BP_FitBayesianCompactness {BoneProfileR}R Documentation

Estimation of Bayesian model of a bone section

Description

Estimation of Bayesian model of a bone section.

Usage

BP_FitBayesianCompactness(
  bone = stop("A result from BP_FitMLCompactness() must be provided"),
  priors = NULL,
  n.iter = 10000,
  n.chains = 1,
  n.adapt = 100,
  thin = 1,
  analysis = 1,
  silent = TRUE
)

Arguments

bone

The bone image to be used

priors

Priors

n.iter

Number of iterations

n.chains

Number of chains

n.adapt

Number of iteration to adapt

thin

Thin parameter for analysis

analysis

Name or rank of analysis

silent

Should some information must me shown ?

Details

BP_FitBayesianCompactness estimates Bayesian model of a bone section

Value

The -Ln L

Author(s)

Marc Girondot marc.girondot@gmail.com

See Also

Other BoneProfileR: BP_AutoFit(), BP_ChooseBackground(), BP_ChooseCenter(), BP_ChooseForeground(), BP_DetectBackground(), BP_DetectCenters(), BP_DetectForeground(), BP_DuplicateAnalysis(), BP_EstimateCompactness(), BP_FitMLCompactness(), BP_FitMLRadialCompactness(), BP_GetFittedParameters(), BP_ListAnalyses(), BP_LnLCompactness(), BP_OpenImage(), BP_Report(), Erinaceus_europaeus, plot.BoneProfileR(), summary.BoneProfileR()

Examples

## Not run: 
# Not run:
 library(BoneProfileR)
 path_Hedgehog <- system.file("extdata", "Erinaceus_europaeus_fem_2-1_small.png", 
                             package = "BoneProfileR")
 bone <- BP_OpenImage(file=path_Hedgehog)
 bone <- BP_DetectBackground(bone=bone, analysis="logistic")
 bone <- BP_DetectForeground(bone=bone, analysis="logistic")
 bone <- BP_DetectCenters(bone=bone, analysis="logistic")
 bone <- BP_EstimateCompactness(bone, analysis="logistic")
 bone <- BP_FitMLCompactness(bone, analysis="logistic")
 plot(bone)
 plot(bone, type="observations")
 plot(bone, type="observations+model", analysis=1)
 fittedpar <- BP_GetFittedParameters(bone, analysis="logistic")
 bone <- BP_DuplicateAnalysis(bone, from="logistic", to="flexit")
 bone <- BP_FitMLCompactness(bone, 
                fitted.parameters=c(fittedpar, K1=1, K2=1), 
                fixed.parameters=NULL, analysis="flexit")
 compare_AIC(Logistic=BP_GetFittedParameters(bone, analysis="logistic", alloptim=TRUE), 
             Flexit=BP_GetFittedParameters(bone, analysis="flexit", alloptim=TRUE))
 out4p <- plot(bone, type="observations+model", analysis="logistic")
 out6p <- plot(bone, type="observations+model", analysis="flexit")
 bone <- BP_FitBayesianCompactness(bone, analysis="logistic")
 plot(bone, type="observations+model", CI="MCMC", analysis="logistic")
 bone <- BP_FitBayesianCompactness(bone, analysis="flexit")
 plot(bone, type="observations+model", CI="MCMC", analysis="flexit")

## End(Not run)

[Package BoneProfileR version 2.4 Index]