Quantification of binary capture histories

Description

The quant.binary family of functions allow to quantify binary capture histories (partial or complete) in terms of a meaningful quantity which can be interpreted as a possibly meaningful behavioral covariate (like memory persistence of previous capture history)

Usage

quant.binary(x)
quant.binary.markov(x, markov.ord)
quant.binary.integer(x)
quant.binary.counts(x)
quant.binary.counts.integer(x)

Arguments

Details

For a more detailed description of instances of meaningful behavioral covariates see Alunni Fegatelli and Tardella (2012) and Alunni Fegatelli (2013)[PhD Thesis]

Value

For quant.binary it returns a numeric value within the unit interval [0,1] and
quant.binary.markov. For quant.binary.integer it returns an integer value .

Author(s)

Danilo Alunni Fegatelli and Luca Tardella

References

Alunni Fegatelli, D. and Tardella, L. (2012) Improved inference on capture recapture models with behavioural effects. Statistical Methods & Applications Applications Volume 22, Issue 1, pp 45-66 10.1007/s10260-012-0221-4

Alunni Fegatelli, D. (2013) New methods for capture-recapture modelling with behavioural response and individual heterogeneity. PhD Thesis. http://padis.uniroma1.it/bitstream/10805/2085/1/TesiDottorato-AlunniFegatelliDanilo.pdf

Examples

## Example of quantification with character input

capt.hist="0110"

quant.binary(capt.hist)
quant.binary.markov(capt.hist,markov.ord=2)
quant.binary.integer(capt.hist)
quant.binary.counts(capt.hist)
quant.binary.counts.integer(capt.hist)

## Example of quantification with numeric input

ch=c(0,1,1,0)

quant.binary(ch)
quant.binary.markov(ch,markov.ord=2)
quant.binary.integer(ch)
quant.binary.counts(ch)
quant.binary.counts.integer(ch)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BBRecapture)
Loading required package: HI
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lme4
Loading required package: Matrix
Loading required package: secr
This is secr 2.10.3. For overview type ?secr
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BBRecapture/quant.binary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: quant.binary
> ### Title: Quantification of binary capture histories
> ### Aliases: quant.binary quant.binary.markov quant.binary.integer
> ###   quant.binary.counts quant.binary.counts.integer
> ### Keywords: Partial capture history quantification
> 
> ### ** Examples
> 
> ## Example of quantification with character input
> 
> capt.hist="0110"
> 
> quant.binary(capt.hist)
[1] 0.4
> quant.binary.markov(capt.hist,markov.ord=2)
[1] 0.3870968
> quant.binary.integer(capt.hist)
[1] 6
> quant.binary.counts(capt.hist)
[1] 0.5
> quant.binary.counts.integer(capt.hist)
[1] 2
> 
> ## Example of quantification with numeric input
> 
> ch=c(0,1,1,0)
> 
> quant.binary(ch)
[1] 0.4
> quant.binary.markov(ch,markov.ord=2)
[1] 0.3870968
> quant.binary.integer(ch)
[1] 6
> quant.binary.counts(ch)
[1] 0.5
> quant.binary.counts.integer(ch)
[1] 2
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>