R/m3-validateMethod-method.R

In jperezrogers/rabbit: An R Package to Create Computational Pipelines to Develop and Evaluate Biomarkers from High Dimensional Genomic Data

# Validate that the input method conform to required standards of the Task class
# 
# More detailed explaination here
# 
# @param method A user-defined \code{function}. This \code{function} must contain input parameters \code{x} (a numerical matrix with \code{n} columns and \code{m} rows), \code{rank} (a numeric vector of length \code{m} that can be used with \code{\link[base]{sort}}). The user can provide additional parameters to the \code{function} but must specify default values in the \code{function}'s definition. \code{method} must return a numerical matrix with the same number of columns (\code{ncol}) and column names (\code{colnames}) as \code{x} (see example below).
# 
# @return Function will execute silently if no errors are detected in \code{libraries}
# 
# @examples
# \dontrun{
# set.seed(1234)
# x <- matrix(rnorm(100),nrow=10)
# colnames(x) <- paste0("sample_",1:10)
# row.names(x) <- paste0("gene_",1:10)
# rank <- 1:10
# 
# method <- function(x,rank){
#  x <- x[rank[1:5],]
#  return(x)
# }
# validateMethodM3(method)
# }
# 
# @keywords internal


validateMethodM3 <- function(method=NULL){
  
  # check that the user defined method
  if(is.null(method)){
    stop("method must be defined")
  }
  
  # check that method is a function
  if(!is.function(method)){
    stop("method must be a function")
  }
  
  # check that method has input parameters x, y, and optionally data
  if(!all(c("x","rank")%in%names(formals(method)))){
    stop("method must have input parameters 'x' and 'rank'")
  }
  
  # extract parameters and defaults from method, setting params with no default to NULL
  f <- lapply(formals(method), function(x){
    if(!is.null(x)){
      if(is.name(x) & !nzchar(x)) NULL else x
    }
  })
  
  # check if x has a default value, if so, issue a warning to the user
  if(!is.null(f[["x"]])){
    warning("'x' should not have a default value. The default provided will be disregarded when invoking the method")
  }
  
  # check if rank has a default value, if so, issue a warning to the user
  if(!is.null(f[["rank"]])){
    warning("'rank' should not have a default value. The default provided will be disregarded when invoking the method")
  }
  
  # if there are additional input parameters to method, make sure they have defaults
  # by default, formals() returns parameters without defaults as a blank character string: ""
  # here, I change "" to NULL and check for is.null, however if a user-defined parameter was
  # to actually have a default value of "", this would get overwritten. This is a known limitation.
  
  # check that all parameters other than x and rank have defaults, if not, issue error
  cond <- f[-which(names(f)%in%c("x","rank"))]
  if(length(cond)>0){
    if(any(unlist(lapply(cond,function(x) is.null(x))))){
      stop("All parameters other than 'x' and 'rank' in 'method' must have default values")
    }    
  }
  
}