) * 0.125, max(xx[, x]) - 0.02) + 1
  yl <- c(1, 1 + length(unique(xx[, y])) * 0.125)

  Text <- paste(textLaby, ": ", xx[, y], "\n", textLabx, ": ", xx[, x])

  if (title == "Most Local Cited References" & values$M$DB[1] == "SCOPUS") {
    xx[, y] <- gsub("^(.+?)\\.,.*\\((\\d{4})\\)$", paste0("\\1", "., ", "\\2"), xx[, y])
  }

  xx[, y] <- substr(xx[, y], 1, string.max)

  g <- ggplot(xx, aes(x = xx[, x], y = xx[, y], label = xx[, x], text = Text)) +
    geom_segment(aes(x = 0, y = xx[, y], xend = xx[, x], yend = xx[, y]), color = "grey50") +
    geom_point(aes(color = -xx[, x], size = xx[, x]), show.legend = FALSE) +
    scale_radius(range = c(5, 12)) +
    geom_text(color = "white", size = 3) +
    scale_y_discrete(limits = rev(xx[, y])) +
    scale_fill_continuous(type = "gradient") +
    labs(title = title, y = textLaby) +
    labs(x = textLabx) +
    expand_limits(y = c(1, length(xx[, y]) + 1)) +
    theme_minimal() +
    theme(axis.text.y = element_text(angle = 0, hjust = 0)) +
    annotation_custom(values$logoGrid, xmin = xl[1], xmax = xl[2], ymin = yl[1], ymax = yl[2])

  return(g)
}

emptyPlot <- function(errortext) {
  g <- ggplot() +
    theme_void() +
    theme(legend.position = "none") +
    annotate("text", x = 4, y = 25, label = errortext, size = 10)
  plot(g)
}

count.duplicates <- function(DF) {
  x <- do.call("paste", c(DF, sep = "\r"))
  ox <- order(x)
  rl <- rle(x[ox])
  cbind(DF[ox[cumsum(rl$lengths)], , drop = FALSE], count = rl$lengths)
}

reduceRefs <- function(A) {
  ind <- unlist(regexec("*V[0-9]", A))
  A[ind > -1] <- substr(A[ind > -1], 1, (ind[ind > -1] - 1))
  ind <- unlist(regexec("*DOI ", A))
  A[ind > -1] <- substr(A[ind > -1], 1, (ind[ind > -1] - 1))
  return(A)
}

notifications <- function() {
  ## check connection and download notifications
  online <- is_online()
  location <- "https://www.bibliometrix.org/bs_notifications/biblioshiny_notifications.csv"
  notifOnline <- NULL
  if (isTRUE(is_online())) {
    ## add check to avoid blocked app when internet connection is to slow
    envir <- environment()
    # setTimeLimit(cpu = 1, elapsed = 1, transient = TRUE)
    # on.exit({
    #   setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE)
    # })
    tryCatch(
      {
        eval(expr = suppressWarnings(notifOnline <- read.csv(location, header = TRUE, sep = ",")), envir = envir)
      },
      error = function(ex) {
        notifOnLine <- NULL
      }
    )
    if (is.null(notifOnline)) {
      online <- FALSE
    } else {
      notifOnline$href[nchar(notifOnline$href) < 6] <- NA
    }
  }

  ## check if a file exists on the local machine and load it
  home <- homeFolder()

  file <- paste(home, "/biblioshiny_notifications.csv", sep = "")
  fileTrue <- file.exists(file)
  if (isTRUE(fileTrue)) {
    suppressWarnings(notifLocal <- read.csv(file, header = TRUE, sep = ","))
    # notifLocal <- readLines(file)
    # linksLocal[nchar(linksLocal)<6] <- NA
  }


  A <- c("noA", "A")
  B <- c("noB", "B")
  status <- paste(A[online + 1], B[fileTrue + 1], sep = "")

  switch(status,
    # missing both files (online and local)
    noAnoB = {
      notifTot <- data.frame(nots = "No notifications", href = NA, status = "info") %>% mutate(status = "info")
    },
    # missing online file. The local one exists.
    noAB = {
      notifTot <- notifLocal %>%
        filter(action == TRUE) %>%
        mutate(status = "info")
    },
    # missing the local file. The online one exists.
    AnoB = {
      # notifOnline <- notifOnline %>%
      #   dplyr::slice_head(n = 5)
      notifTot <- notifOnline %>%
        filter(action == TRUE) %>%
        mutate(status = "danger") %>% 
        dplyr::slice_head(n = 5)
      notifOnline %>%
        filter(action == TRUE) %>%
        write.csv(file = file, quote = FALSE, row.names = FALSE)
    },
    # both files exist.
    AB = {
      notifTot <- left_join(notifOnline %>% mutate(status = "danger"),
        notifLocal %>% mutate(status = "info"),
        by = "nots"
      ) %>%
        mutate(status = tidyr::replace_na(status.y, "danger")) %>%
        rename(
          href = href.x,
          action = action.x
        ) %>%
        select(nots, href, action, status) %>%
        arrange(status) %>%
        filter(action == TRUE) %>%
        dplyr::slice_head(n = 5)
      notifTot %>%
        select(-status) %>%
        write.csv(file = file, quote = FALSE, row.names = FALSE)
    }
  )

  # notifTot <- notifTot[1:(min(5,nrow(notifTot))),]
  return(notifTot)
}

is_online <- function(timeout = 3) {
  RCurl::url.exists("www.bibliometrix.org", timeout = timeout)
}

# is_online <- function(){
#   ## add check to avoid blocked app when internet connection is to slow
#   envir <- environment()
#   setTimeLimit(cpu = 1, elapsed = 1, transient = TRUE)
#   on.exit({
#     setTimeLimit(cpu = Inf, elapsed = Inf, transient = FALSE)
#   })
#   tryCatch({
#     eval(expr=suppressWarnings(resp <- curl::has_internet()), envir = envir)
#   }, error = function(ex) {resp <- FALSE}
#   )
#   return(resp)
# }

initial <- function(values) {
  values$results <- list("NA")
  values$log <- "working..."
  values$load <- "FALSE"
  values$field <- values$cocngrams <- "NA"
  values$citField <- values$colField <- values$citSep <- "NA"
  values$NetWords <- values$NetRefs <- values$ColNetRefs <- matrix(NA, 1, 1)
  values$Title <- "Network"
  values$Histfield <- "NA"
  values$histlog <- "working..."
  values$kk <- 0
  values$histsearch <- "NA"
  values$citShortlabel <- "NA"
  values$S <- list("NA")
  values$GR <- "NA"
  values$nMerge <- NULL
  values$collection_description <- NULL
  ### column to export in TALL
  values$corpusCol <- c("Title" = "TI", "Abstract" = "AB", "Author's Keywords" = "DE")
  values$metadataCol <- c("Publication Year" = "PY", "Document Type" = "DT", "DOI" = "DI", "Open Access" = "OA", "Language" = "LA", "First Author" = "AU1")

  # Chrome enviroment variable
  if (inherits(try(pagedown::find_chrome(), silent=T), "try-error")) {
    values$Chrome_url <- NULL
  }else{
    values$Chrome_url <- pagedown::find_chrome()
  }
  
  return(values)
}

### TALL Export functions ----
tallExport <- function(M, tallFields, tallMetadata, metadataCol) {
  corpus <- NULL
  ## Corpus Fields ##
  if ("Abstract" %in% tallFields) {
    if (!"AB_raw" %in% names(M)) {
      M <- M %>%
        mutate(AB_raw = sapply(AB, capitalize_after_dot, USE.NAMES = FALSE))
    }
    corpus <- c(corpus, "AB_raw")
  }

  if ("Title" %in% tallFields) {
    if (!"TI_raw" %in% names(M)) {
      M <- M %>%
        mutate(TI_raw = sapply(TI, capitalize_after_dot, USE.NAMES = FALSE))
    }
    corpus <- c(corpus, "TI_raw")
  }

  if ("Author's Keywords" %in% tallFields) {
    if (!"DE_raw" %in% names(M)) {
      M <- M %>%
        mutate(DE_raw = sapply(DE, capitalize_after_dot, USE.NAMES = FALSE))
    }
    corpus <- c(corpus, "DE_raw")
  }

  corpus <- c(corpus, as.character(metadataCol[tallMetadata]))

  M <- M %>%
    select(SR, any_of(corpus)) %>%
    rename(doc_id = SR)
  names(M) <- gsub("_raw", "", names(M))

  return(M)
}

capitalize_after_dot <- function(text) {
  # Tutto minuscolo
  text <- tolower(text)

  # Prima lettera della stringa maiuscola
  text <- paste0(toupper(substr(text, 1, 1)), substr(text, 2, nchar(text)))

  # Maiuscola dopo punto (o ! o ?) + spazio
  text <- gsub("([\\.\\!\\?]\\s*)([a-z])", "\\1\\U\\2", text, perl = TRUE)

  return(text)
}


### ANALYSIS FUNCTIONS ####
### Descriptive functions ----

ValueBoxes <- function(M) {
  # calculate statistics for Biblioshiny ValueBoxes
  df <- data.frame(Description = rep(NA, 12), Results = rep(NA, 12))

  ## VB  1 - Time span
  df[1, ] <- c("Timespan", paste(range(M$PY, na.rm = T), collapse = ":"))

  ## VB  2 - Authors
  listAU <- (strsplit(M$AU, ";"))
  nAU <- lengths(listAU)
  listAU <- unique(trimws((unlist(listAU))))
  listAU <- listAU[!is.na(listAU)]
  df[2, ] <- c("Authors", length(listAU))

  ## VB  3 - Author's Keywords (DE)
  if (!"DE" %in% names(M)) {
    M$DE <- ""
  }
  DE <- unique(trimws(gsub("\\s+|\\.|\\,", " ", unlist(strsplit(M$DE, ";")))))
  DE <- DE[!is.na(DE)]

  df[3, ] <- c("Author's Keywords (DE)", length(DE))

  ## VB  4 - Sources
  df[4, ] <- c("Sources (Journals, Books, etc)", length(unique(M$SO)))

  ## VB  5 - Authors of single-authored docs

  df[5, ] <- c("Authors of single-authored docs", length(unique(M$AU[nAU == 1])))

  ## VB  6 - References
  CR <- trimws(gsub("\\s+|\\.|\\,", " ", unlist(strsplit(M$CR, ";"))))
  CR <- CR[nchar(CR) > 0 & !is.na(CR)]
  nCR <- length(unique(CR))
  if (nCR == 1) {
    nCR <- 0
  }
  df[6, ] <- c("References", nCR)

  ## VB  7 - Documents
  df[7, ] <- c("Documents", nrow(M))

  ## VB  8 - International Co-Authorship
  if (!"AU_CO" %in% names(M)) {
    M <- metaTagExtraction(M, "AU_CO")
  }
  AU_CO <- strsplit(M$AU_CO, ";")
  Coll <- unlist(lapply(AU_CO, function(l) {
    length(unique(l)) > 1
  }))
  Coll <- sum(Coll) / nrow(M) * 100
  df[8, ] <- c("International co-authorships %", format(Coll, digits = 4))

  ## VB  9 - Document Average Age
  age <- as.numeric(substr(Sys.Date(), 1, 4)) - M$PY
  df[9, ] <- c("Document Average Age", format(mean(age, na.rm = TRUE), digits = 3))

  ## VB 10 - Annual Growth Rate
  Y <- table(M$PY)
  ny <- diff(range(M$PY, na.rm = TRUE))
  CAGR <- as.numeric(round(((Y[length(Y)] / Y[1])^(1 / (ny)) - 1) * 100, 2))
  df[10, ] <- c("Annual Growth Rate %", CAGR)

  ## VB 11 - Co-Authors per Doc
  df[11, ] <- c("Co-Authors per Doc", format(mean(nAU, na.rm = T), digit = 3))

  ## VB 12 - Average citations per doc
  df[12, ] <- c("Average citations per doc", format(mean(M$TC, na.rm = T), digit = 4))

  DT <- M %>%
    mutate(DT = tolower(DT)) %>%
    count(DT) %>%
    rename(
      Description = DT,
      Results = n
    )

  # Indexed Keywords (ID)
  ID <- unique(trimws(gsub("\\s+|\\.|\\,", " ", unlist(strsplit(M$ID, ";")))))
  ID <- ID[!is.na(ID)]
  df[nrow(df) + 1, ] <- c("Keywords Plus (ID)", length(ID))

  # Single authored docs

  df[nrow(df) + 1, ] <- c("Single-authored docs", sum(nAU == 1))

  df2 <- data.frame(Description = c(
    "MAIN INFORMATION ABOUT DATA", "Timespan", "Sources (Journals, Books, etc)", "Documents",
    "Annual Growth Rate %", "Document Average Age", "Average citations per doc", "References",
    "DOCUMENT CONTENTS", "Keywords Plus (ID)", "Author's Keywords (DE)", "AUTHORS", "Authors", "Authors of single-authored docs",
    "AUTHORS COLLABORATION", "Single-authored docs", "Co-Authors per Doc", "International co-authorships %", "DOCUMENT TYPES"
  ))

  df <- left_join(df2, df, by = "Description") %>%
    rbind(DT) %>%
    mutate(Results = replace_na(Results, ""))

  return(df)
}

countryCollab <- function(M) {
  sep <- ";"
  if (!("AU_CO" %in% names(M))) {
    M <- metaTagExtraction(M, Field = "AU_CO", sep)
  }
  if (!("AU1_CO" %in% names(M))) {
    M <- metaTagExtraction(M, Field = "AU1_CO", sep)
  }

