BoneProfileR (version 3.1)

BP_FitBayesianCompactness: 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
)

Value

The -Ln L

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 ?

Author

Marc Girondot

Details

BP_FitBayesianCompactness estimates Bayesian model of a bone section

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

if (FALSE) {
# 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")
}