fw_package: FWebs

Documented in create.fw.list

#' Download datasets from online database
#'
#' @param db Database: eb (EcoBase), gw (GlobalWeb), wl (Web of Life) and mg (Mangal)
#' @param folder Folder in the working directory to get the dataset files (db=gw and wl)
#' @param mangal_types If db=mg the user should provide the type of interactions to be downloaded; if 'db=all' all mangal interaction types are used
#' @param ecosyst Getting ecosystem information (only for db=gw, db=eb)
#' @param ref references information
#' @param spatial get spatial info (only for )
#' @param code To get the food web code
#' @return Returns a list that might have the following elements (depending on use options): 1. list of interaction matrices, 2. Reference data frame with FW code, first author of original publication, year of publication, full reference (if db='mg': FW code, type of interaction matrix, original ID in mangal, first author of original publication, year of publication); 3. Study site location (for db=wl, db=eb and db=mg); 4. FW code. 
#' @importFrom Hmisc all.is.numeric
#' @importFrom ggplot2 aes ggplot theme annotation_logticks geom_line scale_y_log10 scale_x_log10 element_text labs
#' @importFrom NetIndices GenInd TrophInd
#' @importFrom igraph degree degree_distribution graph_from_adjacency_matrix as_data_frame
#' @importFrom sf st_as_sf st_cast st_geometry st_read st_zm
#' @importFrom sp SpatialPolygons Polygon Polygons
#' @importFrom XML xmlToList xmlTreeParse xpathSApply
#' @importFrom stringr str_extract_all str_length str_sub word str_replace_all
#' @importFrom methods as
#' @importFrom stats na.omit
#' @importFrom utils read.csv tail
#' @importFrom randomcoloR randomColor
#' @importFrom rmangal get_collection search_interactions as.igraph
#' @importFrom plyr ldply
#' @importFrom RCurl basicTextGatherer curlPerform
#' @importFrom magrittr %>%
#' @export
#' @examples #mg2 <- create.fw.list(db="mg", ref=TRUE, spatial=TRUE)


create.fw.list <- function(db, folder = NULL, ecosyst=FALSE, ref=FALSE, spatial=FALSE, code=FALSE, mangal_types = NULL)
  {
  
  #utils::globalVariables(c("model.dissemination_allow", "model.whole_food_web"))
  model.dissemination_allow <- model.whole_food_web <- NULL
  
  #### Arguments  ####
  #db - database - eb (EcoBase), gw (GlobalWeb), wl (Web of Life) and mg (Mangal)
  #folder - folder in the WD to get the dataset files (db=gw and wl).
  #ecosyst - Getting ecosystem information, only for gw, eb
  #ref references information
  #spatial - get spatial info, only for wl, eb and mg
  #mangal_types - if db=mg the user should provide the type of interactions to be downloaded
  
  #### Data Sources ####
  #Global Web: https://www.globalwebdb.com/
  #EcoTroph Example (EcoBase): http://sirs.agrocampus-ouest.fr/EcoTroph/index.php?action=examples
  #Script for EcoBase: http://sirs.agrocampus-ouest.fr/EcoBase/#discoverytools
  #Mangal: #https://mangal-wg.github.io/rmangal/articles/rmangal.html
  #Web of Life: http://www.web-of-life.es/
  
  #### Results  ####
  fwlist <- list()
  
  #### Conditions for data entry  ############################################################
  
  #db
  
  if(!db %in% c("eb","wl","gw","mg"))stop("Argument 'db' must take one of the following values:\n
                                          'wl' - Web of Life
                                          'mg' - mangal
                                          'gw' - globalweb
                                          'eb' - ecobase")
  
  #folder
  if(!db %in% c("wl","gw") & !is.null(folder)) stop("Argument 'folder'can only be used if 'db'= 'wl' or 'gw'!")
  
  #type
  
  #folder
  if(!db %in% c("mg") & !is.null(mangal_types)) stop("Argument 'type'can only be used if 'db'= 'mg'!")
  
  #ecosyst
  
  if(!db %in% c("gw", "eb") & ecosyst==TRUE) stop("Argument 'ecosyst'can only be used if 'db'= 'eb' or 'gw'!")
  
  #ref
  #all
  
  #spatial
  if(!db %in% c("wl", "mg", "eb") & spatial==TRUE) stop("Argument 'spatial'can only be used if 'db'= 'eb', 'mg' 'wl'!")
  