  M$nCO <- as.numeric(unlist(lapply(strsplit(M$AU_CO, ";"), function(l) {
    length(unique(l)) > 1
  })))

  M$AU1_CO <- trim(gsub("[[:digit:]]", "", M$AU1_CO))
  M$AU1_CO <- gsub("UNITED STATES", "USA", M$AU1_CO)
  M$AU1_CO <- gsub("RUSSIAN FEDERATION", "RUSSIA", M$AU1_CO)
  M$AU1_CO <- gsub("TAIWAN", "CHINA", M$AU1_CO)
  M$AU1_CO <- gsub("ENGLAND", "UNITED KINGDOM", M$AU1_CO)
  M$AU1_CO <- gsub("SCOTLAND", "UNITED KINGDOM", M$AU1_CO)
  M$AU1_CO <- gsub("WALES", "UNITED KINGDOM", M$AU1_CO)
  M$AU1_CO <- gsub("NORTH IRELAND", "UNITED KINGDOM", M$AU1_CO)

  df <- M %>%
    group_by(AU1_CO) %>%
    select(AU1_CO, nCO) %>%
    summarize(
      Articles = n(),
      SCP = sum(nCO == 0),
      MCP = sum(nCO == 1)
    ) %>%
    rename(Country = AU1_CO) %>%
    arrange(desc(Articles))

  return(df)
}

Hindex_plot <- function(values, type, input) {
  hindex <- function(values, type, input) {
    switch(type,
      author = {
        # AU <- trim(gsub(",","",names(tableTag(values$M,"AU"))))
        values$H <- Hindex(values$M, field = "author", elements = NULL, sep = ";", years = Inf)$H %>%
          arrange(desc(h_index))
      },
      source = {
        # SO <- names(sort(table(values$M$SO),decreasing = TRUE))
        values$H <- Hindex(values$M, field = "source", elements = NULL, sep = ";", years = Inf)$H %>%
          arrange(desc(h_index))
      }
    )

    return(values)
  }

  values <- hindex(values, type = type, input)

  xx <- values$H
  if (type == "author") {
    K <- input$Hkauthor
    measure <- input$HmeasureAuthors
    title <- "Authors' Local Impact"
    xn <- "Authors"
  } else {
    K <- input$Hksource
    measure <- input$HmeasureSources
    title <- "Sources' Local Impact"
    xn <- "Sources"
  }
  if (K > dim(xx)[1]) {
    k <- dim(xx)[1]
  } else {
    k <- K
  }

  switch(measure,
    h = {
      m <- 2
    },
    g = {
      m <- 3
    },
    m = {
      m <- 4
      xx[, m] <- round(xx[, m], 2)
    },
    tc = {
      m <- 5
    }
  )
  xx <- xx[order(-xx[, m]), ]
  xx <- xx[1:k, c(1, m)]


  g <- freqPlot(xx, x = 2, y = 1, textLaby = xn, textLabx = paste("Impact Measure:", toupper(measure)), title = paste(title, "by", toupper(measure), "index"), values)

  res <- list(values = values, g = g)
  return(res)
}

descriptive <- function(values, type) {
  switch(type,
    "tab2" = {
      TAB <- values$M %>%
        group_by(PY) %>%
        count() %>%
        rename(
          Year = PY,
          Articles = n
        ) %>%
        right_join(data.frame(Year = seq(min(values$M$PY, na.rm = TRUE), max(values$M$PY, na.rm = TRUE))), by = "Year") %>%
        mutate(Articles = replace_na(Articles, 0)) %>%
        arrange(Year) %>%
        as.data.frame()

      ny <- diff(range(TAB$Year))
      values$GR <- round(((TAB[nrow(TAB), 2] / TAB[1, 2])^(1 / (ny)) - 1) * 100, digits = 2)
    },
    "tab3" = {
      listAU <- (strsplit(values$M$AU, ";"))
      nAU <- lengths(listAU)
      fracAU <- rep(1 / nAU, nAU)
      TAB <- tibble(Author = unlist(listAU), fracAU = fracAU) %>%
        group_by(Author) %>%
        summarize(
          Articles = n(),
          AuthorFrac = sum(fracAU)
        ) %>%
        arrange(desc(Articles)) %>%
        as.data.frame()
      names(TAB) <- c("Authors", "Articles", "Articles Fractionalized")
      # print(S$MostProdAuthors)
    },
    "tab4" = {
      y <- as.numeric(substr(Sys.Date(), 1, 4))
      TAB <- values$M %>%
        mutate(TCperYear = TC / (y + 1 - PY)) %>%
        select(SR, DI, TC, TCperYear, PY) %>%
        group_by(PY) %>%
        mutate(NTC = TC / mean(TC)) %>%
        ungroup() %>%
        select(-PY) %>%
        arrange(desc(TC)) %>%
        as.data.frame()
      names(TAB) <- c("Paper", "DOI", "Total Citations", "TC per Year", "Normalized TC")
    },
    "tab5" = {
      TAB <- countryCollab(values$M)
      TAB <- TAB %>%
        mutate(Freq = Articles / sum(Articles)) %>%
        mutate(MCP_Ratio = MCP / Articles) %>%
        drop_na(Country)
    },
    "tab6" = {
      if (!"AU1_CO" %in% names(values$M)) {
        values$M <- metaTagExtraction(values$M, "AU1_CO")
      }
      TAB <- values$M %>%
        select(AU1_CO, TC) %>%
        drop_na(AU1_CO) %>%
        rename(
          Country = AU1_CO,
          TotalCitation = TC
        ) %>%
        group_by(Country) %>%
        summarise("TC" = sum(TotalCitation), "Average Article Citations" = round(sum(TotalCitation) / length(TotalCitation), 1)) %>%
        arrange(-TC) %>%
        as.data.frame(.data)
    },
    "tab7" = {
      TAB <- values$M %>%
        select(SO) %>%
        group_by(SO) %>%
        count() %>%
        arrange(desc(n)) %>%
        rename(
          Sources = SO,
          Articles = n
        ) %>%
        as.data.frame()
    },
    "tab10" = {
      TAB <- mapworld(values$M)$tab
    },
    "tab11" = {
      if (!("AU_UN" %in% names(values$M))) {
        values$M <- metaTagExtraction(values$M, Field = "AU_UN")
      }
      TAB <- data.frame(Affiliation = unlist(strsplit(values$M$AU_UN, ";"))) %>%
        group_by(Affiliation) %>%
        count() %>%
        drop_na(Affiliation) %>%
        arrange(desc(n)) %>%
        rename(Articles = n) %>%
        filter(Affiliation != "NA") %>%
        as.data.frame()
    },
    "tab12" = {
      TAB <- tableTag(values$M, "C1")
      TAB <- data.frame(Affiliations = names(TAB), Articles = as.numeric(TAB))
      TAB <- TAB[nchar(TAB[, 1]) > 4, ]
      # names(TAB)=c("Affiliations", "Articles")
    },
    "tab13" = {
      CR <- localCitations(values$M, fast.search = FALSE, verbose = FALSE)
      TAB <- CR$Authors
      # TAB=data.frame(Authors=names(CR$Authors$Author), Citations=as.numeric(CR$Cited))
    }
  )
  values$TAB <- TAB
  res <- list(values = values, TAB = TAB)
  return(res)
}

AffiliationOverTime <- function(values, n) {
  if (!("AU_UN" %in% names(values$M))) {
    values$M <- metaTagExtraction(values$M, Field = "AU_UN")
  }
  AFF <- strsplit(values$M$AU_UN, ";")
  nAFF <- lengths(AFF)

  AFFY <- data.frame(Affiliation = unlist(AFF), Year = rep(values$M$PY, nAFF)) %>%
    filter(Affiliation != "NA") %>%
    drop_na(Affiliation, Year) %>%
    group_by(Affiliation, Year) %>%
    count() %>%
    group_by(Affiliation) %>%
    arrange(Year) %>%
    ungroup() %>%
    pivot_wider(Affiliation, names_from = Year, values_from = n) %>%
    mutate_all(~ replace(., is.na(.), 0)) %>%
    pivot_longer(cols = !Affiliation, names_to = "Year", values_to = "Articles") %>%
    group_by(Affiliation) %>%
    mutate(Articles = cumsum(Articles))

  Affselected <- AFFY %>%
    filter(Year == max(Year)) %>%
    ungroup() %>%
    slice_max(Articles, n = n)

  values$AffOverTime <- AFFY %>%
    filter(Affiliation %in% Affselected$Affiliation) %>%
    mutate(Year = Year %>% as.numeric())

  Text <- paste(values$AffOverTime$Affiliation, " (", values$AffOverTime$Year, ") ", values$AffOverTime$Articles, sep = "")
  width_scale <- 1.7 * 26 / length(unique(values$AffOverTime$Affiliation))
  x <- c(max(values$AffOverTime$Year) - 0.02 - diff(range(values$AffOverTime$Year)) * 0.15, max(values$AffOverTime$Year) - 0.02) + 1
  y <- c(min(values$AffOverTime$Articles), min(values$AffOverTime$Articles) + diff(range(values$AffOverTime$Articles)) * 0.15)


  values$AffOverTimePlot <- ggplot(values$AffOverTime, aes(x = Year, y = Articles, group = Affiliation, color = Affiliation, text = Text)) +
    geom_line() +
    labs(
      x = "Year",
      y = "Articles",
      title = "Affiliations' Production over Time"
    ) +
    scale_x_continuous(breaks = (values$AffOverTime$Year[seq(1, length(values$AffOverTime$Year), by = ceiling(length(values$AffOverTime$Year) / 20))])) +
    geom_hline(aes(yintercept = 0), alpha = 0.1) +
    labs(color = "Affiliation") +
    theme(
      text = element_text(color = "#444444"),
      legend.text = ggplot2::element_text(size = width_scale),
      legend.box.margin = margin(6, 6, 6, 6),
      legend.title = ggplot2::element_text(size = 1.5 * width_scale, face = "bold"),
      legend.position = "bottom",
      legend.direction = "vertical",
      legend.key.size = grid::unit(width_scale / 50, "inch"),
      legend.key.width = grid::unit(width_scale / 50, "inch"),
      plot.caption = element_text(size = 9, hjust = 0.5, color = "black", face = "bold"),
      panel.background = element_rect(fill = "#FFFFFF"),
      panel.grid.minor = element_line(color = "#EFEFEF"),
      panel.grid.major = element_line(color = "#EFEFEF"),
      plot.title = element_text(size = 24),
      axis.title = element_text(size = 14, color = "#555555"),
      axis.title.y = element_text(vjust = 1, angle = 90),
      axis.title.x = element_text(hjust = 0.95, angle = 0),
      axis.text.x = element_text(size = 10, angle = 90),
      axis.line.x = element_line(color = "black", linewidth = 0.5),
      axis.line.y = element_line(color = "black", linewidth = 0.5)
    ) +
    annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
  return(values)
}

CountryOverTime <- function(values, n) {
  if (!("AU_CO" %in% names(values$M))) {
    values$M <- metaTagExtraction(values$M, Field = "AU_CO")
  }
  AFF <- strsplit(values$M$AU_CO, ";")
  nAFF <- lengths(AFF)

  AFFY <- data.frame(Affiliation = unlist(AFF), Year = rep(values$M$PY, nAFF)) %>%
    drop_na(Affiliation, Year) %>%
    group_by(Affiliation, Year) %>%
    count() %>%
    group_by(Affiliation) %>%
    arrange(Year) %>%
    ungroup() %>%
    pivot_wider(Affiliation, names_from = Year, values_from = n) %>%
    mutate_all(~ replace(., is.na(.), 0)) %>%
    pivot_longer(cols = !Affiliation, names_to = "Year", values_to = "Articles") %>%
    group_by(Affiliation) %>%
    mutate(Articles = cumsum(Articles))

  Affselected <- AFFY %>%
    filter(Year == max(Year)) %>%
    ungroup() %>%
    slice_max(Articles, n = n)

  values$CountryOverTime <- AFFY %>%
    filter(Affiliation %in% Affselected$Affiliation) %>%
    mutate(Year = Year %>% as.numeric()) %>%
    rename(Country = Affiliation)

