server.R

library(shiny)
library(knitr)

# Define server
shinyServer(function(input, output) {
  
  #source("helper.r")
  
  
  # Set seed
  set.seed(sample(1:10000, 1))
  
  # Read in cleaned up words and part of speech / sentiment
  words <- read.csv("joe_words.csv")
  words$word <- tolower(words$word)
  
  # Put everything into lowercase
  adjective <- tolower(words$word[which(words$pos == "adjective")])
  verb <- tolower(words$word[which(words$pos == "verb")])
  noun <- tolower(words$word[which(words$pos == "noun")])
  
  
  # Write function to get words by type
  joe <- function(pos, sentiment = NULL, reg = NULL, neg_reg = NULL, number = 1){
    
    x <- words
    
    if(!is.null(sentiment)){
      x <- x[which(x$pos == pos & x$sentiment == sentiment),]
    }
    if(!is.null(reg)){
      x <- x[which(grepl(reg, x$word)),]
    }
    if(!is.null(neg_reg)){
      x <- x[which(!grepl(neg_reg, x$word)),]
    }
    x <- x$word[which(x$pos == pos)]
    if(length(x) > 0){
      return(sample(x, number))
    } else{
      return(sample(words$word[which(words$pos == pos & words$sentiment == sentiment)], 1))
    }
    
  }
  
  # Write generate paper function
  GeneratePaper <- function(title,
                            author,
                            to,
                            sentiment,
                            journal){
    
    
    ############
    line1 <- paste0("Dear ", to, ",")
    
    ############
    l2nega <- paste0("It was with a great deal of ",
                     joe("noun", "negative"), 
                     " that I read ",
                     author,
                     "'s most ",
                     joe("adjective", "negative"), 
                     " article entitled '",
                     title, "'.")
    l2negb <- paste0("I was very ",
                     joe(pos = "adjective", sentiment = "negative", reg = "ed", neg_reg = "need"),
                     " to read ",
                     author,
                     "'s most ",
                     joe("adjective", "negative"), 
                     " article entitled '",
                     title, "'.")
    l2negc <- paste0(author,
                     "'s ",
                     "most ",
                     joe(pos = "adjective", sentiment = "negative"),
                     " article ('",
                     title, 
                     "')",
                     " was a perfect example of everything that is ",
                     joe("adjective", "negative"),
                     " and ", 
                     joe("adjective", "negative"),
                     " with the field of epidemiology today.")
    
    
    l2posa <- paste0(author, 
                     "'s '",
                     title,
                     "' was a most ",
                     joe("adjective", "positive", reg = "ous", neg_reg = "famous"),                   " break from the typical ",
                     joe("noun", "negative"),
                     " that our field usually produces these days.")
    l2posb <- paste0("I was absolutely ",
                     joe("adjective", "positive"),
                     " upon reading ",
                     author,
                     "'s most ",
                     joe("adjective", "positive"),
                     " article entitled '",
                     title,
                     "'.")
    l2posc <- paste0(author,
                     "'s ",
                     joe("adjective", "positive"),
                     " '",
                     title,
                     "' was a complete ",
                     joe("noun", "positive", neg_reg = "ion"),
                     ", especially when compared to the usual ",
                     joe("noun", "negative"),
                     "  published by this journal",
                     ".")
    
    if(sentiment == "negative"){
      line2 <- sample(c(l2nega, l2negb, l2negc), 1)
    } else{
      line2 <- sample(c(l2posa, l2posb, l2posc), 1)
    }
    
    ############
    l3nega <- paste0("It is rare to come across such a ",
                     joe("adjective", "negative"),
                     " example of ",
                     joe("noun", "negative"),
                     " filled with so many ",
                     joe("noun", "negative", neg_reg = "ness"),
                     "s.")
    l3negb <- paste0("In my many years of reading ",
                     journal, 
                     ", this is the first time I've found myself so ",
                     joe("adjective", "negative", reg = "*ed", neg_reg = "ly"),
                     " by an article that I felt compelled to write.")
    l3negc <- paste0("Even by the standards of ",
                     journal,
                     ", this article was noteworthy for being both ",
                     joe("adjective", "negative"), 
                     " and ",
                     joe("adjective", "negative"),
                     ", a rare combination indeed.")
    
    l3posa <- paste0("What a joy it was to read such a fine example of ",
                     joe("noun", "positive", "inte"),
                     " and ",
                     joe("noun", "positive"),
                     ", a rare combination in today's increasingly ",
                     joe("adjective", "negative", neg_reg="ly"),
                     " field.")
    
    l3posb <- paste0("Few studies so ",
                     joe("adjective", "positive", "succ", neg_reg = "ly"),
                     "ly combine such ",
                     joe("adjective", "positive", reg = NULL, neg_reg = "ly"),
                     " design with ",
                     joe("adjective", "positive"),
                     " analytical approaches.")
    
    l3posc <- paste0("I have never come across a finer example of ",
                     joe("adjective", "positive"), 
                     " methods and ",
                     joe("adjective", "positive"),
                     " writing, and I ",
                     joe("verb", "positive"),
                     " the authors for ",
                     joe("verb", "positive"),
                     "ing in such ",
                     joe("adjective", "positive"),
                     " ways. ")
    if(sentiment == "negative"){
      line3 <- sample(c(l3nega, l3negb, l3negc), 1)
    } else{
      line3 <- sample(c(l3posa, l3posb, l3posc), 1)
    }
    
