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hib_calc_site_contrasts: Calculate differences between sites for a range of environmental variables.

Source: R/hib_site_contrasts.R
hib_calc_site_contrasts.Rd

This function calculates measures of differences between sites within a study, which can then be used as covariates in models of compositional dis/similarity. A data.frame (named site_contrasts) containing the site-contrast pairs (SSBS1, SSBS2) and the associated 'differences' is added to the provided HibDatabase.

Usage

hib_calc_site_contrasts(
  obj,
  metrics,
  custom_metric_specs = NULL,
  baseline_lui = "Primary vegetation_Minimal use",
  overwrite = FALSE
)

Arguments

obj

A HibDatabase object.

metrics

A character vector of 'distance' metrics. Current options are; "lui_contrast", "geogr_dist_hav", "geogr_dist_geod" and "geogr_midpoint", "env_dist".

custom_metric_specs

A named list (or NULL) with each named item containing the specifications for the named custom metric. At present, custom metrics must be based on vegdist distance metrics.
Essential named values within the specifications of a custom metric are:

  • dist_metr - a character indicating the metric of choice;

  • vars - a character vector indicating the site variables to use when calculating the distance metric.

For example:
list(Gower_dist_a = list(dist_metr = "gower", vars = c("env1", "env2", "env3")), Gower_dist_b = list(dist_metr = "gower", vars = c("env4", "env5", "env6")))
Metric names (as specified in the name of the sub-lists) will be converted to sentence-case in the output data.

baseline_lui

A character (can be multiple entries) or NULL, indicating the baseline LUI/s against which differences are calculated per study. Value/s provided should match the value/s used when calculating compositional dis/similarity (hib_calc_div_between).

overwrite

A logical indicating whether or not any current site contrast data should be over-written. Default value is FALSE.

Value

HibDatabase

Details

The function currently returns site1-site2 contrasts for all within-study contrasts where site1 has the baseline_lui. Subsequent, filtering to ensure contrasts are based on the same effort level is recommended and may be incrporated in future releases.

References

https://adrianadepalma.github.io/BII_tutorial

Examples

if (FALSE) { # \dontrun{
  obj <- hib_calc_site_contrasts(obj, 
                                 c("lui_contrast", "geogr_dist_hav"),
                                 baseline_lui = "Primary vegetation_Minimal use")
} # }