## -----------------------------------------------------------------------------------------------
## -----------------------------------------------------------------------------------------------
##
## A fine-tuned global distribution dataset of marine forest species
## J. Assis, E. Fragkopoulou, Frade, D., Neiva, J., A. Oliveira, D. Abecasis, E.A. Serrão
##
## Set of functions in R language to facilitate extraction, listing and visualization of occurrence records. 
## https://github.com/jorgeassis
##
## -----------------------------------------------------------------------------------------------
## -----------------------------------------------------------------------------------------------

listTaxa <- function() {
  
  options(warn=-1)
  
  packages.to.use <- c("shiny")
  
  for(package in packages.to.use) {
    if( ! package %in% rownames(installed.packages()) ) { install.packages( package ) }
    if( package == "robis" & ! "robis" %in% rownames(installed.packages()) ) { devtools::install_github("iobis/robis") }
    if( ! package %in% rownames(installed.packages()) ) { stop("Error on package instalation") }
    library(package, character.only = TRUE)
  }
  
  file.to.download <- "https://github.com/jorgeassis/marineforestsDB/blob/master/Data/listOfTaxa.csv?raw=true"
  
  download.file(file.to.download,destfile=paste0(tempdir(),"/MFTempFileLTaxa.csv"))
  data <- read.table(file=paste0(tempdir(),"/MFTempFileLTaxa.csv"),header=TRUE,sep="\t")
  file.remove(paste0(tempdir(),"/MFTempFileLTaxa.csv"))
  
  mydata <- as.matrix(data)
  
  packages.to.use <- c("shiny")
  
  options(warn=0)
  print(
    shinyApp(
      ui = fluidPage(
        title = "Examples of DataTables",
        DT::dataTableOutput('tbl')),
      server = function(input, output) {
        output$tbl = DT::renderDataTable(
          mydata, options = list( pageLength = 10, lengthMenu = c(10, 50, 100, 1000)) ) # , filter = 'top'
      } )
  )
  
}

# ------------------------------------------------

extractDataset <- function(group,pruned) {
  
  if( missing(group)) { stop("A group must be especifyed (e.g., brownAlgae or seagrasses)") }
  if( missing(pruned)) { stop("Pruned argument must be specifyed (e.g., TRUE or FALSE )") }
  
  if( group != "seagrasses" & group != "brownAlgae") { stop("A valid group must be especifyed (e.g., brownAlgae or seagrasses)")}
  if( pruned != TRUE & pruned != FALSE ) { stop("Pruned argument must be specifyed as TRUE or FALSE")}
  
  options(warn=-1)
  
  packages.to.use <- c("readr","utils","DT")
  
  for(package in packages.to.use) {
    if( ! package %in% rownames(installed.packages()) ) { install.packages( package ) }
    if( package == "robis" & ! "robis" %in% rownames(installed.packages()) ) { devtools::install_github("iobis/robis") }
    if( ! package %in% rownames(installed.packages()) ) { stop("Error on package instalation") }
    library(package, character.only = TRUE)
  }
  
  options(warn=0)
  
  if( pruned ) { 
    
    if( group == "seagrasses" ) {  file.to.download <- "https://github.com/jorgeassis/marineforestsDB/blob/master/Data/dataSeagrassesPruned.RData.zip?raw=true" }
    if( group == "brownAlgae" ) {  file.to.download <- "https://github.com/jorgeassis/marineforestsDB/blob/master/Data/dataBrownAlgaePruned.RData.zip?raw=true" }
    
    if( group == "seagrasses" ) {  file.name <- "dataSeagrassesPruned.RData" }
    if( group == "brownAlgae" ) {  file.name <- "dataBrownAlgaePruned.RData" }
    
    if( group == "seagrasses" ) {  file.name.obj <- "finalDataBaseSPruned" }
    if( group == "brownAlgae" ) {  file.name.obj <- "finalDataBaseBPruned" }
    
  }
  
  if( ! pruned ) { 
    
    if( group == "seagrasses" ) {  file.to.download <- "https://github.com/jorgeassis/marineforestsDB/blob/master/Data/dataSeagrasses.RData.zip?raw=true" }
    if( group == "brownAlgae" ) {  file.to.download <- "https://github.com/jorgeassis/marineforestsDB/blob/master/Data/dataBrownAlgae.RData.zip?raw=true" }
    
    if( group == "seagrasses" ) {  file.name <- "dataSeagrasses.RData" }
    if( group == "brownAlgae" ) {  file.name <- "dataBrownAlgae.RData" }
    
    if( group == "seagrasses" ) {  file.name.obj <- "finalDataBaseS" }
    if( group == "brownAlgae" ) {  file.name.obj <- "finalDataBaseB" }
    
