Reports the sum, mean or other functions on a variable of the SuperIndividualsData
.
ReportSuperIndividuals(
SuperIndividualsData,
TargetVariable = character(),
TargetVariableUnit = character(),
ReportFunction = getReportFunctions(use = "Baseline"),
GroupingVariables = character(),
InformationVariables = character(),
Filter = character(),
RemoveMissingValues = FALSE,
WeightingVariable = character(),
ConditionOperator = character(),
ConditionValue = character(),
FractionOverVariable = character()
)
The SuperIndividualsData
data.
The variable to report.
The unit to use for the TargetVariable
. See RstoxData::StoxUnits for possible units (look for the appropriate quantity, e.g. "length" for IndividualTotalLength, and use the shortname in the TargetVariableUnit
).
The name of a function to report the Baseline process output by. This must be a function returning a single value. See ReportFunctions
for implemented funcitons.
The variables to report by. For most applications GroupingVariables
should include "Survey" and "SpeciesCategory", unless the user needs to sum over all Survey or SpeciesCategory.
Variables to include as columns to the end of the report table. These cannot have more unique combinations than the GroupingVariables
.
A string with an R expression to filter out unwanted rows of the report, e.g. "IndividualAge %notin% NA" or "Survey %notin% NA & SpeciesCategory %notin% NA".
Logical: If TRUE, remove missing values (NAs) from the TargetVariable
. The default (FALSE) implies to report NA if at least one of the values used in the ReportFunction
is NA. Use RemoveMissingValues
= TRUE with extreme caution, as it may lead to under-estimation. E.g., if RemoveMissingValues
= TRUE and a super-individual lacks IndividualRoundWeight
, Biomass
will be NA, and the portion of Abundance
distributed to that super-individual will be excluded when summing Biomass
(but included when summing Abundance
). It is advised to always run with RemoveMissingValues
= FALSE first, and make a thorough investigation to identify the source of any missing values. The function link{ImputeSuperIndividuals}
can be used to impute the missing information from other super-individuals.
The variable to weight by. Only relevant for ReportFunction
"weighted.mean". Note that missing values in the WeightingVariable
results in missing value from the weighted.mean
function as per the documentation of this function, regardles of any RemoveMissingValues
.
Expressions (strings) giving the condition for the ReportFunction
number
and fractionOfOccurrence
. Supported values for ConditionOperator
are "%in%", "%notin%", "==", "!=", "%notequal%", "<", "<=", ">=", ">". The ConditionOperator
and ConditionValue
are pasted for use in data.table.
When ReportFunction
is a fraction ("fractionOfOccurrence" or "fractionOfSum") FractionOverVariable
is a string naming the variable (one of the GroupingVariables
) to sum over in the denominator of the fraction.
A ReportSuperIndividualsData
object.
This function is useful to, e.g, sum Biomass for each SpeciesCategory and IndividualTotalLength, or average IndividualTotalLength for each IndividualAge and Stratum.