R/map_species.R

In samaperrin/analyseslope: Analysis of Slope as Fish Dispersal Barrier

#' Creates a map showing lakes and presence/absence of fish.
#'
#' @title Maps fish occurrence
#' @param connectivity Table showing at the minimum location IDs for your lakes. Can also show presence/absence for different species, and can contain latitude and longitude.
#' @param get.locations If you do not have latitude and longitude, this should be set to TRUE.
#' @param species The species to map. Can be ignored, in which case map will just plot lakes.
#' @param maptype The type of map you would like to use. Defaults to "terrain".
#'
#' @export


#connectivity_raw <- read.csv(file="./Data/sweden_connection_wBarriers_update.csv",sep=',',header=T,row.names=NULL)
#connectivity <- connectivity_raw %>%
#  filter(!is.na(downstreamLakeID))

#species_map(connectivity, get.locations=TRUE,username="sam.perrin",password="vegemite", maptype="terrain")

map_species <- function(connectivity, species = NA, get.locations=FALSE, maptype, zoom=5, username=NA,password=NA)
{
  if (is.na(username)) {username <- getPass::getPass(msg = 'USERNAME: ')}
  if (is.na(password)) {password <- getPass::getPass(msg = 'PASSWORD: ')}

  if (get.locations == TRUE) {
    focal.lakes <- connectivity$locationID
    connect <- dbPool(
      drv = RPostgreSQL::PostgreSQL(),
      user=username,
      password=password,
      host = "vm-srv-wallace.vm.ntnu.no",
      dbname = "nofa",
      options="-c search_path=nofa" # set db schema from where to look
    )
    locations <- tbl(connect, "location")
    locations <- locations %>%
      filter(locationID %in% !!connectivity$locationID) %>%
      select(locationID, decimalLongitude, decimalLatitude) %>%
      collect()
    connectivity <- merge(connectivity, locations, all.x=TRUE, by="locationID")
    }



  left <- min(connectivity$decimalLongitude)
  bottom <- min(connectivity$decimalLatitude)
  right <- max(connectivity$decimalLongitude)
  top <- max(connectivity$decimalLatitude)
  width <- max(connectivity$decimalLongitude)-min(connectivity$decimalLongitude)
  depth <- max(connectivity$decimalLatitude)-min(connectivity$decimalLatitude)

  box_map <- get_map(location = c(left-width/4,bottom-depth/4,right+width/4,top+depth/4), maptype=maptype,zoom=zoom)
  if (is.na(species)) {
  d <- data.frame(Latitude=connectivity$decimalLatitude, Longitude=connectivity$decimalLongitude)
  p <- ggmap(box_map) + geom_point(data=d, aes(Longitude,Latitude),col='black',alpha=0.5)

  } else {
    d1 <- data.frame(Latitude=connectivity[connectivity[,species] == 1,]$decimalLatitude,
                     Longitude=connectivity[connectivity[,species] == 1,]$decimalLongitude)
    d0 <- data.frame(Latitude=connectivity[connectivity[,species] == 0,]$decimalLatitude,
                     Longitude=connectivity[connectivity[,species] == 0,]$decimalLongitude)
    p <- ggmap(box_map) + geom_point(data=d1, aes(Longitude,Latitude),col='blue') + geom_point(data=d0, aes(Longitude,Latitude),col='red')
  }
  return(p)
  }