R/iBMA.surv.R

In hanase/BMA: Bayesian Model Averaging

iBMA.surv<- function(x, ...)
UseMethod("iBMA.surv")

iBMA.surv.data.frame <-
function (x, surv.t, cens, wt = rep(1, nrow(X)), thresProbne0 = 5, 
    maxNvar = 30, nIter = 100, verbose = FALSE, sorted = FALSE, 
    factor.type = TRUE, ...) 
{
    printCGen <- function(printYN) {
        printYN <- printYN
        return(function(x) if (printYN) cat(paste(paste(x, sep = "", 
            collapse = " "), "\n", sep = "")))
    }


# CF namespcae unlock from https://gist.github.com/wch/3280369
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

inc <- '
/* This is taken from envir.c in the R 2.15.1 source
https://github.com/SurajGupta/r-source/blob/master/src/main/envir.c
*/
#define FRAME_LOCK_MASK (1<<14)
#define FRAME_IS_LOCKED(e) (ENVFLAGS(e) & FRAME_LOCK_MASK)
#define UNLOCK_FRAME(e) SET_ENVFLAGS(e, ENVFLAGS(e) & (~ FRAME_LOCK_MASK))
'
 
src <- '
if (TYPEOF(env) == NILSXP)
error("use of NULL environment is defunct");
if (TYPEOF(env) != ENVSXP)
error("not an environment");
 
UNLOCK_FRAME(env);
 
// Return TRUE if unlocked; FALSE otherwise
SEXP result = PROTECT( Rf_allocVector(LGLSXP, 1) );
LOGICAL(result)[0] = FRAME_IS_LOCKED(env) == 0;
UNPROTECT(1);
 
return result;
'

unlockEnvironment <- cfunction(signature(env = "environment"),
includes = inc,
body = src)
    
    nsEnv <- asNamespace('BMA')
    unlockEnvironment(nsEnv)
    nsEnv$glob <- function() {
        utils::globalVariables(parent.env(environment()))
    }
    environment(nsEnv$glob) <- nsEnv
    pkgEnv <- as.environment('package:BMA')
    unlockEnvironment(pkgEnv)
    pkgEnv$glob <- nsEnv$glob
    exportEnv <- nsEnv$.__NAMESPACE__.$exports
    exportEnv$glob <- c(glob="glob")
#::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

    utils::globalVariables("nastyHack_x.df")
    sortX <- function(surv.t, cens, X, wt) {
        fitvec <- rep(NA, times = ncol(X))
        nastyHack_x.df <- data.frame(X)
        scp <- formula(paste("~", paste(colnames(X), sep = "", 
            collapse = " + ")))
        cox.out <- coxph(Surv(surv.t, cens) ~ 1, weights = wt, 
            method = "breslow", iter.max = 30, data = nastyHack_x.df)
        addcox <- add1(cox.out, scope = scp, test = "Chisq", 
            data = nastyHack_x.df)
        fitvec <- addcox[-1, grep("^P.*Chi", names(addcox))]
        initial.order <- order(fitvec, decreasing = FALSE)
        sortedX <- X[, initial.order]
        return(list(sortedX = sortedX, initial.order = initial.order))
    }
    X <- x
    cl <- match.call()
    printC <- printCGen(verbose)
    if (factor.type == FALSE) {
        x.df <- data.frame(X)
        X <- model.matrix(terms.formula(~., data = x.df), data = x.df)[, 
            -1]
    }
    if (!sorted) {
        printC("sorting X")
        sorted <- sortX(surv.t, cens, X, wt = wt)
        sortedX <- sorted$sortedX
        initial.order <- sorted$initial.order
    }
    else {
        sortedX <- X
        initial.order <- 1:ncol(sortedX)
    }
    nVar <- ncol(sortedX)
    maxNvar <- min(maxNvar, nVar)
    stopVar <- 0
    nextVar <- maxNvar + 1
    current.probne0 <- rep(0, maxNvar)
    maxProbne0 <- rep(0, times = nVar)
    nTimes <- rep(0, times = nVar)
    currIter <- 0
    first.in.model <- rep(NA, times = nVar)
    new.vars <- 1:maxNvar
    first.in.model[new.vars] <- currIter + 1
    iter.dropped <- rep(NA, times = nVar)
    currentSet <- NULL
    current_state <- list(surv.t = surv.t, cens = cens, sortedX = sortedX, 
        wt = wt, call = cl, initial.order = initial.order, thresProbne0 = thresProbne0, 
        maxNvar = maxNvar, nIter = nIter, verbose = verbose, 
        nVar = nVar, currentSet = currentSet, new.vars = new.vars, 
        stopVar = stopVar, nextVar = nextVar, current.probne0 = current.probne0, 
        maxProbne0 = maxProbne0, nTimes = nTimes, currIter = currIter, 
        first.in.model = first.in.model, iter.dropped = iter.dropped)
    class(current_state) <- "iBMA.intermediate.surv"
    result <- iBMA.surv.iBMA.intermediate.surv(current_state, 
        ...)
    result
}


