View source: R/validate_get_twcv.R

validate_get_twcv | R Documentation |

Checks if passed color data are valid, i. e. are bountiful and varied enough according to passed validation criteria. This function is normally only used indirectly through 'Participant$check_valid_get_twcv()' or 'ParticipantGroup$get_valid_twcv()'.

```
validate_get_twcv(
color_matrix,
dbscan_eps = 20,
dbscan_min_pts = 4,
max_var_tight_cluster = 150,
max_prop_single_tight_cluster = 0.6,
safe_num_clusters = 3,
safe_twcv = 250
)
```

`color_matrix` |
An n-by-3 numerical matrix where each row corresponds to a single point in 3D color space. |

`dbscan_eps` |
One-element numerical vector: radius of ‘epsilon neighborhood’ when applying DBSCAN clustering. |

`dbscan_min_pts` |
One-element numerical vector: Minimum number of points required in the epsilon neighborhood for core points (including the core point itself). |

`max_var_tight_cluster` |
One-element numerical vector: maximum variance for a cluster to be considered 'tight-knit'. |

`max_prop_single_tight_cluster` |
One-element numerical vector: maximum proportion of points allowed to be within a 'tight-knit' cluster (if this threshold is exceeded, the data are categorized as invalid). |

`safe_num_clusters` |
One-element numerical vector: minimum number of clusters that guarantees validity if points are 'non-tight-knit'. |

`safe_twcv` |
One-element numerical vector: minimum total within-cluster variance (TWCV) score that guarantees validity if points are 'non-tight-knit'. |

A list with components

`valid` |
One-element logical vector |

`reason_invalid` |
One-element character vector, empty if valid is TRUE |

`twcv` |
One-element numeric (or NA if can't be calculated) vector, indicating TWCV |

`num_clusters` |
One-element numeric (or NA if can't be calculated) vector, indicating the number of identified clusters counting toward the tally compared with 'safe_num_clusters' |

This function relies heavily on the DBSCAN algorithm and its implementation in the R package 'dbscan', for clustering color points. For further information regarding the 'dbscan_eps' and 'dbscan_min_pts' parameters as well as DBSCAN itself, please see the 'dbscan' documentation. Once clustering is done, passed validation criteria are applied:

If too high a proportion of all color points (cut-off specified with ‘max_prop_single_tight_cluster') fall within a single ’tight-knit' cluster (with a cluster variance less than or equal to 'max_var_tight_cluster'), then the data are always classified as invalid.

If the first criterion is cleared,

*and*points form more than 'safe_num_cluster' clusters, data are always classified as valid.If the first criterion is cleared,

*and*the Total Within-Cluster Variance (TWCV) score is greater than or equal to 'safe_twcv', data are always classified as valid.

Note that this means data can be classified as valid by either having
at least 'safe_num_cluster' clusters, *or* by having points composing
a smaller number of clusters but spaced relatively far apart
*within* these clusters.

The DBSCAN 'noise' cluster only counts towards the 'cluster tally' (compared with 'safe_num_cluster') if it includes at least 'dbscan_min_pts' points. Points in the noise cluster are however always included in other calculations, e. g. total within-cluster variance (TWCV).

`point_3d_variance`

for single-cluster variance,
`total_within_cluster_variance`

for TWCV.

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