compute.design.data: Compute design data for a specific parameter in the MARK...

In RMark: R Code for Mark Analysis

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,
  events = NULL,
  use.events = NULL,
  mscale = 1,
  subtract.events = 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 or for HidMarkov it is the strata computed by subtraction for pi parameter
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
events	vector of events if needed for parameter
use.events	if TRUE, adds events to design data
mscale	scalar for multi-scale occupancy model (number of mixtures)
subtract.events	for each stratum either the stratum or event to compute by subtraction for mlogit parameter

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.

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

Author(s)

Jeff Laake

See Also

make.design.data, add.design.data

RMark documentation built on Aug. 14, 2022, 1:05 a.m.