  }
  
  download.file(file.to.download,destfile=paste0(tempdir(),"/MFTempFile.zip"))
  unzip(paste0(tempdir(),"/MFTempFile.zip"),exdir=tempdir(),overwrite=TRUE)
  
  load(paste0(tempdir(),"/",file.name))
  myData <- get(file.name.obj)
  
  file.remove(paste0(tempdir(),"/MFTempFile.zip"))
  file.remove(paste0(tempdir(),"/",file.name))
  return(myData)
  
}

# ------------------------------------------------

subsetDataset <- function(data,taxa,status) {
  
  if( missing(data)) { stop("A dataset must be provided. Use extractDataset() function") }
  if( missing(taxa)) { stop("A taxa name must be provided") }
  if( missing(status)) { status <- "accepted" }
  
  if( status == "accepted" ) { 
    
    if( length(which(dataset$acceptedName == taxa)) == 0 ) { stop("Taxa not found in dataset") }
    data <- data[ which(data$acceptedName == taxa) ,] 
  }
  if( status != "accepted" ) { 
    
    if( length(which(dataset$name == taxa)) == 0 ) { stop("Taxa not found in dataset") }
    data <- data[ which(data$name == taxa) ,] 
    
  }

  return(data)
  
}

# ------------------------------------------------

listDataMap <- function(data,taxa,status,radius,color,zoom) {
  
  zoom.define <- TRUE
  
  if( missing(radius)) { radius <- 2 }
  if( missing(color)) { color <- "black" }
  if( missing(zoom)) { zoom <- FALSE }
  if( missing(taxa)) { taxa <- NULL }
  if( missing(status)) { status <- "accepted" }
  
  packages.to.use <- c("shiny","leaflet")
  
  options(warn=-1)
  
  for(package in packages.to.use) {
    if( ! package %in% rownames(installed.packages()) ) { install.packages( package ) }
    if( package == "robis" & ! "robis" %in% rownames(installed.packages()) ) { devtools::install_github("iobis/robis") }
    if( ! package %in% rownames(installed.packages()) ) { stop("Error on package instalation") }
    library(package, character.only = TRUE)
  }
  
  if( status == "accepted" ) { 
    
    if( length(which(dataset$acceptedName == taxa)) == 0 ) { stop("Taxa not found in dataset") }
    
    data <- data[ which(data$acceptedName == taxa) ,] 
    
  }
  if( status != "accepted" ) { 
    
    if( length(which(dataset$name == taxa)) == 0 ) { stop("Taxa not found in dataset") }
    
    data <- data[ which(data$name == taxa) ,] 
    
  }
  
  species.name <- unlist(data$name)
  species.status <- unlist(data$taxonomicStatus)
  species.wormsid <- data$aphiaID
  
  temp.record.site <- data$locality
  temp.record.country <- data$country
  temp.record.year <- data$year
  temp.record.depth <- data$verbatimDepth
  temp.record.reference <- data$sourceType
  temp.record.reference.id <- data$bibliographicCitation
  
  popup = paste0(
    paste0("Species: <i>", species.name,"</i><br>"),
    paste0("aphiaID: ", species.wormsid,"<br>"),
    paste0("Status: ", species.status,"<br>"),
    paste0("<hr noshade size='1'/>"),
    ifelse( temp.record.site != "" & ! is.na(temp.record.site), paste0("Site: ", temp.record.site , " (",temp.record.country ,")","<br>"), as.character("") ),
    ifelse( !is.na(temp.record.year), paste0("Year: ", temp.record.year , "<br>"), as.character("") ),
    ifelse( !is.na(temp.record.depth), paste0("Depth: ", temp.record.depth , "<br>"), as.character("") ),
    paste0(temp.record.reference , ": ",temp.record.reference.id ,"","<br>")
    
  )
  
  epsg3006 <- leafletCRS(crsClass = "L.Proj.CRS", code = "EPSG:4326",
                         proj4def = "+proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0",
                         resolutions = 2^(13:-1), # 8192 down to 0.5
                         origin = c(0, 0)
  )
  
  data <- as.matrix(data)
  
  if( zoom.define ) { m <- leaflet() %>% setView(lng=mean(as.numeric(data[,"decimalLongitude"])),lat=mean(as.numeric(data[,"decimalLatitude"])),zoom=zoom)  }
  if(! zoom.define ) { m <- leaflet()  }
  
  m <- addTiles(m)
  m <- addCircleMarkers(m, 
                        lng=as.numeric(data[,"decimalLongitude"]), 
                        lat=as.numeric(data[,"decimalLatitude"]), 
                        popup= popup , 
                        radius = radius, 
                        color = color , 
                        stroke = FALSE, 
                        fillOpacity = 0.5 )
  
  options(warn=0)
  
  return(m)
  
