Add Polygons to Points

#Required Libraries. Uncomment to install only the first time you use.
#install.packages("sp")
#install.packages("maptools")
#install.packages("rgeos")
#install.packages("rgdal")

#Install Required Packages
library(sp)
library(maptools)
library(rgeos)
library(rgdal)
library(plyr)

#Defines location of input files
directory = "/Users/msolbrig/Documents/Bairros_Algar_Concessao_region"
polygon_file = "Bairros_Algar_Concessao_region"
point_file = "points.csv"
output_name = "outfile.csv"
combine_points_poly = FALSE

#Function for importing shapefiles to R and dealing with projection
ImportToR <- function(dsn, layer){
  setwd(dsn)
  ShapeFile <- readOGR(dsn = dsn, layer = layer)
  if(!is.na(is.projected(ShapeFile)) && is.projected(ShapeFile)){
    standard <- CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0")
    ShapeFile<- spTransform(ShapeFile, standard)
  }
  return(ShapeFile)
}


#Gets and formats data
setwd(directory)
polygons <- ImportToR(directory, polygon_file)
points <- read.csv(file=point_file)

#separate values with nulls in lat/lon from rest of data
points_null_lat = points[is.na(points['Lat']),]
points_has_lat = points[!is.na(points['Lat']),]

#turns into spatial data type
points_coords = subset(points_has_lat, select = c(Lon, Lat))
points_data = subset(points_has_lat, select=-c(Lon, Lat))
pts = SpatialPointsDataFrame(points_coords, points_data)
proj4string(pts) <- proj4string(polygons) #Ensures that the projections match

#Adds the polygon to the points
pts_with_polygon <- cbind(as.data.frame(pts), over(pts, polygons))

#Adds the rows with Null lat/lon back in
output = rbind.fill(pts_with_polygon, points_null_lat)


#Write to CSV
if(combine_points_poly):
  # function for reshaping the polygons for Tableau
  ReshapePolygons <- function(ShapeFile){}
    
    Data <- as(ShapeFile, "data.frame")
    Data$ObjectID <- as.numeric(rownames(Data))
    
    #extracts the coodinates and polygon IDs
    ObjectList <- slot(ShapeFile,"polygons")
    coordinates <- list(Latitude = numeric(0),
                        Longitude = numeric(0),
                        PolygonID = numeric(0),
                        ObjectID = numeric(0),
                        PlotOrder = numeric(0))
    
    #Loops over Objects to extract coordinates
    PolygonID <- 0
    for(i in 1:length(ObjectList)){
      Object <- ObjectList[[i]]
      ObjectID <- slot(Object, "ID")
      #Loops over Polygons in Object to extract coordinates
      for(j in 1:length(slot(Object,"Polygons"))){
        Polygon <- slot(Object,"Polygons")[[j]]
        #excludes holes. This could be made an option.
        if(!slot(Polygon,"hole")){
          coords <- data.frame(slot(Polygon,"coords"))
          coords$PlotOrder <- c(1:nrow(coords))
          coordinates$PlotOrder <- c(coordinates$PlotOrder, c(1:nrow(coords)))
          coordinates$Longitude <- c(coordinates$Longitude, coords[,1])
          coordinates$Latitude <- c(coordinates$Latitude, coords[,2])
          coordinates$ObjectID <- c(coordinates$ObjectID, rep(ObjectID,nrow(coords)))
          coordinates$PolygonID <-c(coordinates$PolygonID, rep(PolygonID,nrow(coords)))
          PolygonID <- PolygonID + 1
        }
      }
    }
    coordinates <- data.frame(coordinates)
    CombinedData <- merge(Data,coordinates)
    return(CombinedData)
  }
  polydata <- ReshapePolygons(polygons)
  ouput <- 
  
  
  
write.csv(output, file = output_name)