Clusterising sites using coordinates"

In DivInsight: Diversity Index Calculation & Visualisation for Taxa and Location

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(DivInsight)
data("Colombia")

To subset data for an exact location a pair of longitude/latitude coordinates can be used with subset_by_coordinate_ref().

The coordinate_reference argument will mark the centre of the location and the distance_threshold will mark the radius of the location in metres.

Below this function is used as an argument value in the clusterise_sites() function to get clusterised data for two locations in Colombia. The radius of each location is set to 50km.

# clusterise data for a specific location 
Colombia_coordinate_ref_1 <- clusterise_sites(

  dataframe =
    subset_by_coordinate_ref(
      dataframe = Colombia,
      coordinate_reference = c(-73.325377, 3.956982),
      distance_threshold = 50000
    ),

  cluster_min_length = 30 

)

# repeat the process with different coordinates
Colombia_coordinate_ref_2 <- clusterise_sites(

  dataframe = 
    subset_by_coordinate_ref(
      dataframe = Colombia,
      coordinate_reference = c(-71.889919, 4.470524),
      distance_threshold = 50000
    ),

  cluster_min_length = 30 

)

The diversity over time for both sites can then be plotted.

# scatter plot for reference site 1
plot_sites_scatter_H(

  clusterised_object = Colombia_coordinate_ref_1,
  main = "Coordinate Reference Site #1"

) 

# scatter plot for reference site 2
plot_sites_scatter_H(

  clusterised_object = Colombia_coordinate_ref_2,
  main = "Coordinate Reference Site #2"

) 

The see where these patterns are happening a map can be created.

# create a new map using coordinates from first reference site
Colombia_coordinate_ref_map <-

  map_start(

    clusterised_object = Colombia_coordinate_ref_1,
    site_name = "Ref#1",    
    colour = "purple"

  )

# add to the existing map using information from the second reference site
Colombia_coordinate_ref_map <-

  map_add(

    existing_map = Colombia_coordinate_ref_map,

    clusterised_object = Colombia_coordinate_ref_2,
    site_name = "Ref#2",
    colour = "darkred"

  )

The map is ready to be viewed.

# view the interactive map
Colombia_coordinate_ref_map

DivInsight documentation built on Aug. 12, 2023, 9:06 a.m.