Glossary

dataset

A CSV file containing at least three columns: coord_x, coord_y, and species (or any column specified with categorical_col config key instead). Column individuals (or alternative specified with quantity_col instead) is necessary for abundance analysis and Bray–Curtis formula of dissimilarity analysis. It is also optional for the overview analysis. See the datasets folder for examples.

encounter

Single observation within study grid.

extent

Distance between two most distant sampled areas in a spatial observation. In the context of seal distance between the most distant quadrats in the ongoing step of analysis using chosen metric.

grain

Smallest unit of observation, within context of seal typically size of one quadrat in currently analysed grid.

level

A specific stage of transformation. It determines the degree of aggregation of the original sampling units and therefore the spatial grain represented at that level. Higher levels generally correspond to larger grain.

quadrat

A sampling unit, usually a rectangular subset of a study grid.

quadrat coordinates

Coordinates identifying the position of a quadrat within a study grid. The x-coordinate identifies its transect and the y-coordinate its zone. Coordinates are zero-based and may be reassigned during transformation.

quadrat list

A CSV file with list of quadrats in the study corresponding with dataset. Providing one is optional but recommended. Must contain the following fields: coord_x, coord_y; optional column is quadrat_type. See the datasets/qlists folder for examples.

strategy

A set of rules defining how the study grid is transformed across levels to create sampling configurations with different grain and extent. Designed to answer questions like “How would analysis results differ if we only measured every 2^nd quadrat?” or “What would happen if we made quadrats larger and sparsely placed?”

study grid

Spatially arranged set of sampling units divided into independently surveyed quadrats. Usually referred to simply as “grid” in this documentation.

subgrid

Subset of observation units from the study grid in a specific configuration. Subgrids consisting of four or two quadrats are analysed in the richness analysis, while subgrids of 16 or four quadrats are used in the spatial analysis.

transect

A path along which the occurrence of objects is counted. Typically, either objects that intersect with the line marking the transect, or those within a certain distance from it, are counted. In the context of seal transects are defined as all quadrats sharing the same x-coordinate. Transect-based transformation strategies aggregate these quadrats into one-dimensional sampling units extending along the y-axis.

When certain strategies are applied, the grid is adjusted by connecting quadrats with the same x-coordinate, forming a new grid composed only of transects.

transformation

The process by which seal modifies the original study grid according to a selected strategy, creating new sampling units with different grain and spatial arrangement.

zone

A set of quadrats sharing the same y-coordinate and extending perpendicular to the transects.

Notation

\(l\)

Currently processed level.

\(L\)

Set of all analysed levels.

\(q_{2,0}\)

Quadrat at coordinates [2,0].

\(Q_{3,2}\)

Set of species encountered in \(q_{3,2}\).

\(t\)

Number of transects within input study grid.

\(t'\)

Number of transects within study grid post-transformation.

\(z\)

Number of zones within input study grid.