MacroAlgaeIndicator: Macroalgae indicators

Description Usage Arguments Value Examples

View source: R/MacroAlgaeIndicator_CumulativeCover.R

Description

Macroalgae indicators

Usage

1
2
3
MacroAlgaeIndicator(indicator = c("CumulativeCover", "PropOpportunist",
  "NPerennials"), df, boundaries, depth_cutoff, std_depth = 7,
  std_haardsub = 50, n_iter = 10000, Indicator_pred_pct = 0.5)

Arguments

indicator

Name of the indicator to be calculated. Possible values are "CumulativeCover", "PropOpportunist", and "NPerennials"

df

A dataframe with monitoring data for macroalgae according to the Danish National Marine Monitoring Program. The dataframe should contain the following variables:

kildestationnavn

An identifier for the monitoring transect name.

dato

Date of the sampling.

dybde

Depth of the observation in meter.

hardbund_daekpct

Percentage cover of suitable substrate for macroalgae.

totcover_daekpct

Total cover of macroalgae relative to the suitable substrate.

proevetager

Identifier of the person carrying out the monitoring transect.

steneck

The Steneck number of the species.

growth_strategy

Either "P" for perennial, "O" for opportunist or "C" for crustforming algae.

boundaries

A vector of length 4 giving the status class boundary values of the standardized indicator. The boundary values should be given in the order high-good, good-moderate, moderate-poor, poor-bad.

depth_cutoff

The cut-off depth for physical exposure. Observations whith depths shallower than this value are not used in the indicator calculation.

std_depth

The depth for which the indication is calculated. Default is 7 meters.

std_haardsub

The suitable substrate percentage for which the indicator if calculated. Default it 0.5.

n_iter

Maximum number of iteration for Montecarlo simulation.

Indicator_pred_pct

Probability for predicting the percentile in the simulated distribution. Default is 0.5 for the median.

Value

TODO

Examples

1
2
data("alsfjord_2013_2016")
indicator <- MacroAlgaeIndicator("CumulativeCover", alsfjord_2013_2016, boundaries = c(74.4, 40.8, 20.4, 13.8), depth_cutoff = 1)

PMassicotte/makroalgaeindicators documentation built on May 20, 2019, 10:19 p.m.