estg: Estimate all carcass-level detection rates and arrival...

In GenEst: Generalized Mortality Estimator

Estimate all carcass-level detection rates and arrival intervals

Description

Estimate g values and arrival intervals for a set of carcasses from fitted pk and cp models and search data

Usage

estg(
  data_CO,
  COdate,
  data_SS,
  SSdate = NULL,
  model_SE,
  model_CP,
  model_DWP = NULL,
  sizeCol = NULL,
  unitCol = NULL,
  IDcol = NULL,
  nsim = 1000,
  max_intervals = 8
)

Arguments

data_CO	Carcass Observation data
COdate	Column name for the date found data
data_SS	Search Schedule data
SSdate	Column name for the date searched data. Optional. If not provided, estg will try to find the SSdate among the columns in data_SS. See prepSS.
model_SE	Searcher Efficiency model (or list of models if there are multiple carcass classes)
model_CP	Carcass Persistence model (or list of models if there are multiple carcass classes)
model_DWP	Density weighted proportion model (or list of models if there are multiple carcass classes)
sizeCol	Name of column in data_CO where the carcass classes are recorded. Optional. If not provided, no distinctions are made among sizes. sizeCol not only identifies what the name of the size segregating class
unitCol	Column name for the unit indicator
IDcol	Column name for unique carcass IDs (required)
nsim	the number of simulation draws
max_intervals	maximum number of arrival interval intervals to consider for each carcass. Optional. Limiting the number of search intervals can greatly increase the speed of calculations with only a slight reduction in accuracy in most cases.

Value

list of [1] g estimates (ghat) and [2] arrival interval estimates (Aj) for each of the carcasses. The row names of the Aj matrix are the units at which carcasses were found. Row names of ghat are the carcass IDs (in data_CO).

Examples

 data(mock)
 model_SE <- pkm(formula_p = p ~ HabitatType, formula_k = k ~ 1,
              data = mock$SE)
 model_CP <- cpm(formula_l = l ~ Visibility, formula_s = s ~ Visibility, 
               data = mock$CP, dist = "weibull",
               left = "LastPresentDecimalDays", 
               right = "FirstAbsentDecimalDays"
             )
 ghat <- estg(data_CO = mock$CO, COdate = "DateFound",  data_SS = mock$SS,
      model_SE = model_SE, model_CP = model_CP, unitCol = "Unit", nsim = 100)

GenEst documentation built on June 7, 2023, 6:35 p.m.