  Text <- paste(values$CountryOverTime$Country, " (", values$CountryOverTime$Year, ") ", values$CountryOverTime$Articles, sep = "")
  width_scale <- 1.7 * 26 / length(unique(values$CountryOverTime$Country))
  x <- c(max(values$CountryOverTime$Year) - 0.02 - diff(range(values$CountryOverTime$Year)) * 0.15, max(values$CountryOverTime$Year) - 0.02) + 1
  y <- c(min(values$CountryOverTime$Articles), min(values$CountryOverTime$Articles) + diff(range(values$CountryOverTime$Articles)) * 0.15)


  values$CountryOverTimePlot <- ggplot(values$CountryOverTime, aes(x = Year, y = Articles, group = Country, color = Country, text = Text)) +
    geom_line() +
    labs(
      x = "Year",
      y = "Articles",
      title = "Country Production over Time"
    ) +
    scale_x_continuous(breaks = (values$CountryOverTime$Year[seq(1, length(values$CountryOverTime$Year), by = ceiling(length(values$CountryOverTime$Year) / 20))])) +
    geom_hline(aes(yintercept = 0), alpha = 0.1) +
    labs(color = "Country") +
    theme(
      text = element_text(color = "#444444"),
      legend.text = ggplot2::element_text(size = width_scale),
      legend.box.margin = margin(6, 6, 6, 6),
      legend.title = ggplot2::element_text(size = 1.5 * width_scale, face = "bold"),
      legend.position = "bottom",
      legend.direction = "vertical",
      legend.key.size = grid::unit(width_scale / 50, "inch"),
      legend.key.width = grid::unit(width_scale / 50, "inch"),
      plot.caption = element_text(size = 9, hjust = 0.5, color = "black", face = "bold"),
      panel.background = element_rect(fill = "#FFFFFF"),
      panel.grid.minor = element_line(color = "#EFEFEF"),
      panel.grid.major = element_line(color = "#EFEFEF"),
      plot.title = element_text(size = 24),
      axis.title = element_text(size = 14, color = "#555555"),
      axis.title.y = element_text(vjust = 1, angle = 90),
      axis.title.x = element_text(hjust = 0.95, angle = 0),
      axis.text.x = element_text(size = 10, angle = 90),
      axis.line.x = element_line(color = "black", linewidth = 0.5),
      axis.line.y = element_line(color = "black", linewidth = 0.5)
    ) +
    annotation_custom(values$logoGrid, xmin = x[1], xmax = x[2], ymin = y[1], ymax = y[2])
  return(values)
}

wordlist <- function(M, Field, n, measure, ngrams, remove.terms = NULL, synonyms = NULL) {
  switch(Field,
    ID = {
      v <- tableTag(M, "ID", remove.terms = remove.terms, synonyms = synonyms)
    },
    DE = {
      v <- tableTag(M, "DE", remove.terms = remove.terms, synonyms = synonyms)
    },
    KW_Merged = {
      v <- tableTag(M, "KW_Merged", remove.terms = remove.terms, synonyms = synonyms)
    },
    TI = {
      if (!("TI_TM" %in% names(M))) {
        v <- tableTag(M, "TI", ngrams = ngrams, remove.terms = remove.terms, synonyms = synonyms)
      }
    },
    AB = {
      if (!("AB_TM" %in% names(M))) {
        v <- tableTag(M, "AB", ngrams = ngrams, remove.terms = remove.terms, synonyms = synonyms)
      }
    },
    WC = {
      v <- tableTag(M, "WC")
    }
  )
  names(v) <- tolower(names(v))
  # v=tableTag(values$M,"ID")
  n <- min(c(n, length(v)))
  Words <- data.frame(Terms = names(v)[1:n], Frequency = (as.numeric(v)[1:n]), stringsAsFactors = FALSE)
  W <- Words
  switch(measure,
    identity = {},
    sqrt = {
      W$Frequency <- sqrt(W$Frequency)
    },
    log = {
      W$Frequency <- log(W$Frequency + 1)
    },
    log10 = {
      W$Frequency <- log10(W$Frequency + 1)
    }
  )

  results <- list(v = v, W = W, Words = Words)
  return(results)
}

readStopwordsFile <- function(file, sep = ",") {
  if (!is.null(file)) {
    req(file$datapath)
    remove.terms <- unlist(strsplit(readr::read_lines(file$datapath), sep))
  } else {
    remove.terms <- NULL
  }
  return(remove.terms)
}

readSynWordsFile <- function(file, sep = ",") {
  if (!is.null(file)) {
    req(file$datapath)
    syn.terms <- readr::read_lines(file$datapath)
    if (sep != ";") syn.terms <- gsub(sep, ";", syn.terms)
  } else {
    syn.terms <- NULL
  }
  return(syn.terms)
}

mapworld <- function(M, values) {
  if (!("AU_CO" %in% names(M))) {
    M <- metaTagExtraction(M, "AU_CO")
  }
  CO <- as.data.frame(tableTag(M, "AU_CO"))
  CO$Tab <- gsub("[[:digit:]]", "", CO$Tab)
  CO$Tab <- gsub(".", "", CO$Tab, fixed = TRUE)
  CO$Tab <- gsub(";;", ";", CO$Tab, fixed = TRUE)
  CO$Tab <- gsub("UNITED STATES", "USA", CO$Tab)
  CO$Tab <- gsub("RUSSIAN FEDERATION", "RUSSIA", CO$Tab)
  CO$Tab <- gsub("TAIWAN", "CHINA", CO$Tab)
  CO$Tab <- gsub("ENGLAND", "UNITED KINGDOM", CO$Tab)
  CO$Tab <- gsub("SCOTLAND", "UNITED KINGDOM", CO$Tab)
  CO$Tab <- gsub("WALES", "UNITED KINGDOM", CO$Tab)
  CO$Tab <- gsub("NORTH IRELAND", "UNITED KINGDOM", CO$Tab)
  CO$Tab <- gsub("UNITED KINGDOM", "UK", CO$Tab)
  CO$Tab <- gsub("KOREA", "SOUTH KOREA", CO$Tab)


  map.world <- map_data("world")
  map.world$region <- toupper(map.world$region)

  # dplyr::anti_join(CO, map.world, by = c('Tab' = 'region'))

  country.prod <- dplyr::left_join(map.world, CO, by = c("region" = "Tab"))

  tab <- data.frame(country.prod %>%
    dplyr::group_by(region) %>%
    dplyr::summarise(Freq = mean(Freq)))

  tab <- tab[!is.na(tab$Freq), ]

  tab <- tab[order(-tab$Freq), ]

  # breaks=as.numeric(round(quantile(CO$Freq,c(0.2,0.4,0.6,0.8,1))))
  # names(breaks)=breaks
  # breaks=log(breaks)
  breaks <- as.numeric(cut(CO$Freq, breaks = 10))
  names(breaks) <- breaks

  g <- ggplot(country.prod, aes(x = long, y = lat, group = group, text = paste("Country: ", region, "\nN.of Documents: ", Freq))) +
    geom_polygon(aes(fill = Freq, group = group)) +
    scale_fill_continuous(low = "#87CEEB", high = "dodgerblue4", breaks = breaks, na.value = "grey80") +
    guides(fill = guide_legend(reverse = T)) +
    # geom_text(data=centroids, aes(label = centroids$Tab, x = centroids$long, y = centroids$lat, group=centroids$Tab)) +
    labs(
      fill = "N.Documents",
      title = "Country Scientific Production",
      x = NULL,
      y = NULL
    ) +
    theme(
      text = element_text(color = "#333333"),
      plot.title = element_text(size = 28),
      plot.subtitle = element_text(size = 14),
      axis.ticks = element_blank(),
      axis.text = element_blank(),
      panel.grid = element_blank(),
      panel.background = element_rect(fill = "#FFFFFF") #' #333333'
      , plot.background = element_rect(fill = "#FFFFFF"),
      legend.position = "none"
      # ,legend.background = element_blank()
      # ,legend.key = element_blank()
    ) +
    annotation_custom(values$logoGrid, xmin = 143, xmax = 189.5, ymin = -69, ymax = -48)

  results <- list(g = g, tab = tab)
  return(results)
}

### Structure fuctions ----
CAmap <- function(input, values) {
  if ((input$CSfield %in% names(values$M))) {
    if (input$CSfield %in% c("TI", "AB")) {
      ngrams <- as.numeric(input$CSngrams)
    } else {
      ngrams <- 1
    }

    ### load file with terms to remove
    if (input$CSStopFile == "Y") {
      remove.terms <- trimws(values$CSremove.terms$stopword)
    } else {
      remove.terms <- NULL
    }
    # values$CSremove.terms <- remove.terms
    ### end of block
    ### load file with synonyms
    if (input$FASynFile == "Y") {
      synonyms <- values$FAsyn.terms %>%
        group_by(term) %>%
        mutate(term = paste0(term, ";", synonyms)) %>%
        select(term)
      synonyms <- synonyms$term
    } else {
      synonyms <- NULL
    }
    # values$FAsyn.terms <- synonyms
    ### end of block

    tab <- tableTag(values$M, input$CSfield, ngrams = ngrams)
    if (length(tab >= 2)) {
      minDegree <- as.numeric(tab[input$CSn])

      values$CS <- conceptualStructure(values$M,
        method = input$method, field = input$CSfield, minDegree = minDegree, clust = input$nClustersCS,
        k.max = 8, stemming = F, labelsize = input$CSlabelsize / 2, documents = input$CSdoc, graph = FALSE, ngrams = ngrams,
        remove.terms = remove.terms, synonyms = synonyms
      )
      if (input$method != "MDS") {
        CSData <- values$CS$docCoord
        CSData <- data.frame(Documents = row.names(CSData), CSData)
        CSData$dim1 <- round(CSData$dim1, 2)
        CSData$dim2 <- round(CSData$dim2, 2)
        CSData$contrib <- round(CSData$contrib, 2)
        values$CS$CSData <- CSData
      } else {
        values$CS$CSData <- data.frame(Docuemnts = NA, dim1 = NA, dim2 = NA)
      }


      switch(input$method,
        CA = {
          WData <- data.frame(
            word = row.names(values$CS$km.res$data.clust), values$CS$km.res$data.clust,
            stringsAsFactors = FALSE
          )
          names(WData)[4] <- "cluster"
        },
        MCA = {
          WData <- data.frame(
            word = row.names(values$CS$km.res$data.clust), values$CS$km.res$data.clust,
            stringsAsFactors = FALSE
          )
          names(WData)[4] <- "cluster"
        },
        MDS = {
          WData <- data.frame(
            word = row.names(values$CS$res), values$CS$res,
            cluster = values$CS$km.res$cluster
          )
        }
      )

      WData$Dim1 <- round(WData$Dim1, 2)
      WData$Dim2 <- round(WData$Dim2, 2)
      values$CS$WData <- WData
    } else {
      emptyPlot("Selected field is not included in your data collection")
      values$CS <- list("NA")
    }
  } else {
    emptyPlot("Selected field is not included in your data collection")
    values$CS <- list("NA")
  }
  return(values)
}

historiograph <- function(input, values) {
  min.cit <- 0

  # if (values$Histfield=="NA"){
  values$histResults <- histNetwork(values$M, min.citations = min.cit, sep = ";")
  # values$Histfield="done"
  # }

  # titlelabel <- input$titlelabel
  values$histlog <- (values$histPlot <- histPlot(values$histResults, n = input$histNodes, size = input$histsize, remove.isolates = (input$hist.isolates == "yes"), labelsize = input$histlabelsize, label = input$titlelabel, verbose = FALSE))
  values$histResults$histData$DOI <- paste0('<a href=\"https://doi.org/', values$histResults$histData$DOI, '\" target=\"_blank\">', values$histResults$histData$DOI, "</a>")
  values$histResults$histData <- values$histResults$histData %>%
    left_join(
      values$histPlot$layout %>%
        select(name, color),
      by = c("Paper" = "name")
    ) %>%
    drop_na(color) %>%
    mutate(cluster = match(color, unique(color))) %>%
    select(!color) %>%
    group_by(cluster) %>%
    arrange(Year, .by_group = TRUE)
  return(values)
}


### Network functions ----
degreePlot <- function(net) {
  # deg <- data.frame(node = names(net$nodeDegree), x= (1:length(net$nodeDegree)), y = net$nodeDegree)
  ma <- function(x, n = 5) {
    stats::filter(x, rep(1 / n, n), sides = 1)
  }

  deg <- net$nodeDegree %>%
    mutate(x = row_number())

  p <- ggplot(data = deg, aes(
    x = x, y = degree,
    text = paste(node, " - Degree ", round(degree, 3), sep = "")
  )) +
    geom_point() +
    geom_line(aes(group = "NA"), color = "#002F80", alpha = .5) +
    # geom_hline(yintercept=cutting$degree, linetype="dashed",color = '#002F80', alpha = .5)+
    theme(
      text = element_text(color = "#444444"),
      panel.background = element_rect(fill = "#FFFFFF"),
      panel.grid.minor = element_line(color = "#EFEFEF"),
      panel.grid.major = element_line(color = "#EFEFEF"),
      plot.title = element_text(size = 24),
      axis.title = element_text(size = 14, color = "#555555"),
      axis.title.y = element_text(vjust = 1, angle = 0),
      axis.title.x = element_text(hjust = 0),
      axis.line.x = element_line(color = "black", linewidth = 0.5),
      axis.line.y = element_line(color = "black", linewidth = 0.5)
    ) +
    labs(x = "Node", y = "Cumulative Degree", title = "Node Degrees")
  return(p)
}

cocNetwork <- function(input, values) {
  n <- input$Nodes
  label.n <- input$Labels