  #code
  if(!db %in% c("wl", "mg", "gw") & code==TRUE) stop("Argument 'code'can only be used if 'db'= 'wl', 'mg'', 'gw'!")
  
  #mangal_types
  if("mg" %in% db & is.null(mangal_types)) message("No value defined for the 'mangal_types' argument! \n Will assume types 'predation' and 'herbivory'.")
  if(!"mg" %in% db & !is.null(mangal_types)) stop("Argument 'mangal_types'can only be used if 'db'= 'mg'!")
  
  ############################################################################################
  #Updating each dataset database
  
  #GlobalWeb
  if (db == "gw"){
    message("####################### GLOBALWEB DATABASE #######################\n\n")
    
    message("Fetching info from the provided folder!")
    files_gw <- list.files(path = folder, pattern = "WEB")
    ngw <- length(files_gw)
    message (paste0("There are ", ngw, " food web files in the folder!"))
    message ("You should have downloaded the file 'Current Food Web List' from the GlobalWeb website
             \n and converted it to csv.")
    
    
    #Load files into list
    #And create vector of references
    if (ref==TRUE) reflist_gw <- c()
    
    names_gw <- c()#FW names
    
    #getting the files into R
    for(i in 1:ngw){
      
      message(paste0("Fetching food web ", i, " in ", ngw, "!"))
      
      dfgw <- read.csv(paste0(folder,"/",files_gw[i]), header = FALSE)  # read csv file
      dfgw <- dfgw[, colSums( is.na(dfgw) ) <=1]#Remove columns with all NA
      #dfgw <- dfgw[colSums( is.na(dfgw) ) <=1,]#Remove rows with no data
      
      #Get the FW name
      names_gw[i] <- as.character(dfgw[2,1])
      
      #Get the reference to the vector
      if (ref==TRUE) reflist_gw[i] <- as.character(dfgw[1,1])
      
      #to name the columns
      names_gw_c <- c()
      n1 <- ncol(dfgw)-1
      for(j in 1:n1){
        names_gw_c[j] <- as.character(dfgw[2,j+1])
      }
      
      #to name the rows
      names_gw_r <- c()
      n2 <- nrow(dfgw)-2
      for(j in 1:n2){
        names_gw_r[j] <- as.character(dfgw[j+2, 1])
      }
      
      dfgw <- dfgw[-c(1,2),-1]
      
      #Remove columns with NA
      dfgw[dfgw==""] <- NA
      dfgw <- na.omit(dfgw)
      
      if(i==281){names_gw_r <- names_gw_r[-c(36,37)]}#the FW on i=281 has a note at the bottom
      
      #Delete the 'empty names'
      names_gw_c <- names_gw_c[names_gw_c!=""]
      names_gw_r <- names_gw_r[names_gw_r!=""]
      
      #Same names in rows or columns?
      #if(length(unique(names_gw_r)) < length(names_gw_r)) rown[i] <- as.character(i)
      #if(length(unique(names_gw_c)) < length(names_gw_c)) coln[i] <- as.character(i)
      
      #For some strange reason some rows and columns have the same name
      names_gw_c <- paste0("sp_", as.character(1:length(names_gw_c)), "_",names_gw_c)
      names_gw_r <- paste0("sp_", as.character(1:length(names_gw_r)), "_",names_gw_r)
      
      colnames(dfgw) <- names_gw_c
      rownames(dfgw) <- names_gw_r
      
      fwlist[[i]] <- dfgw
      
    }
    
    #Name the list
    names(fwlist) <- names_gw
    
    if(ref==TRUE){
      
      references <- as.data.frame(matrix(ncol = 4))
      names(references) <- c("FW code", "first_author", "year", "full_ref" )
      
      files_gw <- list.files(folder, pattern = "WEB")
      
      message("Fetching references from the dataset files!")
      
      for(w in 1:ngw){
        
        dfgw <- read.csv(paste0(folder,"/",files_gw[w]), header = FALSE)  # read csv file
        #message(paste0("Reading file ", files_gw[w]))
        dfgw <- dfgw[, colSums( is.na(dfgw) ) <=1]#Remove columns with all NA
        
