create.dm: Creates a design matrix for a parameter
In marked: Mark-Recapture Analysis for Survival and Abundance Estimation

create.dm

R Documentation

Creates a design matrix for a parameter

Description

Creates a design matrix using the design dataframe, a formula and any intervals defined for time, cohort and age.

Usage

create.dm(x, formula, time.bins=NULL, cohort.bins=NULL, age.bins=NULL, 
                  chunk_size=1e7, remove.intercept=NULL,remove.unused.columns=TRUE)
       
       create.dml(ddl,model.parameters,design.parameters,restrict=FALSE,
             chunk_size=1e7,use.admb=FALSE,remove.unused.columns=TRUE,simplify=FALSE)

Arguments

`x`	design dataframe created by `create.dmdf`
`formula`	formula for model in R format
`time.bins`	any bins of time to collapse values
`cohort.bins`	any bins of cohort to collapse values
`age.bins`	any bins of cohort to collapse values
`chunk_size`	specifies amount of memory to use in creating design matrices; amount used is 8*chunk_size/1e6 MB (default 80MB)
`remove.intercept`	if TRUE, forces removal of intercept in design matrix
`remove.unused.columns`	if TRUE, unused columns are removed; otherwise they are left
`ddl`	Design data list which contains a list element for each parameter type; if NULL it is created
`design.parameters`	Specification of any grouping variables for design data for each parameter
`model.parameters`	List of model parameter specifications
`restrict`	if TRUE, only use design data with Time >= Cohort
`use.admb`	if TRUE uses mixed.model.admb for random effects; otherwise mixed.model
`simplify`	if TRUE simplies real parameter structure for some models; at this time it is not more efficient so ignore

Value

create.dm returns a fixed effect design matrix constructed with the design dataframe and the formula for a single parametre. It excludes any columns that are all 0. create.dml returns a list with an element for for each parameter with a sub-list for the fixed effect (fe) and random effects. The re structure depends on switch use.admb. When TRUE, it contains a single design matrix (re.dm) and indices for random effects (re.indices). When FALSE, it returns re.list which is a list with an element for each random component containing re.dm and indices for that random effect (eg (1|id) + (1|time) would produce elements for id and time.