R Under development (unstable) (2024-08-21 r87038 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("DoseFinding")
Loading required package: DoseFinding
> ########################################################################
> #### multContTest
> # functions to sample random DF data
> getDosSampSiz <- function(){
+   # generate dose levels
+   mD <- runif(1, 0, 1500)
+   nD <- max(rpois(1, 5), 4)
+   p <- rgamma(nD, 3)
+   p <- cumsum(p/sum(p))
+   doses <- signif(c(0, mD*p), 3)
+   # sample size allocations
+   totSS <- rpois(1, rexp(1, 1/250))
+   totSS <- max(totSS, 50)
+   p <- rgamma(nD+1, 3);p <- p/sum(p)
+   n <- round(p*totSS)
+   n[n==0] <- rpois(sum(n==0), 1)+1
+   list(doses=doses, n=n)
+ }
> getDFdataSet <- function(doses, n){
+   ll <- getDosSampSiz()
+   e0 <- rnorm(1, 0, 10)
+   eMax <- rgamma(1, abs(e0)*0.5, 0.5)*I(runif(1)<0.25)
+   if(eMax > 0){ sig <- eMax/runif(1, 0.5, 5)}
+   else { sig <- rgamma(1, abs(e0)*0.5, 0.5) }
+   dosVec <- rep(ll$doses, ll$n)
+   if(runif(1)<0.3){
+     mnVec <- betaMod(dosVec, e0=e0, eMax=eMax, delta1=runif(1, 0.5, 5),
+                      delta2=runif(1, 0.5, 5), scal=1.2*max(ll$doses))
+   } else {
+     mnVec <- logistic(dosVec, e0 = e0, eMax = eMax,
+                       ed50=runif(1, 0.05*max(ll$doses), 1.5*max(ll$doses)),
+                       delta=runif(1, 0.5, max(ll$doses)/2))
+   }
+   resp <- rnorm(sum(ll$n), mnVec, sig)
+   N <- sum(ll$n)
+   cov1 <- as.factor(rpois(N, 5))
+   cov2 <- runif(N, 1, 100)
+   aa <- data.frame(x= dosVec, y=resp, cov1=cov1, cov2=cov2)
+   aa[sample(1:nrow(aa)),]  
+ }
> 
> #### simulate data
> set.seed(10)
> dd <- getDFdataSet()
> bet <- guesst(0.9*max(dd$x), p=0.8, "betaMod", scal = 1.2*max(dd$x),
+               dMax = 0.7*max(dd$x), Maxd = max(dd$x))
> sE <- guesst(c(0.5*max(dd$x), 0.7*max(dd$x)) , p=c(0.5, 0.9), "sigEmax")
> models <- Mods(linear = NULL, betaMod = bet, sigEmax = sE,
+                doses = sort(unique(dd$x)),
+                addArgs=list(scal = 1.2*max(dd$x)))
> obj <- MCPMod(x,y, dd, models=models, addCovars = ~cov1+cov2, alpha=0.05, Delta=0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> obj <- MCPMod(dd$x,dd$y, models=models, alpha=0.05, Delta=0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> #### different model set
> set.seed(10)
> dd <- getDFdataSet()
> mD <- max(dd$x)
> lg1 <- guesst(c(0.3*mD, 0.4*mD), c(0.3, 0.9), "logistic")
> lg2 <- guesst(c(0.3*mD, 0.4*mD), c(0.3, 0.5), "logistic")
> expo <- guesst(c(0.9*mD), c(0.7), "exponential", Maxd=mD)
> quad <- guesst(c(0.6*mD), c(1), "quadratic")
> models <- Mods(linlog = NULL, logistic = rbind(lg1, lg2),
+                    exponential = expo, quadratic = quad,
+                    doses = sort(unique(dd$x)), addArgs=list(off = 0.2*max(dd$x)))
> 
> obj <- MCPMod(x,y, dd, models=models, addCovars = ~cov1+cov2, alpha = 0.2, Delta=0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> obj <- MCPMod(dd$x,dd$y, models=models, addCovars = ~1, alpha = 0.2, Delta=0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> ########################################################################
> #### some binary test cases
> getDFdataSet.bin <- function(doses, n){
+   ll <- getDosSampSiz()
+   ll$n <- ll$n+10
+   e0 <- rnorm(1, 0, sqrt(3.28))
+   eMax <- rnorm(1, 0, 5)
+   dosVec <- rep(ll$doses, ll$n)
+   if(runif(1)<0.3){
+     mn <- betaMod(dosVec, e0 = e0, eMax = eMax, delta1=runif(1, 0.5, 5),
+                   delta2=runif(1, 0.5, 5), scal=1.2*max(ll$doses))
+   } else {
+     mn <- logistic(dosVec, e0 = e0,
+                    eMax = eMax, ed50=runif(1, 0.05*max(ll$doses), 1.5*max(ll$doses)),
+                    delta=runif(1, 0.5, max(ll$doses)/2))
+   }
+   resp <- rbinom(length(ll$n), ll$n, 1/(1+exp(-mn)))
+   aa <- data.frame(dose = ll$doses, resp = resp)    
