Mizer provides a range of functions to calculate indicators from a MizerSim or MizerParams object.
Details
When called with a MizerSim object, these functions return a time series
of values. When called with a MizerParams object, they return a single
value calculated from the initial abundances stored in the params object.
A list of available indicator functions is given in the table below
| Function | Returns | Description |
getProportionOfLargeFish() | A vector with values at each time step (or a single value for MizerParams). | Calculates the proportion of large fish through time. The threshold value can be specified. It is possible to calculation the proportion of large fish based on either length or weight. |
getMeanWeight() | A vector with values at each saved time step (or a single value for MizerParams). | The mean weight of the community through time. This is calculated as the total biomass of the community divided by the total abundance. |
getMeanMaxWeight() | Depends on the measure argument. If measure = “both” then you get a matrix with two columns, one with values by numbers, the other with values by biomass at each saved time step (or a named vector for MizerParams). If measure = “numbers” or “biomass” you get a vector of the respective values at each saved time step (or a single value for MizerParams). | The mean maximum weight of the community through time. This can be calculated by numbers or by biomass. See the help file for more details. |
getCommunitySlope() | A data.frame with four columns: time step, slope, intercept and the coefficient of determination (or a single-row data.frame for MizerParams). | Calculates the slope of the community abundance spectrum through time by performing a linear regression on the logged total numerical abundance and logged body size. |