BP_Report {BoneProfileR}R Documentation

Generate a pdf report for the analyzed bone

Description

Generate a docx, xlsx, or pdf report.

Usage

BP_Report(
  bone = stop("A bone section must be provided"),
  control.plot = list(message = NULL, show.centers = TRUE, show.colors = TRUE, show.grid
    = TRUE, CI = "ML", show.legend = TRUE),
  analysis = 1,
  docx = file.path(getwd(), "report.docx"),
  pdf = file.path(getwd(), "report.pdf"),
  xlsx = file.path(getwd(), "report.xlsx"),
  author = NULL,
  title = attributes(bone)$name
)

Arguments

bone

The bone image

control.plot

A list with the parameters used for plot

analysis

Indicate analysis name or rank that you want report

docx

Name of Word file

pdf

Name of pdf file

xlsx

Name of Excel file

author

Name indicated in the report

title

Title of the report

Details

BP_Report save a pdf report for the analyzed bone

Value

Nothing

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_FitMLCompactness(), BP_FitMLRadialCompactness(), BP_GetFittedParameters(), BP_ListAnalyses(), BP_LnLCompactness(), BP_OpenImage(), 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")
 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))
 bone <- BP_FitMLRadialCompactness(bone, analysis="logistic")
 # Test using the change of orientation using default.angle from BP_EstimateCompactness():
 bone <- BP_DuplicateAnalysis(bone, from="logistic", to="logistic_rotation_pi")
 # With a pi rotation, the top moves to the bottom and the left moves to the right
 bone <- BP_EstimateCompactness(bone, rotation.angle=pi, analysis="logistic_rotation_pi")
 bone <- BP_FitMLRadialCompactness(bone, analysis="logistic_rotation_pi")
 BP_Report(bone=bone, 
           analysis=1,
           docx=NULL, 
           pdf=NULL, 
           xlsx=file.path(getwd(), "report.xlsx"), 
           author="Marc Girondot", 
           title=attributes(bone)$name)
           
 BP_Report(bone=bone, 
           analysis=1,
           docx=NULL, 
           pdf=file.path(getwd(), "report.pdf"), 
           xlsx=NULL, 
           author="Marc Girondot", 
           title=attributes(bone)$name)
           
 BP_Report(bone=bone, 
           analysis=1,
           docx=file.path(getwd(), "report.docx"), 
           pdf=NULL, 
           xlsx=NULL, 
           author="Marc Girondot", 
           title=attributes(bone)$name)

## End(Not run)

[Package BoneProfileR version 2.4 Index]