Helper functions to isolate particular components of a population dynamics model, such as the reproduction terms, transition/growth terms, or particular life stages from an abundance vector, such as pre- or post-reproductive stages.
reproduction(matrix, dims = NULL)
survival(matrix, dims = NULL)
transition(matrix, dims = NULL)
all_cells(matrix, dims = NULL)
all_classes(matrix, dims = NULL)
combine(...)a population dynamics matrix for which a particular mask is required. Only used to determine mask dimensions, so can be any matrix with appropriate dimensions
a numeric value or vector identifying subsets of cells to include in a given mask
a set of masks or masking functions
to be combined into a single mask by one of the
combine methods
To be completed.
# define a population
nclass <- 5
popmat <- matrix(0, nrow = nclass, ncol = nclass)
popmat[reproduction(popmat, dims = 4:5)] <- c(10, 20)
popmat[transition(popmat)] <- c(0.25, 0.3, 0.5, 0.65)
# pull out reproductive elements
reproduction(popmat)
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] FALSE TRUE TRUE TRUE TRUE
#> [2,] FALSE FALSE FALSE FALSE FALSE
#> [3,] FALSE FALSE FALSE FALSE FALSE
#> [4,] FALSE FALSE FALSE FALSE FALSE
#> [5,] FALSE FALSE FALSE FALSE FALSE
#> attr(,"class")
#> [1] "mask" "matrix" "array"
# what if only 4 and 5 year olds reproduce?
reproduction(popmat, dims = 4:5)
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] FALSE FALSE FALSE TRUE TRUE
#> [2,] FALSE FALSE FALSE FALSE FALSE
#> [3,] FALSE FALSE FALSE FALSE FALSE
#> [4,] FALSE FALSE FALSE FALSE FALSE
#> [5,] FALSE FALSE FALSE FALSE FALSE
#> attr(,"class")
#> [1] "mask" "matrix" "array"
# define survival elements
survival(popmat)
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] TRUE FALSE FALSE FALSE FALSE
#> [2,] FALSE TRUE FALSE FALSE FALSE
#> [3,] FALSE FALSE TRUE FALSE FALSE
#> [4,] FALSE FALSE FALSE TRUE FALSE
#> [5,] FALSE FALSE FALSE FALSE TRUE
#> attr(,"class")
#> [1] "mask" "matrix" "array"
# what if 1 and 2 year olds always transition?
survival(popmat, dims = 3:5)
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] FALSE FALSE FALSE FALSE FALSE
#> [2,] FALSE FALSE FALSE FALSE FALSE
#> [3,] FALSE FALSE TRUE FALSE FALSE
#> [4,] FALSE FALSE FALSE TRUE FALSE
#> [5,] FALSE FALSE FALSE FALSE TRUE
#> attr(,"class")
#> [1] "mask" "matrix" "array"
# and transitions
transition(popmat)
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] FALSE FALSE FALSE FALSE FALSE
#> [2,] TRUE FALSE FALSE FALSE FALSE
#> [3,] FALSE TRUE FALSE FALSE FALSE
#> [4,] FALSE FALSE TRUE FALSE FALSE
#> [5,] FALSE FALSE FALSE TRUE FALSE
#> attr(,"class")
#> [1] "mask" "matrix" "array"
# combine transitions and reproduction of 4 and 5 year olds
combine(reproduction(popmat, dims = 4:5), transition(popmat))
#> [,1] [,2] [,3] [,4] [,5]
#> [1,] FALSE FALSE FALSE TRUE TRUE
#> [2,] TRUE FALSE FALSE FALSE FALSE
#> [3,] FALSE TRUE FALSE FALSE FALSE
#> [4,] FALSE FALSE TRUE FALSE FALSE
#> [5,] FALSE FALSE FALSE TRUE FALSE
#> attr(,"class")
#> [1] "mask" "matrix" "array"
# can also mask the population vector in this way
# pull out all classes
all_classes(popmat)
#> [,1]
#> [1,] TRUE
#> [2,] TRUE
#> [3,] TRUE
#> [4,] TRUE
#> [5,] TRUE
#> attr(,"class")
#> [1] "mask" "matrix" "array"
# and just 3-5 year olds
all_classes(popmat, dims = 3:5)
#> [,1]
#> [1,] FALSE
#> [2,] FALSE
#> [3,] TRUE
#> [4,] TRUE
#> [5,] TRUE
#> attr(,"class")
#> [1] "mask" "matrix" "array"