lllcrc: Local Log-linear Models for Capture-Recapture

Applies local log-linear capture-recapture models (LLLMs) for closed populations, as described in the doctoral thesis of Zachary Kurtz. The method is relevant when there are 3-5 capture occasions, with auxiliary covariates available for all capture occasions. As part of estimating the number of missing population units, the method estimates the "rate of missingness" as it varies over the covariate space. In addition, user-friendly functions are provided to recreate (approximately) the method of Zwane and van der Heijden (2004), which applied the VGAM package in a way that is closely related to LLLMs.

Author
Zach Kurtz
Date of publication
2014-10-06 00:53:14
Maintainer
Zach Kurtz <zkurtz@gmail.com>
License
GPL-2
Version
1.2

View on CRAN

Man pages

age.sex.zip
Simulate CRC data with age, sex, and zip code
AICc.vgam
Compute the AICc for a VGAM model
apply.ic.fit
Select an LLLM at each point
apply.local.ml
Fit LLLMs
as.num
Conversion to numeric
captures
Simulating captures
construct.vgam
Make a VGAM model
extract.CI
Use bootstrap output to get CI
flat.IC
Select an LLM
flat.log.linear
Fit an LLM
formatdata
Format the CRC data
french.1
A fake dataset, french.1
get.IC
Compute an information criterion
ic.all
Compute an IC for several LLMs
ic.fit
Select and fit an LLM
ic.wghts
Information criterion model weights
initialize.u.vec
Initialize log-linear parameters
init.pop
Set up a fake population
llcrc.flat.boots
Bootstrapping LLMs
lllcrc
Local log-linear models (LLLMs) for capture-recapture (CRC)
lllcrc.boots
Bootstrap for LLLMs
lllcrc-package
Local Log-linear Models for Capture-Recapture
llm.sim
Simulate basic log-linear CRC experiments
local.ml
Maximum likelihood estimation for fixed LLLMs
make.design.matrix
Construct standard LLM design matrix.
make.hierarchical.term.sets
Generate a universe of hierarchical models.
make.patterns.template
Template for capture-pattern counts
micro.post.stratify
Collapse CRC data through micro post-stratification
odd.evens
Determine the even-ness of capture patterns
patterns
Collapse capture events into capture patterns (strings)
patterns.possible
Generate all observable capture patterns
pirls
Maximum likelihood for log-linear coefficients
plot
Plot LLLMs
plot.llsim
Plot the output of 'llm.sim'
pop.to.counts
Put CRC data into LLM vector
poptop
Simulate a CRC experiment
rates.by.category
Display estimated rates of missingness by category
resample.captures
Tool for bootstrapping
saturated.local
Use odd-even formula to fit saturated LLM
smooth.patterns
Local averaging for LLLMs
stackydens
Stack local capture pattern frequencies for plotting
string.to.array
Put LLM vector into a LLM design matrix
summarize.by.factors
Summarize LLLM by factor
summary
Summary of LLLM or VGAM CRC analysis
vgam.crc
Build a VGAM CRC model
vgam.crc.boots
Bootstrapping for a VGAM CRC model
y.string.to.y.glm
Capture patterns to design matrix
zglm
Maximum likelihood for log-linear coefficients

Files in this package

lllcrc
lllcrc/NAMESPACE
lllcrc/R
lllcrc/R/regression.R
lllcrc/R/ic.R
lllcrc/R/llsimulate.R
lllcrc/R/lllcrc-package.R
lllcrc/R/zvgam.R
lllcrc/R/boots.R
lllcrc/R/graph.R
lllcrc/R/local_ml.R
lllcrc/R/design.R
lllcrc/R/simulate.R
lllcrc/R/user.R
lllcrc/MD5
lllcrc/DESCRIPTION
lllcrc/man
lllcrc/man/poptop.Rd
lllcrc/man/ic.wghts.Rd
lllcrc/man/y.string.to.y.glm.Rd
lllcrc/man/smooth.patterns.Rd
lllcrc/man/AICc.vgam.Rd
lllcrc/man/construct.vgam.Rd
lllcrc/man/as.num.Rd
lllcrc/man/zglm.Rd
lllcrc/man/vgam.crc.boots.Rd
lllcrc/man/stackydens.Rd
lllcrc/man/ic.all.Rd
lllcrc/man/init.pop.Rd
lllcrc/man/make.design.matrix.Rd
lllcrc/man/resample.captures.Rd
lllcrc/man/rates.by.category.Rd
lllcrc/man/vgam.crc.Rd
lllcrc/man/local.ml.Rd
lllcrc/man/llm.sim.Rd
lllcrc/man/string.to.array.Rd
lllcrc/man/pop.to.counts.Rd
lllcrc/man/get.IC.Rd
lllcrc/man/extract.CI.Rd
lllcrc/man/micro.post.stratify.Rd
lllcrc/man/make.patterns.template.Rd
lllcrc/man/patterns.possible.Rd
lllcrc/man/formatdata.Rd
lllcrc/man/saturated.local.Rd
lllcrc/man/apply.ic.fit.Rd
lllcrc/man/flat.IC.Rd
lllcrc/man/plot.llsim.Rd
lllcrc/man/lllcrc.Rd
lllcrc/man/lllcrc-package.Rd
lllcrc/man/make.hierarchical.term.sets.Rd
lllcrc/man/lllcrc.boots.Rd
lllcrc/man/ic.fit.Rd
lllcrc/man/patterns.Rd
lllcrc/man/pirls.Rd
lllcrc/man/french.1.Rd
lllcrc/man/plot.Rd
lllcrc/man/summarize.by.factors.Rd
lllcrc/man/captures.Rd
lllcrc/man/odd.evens.Rd
lllcrc/man/flat.log.linear.Rd
lllcrc/man/age.sex.zip.Rd
lllcrc/man/llcrc.flat.boots.Rd
lllcrc/man/summary.Rd
lllcrc/man/apply.local.ml.Rd
lllcrc/man/initialize.u.vec.Rd