Rearrange stages of a matrix population model to segregate reproductive and non-reproductive stages

Rearrange stages of a matrix population model so that all inter-reproductive stages fall in the final rows/columns of the matrix. This is a preparatory step to collapsing the matrix model into a standardized set of stages (e.g., propagule, pre-reproductive, reproductive, and post-reproductive).

mpm_rearrange(matU, matF, matC = NULL, repro_stages, matrix_stages)

Arguments

matU

The survival component of a matrix population model (i.e., a square projection matrix reflecting survival-related transitions; e.g., progression, stasis, and retrogression)

matF

The sexual component of a matrix population model (i.e., a square projection matrix reflecting transitions due to sexual reproduction)

matC

The clonal component of a matrix population model (i.e., a square projection matrix reflecting transitions due to clonal reproduction). Defaults to NULL, indicating no clonal reproduction (i.e., matC is a matrix of zeros).

repro_stages

Logical vector of length ncol(matU) indicating which stages are reproductive. Alternatively, a vector of stage indices or stage names of the reproductive classes.

matrix_stages

A character vector identifying organized matrix stages.

Value

Returns a list with 6 elements:

matU

Rearranged survival matrix

matF

Rearranged sexual reproduction matrix

matC

Rearranged clonal reproduction matrix

matrix_stages

Rearranged vector of organized matrix stages

repro_stages

Rearranged logical vector of reproductive stages

nonRepInterRep

Numeric index for any rearranged inter-reproductive stages

See also

mpm_standardize

Other transformation: is_leslie_matrix(), leslie_collapse(), mpm_collapse(), mpm_split(), mpm_standardize(), name_stages(), repro_stages(), standard_stages()

Author

Rob Salguero-Gómez <rob.salguero@zoo.ox.ac.uk>

Examples

matU <- rbind(
  c(0.1, 0, 0, 0, 0),
  c(0.5, 0.2, 0.1, 0, 0),
  c(0, 0.3, 0.3, 0.1, 0),
  c(0, 0, 0.4, 0.4, 0.1),
  c(0, 0, 0, 0.1, 0.4)
)

matF <- rbind(
  c(0, 1.1, 0, 1.6, 0),
  c(0, 0.8, 0, 0.4, 0),
  c(0, 0, 0, 0, 0),
  c(0, 0, 0, 0, 0),
  c(0, 0, 0, 0, 0)
)

repro_stages <- c(2, 4)
matrix_stages <- c("prop", "active", "active", "active", "active")

mpm_rearrange(matU, matF,
  repro_stages = repro_stages,
  matrix_stages = matrix_stages
)
#> $matU
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]  0.1  0.0  0.0  0.0  0.0
#> [2,]  0.5  0.2  0.0  0.0  0.1
#> [3,]  0.0  0.0  0.4  0.1  0.4
#> [4,]  0.0  0.0  0.1  0.4  0.0
#> [5,]  0.0  0.3  0.1  0.0  0.3
#> 
#> $matF
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    0  1.1  1.6    0    0
#> [2,]    0  0.8  0.4    0    0
#> [3,]    0  0.0  0.0    0    0
#> [4,]    0  0.0  0.0    0    0
#> [5,]    0  0.0  0.0    0    0
#> 
#> $matC
#>      [,1] [,2] [,3] [,4] [,5]
#> [1,]    0    0    0    0    0
#> [2,]    0    0    0    0    0
#> [3,]    0    0    0    0    0
#> [4,]    0    0    0    0    0
#> [5,]    0    0    0    0    0
#> 
#> $matrix_stages
#> [1] "prop"   "active" "active" "active" "active"
#> 
#> $repro_stages
#> [1] FALSE  TRUE  TRUE FALSE FALSE
#> 
#> $nonRepInterRep
#> [1] 3
#>