Adds columns to the data slot of a CompadreDB object that flag potential problems in the matrix population models. These columns can subsequently be used to subset the database by logical argument.
Optional checks include:
check_NA_A: missing values in matA?
check_NA_U: missing values in matU?
check_NA_F: missing values in matF?
check_NA_C: missing values in matC?
check_zero_U: matU all zeros (including NA)?
check_singular_U: matU singular (i.e. non-invertable)?
check_component_sum: do matU/matF/matC components sum to matA
(see Details)?
check_ergodic: is matA ergodic (see
isErgodic)?
check_irreducible: is matA irreducible (see
isIrreducible)?
check_primitive: is matA primitive (see
isPrimitive)?
check_surv_gte_1: does matU contains values that are equal to or greater than 1?
cdb_flag( cdb, checks = c("check_NA_A", "check_NA_U", "check_NA_F", "check_NA_C", "check_zero_U", "check_singular_U", "check_component_sum", "check_ergodic", "check_irreducible", "check_primitive", "check_surv_gte_1") )
| cdb | A CompadreDB object |
|---|---|
| checks | Character vector specifying which checks to run. Defaults to all, i.e. |
Returns cdb with extra columns appended to the data slot
(columns have the same names as the corresponding elements of
checks) to indicate (TRUE/FALSE) whether there are potential
problems with the matrices corresponding to a given row of the data.
For the flag check_component_sum, a value of NA will be
returned if the matrix sum of matU, matF, and matC consists only of zeros
and/or NA, indicating that the matrix has not been split.
Other data checking:
cdb_check_species(),
cdb_collapse(),
cdb_compare(),
mpm_methods
Owen Jones <jones@biology.sdu.dk>
Julia Jones <juliajones@biology.sdu.dk>
Roberto Salguero-Gomez <rob.salguero@zoo.ox.ac.uk>
Danny Buss <dlb50@cam.ac.uk>
Patrick Barks <patrick.barks@gmail.com>
CompadreFlag <- cdb_flag(Compadre) # only check whether matA has missing values, and whether matA is ergodic CompadreFlag <- cdb_flag(Compadre, checks = c("check_NA_A", "check_ergodic"))