Calculate_demography {SharkDemography}

The base function for calculating demographic traits using a Leslie matrix method

Description

Using provided life history estimates from various sources, a demographic analysis is performed using Leslie matrix methods. This function can be run as stand alond and will given the outputs of a stochastic matrix model given the provided life history parameters and their associated error. However, the main purpose of this function is to be used in other simulation functions provided in this package. In each use this function will calculate:

lambda

The finite rate of population growth

R0

The reproductive value of the population

G

The generation length of the population

elast.fecund

The mean elasticity of the fecundity elements

elast.juv.survival

The mean elasticity of the juvenile survivoship elements

juv.ratio

The ratio of fecundity to juvenile elasticities

adult.ratio

The ratio of fecundity to adult elasticities

M.estimator

The natural mortality estimator randomly used in this analysis

Usage

Calculate_demography(
  data,
  AAFC = NULL,
  F. = 0,
  AALC = NULL,
  M.estimators = NULL
)

Arguments

data

A multi-level list of the class 'Demography.inputs' produced from the 'create_data_input' function and then manually completed.

AAFC

Age-at-first-capture which can be specified by the user or automated in the 'Simulate_AAFC' function. Must be an integer age which can include zero to indicate the availability of the population to capture from birth.

F.

The instantaneous rate of fishing mortality 'F'. This will be applied to all ages available to capture as defined by either the AALC or AAFC arguments.

AALC

Age-at-last-capture which can be specified by the user or automated in the 'Simulate_AALC' function. Must be an integer age which can include zero.

M.estimators

Any specific natural mortality estimators to be included in the analysis. Only one will be used in each run which is randomly selected. In the simulation functions these will be varied among simulations. Must be a single estimator or a vector of estimators. These can include: "Pet.Wro","Jensen.mat","Chen.Yuan","Then_hoenig","Then_pauly", " Jensen.mat","Charnov" or "Chen.Want". If none are specified then all applicable estimators could be chosen.

Value

A list of parameters including:

lambda

The finite rate of population growth

R0

The reproductive value of the population

G

The generation length of the population

elast.fecund

The mean elasticity of the fecundity elements

elast.juv.survival

The mean elasticity of the juvenile survivoship elements

juv.ratio

The ratio of fecundity to juvenile elasticities

adult.ratio

The ratio of fecundity to adult elasticities

M.estimator

The natural mortality estimator randomly used in this analysis

Examples

# load Silky shark data produced by create_data_input()
# Type `?create_data_input()` for details
data("Silky_data")

# run a single Leslie Matrix analysis with random draws from biological data
# distributions. Use `Simulate_demography()` to run Monte Carlo Simulations
# using this function

Calculate_demography(Silky_data)