R Under development (unstable) (2024-08-21 r87038 ucrt) -- "Unsuffered Consequences"
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Platform: x86_64-w64-mingw32/x64

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> ## require("DoseFinding")
> 
> ## ## commented out for time reasons
> 
> ## resp <- c(1.23, 1.31, 1.32, 1.36, 1.38)
> ## dose <- c(0, 1.25, 2.5, 5, 10)
> ## sdev <- c(0.015, 0.014, 0.015, 0.016, 0.015)
> ## V <- diag(sdev^2)
> ## mods <- Mods(emax=c(2.65, 12.5), linear=NULL, linInt = c(1, 1, 1, 1),
> ##              logistic=c(29, 9.55), quadratic = -0.0075,
> ##              doses=dose)
> ## mmfit <- MCPMod(dose, resp, S=V, type="general", models=mods, Delta=0.12)
> ## efit <- mmfit$mods$emax
> ## plot(efit, plotData = "meansCI", CI=TRUE)
> ## plot(efit, plotData = "meansCI", CI=FALSE)
> ## ## plot(efit, plotData = "raw") # should throw an error
> ## plot(efit, plotData = "means", CI = TRUE)
> ## plot(efit, plotData = "means", CI = FALSE)
> ## plot(efit, plotData = "none", CI =TRUE)
> ## plot(efit, plotData = "none", CI =FALSE)
> 
> ## plot(mmfit, plotData = "meansCI", CI=TRUE)
> ## plot(mmfit, plotData = "meansCI", CI=FALSE)
> ## ## plot(mmfit, plotData = "raw") # should throw an error
> ## plot(mmfit, plotData = "means", CI = TRUE)
> ## plot(mmfit, plotData = "means", CI = FALSE)
> ## plot(mmfit, plotData = "none", CI =TRUE)
> ## plot(mmfit, plotData = "none", CI =FALSE)
> 
> ## data(IBScovars)
> ## models <- Mods(emax = c(0.5, 1), betaMod=c(1,1), linear = NULL, doses=c(0,4))
> ## mmfit <- MCPMod(dose, resp, data=IBScovars, models=models, Delta=0.12)
> ## efit <- mmfit$mods$emax
> ## plot(efit, plotData = "meansCI", CI=TRUE)
> ## plot(efit, plotData = "meansCI", CI=FALSE)
> ## plot(efit, plotData = "raw", CI=FALSE)
> ## plot(efit, plotData = "raw", CI=TRUE)
> ## plot(efit, plotData = "means", CI = TRUE)
> ## plot(efit, plotData = "means", CI = FALSE)
> ## plot(efit, plotData = "none", CI =TRUE)
> ## plot(efit, plotData = "none", CI =FALSE)
> 
> ## plot(mmfit, plotData = "meansCI", CI=TRUE)
> ## plot(mmfit, plotData = "meansCI", CI=FALSE)
> ## plot(mmfit, plotData = "raw", CI=TRUE)
> ## plot(mmfit, plotData = "raw", CI=FALSE)
> ## plot(mmfit, plotData = "means", CI = TRUE)
> ## plot(mmfit, plotData = "means", CI = FALSE)
> ## plot(mmfit, plotData = "none", CI =TRUE)
> ## plot(mmfit, plotData = "none", CI =FALSE)
> 
> ## data(IBScovars)
> ## models <- Mods(emax = c(0.5, 1), betaMod=c(1,1), linInt = c(1, 1, 1, 1),
> ##                linear = NULL, doses=0:4)
> ## anovaMod <- lm(resp~factor(dose)+gender, data=IBScovars)
> ## drFit <- coef(anovaMod)[2:5] # placebo adjusted estimates at doses
> ## vCov <- vcov(anovaMod)[2:5,2:5]
> ## dose <- sort(unique(IBScovars$dose))[-1]
> ## mmfit <- MCPMod(dose, drFit, S=vCov, type = "general", models=models, Delta=0.12, placAdj=TRUE)
> ## efit <- mmfit$mods$emax
> ## plot(efit, plotData = "meansCI", CI=TRUE)
> ## plot(efit, plotData = "meansCI", CI=FALSE)
> ## ## plot(efit, plotData = "raw", CI=FALSE) # should throw an error
> ## ## plot(efit, plotData = "raw", CI=TRUE) # should throw an error
> ## plot(efit, plotData = "means", CI = TRUE)
> ## plot(efit, plotData = "means", CI = FALSE)
> ## plot(efit, plotData = "none", CI =TRUE)
> ## plot(efit, plotData = "none", CI =FALSE)
> 
> ## plot(mmfit, plotData = "meansCI", CI=TRUE)
> ## plot(mmfit, plotData = "meansCI", CI=FALSE)
> ## ## plot(mmfit, plotData = "raw", CI=TRUE) # should throw an error
> ## ## plot(mmfit, plotData = "raw", CI=FALSE) # should throw an error
> ## plot(mmfit, plotData = "means", CI = TRUE)
> ## plot(mmfit, plotData = "means", CI = FALSE)
> ## plot(mmfit, plotData = "none", CI =TRUE)
> ## plot(mmfit, plotData = "none", CI =FALSE)
> 
> ## ## neurodeg example (in 0.9-6 not all means were visible)
> ## doses <- c(0,1,3,10,30)
> ## muH  <- c(-5.099, -4.581, -3.22, -2.879, -3.52)     # estimated slope
> ## covH <- structure(c(0.149, 0.009, 0.009, 0.009, 0.009, 0.009, 0.149, 
> ##                     0.009, 0.009, 0.009, 0.009, 0.009, 0.149, 0.009,
> ##                     0.009, 0.009, 0.009, 0.009, 0.149, 0.009, 0.009,
> ##                     0.009, 0.009, 0.009, 0.149), .Dim = c(5L, 5L))
> ## fit <- fitMod(doses, muH, S=covH, model="emax", type = "general")
> ## plot(fit, plotData="meansCI", CI=TRUE)
> 
> 
> proc.time()
   user  system elapsed 
   0.15    0.09    0.21