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Report length at age

Source: R/StoxReportFunctions.R
ReportRecaLengthAtAge.Rd

Tabulates summary statistics for mean length at age from MCMC simulations using Reca. MCMC simulations are typically obtained with RunRecaModels. Summary statistics are obtained from the posterior distribution, and the interval is reported as equal-tailed credible intervals are reported.

Mean length for plus-groups are a weighted by the relative catch-at-age in each composite age group. For iterations where all of the plus-group ages have a zero catch at age, this weight is not defined, and summary statistics are obtained from the remaining iterations.

If 'RecaCatchAtAge' contains estimate for a set of aggregation variables, such as area, gear, stock, etc., summary statistics will be presented similarly.

Rounding of numbers according to the argument 'Decimals' is done with round, so that negative numbers specify rounding to powers of ten, and rounding of the digit 5 is towards the even digit.

The units considered valid for mean lengths are those listed for quantity 'length' in StoxUnits

Usage

ReportRecaLengthAtAge(
  RecaCatchAtAge,
  PlusGroup = integer(),
  IntervalWidth = numeric(),
  Decimals = integer(),
  Threshold = numeric(),
  Unit = RstoxData::getUnitOptions("length", conversionRange = c(1e-07, 10))
)

Arguments

RecaCatchAtAge

Results from MCMC simulations (RecaCatchAtAge).

PlusGroup

If given, ages 'PlusGroup' or older are included in a plus group.

IntervalWidth

The width of the reported credible interval. A value of 0.9 gives 90 per cent credible intervals. Defaults to `r stoxFunctionAttributes$ReportRecaLengthAtAge$functionParameterDefaults$IntervalWidth`.

Decimals

integer specifying the number of decimals to report for 'MeanIndividualLength', 'SD', 'Low' and 'High'. Defaults to `r stoxFunctionAttributes$ReportRecaLengthAtAge$functionParameterDefaults$Decimals`.

Threshold

threshold for reporting mean weight. Rows with an estimated Catch At Age (number of individuals) lower than this will have NA reported for their mean length Defaults to `r stoxFunctionAttributes$ReportRecaLengthAtAge$functionParameterDefaults$Threshold`.

Unit

unit for 'MeanIndividualLength', 'SD', 'Low' and 'High'

Value

ReportFdaLengthAtAgeData

See also

RunRecaModels for running Reca-analysis

Examples

  lengthAtAge <- ReportRecaLengthAtAge(RstoxFDA::RecaCatchAtAgeExample, 
        PlusGroup = 13, Unit="cm", Decimals = 0)
  lengthAtAge$MeanLengthByAge
#>     AgeGroup   Age MeanIndividualLength    SD   Low  High
#>       <char> <num>                <num> <num> <num> <num>
#>  1:    Age 1     1                   28     2    25    32
#>  2:    Age 2     2                   38     4    35    41
#>  3:    Age 3     3                   47     1    45    48
#>  4:    Age 4     4                   51     1    50    52
#>  5:    Age 5     5                   56     1    55    57
#>  6:    Age 6     6                   61     1    60    62
#>  7:    Age 7     7                   67     1    65    67
#>  8:    Age 8     8                   71     1    70    72
#>  9:    Age 9     9                   75     1    73    76
#> 10:   Age 10    10                   79     1    77    80
#> 11:   Age 11    11                   82     1    81    83
#> 12:   Age 12    12                   85     1    84    87
#> 13:  Age 13+    13                   95     2    92    98