Outputs basic parameters or mortalities from a rpath() object to a .csv or .RData file.
Arguments
- x
Rpath model object generated by
rpath().- file
file name for resultant file. Need to specify ".csv" or ".RData".
- morts
Logical value whether to output basic parameters or mortalities.
Value
Writes a list object or file with the basic parameters or mortalities from an Rpath object.
If morts = F, output reflects the basic parameters of the mass-balanced model, namely:
- Group
Vector of group names
- type
Vector of group types: 0 = consumer, 1 = producer, 2 = detritus, 3 = fishery
- TL
Vector of trophic level for each group, calculated based on mass balance
- Biomass
Vector of biomass values for each modeled group
- PB
Vector of production:biomass ratios for each modeled group
- QB
Vector of consumption:biomass ratios for each modeled group
- EE
Vector of ecotrophic efficiency values for each modeled group
- GE
Vector of gross efficiency values (production:comsumption ratios) for each modeled group
- Removals
Vector of total fishery removals for each modeled group
If morts = T, output reflects calculated mortality values for each group.
The number of columns will vary based on how many predators are in the model.
- Group
Vector of group names
- M0
Vector of natural mortality for each group. Natural mortality = PB * (1-EE)
- Fmort
Vector of fishing mortality for each group
- M2.XX
Vector of predation mortality, where XX is the name of a predator group
See also
Other Rpath functions:
MTI(),
check.rpath.params(),
create.rpath.params(),
frate.table(),
read.rpath.params(),
rpath(),
rpath.consumers(),
rpath.detrital(),
rpath.gears(),
rpath.groups(),
rpath.living(),
rpath.mixotrophs(),
rpath.producers(),
rpath.stanzas(),
stanzaplot(),
webplot(),
write.rpath.params()
Examples
if (FALSE) { # \dontrun{
# Read in Rpath parameter file, generate model object
x <- rpath(AB.params)
# Saves basic model parameters for all groups to the root directory of users project
write.Rpath(x, file = "output.csv", morts = F)
# Calculates natural mortality (M0), fishing mortality by fleet, and predation mortality by predator (M2) on each group
# Writes output to an Rdata file in the root directory of users project
write.Rpath(x, file = here::here("output.RData"), morts = T)
} # }