### this function does a set number of iterations of iBMA, returning an intermediate result unless it is finished,
### in which case it returns a final result
        

iBMA.surv.iBMA.intermediate.surv<- function (x, nIter = NULL, verbose = NULL, ...) 
{

   printCGen<- function(printYN)
   {
        printYN<- printYN
        return(function(x) if (printYN) cat(paste(paste(x,sep="", collapse = " "),"\n", sep="")))
   }
   
   
   cs<- x
      
   # check if nIter has been redefined
   if (!is.null(nIter)) cs$nIter<- nIter
   if (!is.null(verbose)) cs$verbose<- verbose
   printC<- printCGen(cs$verbose)
   
   
   finalIter<- cs$currIter + cs$nIter
   
### iterate until a final result is produced (cs$stopVar == 1) or nIter more iterations have been done
   while (cs$stopVar == 0 && cs$currIter < finalIter) 
   {
   
        # add in the new variables
        nextSet<- c(cs$currentSet, cs$new.vars)
        cs$currIter<- cs$currIter + 1    
        
        printC(paste("\n\n starting iteration ",cs$currIter,"   nextVar =",cs$nextVar))
        printC("applying bic.surv now")
    
        currentX<- cs$sortedX[,nextSet]
        colnames(currentX)<- colnames(cs$sortedX)[nextSet]
      
    
        ret.bic<- bic.surv(x = currentX, surv.t = cs$surv.t, cens = cs$cens, maxCol = cs$maxNvar + 1, ...)
          
        printC(ret.bic$probne0)

        cs$maxProbne0[nextSet]<- pmax(ret.bic$probne0, cs$maxProbne0[nextSet])
        cs$nTimes[nextSet]<- cs$nTimes[nextSet] + 1
        cs$rmVector <- ret.bic$probne0 < cs$thresProbne0

        # adaptive threshold
        if (any(cs$rmVector) == FALSE) 
        {
            # no var to swap in!!, increase threshold
            currMin <- min (ret.bic$probne0)
            printC (paste("no var to swap! Min probne0 = ", currMin, sep=""))
            newThresProbne0 <- currMin + 1
            printC(paste("new probne0 threshold = ", newThresProbne0, sep=""))
            cs$rmVector <- ret.bic$probne0 < newThresProbne0
            
            # check that we do not drop everything!
            if (all(cs$rmVector))
                cs$rmVector<- c(rep(FALSE, times = length(cs$rmVector)-1), TRUE)
                
        }

        # drop the bad ones...
        cs$iter.dropped[nextSet[cs$rmVector]]<- cs$currIter
        cs$currentSet<- nextSet[!cs$rmVector]

        # now if there are more variables to examine add the new set of variables to the current set
        
        if ( cs$nextVar <= cs$nVar) 
        {
  
            # set up new X
            printC ("generating next set of variables")
            lastVar<- sum(cs$rmVector) + cs$nextVar - 1
            
            # add in bulk if we are not close to the end of the variables,
            if (lastVar <= cs$nVar) 
            {
                cs$new.vars<- cs$nextVar:lastVar
                cs$first.in.model[cs$new.vars]<- cs$currIter + 1
                cs$nextVar <- lastVar + 1
            } 
            # add in one by one until no variables left
            else 
            {
                cs$new.vars<- NULL
                for (i in length(cs$rmVector):1) 
                {
                   if (cs$rmVector[i] == TRUE && cs$nextVar <= cs$nVar) 
                   {
                        cs$new.vars<- c(cs$new.vars, cs$nextVar)
                        cs$first.in.model[cs$nextVar]<- cs$currIter + 1
                        cs$nextVar <- cs$nextVar + 1
                   }
                }
            }
        }
        else 
        {
            # exhausted all data
            cs$stopVar <- 1
            cs$new.vars = NULL
        }
    }
 
   # if we have finished (all variables) do some wrap-up and generate output values 
   if (cs$stopVar == 1) 
   {
   
        printC("finished iterating")
        
        
        
    
        currentX<- cs$sortedX[,cs$currentSet]
        colnames(currentX)<- colnames(cs$sortedX)[cs$currentSet]
        
        ret.bic<- bic.surv(x = currentX, surv.t = cs$surv.t, cens = cs$cens, maxCol = cs$maxNvar + 1, ...)
         
        output<- cs
        output$bma<- ret.bic
        output$selected<- cs$currentSet
        output$nIterations<- cs$currIter
        class(output)<- "iBMA.surv"
   }
   
   else
   {
        output<- cs
        class(output)<- "iBMA.intermediate.surv"
   }
   output
}





iBMA.surv.matrix<- iBMA.surv.data.frame