| 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)