library("tm")

library("SnowballC")

library("ggplot2")

library("wordcloud")

library("cluster")

require("stats")

setwd("C:/Users/cloud/Downloads")

ctcl <- read.csv("ctsampleinds_cleaned (2).csv", header = F)

ctclwtri <- read.csv("ctsampleinds_cleaned.csv", header = F)

accruals <- read.csv("ctsampledata (1).csv", header = F)

setwd("C:/Users/cloud/Downloads/ClusterSentCritFinalRun3")

###NOTE: IF the words "inclusion criterion" or "exclusion criterion" actually appear in your data file,

#then pick different words to use for the below loops

n <- 1

s <- seq(1, ncol(ctcl), by = 2)

for (i in 1:nrow(ctcl)) {

  for (j in s) {

    if (!is.na(ctcl[i,j])) {

      if (ctcl[i,j] != "") {

        n <- as.character(n)

        str <- paste("s", n, ".txt", sep = "")

        incexc <- "UNKNOWN WHETHER INCLUSION CRITERION OR EXCLUSION CRITERION"

        if (!is.na(ctcl[i,j+1])) {

          if (ctcl[i,j+1] != "") {

            if (ctcl[i,j+1] == "TRUE") {

              incexc <- "INCLUSION CRITERION"

            }

            if (ctcl[i,j+1] == "FALSE") {

              incexc <- "EXCLUSION CRITERION"

            }

          }

        }

        trial <- ctclwtri[i,1]

        accrual <- "No accrual data found"

        for (k in 1:nrow(accruals)) {

          if (trial == accruals[k,1]) {

            accrual <- accruals[k,2]

          }

        }

        write.table(as.data.frame(paste(ctcl[i,j], incexc, "Accruals:", accrual, sep = " ")),file = str, row.names = F, col.names = F)

        n <- as.numeric(n)

        n <- n + 1

      }

    }

  }

}

sentdocs <- Corpus(DirSource("C:/Users/cloud/Downloads/ClusterSentCritFinalRun3"))

writeLines(as.character(sentdocs[[9770]]))

sentdocs <- tm_map(sentdocs,content_transformer(tolower))

toSpace <- content_transformer(function(x, pattern) { return (gsub(pattern, " ", x))})

sentdocs <- tm_map(sentdocs, toSpace, '"')

sentdocs <- tm_map(sentdocs, toSpace, 'inclusion criterion')

sentdocs <- tm_map(sentdocs, toSpace, 'exclusion criterion')

sentdocs <- tm_map(sentdocs, toSpace, 'accruals: \\d+')

sentdocs <- tm_map(sentdocs, toSpace, 'no accrual data found')

sentdocs <- tm_map(sentdocs, removeWords, stopwords("english"))

sentdocs <- tm_map(sentdocs, stripWhitespace)

sentdocs <- tm_map(sentdocs,stemDocument)

sentdtm <- DocumentTermMatrix(sentdocs)

sentm <- as.matrix(sentdtm)

#Clust number selection

library("NbClust")

sentmdf <- as.data.frame(sentm)

minnum <- 10

maxnum <- 50

nb1 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "kl", alphaBeale = 0.1)

nb2 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "ch", alphaBeale = 0.1)

nb3 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "hartigan", alphaBeale = 0.1)

nb4 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "ccc", alphaBeale = 0.1)

nb5 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "scott", alphaBeale = 0.1)

nb6 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "marriot", alphaBeale = 0.1)

nb7 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "trcovw", alphaBeale = 0.1)

nb8 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "tracew", alphaBeale = 0.1)

nb9 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

               method = "ward.D", index = "friedman", alphaBeale = 0.1)

nb10 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "rubin", alphaBeale = 0.1)

nb11 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "cindex", alphaBeale = 0.1)

nb12 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "db", alphaBeale = 0.1)

nb13 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "silhouette", alphaBeale = 0.1)

