# Get the total fishing mortality rate from all fishing gears by time, species and size. Calculates the total fishing mortality (in units 1/year) from all gears by species and size and possibly time. See `setFishing()` for details of how fishing gears are set up. ```r getFMort(object, effort, time_range, drop = TRUE) ``` ## Arguments - `object`: A `MizerParams` object or a `MizerSim` object - `effort`: The effort of each fishing gear. Only used if the object argument is of class `MizerParams`. See notes below. - `time_range`: Subset the returned fishing mortalities by time. The time range is either a vector of values, a vector of min and max time, or a single value. Default is the whole time range. Only used if the `object` argument is of type `MizerSim`. - `drop`: Only used when object is of type `MizerSim`. Should dimensions of length 1 be dropped, e.g. if your community only has one species it might make presentation of results easier. Default is TRUE. ## Returns An array. If the effort argument has a time dimension, or object is of class `MizerSim`, the output array has three dimensions (time x species x size). If the effort argument does not have a time dimension, the output array has two dimensions (species x size). The `effort` argument is only used if a `MizerParams` object is passed in. The `effort` argument can be a two dimensional array (time x gear), a vector of length equal to the number of gears (each gear has a different effort that is constant in time), or a single numeric value (each gear has the same effort that is constant in time). The order of gears in the `effort` argument must be the same as in the `MizerParams` object. If the object argument is of class `MizerSim` then the effort slot of the `MizerSim` object is used and the `effort` argument is not used. ## Details The total fishing mortality is just the sum of the fishing mortalities imposed by each gear, $\mu_{f.i}(w)=\sum_g F_{g,i,w}$. The fishing mortality for each gear is obtained as catchability x selectivity x effort. ## Your own fishing mortality function By default `getFMort()` calls `mizerFMort()`. However you can replace this with your own alternative fishing mortality function. If your function is called `"myFMort"` then you register it in a MizerParams object `params` with ``` params <- setRateFunction(params, "FMort", "myFMort") ``` Your function will then be called instead of `mizerFMort()`, with the same arguments. ## Examples ```r params <- NS_params # Get the total fishing mortality in the initial state F <- getFMort(params, effort = 1) str(F) # Get the initial total fishing mortality when effort is different # between the four gears: F <- getFMort(params, effort = c(0.5,1,1.5,0.75)) # Get the total fishing mortality when effort is different # between the four gears and changes with time: effort <- array(NA, dim = c(20,4)) effort[, 1] <- seq(from = 0, to = 1, length = 20) effort[, 2] <- seq(from = 1, to = 0.5, length = 20) effort[, 3] <- seq(from = 1, to = 2, length = 20) effort[, 4] <- seq(from = 2, to = 1, length = 20) F <- getFMort(params, effort = effort) str(F) # Get the total fishing mortality using the effort already held in a # MizerSim object. sim <- project(params, t_max = 20, effort = 0.5) F <- getFMort(sim) F <- getFMort(sim, time_range = c(10, 20)) ``` ## See Also Other rate functions: `getEGrowth()`, `getERepro()`, `getEReproAndGrowth()`, `getEncounter()`, `getFMortGear()`, `getFeedingLevel()`, `getMort()`, `getPredMort()`, `getPredRate()`, `getRDD()`, `getRDI()`, `getRates()`, `getResourceMort()`

getFMort function