Description Usage Arguments Details Partitional Hierarchical TADPole

Control parameters for fine-grained control.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | ```
partitional_control(
pam.precompute = TRUE,
iter.max = 100L,
nrep = 1L,
symmetric = FALSE,
packages = character(0L),
distmat = NULL,
pam.sparse = FALSE,
version = 2L
)
hierarchical_control(
method = "average",
symmetric = FALSE,
packages = character(0L),
distmat = NULL
)
fuzzy_control(
fuzziness = 2,
iter.max = 100L,
delta = 0.001,
packages = character(0L),
symmetric = FALSE,
version = 2L,
distmat = NULL
)
tadpole_control(dc, window.size, lb = "lbk")
tsclust_args(preproc = list(), dist = list(), cent = list())
``` |

`pam.precompute` |
Logical flag. Precompute the whole distance matrix once and reuse it on each iteration if using PAM centroids. Otherwise calculate distances at every iteration. See details. |

`iter.max` |
Integer. Maximum number of allowed iterations for partitional/fuzzy clustering. |

`nrep` |
Integer. How many times to repeat clustering with different starting points (i.e., different random seeds). |

`symmetric` |
Logical flag. Is the distance function symmetric? In other words, is |

`packages` |
Character vector with the names of any packages required for custom |

`distmat` |
If available, the cross-distance matrix can be provided here. Only relevant for partitional with PAM centroids, fuzzy with FCMdd centroids, or hierarchical clustering. |

`pam.sparse` |
Attempt to use a sparse matrix for PAM centroids. See details. |

`version` |
Which version of partitional/fuzzy clustering to use. See details. |

`method` |
Character vector with one or more linkage methods to use in hierarchical procedures
(see |

`fuzziness` |
Numeric. Exponent used for fuzzy clustering. Commonly termed |

`delta` |
Numeric. Convergence criterion for fuzzy clustering. |

`dc` |
The cutoff distance for the TADPole algorithm. |

`window.size` |
The window.size specifically for the TADPole algorithm. |

`lb` |
The lower bound to use with TADPole. Either |

`preproc` |
A list of arguments for a preprocessing function to be used in |

`dist` |
A list of arguments for a distance function to be used in |

`cent` |
A list of arguments for a centroid function to be used in |

The functions essentially return their function arguments in a classed list, although some checks are performed.

Regarding parameter `version`

: the first version of partitional/fuzzy clustering implemented
in the package always performed an extra iteration, which is unnecessary. Use version 1 to mimic
this previous behavior.

When `pam.precompute = FALSE`

, using `pam.sparse = TRUE`

defines a sparse matrix (refer to
`Matrix::sparseMatrix()`

) and updates it every iteration (except for `"dtw_lb"`

distance). For
most cases, precomputing the whole distance matrix is still probably faster. See the timing
experiments in `browseVignettes("dtwclust")`

.

Parallel computations for PAM centroids have the following considerations:

If

`pam.precompute`

is`TRUE`

, both distance matrix calculations and repetitions are done in parallel, regardless of`pam.sparse`

.If

`pam.precompute`

is`FALSE`

and`pam.sparse`

is`TRUE`

, repetitions are done sequentially, so that the distance calculations can be done in parallel and the sparse matrix updated iteratively.If both

`pam.precompute`

and`pam.sparse`

are`FALSE`

, repetitions are done in parallel, and each repetition performs distance calculations sequentially, but the distance matrix cannot be updated iteratively.

There are some limitations when using a custom hierarchical function in `method`

: it will
receive the lower triangular of the distance matrix as first argument (see `stats::as.dist()`

)
and the result should support the `stats::as.hclust()`

generic. This functionality was added
with the cluster package in mind, since its functions follow this convention, but other
functions could be used if they are adapted to work similarly.

When using TADPole, the `dist`

argument list includes the `window.size`

and specifies `norm = "L2"`

.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.