nb14 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "duda", alphaBeale = 0.1)

nb15 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "pseudot2", alphaBeale = 0.1)

nb16 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "beale", alphaBeale = 0.1)

nb17 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "ratkowsky", alphaBeale = 0.1)

nb18 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "ball", alphaBeale = 0.1)

nb19 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "ptbiserial", alphaBeale = 0.1)

nb20 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "gap", alphaBeale = 0.1)

nb21 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "frey", alphaBeale = 0.1)

nb22 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "mcclain", alphaBeale = 0.1)

nb23 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "gamma", alphaBeale = 0.1)

nb24 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "gplus", alphaBeale = 0.1)

nb25 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "tau", alphaBeale = 0.1)

nb26 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "dunn", alphaBeale = 0.1)

nb27 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "hubert", alphaBeale = 0.1)

nb28 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "sdindex", alphaBeale = 0.1)

nb29 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "dindex", alphaBeale = 0.1)

nb30 <- NbClust(data = sentmdf, diss = NULL, distance = "euclidean", min.nc = minnum, max.nc = maxnum, 

                method = "ward.D", index = "sdbw", alphaBeale = 0.1)

list1 <- unlist(list(if(exists("nb1")) { if(!is.null(nb1$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb1$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb1$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb2")) { if(!is.null(nb2$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb2$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb2$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb3")) { if(!is.null(nb3$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb3$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb3$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb4")) { if(!is.null(nb4$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb4$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb4$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb5")) { if(!is.null(nb5$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb5$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb5$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb6")) { if(!is.null(nb6$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb6$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb6$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb7")) { if(!is.null(nb7$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb7$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb7$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb8")) { if(!is.null(nb8$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb8$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb8$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb9")) { if(!is.null(nb9$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb9$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb9$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb10")) { if(!is.null(nb10$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb10$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb10$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb11")) { if(!is.null(nb11$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb11$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb11$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb12")) { if(!is.null(nb12$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb12$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb12$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb13")) { if(!is.null(nb13$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb13$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb13$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb14")) { if(!is.null(nb14$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb14$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb14$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb15")) { if(!is.null(nb15$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb15$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb15$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb16")) { if(!is.null(nb16$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb16$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb16$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb17")) { if(!is.null(nb17$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb17$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb17$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb18")) { if(!is.null(nb18$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb18$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb18$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb19")) { if(!is.null(nb19$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb19$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb19$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb20")) { if(!is.null(nb20$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb20$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb20$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb21")) { if(!is.null(nb21$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb21$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb21$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb22")) { if(!is.null(nb22$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb22$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb22$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb23")) { if(!is.null(nb23$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb23$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb23$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb24")) { if(!is.null(nb24$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb24$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb24$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb25")) { if(!is.null(nb25$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb25$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb25$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb26")) { if(!is.null(nb26$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb26$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb26$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb27")) { if(!is.null(nb27$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb27$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb27$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb28")) { if(!is.null(nb28$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb28$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb28$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb29")) { if(!is.null(nb29$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb29$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb29$Best.nc[1]), "Number_clusters")))}}},

                     if(exists("nb30")) { if(!is.null(nb30$Best.nc)) { if ( !is.infinite(as.numeric(unlist(strsplit(as.character(nb30$Best.nc[1]), "Number_clusters"))))) {as.numeric(unlist(strsplit(as.character(nb30$Best.nc[1]), "Number_clusters")))}}}))

round2 = function(x, n) {

  posneg = sign(x)

  z = abs(x)*10^n

  z = z + 0.5

  z = trunc(z)

  z = z/10^n

  z*posneg

}

round2(median(list1), 0)

round2(mean(list1), 0)

cutnum <- round2(mean(list1), 0)