        #Get the reference to the vector
        full_ref1 <- as.character(dfgw[1,1])
        references[w,4] <- full_ref1#full reference
        references[w,1] <- files_gw[w]#fw code
        references[w,2] <- str_sub(word(full_ref1, start = 1), 1, str_length(word(full_ref1, start = 1))-1)#fisrt author
        references[w,3] <- regmatches(x = full_ref1,gregexpr("[0-9]+",text = full_ref1))[[1]][1]#year
        #references[w,3] <- gsub('.+\\(([0-9]+)\\).+?$', '\\1', full_ref1)#year
        
      }#end loop to add refs
      
    }#end gw refs
    
    #ECOSYSTEM
    if(ecosyst==TRUE){
      message("Searching for 'gw_list.csv' file...")
      
      if (!file.exists(paste0(folder, "/gw_list.csv"))) stop("\nDownload the file 'Current Food Web List' from the website
                                                             \nand convert to a csv named 'gw_list.csv' please!")
      
      #I had to conver the gw_list.pdf file to excel (csv), since I could not install tabulizes to extract pdf tables
      gw_eco <- read.csv(paste0(folder,"/","gw_list.csv"), header = TRUE, sep = ";")  # read csv file
      
      filn <- paste0("WEB", as.character(gw_eco[,1]), ".csv")
      
      gw_eco2 <- gw_eco[,1:3]
      gw_eco2[,1] <- filn
      
      names(gw_eco2)[1] <- "FW"
      
      #yes... I do know the following few lines are 'ugly'...
      filn <- as.data.frame(cbind(filn, filn))
      
      names(filn) <- c("filn1","filn2")
      
      #files_gw <- list.files(path = folder, pattern = "WEB")
      
      ecosystem <- merge(x=filn, y=gw_eco2, by.x= "filn2", by.y = "FW")
      
      ecosystem <- ecosystem[,c(2, 3, 4)]
      
      names(ecosystem)[1] <- "Food web"
      
    }
    
  }#end of gw
  
  #Web of Life
  if (db == "wl"){
    
    message("####################### WEB OF LIFE DATABASE #######################\n\n")
    
    files_wl <- list.files(path = folder, pattern = ".csv")
    
    files_wl <- files_wl[files_wl != "references.csv"]
    
    nwl <- length(files_wl)
    message (paste0("There are ", nwl, " food web files in the folder!"))
    
    #Get refs and metrics table
    if (file.exists(paste0(folder, "/references.csv"))) {
      table_wl <- read.csv(paste0(folder, "/references.csv"), header = TRUE)  # read csv file
    } else {
      stop("There is no 'references.csv' file on the folder, as provided by the website!")
    }
    
    #FW names
    names_wl <- as.character(table_wl[,8])
    
    #Load files
    for(i in 1:nwl){
      message(paste0("Fetching food web ", i, " in ", nwl, "!"))
      dfwl <- read.csv(paste0(folder, "/",files_wl[i]), header = TRUE, row.names=1)  # read csv file
      #row.names(dfwl) <- as.character(dfwl[,1])
      #dfwl <- dfwl[,-1]
      dfwl[is.na(dfwl)] <- 0
      fwlist[[i]] <- dfwl
    }
    
    names(fwlist) <- names_wl
    
    #REFERENCES
    if(ref==TRUE){
      
      references <- as.data.frame(matrix(ncol = 4))
      names(references) <- c("FW code", "first_author", "year", "full_ref" )
      
      message("Fetching references from the 'references.csv' file!")
      message("Checking the presence of the 'references.csv' file...")
      if(!file.exists(paste0(folder, "/references.csv"))==TRUE)stop("Can't retrieve reference details... \n File not present!")
      
      ref_file <- read.csv(paste0(folder, "/references.csv"), header = TRUE)  # read csv file
      
      for(w in 1:nwl){
        
        full_ref1 <- as.character(ref_file[w,7])
        references[w,4] <- full_ref1#full reference
        references[w,1] <- as.character(ref_file[w,1])#fw code
        references[w,2] <- stringr::str_sub(stringr::word(full_ref1, start = 1), 1, stringr::str_length(stringr::word(full_ref1, start = 1))-1)#fisrt author
        references[w,3] <- regmatches(x = full_ref1,gregexpr("[0-9]+",text = full_ref1))[[1]][1]#year
        #references[w,3] <- gsub('.+\\(([0-9]+)\\).+?$', '\\1', full_ref1)#year
        
      }#end loop to add refs
      
      
    }#end wl refs
    
    #SPATIAL
    if(spatial==TRUE){
      
      message("Fetching the spatial information from the 'references.csv' file!")
      message("Checking the presence of the 'references.csv' file...")
      if(!file.exists(paste0(folder, "/references.csv"))==TRUE)stop("Can't retrieve spatial info... \n File not present!")
      
