RMark (version 2.1.12)

compute.design.data: Compute design data for a specific parameter in the MARK model (internal use)

Description

For a specific type of parameter (e.g., Phi, p, r etc), it creates a data frame containing design data for each parameter of that type in the model as structured by an all different PIM (parameter information matrix). The design data are used in constructing the design matrix for MARK with user-specified model formulae as in make.mark.model.

Usage

compute.design.data(data, begin, num, type = "Triang", mix = FALSE,
  rows = 0, pim.type = "all", secondary, nstrata = 1, tostrata = FALSE,
  strata.labels = NULL, subtract.stratum = strata.labels,
  common.zero = FALSE, sub.stratum = 0, limits = NULL)

Arguments

data

data list created by process.data

begin

0 for survival type, 1 for capture type

num

number of parameters relative to number of occasions (0 or -1)

type

type of parameter structure (Triang (STriang) or Square)

mix

if TRUE this is a mixed parameter

rows

number of rows relative to number of mixtures

pim.type

type of pim structure; either all (all-different) or time

secondary

TRUE if a parameter for the secondary periods of robust design

nstrata

number of strata for multistrata

tostrata

set to TRUE for transition parameters

strata.labels

labels for strata as identified in capture history

subtract.stratum

for each stratum, the to.strata that is computed by subtraction

common.zero

if TRUE, uses a common begin.time to set origin (0) for Time variable defaults to FALSE for legacy reasons but should be set to TRUE for models that share formula like p and c with the Time model

sub.stratum

the number of strata to subtract for parameters that use mlogit across strata like pi and Omega for RDMSOpenMisClass

limits

For RDMSOccRepro values that set row and col (if any) start on states

Value

• design.data: a data frame containing all of the design data fields for a particular type of parameter
• group
  group factor level
• age
  age factor level
• time
  time factor level
• cohort
  cohort factor level
• Age
  age as a continuous variable
• Time
  time as a continuous variable
• Cohort
  cohort as a continuous variable
• mixture
  mixture factor level
• other fields
  any factor variables used to define groups

Details

This function is called by make.design.data to create all of the default design data for a particular type of model and by add.design.data to add binned design data fields for a particular type of parameter. The design data created by this function include group, age, time and cohort as factors variables and continuous (non-factor) versions of all but group. In addition, if groups have been defined for the data, then a data column is added for each factor variable used to define the groups. Also for specific closed capture heterogeneity models (model="HetClosed", "FullHet", "HetHug", "FullHetHug") the data column mixture is added to the design data. The arguments for this function are defined for each model by the function setup.model.

See Also

make.design.data, add.design.data