SCRAPI: SCRAPI v2.2: The smolt companion to SCOBI

In mackerman44/SCOBI: Salmonid Composition Bootstrap Intervals

Description

Perform compositional analyses of smolts at Lower Granite Dam.

Usage

SCRAPI(smoltData = NULL, Dat = "CollectionDate", Rr = "Rear",
  Primary = "GenStock", Secondary = NA, passageData = NULL,
  strat = "Week", dat = "SampleEndDate", tally = "SampleCount",
  samrate = "SampleRate", guidance = "GuidanceEfficiency",
  collaps = "Collapse", Run = "output", RTYPE = "W", REARSTRAT = TRUE,
  alph = 0.1, B = 5000, dateFormat = "%m/%d/%Y")

Arguments

smoltData	the .csv file containing the biological data for the smolts to be analyzed. The file should contain data for all smolts trapped in a given migratory year and for a given 'species' (sthd, ch0, or ch1). The function lgr2SCRAPI() can be used to format raw smolt data exported from the LGTrappingDB to make it ready for the SCRAPI() function
Dat	speciy the column in smoltData that contains the sample date for each smolt
Rr	specify the column in smoltData that contains the rear type (W or HNC) for each smolt
Primary	specify the primary category in smoltData to be estimated. i.e., after RTYPE what category would you like to decompose?
Secondary	the secondary category in the smoltData to be estimated. i.e. after Primary what category would you like to decompose next? Use Secondary = NA if no secondary decomposition is desired
passageData	the .csv file containg the smolt passage data. The file should contain the sampling date for each day of the season and for each date the 1) calendar week, 2) sampling rate, 3) count of smolts in the trap, and 4) the juvenile bypass system guidance efficiency. passageData should also contain the collapsing scheme to be used.
strat	specify the column in passageData that contains the calendar weeks
dat	specify the column in passageData that contains the sampling dates
tally	specify the column in passageData containg the daily count of smolts in the trap
samrate	specify the column in passageData containing the daily trap sample rate
guidance	specify the column in passageData containing the daily guidance efficiency estimates
collaps	specify the column in passageData containing the collapsing scheme to be used
Run	synopsis of the run being conducted. This will be used as the prefix for all of your output files
RTYPE	which rear type (wild [H] or hatchery unclipped [HNC]) would you like to perform analysis on
REARSTRAT	would you like pWild calculated on a time-stratified basis (TRUE) or across the entire emigration (FALSE)
alph	the alpha used for confidence intervals (e.g., alph = 0.10 results in 90 percent CIs)
B	the desired number of bootstraps
dateFormat	What format are the dates in your fish and passage data? The default format used in the LGTrappingDB is 01/01/1900

Author(s)

Kirk Steinhorst and Mike Ackerman

Examples

SCRAPI(smoltData = sthdScrapiInput, Primary = "GenStock", Secondary = "fwAge",
passageData = sthdSmoltPassData, Run = "sthdSmoltTest", RTYPE = "W", alph = 0.1, B = 200)

SCRAPI(smoltData = chnkScrapiInput, Primary = "GenStock", Secondary = "GenSex",
passageData = sthdSmoltPassData, Run = "ch1SmoltTest", RTYPE = "W", alph = 0.1, B = 200)

mackerman44/SCOBI documentation built on July 20, 2019, 2:48 p.m.