      ref_file <- read.csv(paste0(folder, "/references.csv"), header = TRUE)  # read csv file
      spatial1 <- ref_file[,c(1,9,10)]
      
    }#end of spatial
    
  }#end of wl
  
  #EcoBase
  if(db == "eb"){
    
    message("####################### ECOBASE DATABASE #######################\n\n")
    
    message("Fetching info from the EcoBase website!")
    suppressWarnings({
      
      #To obtain the list of available models
      
      suppressMessages({
        h=basicTextGatherer()
        curlPerform(url = 'http://sirs.agrocampus-ouest.fr/EcoBase/php/webser/soap-client_3.php',writefunction=h$update)
        data1 <- xmlTreeParse(h$value(),useInternalNodes=TRUE)
        liste_mod <- ldply(xmlToList(data1),data.frame)#liste_mod contains a list and decription
      })
      
      #Select only those allowing dissemination
      l2 <- subset(liste_mod, model.dissemination_allow =="true")#only those of which dissemination is allowed
      message("Sellected only those to which model dissemination is allowed!")
      
      #Select only those with whole food webs
      l3 <- subset(l2, model.whole_food_web =="true")#only those with the full food web
      message("Sellected only those to which the whole food web is available!")
      
      #Get model names
      model.name <- as.character(l3$model.model_name)
      input_list <- list()
      id <- as.numeric(as.character(l3$model.model_number))
      
      #Loop to get input list
      for(i in 1:nrow(l3)){
        
        message(paste0("Fetching information on food web ",i, " of ", nrow(l3)))
        
        suppressMessages({
          h=basicTextGatherer()
          mymodel <- id[i]
          curlPerform(url = paste('http://sirs.agrocampus-ouest.fr/EcoBase/php/webser/soap-client.php?no_model=',mymodel,sep=''),writefunction=h$update,verbose=TRUE)
          data2 <- xmlTreeParse(h$value(),useInternalNodes=TRUE)
          input1 <- xpathSApply(data2,'//group',function(x) xmlToList(x))
        })
        
        #need do name the columns
        names_input <- as.character(input1[1,])
        input1 <- as.data.frame(input1)
        colnames(input1) <- names_input
        input1 <- input1[-1,]
        input_list[[i]] <- input1
      }#end of loop to get input list
      
      mnames <- names(input_list)
      
      for (i in 1:length(input_list)){
        
        m2 <- input_list[[i]] #get the model
        
        nnodes <- length(m2)
        node_names <- names(m2)
        
        # if (biomass == TRUE)
        #    {
        #    nodes_biomass <- as.data.frame(matrix(ncol=3, nrow=nnodes))
        #    names(nodes_biomass) <- c("id", "name", "biomass")
        #    }
        
        int_matrix <- as.data.frame(matrix(ncol=nnodes, nrow=nnodes))
        
        for(j in 1:length(m2)){
          
          node1 <- m2[[j]]
          node_id <- as.numeric(node1$group_seq)
          #node1_biomass <- as.numeric(node1$biomass)
          node_name <- node_names[j]
          
          #biomass
          #if (biomass == TRUE)
          #{
          #nodes_biomass[node_id, 1] <- node_id
          #nodes_biomass[node_id, 2] <- node_name
          #nodes_biomass[node_id, 3] <- node1_biomass
          #}
          
          #matrix
          colnames(int_matrix)[node_id] <- node_name
          rownames(int_matrix)[node_id] <- node_name
          
          diet_node1 <- node1$diet_descr
          nr_food_items <- length(diet_node1)
          
          for(a in 1:nr_food_items){
            item1 <- diet_node1[[a]]
            id_item1 <- as.numeric(item1$prey_seq)
            proportion_item1 <- as.numeric(item1$proportion)
            detritus_item1 <- as.numeric(item1$detritus_fate)
            #send to matrix
            int_matrix[id_item1,node_id] <- proportion_item1
          }
          
        }
        
        int_matrix[is.na(int_matrix)] <- 0#replacing NA with 0
        
        #if(db=="eb" && biomass == TRUE) fwlist[[i]] <- list(biomass=nodes_biomass, trophic_relations=int_matrix)
        #if(db=="eb" && biomass == FALSE) fwlist[[i]] <- int_matrix
        fwlist[[i]] <- int_matrix
        