    ############
    l4negasub1 <- paste0("The authors lack any and all ", 
                         joe("adjective", "positive"),
                         " evidence for their secondary findings. ")
    l4negasub2 <- paste0("The authors' methods are both ", 
                         joe("adjective", "negative"),
                         " and ",
                         joe("adjective", "negative", "ed"),
                         ". ")
    l4negasub3 <- paste0("The authors' insistence on the ",
                         joe("noun", "positive", "ence"),
                         " of their findings ignore nearly a decade of ",
                         joe("adjective", "positive", neg_reg = "ly"),
                         " work in an increasingly ",
                         joe("adjective", "positive"),
                         " field. ")
    l4negasub4 <- paste0("The authors' conclusions are not only unsupported by their (",
                         joe("adjective", "negative"),
                         ") data, but they also appear to contradict it ",
                         joe("adjective", "negative", neg_reg = "ly"),
                         "ly. ")
    
    
    l4nega <- paste0("The article's shortcomings are three-fold: 1) ",
                     l4negasub1, " 2) ",
                     l4negasub2, " 3) ",
                     l4negasub3)
    l4negb <- paste0("The article has two ",
                     joe("adjective", "negative"),
                     " shortcomings: 1) ",
                     l4negasub4, " 2) ",
                     l4negasub2)
    
    l4posasub4 <- paste0("the authors' ",
                         joe("adjective", "positive", neg_reg = "ly"),
                         " analysis and ",
                         joe("adjective", "positive", neg_reg = "ly"),
                         " interpretation of their results more than adequately compensate ",
                         "for the ",
                         joe("noun", "negative", "ence"), 
                         " of their study design. ")
    
    l4posa <- paste0(l4negasub3,
                     " That said, ",
                     l4posasub4)
    l4posb <- paste0("The authors'",
                     joe("adjective", "positive", neg_reg = "ly"),
                     " analysis and ",
                     joe("adjective", "positive", neg_reg = "ly"),
                     " interpretation of their results more than adequately compensate ",
                     "for the ",
                     joe("noun", "negative", "ence"), 
                     " of their study design.  That said, it is worth pointing out ",
                     "2 noteworthy problems: ",
                     "1) ",
                     l4negasub4, 
                     " 2) ",
                     l4negasub3,
                     " These criticsms should not detract from ", 
                     author,
                     "'s ",
                     "overall message (which I found to be ",
                     joe("adjective", "positive"),
                     ") or the article's ",
                     joe("noun", "positive", "est"),
                     ". ")
    
    if(sentiment == "negative"){
      line4 <- sample(c(l4nega, l4negb), 1)
    } else{
      line4 <- sample(c(l4posa, l4posb), 1)
    }
    
    ############
    l5nega <- paste0("I sincerely hope that ",
                     author,
                     " will reconsider their conclusions, and that in the future ",
                     journal,
                     " will be a bit more careful in selecting articles they deem ",
                     joe("adjective", "positive"),
                     " enough for publication. ")
    l5negb <- paste0("Though this article contains elements of ",
                     joe("adjective", "positive", neg_reg = "ly"),
                     " insight, ",
                     author,
                     " muddled their message with ",
                     joe("adjective", "negative", neg_reg = "ly"),
                     "ly ", 
                     joe("adjective", "negative"),
                     " analyses of otherwise ",
                     joe("adjective", "positive"),
                     " data. ")
    l5negc <- paste0("I encourage ",
                     author,
                     " to withdraw their paper from publication, given the ",
                     joe("adjective", "negative"), 
                     " flaws in the design, analysis and interpretation of",
                     " what otherwise could have been a ",
                     joe("adjective", "positive"), 
                     " contribution to our field. ")
    l5negd <- paste0("J'accuse ",
                     author,
                     " of ",
                     joe("adjective", "negative"), " ",
                     joe("noun", "negative", "ism"),
                     " and implore ",
                     journal,
                     " to withdraw this article's publication entirely. ")
    
    l5posa <- paste0("I applaud ",
                     author,
                     " for their ",
                     joe("adjective", "positive"),
                     " contribution to our field, ",
                     " and encourage others to follow their example. ")
    l5posb <- paste0(author,
                     "'s study represents a ",
                     joe("adjective", "positive"),
                     " and ",
                     joe("adjective", "positive"),
                     " shift in the way epidemiologists ",
                     joe("verb", "positive", "ize"),
                     " our understanding of ",
                     joe("noun", "positive", "ism"),
                     ". ")
    l5posc <- paste0(author,
                     "'s most serious shortcoming was that they did not fully ",
                     joe("verb", "positive", "ize"), 
                     " the ",
                     joe("noun", "positive", "ance"),
                     " of their findings. ")
    l5posd <- paste0("'",
                     title,
                     "'",
                     " deserves widespread dissemination for its ",
                     joe("verb", "positive", neg_reg = "ly"),
                     "ly ",
                     joe("adjective", "positive"),
                     " implications for future studies of the population in question. ")
    
    l5pos1 <- sample(c(l5posb, l5posc), 1)
    l5pos2 <- sample(c(l5posa, l5posd), 1)
    
    l5neg1 <- l5negb
    l5neg2 <- sample(c(l5nega, l5negc, l5negd), 1)
    
    if(sentiment == "negative"){
      line5 <- paste0(l5neg1, l5neg2)
    } else{
      line5 <- paste0(l5pos1, l5pos2)
    }
    
    x <- list(line1, line2, line3, line4, line5)
    return(x)
    
  }
  
  
  
  
  
  
  
  
  output$downloadPDF <-
    downloadHandler(filename = "report.pdf",
                    content = function(file){
                      # generate PDF
                      knit2pdf("report.Rnw")

                      # copy pdf to 'file'
                      file.copy("report.pdf", file)

                      # delete generated files
                      file.remove("report.pdf", "report.tex",
                                  "report.aux", "report.log")

                      # delete folder with plots
                      unlink("figure", recursive = TRUE)
                    },
                    contentType = "application/pdf"
  )
  

  
})