prep_for_fit: Trim sites that do not fit the criteria for model fitting

In dsjohnson/agTrendTMB: Interpolate Survey Counts For Site-Level Aggregating

Description

Trim sites that do not fit the criteria for model fitting

Usage

prep_for_fit(
  x,
  site.name = "SITE",
  abund.name = "counts",
  time.name = "year",
  model.cuts = c(5, 10),
  non.zero = 2,
  total = 10
)

Arguments

x	Steller sea lion count data for one DPS and age class, e.g., eDPS nonpups
site.name	Name of column with site names
abund.name	Name of the column with the abundance counts
time.name	Name of the column with the time (e.g., year) data
model.cuts	Number of nonzero surveys for each model type (see Details)
non.zero	Minimum number of nonzero counts for inclusion in model fitting. Must be >2.
total	Minimum total number of sea lions observed at the site over the time span considered

Details

The model.cuts is a 2-vector argument that provides the boundaries for each model type, 'const' (constant meand term), 'lin' (linear slope mean term) or 'gp' (Gaussian process mean term). E.g., the default value is model.cuts=c(3,10) which means that any site with less than or equal to 3 nonzero survey values with be fit with a 'const' model and if the number of nonzero counts is in (3,10] a 'lin' model is fitted, and so on.

dsjohnson/agTrendTMB documentation built on Jan. 1, 2021, 12:07 a.m.