BoneProfileR (version 4.0)

summary.BoneProfileR: Plot a bone section

Description

Display information of bone section

Usage

# S3 method for BoneProfileR
summary(
  object,
  analysis = 1,
  periodic.angles = "all",
  periodic.angles.replicate.CI = 2000,
  ...
)

Value

An invisible list with recorded information

Arguments

object

The bone image

analysis

The analysis to report the compactness

periodic.angles

A vector indicating which angle to report for periodic analysis

periodic.angles.replicate.CI

Number of replicates to estimate CI

...

Not used

Author

Marc Girondot

Details

summary.BoneProfileR displays 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_FitBayesianCompactness(), BP_FitBayesianPeriodicCompactness(), BP_FitMLCompactness(), BP_FitMLPeriodicCompactness(), BP_FitMLRadialCompactness(), BP_GetFittedParameters(), BP_ListAnalyses(), BP_LnLCompactness(), BP_OpenImage(), BP_Report(), Erinaceus_europaeus, plot.BoneProfileR()

Examples

if (FALSE) {
# Not run:
library(BoneProfileR)
 bone <- BP_OpenImage()
 # or 
 path_Hedgehog <- system.file("extdata", "Erinaceus_europaeus_fem_2-1_small.png", 
                             package = "BoneProfileR")
 bone <- BP_OpenImage(file=path_Hedgehog)
 summary(bone)
 
 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", cut.angle = 60)
 bone <- BP_FitMLCompactness(bone, analysis="logistic", twosteps=TRUE)
 plot(bone, type="observations+model", analysis="logistic")
 par <- BP_GetFittedParameters(bone, analysis="logistic", ML=TRUE, return.all=FALSE)[, "mean"]
 options(mc.cores=parallel::detectCores())
 
 #############################################
 # Periodic analysis
 #############################################
 bone <- BP_FitMLPeriodicCompactness(bone, analysis="logistic", control.optim=list(trace=2), 
                                     fitted.parameters=c(par, PSin=0.001, PCos=0.001, 
                                     SSin=0.001, SCos=0.001, MinSin=0.001, MinCos=0.001, 
                                     MaxSin=0.001, MaxCos=0.001), replicates.CI=2000)
 bone <- BP_FitBayesianPeriodicCompactness(bone, analysis="logistic", replicates.CI=2000)
 
 summary(object=bone, analysis="logistic")
 summary(object=bone, analysis="logistic", 
         periodic.angles=seq(from=-0.1, to=0.1, length.out=10))
}