Split reference list helper for pilot and collaborative screening rounds

by Coralie Williams

When screening for a systematic review or meta-analysis, we conduct several pilot screening rounds. Pilot screenings help us refine our search string, decision tree, and increase the overall accuracy of our screening for literature reviews [check out this nice guide from the I-DEEL team for more info: Foo et al, 2021].

During a pilot screening, we want to select a random subset of references that would be a representative sample of the full set. When possible, screening rounds are conducted in collaboration with another reviewer. To speed up the screening process, we sometimes want to randomly allocate a subset of papers to a collaborator by splitting a reference list into subsets.

There are two reasons we’d want to automate the selection and splitting of a reference list:

1. It is time consuming to randomly select papers (>100 papers is tedious to select by hand!)
2. We are not really good at selecting things at random (actually computers aren’t really good at selecting truly at random either*)

​Below is the R (www.r-project.org) code to run two functions that may come in useful when conducting your pilot and collaborative screenings with Rayyan (https://rayyan.ai/), or any other software where you can upload your pilot reference list.

1. Select random pilot set:

First, load the getpilotref function below in your environment:
​

# -----------------------------------
# getpilotref function 
# -----------------------------------
## Description: 
#     Function to obtain a random subset of references for pilot screening.
#
# Arguments
# - x: data frame with reference list
# - n: number of papers for pilot subset (default is 10)
# - write: logical argument whether to save the pilot list as a csv file 
#   in the current working directory (default is FALSE).
# - fileName: name of file (default is "pilot")

getpilotref <- function(x, n=10, write=FALSE, fileName="pilot"){
  
  if (length(n) == 1L && n%%1==0 && n>0 && n<=nrow(x)) { 
    
    # sample randomly the vector n of row indexes and remove id column in the final dataset
    x$ids <- 1:nrow(x)
    pdat <- x[which(x$ids %in% sample(x$ids, n)),]
    pilot <- pdat[,-which(colnames(pdat)=="ids")]
    
    } else {
      # error message n value provided is not valid 
      stop("Incompatible value n supplied, please check. 
      #n must be a positive integer no higher than the total number of references provided.") 
    }
  
  if (write==T){
    
    # save generated pilot list in working directory using the name provided
    write_csv(pilot, paste(fileName, ".csv", sep=""), na="")
    
    # print out summary of saved file name
    cat(paste("Pilot random sample set of ", n, " articles is saved as: ", fileName, ".csv", sep=""))
    
  }
  
  return(pilot)
}

​Let’s try it out
Load example csv file that was exported from Rayyan (a reference list of papers in Ecology & Evolutionary Biology having the word “butterflies” in their title):

# Read example butterfly reference list
articles<-read.csv("https://raw.githubusercontent.com/coraliewilliams/2022/main/data/articles_butterfly.csv")

​First, let’s obtain a random set of 10 papers without saving it as a csv file:

p10 <- getpilotref(articles)

Now, let’s obtain a subset of 100 papers for a pilot screening and save the subset as a csv file called pilot100.csv. Make sure you have the readr package installed and loaded in your environment.

library(readr)
p100 <- getpilotref(articles, n=100, write=T, fileName="pilot100")

## Pilot random sample set of 100 articles is saved as: pilot100.csv

This will save a csv file pilot100.csv in your working directory. If you are unsure where is your working directory run this command getwd() in your console.

2. Split reference list with another collaborator​

Load the splitref_prop function in your environment:

# -----------------------------------
# splitref_prop function 
# -----------------------------------
## Description: 
#     Function to split in two a reference list based on input proportions.
#
## Arguments: 
# - x: data frame with reference list
# - p: vector of two numerical proportions for each split, it must have two positive numerical values that sum to 1.
# - write: logical argument whether to save the pilot list as csv in current working directory.
# - fileName: name to give to the suffix of the two split csv files.

splitref_prop <- function(x, p=c(0.5, 0.5), write=F, sname="split") {
  
    if (length(p) == 2L && is.numeric(p) && sum(p) == 1 && all(p > 0)) {
      
      # randomly allocated a numerical id to each reference
      rids <- sample(1:nrow(x))
      
      # get index of row to split on using the proportion values provided
      spl <- floor(p[-length(p)] * nrow(x))
      
      # get indices of two data frames based on split ids
      indx1 <- rids[1:spl]
      indx2 <- rids[(spl + 1):nrow(x)]
      
      # save split subsets in two separate datasets
      split1 <<- x[indx1,]
      split2 <<- x[indx2,]
      
      # print out summary message
      cat(paste(c("Reference list was randomly split into",length(p), "proportions of", p[1]*100, "% and", p[2]*100, "%")))
      
      if (write == T) {
        # save files
        write_csv(split1, paste(sname, "_set1", ".csv", sep = ""), na ="")
        write_csv(split2, paste(sname, "_set2", ".csv", sep = ""), na ="")
        }
      
      } else {
      # error message if provided n value is not valid
      stop("Incompatible values for p (proportions) supplied, please check.
           Proportion values must be positive integers less than 1, and the total sum of all proportions should equal to 1.")
        
    }
}

​Let’s try it out
Using the example butterfly reference list, let’s first split the reference list in two equal splits (50% each):

splitref_prop(articles)

## Reference list was randomly split into 2 proportions of 50 % and 50 %

This will give you two separate data frames to share between two reviewers: split1 and split2.

Now let’s get 30% of references in the first subset (split1) and 70% in the second subset (split2), for example if one reviewer has more time to spend on the screening:

splitref_prop(articles, p=c(0.3,0.7))

## Reference list was randomly split into 2 proportions of 30 % and 70 %

Let’s save the 30% and 70% split list of references as csv files with the suffix “testsplit”:

splitref_prop(articles, p=c(0.3,0.7), write=T, sname="testsplit")

## Reference list was randomly split into 2 proportions of 30 % and 70 %

This will save two csv files, testsplit_set1.csv and testsplit_set2.csv, in your working directory.

*computers aren’t really good at selecting truly at random…Random number generators from most computer programs are actually “pseudo-random”, meaning they are produced from a deterministic mathematical model or algorithm. The R code above uses a pseudo-random number generator. Pseudo-random number generators are usually good enough for their intended purpose (basically better than what any human could do). A good pseudo-random number generator will reproduce statistics that are consistent with true randomness, but they are not truly random. A truly random number can be generated based on a constantly changing physical process that can’t be modelled as an algorithm. If you’re curious about true randomness check out these websites: https://www.random.org/; https://qrng.anu.edu.au/random-colours/.


(Any comments, questions or feedback, you can reach me at: [email protected])