  ### load file with terms to remove
  if (input$COCStopFile == "Y") {
    remove.terms <- trimws(values$COCremove.terms$stopword)
  } else {
    remove.terms <- NULL
  }
  # values$COCremove.terms <- remove.terms
  ### end of block
  ### load file with synonyms
  if (input$COCSynFile == "Y") {
    synonyms <- values$COCsyn.terms %>%
      group_by(term) %>%
      mutate(term = paste0(term, ";", synonyms)) %>%
      select(term)
    synonyms <- synonyms$term
  } else {
    synonyms <- NULL
  }
  # values$COCsyn.terms <- synonyms
  ### end of block

  if ((input$field %in% names(values$M))) {
    if ((dim(values$NetWords)[1]) == 1 | !(input$field == values$field) | !(input$cocngrams == values$cocngrams) | ((dim(values$NetWords)[1]) != input$Nodes)) {
      values$field <- input$field
      values$ngrams <- input$cocngrams

      switch(input$field,
        ID = {
          values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "keywords", n = n, sep = ";", remove.terms = remove.terms, synonyms = synonyms)
          values$Title <- "Keywords Plus Network"
        },
        DE = {
          values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "author_keywords", n = n, sep = ";", remove.terms = remove.terms, synonyms = synonyms)
          values$Title <- "Authors' Keywords network"
        },
        KW_Merged ={
          values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "all_keywords", n = n, sep = ";", remove.terms = remove.terms, synonyms = synonyms)
          values$Title <- "All Keywords network"
        },
        TI = {
          # if(!("TI_TM" %in% names(values$M))){
          values$M <- termExtraction(values$M, Field = "TI", verbose = FALSE, ngrams = as.numeric(input$cocngrams), remove.terms = remove.terms, synonyms = synonyms)
          # }
          values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "titles", n = n, sep = ";")
          values$Title <- "Title Words network"
        },
        AB = {
          # if(!("AB_TM" %in% names(values$M))){
          values$M <- termExtraction(values$M, Field = "AB", verbose = FALSE, ngrams = as.numeric(input$cocngrams), remove.terms = remove.terms, synonyms = synonyms)
          # }
          values$NetWords <- biblioNetwork(values$M, analysis = "co-occurrences", network = "abstracts", n = n, sep = ";")
          values$Title <- "Abstract Words network"
        },
        WC = {
          WSC <- cocMatrix(values$M, Field = "WC", binary = FALSE)
          values$NetWords <- crossprod(WSC, WSC)
          values$Title <- "Subject Categories network"
        }
      )
    }

    if (label.n > n) {
      label.n <- n
    }
    if (input$normalize == "none") {
      normalize <- NULL
    } else {
      normalize <- input$normalize
    }
    if (input$label.cex == "Yes") {
      label.cex <- TRUE
    } else {
      label.cex <- FALSE
    }
    if (input$coc.curved == "Yes") {
      curved <- TRUE
    } else {
      curved <- FALSE
    }
    
    values$cocnet <- networkPlot(values$NetWords,
      normalize = normalize, Title = values$Title, type = input$layout,
      size.cex = TRUE, size = 5, remove.multiple = F, edgesize = input$edgesize * 3, labelsize = input$labelsize, label.cex = label.cex,
      label.n = label.n, edges.min = input$edges.min, label.color = F, curved = curved, alpha = input$cocAlpha,
      cluster = input$cocCluster, remove.isolates = (input$coc.isolates == "yes"),
      community.repulsion = input$coc.repulsion / 2, verbose = FALSE
    )
    if (input$cocyears == "Yes") {
      Y <- fieldByYear(values$M, field = input$field, graph = FALSE)
      g <- values$cocnet$graph
      label <- igraph::V(g)$name
      ind <- which(tolower(Y$df$item) %in% label)
      df <- Y$df[ind, ]

      col <- hcl.colors((diff(range(df$year_med)) + 1) * 10, palette = "Blues 3")
      igraph::V(g)$color <- col[(max(df$year_med) - df$year_med + 1) * 10]
      igraph::V(g)$year_med <- df$year_med
      values$cocnet$graph <- g
    }
  } else {
    emptyPlot("Selected field is not included in your data collection")
  }
  return(values)
}

intellectualStructure <- function(input, values) {
  n <- input$citNodes
  label.n <- input$citLabels

  if ((dim(values$NetRefs)[1]) == 1 | !(input$citField == values$citField) | !(input$citSep == values$citSep) | !(input$citShortlabel == values$citShortlabel) | ((dim(values$NetRefs)[1]) != input$citNodes)) {
    values$citField <- input$citField
    values$citSep <- input$citSep
    if (input$citShortlabel == "Yes") {
      shortlabel <- TRUE
    } else {
      shortlabel <- FALSE
    }
    values$citShortlabel <- input$citShortlabel
    switch(input$citField,
      CR = {
        values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "references", n = n, sep = input$citSep, shortlabel = shortlabel)
        values$Title <- "Cited References network"
      },
      CR_AU = {
        if (!("CR_AU" %in% names(values$M))) {
          values$M <- metaTagExtraction(values$M, Field = "CR_AU", sep = input$citSep)
        }
        values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "authors", n = n, sep = input$citSep)
        values$Title <- "Cited Authors network"
      },
      CR_SO = {
        if (!("CR_SO" %in% names(values$M))) {
          values$M <- metaTagExtraction(values$M, Field = "CR_SO", sep = input$citSep)
        }
        values$NetRefs <- biblioNetwork(values$M, analysis = "co-citation", network = "sources", n = n, sep = input$citSep)
        values$Title <- "Cited Sources network"
      }
    )
  }

  if (label.n > n) {
    label.n <- n
  }
  if (input$citlabel.cex == "Yes") {
    label.cex <- TRUE
  } else {
    label.cex <- FALSE
  }
  if (input$cocit.curved == "Yes") {
    curved <- TRUE
  } else {
    curved <- FALSE
  }

  values$cocitnet <- networkPlot(values$NetRefs,
    normalize = NULL, Title = values$Title, type = input$citlayout,
    size.cex = TRUE, size = 5, remove.multiple = F, edgesize = input$citedgesize * 3,
    labelsize = input$citlabelsize, label.cex = label.cex, curved = curved,
    label.n = label.n, edges.min = input$citedges.min, label.color = F, remove.isolates = (input$cit.isolates == "yes"),
    alpha = 0.7, cluster = input$cocitCluster,
    community.repulsion = input$cocit.repulsion / 2, verbose = FALSE
  )
  return(values)
}

socialStructure <- function(input, values) {
  n <- input$colNodes
  label.n <- input$colLabels

  if ((dim(values$ColNetRefs)[1]) == 1 | !(input$colField == values$colField) | ((dim(values$ColNetRefs)[1]) != input$colNodes)) {
    values$colField <- input$colField


    # values$cluster="walktrap"
    switch(input$colField,
      COL_AU = {
        values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "authors", n = n, sep = ";")
        values$Title <- "Author Collaboration network"
      },
      COL_UN = {
        if (!("AU_UN" %in% names(values$M))) {
          values$M <- metaTagExtraction(values$M, Field = "AU_UN", sep = ";")
        }
        values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "universities", n = n, sep = ";")
        values$Title <- "Edu Collaboration network"
      },
      COL_CO = {
        if (!("AU_CO" %in% names(values$M))) {
          values$M <- metaTagExtraction(values$M, Field = "AU_CO", sep = ";")
        }
        values$ColNetRefs <- biblioNetwork(values$M, analysis = "collaboration", network = "countries", n = n, sep = ";")
        values$Title <- "Country Collaboration network"
        # values$cluster="none"
      }
    )
  }

  if (label.n > n) {
    label.n <- n
  }
  if (input$colnormalize == "none") {
    normalize <- NULL
  } else {
    normalize <- input$colnormalize
  }
  if (input$collabel.cex == "Yes") {
    label.cex <- TRUE
  } else {
    label.cex <- FALSE
  }
  if (input$soc.curved == "Yes") {
    curved <- TRUE
  } else {
    curved <- FALSE
  }

  type <- input$collayout
  if (input$collayout == "worldmap") {
    type <- "auto"
  }

  values$colnet <- networkPlot(values$ColNetRefs,
    normalize = normalize, Title = values$Title, type = type,
    size.cex = TRUE, size = 5, remove.multiple = F, edgesize = input$coledgesize * 3,
    labelsize = input$collabelsize, label.cex = label.cex, curved = curved,
    label.n = label.n, edges.min = input$coledges.min, label.color = F, alpha = input$colAlpha,
    remove.isolates = (input$col.isolates == "yes"), cluster = input$colCluster,
    community.repulsion = input$col.repulsion / 2, verbose = FALSE
  )

  return(values)
}

countrycollaboration <- function(M, label, edgesize, min.edges, values) {
  M <- metaTagExtraction(M, "AU_CO")
  net <- biblioNetwork(M, analysis = "collaboration", network = "countries")
  CO <- data.frame(Tab = rownames(net), Freq = diag(net))
  bsk.network <- igraph::graph_from_adjacency_matrix(net, mode = "undirected")
  COedges <- as.data.frame(igraph::ends(bsk.network, igraph::E(bsk.network), names = TRUE))

  map.world <- map_data("world")
  map.world$region <- toupper(map.world$region)
  map.world$region <- gsub("^UK$", "UNITED KINGDOM", map.world$region)
  map.world$region <- gsub("^SOUTH KOREA$", "KOREA", map.world$region)

  country.prod <- dplyr::left_join(map.world, CO, by = c("region" = "Tab"))

  # breaks <- as.numeric(round(quantile(CO$Freq,seq(0.1,1,by=0.1))))
  breaks <- as.numeric(cut(CO$Freq, breaks = 10))
  names(breaks) <- breaks
  # breaks=breaks
  data("countries", envir = environment())
  names(countries)[1] <- "Tab"

  COedges <- dplyr::inner_join(COedges, countries, by = c("V1" = "Tab"))
  COedges <- dplyr::inner_join(COedges, countries, by = c("V2" = "Tab"))
  COedges <- COedges[COedges$V1 != COedges$V2, ]
  COedges <- count.duplicates(COedges)
  tab <- COedges
  COedges <- COedges[COedges$count >= min.edges, ]
  COedges$region <- paste("\nCollaboration between\n", COedges$V1, "\n and \n", COedges$V2)

  g <- ggplot(country.prod, aes(x = long, y = lat, group = group, text = paste("Country: ", region))) +
    geom_polygon(aes(fill = Freq)) +
    scale_fill_continuous(low = "#87CEEB", high = "dodgerblue4", breaks = breaks, na.value = "grey80") +
    # guides(fill = guide_legend(reverse = T)) +
    guides(colour = FALSE, fill = FALSE) +
    # geom_curve(data=COedges, aes(x = Longitude.x , y = Latitude.x, xend = Longitude.y, yend = Latitude.y,     # draw edges as arcs
    #                              color = "firebrick4", size = count, group=continent.x),
    #            curvature = 0.33,
    #            alpha = 0.5) +
    geom_segment(
      data = COedges, aes(
        x = Longitude.x, y = Latitude.x, xend = Longitude.y, yend = Latitude.y, # draw edges as arcs
        size = count, group = continent.x
      ),
      color = "orangered4", # FFB347",
      # curvature = 0.33,
      alpha = 0.3
    ) +
    scale_size_continuous(guide = FALSE, range = c(0.25, edgesize)) +
    labs(title = NULL, x = "Latitude", y = "Longitude") +
    theme(
      text = element_text(color = "#333333"),
      plot.title = element_text(size = 28),
      plot.subtitle = element_text(size = 14),
      axis.ticks = element_blank(),
      axis.text = element_blank(),
      panel.grid = element_blank(),
      panel.background = element_rect(fill = "#FFFFFF") #' #333333'
      , plot.background = element_rect(fill = "#FFFFFF"),
      legend.position = c(.18, .36),
      legend.background = element_blank(),
      legend.key = element_blank()
    ) +
    annotation_custom(values$logoGrid, xmin = 143, xmax = 189.5, ymin = -69, ymax = -48)
  if (isTRUE(label)) {
    CO <- dplyr::inner_join(CO, countries, by = c("Tab" = "Tab"))
    g <- g +
      # ggrepel::geom_text_repel(data=CO, aes(x = Longitude, y = Latitude, label = Tab, group=continent),             # draw text labels
      #                          hjust = 0, nudge_x = 1, nudge_y = 4,
      #                          size = 3, color = "orange", fontface = "bold")
      ggrepel::geom_text(
        data = CO, aes(x = Longitude, y = Latitude, label = Tab, group = continent), # draw text labels
        hjust = 0, nudge_x = 1, nudge_y = 4,
        size = 3, color = "orange", fontface = "bold"
      )
  }

  results <- list(g = g, tab = tab)
  return(results)
}
### visNetwork tools ----
netLayout <- function(type) {
  switch(type,
    auto = {
      l <- "layout_nicely"
    },
    circle = {
      l <- "layout_in_circle"
    },
    mds = {
      l <- "layout_with_mds"
    },
    star = {
      l <- "layout_as_star"
    },
    sphere = {
      l <- "layout_on_sphere"
    },
    fruchterman = {
      l <- "layout_with_fr"
    },
    kamada = {
      l <- "layout_with_kk"
    }
  )
  return(l)
}

savenetwork <- function(con, VIS) {
  VIS %>%
    visOptions(height = "800px") %>%
    visNetwork::visSave(con)
}

igraph2vis <- function(g, curved, labelsize, opacity, type, shape, net, shadow = TRUE, edgesize = 5, noOverlap = TRUE) {
  LABEL <- igraph::V(g)$name

  LABEL[igraph::V(g)$labelsize == 0] <- ""

  vn <- visNetwork::toVisNetworkData(g)

  vn$nodes$label <- LABEL
  vn$edges$num <- 1
  vn$edges$dashes <- FALSE
  vn$edges$dashes[vn$edges$lty == 2] <- TRUE

  ## opacity
  vn$nodes$color <- adjustcolor(vn$nodes$color, alpha.f = min(c(opacity, 1)))
  ## set a darkest gray for iter-cluster edges
  vn$edges$color <- paste(substr(vn$edges$color, 1, 7), "90", sep = "")
  vn$edges$color[substr(vn$edges$color, 1, 7) == "#B3B3B3"] <- "#69696960"
  vn$edges$color <- adjustcolor(vn$edges$color, alpha.f = opacity)

  ## removing multiple edges
  vn$edges <- unique(vn$edges)

  vn$edges$width <- vn$edges$width^2 / (max(vn$edges$width^2)) * (10 + edgesize)

