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Combine prior and data for fertility matrix

Source: R/fill_matrix.R
fill_fertility.Rd

fill_fertility returns the expected value of the fertility matrix combining observed recruits for one time step and a Gamma prior for each column.

Usage

fill_fertility(
  TF,
  N,
  alpha = 1e-05,
  beta = 1e-05,
  priorweight = -1,
  returnType = "F"
)

Arguments

TF

A list of two matrices, T and F, as ouput by projection.matrix.

N

A vector of observed stage distribution.

alpha

A matrix of the prior parameter for each stage. Impossible stage combinations marked with NA_real_.

beta

A matrix of the prior parameter for each stage. Impossible stage combinations marked with NA_real_.

priorweight

total weight for each column of prior as a percentage of sample size or 1 if negative

returnType

A character vector describing the desired return value. Defaults to "F" the fertility matrix

Value

The return value depends on parameter returnType.

  • A - the summed matrix "filled in" using a Gamma prior

  • F - just the filled in fertility matrix

  • ab - the posterior parameters alpha and beta as a list.

Details

Assumes that only one stage reproduces ... needs generalizing.

Examples

# Build a simple 3-stage TF list (transition + fertility matrices)
T_mat <- matrix(c(0.5, 0.3, 0.0,
                  0.2, 0.4, 0.1,
                  0.0, 0.1, 0.7), nrow = 3, ncol = 3)
F_mat <- matrix(c(0.0, 0.0, 1.5,
                  0.0, 0.0, 0.0,
                  0.0, 0.0, 0.0), nrow = 3, ncol = 3)
TF <- list(T = T_mat, F = F_mat)
N  <- c(10, 5, 8)

# Only adults (stage 3) reproduce; mark non-reproducing entries with NA
alpha_mat <- matrix(c(NA, NA, 0.5,
                      NA, NA, NA,
                      NA, NA, NA), nrow = 3, ncol = 3)
beta_mat  <- matrix(c(NA, NA, 1.0,
                      NA, NA, NA,
                      NA, NA, NA), nrow = 3, ncol = 3)

# Default: return filled fertility matrix F
fill_fertility(TF, N, alpha = alpha_mat, beta = beta_mat)
#>          [,1] [,2] [,3]
#> [1,] 0.000000    0    0
#> [2,] 0.000000    0    0
#> [3,] 1.409091    0    0

# Return the full population matrix A = T + F
fill_fertility(TF, N, alpha = alpha_mat, beta = beta_mat, returnType = "A")
#>          [,1] [,2] [,3]
#> [1,] 0.500000  0.2  0.0
#> [2,] 0.300000  0.4  0.1
#> [3,] 1.409091  0.1  0.7

# Return the posterior alpha and beta parameters
fill_fertility(TF, N, alpha = alpha_mat, beta = beta_mat, returnType = "ab")
#> $alpha
#>      [,1] [,2] [,3]
#> [1,]   NA   NA   NA
#> [2,]   NA   NA   NA
#> [3,] 15.5   NA   NA
#> 
#> $beta
#>      [,1] [,2] [,3]
#> [1,]   NA   NA   NA
#> [2,]   NA   NA   NA
#> [3,]   11   NA   NA
#>