estM {GenEst}

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 = NULL,
  frac = 1,
  COdate = "DateFound",
  model_SE,
  model_CP,
  model_DWP = NULL,
  unitCol = NULL,
  SSdate = NULL,
  sizeCol = NULL,
  IDcol = NULL,
  DWPCol = NULL,
  nsim = 1000,
  max_intervals = 8
)

Arguments

data_CO

Carcass Observation data

data_SS

Search Schedule data

data_DWP

Survey unit (rows) by carcass class (columns) density weighted proportion table

frac

fraction carcasses on ground that was surveyed but not accounted for in DWP

COdate

Column name for the date found data

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

fitted dwp model (optional)

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 carcass classes are recorded. Optional. If none provided, it is assumed there is no distinctions among carcass classes.

IDcol

column with unique carcass (CO) identifier

DWPCol

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

nsim

the number of simulation draws

max_intervals

maximum number of arrival intervals to consider for each carcass

Value

list of Mhat, Aj, ghat, DWP (by carcass), and Xtot = total number of carcasses observe

Examples

 ## 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
       )
 
## End(Not run)