      }
      
      names(fwlist) <- model.name
      
    })#end of outer suppressWarnings
    
    #REFERENCES
    if(ref==TRUE){
      
      references <- as.data.frame(matrix(ncol = 4))
      names(references) <- c("FW code", "first_author", "year", "full_ref" )
      
      message("Fetching the references information!")
      
      for(w in 1:nrow(l3)){
        
        #Get the reference to the vector
        full_ref1 <- as.character(l3$model.reference)[w]
        references[w,4] <- full_ref1#full reference
        references[w,1] <- as.numeric(as.character(l3$model.model_number[w]))#fw code
        references[w,2] <- as.character(l3$model.author[w])#fisrt author
        references[w,3] <- regmatches(x = full_ref1,gregexpr("[0-9]+",text = full_ref1))[[1]][1]#year
        #references[w,3] <- gsub('.+\\(([0-9]+)\\).+?$', '\\1', full_ref1)#year
        
      }#end loop to add refs
      
      
    }#end of eb refs
    
    #ECOSYSTEM
    if(ecosyst==TRUE){
      
      ecosystem <- data.frame(l3$model.model_number, l3$model.country, l3$model.ecosystem_type)
      
      names(ecosystem) <- c("Food web", "Location", "Ecosystem")
      
    }#end of eb ecosystem
    
    #SPATIAL
    if(spatial==TRUE){
      
      message("Fetching spatial information from the EcoBase website...")
      
      #Get actual polygons
      #message("Downloading 'ecobase_spatial_info.kml' file to working directory!")
      #download.file("http://sirs.agrocampus-ouest.fr/EcoBase/php/protect/extract_kml.php", destfile = "ecobase_spatial_info.kml")
      if(!file.exists("ecobase_areas.shp")){
        
        stop("If you need the spatial information on each dataset you have to:\n
             1. Download the kml file from http://sirs.agrocampus-ouest.fr/EcoBase/php/protect/extract_kml.php;\n
             (file name is 'location.kml')\n
             2. Convert it to a shapefile in any GIS;\n
             3. Name it 'ecobase_areas.shp';\n
             4. Place it in the working directory;\n
             ... I know, it is not ideal!...
             ")
        
      }else EcoBase_shape <- sf::st_read("ecobase_areas.shp")
      
      ebd <- EcoBase_shape$Name
      
      #Getting the model numbers
      nmr <- list()
      for(i in 1:length(ebd)){
        nr <- strsplit(as.character(ebd[i]), "--::")[[1]][1]
        nr <- as.numeric(str_extract_all(nr, "\\d+")[[1]])
        nmr[[i]] <- nr
      }
      
      nmr2 <- c()#line rows for each model
      for(i in 1:length(nmr)){
        a <- nmr[[i]]
        b <- length(a)
        c1 <- rep(i,b)
        nmr2 <- c(nmr2, c1)
      }
      
      #In Which row in ecobase geo file is the model?
      nmr <- unlist(nmr)
      table1 <- as.data.frame(cbind(nmr2, nmr))
      colnames(table1) <- c("row_n","id")
      
      #In which row does model.model_number with a given Id occurs?
      lines_n <- c()
      for (i in 1:nrow(liste_mod)){
        id <- as.numeric(as.character(liste_mod$model.model_number[i]))
        lines_n[i] <- as.numeric(table1[table1$id==id,][1])
      }
      
      ecobase_poly2 <- list()
      for(i in 1:length(lines_n)){
        ecobase_poly2[i] <- st_geometry(EcoBase_shape)[lines_n[i]]
        #plot(st_geometry(EcoBase_shape)[lines_n[i]], border="green", add=TRUE)
      }
      
      #if no polygon then bounding box
      #into here ecobase_poly2
      for(i in 1:length(ecobase_poly2)){
        if(is.na(lines_n[i])){
          #create a bounding box geographic thing
          z1 <- as.numeric(unlist(regmatches(liste_mod$model.geographic_extent[[i]],gregexpr("[[:digit:]]+\\.*[[:digit:]]*",liste_mod$model.geographic_extent[[i]]))))
          z2 <- c(z1[4], z1[1], z1[2], z1[1], z1[2], z1[3], z1[4], z1[3])
          x1 <- as.data.frame(matrix(z2, ncol=2, byrow=TRUE))
          x1 <- cbind(x1[2], x1[1])#had to change lat and long... I had this the other way around...
          p1 <- Polygon(x1)
          ps1 <- Polygons(list(p1),1)
          ecobase_poly2[[i]] <- st_as_sf(SpatialPolygons(list(ps1)))
        }
        ecobase_poly2[[i]] <- ecobase_poly2[[i]]
      }
      