}

# ------------------------------------------------

listData <- function(data,taxa,status) {
  
  if( missing(taxa)) { taxa <- NULL }
  if( missing(status)) { status <- "accepted" }
  
  packages.to.use <- c("shiny","DT")
  
  options(warn=-1)
  
  for(package in packages.to.use) {
    if( ! package %in% rownames(installed.packages()) ) { install.packages( package ) }
    if( package == "robis" & ! "robis" %in% rownames(installed.packages()) ) { devtools::install_github("iobis/robis") }
    if( ! package %in% rownames(installed.packages()) ) { stop("Error on package instalation") }
    library(package, character.only = TRUE)
  }
  
  if( status == "accepted" ) { 
    
    if( length(which(dataset$acceptedName == taxa)) == 0 ) { stop("Taxa not found in dataset") }
    data <- data[ which(data$acceptedName == taxa) ,] 
  }
  if( status != "accepted" ) { 
    
    if( length(which(dataset$name == taxa)) == 0 ) { stop("Taxa not found in dataset") }
    data <- data[ which(data$name == taxa) ,] }
  
  options(warn=0)
  
  shinyApp(
    ui = fluidPage(
      title = "Examples of DataTables",
      DT::dataTableOutput('tbl')),
    server = function(input, output) {
      output$tbl = DT::renderDataTable(
        data, options = list( pageLength = 10, lengthMenu = c(10, 50, 100, 1000)) ) # , filter = 'top'
    } )
  
}

# ------------------------------------------------

exportData <- function(data,taxa,status,type,file) {
  
  packages.to.use <- c("sp","raster","rgdal")
  
  for(package in packages.to.use) {
    if( ! package %in% rownames(installed.packages()) ) { install.packages( package ) }
    if( package == "robis" & ! "robis" %in% rownames(installed.packages()) ) { devtools::install_github("iobis/robis") }
    if( ! package %in% rownames(installed.packages()) ) { stop("Error on package instalation") }
    library(package, character.only = TRUE)
  }
  
  if( missing(taxa)) { taxa <- NULL }
  if( missing(status)) { status <- NULL }
  if( missing(file)) { stop("A filename must be provided") }
  if( missing(type)) { type <- "csv" }
  
  if( !is.null(status) & status != "accepted" & status != "unaccepted" ) { stop("Status must be accepted or unaccepted")  }
  if( type != "csv" & type != "shp" ) { stop("Status must be csv or shp")  }
  
  if( ! is.null(status) ) {  
    
    if( status == "accepted" ) { 
      
      if( length(which(dataset$acceptedName == taxa)) == 0 ) { stop("Taxa not found in dataset") }
      data <- data[ which(data$acceptedName == taxa) ,] 
    }
    if( status != "accepted" ) { 
      
      if( length(which(dataset$name == taxa)) == 0 ) { stop("Taxa not found in dataset") }
      data <- data[ which(data$name == taxa) ,] }
    
  }
  
  if(type == "csv") {
    
    write.table(data,file=file, row.names = FALSE, quote=FALSE,sep = ";",col.names = TRUE)
    
  }
  if(type == "shp") {
    
    main.results.sp <- SpatialPointsDataFrame(data.frame(Lon=as.numeric(as.character(data$decimalLongitude)),Lat=as.numeric(as.character(data$decimalLatitude))),data)   
    crs(main.results.sp) <- "+proj=longlat +datum=WGS84 +no_defs +ellps=WGS84 +towgs84=0,0,0" 
    writeOGR(main.results.sp, ".", file, driver="ESRI Shapefile",overwrite_layer=TRUE)
    
  }
}

# ------------------------------------------------

getTaxonomyWorms <- function(name) {
  
  packages.to.use <- "worms"
  
  options(warn=-1)
  
  for(package in packages.to.use) {
    if( ! package %in% rownames(installed.packages()) ) { install.packages( package ) }
    if( ! package %in% rownames(installed.packages()) ) { stop("Error on package instalation") }
    library(package, character.only = TRUE)
  }
  
  tryCatch( worms.query <- wormsbynames( name , verbose = FALSE )
            , error=function(e) { } )
  
  options(warn=0)
  
  if( exists("worms.query") ) { 
    
    cat('\n')
    cat('\n')
    cat('----------------------------------------------------------------------')
    cat('\n')
    cat('Processing taxonomy for', name )
    cat('\n')
    cat('\n')
    cat('\n')
    
    return(data.frame(
      aphiaID = worms.query$AphiaID,
      name = worms.query$scientificname,
      authority = worms.query$authority,
      status = worms.query$status,
      taxKingdom = worms.query$kingdom,
      taxPhylum = worms.query$phylum,
      taxClass = worms.query$class,
      taxOrder = worms.query$order,
      taxFamily = worms.query$family,
      taxGenus = worms.query$genus,
      revisionByWormsDate = Sys.Date(),
      acceptedAphiaID = worms.query$valid_AphiaID,
      acceptedName = worms.query$valid_name
    ))
    
  } else {         
    
    cat('\n')
    cat('\n')
    cat('----------------------------------------------------------------------')
    cat('\n')
    cat('Taxonomy for',name,'not found')
    cat('\n')
    cat('\n')
    cat('\n')
    
  }
}