assignLifeStage: assignLifeStage

In tmcd82070/CAMP_RST: CAMP RST R Routines

assignLifeStage

Description

This function will be called within F.get.catch.data The purpose is to replace the life stage column with an updated assignment based on a clustering routine.

Usage

assignLifeStage(
  DATA,
  groupN = 1,
  USEWeight = NULL,
  output.file = output.file,
  ...
)

Arguments

DATA	A data frame of the catch data with the weight measurement, as returned from getCatchDataWeight.
groupN	The number of life stage groups to be estimated, see details.
USEWeight	Indicate whether weight should not (FALSE) be used in the analytical assignment or allow (NULL) weight to be used, see details.
output.file	A text string indicating a prefix to append to all output.
...	Arguments passed to assignLSCompare.

Details

The function expects the data frame DATA to have column names: lifeStage, SampleDate, FinalRun, forkLength, weight, Unmarked. The lifeStage column is overwritten with the new analytical life stage assignment.

The life stage assignment is done by each unique value in the FinalRun column. If the final run is unassigned, no estimation is done and the life stage is set to Unassigned.

This function relies on several global variables as set by GlobalVars: sample.size.forkLength, sample.size.forkLengthAndWeight, weight.prop.forkLength, forkLength.mean.diff, see GlobalVars for default values.

If the number of fish with a fork length value is less than sample.size.forkLength the life stage is set to Unassigned, else the life stage assignment will continue.

If USEWeight=FALSE the life stage is analytically assigned using fork length and date only. If USEWeight=NULL the weight variable is also used to assign life stage if the number of fish with a weight measurement divided by the number of fish with a fork length measurement is greater than weight.prop.forkLength AND the number of fish with a weight and fork length measurements is greater than sample.size.forkLengthAndWeight. It is not recommend for the user to specify USEWeight=TRUE, if done, weight is only used if the number of fish with a weight measurement is greater than sample.size.forkLengthAndWeight else weight is not used. In all cases fork length and date are used in the life stage assignment and based on user input and these conditions weight might also be used to assign life stage.

groupN may take the values 2, 3, or NULL. If 2 or 3 the analytical life stage is done with that number of groups. If 2, the group names are Small and Large, if 3 the group names are Small, Medium, and Large. These names are chosen to distinguish from the morphometric life stage names. If groupN=NULL the analytical life stage begins with 3 groups. If the minimum pairwise fork length mean difference is less than forkLength.mean.diff the number of groups fit is reduced by one. In this protocol the number of groups can be one, in which case the group name is All.

The analytical assignment is done through a call to the Mclust function in the mclust package. The Mclust function is fitting a mixture of multivariate normal distributions. The number of distribution fit corresponds to the number of life stage groups. The Mclust function returns mean vectors and variance covariance matrices for each group and the group member ship for each fish used in the mixture distribution estimation. The group names are assigned based on the means of the fork length, smallest mean is label as Small, etc.

In some cases not all of the fish are used in the mixture distribution estimation. For example if weight is to be used, there could be some fish without a weight measurement and complete observations are needed for the Mclust function. For these fish a minimum Mahalanobis distance is used for the life stage assignment. For each fish not used in the mixture distribution estimation, but have at least a fork length or weight, the Mahalanobis distance from the fish to each of the group means is calculated. The minimum distance indicates which group that fish will be assigned too. The concept is that all fish with a recorded fork length will have a group assignment.

The analytical and morphometric life stage assignments are compared with a call to assignLSCompare.

Value

The data frame DATA is returned with the lifeStage column being updated by the analytical assignment.

Author(s)

Jared Studyvin, WEST Inc.

See Also

assignLSCompare, GlobalVars

Examples

## Not run: 
assignLifeStage(DATA,groupN,USEWeight)


## End(Not run)

tmcd82070/CAMP_RST documentation built on April 6, 2022, 12:07 a.m.