View source: R/BP_FitBayesianCompactness.R
BP_FitBayesianCompactness | R Documentation |
Estimation of Bayesian model of a bone section.
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 )
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 ? |
BP_FitBayesianCompactness estimates Bayesian model of a bone section
The -Ln L
Marc Girondot marc.girondot@gmail.com
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()
## 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)
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