R Under development (unstable) (2024-03-22 r86169 ucrt) -- "Unsuffered Consequences"
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> # This file is part of the standard setup for testthat.
> # It is recommended that you do not modify it.
> #
> # Where should you do additional test configuration?
> # Learn more about the roles of various files in:
> # * https://r-pkgs.org/testing-design.html#sec-tests-files-overview
> # * https://testthat.r-lib.org/articles/special-files.html
> 
> library(testthat)
> library(TCPMOR)
> 
> # Generate simulated data dataC
> dataC <- createData(200)
> 
> # Fit the semi-parametric model
> spm.fit <- fitSemiParamModel(dataC)
iteration 1
iteration 2
iteration 3
iteration 4
iteration 5
> plot(spm.fit,ylab = "lnOR",xlab = "age",shade = FALSE)
> summary(spm.fit)


Summary for non-linear components:

                df  spar knots
f(dataC$age) 2.849 53.19    39

Note this includes 1 df for the intercept.


> 
> # Find two cut-off points
> dataC <- findCutoffs(spm.fit, dataC)
> 
> # Calculate the two cut-off points after limiting sensitivity se and specificity sp
> result <- calculateCutoffs(dataC)
> cutoffs <- result$cutoffs
> dataC2 <- result$filteredData
> print(cutoffs)
[1] 32.00421 64.42158
> 
> # Discretize age variable based on the two cutoffs
> dataC2 <- discretizeAge(dataC2, cutoffs)
> 
> # Fitting logistic regression models and obtaining OR values and 95% confidence intervals
> OR_Results <- fitLogisticRegression(dataC2)
> print(round(OR_Results, 3))
               OR 2.5 % 97.5 %
(Intercept) 0.333 0.035  3.205
age_p       3.474 0.354 34.093
> 
> proc.time()
   user  system elapsed 
   1.21    0.17    1.37