Function to download biotic interaction datasets

February 6, 2020
By

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I work in ecology, biogeography, etc… Biotic interactions (interactions between species) and its repercussions on species distributions is my main research interest.

As such, I had, at some point, to download datasets on species interactions. I wanted to be able to produce a uniform (more or less, not as much as I would like) R object whatever the database I used. I created this function to do just that!

It can be used to download from database website or upload csv files into R (depending on the database). It currently uses the following databases:

  1. EcoBase – The database for the models using Ecopath with Ecosim. These are really good, have good metadata and spatial information (polygons) (Christensen & Walters, 2004Heymans et al. 2016).
  2. Web of Life – To be really honest I don’t know this database all that much. However it also provides information on the dataset location, but it does not provide details on the ecosystem where it occurs (Fortuna et al. 2014).
  3. Global Web – This database provides details on the ecosystem where the interaction dataset occur, bu no details on spatial location are provided (Thompson et al. 2012).
  4. Mangal – This database provides lots of information on the biotic interactions datasets (Poisot et al. 2015).

In order to write this function I relied on work previously done by others. Namely the code to download EcoBase interaction datasets was obtained here. In what concerns the mangal database I relied on the work done in the package rmangal.

NOTE: This is important! Be sure to check the results of the function! I’m still working on it, so this is a provisional version. But I think it works pretty good though.

(Somewhere in the future it might be available in my GitHub.)

create.fw.list <- function(db, folder = NULL, type = NULL, ecosyst=FALSE, ref=FALSE, spatial=FALSE, code=FALSE)
  {
  
  #### 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).
  #'type' - if db=mg the user should provide the type of interactions to be downloaded
  # 'ecosyst' - Getting ecosystem information, only for gw, eb
  #'ref' references information
  #'spatial' - get spatial info, only for wl, eb and mg
  
  #### 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(type)) 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'!")
  
  ############################################################################################
  #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!"))
    
    #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
      
      #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("\nThe pdf 'gw_list.pdf' has to be previously converted to a csv file...")
      
      #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 = "FW")
    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)  # 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] <- 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 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
      EcoBase_shape <- sf::st_read("http://sirs.agrocampus-ouest.fr/EcoBase/php/protect/extract_kml.php")
      
      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]])#Alternative to Numextract
        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(Numextract(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! \n\n Types 'predation' and 'herbivory' by default... \n but run mangal function 'avail_type' to check available types...\n\nThis operation might take a long time!")
    
    ntypes <- length(type)
    
    net_info <- list()
    
    for(i in 1:ntypes){
      
      message(paste0("\n\nFetching information from interactions of the type ","'",type[i], "'!"))
      
      fwlist1 <- search_interactions(type = type[i]) %>% get_collection()
        
      net_info <- rbind(net_info, fwlist1)

      fwlist2 <- as.igraph(fwlist1)
      
      fwlist <- c(fwlist, fwlist2)
      
      #class(fwlist)
      
    }
    
    #Converting igraph objects to data frame
    for(i in 1:length(fwlist)){
      fw2 <- fwlist[[i]]
      #convert each igraph to a data frame
      fw3 <- as_data_frame(fw2, what = "both")
      id_name <- fw3$vertices[,1:2]
      
      for(j in 1:nrow(id_name)){#clean the names
        
        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 = 4))
      names(references) <- c("Dataset 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,2] <- first_author
      references[j,3] <- year_mng
      references[j,4] <- doi_mng
      
      references <- references[order(references$`Dataset ID`),]
      rownames(references) <- 1:nrow(references)
      }
      
    }#End of mg refs
    
    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

 

 

 

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