summary.BoneProfileR {BoneProfileR} | R Documentation |
Plot a bone section
Description
Display information of bone section
Usage
## S3 method for class 'BoneProfileR'
summary(
object,
analysis = 1,
periodic.angles = "all",
periodic.angles.replicate.CI = 2000,
...
)
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 |
Details
summary.BoneProfileR displays a bone section
Value
An invisible list with recorded information
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_FitBayesianCompactness()
,
BP_FitBayesianPeriodicCompactness()
,
BP_FitMLCompactness()
,
BP_FitMLPeriodicCompactness()
,
BP_FitMLRadialCompactness()
,
BP_GetFittedParameters()
,
BP_ListAnalyses()
,
BP_LnLCompactness()
,
BP_OpenImage()
,
BP_Report()
,
Erinaceus_europaeus
,
plot.BoneProfileR()
Examples
## Not run:
# 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))
## End(Not run)