# Generate a pdf report for the analyzed bone Generate a docx, xlsx, or pdf report. In the xlsx report, the observed compactness is simply the ratio of the number of mineralized pixels to the number of total pixels. The corrected modelled compactness is the compactness if the bone had the same number of pixels in the centre as on the periphery So it's a compactness that corrects for the shape of the bone. ```r 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 ## Returns Nothing ## Details BP_Report save a pdf report for the analyzed bone ## Examples ```r ## 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", ML=TRUE, return.all = FALSE)[, "mean"] 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", ML=TRUE, return.all = TRUE), Flexit=BP_GetFittedParameters(bone, analysis="flexit", ML=TRUE, return.all = 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") # Periodic analysis par <- BP_GetFittedParameters(bone, analysis="logistic", ML=TRUE, return.all = FALSE)[, "mean"] options(mc.cores=parallel::detectCores()) 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) 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) ``` ## 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()`, `Erinaceus_europaeus`, `plot.BoneProfileR()`, `summary.BoneProfileR()` ## Author(s) Marc Girondot marc.girondot@gmail.com

BP_Report function