nhclu_kmeans {bioregion} | R Documentation |

## Non hierarchical clustering: k-means analysis

### Description

This function performs non hierarchical clustering on the basis of dissimilarity with a k-means analysis.

### Usage

```
nhclu_kmeans(
dissimilarity,
index = names(dissimilarity)[3],
seed = NULL,
n_clust = c(1, 2, 3),
iter_max = 10,
nstart = 10,
algorithm = "Hartigan-Wong",
algorithm_in_output = TRUE
)
```

### Arguments

`dissimilarity` |
the output object from |

`index` |
name or number of the dissimilarity column to use. By default,
the third column name of |

`seed` |
for the random number generator (NULL for random by default). |

`n_clust` |
an |

`iter_max` |
an |

`nstart` |
an |

`algorithm` |
a |

`algorithm_in_output` |
a |

### Details

This method partitions the data into k groups such that that the sum of squares of euclidean distances from points to the assigned cluster centers is minimized. k-means cannot be applied directly on dissimilarity/beta-diversity metrics, because these distances are not euclidean. Therefore, it requires first to transform the dissimilarity matrix with a Principal Coordinate Analysis (using the function pcoa), and then applying k-means on the coordinates of points in the PCoA. Because this makes an additional transformation of the initial matrix of dissimilarity, the partitioning around medoids method should be preferred (nhclu_pam)

### Value

A `list`

of class `bioregion.clusters`

with five slots:

**name**:`character`

containing the name of the algorithm**args**:`list`

of input arguments as provided by the user**inputs**:`list`

of characteristics of the clustering process**algorithm**:`list`

of all objects associated with the clustering procedure, such as original cluster objects**clusters**:`data.frame`

containing the clustering results

In the `algorithm`

slot, if `algorithm_in_output = TRUE`

, users can
find the output of
kmeans.

### Author(s)

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

### See Also

### 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")
clust1 <- nhclu_kmeans(dissim, n_clust = 2:10, index = "Simpson")
clust2 <- nhclu_kmeans(dissim, n_clust = 2:15, index = "Simpson")
partition_metrics(clust2, dissimilarity = dissim,
eval_metric = "pc_distance")
partition_metrics(clust2, net = comnet, species_col = "Node2",
site_col = "Node1", eval_metric = "avg_endemism")
```

*bioregion*version 1.1.1 Index]