Extract stage-class information from CompadreMat or CompadreDB objects

Source: R/mpm_methods.R

Methods for extracting stage-class information from CompadreMat or CompadreDB objects, including whether the matrix population model includes one or more propagule stages (mpm_has_prop), dormant stages (mpm_has_dorm), or active stages (mpm_has_active), and the integer index of the first active stage class (mpm_first_active).

These methods will return a single value if passed a CompadreMat object, or a vector of values if passed a CompadreDB object (one value for every CompadreMat object within the column 'mat').

mpm_has_prop(object)

# S4 method for CompadreMat
mpm_has_prop(object)

# S4 method for CompadreDB
mpm_has_prop(object)

mpm_has_active(object)

# S4 method for CompadreMat
mpm_has_active(object)

# S4 method for CompadreDB
mpm_has_active(object)

mpm_has_dorm(object)

# S4 method for CompadreMat
mpm_has_dorm(object)

# S4 method for CompadreDB
mpm_has_dorm(object)

mpm_first_active(object)

# S4 method for CompadreMat
mpm_first_active(object)

# S4 method for CompadreDB
mpm_first_active(object)

Arguments

object

A CompadreMat or CompadreDB object

Value

No return value, called for side effects

See also

Other data checking: cdb_check_species(), cdb_collapse(), cdb_compare(), cdb_flag()

Author

Patrick Barks <patrick.barks@gmail.com>

Examples

# with CompadreMat object
mpm_has_prop(Compadre$mat[[1]])

#> [1] FALSE
mpm_has_active(Compadre$mat[[1]])

#> [1] TRUE
mpm_has_dorm(Compadre$mat[[1]])

#> [1] FALSE
mpm_first_active(Compadre$mat[[1]])

#> [1] 1

# with CompadreDB object
mpm_has_prop(Compadre)

#>   [1] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE
#>  [13] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE
#>  [25] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE
#>  [37]  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE
#>  [49] FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE
#>  [61] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE
#>  [73] FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE
#>  [85]  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE
#>  [97]  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE
#> [109]  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE
#> [121]  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE
#> [133] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE
#> [145]  TRUE FALSE FALSE FALSE  TRUE FALSE
mpm_has_active(Compadre)

#>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [25]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [37]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [49]  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [61]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [73]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [85]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#>  [97]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#> [109]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#> [121]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#> [133]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
#> [145]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
mpm_has_dorm(Compadre)

#>   [1] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [13] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE
#>  [25] FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE
#>  [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [49] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [61] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#>  [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE
#>  [97]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [109] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE
#> [121] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [133] FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
#> [145] FALSE FALSE  TRUE FALSE FALSE  TRUE
mpm_first_active(Compadre)

#>   [1]  1  2  1  1  1  1  1  1  1  1  2  2  1  1  2  2  1  1 NA  1  1  2  1  1  1
#>  [26]  1  1  1  1  1  1  1  1  2  1  1  2  1  2  1  2  1  1  1  4  1  2  1  1  2
#>  [51]  2 NA  2  1  2  2  1  2  2  1  1  1  2  1  1  1  1  1  2  1  1  2  1  1  2
#>  [76]  1  3  2  1  1  1  1  2  1  2  1  1  1  1  1  2  1  1  2  2  1  2  1  1  1
#> [101]  1  1  3  2  1  1  1  1  2  2  1  1  2  1  1  1  1  1  1  2  2  1  1  3  1
#> [126]  3  2  1  4  1  2  5  1  1  2  2  1  1  1  1  1  1  2  2  2  1  1  1  2  1