R/sequester.R

In OmicsMarkeR: Classification and Feature Selection for 'Omics' Datasets

#' @title Sequester Additional Parameters
#' @description When the user provides additional arguments to either 
#' \code{fs.stability} or \code{fs.ensembl.stability} this function will 
#' extract the parameters to be fit if optimization is not used i.e. 
#' \code{optimize = FALSE}.
#' @param theDots List of additional arguments
#' @param method Vector of strings listing models to be fit
#' @return Returns a list of the following elements
#' @return \item{parameters}{The parameters that will be fit to models}
#' @return \item{pnames}{The names of the specific parameters}

sequester <- function(theDots, method){
    
    Value <- vector("list", length(method))
    pnames <- vector()
    names(Value) <- method
    
    for(m in seq(along = method)){
        vals <- 
            switch(tolower(method[m]),
                   plsda =
{
    x <- which(names(theDots) == ".ncomp")
    if(length(x) < 1){
        stop("Error: If not autotuning or providing a grid, 
             PLSDA requires you to specify 'ncomp'")
    }
    Value[[m]] <- theDots[x]
    pnames <- c(pnames, "ncomp")
    },

gbm =
{
    x <- which(names(theDots) 
               %in% c(".n.trees", 
                      ".interaction.depth", 
                      ".shrinkage"))
    if(length(x) < 3){
        stop("Error: If not autotuning or providing a grid, 
             GBM requires you to specify 'n.trees', 
             'interaction.depth', and 'shrinkage' values")
    }
    Value[[m]] <- theDots[x]
    pnames <- c(pnames, 
                c("n.trees", "interaction.depth", "shrinkage"))
    },

rf =
{
    x <- which(names(theDots) == ".mtry")
    if(length(x) < 1){
        stop("Error: If not autotuning or providing a grid, 
             RandomForest requires you to specify 'mtry'")
    }
    Value[[m]] <- theDots[x]
    pnames <- c(pnames, "mtry")
    },

svm = 
{
    x <- which(names(theDots) == ".C")
    if(length(x) < 1){
        stop("Error: If not autotuning or providing a grid, 
             SVM requires you to specify 'C'")
    }
    Value[[m]] <- theDots[x]
    pnames <- c(pnames, "C")
    },

glmnet = 
{
    x <- which(names(theDots) %in% c(".lambda", ".alpha"))
    if(length(x) < 1){
        stop("Error: If not autotuning or providing a grid, 
             glmnet requires you to specify 'lambda' and 'alpha'")
                 }
                 Value[[m]] <- theDots[x]
                 pnames <- c(pnames, c("lambda", "alpha"))
               },
             
             pam = 
               {
                 x <- which(names(theDots) == ".threshold")
                 if(length(x) < 1){
                   stop("Error: If not autotuning or providing a grid, 
                        PAM requires you to specify 'threshold'")
                 }
                 Value[[m]] <- theDots[x]
                 pnames <- c(pnames, "threshold")
               }
    )
  }
 out <- list(parameters = Value,
             pnames = pnames)
  out
  
}