SRpresto: Sea Lamprey Status Report Generation
In JVAdams/GLFC: Great Lakes Fishery Commission

SRpresto

R Documentation

Sea Lamprey Status Report Generation

Description

Carry out a series of steps in the Sea Lamprey Status Report generation process in one fell swoop.

Usage

SRpresto(
  FOLDER,
  INDEX.LAKE,
  INDEX.STREAM,
  MAXLARVAE,
  CONTROL = "ControlTable.csv",
  TROUTSUP = "TroutSuperior.csv",
  TROUTMIC = "TroutMichigan.csv",
  TROUTHUR = "TroutHuron.csv",
  TROUTERI = "TroutErie.csv",
  TROUTONT = "TroutOntario.csv",
  AXISRANGES = "AxisRanges.xls"
)

Arguments

`FOLDER`	A character scalar identifying the path where all the files are stored, e.g., `DIRECTORY = "C:\\temp\\mydir"`.
`INDEX.LAKE`	A character scalar identifying the name of the csv file with historic lake-wide sea lamprey adult index data, typically `AdultLakeThruYYYY.csv` the output from `AIpresto`.
`INDEX.STREAM`	A character scalar identifying the name of the csv file with historic stream-specific sea lamprey adult index data, typically `AdultStreamThruYYYY.csv` the output from `AIpresto`.
`MAXLARVAE`	A character scalar identifying the name of the Excel spreadsheet with stream-specific maximum age-1 and older sea lamprey larvae population estimates from QAS/RS data, typically dating back to 1995. Column headers should include: "Lake", "Stream", "Estimate", "STREAM_NAM", "LATITUDE", and "LONGITUDE".
`CONTROL`	A character scalar identifying the name of the csv file with historic lake-wide sea lamprey control data, default "ControlTable.csv". The first column is the year of control. The remaining columns are "Field Days", "TFM", and "Bayer" repeated for each Great Lake (columns 2-4 for Superior, 5-7 Michigan, 8-10 Huron, 11-13 Erie, 14-16 Ontario) and the totals across all five lakes (columns 17-19). ??? UNITS
`TROUTSUP`	A character scalar identifying the name of the csv file with historic lake-wide lake trout data for Lake Superior (both catch per unit effort and sea lamprey wounding rate), default "TroutSuperior.csv". Column headers should include: "year", "cpe", "lo", "hi", and "wound".
`TROUTMIC`	A character scalar identifying the name of the csv file with historic lake-wide lake trout data for Lake Michigan (both catch per unit effort and sea lamprey wounding rate), default "TroutMichigan.csv". Column headers should include: "year", "cpe", "lo", "hi", "wound", "wound.upper", and "wound.lower".
`TROUTHUR`	A character scalar identifying the name of the csv file with historic lake-wide lake trout data for Lake Huron (both catch per unit effort and sea lamprey wounding rate), default "TroutHuron.csv". Column headers should include: "year", "cpe", "lo", "hi", and "wound".
`TROUTERI`	A character scalar identifying the name of the csv file with historic lake-wide lake trout data for Lake Erie (both catch per unit effort and sea lamprey wounding rate), default "TroutErie.csv". Column headers should include: "year", "cpe", "wound", "wound.upper", and "wound.lower".
`TROUTONT`	A character scalar identifying the name of the csv file with historic lake-wide lake trout data for Lake Ontario (both catch per unit effort and sea lamprey wounding rate), default "TroutOntario.csv". Column headers should include: "year", "cpe", "wound", "wound.upper", and "wound.lower".
`AXISRANGES`	A character scalar identifying the name of the Excel spreadsheet with specified axis ranges for the plots in the Status Report, default "AxisRanges.xls". Column headers should include: "order", "metric", "order", "lake", "from", "to", "by", "from", "to", and "by" corresponding to the metric order and name, lake order and name, then the minimum (from), maximum (to) and spacing (by) tick marks for individual graphs (columns 5-7) and the big one-page graphs (columns 8-10).

Value

Two data summaries are saved as csv files to FOLDER:

StatusTargetsdd-Mon-YYYY.csv) - Lake-wide lake trout wounding rate targets and sea lamprey Adult Index targets.
StatusMetricsdd-Mon-YYYY.csv - Annual lake-wide summary of all the Status Report metrics.

One rich text documents are saved as doc files (so that MS Word will open them automatically) to FOLDER:

Status Report Rough Draft dd-Mon-YYYY.doc - Rough draft of the sea lamprey Status Report.

Examples

## Not run: 
SRpresto(
  FOLDER="C:/JVA/GLFC/People/Siefkes/Status graphs/",
  INDEX.LAKE="AdultLakeThru2016.csv",
  INDEX.STREAM="AdultStreamThru2016.csv",
  MAXLARVAE="MaxLarvalEstimatesSummary2013mod2016-08-25.xls"
)

## End(Not run)

JVAdams/GLFC documentation built on Jan. 5, 2023, 12:59 a.m.