  # if (edgesize==0){
  #   vn$edges$hidden <- TRUE
  #   }else{vn$edges$hidden <- FALSE}

  ## labelsize
  vn$nodes$font.size <- vn$nodes$deg
  scalemin <- 20
  scalemax <- 150
  Min <- min(vn$nodes$font.size)
  Max <- max(vn$nodes$font.size)
  if (Max > Min) {
    size <- (vn$nodes$font.size - Min) / (Max - Min) * 15 * labelsize + 10
  } else {
    size <- 10 * labelsize
  }
  size[size < scalemin] <- scalemin
  size[size > scalemax] <- scalemax
  vn$nodes$font.size <- size
  l <- netLayout(type)

  ### TO ADD SHAPE AND FONT COLOR OPTIONS
  coords <- net$layout

  vn$nodes$size <- vn$nodes$font.size * 0.7

  # vn$nodes$font.color <- adjustcolor("black", alpha.f = min(c(opacity,1)))

  if (shape %in% c("dot", "square")) {
    vn$nodes$font.vadjust <- -0.7 * vn$nodes$font.size
  } else {
    vn$nodes$font.vadjust <- 0
  }

  opacity_font <- sqrt((vn$nodes$font.size - min(vn$nodes$font.size)) / diff(range(vn$nodes$font.size))) * opacity + 0.3
  if (is.nan(opacity_font[1])) opacity_font <- rep(0.3, length(opacity_font))

  if (labelsize > 0) {
    vn$nodes$font.color <- unlist(lapply(opacity_font, function(x) adjustcolor("black", alpha.f = x)))
  } else {
    vn$nodes$font.color <- adjustcolor("black", alpha.f = 0)
  }
  ## avoid label overlaps
  if (noOverlap) {
    threshold <- 0.05
    ymax <- diff(range(coords[, 2]))
    xmax <- diff(range(coords[, 1]))
    threshold2 <- threshold * mean(xmax, ymax)
    w <- data.frame(x = coords[, 1], y = coords[, 2], labelToPlot = vn$nodes$label, dotSize = size, row.names = vn$nodes$label)
    labelToRemove <- avoidNetOverlaps(w, threshold = threshold2)
  } else {
    labelToRemove <- ""
  }

  vn$nodes <- vn$nodes %>%
    mutate(
      label = ifelse(label %in% labelToRemove, "", label),
      title = id
    )
  ##

  VIS <-
    visNetwork::visNetwork(nodes = vn$nodes, edges = vn$edges, type = "full", smooth = TRUE, physics = FALSE) %>%
    visNetwork::visNodes(shadow = shadow, shape = shape, font = list(color = vn$nodes$font.color, size = vn$nodes$font.size, vadjust = vn$nodes$font.vadjust)) %>%
    visNetwork::visIgraphLayout(layout = "layout.norm", layoutMatrix = coords, type = "full") %>%
    visNetwork::visEdges(smooth = list(type = "horizontal")) %>%
    visNetwork::visOptions(highlightNearest = list(enabled = T, hover = T, degree = 1), nodesIdSelection = T) %>%
    visNetwork::visInteraction(dragNodes = TRUE, navigationButtons = F, hideEdgesOnDrag = TRUE, zoomSpeed = 0.4) %>%
    visNetwork::visOptions(manipulation = curved, height = "100%", width = "100%")

  return(list(VIS = VIS, vn = vn, type = type, l = l, curved = curved))
}

## function to avoid label overlapping ----
avoidNetOverlaps <- function(w, threshold = 0.10) {
  w[, 2] <- w[, 2] / 2

  Ds <- dist(
    w %>%
      dplyr::filter(labelToPlot != "") %>%
      select(1:2),
    method = "manhattan", upper = T
  ) %>%
    dist2df() %>%
    rename(
      from = row,
      to = col,
      dist = value
    ) %>%
    left_join(
      w %>% dplyr::filter(labelToPlot != "") %>%
        select(labelToPlot, dotSize),
      by = c("from" = "labelToPlot")
    ) %>%
    rename(w_from = dotSize) %>%
    left_join(
      w %>% dplyr::filter(labelToPlot != "") %>%
        select(labelToPlot, dotSize),
      by = c("to" = "labelToPlot")
    ) %>%
    rename(w_to = dotSize) %>%
    filter(dist < threshold)

  if (nrow(Ds) > 0) {
    st <- TRUE
    i <- 1
    label <- NULL
    case <- "n"

    while (isTRUE(st)) {
      if (Ds$w_from[i] > Ds$w_to[i] & Ds$dist[i] < threshold) {
        case <- "y"
        lab <- Ds$to[i]
      } else if (Ds$w_from[i] <= Ds$w_to[i] & Ds$dist[i] < threshold) {
        case <- "y"
        lab <- Ds$from[i]
      }

      switch(case,
        "y" = {
          Ds <- Ds[Ds$from != lab, ]
          Ds <- Ds[Ds$to != lab, ]
          label <- c(label, lab)
        },
        "n" = {
          Ds <- Ds[-1, ]
        }
      )

      if (i >= nrow(Ds)) {
        st <- FALSE
      }
      case <- "n"
      # print(nrow(Ds))
    }
  } else {
    label <- NULL
  }
  label
}




## visnetwork for subgraphs
igraph2visClust <- function(g, curved = FALSE, labelsize = 3, opacity = 0.7, shape = "dot", shadow = TRUE, edgesize = 5) {
  LABEL <- igraph::V(g)$name

  LABEL[igraph::V(g)$labelsize == 0] <- ""

  vn <- visNetwork::toVisNetworkData(g)

  vn$nodes$label <- LABEL
  vn$edges$num <- 1
  vn$edges$dashes <- FALSE
  vn$edges$dashes[vn$edges$lty == 2] <- TRUE

  ## opacity
  vn$nodes$color <- adjustcolor(vn$nodes$color, alpha.f = min(c(opacity, 1)))
  ## set a darkest gray for iter-cluster edges
  vn$edges$color <- paste(substr(vn$edges$color, 1, 7), "90", sep = "")
  vn$edges$color[substr(vn$edges$color, 1, 7) == "#B3B3B3"] <- "#69696960"
  vn$edges$color <- adjustcolor(vn$edges$color, alpha.f = opacity)

  ## removing multiple edges
  vn$edges <- unique(vn$edges)

  vn$edges$width <- vn$edges$width^2 / (max(vn$edges$width^2)) * (5 + edgesize)

  ## labelsize
  scalemin <- 20
  scalemax <- 100
  # aggiunta
  vn$nodes$font.size <- vn$nodes$deg
  #
  Min <- min(vn$nodes$font.size)
  Max <- max(vn$nodes$font.size)
  if (Max > Min) {
    size <- (vn$nodes$font.size - Min) / (Max - Min) * 15 * labelsize #+10
  } else {
    size <- 5 * labelsize
  }
  size[size < scalemin] <- scalemin
  size[size > scalemax] <- scalemax
  vn$nodes$font.size <- size
  # l<-netLayout(type)

  ### TO ADD SHAPE AND FONT COLOR OPTIONS

  vn$nodes$size <- vn$nodes$font.size * 0.4

  if (shape %in% c("dot", "square")) {
    vn$nodes$font.vadjust <- -0.7 * vn$nodes$font.size
  } else {
    vn$nodes$font.vadjust <- 0
  }

  opacity_font <- sqrt((vn$nodes$font.size - min(vn$nodes$font.size)) / diff(range(vn$nodes$font.size))) * opacity + 0.3
  if (is.nan(opacity_font[1])) opacity_font <- rep(0.3, length(opacity_font))

  if (labelsize > 0) {
    vn$nodes$font.color <- unlist(lapply(opacity_font, function(x) adjustcolor("black", alpha.f = x)))
  } else {
    vn$nodes$font.color <- adjustcolor("black", alpha.f = 0)
  }

  VIS <-
    visNetwork::visNetwork(nodes = vn$nodes, edges = vn$edges, type = "full", smooth = TRUE, physics = FALSE) %>%
    visNetwork::visNodes(shadow = shadow, shape = shape, font = list(color = vn$nodes$font.color, size = vn$nodes$font.size, vadjust = vn$nodes$font.vadjust)) %>%
    visNetwork::visIgraphLayout(layout = "layout_nicely", type = "full") %>%
    visNetwork::visEdges(smooth = list(type = "horizontal")) %>%
    visNetwork::visOptions(highlightNearest = list(enabled = T, hover = T, degree = 1), nodesIdSelection = T) %>%
    visNetwork::visInteraction(dragNodes = TRUE, navigationButtons = F, hideEdgesOnDrag = TRUE, zoomSpeed = 0.4) %>%
    visNetwork::visOptions(manipulation = curved, height = "100%", width = "100%")

  return(list(VIS = VIS, vn = vn))
}


hist2vis <- function(net, labelsize = 2, nodesize = 2, curved = FALSE, shape = "dot", opacity = 0.7, labeltype = "short", timeline = TRUE) {
  LABEL <- igraph::V(net$net)$id

  LABEL[igraph::V(net$net)$labelsize == 0] <- ""

  layout <- net$layout %>%
    dplyr::select(x, y, color, name)

  vn <- visNetwork::toVisNetworkData(net$net)

  vn$nodes$short_label <- LABEL
  
  if (labeltype != "short") {
    vn$nodes$label <- paste0(vn$nodes$years, ": ", LABEL)
  } else {
    vn$nodes$label <- LABEL
  }

  vn$nodes <- dplyr::left_join(vn$nodes, layout, by = c("id" = "name"))

  vn$edges$num <- 1
  vn$edges$dashes <- FALSE
  vn$edges$dashes[vn$edges$lty == 2] <- TRUE
  vn$edges$color <- "grey"

  ## opacity
  vn$nodes$font.color <- vn$nodes$color

  vn$nodes$color <- adjustcolor(vn$nodes$color, alpha.f = min(c(opacity - 0.2, 1)))
  vn$edges$color <- adjustcolor(vn$edges$color, alpha.f = opacity - 0.2)
  vn$edges$smooth <- curved

  ## removing multiple edges
  vn$edges <- unique(vn$edges)

  ## labelsize
  scalemin <- 20
  scalemax <- 150
  size <- 10 * labelsize
  size[size < scalemin] <- scalemin
  size[size > scalemax] <- scalemax
  vn$nodes$font.size <- size * 0.5
  vn$nodes$size <- nodesize * 2

  if (shape %in% c("dot", "square")) {
    vn$nodes$font.vadjust <- -0.7 * vn$nodes$font.size
  } else {
    vn$nodes$font.vadjust <- 0
  }

  text_data <- net$graph.data %>%
    select(Label, DOI, LCS, GCS) %>%
    rename(id = Label) %>%
    filter(!duplicated(id))

  vn$nodes <- vn$nodes %>% left_join(text_data, by = "id")

  ## split node tooltips into two strings
  title <- strsplit(stringi::stri_trans_totitle(vn$nodes$title), " ")

  vn$nodes$title <- unlist(lapply(title, function(l) {
    n <- floor(length(l) / 2)
    paste0(paste(l[1:n], collapse = " ", sep = ""), "<br>", paste(l[(n + 1):length(l)], collapse = " ", sep = ""))
  }))

  vn$nodes <- vn$nodes %>%
    mutate(title_orig = title,
      title = paste("<b>Title</b>: ",
      title,
      "<br><b>DOI</b>: ",
      paste0(
        '<a href=\"https://doi.org/',
        DOI,
        '\" target=\"_blank\">',
        # "DOI: ",
        DOI, "</a>"
      ),
      "<br><b>GCS</b>: ",
      GCS, "<br><b>LCS</b>: ",
      LCS,
      sep = ""
    ))

  ## add time line
  vn$nodes$group <- "normal"
  vn$nodes$shape <- "dot"
  vn$nodes$shadow <- TRUE

  # nr <- nrow(vn$nodes)
  # y <- max(vn$nodes$y)
  # vn$nodes[nr + 1, c("id", "title", "label", "color", "font.color")] <-
  #   c(rep("logo", 3), "black", "white")
  # vn$nodes$x[nr + 1] <- max(vn$nodes$x, na.rm = TRUE) + 1
  # vn$nodes$y[nr + 1] <- y
  # vn$nodes$size[nr + 1] <- vn$nodes$size[nr] * 4
  # vn$nodes$years[nr + 1] <- as.numeric(vn$nodes$x[nr + 1])
  # vn$nodes$font.size[nr + 1] <- vn$nodes$font.size[nr]
  # vn$nodes$group[nr + 1] <- "logo"
  # vn$nodes$shape[nr + 1] <- "image"
  # vn$nodes$image[nr + 1] <- "logo.jpg"
  # vn$nodes$fixed.x <- TRUE
  # vn$nodes$fixed.y <- FALSE
  # vn$nodes$fixed.y[nr + 1] <- TRUE
  # vn$nodes$shadow[nr + 1] <- FALSE

  # coords <- vn$nodes[, c("x", "y")] %>%
  #   as.matrix()
  # 
  # coords[, 2] <- coords[, 2]^(1 / 2)

  tooltipStyle <- ("position: fixed;visibility:hidden;padding: 5px;white-space: nowrap;
                  font-size:12px;font-color:black;background-color:white;")