      #convert all to class sf
      for(i in 1:length(ecobase_poly2)){
        if(!any(class(ecobase_poly2[[i]])=='sf')){
          t2 <- ecobase_poly2[[i]]
          t3 <- st_cast(t2, to="POLYGON")
          ecobase_poly2[[i]] <- st_as_sf(as(st_zm(st_geometry(t3)), "Spatial"))
        }
        else message("Ok!")
      }
      
      #line.Id correspondence
      table2 <- as.data.frame(cbind(1:length(ecobase_poly2),as.numeric(as.character(liste_mod$model.model_number))))
      names(table2) <- c("row","id")
      
      #select the corresponding polygons
      id_selected <- as.numeric(as.character(l3$model.model_number))
      
      #Which rows?
      rows_selected <- c()
      for(i in 1:length(id_selected)){
        rows_selected[i]  <- as.numeric(table2[table2["id"]==id_selected[i],][1])
      }
      
      spatial1 <- ecobase_poly2[rows_selected]
      
    }#end of eb spatial
    
  }#end of eb
  
  #MANGAL
  if(db == "mg"){
    
    message("####################### MANGAL DATABASE #######################\n\n")
    
    message("Fetching datasets from the Mangal website! \nThis operation might take a long time!")
    
    #type <- mangal_types
    
    #Default value
    if(is.null(mangal_types)) mangal_types <- c("predation", "herbivory")
    
    if("all" %in% mangal_types) {
      
      mangal_types <- c("competition", "predation", "herbivory",
                        "amensalism", "neutralism", "commensalism",
                        "mutualism", "parasitism", "symbiosis",
                        "scavenger", "detritivore")
      
      message("You are downloading the all types of interactions in the mangal database:
              competition, predation, herbivory, amensalism, neutralism, commensalism,
              mutualism, parasitism, symbiosis, scavenger, detritivore")
    }else mangal_types <- mangal_types
    
    ntypes <- length(mangal_types)
    
    net_info <- list()
    type_info <- c()
    
    for(i in 1:ntypes){#Going through the interaction types
      
      message(paste0("\n\nFetching information from interactions of the type ","'",mangal_types[i], "'!"))
      
      #fwlist1 <- rmangal::search_interactions(type = type[i]) %>% rmangal::get_collection()
      #Get all networks containing competition
      df_inter <- search_interactions(type = mangal_types[i], verbose = TRUE)
      
      if(nrow(df_inter)>0) fwlist1 <- get_collection(df_inter, verbose = TRUE)
      
      #if(nrow(df_inter)>0) net_info <- rbind(net_info, fwlist1)
      if(nrow(df_inter)>0) net_info <- c(net_info, fwlist1)
      
      if(nrow(df_inter)>0) fwlist2 <- rmangal::as.igraph(fwlist1)
      
      if(nrow(df_inter)>0) type_info <- c(type_info, rep(mangal_types[i], length(fwlist2)))
      
      if(nrow(df_inter)>0) fwlist <- c(fwlist, fwlist2)
      
    }#END of going through types
    
    #Converting igraph objects to data frame
    for(i in 1:length(fwlist)){
      fw2 <- fwlist[[i]]
      #convert each igraph to a data frame
      fw3 <- igraph::as_data_frame(fw2, what = "both")
      id_name <- fw3$vertices[,1:2]
      
      for(j in 1:nrow(id_name)){#clean the names
        
        node_name <- (paste0(id_name$original_name[j],"_" , id_name$name[j]))
        #node_name <- id_name$original_name[j]
        
        if (grepl(":", node_name, fixed=TRUE)) {
          node_name <- tail(strsplit(node_name, ": "))[[1]]
          id_name[j,2] <- node_name[2]
        } else id_name[j,2] <- node_name
        
        
      }#end clean names
      
      id_edges <- fw3$edges[,1:3]
      int_matrix <- as.data.frame(matrix(ncol = nrow(id_name), nrow = nrow(id_name)))
      colnames(int_matrix) <- id_name$original_name
      rownames(int_matrix) <- id_name$original_name
      
