GenEst (version 1.2.0)

estM: Estimate mortality

Description

Given given fitted Searcher Efficiency and Carcass Persistence models; Search Schedule, Density Weighted Proportion, and Carcass Observation data; and information about the fraction of the the facility that was surveyed.

Usage

estM(data_CO, data_SS, data_DWP, frac = 1, COdate = "DateFound",
  model_SE, model_CP, unitCol = NULL, SSdate = NULL, sizeCol = NULL,
  DWPCol = NULL, seed_SE = NULL, seed_CP = NULL, seed_g = NULL,
  seed_M = NULL, nsim = 1000, max_intervals = 8)

Arguments

data_CO

Carcass Observation data

data_SS

Search Schedule data

data_DWP

Survey unit (rows) by size (columns) density weighted proportion table

frac

fraction of facility (by units or by area) surveyed

COdate

Column name for the date found data

model_SE

Searcher Efficiency model (or list of models if there are multiple size classes)

model_CP

Carcass Persistence model (or list of models if there are multiple size classes)

unitCol

Column name for the unit indicator (optional)

SSdate

Column name for the date searched data

sizeCol

Name of colum in data_CO where the size classes are recorded. Optional. If none provided, it is assumed there is no distinctions among size classes.

DWPCol

Column name for the DWP values in the DWP table when no size class is used and there is more than one column in data_DWP that could be interpreted as DWP.

seed_SE

seed for random draws of the SE model

seed_CP

seed for random draws of the CP model

seed_g

seed for random draws of the gs

seed_M

seed for the random draws of the Mhats

nsim

the number of simulation draws

max_intervals

maximum number of arrival intervals to consider for each carcass

Value

list of Mhat, Aj, ghat

Examples

# NOT RUN {
 
# }
# NOT RUN {
 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"
             )
 eM <- estM(nsim = 1000, data_CO = mock$CO, data_SS = mock$SS, 
         data_DWP = mock$DWP, frac = 1, model_SE = model_SE, 
         model_CP = model_CP, COdate = "DateFound",
         DWPCol = "S", sizeCol = NULL
       )
 
# }
# NOT RUN {
# }

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