R/ds.dist.R

In FlorianSchw/dsClusterAnalysisClient: DataSHIELD client side functions for the dsClusterAnalysisClient package

#'
#' @title Computes the distance matrix of a given data set
#' @description This function is similar to the native R function from stats
#' @details The function calls the server-side function \code{distDS} that computes the
#' distance matrix of a data set (type data.frame or matrix) and assigns the new object to the server-side, which will be of class 'dist'.
#' The new object is named by the user using the \code{newobj} argument, otherwise it is named \code{dist.newobj} by default.
#' @param df.name is a string character of the data set (either a data.frame or a matrix)
#' @param method specifies the method for the distance matrix calculation and can be either 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary' or 'minkowski'
#' @param newobj is the name of the new object which is created with this function
#' @param datasources a list of \code{\link{DSConnection-class}} objects obtained after login
#' @return the object specified by the \code{newobj} argument of \code{ds.dist} or default name \code{dist.newobj}
#' @author Florian Schwarz for the German Institute of Human Nutrition
#' @import DSI
#' @import dsBaseClient
#' @import methods
#' @export
#' 


ds.dist <- function(df.name=NULL, method = "euclidean", newobj=NULL, datasources=NULL){
  
  # look for DS connections
  if(is.null(datasources)){
    datasources <- datashield.connections_find()
  }
  
  
  # ensure datasources is a list of DSConnection-class
  if(!(is.list(datasources) && all(unlist(lapply(datasources, function(d) {methods::is(d,"DSConnection")}))))){
    stop("The 'datasources' were expected to be a list of DSConnection-class objects", call.=FALSE)
  }
  
  
  if(is.null(df.name)){
    stop("Please provide the name of the input object!", call.=FALSE)
  }
  
  
  defined <- dsBaseClient:::isDefined(datasources, df.name)
  
  
  # call the internal function that checks the input object is of the same class in all studies.
  typ <- dsBaseClient:::checkClass(datasources, df.name)
  
  
  # Check whether the input is either of type data frame or matrix
  if(!('data.frame' %in% typ) && !('matrix' %in% typ)){
    stop("Only objects of type 'data frame' or 'matrix' are allowed.", call.=FALSE)
  }
  
  
  
  checkColumnsDF1(df.name = df.name, datasources = datasources)
  
  
  
  # create a name by default if the user does not provide a name for the new variable
  if(is.null(newobj)){
    newobj <- "dist.newobj"
  }
  
  
  # Needs to be checked for one of the six methods in a list
  allowedmethods <- c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")
  
  if(!(method %in% allowedmethods)){
    stop("Method needs to be one of the following: 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary' or 'minkowski'.", call.=FALSE)
  }
  
  
  # call the server side function that does the operation
  cally <- call("distDS", df.name, method)
  DSI::datashield.assign(datasources, newobj, cally)

  
}