demography_dynamics_functions: Functions to modify the demography in a state object.

Description Usage Arguments Examples

Description

Pre-defined functions to operate on a population demography during a simulation.

Usage

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environmental_stochasticity(transition_matrix, stochasticity = 0)

density_dependence(transition_matrix, fecundity_fraction = 1,
  survival_fraction = 1)

surv_fec_modify(transition_matrix, surv_layers, fec_layers)

Arguments

transition_matrix

A life-stage transition matrix.

stochasticity

A matrix with standard deviations (consistent or varying) around the transition means with dimensions matched to the life-stage transition matrix or a number representing a consistent standard deviation to apply to all transitions (default is 0).

fecundity_fraction

A multiplier value between 0 and 1 for fecundity values in the transition matrix.

survival_fraction

A multiplier value between 0 and 1 for survival values in the transition matrix.

surv_layers

a list of raster stacks with multipliers for survival equal to the number of life-stages.

fec_layers

a list of raster stacks with multipliers for fecundities equal to the number of life-stages. Note, life-stages that do not reproduce will have NULL in place of the raster stack.

Examples

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library(steps)

mat <- matrix(c(0.000,0.000,0.302,0.302,
                0.940,0.000,0.000,0.000,
                0.000,0.884,0.000,0.000,
                0.000,0.000,0.793,0.793),
              nrow = 4, ncol = 4, byrow = TRUE)
colnames(mat) <- rownames(mat) <- c('Stage_1','Stage_2','Stage_3','Stage_4')

mat_sd <- .01

# Use the demo_environmental_stochasticity function to modify the transition
# matrix with specified environmental stochasticity:
test_demo_es <- demo_environmental_stochasticity(transition_matrix = mat,
                                    stochasticity = mat_sd)

# Use the demo_density_dependence function to modify the transition
# matrix once carrying capacity is reached:
test_demo_dd <- demo_density_dependence(transition_matrix = mat,
                                        fecundity_fraction = 1,
                                        survival_fraction = 0.5)

# Use the demo_surv_fec_modify function to modify the  
# demography using explicit survival and fecundity layers:
test_survfec <- demo_surv_fec_modify(transition_matrix = mat,
                                    surv_layers = surv,
                                    fec_layers = fec)

skiptoniam/dlmpr documentation built on Sept. 26, 2018, 3:11 p.m.