R Under development (unstable) (2024-08-21 r87038 ucrt) -- "Unsuffered Consequences"
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> ## ## commented out for time-reasons
> 
> ## ################################################################################
> ## ## test 1: "validation" using fitMod and vcov.DRMod and predict.DRMod
> ## model <- "emax"
> ## sigma <- 1
> ## n <- c(100,50,50,50,100)
> ## doses <- c(0,10,20,40,50)
> ## cf <- c(0,1,10)
> ## V <- DoseFinding:::aprCov(doses, model, cf, S=diag(1/n))
> ## DoseFinding:::getPredVar(model, cf, V=V, pDose=50)
> 
> ## ## now validation using the formulas in fitMod
> ## doseVec <- rep(doses, n)
> ## respVec <- rnorm(length(doseVec))
> ## dd <- fitMod(doseVec, respVec, model="emax")
> ## ## now change to achieve desired values
> ## dd$coefs <- cf
> ## dd$df <- dd$RSS <- sum(n)
> ## vcov(dd)
> ## predict(dd, predType = "effect-curve", doseSeq=50, se.fit=TRUE)$se.fit^2
> 
> ## ################################################################################
> ## ## test 2: "validation" using simulation
> ## model <- "emax"
> ## sigma <- 1
> ## ## select very large sample size (to validate asymptotics)
> ## n <- c(100000, 50000, 50000, 50000, 100000)
> ## n <- c(100, 50, 50, 50, 100)
> ## doses <- c(0,10,20,40,50)
> ## cf <- c(0,0.4,10)
> ## Delta <- 0.2
> 
> ## V <- DoseFinding:::aprCov(doses, model, cf, S=diag(0.3^2/n))
> ## tdvar <- DoseFinding:::getTDVar(model, cf, V=V, Delta=Delta, scale = "unrestricted")
> ## edvar <- DoseFinding:::getEDVar(model, cf, V=V, p=0.5, maxD=50, scale = "unrestricted")
> ## pavar <-  DoseFinding:::getPredVar(model, cf, V=V, pDose=50)
> ## tdvart <- DoseFinding:::getTDVar(model, cf, V=V,scale = "log", Delta=Delta)
> ## edvart <- DoseFinding:::getEDVar(model, cf, V=V,scale = "logit", p=0.5, maxD=50)
> 
> ## ## simulation
> ## mn <- emax(doses, cf[1], cf[2], cf[3])
> ## doseVec <- rep(doses, n)
> ## mnVec <- rep(mn, n)
> ## td <- pl <- ed <- numeric(10000)
> ## for(i in 1:10000){
> ##   respVec <- mnVec + rnorm(length(mnVec),0,0.3)
> ##   ff <- fitMod(doseVec, respVec, model="emax", bnds = c(0.05, 75))
> ##   ed[i] <- ED(ff, p=0.5)
> ##   td[i] <- TD(ff, Delta = Delta)
> ##   pl[i] <- predict(ff, doseSeq=50, predType = "effect-curve")
> ##   pb <- txtProgressBar(min=1, max=1000, char="*", width = 20, style = 3)
> ##   setTxtProgressBar(pb, i)
> ## }
> ## cat("\n")
> 
> 
> ## mm <- Mods(emax=cf[3], doses=doses, placEff=0, maxEff=emax(50,cf[1],cf[2],cf[3]))
> ## edt <- ED(mm, p=0.5)
> ## edt7 <- ED(mm, p=0.7)
> ## edt3 <- ED(mm, p=0.3)
> ## tdt <- TD(mm, Delta=Delta)
> ## hist(td[td < 100], freq=FALSE, breaks = 21)
> ## curve(dnorm(x, tdt, sqrt(tdvar)), add=TRUE)
> ## hist(ed, freq=FALSE, breaks = 101)
> ## curve(dnorm(x, edt, sqrt(edvar)), add=TRUE)
> ## hist(pl, freq=FALSE, breaks = 21)
> ## curve(dnorm(x, emax(50,cf[1],cf[2],cf[3]), sqrt(pavar)), add=TRUE)
> 
> ## hist(td[td < 100], freq=FALSE, breaks = 101)
> ## curve(dlnorm(x, log(tdt), sqrt(tdvart)), add=TRUE)
> ## hist(ed, freq=FALSE, breaks = 101)
> ## ## plot against logit-normal distribution
> 
> ## mean(ed < edt7 & ed > edt3)
> ## pnorm(edt7, edt, sqrt(edvar))-pnorm(edt3, edt, sqrt(edvar))
> 
> ## ################################################################################
> ## ## test 3: study example
