F.passageWithLifeStageAssign: F.passageWithLifeStageAssign

In tmcd82070/CAMP_RST: CAMP RST R Routines

F.passageWithLifeStageAssign

Description

Estimate annual passage / production estimates between days specified.

Usage

F.passageWithLifeStageAssign(
  site,
  taxon,
  min.date,
  max.date,
  output.file,
  ci = TRUE,
  autols = FALSE,
  nls = NULL,
  weightuse = NULL,
  enhmodel = TRUE
)

Arguments

site	The identification number of the site for which estimates are required.
taxon	The species identifier indicating the type of fish of interest. This is always 161980; i.e., Chinook Salmon.
min.date	The start date for data to include. This is a text string in the format %Y-%m-%d, or YYYY-MM-DD.
max.date	The end date for data to include. Same format as min.date.
output.file	The name of the file prefix under which output is to be saved. Set to NA to plot to the Plot window.
ci	A logical indicating if 95% bootstrapped confidence intervals should be estimated along with passage estimates.
autols	Default of FALSE leads to no assigning of no analytical life stage. If TRUE, assignment of analytical life stage is done. See Details.
nls	Number of life stage groups to estimate. Ignored if autols=FALSE. See Details.
weightuse	A logical indicating if variable weight should be used for the analytical life stage assignment; the default is NULL. Ignored if autols=FALSE. See Details.
enhmodel	A logical indicating if enhanced efficiency models should be used to estimate trap efficiencies. Default is TRUE.

Details

The date range difference specified via max.date and min.date must be less than or equal to 366 days. Note that this cutoff allows for leap-year annual estimates.

Passage requires the division of a non-zero catch by a non-zero efficiency. A non-zero catch numerator ensures that passage estimates are greater than zero, while a non-zero efficiency denominator ensures that passage estimates are less than infinity. The program exits if either of these conditions are violated.

Assuming validity, catch data are summarized via unique combinations of trapVisitID, FinalRun, and lifeStage. After summarizing, all catch data are collapsed so as to have one line per combination of these variables. The use of a plus-count algorithm divvies up non-randomly selected fish into appropriate FinalRun and lifeStage categories. In this way, all fish are ultimately utilized in all pasasge estimates by life stage and run.

Observed fish are also corrected for half-cone operations, in which the intake of fish is reduced to half of a cone's aperture being covered, so as to reduce flow, and thus captured fish. Generally, all fish captured during half-cone operations are multiplied by the value of the global halfConeMulti variable, which serves as a multiplier to correct for fish missed. Variable halfConeMulti is set to 2.

The unique combinations of run and life stage in the catch data dictate the reports generated. Thus, reports spanning different time periods and sites may report different run and life stage passage combinations.

In the case when autols=TRUE, the life stage is assigned analytically. Note that the only numbers of groups allowed by argument (nls) is two or three. If NULL, the function assignLifeStage determines the number of groups utilized.

If weightuse is FALSE, any recorded weight measurements are not used in the analytical life stage assignment. If weightuse is NULL, the function assignLifeStage will determine if variable weight will be used or not.

Value

A data frame containing daily passage estimates, corrected for times not fishing, along with associated standard errors.

A bar chart displaying relative proportions over both run and life stage.

For each unique combination of run and life stage containing at least one fish, a graph png of catch over time, a csv of daily catch and passage.

A graphical display of efficiency over time, for each trap, along with an accompanying csv tabular datasheet.

In the case when autols=TRUE, a plot (pdf) and a confusion matrix (csv) comparing the analytical and morphometric life stage assignments.

Author(s)

WEST Inc.

See Also

assignLifeStage, assignlsCompare, F.run.passage

Examples

## Not run: 

#  ---- For the WallaWalla workshop
site <- 1000
taxon <- "161980"
min.date <- "2018-01-01"
max.date <- "2018-08-01"
output.file <- "passageWithLifeStageAssign_Imnaha_2019-10-31_15-33-50"
ci <- TRUE
autols <- FALSE
nls <- 1
weightuse <- TRUE
enhmodel <- FALSE

ans <- F.passageWithLifeStageAssign(site, taxon, min.date, max.date, output.file, ci, autols, nls, weightuse, enhmodel)

#   ---- Estimate passage on the American by life stage and run.
site <- 57000
taxon <- 161980
min.date <- "2013-01-01"
max.date <- "2013-06-01"
output.file <- "American"
ci <- TRUE
nls <- NULL
weightuse <- NULL
autols <- FALSE
passageWithLifeStageAssign(site,taxon,min.date,max.date,output.file,ci,
  weightuse,autols)

## End(Not run)

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