The function addNewData.R modifies a data frame with a lookup table. This is useful where you want to supplement data loaded from file with other data, e.g. to add details, change treatment names, or similar. The function readNewData is also included. This function runs some checks on the new table to ensure it has correct variable names and val…

addNewData.R

##' Modifies 'data' by adding new values supplied in newDataFileName
##'
##' newDataFileName is expected to have columns 
##' c(lookupVariable,lookupValue,newVariable,newValue,source)
##' 
##' Within the column 'newVariable', replace values that
##' match 'lookupValue' within column 'lookupVariable' with the value
##' newValue'.  If 'lookupVariable' is NA, then replace *all* elements
##' of 'newVariable' with the value 'newValue'.
##'
##' Note that lookupVariable can be the same as newVariable.
##'
##' @param newDataFileName name of lookup table
##' @param data existing data.frame
##' @param allowedVars vector of permissible variable names for newVariable
##' @return modified data.frame
addNewData <- function(newDataFileName, data, allowedVars){

  import <- readNewData(newDataFileName, allowedVars)

  if( !is.null(import)){    
    for(i in seq_len(nrow(import))){  #Make replacements
      col.to <- import$newVariable[i] 
      col.from <- import$lookupVariable[i]
      if(is.na(col.from)){ # apply to whole column
        data[col.to] <- import$newValue[i]
      } else { # apply to subset
        rows <- data[[col.from]] == import$lookupValue[i]
        data[rows,col.to] <- import$newValue[i]
      }
    }   
  }      
  data
}

##' Utility function to read/process newDataFileName for addNewData
##' 
##' @param newDataFileName name of lookup table
##' @param allowedVars vector of permissible variable names for newVariable
##' @return data.frame with columns c(lookupVariable,lookupValue,newVariable,newValue,source)
readNewData <- function(newDataFileName, allowedVars){
  
  if( file.exists(newDataFileName)){
    import <- read.csv(newDataFileName, header=TRUE, stringsAsFactors=FALSE,
                       strip.white=TRUE)
    if( nrow(import)> 0 ){
      
      #Check columns names for import are right
      expectedColumns<- c("lookupVariable","lookupValue","newVariable","newValue")
      nameIsOK <-  expectedColumns %in% names(import)
      if(any(!nameIsOK))
        stop("Incorrect name in lookup table for ",
             newDataFileName, "--> ", paste(expectedColumns[!nameIsOK],
                                            collapse=", "))
      
      #Check values of newVariable are in list of allowed variables
      import$lookupVariable[import$lookupVariable == ""] <- NA
      nameIsOK <- import$newVariable %in% allowedVars
      if(any(!nameIsOK))
        stop("Incorrect name(s) in newVariable column of ",
             newDataFileName, "--> ", paste(import$newVariable[!nameIsOK],
                                      collapse=", "))
    } else {
      import <- NULL
    }
  } else {
    import <- NULL
  }
  import
}

dataNew.csv

installation.md

To install the code, do one of the following:

1. Download it then load with source(addNewData.R)
2. Load it directly from github

library(devtools, quietly=TRUE)
source_gist("https://gist.github.com/dfalster/5589956")

To use it, simply type

addNewData("dataNew.csv", myData, allowedVars)

where allowedVars is vector of permissible variable names for the columns of myData.