      #Fill the matrix
      for(a in 1:nrow(id_edges)){
        edge1 <- as.numeric(id_edges[a,1:2])
        name1 <- id_name[as.character(edge1[1]),][,2]
        name2 <- id_name[as.character(edge1[2]),][,2]
        int_matrix[name1,name2] <- 1
      }
      
      int_matrix[is.na(int_matrix)] <- 0 #convert all NA to zero
      
      fwlist[[i]] <- int_matrix
      
    }#end of loop to convert to a data frame
    
    #if(ref==TRUE){
    references <- as.data.frame(matrix(ncol = 6))
    names(references) <- c("Dataset ID", "Type of interaction", "Original ID","first_author", "year", "DOI")
    
    message("Fetching references!")
    
    for(j in 1:length(net_info)){
      dataset_id <- net_info[[j]]$dataset$dataset_id
      first_author <- net_info[[j]]$reference$first_author
      year_mng <- as.numeric(net_info[[j]]$reference$year)
      doi_mng <- net_info[[j]]$reference$doi
      #references[j,1] <- dataset_id
      references[j,3] <- dataset_id
      references[j,4] <- first_author
      references[j,5] <- year_mng
      references[j,6] <- doi_mng
      
      references <- references[order(references$`Dataset ID`),]
      rownames(references) <- 1:nrow(references)
    }
    
    references[,1] <- paste0("mg_",1:nrow(references))
    references[,2] <- type_info
    
    #}#End of mg refs
    
    names(fwlist) <-  paste0("mg_", references[,1])
    
    if(spatial==TRUE){
      spatial1 <- as.data.frame(matrix(ncol = 4))
      names(spatial1) <- c("Dataset ID", "first_author", "lat", "long")
      message("Fetching coordinates!")
      
      for(z in 1: length(net_info)){
        dataset_id <- net_info[[z]]$dataset$dataset_id
        lat_mng <- net_info[[z]]$network$geom_lat
        long_mng <-  net_info[[z]]$network$geom_lon
        first_author <- net_info[[z]]$reference$first_author
        if(length(unlist(lat_mng))>1){
          
          spatial2 <- as.data.frame(matrix(ncol = 4))
          names(spatial2) <- c("Dataset ID", "first_author", "long", "lat" )
          
          for(b in 1:length(unlist(lat_mng))){
            spatial2[b,3] <- long_mng[[1]] [b]
            spatial2[b,4] <- lat_mng [[1]] [b]
          }
          
          spatial2[,1] <- dataset_id
          spatial2[,2] <- first_author
          
          spatial1 <- rbind(spatial1, spatial2)
          
        }
        spatial1[z,1] <- dataset_id
        spatial1[z,2] <- first_author
        if(length(unlist(lat_mng))==1) spatial1[z,3] <- lat_mng
        if(length(unlist(lat_mng))==1) spatial1[z,4] <- long_mng
      }
      
      spatial1 <- spatial1[order(spatial1$`Dataset ID`),]
      rownames(spatial1) <- 1:nrow(spatial1)
      
    }#End of mg spatial
    
    #if (exists("references") & exists("spatial1")) (if(nrow(references)!=nrow(spatial1)) message("WARNING: There are more than on FW in some datasets! References and Spatial data frames have different number of rows."))
    
  }#end of mangal
  
  message(paste0("DONE! \n\nOverall the list stores ", length(fwlist), " datasets!"))
  
  master_list <- list()
  master_list[["int_matrix"]] <- fwlist
  
  if(ecosyst==TRUE) {
    master_list[["ecosystem"]] <- ecosystem
    message ("\n Additional element in the results: \n\n The vector with information on the ecosystems.")
  }
  
  if(ref==TRUE) {
    master_list[["references"]] <- references
    message ("Additional element in the results! \nA data frame with information on the references.")
  }
  
  if(spatial==TRUE) {
    master_list[["spatial_info"]] <- spatial1
    message ("\n Additional element in the results: \n\n Spatial information was added.")
  }
  
  if(code==TRUE) {
    if(db == "gw") master_list[["code"]] <- files_gw
    if(db == "wl") master_list[["code"]] <- files_wl
    if(db == "mg") master_list[["code"]] <- references[,1]
    
    message ("Added food web code information.")
  }
  
  #Return results
  if(length(master_list)==1) return(fwlist)
  if(length(master_list)!=1) return(master_list)
  
  message("####################### DONE! #######################")
  
  
  }#END OF FUNCTION create.fw.list