  ## Font opacity
  vn$nodes$LCS[is.na(vn$nodes$LCS)] <- max(vn$nodes$LCS, na.rm = TRUE)
  opacity_font <- sqrt((vn$nodes$LCS - min(vn$nodes$LCS)) / diff(range(vn$nodes$LCS))) * 0.6 + 0.4

  vn$nodes$size <- opacity_font * 5 * nodesize
  vn$nodes$size[nrow(vn$nodes)] <- max(5 * nodesize)

  for (i in 1:nrow(vn$nodes)) vn$nodes$font.color[i] <- adjustcolor(vn$nodes$font.color[i], alpha.f = opacity_font[i])
  
  x <- vn$nodes$x
  y <- vn$nodes$y
  vn$nodes$x <- y
  vn$nodes$y <- x
  
  vn$nodes <- assign_horizontal_coords_clusters_adaptive(vn$nodes)

  vn$nodes$fixed.x <- FALSE
  vn$nodes$fixed.y <-TRUE
  
  coords <- vn$nodes[, c("x", "y")] %>%
    as.matrix()
  coords[,2] <- coords[,2]
  
  VIS <-
    visNetwork::visNetwork(nodes = vn$nodes, edges = vn$edges, type = "full", smooth = TRUE, physics = FALSE) %>%
    visNetwork::visNodes(shadow = vn$nodes$shadow, shape = shape, size = vn$nodes$size, font = list(color = vn$nodes$font.color, size = vn$nodes$font.size, vadjust = vn$nodes$font.vadjust)) %>%
    visNetwork::visIgraphLayout(layout = "layout.norm", layoutMatrix = coords, type = "full") %>%
    #visNetwork::visEdges(smooth = list(type = "horizontal"), arrows = list(to = list(enabled = TRUE, scaleFactor = 0.5))) %>%
    visNetwork::visEdges(smooth = list(enabled = TRUE, type = "dynamic", roundness = 0.3),
                         arrows = list(to = list(enabled = TRUE, scaleFactor = 0.5))) %>%
    visNetwork::visInteraction(dragNodes = T, navigationButtons = F, hideEdgesOnDrag = F, tooltipStyle = tooltipStyle, zoomSpeed = 0.2) %>%
    visNetwork::visOptions(
      highlightNearest = list(enabled = T, hover = T, degree = list(from = 1), algorithm = "hierarchical"), nodesIdSelection = F,
      manipulation = FALSE, height = "100%", width = "100%"
    )

  return(list(VIS = VIS, vn = vn, type = "historiograph", curved = curved))
}

## calculate node coordinates in historiograph
assign_horizontal_coords_clusters_adaptive <- function(nodes_df, spacing_base = 1.0, cluster_spacing = 6, tol=0.15) {
  
  clusters <- nodes_df %>%
    count(color, name = "n_cluster") %>%
    arrange(desc(n_cluster)) %>%
    mutate(cluster_id = row_number(),
           cluster_center = (cluster_id - mean(cluster_id)) * cluster_spacing)
  
  nodes_df <- nodes_df %>%
    left_join(clusters, by = "color")
  
  nodes_df <- nodes_df %>%
    group_by(years, color) %>%
    mutate(
      n_nodes = n(),
      spacing = spacing_base * n_nodes,  # USA direttamente il numero di nodi
      x = (cluster_center[1] + spacing[1] * (row_number() - (n() + 1)/2))*runif(1,1-tol,1+tol)
    ) %>%
    ungroup()
  
  return(nodes_df)
}

## Pajek Export
graph2Pajek <- function(graph, filename = "my_pajek_network") {
  nodes <- igraph::as_data_frame(graph, what = c("vertices")) %>%
    mutate(id = row_number())

  edges <- igraph::as_data_frame(graph, what = c("edges"))
  edges <- edges %>%
    left_join(nodes %>% select(id, name), by = c("from" = "name")) %>%
    rename(id_from = id) %>%
    left_join(nodes %>% select(id, name), by = c("to" = "name")) %>%
    rename(id_to = id)

  ### Creation of NET file
  file <- paste0(filename, ".net")

  # Nodes
  write(paste0("*Vertices ", nrow(nodes)), file = file)
  write(paste0(nodes$id, ' "', nodes$name, '"'), file = file, append = T)

  # Edges
  write(paste0("*Edges ", nrow(nodes)), file = file, append = T)
  write(paste0(edges$id_from, " ", edges$id_to, " ", edges$weight), file = file, append = T)

  ### Creation of VEC file
  file <- paste0(filename, ".vec")

  # Nodes
  write(paste0("*Vertices ", nrow(nodes)), file = file)
  write(paste0(nodes$deg), file = file, append = T)

  ### Creation of CLU file
  file <- paste0(filename, ".clu")

  # Nodes
  write(paste0("*Vertices ", nrow(nodes)), file = file)
  write(paste0(nodes$community), file = file, append = T)
}


## Dendogram to Visnetwork
dend2vis <- function(hc, labelsize, nclusters = 1, community = FALSE) {
  # community = TRUE means that hc is an igraph community detection object
  # community = FALSE mean that hc is a hclust object

  # transform and plot a community igraph object using dendrogram
  if (community) {
    hc <- as.hclust(hc, use.modularity = TRUE)
  }

  h_tail <- round((max(hc$height) * 0.12), 1)

  hc$height <- hc$height + h_tail

  VIS <- visHclust(hc, cutree = nclusters, colorEdges = "grey60", horizontal = TRUE, export = FALSE)
  VIS$x$edges <- data.frame(color = unique(VIS$x$edges$color)) %>%
    mutate(new_color = colorlist()[1:nrow(.)]) %>%
    right_join(VIS$x$edges, by = "color") %>%
    select(-color) %>%
    rename(color = new_color)
  VIS$x$nodes <- VIS$x$nodes %>%
    mutate(
      label = ifelse(group != "individual", NA, label),
      group = ifelse(group == "individual", "word", group),
      title = gsub("individuals", "words", title),
      value = 1,
      scaling.min = 10,
      scaling.max = 10
    )
  coords <- VIS$x$nodes %>%
    select(x, y) %>%
    as.matrix()

  edges <- VIS$x$edges
  nodes <- VIS$x$nodes %>%
    select(id, label) %>%
    dplyr::filter(label != "1")

  VIS$x$edges <- edges %>%
    select(-id) %>%
    left_join(nodes, by = c("to" = "id")) %>%
    select(-label.x) %>%
    rename(label = label.y) %>%
    mutate(
      value = 10,
      font.color = color,
      font.size = labelsize * 10,
      font.vadjust = -0.2 * font.size,
      label = ifelse(is.na(label), "", label)
    )

  VIS <- VIS %>%
    visGroups(
      groupname = "group", color = "gray90",
      shape = "dot", size = 10
    ) %>%
    visGroups(
      groupname = "word",
      font = list(size = 0),
      color = list(
        background = "white", border = "#80B1D3",
        highlight = "#e2e9e9", hover = "orange"
      ), shape = "box"
    ) %>%
    visNodes(font = list(align = VIS$x$nodes$font.align)) %>%
    visNetwork::visOptions(
      highlightNearest = list(enabled = T, hover = T, degree = list(to = 1000, from = 0), algorithm = "hierarchical"), nodesIdSelection = FALSE,
      manipulation = FALSE, height = "100%", width = "100%"
    ) %>%
    visNetwork::visInteraction(dragNodes = FALSE, navigationButtons = F, hideEdgesOnDrag = TRUE, zoomSpeed = 0.4) %>%
    visIgraphLayout(layout = "layout.norm", layoutMatrix = coords, type = "full") %>%
    visEdges(font = list(align = "top", size = VIS$x$edges$font.size)) %>%
    visEvents(click = "function(nodes){
                  Shiny.onInputChange('click_dend', nodes.nodes[0]);
                  ;}")

  for (i in 1:nrow(VIS$x$nodes)) {
    if (VIS$x$nodes$group[i] == "group") {
      old_inertia <- as.character(VIS$x$nodes$inertia[i])
      inertia <- as.character(VIS$x$nodes$inertia[i] - h_tail)
      VIS$x$nodes$title[i] <- gsub(old_inertia, inertia, VIS$x$nodes$title[i])
    }
  }

  VIS
}

## Factorial Analysis dynamic plots
ca2plotly <- function(CS, method = "MCA", dimX = 1, dimY = 2, topWordPlot = Inf, threshold = 0.10, labelsize = 16, size = 5) {
  LABEL <- CS$WData$word
  switch(method,
    CA = {
      contrib <- rowSums(CS$coord$contrib %>% as.data.frame()) / 2
      wordCoord <- CS$coord$coord[, 1:2] %>%
        data.frame() %>%
        mutate(
          label = LABEL,
          contrib = contrib
        ) %>%
        select(c(3, 1, 2, 4))
      row.names(wordCoord) <- LABEL
      xlabel <- paste0("Dim 1 (", round(CS$res$eigCorr$perc[1], 2), "%)")
      ylabel <- paste0("Dim 2 (", round(CS$res$eigCorr$perc[2], 2), "%)")
    },
    MCA = {
      contrib <- rowSums(CS$coord$contrib %>% as.data.frame()) / 2
      wordCoord <- CS$coord$coord[, 1:2] %>%
        data.frame() %>%
        mutate(
          label = LABEL,
          contrib = contrib
        ) %>%
        select(c(3, 1, 2, 4))
      row.names(wordCoord) <- LABEL
      xlabel <- paste0("Dim 1 (", round(CS$res$eigCorr$perc[1], 2), "%)")
      ylabel <- paste0("Dim 2 (", round(CS$res$eigCorr$perc[2], 2), "%)")
    },
    MDS = {
      contrib <- size
      xlabel <- "Dim 1"
      ylabel <- "Dim 2"
      wordCoord <- CS$WData %>%
        data.frame() %>%
        select(1:3) %>%
        mutate(contrib = contrib / 2) %>%
        rename(label = "word")
    }
  )

  dimContrLabel <- paste0("Contrib", c(dimX, dimY))
  ymax <- diff(range((wordCoord[, 3])))
  xmax <- diff(range((wordCoord[, 2])))
  threshold2 <- threshold * mean(xmax, ymax)

  # scaled size for dots
  dotScale <- (wordCoord$contrib) + size

  # Threshold labels to plot
  thres <- sort(dotScale, decreasing = TRUE)[min(topWordPlot, nrow(wordCoord))]

  names(wordCoord)[2:3] <- c("Dim1", "Dim2")

  wordCoord <- wordCoord %>%
    mutate(
      dotSize = dotScale,
      groups = CS$km.res$cluster,
      labelToPlot = ifelse(dotSize >= thres, label, ""),
      font.color = ifelse(labelToPlot == "", NA, adjustcolor(colorlist()[groups], alpha.f = 0.85)),
      font.size = round(dotSize * 2, 0)
    )

  ## Avoid label overlapping
  labelToRemove <- avoidOverlaps(wordCoord, threshold = threshold2, dimX = dimX, dimY = dimY)
  wordCoord <- wordCoord %>%
    mutate(labelToPlot = ifelse(labelToPlot %in% labelToRemove, "", labelToPlot)) %>%
    mutate(
      label = gsub("_1", "", label),
      labelToPlot = gsub("_1", "", labelToPlot)
    )

  hoverText <- paste(" <b>", wordCoord$label, "</b>\n Contribute: ", round(wordCoord$contrib, 3), sep = "")

  fig <- plot_ly(
    data = wordCoord, x = wordCoord[, "Dim1"], y = wordCoord[, "Dim2"], # customdata=results$wordCoord,
    type = "scatter",
    mode = "markers",
    marker = list(
      size = dotScale,
      color = adjustcolor(colorlist()[wordCoord$groups], alpha.f = 0.3), #' rgb(79, 121, 66, .5)',
      line = list(
        color = adjustcolor(colorlist()[wordCoord$groups], alpha.f = 0.3), #' rgb(79, 121, 66, .8)',
        width = 2
      )
    ),
    text = hoverText,
    hoverinfo = "text",
    alpha = .3
  )

  fig <- fig %>% layout(
    yaxis = list(title = ylabel, showgrid = TRUE, showline = FALSE, showticklabels = TRUE, domain = c(0, 1)),
    xaxis = list(title = xlabel, zeroline = TRUE, showgrid = TRUE, showline = FALSE, showticklabels = TRUE),
    plot_bgcolor = "rgba(0, 0, 0, 0)",
    paper_bgcolor = "rgba(0, 0, 0, 0)"
  )

  for (i in seq_len(max(wordCoord$groups))) {
    if (method == "MDS") {
      w <- wordCoord %>%
        dplyr::filter(groups == i) %>%
        mutate(
          Dim1 = Dim1 + 0.005,
          Dim2 = Dim2 + 0.005
        )
    } else {
      w <- wordCoord %>%
        dplyr::filter(groups == i) %>%
        mutate(
          Dim1 = Dim1 + dotSize * 0.005,
          Dim2 = Dim2 + dotSize * 0.01
        )
    }

    if (max(CS$hull_data$clust) > 1) {
      hull_df <- CS$hull_data %>% dplyr::filter(clust == i)
      fig <- fig %>% add_polygons(
        x = hull_df$Dim1, y = hull_df$Dim2, inherit = FALSE, showlegend = FALSE,
        color = I(hull_df$color[1]), opacity = 0.3, line = list(width = 2),
        text = paste0("Cluster ", i), hoverinfo = "text", hoveron = "points"
      )
    }
    fig <- fig %>%
      add_annotations(
        data = w, x = ~Dim1, y = ~Dim2, xref = "x1", yref = "y",
        text = ~labelToPlot,
        font = list(family = "sans serif", size = labelsize, color = w$font.color[1]), #' rgb(79, 121, 66)'),
        showarrow = FALSE
      )
  }

  fig <- fig %>%
    config(
      displaylogo = FALSE,
      modeBarButtonsToRemove = c(
        #' toImage',
        "sendDataToCloud",
        "pan2d",
        "select2d",
        "lasso2d",
        "toggleSpikelines",
        "hoverClosestCartesian",
        "hoverCompareCartesian"
      )
    ) %>%
    event_register("plotly_selecting")
  return(fig)
}


