getFleetG: getFleetG - Compute all-site (fleetwide) Evidence of Absence...
In tmcd82070/evoab: Evidence of Absence (EoA)

Description Usage Arguments Details Value Examples

Compute a single all-site g value from site-season specifice g values.

1 2	getFleetG(siteYearResults, species = "LBBA", weights = NULL, yearWeights = NULL)

`siteYearResults`	A data frame containing site-season results. One usually obtains this by running the site-year module of the `eoa` package on every combination of year and site. To assist with this, we at WEST have a python app which copies and pastes the input parameters from CSV files into the interface of `eoa`. Once site-year g-values are computed (using the auto-copy-paste routine), we have a "scraper" function in R which pulls parameters from all the text files that `eoa` produces. This parameter is a data frame containing the output CSV results from the "scraper". At a minimum, `siteYearResults` must contain the following columns: `$species`, `$facility`, `$gFac.a` = the alpha paramters of this facility's beta distribution, `$gFac.b` = the beta parameter of this facility's beta distribution, and `$year`.
`species`	Species abbreviation to run.
`weights`	A scalar or data frame containing weights for each facility in the fleet. One row per facility. This is the "DWP" field of `eoa`. If `weights` = NULL, all facilities receive equal weight. Otherwise, `weights` must be a data frame containing `$facility` and `$weight` columns. This is merged with `siteYearResults` using `$facility` as the key. These weights are re-scaled to sum to 1.0 in the `mixtureBeta` function.
`yearWeights`	When more than one year at a facility is present, this parameter allows different weights to be applied across years. The length of this vector must be equal to the number of years of data for all facilities that have multiple years of data. That is, an individual facility can have either 1 or length(yearWeights) rows in siteYearResults. If yearWeights == NULL, equal weights are use. These weights are re-scaled to sum to 1.0 inside the `mixtureBeta` function.

Seasons are summarized first. That is, if a site appears more than once for a species, we assume each line is a separate season for that species. g is averaged over those lines first. At the end, this average goes into the multi-site g average.

The fleet-wide g-value for a particular species. This value can then go into estimateL.eoa.

syr <- data.frame(species=c("LBBA","LBBA","LBBA"),
   facility=c("f1","f2","f2"),
   gFac.a = c( 69.9299, 63.5035,  84.6997),
   gFac.b = c(  736.4795,  318.3179, 759.9333 ),
   year = c(2015,2015,2016))
getFleetG(syr, "LBBA")