Predict missing life-history based on taxonomic information and hierarchical model fitted to FishBase life-history parameters
Usage
LH2OM(
OM,
dist = c("unif", "norm"),
filterMK = FALSE,
plot = TRUE,
Class = "predictive",
Order = "predictive",
Family = "predictive",
msg = TRUE,
db = MSEtool::LHdatabase
)
predictLH(
inpars = list(),
Genus = "predictive",
Species = "predictive",
nsamp = 100,
db = MSEtool::LHdatabase,
dist = c("unif", "norm"),
filterMK = TRUE,
plot = TRUE,
Class = "predictive",
Order = "predictive",
Family = "predictive",
msg = TRUE
)Arguments
- OM
An object of class 'OM'
- dist
Character. Should parameters be sampled from a uniform (
unif) or normal (norm) distribution?- filterMK
Logical or numeric specifying percentiles. See Details. e.g.
OM@MandOM@K. Empty slots or slots with all values of 0 are considered unknown.- plot
Logical. Should the plot be produced?
- Class
Optional higher order taxonomic information
- Order
Optional higher order taxonomic information
- Family
Optional higher order taxonomic information
- msg
Logical. Should messages be printed?
- db
Database from FishLife model with fitted model results
- inpars
A named list with lower and upper bounds of provided parameters: Linf, L50, K and M (must be length 2). Unknown or missing parameters should not be included. For example, an empty list assumes that all four life history parameters are unknown and need to be estimated. See Details below for more information.
- Genus
Character string specifying the Genus name. Optional. Default is 'predictive'
- Species
Character string specifying the Species name. Optional. Default is 'predictive'. If full species name (Genus + Species) is not found if FishLife database (based on FishBase) higher order taxonomy will be used (e.g., Family) for the predictions.
- nsamp
The number of samples to return
Value
LH2OM: An OM with OM@cpars populated with OM@nsim samples of M, K, Linf and L50
predictLH: A data.frame with nsamp rows with Linf, L50, K, and M values.
Details
filterMK
If filterMK is logical: Should the predicted M and K parameters be filtered within the range specified in inparsor OM?
Otherwise, filterMK must be numeric vector of length(2) specifying lower and upper percentiles that will be applied to the predicted M or K values
The model predicts missing life-history parameters based on provided parameters and taxonomic information.
If both M and K are provided in inpars or OM, K values are predicted and predictions filtered
so that resulting K values are within bounds specified in inpars$K or OM@K (see filterMK).
If both Linf and L50 are provided in inpars or OM, L50 values are predicted and values in inpars$L50
or OM@L50 are ignored.
Functions
LH2OM(): Predict missing life-history and populateOM@cparspredictLH(): Predict missing life-history based on taxonomic information and hierarchical model fitted to FishBase life-history parameters