## function to avoid label overlapping ----
avoidOverlaps <- function(w, threshold = 0.10, dimX = 1, dimY = 2) {
  w[, "Dim2"] <- w[, "Dim2"] / 3

  Ds <- dist(
    w %>%
      dplyr::filter(labelToPlot != "") %>%
      select(Dim1, Dim2),
    method = "manhattan", upper = T
  ) %>%
    dist2df() %>%
    rename(
      from = row,
      to = col,
      dist = value
    ) %>%
    left_join(
      w %>% dplyr::filter(labelToPlot != "") %>%
        select(labelToPlot, dotSize),
      by = c("from" = "labelToPlot")
    ) %>%
    rename(w_from = dotSize) %>%
    left_join(
      w %>% dplyr::filter(labelToPlot != "") %>%
        select(labelToPlot, dotSize),
      by = c("to" = "labelToPlot")
    ) %>%
    rename(w_to = dotSize) %>%
    filter(dist < threshold)

  st <- TRUE
  i <- 1
  label <- NULL
  case <- "n"

  while (isTRUE(st)) {
    if (Ds$w_from[i] > Ds$w_to[i] & Ds$dist[i] < threshold) {
      case <- "y"
      lab <- Ds$to[i]
    } else if (Ds$w_from[i] <= Ds$w_to[i] & Ds$dist[i] < threshold) {
      case <- "y"
      lab <- Ds$from[i]
    }

    switch(case,
      "y" = {
        Ds <- Ds[Ds$from != lab, ]
        Ds <- Ds[Ds$to != lab, ]
        label <- c(label, lab)
      },
      "n" = {
        Ds <- Ds[-1, ]
      }
    )

    if (i >= nrow(Ds)) {
      st <- FALSE
    }
    case <- "n"
    # print(nrow(Ds))
  }

  label
}

## convert a distance object into a data.frame ----
dist2df <- function(inDist) {
  if (class(inDist) != "dist") stop("wrong input type")
  A <- attr(inDist, "Size")
  B <- if (is.null(attr(inDist, "Labels"))) sequence(A) else attr(inDist, "Labels")
  if (isTRUE(attr(inDist, "Diag"))) attr(inDist, "Diag") <- FALSE
  if (isTRUE(attr(inDist, "Upper"))) attr(inDist, "Upper") <- FALSE
  data.frame(
    row = B[unlist(lapply(sequence(A)[-1], function(x) x:A))],
    col = rep(B[-length(B)], (length(B) - 1):1),
    value = as.vector(inDist)
  )
}

### Excel report functions
addDataWb <- function(list_df, wb, sheetname) {
  l <- length(list_df)
  startRow <- 1
  for (i in 1:l) {
    df <- list_df[[i]]
    n <- nrow(df)
    writeDataTable(wb, sheetname, df, startRow = startRow, startCol = 1, tableStyle = "TableStyleMedium20")
    startRow <- startRow + n + 3
  }
  return(wb)
}

addDataScreenWb <- function(list_df, wb, sheetname) {
  ind <- which(regexpr(sheetname, wb$sheet_names) > -1)
  if (length(ind) > 0) {
    sheetname <- paste(sheetname, "(", length(ind) + 1, ")", sep = "")
  }
  addWorksheet(wb = wb, sheetName = sheetname, gridLines = FALSE)
  if (!is.null(list_df)) {
    addDataWb(list_df, wb, sheetname)
    col <- max(unlist(lapply(list_df, ncol))) + 2
  } else {
    col <- 1
  }

  results <- list(wb = wb, col = col, sheetname = sheetname)
  return(results)
}

addGgplotsWb <- function(list_plot, wb, sheetname, col, width = 10, height = 7, dpi = 75) {
  l <- length(list_plot)
  startRow <- 1
  for (i in 1:l) {
    fileName <- tempfile(
      pattern = "figureImage",
      fileext = ".png"
    )
    if (inherits(list_plot[[i]], "ggplot")) {
      ggsave(
        plot = list_plot[[i]], filename = fileName, width = width, height = height,
        units = "in", dpi = dpi
      )
    }
    if (inherits(list_plot[[i]], "igraph")) {
      igraph2PNG(x = list_plot[[i]], filename = fileName, width = width, height = height, dpi = dpi)
    }
    if (inherits(list_plot[[i]], "bibliodendrogram")) {
      # print("dendrogram plot")
      # 1. Open jpeg file
      png(filename = fileName, width = width, height = height, res = 300, units = "in")
      # 2. Create the plot
      plot(list_plot[[i]])
      # 3. Close the file
      dev.off()
    }
    insertImage(
      wb = wb, sheet = sheetname, file = fileName, width = width,
      height = height, startRow = startRow, startCol = col,
      units = "in", dpi = dpi
    )
    startRow <- startRow + (height * 6) + 1
  }
  return(wb)
}

screenSh <- function(p, zoom = 2, type = "vis") {
  tmpdir <- tempdir()
  fileName <- tempfile(
    pattern = "figureImage",
    tmpdir = tmpdir,
    fileext = ".png"
  ) # %>% substr(.,2,nchar(.))

  plot2png(p, filename = fileName, zoom = zoom, type = type, tmpdir = tmpdir)

  return(fileName)
}

screenShot <- function(p, filename, type) {
  home <- homeFolder()
  
  # setting up the main directory
  # filename <- paste0(file.path(home,"downloads/"),filename)
  if ("downloads" %in% tolower(dir(home))) {
    filename <- paste0(file.path(home, "downloads"), "/", filename)
  } else {
    filename <- paste0(home, "/", filename)
  }

  plot2png(p, filename, zoom = 2, type = type, tmpdir = tempdir())
}

plot2png <- function(p, filename, zoom = 2, type = "vis", tmpdir) {
  html_name <- tempfile(
    fileext = ".html",
    tmpdir = tmpdir
  )
  switch(type,
    vis = {
      visSave(p, html_name)
    },
    plotly = {
      htmlwidgets::saveWidget(p, file = html_name)
    }
  )
  biblioShot(url = html_name, zoom = zoom, file = filename) # , verbose=FALSE)

  popUpGeneric(
    title = NULL, type = "success", color = c("#1d8fe1"),
    subtitle = paste0("Plot was saved in the following path: ", filename),
    btn_labels = "OK", size = "40%"
  )
}

addScreenWb <- function(df, wb, width = 14, height = 8, dpi = 75) {
  names(df) <- c("sheet", "file", "n")
  if (nrow(df) > 0) {
    sheet <- unique(df$sheet)
    for (i in 1:length(sheet)) {
      sh <- sheet[i]
      df_sh <- df %>% dplyr::filter(sheet == sh)
      l <- nrow(df_sh)
      startRow <- 1
      for (j in 1:l) {
        fileName <- df_sh$file[j]
        insertImage(
          wb = wb, sheet = sh, file = fileName, width = width,
          height = height, startRow = startRow, startCol = df_sh$n[j],
          units = "in", dpi = dpi
        )
        startRow <- startRow + (height * 10) + 3
      }
    }
  }
  return(wb)
}

addSheetToReport <- function(list_df, list_plot, sheetname, wb, dpi = 75) {
  ind <- which(regexpr(sheetname, wb$sheet_names) > -1)
  if (length(ind) > 0) {
    sheetname <- paste(sheetname, "(", length(ind) + 1, ")", sep = "")
  }
  addWorksheet(wb, sheetname, gridLines = FALSE)

  if (!is.null(list_df)) {
    col <- max(unlist(lapply(list_df, ncol))) + 2
    wb <- addDataWb(list_df, wb = wb, sheetname = sheetname)
  } else {
    col <- 1
  }

  if (!is.null(list_plot)) {
    wb <- addGgplotsWb(list_plot, wb = wb, sheetname = sheetname, col = col, dpi = dpi)
  }
  # values$sheet_name <- sheetname
  return(wb)
}

short2long <- function(df, myC) {
  z <- unlist(lapply(myC, function(x) {
    y <- gsub(r"{\s*\([^\)]+\)}", "", x)
    gsub(y, df$long[df$short == y], x)
  }))
  names(myC) <- z
  return(myC)
}

dfLabel <- function() {
  short <- c(
    "Empty Report", "MissingData", "MainInfo", "AnnualSciProd", "AnnualCitPerYear", "ThreeFieldsPlot", "MostRelSources", "MostLocCitSources", "BradfordLaw", "SourceLocImpact",
    "SourceProdOverTime", "MostRelAuthors", "MostLocCitAuthors", "AuthorProdOverTime", "LotkaLaw", "AuthorLocImpact", "MostRelAffiliations", "AffOverTime",
    "CorrAuthCountries", "CountrySciProd", "CountryProdOverTime", "MostCitCountries", "MostGlobCitDocs", "MostLocCitDocs", "MostLocCitRefs", "RPYS",
    "MostFreqWords", "WordCloud", "TreeMap", "WordFreqOverTime", "TrendTopics", "CouplingMap", "CoWordNet", "ThematicMap", "ThematicEvolution",
    "TE_Period_1", "TE_Period_2", "TE_Period_3", "TE_Period_4", "TE_Period_5", "FactorialAnalysis", "CoCitNet", "Historiograph", "CollabNet", "CollabWorldMap"
  )

  long <- c(
    "Empty Report", "Missing Data Table", "Main Information", "Annual Scientific Production", "Annual Citation Per Year", "Three-Field Plot", "Most Relevant Sources", "Most Local Cited Sources", "Bradfords Law", "Sources Local Impact",
    "Sources Production over Time", "Most Relevant Authors", "Most Local Cited Authors", "Authors Production over Time", "Lotkas Law", "Authors Local Impact", "Most Relevant Affiliations", "Affiliations Production over Time",
    "Corresponding Authors Countries", "Countries Scientific Production", "Countries Production over Time", "Most Cited Countries", "Most Global Cited Documents", "Most Local Cited Documents", "Most Local Cited References", "Reference Spectroscopy",
    "Most Frequent Words", "WordCloud", "TreeMap", "Words Frequency over Time", "Trend Topics", "Clustering by Coupling", "Co-occurence Network", "Thematic Map", "Thematic Evolution",
    "TE_Period_1", "TE_Period_2", "TE_Period_3", "TE_Period_4", "TE_Period_5", "Factorial Analysis", "Co-citation Network", "Historiograph", "Collaboration Network", "Countries Collaboration World Map"
  )
  data.frame(short = short, long = long)
}

## Generic PopUp
popUpGeneric <- function(title = NULL, type = "success", color = c("#1d8fe1", "#913333", "#FFA800"),
                         subtitle = "",
                         btn_labels = "OK", size = "40%") {
  showButton <- TRUE
  timer <- NA
  show_alert(
    title = title,
    text = subtitle,
    type = type,
    size = size,
    closeOnEsc = TRUE,
    closeOnClickOutside = TRUE,
    html = FALSE,
    showConfirmButton = showButton,
    showCancelButton = FALSE,
    btn_labels = btn_labels,
    btn_colors = color,
    timer = timer,
    imageUrl = "",
    animation = TRUE
  )
}


## Ad to Report PopUp
popUp <- function(title = NULL, type = "success", btn_labels = "OK") {
  switch(type,
    success = {
      title <- paste(title, "\n added to report", sep = "")
      subtitle <- ""
      btn_colors <- "#1d8fe1"
      showButton <- TRUE
      timer <- 3000
    },
    error = {
      title <- "No results to add to the report "
      subtitle <- "Please Run the analysis and then Add it to the report"
      btn_colors <- "#913333"
      showButton <- TRUE
      timer <- 3000
    },
    waiting = {
      title <- "Please wait... "
      subtitle <- "Adding results to report"
      btn_colors <- "#FFA800"
      showButton <- FALSE
      btn_labels <- NA
      timer <- NA
    }
  )

  show_alert(
    title = title,
    text = subtitle,
    type = type,
    size = "s",
    closeOnEsc = TRUE,
    closeOnClickOutside = TRUE,
    html = FALSE,
    showConfirmButton = showButton,
    showCancelButton = FALSE,
    btn_labels = btn_labels,
    btn_colors = btn_colors,
    timer = timer,
    imageUrl = "",
    animation = TRUE
  )
}

colorlist <- function() {
  c(
    "#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#A65628", "#F781BF", "#999999", "#66C2A5", "#FC8D62", "#8DA0CB", "#E78AC3", "#A6D854", "#FFD92F",
    "#B3B3B3", "#A6CEE3", "#1F78B4", "#B2DF8A", "#33A02C", "#FB9A99", "#E31A1C", "#FDBF6F", "#FF7F00", "#CAB2D6", "#6A3D9A", "#B15928", "#8DD3C7", "#BEBADA",
    "#FB8072", "#80B1D3", "#FDB462", "#B3DE69", "#D9D9D9", "#BC80BD", "#CCEBC5"
  )
}

overlayPlotly <- function(VIS) {
  # colorscale_VOS=matrix(c(0, 'rgba(66,65,135,255)', 0.1, 'rgba(34,170,134,255)',
  #                         0.3, 'rgba(202,224,31,255)',
  #                         1, 'rgba(244,227,92,255)'),4,2, byrow=T)

