Case study 1: Different biodiversity hotspots and their congruence.

Mihai Valcu

2019-03-26

Appendix S2

Supporting information in Valcu, M., Dale, J., and Kempenaers, B. (2012). rangeMapper: a platform for the study of macroecology of life-history traits. Global Ecology and Biogeography 21, 945-951.

The example shown here is run on the wrens dataset which is part of the package. The wrens dataset has 84 species while the case study presented in the paper was run on 8434 bird species. Therefore both the settings and the results shown below are not identical with the results presented in Valcu et al 2012.

Project Set Up

Initiates a new rangeMapper project (wrens.sqlite) into a temporary directory

## Loading required package: rangeMapper
## Loading required package: RSQLite
## This is rangeMapper 0.3-5
## New session 2019-03-26 17:22:19
## PROJECT: wrens.sqlite 
## DIRECTORY: /tmp/Rtmp6x8Ng1

Saves the global bounding box as the union of all species bounding boxes.

## Computing global bounding box for 1 ranges...
## Checking for proj4 string differences...
## Done!
## [1] TRUE

Saves the grid size (i.e. the size of a canvas cell) using the default value. The grid size can be specified by e.g. gridSize.save(dbcon, gridSize = 2.5)

## Warning in .local(object, ...): Default grid size used!
## Grid size set to 1.1728375626 map units.

Saves the canvas grid using the global bounding box and the grid size.

## Canvas uploaded.

Performs vector range maps interpolation with the canvas.

## Warning: executing %dopar% sequentially: no parallel backend registered
## Writing overlay output to project...
## 84 out of 84 ranges updated; Elapsed time: 0 mins
## Extracting metadata...

Uploads to the existing project a data.frame containing life history data

## Table wrens saved as a  BIO_ table

Define Hotspots Parameters

(i.e. the quantile of the given parameter used as a threshold value)

HOTSPOTS CONGRUENCE

  1. Find threshold values
  1. Save cumulative hotspot congruence satisfying all three criteria
## [1] TRUE
  1. Species richness & endemics richness congruence (two criteria are satified)
## [1] TRUE
  1. Endemics richness & body mass diversity congruence
## [1] TRUE
  1. Species richness & body mass diversity congruence
## [1] TRUE
  1. Retrieve all the map objects.
  1. Compute hotspots congruence

Species richness & body mass diversity congruence (%)

## [1] 18.35821

Endemics richness & body mass diversity congruence (%)

## [1] 5.306122

Species richness & endemics richness congruence (%)

## [1] 4.583333

Cumulative congruence (%)

## [1] 1.648746