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Calculate metrics for one or several partitions

Source: R/partition_metrics.R
partition_metrics.Rd

This function aims at calculating metrics for one or several partitions, usually on outputs from netclu_, hclu_ or nhclu_ functions. Metrics may require the users to provide either a similarity or dissimilarity matrix, or to provide the initial species-site table.

Usage

partition_metrics(
  cluster_object,
  dissimilarity = NULL,
  dissimilarity_index = NULL,
  net = NULL,
  site_col = 1,
  species_col = 2,
  eval_metric = c("pc_distance", "anosim", "avg_endemism", "tot_endemism")
)

Arguments

cluster_object

a bioregion.clusters object

dissimilarity

a dist object or a bioregion.pairwise.metric object (output from similarity_to_dissimilarity()). Necessary if eval_metric includes pc_distance and tree is not a bioregion.hierar.tree object

dissimilarity_index

a character string indicating the dissimilarity (beta-diversity) index to be used in case dist is a data.frame with multiple dissimilarity indices

net

the species-site network (i.e., bipartite network). Should be provided if eval_metric includes "avg_endemism" or "tot_endemism"

site_col

name or number for the column of site nodes (i.e. primary nodes). Should be provided if eval_metric includes "avg_endemism" or "tot_endemism"

species_col

name or number for the column of species nodes (i.e. feature nodes). Should be provided if eval_metric includes "avg_endemism" or "tot_endemism"

eval_metric

character string or vector of character strings indicating metric(s) to be calculated to investigate the effect of different number of clusters. Available options: "pc_distance", "anosim", "avg_endemism" and "tot_endemism"

Value

a list of class bioregion.partition.metrics with two to three elements:

  • args: input arguments

  • evaluation_df: the data.frame containing eval_metric for all explored numbers of clusters

  • endemism_results: if endemism calculations were requested, a list with the endemism results for each partition

Details

Evaluation metrics:

  • pc_distance: this metric is the method used by Holt2013bioregion. It is a ratio of the between-cluster sum of dissimilarity (beta-diversity) versus the total sum of dissimilarity (beta-diversity) for the full dissimilarity matrix. In other words, it is calculated on the basis of two elements. First, the total sum of dissimilarity is calculated by summing the entire dissimilarity matrix (dist). Second, the between-cluster sum of dissimilarity is calculated as follows: for a given number of cluster, the dissimilarity is only summed between clusters, not within clusters. To do that efficiently, all pairs of sites within the same clusters have their dissimilarity set to zero in the dissimilarity matrix, and then the dissimilarity matrix is summed. The pc_distance ratio is obtained by dividing the between-cluster sum of dissimilarity by the total sum of dissimilarity.

  • anosim: This metric is the statistic used in Analysis of Similarities, as suggested in Castro-Insua2018bioregion (see vegan::anosim()). It compares the between-cluster dissimilarities to the within-cluster dissimilarities. It is based based on the difference of mean ranks between groups and within groups with the following formula: R = (r_B - r_W)/(N (N-1) / 4)R = (r_B - r_W)/(N (N-1) / 4), where r_Br_B and r_Wr_W are the average ranks between and within clusters respectively, and NN is the total number of sites. Note that the function does not estimate the significance here, it only computes the statistic - for significance testing see vegan::anosim().

  • avg_endemism: this metric is the average percentage of endemism in clusters as recommended by Kreft2010bioregion. Calculated as follows: End_mean = _i=1^K E_i / S_iKPc_endemism_mean = sum(Ei / Si) / K where E_iEi is the number of endemic species in cluster i, S_iSi is the number of species in cluster i, and K the maximum number of clusters.

  • tot_endemism: this metric is the total endemism across all clusters, as recommended by Kreft2010bioregion. Calculated as follows: End_tot = ECEndemism_total = E/Cwhere EE is total the number of endemics (i.e., species found in only one cluster) and CC is the number of non-endemic species.

References

Castro-Insua2018bioregion

Ficetola2017bioregion

Holt2013bioregion

Kreft2010bioregion

Langfelder2008bioregion

See also

compare_partitions

Author

Boris Leroy (leroy.boris@gmail.com), Maxime Lenormand (maxime.lenormand@inrae.fr) and Pierre Denelle (pierre.denelle@gmail.com)

Examples

comat <- matrix(sample(0:1000, size = 500, replace = TRUE, prob = 1/1:1001),
20, 25)
rownames(comat) <- paste0("Site",1:20)
colnames(comat) <- paste0("Species",1:25)

comnet <- mat_to_net(comat)

dissim <- dissimilarity(comat, metric = "all")

# User-defined number of clusters
tree1 <- hclu_hierarclust(dissim, 
                          n_clust = 2:20, index = "Simpson")
#> Building the iterative hierarchical consensus tree... Note that this process can take time especially if you have a lot of sites.
#> 
#> Final tree has a 0.4589 cophenetic correlation coefficient with the initial dissimilarity
#>       matrix
#> Warning: The requested number of cluster could not be found
#>                          for k = 15. Closest number found: 14
#> Warning: The requested number of cluster could not be found
#>                          for k = 16. Closest number found: 14
#> Warning: The requested number of cluster could not be found
#>                          for k = 17. Closest number found: 14
#> Warning: The requested number of cluster could not be found
#>                          for k = 18. Closest number found: 14
#> Warning: The requested number of cluster could not be found
#>                          for k = 19. Closest number found: 14
#> Warning: The requested number of cluster could not be found
#>                          for k = 20. Closest number found: 14
tree1
#> Clustering results for algorithm : hclu_hierarclust 
#> 	(hierarchical clustering based on a dissimilarity matrix)
#>  - Number of sites:  20 
#>  - Name of dissimilarity metric:  Simpson 
#>  - Tree construction method:  average 
#>  - Randomization of the dissimilarity matrix:  yes, number of trials 100 
#>  - Method to compute the final tree:  Iterative consensus hierarchical tree 
#>  - Cophenetic correlation coefficient:  0.459 
#>  - Number of clusters requested by the user:  2 3 4 5 6 7 8 9 10 11 ... (with 9 more values) 
#> Clustering results:
#>  - Number of partitions:  19 
#>  - Partitions are hierarchical
#>  - Number of clusters:  2 3 4 5 6 7 8 9 10 11 ... (with 9 more values) 
#>  - Height of cut of the hierarchical tree: 0.125 0.109 0.102 0.094 0.086 0.078 0.062 0.053 0.047 0.045 ... (with 9 more values) 

a <- partition_metrics(tree1, dissimilarity = dissim, net = comnet,
                       site_col = "Node1", species_col = "Node2",
                       eval_metric = c("tot_endemism", "avg_endemism",
                                      "pc_distance", "anosim"))
#> Computing similarity-based metrics...
#>   - pc_distance OK
#>   - anosim OK
#> Computing composition-based metrics...
#>   - avg_endemism OK
#>   - tot_endemism OK
a
#> Partition metrics:
#>  - 19  partition(s) evaluated
#>  - Range of clusters explored: from  2  to  14 
#>  - Requested metric(s):  tot_endemism avg_endemism pc_distance anosim 
#>  - Metric summary:
#>      tot_endemism avg_endemism pc_distance    anosim
#> Min    0.00000000  0.000000000   0.1521221 0.3640700
#> Mean   0.01263158  0.005964912   0.8313228 0.6812192
#> Max    0.20000000  0.100000000   1.0000000 0.8729282
#> 
#> Access the data.frame of metrics with your_object$evaluation_df
#> Details of endemism % for each partition are available in 
#>         your_object$endemism_results