Todos for topepo/caret

These are TODOs that are seen in the code

predictionFunction.R
          
             = param)
  ## TODO convert to character with classification
  out 
}



          
      
BoxCoxTrans.R
          
            BoxCoxTrans <- function(y, ...) UseMethod("BoxCoxTrans")


##TODO add an epsilon?
## TODO add
          
      
sensitivity.R
          
            (reference) | !is.factor(data)) 
    stop("inputs must be factors")

  ## todo: relax the =2 constraint
          
      
specificity.R
          
            (reference) | !is.factor(data)) 
      stop("input data must be a factor")

   ## todo: relax the
          
      
bagEarth.R
          
             <- x[-index,, drop = FALSE]
      subY <- y[-index]
      ## todo
      predY <- if(is.null(fit$levels
          
      
extractProb.R
          
            ## TODO use foreach to parallelize

extractProb <- function(models, 
                        testX
          
      
filterVarImp.R
          
            ## todo start using foreach here

oldfilterVarImp <- function(x, y, nonpara = FALSE
          
      
preProcess.R
          
             frame? 
## TODO let inputs vars be regex's

ppMethods <- c("BoxCox", "YeoJohnson", "expoTrans
          
          
            
  
  ## TODO This should be moved inside of pca or ica code 
  ## and done after centering and scaling
          
      
heldout.R
          
            ###################################################################
##

## Todo: 
## X. Make an
          
      
train.default.R
          
            ") nrow(y) else length(y)
  
  ## TODO add check method and execute here
  
  ## Some models that use
          
          
            ))
    stop("Out of bag estimates are not implemented for this model")
  
  ## SURV TODO: make resampling
          
      
gafs.R
          
            
  
  ###################################################################
  ## From GA package:
  
  ## TODO make input
          
          
             = i,
                                             ...) 
                                } ## loop over chromosomes
    
    ## TODO
          
      
adaptive.R
          
            ## TODO: clean up code duplication?
##       add na.action to all eval functions
##       change
          
          
            ],
                        ## TODO check this for seq models
                        gsub("^\\.", "", colnames(info$loop
          
      
ggplot.R
          
            (paste(strip_lab[i], dat[, strip_vars[i]], sep = ": "))
    }
    ## TODO: use factor(format(x)) to
          
      
aaa.R
          
             class-wise stats
  #Todo: add weights
  # RES: support two classes here as well
  #browser() # Debug
          
      
safs.R
          
            $holdout,
                lvl = classLevels,
                ...)
    }
    
    ## TODO save only
          
          
             containers for
    ## the remaining iterations
    if(i == 1) {  ##TODO check for name and modify if needed
          
      
workflows.R
          
             <- ddply(resamples[,!grepl("^cell|Resample", colnames(resamples)),drop = FALSE],
               ## TODO
          
      
rfe.R
          
            ")) ##todo: get away from this since it finds object in other spaces
        {
          if