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Calculate Biodiversity Indicators Over Time

Source: R/calc_ts_methods.R, R/generic_functions.R
calc_ts.Rd

This function provides a flexible framework for calculating various biodiversity indicators over time. It prepares the data, creates a grid, calculates indicators, and formats the output into an appropriate S3 object ('indicator_ts'). Specific implementations for different indicator types are provided using the appropriate wrappers.

Usage

# Default S3 method
calc_ts(x, ...)

# S3 method for class 'completeness'
calc_ts(x, ...)

# S3 method for class 'hill0'
calc_ts(x, ...)

# S3 method for class 'hill1'
calc_ts(x, ...)

# S3 method for class 'hill2'
calc_ts(x, ...)

# S3 method for class 'obs_richness'
calc_ts(x, ...)

# S3 method for class 'cum_richness'
calc_ts(x, ...)

# S3 method for class 'total_occ'
calc_ts(x, ...)

# S3 method for class 'spec_richness_density'
calc_ts(x, ...)

# S3 method for class 'occ_density'
calc_ts(x, ...)

# S3 method for class 'newness'
calc_ts(x, ...)

# S3 method for class 'williams_evenness'
calc_ts(x, ...)

# S3 method for class 'pielou_evenness'
calc_ts(x, ...)

# S3 method for class 'ab_rarity'
calc_ts(x, ...)

# S3 method for class 'area_rarity'
calc_ts(x, ...)

# S3 method for class 'spec_occ'
calc_ts(x, ...)

# S3 method for class 'spec_range'
calc_ts(x, ...)

# S3 method for class 'relative_occupancy'
calc_ts(x, occ_type = 0, ...)

# S3 method for class 'tax_distinct'
calc_ts(x, set_rows = 1, ...)

# S3 method for class 'occ_turnover'
calc_ts(x, ...)

calc_ts(x, ...)

Arguments

x

A data cube object ('processed_cube').

...

Additional arguments passed to specific indicator calculation functions.

occ_type

Integer controlling the occupancy denominator (default 0):

  • 0 — Total-area occupancy: number of cells occupied by species / total number of grid cells in the study region (including unsampled cells). This is the most conservative measure. Presence-only caveat: empty cells cannot be assumed to be truly unoccupied; they may simply lack sampling effort.

  • 1 — Relative-to-ever-occupied occupancy: number of cells occupied by species / number of cells with at least one occurrence (any species) anywhere in the time window. This conditions on cells where some sampling effort is documented but the denominator is still constant across years.

  • 2 — Annual occupancy: for each year, number of cells occupied by species / number of cells with at least one occurrence (any species) in that year. The denominator therefore varies by year, reflecting changes in sampling footprint over time.

Note on presence-only data: All three types are computed from presence-only occurrence data. A cell with no records cannot be assumed to be truly unoccupied; it may be unsampled or under-surveyed. Types 1 and 2 partially address this by restricting the denominator to cells with documented occurrences, but they still reflect recording effort rather than true absence. Interpret all types with care.

Note on cell aggregation: When a coarser cell_size is chosen, data are aggregated to coarser grid cells before this calculation. The denominator counts post-aggregation cells (cellid), not original cube cells (cellCode).

set_rows

Automatically select which taxonomic information to keep when there are multiple options. Default value of 1 keeps the first option, which is usually the best.

Value

An S3 object of the class 'indicator_ts' containing the calculated indicator values and metadata.

Examples

total_occurrences_trend <- total_occ_ts(example_cube_1)
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  3 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  4 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  3 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  2 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  5 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  1 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  4 \n Cannot calculate confidence intervals"
#> [1] "All values of t are equal to  3 \n Cannot calculate confidence intervals"
plot(total_occurrences_trend, min_year=1980)