  # colorscale_Our=matrix(c(0, 'rgba(238,238,238,255)',
  #                         0.1, 'rgba(232,202,177,255)',
  #                         0.2, 'rgba(217,137,100,255)',
  #                         0.6, 'rgba(199,107,90,255)',
  #                         0.9, 'rgba(164,38,39,255)',
  #                         1,   'rgba(178,34,34,255)'),
  #                       6,2, byrow=T)

  Reds <- matrix(
    c(
      "0", "rgb(255,255,255)",
      "0.05", "rgb(238,238,238)",
      "0.125", "rgb(254,224,210)",
      "0.25", "rgb(252,187,161)",
      "0.375", "rgb(252,146,114)",
      "0.5", "rgb(251,106,74)",
      "0.625", "rgb(239,59,44)",
      "0.75", "rgb(203,24,29)",
      "0.875", "rgb(165,15,21)",
      "1", "rgb(103,0,13)"
    )
  )

  nodes <- VIS$x$nodes %>%
    mutate(
      y = y * (-1),
      font.size = (((font.size - min(font.size)) / diff(range(font.size))) * 20) + 10
    )

  colori <- c(
    "Blackbody", "Bluered", "Blues", "Cividis", "Earth", "Electric", "Greens", "Greys", "Hot", "Jet", "Picnic", "Portland",
    "Rainbow", "RdBu", "Reds", "Viridis", "YlGnBu", "YlOrRd"
  )

  nodes2 <- nodes %>%
    group_by(id) %>%
    mutate(log = ceiling(log(deg))) %>%
    slice(rep(1, each = log))

  p <- plot_ly(nodes2, x = ~x, y = ~y) %>%
    add_histogram2d(
      histnorm = "density", zsmooth = "fast",
      colorscale = Reds,
      # colorscale=colori[15],
      showscale = FALSE
    )

  for (i in 1:nrow(nodes)) {
    p <- p %>%
      add_annotations(
        xref = "x1", yref = "y",
        x = nodes$x[i], y = nodes$y[i],
        text = nodes$label[i],
        font = list(family = "Arial", size = nodes$font.size[i], color = adjustcolor(nodes$font.color[i], alpha.f = 0.8)),
        showarrow = FALSE
      )
  }
  p <- p %>%
    layout(
      yaxis = list(
        title = "", zeroline = FALSE, showgrid = FALSE, showline = FALSE,
        showticklabels = FALSE, domain = c(-1, 1), gridcolor = "#FFFFFF",
        tickvals = list(NA)
      ),
      xaxis = list(
        title = "", zeroline = FALSE, showgrid = FALSE, showline = FALSE,
        showticklabels = FALSE, domain = c(-1, 1), gridcolor = "#FFFFFF",
        tickvals = list(NA)
      ),
      plot_bgcolor = "rgba(0, 0, 0, 0)",
      paper_bgcolor = "rgba(0, 0, 0, 0)",
      showlegend = FALSE
    ) %>%
    style(hoverinfo = "none") %>%
    config(
      displaylogo = FALSE,
      modeBarButtonsToRemove = c(
        #' toImage',
        "sendDataToCloud",
        "pan2d",
        "select2d",
        "lasso2d",
        "toggleSpikelines",
        "hoverClosestCartesian",
        "hoverCompareCartesian"
      )
    )
  return(p)
}


menuList <- function(values) {
  TC <- ISI <- MLCS <- MLCA <- AFF <- MCC <- DB_TC <- DB_CR <- CR <- FALSE
  if (!"TC" %in% values$missTags) TC <- TRUE
  if ("ISI" %in% values$M$DB[1] & !"CR" %in% values$missTags) MLCS <- TRUE
  if ("ISI" %in% values$M$DB[1] & !"CR" %in% values$missTags) MLCA <- TRUE
  if ("ISI" %in% values$M$DB[1]) ISI <- TRUE
  if (!"C1" %in% values$missTags) AFF <- TRUE
  if (!"CR" %in% values$missTags) CR <- TRUE
  if (!"TC" %in% values$missTags & !"C1" %in% values$missTags) MCC <- TRUE
  if (sum(c("SCOPUS", "ISI") %in% values$M$DB[1]) > 0) DB_CR <- TRUE
  if (sum(c("SCOPUS", "ISI", "OPENALEX", "LENS") %in% values$M$DB[1]) > 0) DB_TC <- TRUE


  # out <- list(TC,ISI,MLCS,AFF,MCC,DB_TC,DB_CR,CR)
  out <- NULL

  L <- list()

  L[[length(L) + 1]] <-
    menuItem("Filters", tabName = "filters", icon = fa_i(name = "filter"))

  L[[length(L) + 1]] <-
    menuItem("Overview",
      tabName = "overview", icon = fa_i(name = "table"), startExpanded = FALSE,
      menuSubItem("Main Information", tabName = "mainInfo", icon = icon("chevron-right", lib = "glyphicon")),
      menuSubItem("Annual Scientific Production", tabName = "annualScPr", icon = icon("chevron-right", lib = "glyphicon")),
      if (isTRUE(TC)) {
        menuSubItem("Average Citations per Year", tabName = "averageCitPerYear", icon = icon("chevron-right", lib = "glyphicon"))
      },
      menuSubItem("Three-Field Plot", tabName = "threeFieldPlot", icon = icon("chevron-right", lib = "glyphicon"))
    )

  L[[length(L) + 1]] <-
    menuItem("Sources",
      tabName = "sources", icon = fa_i(name = "book"), startExpanded = FALSE,
      menuSubItem("Most Relevant Sources", tabName = "relevantSources", icon = icon("chevron-right", lib = "glyphicon")),
      if (isTRUE(MLCS)) {
        menuSubItem("Most Local Cited Sources", tabName = "localCitedSources", icon = icon("chevron-right", lib = "glyphicon"))
      },
      menuSubItem("Bradford's Law", tabName = "bradford", icon = icon("chevron-right", lib = "glyphicon")),
      if (isTRUE(TC)) {
        menuSubItem("Sources' Local Impact", tabName = "sourceImpact", icon = icon("chevron-right", lib = "glyphicon"))
      },
      menuSubItem("Sources' Production over Time", tabName = "sourceDynamics", icon = icon("chevron-right", lib = "glyphicon"))
    )

  AU <-
    menuItem("Authors",
      tabName = "authors", icon = fa_i(name = "user"), startExpanded = FALSE,
      "Authors",
      menuSubItem("Most Relevant Authors", tabName = "mostRelAuthors", icon = icon("chevron-right", lib = "glyphicon")),
      if (isTRUE(MLCA)) {
        menuSubItem("Most Local Cited Authors", tabName = "mostLocalCitedAuthors", icon = icon("chevron-right", lib = "glyphicon"))
      },
      menuSubItem("Authors' Production over Time", tabName = "authorsProdOverTime", icon = icon("chevron-right", lib = "glyphicon")),
      menuSubItem("Lotka's Law", tabName = "lotka", icon = icon("chevron-right", lib = "glyphicon")),
      if (isTRUE(TC)) {
        menuSubItem("Authors' Local Impact", tabName = "authorImpact", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(AFF)) {
        "Affiliations"
      },
      if (isTRUE(AFF)) {
        menuSubItem("Most Relevant Affiliations", tabName = "mostRelAffiliations", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(AFF)) {
        menuSubItem("Affiliations' Production over Time", tabName = "AffOverTime", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(AFF)) {
        "Countries"
      },
      if (isTRUE(AFF)) {
        menuSubItem("Corresponding Author's Countries", tabName = "correspAuthorCountry", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(AFF)) {
        menuSubItem("Countries' Scientific Production", tabName = "countryScientProd", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(AFF)) {
        menuSubItem("Countries' Production over Time", tabName = "COOverTime", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(MCC)) {
        menuSubItem("Most Cited Countries", tabName = "mostCitedCountries", icon = icon("chevron-right", lib = "glyphicon"))
      }
    )

  L[[length(L) + 1]] <- AU

  DOC <-
    menuItem("Documents",
      tabName = "documents", icon = fa_i(name = "layer-group"), startExpanded = FALSE,
      if (isTRUE(TC) | isTRUE(DB_TC)) {
        "Documents"
      },
      if (isTRUE(TC)) {
        menuSubItem("Most Global Cited Documents", tabName = "mostGlobalCitDoc", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(DB_TC) & isTRUE(CR) & isTRUE(TC)) {
        menuSubItem("Most Local Cited Documents", tabName = "mostLocalCitDoc", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(DB_CR)) {
        "Cited References"
      },
      if (isTRUE(DB_CR)) {
        menuSubItem("Most Local Cited References", tabName = "mostLocalCitRef", icon = icon("chevron-right", lib = "glyphicon"))
      },
      if (isTRUE(DB_CR)) {
        menuSubItem("References Spectroscopy", tabName = "ReferenceSpect", icon = icon("chevron-right", lib = "glyphicon"))
      },
      "Words",
      menuSubItem("Most Frequent Words", tabName = "mostFreqWords", icon = icon("chevron-right", lib = "glyphicon")),
      menuSubItem("WordCloud", tabName = "wcloud", icon = icon("chevron-right", lib = "glyphicon")),
      menuSubItem("TreeMap", tabName = "treemap", icon = icon("chevron-right", lib = "glyphicon")),
      menuSubItem("Words' Frequency over Time", tabName = "wordDynamics", icon = icon("chevron-right", lib = "glyphicon")),
      menuSubItem("Trend Topics", tabName = "trendTopic", icon = icon("chevron-right", lib = "glyphicon"))
    )

  L[[length(L) + 1]] <- DOC

  L[[length(L) + 1]] <-
    menuItem("Clustering",
      tabName = "clustering", icon = fa_i(name = "spinner"), startExpanded = FALSE,
      menuSubItem("Clustering by Coupling", tabName = "coupling", icon = icon("chevron-right", lib = "glyphicon"))
    )

  L[[length(L) + 1]] <-
    menuItem("Conceptual Structure",
      tabName = "concepStructure", icon = fa_i(name = "spell-check"), startExpanded = FALSE,
      "Network Approach",
      menuSubItem("Co-occurence Network", tabName = "coOccurenceNetwork", icon = icon("chevron-right", lib = "glyphicon")),
      menuSubItem("Thematic Map", tabName = "thematicMap", icon = icon("chevron-right", lib = "glyphicon")),
      menuSubItem("Thematic Evolution", tabName = "thematicEvolution", icon = icon("chevron-right", lib = "glyphicon")),
      "Factorial Approach",
      menuSubItem("Factorial Analysis", tabName = "factorialAnalysis", icon = icon("chevron-right", lib = "glyphicon"))
    )

  if (!"CR" %in% values$missTags) {
    L[[length(L) + 1]] <-
      menuItem("Intellectual Structure",
        tabName = "intStruct", icon = fa_i(name = "gem"), startExpanded = FALSE,
        menuSubItem("Co-citation Network", tabName = "coCitationNetwork", icon = icon("chevron-right", lib = "glyphicon")),
        if (isTRUE(DB_TC) & isTRUE(CR)) {
          menuSubItem("Historiograph", tabName = "historiograph", icon = icon("chevron-right", lib = "glyphicon"))
        }
      )
  }

  L[[length(L) + 1]] <-
    menuItem("Social Structure",
      tabName = "socialStruct", icon = fa_i("users"), startExpanded = FALSE,
      menuSubItem("Collaboration Network", tabName = "collabNetwork", icon = icon("chevron-right", lib = "glyphicon")),
      if (isTRUE(AFF)) {
        menuSubItem("Countries' Collaboration World Map", tabName = "collabWorldMap", icon = icon("chevron-right", lib = "glyphicon"))
      }
    )

  L[[length(L) + 1]] <- menuItem("Report", tabName = "report", icon = fa_i(name = "list-alt"))

  L[[length(L) + 1]] <- menuItem("TALL Export", tabName = "tall", icon = icon("text-size", lib = "glyphicon"))

  # L[[length(L) + 1]] <- menuItem("Settings", tabName = "settings", icon = fa_i(name = "sliders"))

  if (!isTRUE(TC)) {
    out <- c(
      out, "Average Citations per Year", "Sources' Local Impact", "Authors' Local Impact",
      "Most Global Cited Documents"
    )
  }
  if (!isTRUE(MLCS)) {
    out <- c(out, "Most Local Cited Sources")
  }
  if (!isTRUE(ISI)) {
    out <- c(out, "Most Local Cited Authors")
  }
  if (!isTRUE(AFF)) {
    out <- c(
      out, "Most Relevant Affiliations", "Affiliations' Production over Time",
      "Corresponding Author's Countries", "Countries' Scientific Production",
      "Countries' Production over Time", "Countries' Collaboration World Map"
    )
  }
  if (!isTRUE(MCC)) {
    out <- c(out, "Most Cited Countries")
  }
  if (!(isTRUE(DB_TC) & isTRUE(CR) & isTRUE(TC))) {
    out <- c(out, "Most Local Cited Documents")
  }
  if (!isTRUE(DB_CR)) {
    out <- c(out, "Most Local Cited References", "References Spectroscopy")
  }
  if (!isTRUE(CR)) {
    out <- c(out, "Co-citation Network")
  }
  if (!(isTRUE(DB_TC) & isTRUE(CR))) {
    out <- c(out, "Historiograph")
  }

  values$out <- out

  return(L)
}


# find home folder
homeFolder <- function() {
  switch(Sys.info()[["sysname"]],
         Windows = {
           home <- Sys.getenv("R_USER")
         },
         Linux = {
           home <- Sys.getenv("HOME")
         },
         Darwin = {
           home <- Sys.getenv("HOME")
         }
  )
  return(home)
}


