Returns a set of standard rules to be used by the verify method for an object of a given class.
Arguments
- object
An object of any FLR class for which the method has been defined.
- ...
Names of positions in the standard list to subset.
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.
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>
#>
#>