> ## nSim <- 100
> ## doses <- c(0,1,3,10,30,50,75,150,300,450)
> ## n <- c(100,rep(38,8),100)
> ## sigma <- 380
> ## mm <- Mods(sigEmax = rbind(c(100,6),c(170,4), c(80,3), c(290,5)),
> ##            emax = c(5,20,50,120), linear=NULL, doses=doses,
> ##            placEff=0, maxEff=150)
> 
> ## model <- "sigEmax"
> ## pp <- planMod(model, mm, n, sigma, doses=doses,
> ##               simulation = TRUE, cores = 4,
> ##               alpha = 0.025, nSim = nSim,
> ##               p = 0.5, pLB = 0.25, pUB = 0.75)
> ## print(pp)
> ## summary(pp, Delta = 130, p = 0.5)
> ## plot(pp)
> ## plot(pp, type="ED", 0.5)
> ## plot(pp, type="TD", Delta = 130, direction = "increasing")
> 
> ## model <- "emax"
> ## pp <- planMod(model, mm, n, sigma, doses=doses,
> ##               simulation = TRUE, cores = 4,
> ##               alpha = 0.025, 
> ##               p = 0.5, pLB = 0.25, pUB = 0.75)
> 
> ## model <- "linear"
> ## pp <- planMod(model, mm, n, sigma, doses=doses,
> ##               simulation = TRUE, cores = 4,
> ##               alpha = 0.025, nSim = nSim,
> ##               p = 0.5, pLB = 0.25, pUB = 0.75)
> 
> ## ## now model selection
> ## model <- c("sigEmax", "emax")
> ## pp1 <- planMod(model, mm, n, sigma, doses=doses, asyApprox = FALSE,
> ##               simulation = TRUE,  cores = 4,
> ##               alpha = 0.025, nSim = nSim,
> ##               p = 0.5, pLB = 0.25, pUB = 0.75)
> ## print(pp1)
> ## summary(pp1)
> ## plot(pp1)
> ## plot(pp1, type="ED", 0.5)
> ## plot(pp1, type="TD", Delta = 130, direction = "increasing")
> 
> 
> ## ## ################################################################################
> ## ## ## test 4: study example
> ## doses <- c(0,10,25,50,100,150)
> ## fmodels <- Mods(linear = NULL, emax = 25,
> ##                 logistic = c(50, 10.88111), exponential= 85,
> ##                 betaMod=rbind(c(0.33,2.31),c(1.39,1.39)),
> ##                 doses = doses, addArgs=list(scal = 200),
> ##                 placEff = 0, maxEff = 0.4)
> ## sigma <- 1
> ## n <- rep(62, 6)*2
> 
> ## ## use all models not used previously
> ## model <- c("linear", "quadratic", "exponential", "betaMod", "logistic", "linlog")
> ## altb <- defBnds(200)
> ## pp <- planMod(model, fmodels, n, sigma, doses=doses,
> ##               asyApprox = FALSE, simulation = TRUE, cores = 4,
> ##               alpha = 0.025, nSim = nSim, bnds=altb,
> ##               p = 0.5, pLB = 0.25, pUB = 0.75)
> ## pp
> ## summary(pp, p = 0.5, Delta = 0.3)
> ## plot(pp)
> ## plot(pp, type = "TD", Delta=0.3, direction = "i")
> ## plot(pp, type = "ED", p = 0.5)
> 
> ## ########################################################################
> ## ## test 5: C's example
> ## models <- Mods(linear = NULL, linlog = NULL, emax = c(8, 10),
> ##                sigEmax = c(10, 2),
> ##                doses = c(0, 10,20, 50, 100),
> ##                placEff=0, maxEff=-2)
> ## pObj <- planMod("sigEmax",models,n=100,sigma=1.2,
> ##                 simulation=TRUE,nSim=100, cores=4)
> ## summary(pObj,Delta=-1.1) ## this should fail
> ## summary(pObj,Delta=1.1)
> ## plot(pObj)
> ## plot(pObj, type = "TD", Delta=-1.1) ## this should fail
> ## plot(pObj, type = "TD", Delta=1.1)
> ## plot(pObj, type = "ED", p=0.5)
> 
> proc.time()
   user  system elapsed 
   0.14    0.07    0.20