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Set of verify rules for an FLR class

Source: R/genericMethods.R, R/FLStock.R
ruleset.Rd

Returns a set of standard rules to be used by the verify method for an object of a given class.

Usage

ruleset(object, ...)

# S4 method for FLStock
ruleset(object, ...)

Arguments

object

An object of any FLR class for which the method has been defined.

...

Names of positions in the standard list to subset.

Value

A named list containing the rules defined for for the class object belongs to.

Details

A standard minimal set of rules to check FLStock objects against using the verify method. The included rules are (with names in italics) check that:

  • there are no NAs in any slot, anyna.

  • catch.wt, landings.wt, discards.wt and stock.wt > 0.

  • mat, m.spwn and harvest.spwn values are between 0 and 1.

  • harvest >= 0.

  • cohorts in the stock.n slot contain decreasing numbers, except for the plusgroup age.

Author

The FLR Team

Examples

data(ple4)
ruleset(ple4)
#> $anyna
#> $anyna$rule
#> [1] "!anyna"
#> 
#> $anyna$anyna
#> function(x)
#>       unlist(qapply(x, function(y) sum(is.na(y), na.rm=TRUE) > 0))
#> <bytecode: 0x558826867a30>
#> <environment: 0x55884b7971f0>
#> 
#> 
#> $catch.wt
#> ~catch.wt > 0
#> <environment: 0x55884b7971f0>
#> 
#> $landings.wt
#> ~landings.wt > 0
#> <environment: 0x55884b7971f0>
#> 
#> $discards.wt
#> ~discards.wt > 0
#> <environment: 0x55884b7971f0>
#> 
#> $stock.wt
#> ~stock.wt > 0
#> <environment: 0x55884b7971f0>
#> 
#> $mat
#> ~mat <= 1 & mat >= 0
#> <environment: 0x55884b7971f0>
#> 
#> $harvest.spwn
#> ~harvest.spwn <= 1 & harvest.spwn >= 0
#> <environment: 0x55884b7971f0>
#> 
#> $m.spwn
#> ~m.spwn <= 1 & m.spwn >= 0
#> <environment: 0x55884b7971f0>
#> 
#> $harvest
#> ~harvest >= 0
#> <environment: 0x55884b7971f0>
#> 
#> $cohorts
#> $cohorts$rule
#> ~ccohorts(stock.n)
#> <environment: 0x55884b7971f0>
#> 
#> $cohorts$ccohorts
#> function(x) {
#>         if(dim(x)[2] < dim(x)[1])
#>           return(NA)
#>         #   DROP plusgroup, SELECT full cohorts
#>         x <- FLCohort(x)[-dim(x)[1], seq(dim(x)[1], dim(x)[2] - dim(x)[1])]
#>         # CHECK cohort change in abundances
#>         return((x[-1, ] / x[-dim(x)[1],]) < 1)
#>       }
#> <bytecode: 0x55882686c6a8>
#> <environment: 0x55884b7971f0>
#> 
#> 
#> $uoms
#> $uoms$rule
#> [1] "uoms"
#> 
#> $uoms$uoms
#> function(x)
#>       uomUnits(unlist(units(x)))
#> <bytecode: 0x55882686ee98>
#> <environment: 0x55884b7971f0>
#> 
#> 
# Extract single rule by name
ruleset(ple4, 'anyna')
#> $anyna
#> $anyna$rule
#> [1] "!anyna"
#> 
#> $anyna$anyna
#> function(x)
#>       unlist(qapply(x, function(y) sum(is.na(y), na.rm=TRUE) > 0))
#> <bytecode: 0x558826867a30>
#> <environment: 0x55884db9a958>
#> 
#>