+   aa <- data.frame(x= aa$dose, y=aa$resp/ll$n, n=ll$n)
+   aa[sample(1:nrow(aa)),]  
+ }
> 
> set.seed(1909)
> dd <- getDFdataSet.bin()
> bet <- guesst(0.9*max(dd$x), p=0.8, "betaMod", scal = 1.2*max(dd$x), dMax = 0.7*max(dd$x),
+               Maxd = max(dd$x))
> sE <- guesst(c(0.5*max(dd$x), 0.7*max(dd$x)) , p=c(0.5, 0.9), "sigEmax")
> models <- Mods(linear = NULL, betaMod = bet, sigEmax = sE,
+                    doses = sort(unique(dd$x)), addArgs=list(scal = 1.2*max(dd$x)))
> logReg <- glm(y~as.factor(x)-1, family=binomial, data=dd, weights = n)
> dePar <- coef(logReg)
> vCov <- vcov(logReg)
> dose <- sort(unique(dd$x))
> obj <- MCPMod(dose, dePar, S=vCov, models=models, type="general",
+                df=Inf, alpha = 0.3, Delta = 0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> set.seed(1997)
> dd <- getDFdataSet.bin()
> bet <- guesst(0.9*max(dd$x), p=0.8, "betaMod", scal = 1.2*max(dd$x),
+               dMax = 0.7*max(dd$x), Maxd = max(dd$x))
> sE <- guesst(c(0.5*max(dd$x), 0.7*max(dd$x)) , p=c(0.5, 0.9), "sigEmax")
> models <- Mods(linear = NULL, betaMod = bet, sigEmax = sE,direction = "decreasing",
+                    addArgs=list(scal = 1.2*max(dd$x)), doses = sort(unique(dd$x)))
> logReg <- glm(y~as.factor(x)-1, family=binomial, data=dd, weights = n)
> dePar <- coef(logReg)
> vCov <- vcov(logReg)
> dose <- sort(unique(dd$x))
> obj <- MCPMod(dose, dePar, S=vCov, models=models, type = "general",
+                pVal = TRUE, df=Inf, alpha = 0.2, Delta = 0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> set.seed(1)
> dd <- getDFdataSet.bin()
> bet <- guesst(0.9*max(dd$x), p=0.8, "betaMod", scal = 1.2*max(dd$x),
+               dMax = 0.7*max(dd$x), Maxd = max(dd$x))
> sE <- guesst(c(0.5*max(dd$x), 0.7*max(dd$x)) , p=c(0.5, 0.9), "sigEmax")
> models <- Mods(linear = NULL, betaMod = bet, sigEmax = sE,
+                    doses = sort(unique(dd$x)), addArgs=list(scal = 1.2*max(dd$x)))
> logReg <- glm(y~as.factor(x)-1, family=binomial, data=dd, weights = n)
> dePar <- coef(logReg)
> vCov <- vcov(logReg)
> dose <- sort(unique(dd$x))
> obj <- MCPMod(dose, dePar, S=vCov, models=models, type = "general",
+                pVal = T, df=Inf, alpha = 0.4, Delta = 0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> ########################################################################
> ## placebo-adjusted scale
> ## two blocks below should give equal results
> data(IBScovars)
> modlist <- Mods(emax = 0.05, linear = NULL, 
+                 linInt = c(0, 1, 1, 1), doses = c(0, 1, 2, 3, 4))
> ancMod <- lm(resp~factor(dose)+gender, data=IBScovars)
> drEst <- coef(ancMod)[2:5]
> vc <- vcov(ancMod)[2:5, 2:5]
> doses <- (1:4)
> obj <- MCPMod(doses, drEst, S = vc, models = modlist, placAdj = TRUE,
+               type = "general", df = Inf, Delta=0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> ## now unordered
> ord <- c(3,4,1,2)
> drEst2 <- drEst[ord]
> vc2 <- vc[ord,ord]
> doses2 <- doses[ord]
> obj <- MCPMod(doses2, drEst2, S = vc2, models = modlist, placAdj = TRUE,
+               type = "general", df = Inf, Delta = 0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> ## unadjusted scale
> ## two blocks below should give equal results
> ancMod <- lm(resp~factor(dose)-1, data=IBScovars)
> drEst <- coef(ancMod)
> vc <- vcov(ancMod)
> doses <- 0:4
> obj <- MCPMod(doses, drEst, S = vc, models = modlist,
+               type = "general", df = Inf, Delta = 0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> ord <- c(3,4,1,2,5)
> drEst2 <- drEst[ord]
> vc2 <- vc[ord,ord]
> doses2 <- doses[ord]
> obj <- MCPMod(doses2, drEst2, S = vc2, models = modlist,
+               type = "general", df = Inf, Delta = 0.5)
> plot(obj, plotData="meansCI", CI=TRUE)
> 
> proc.time()
   user  system elapsed 
   2.87    0.32    3.20