F.summarize.fish.visit: F.summarize.fish.visit

In tmcd82070/CAMP_RST: CAMP RST R Routines

F.summarize.fish.visit

Description

Summarize fish count and fork lengths over visits.

Usage

F.summarize.fish.visit(catch, variable)

Arguments

catch	A data frame containing one record per fish or fish group, where each record or fish group contains identical fork lengths. This data frame results from F.get.catch.data.
variable	The type of fish for which summary is required.

Details

Results from the catch-query series summarize the number of fish per trapVisitID, lifeStage, FinalRun, and forkLength. See section Structured Query Language (SQL) Queries in F.run.sqlFile for more information. Following the initial queries, these need to be summarized, depending on the type of fish, for further processing. Types of fish summarized by F.summarize.fish.visit include counts under variables unassigned, inflated, assigned, halfConeAssignedCatch, halfConeUnassignedCatch, assignedCatch, unassignedCatch, modAssignedCatch, and modUnassignedCatch. See section Value under function F.get.catch.data for more information on these variables.

An index comprised of variables trapVisitID, FinalRun, and Unassd summarizes assigned fish. Note that here, assigned fish are assumed to have only their run assigned, and not necessarily their life stage. Assigned fish are separate from unassigned fish, meaning they were randomly selected, and thus form the basis of sampling proportions of run and life stage utilized via the plus-count algorithm.

Unassigned fish are summarized via an index comprised of variables trapVisitID, FinalRun, lifeStage, and Unassd.

Inflated fish (all captured fish, including plus-counts) are summarized via an index comprised of trapVisitID, FinalRun, and lifeStage. Because inflated fish include plus-counted fish that have been re-assigned to sampled-based counts of run and life stage, indexing by variable Unassd is unnecessary.

Finally, the other fish types for which summaries are required, namely those involved with the adjustment for half-cone operations, have an index of trapVisitID, FinalRun, and lifeStage.

"Half-cone fish" and the "mod" variables listed above comprise additive adjustments to the observed counts of fish due to those fish being associated with half-cone operations. Generally, these fish equal the amount actually captured; together, the sum of captured fish and half-cone fish equals twice the number of captured fish, where the multiplier of two originates from the halfConeMulti global variable set in function GlobalVars. See F.get.catch.data.

Weighted fork lengths are recorded to the nearest millimeter. Each is calculated over unique indices and weighted on the number of fish.

Value

A data frame with one line per visit, with catch summarized. Summary statistics for each fish record or group of fish include N, mean fork length, and standard deviation of fork length.

Author(s)

WEST Inc.

See Also

F.get.catch.data

Examples

## Not run: 
#   ---- Summarize fish and obtain simple statistics for unassigned
#   ---- fish broken out by run, and possibly life stage as well,
#   ---- in data frame catch.  
catch.df0 <- F.summarize.fish.visit(catch,"unassigned")

## End(Not run)

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