numbo <- 1

gsubin <- function(x){gsub("INCLUSION CRITERION", "", x)}

gsubex <- function(x){gsub("EXCLUSION CRITERION", "", x)}

gsubacc <- function(x){gsub("Accruals: \\d+", "", x)}

gsubacc2 <- function(x){gsub("No accrual data found", "", x)}

groups <- cutree(hclust(dist(sentm),method="ward.D"), k=cutnum)

clust_list <- lapply(sort(unique(groups)), function(x) which(groups==x))

hc1 <- hclust(dist(sentm), method = "ward.D")

id1 <- idendro(hc1)

for (numbo in 1:cutnum) {

cdf <- as.data.frame(clust_list[[numbo]])

gsubsen <- function(x) {gsub("s\\d+ .. ", "", x)}

row.names(cdf) <- lapply(row.names(cdf), gsubsen)

cdf[] <- lapply(cdf, as.character)

cdf[,1] <- row.names(cdf)

setwd("C:/Users/cloud/Downloads/ClusterSentCritFinalRun3")

require(data.table)

for (i in 1:nrow(cdf)) {

  if ((file.info(paste(cdf[i,1],"",sep=""))$size) > 0) {

    if (as.character(read.table(paste(cdf[i,1],"",sep=""), header = F)[1,1]) %like% "INCLUSION CRITERION") {

      incexc2 <- "Inclusion criterion"

    }

    if (as.character(read.table(paste(cdf[i,1],"",sep=""), header = F)[1,1]) %like% "EXCLUSION CRITERION") {

      incexc2 <- "Exclusion criterion"

    }

    cdf[i,2] <- as.character(read.table(paste(cdf[i,1],"",sep=""), header = F)[1,1])  

    cdf[i,2] <- gsubin(cdf[i,2])

    cdf[i,2] <- gsubex(cdf[i,2])

    cdf[i,3] <- incexc2

  }

} 

cdf <- cdf[,c(1,2,3)]

setwd("C:/Users/cloud/Downloads/NewClusterRun5")

if (nrow(cdf)>1) {

n <- as.character(numbo)

str <- paste("cluster", n, ".txt", sep = "")

write.table(cdf,file = str, row.names = F, col.names = F)

}else {

  write.table(cdf,file = "clustersingletons.txt", row.names = F, col.names = F, append = TRUE)

}

}

cbindPad <- function(...){

  args <- list(...)

  n <- sapply(args,nrow)

  mx <- max(n)

  pad <- function(x, mx){

    if (nrow(x) < mx){

      nms <- colnames(x)

      padTemp <- matrix(NA, mx - nrow(x), ncol(x))

      colnames(padTemp) <- nms

      if (ncol(x)==0) {

        return(padTemp)

      } else {

        return(rbind(x,padTemp))

      }

    }

    else{

      return(x)

    }

  }

  rs <- lapply(args,pad,mx)

  return(do.call(cbind,rs))

}

numbo <- 1

while (numbo <= (cutnum +1)) {

  if (numbo <= cutnum) {

  str2 <- paste("cluster", numbo, ".txt", sep = "")

  }else {

    str2 <- "clustersingletons.txt"

  }

  setwd("C:/Users/cloud/Downloads/NewClusterRun5")

  res <- try(read.table(str2),silent = TRUE)

  if (!inherits(res, 'try-error')) {

    b <- read.table(str2)

    b <- b[,2, drop = F] 

    b[] <- lapply(b, as.character)

    b[] <- lapply(b, tolower)

    l <- as.data.frame(matrix(0, ncol = 1, nrow = (nrow(b))))

    for (i in 1:nrow(b)) {

      if (length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))) > ncol(l)) {

        l <- as.data.frame(matrix(0, ncol = length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))), nrow = (nrow(b))))

      }

    }

    n <- 1

    for (i in 1:nrow(b)) {

      n <- as.numeric(as.numeric(ncol(l)) - as.numeric(length( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE)))))

      l[i,] <- c( unlist(strsplit(unlist(strsplit (b[i,1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE)), rep("IGNORE", times = as.numeric(n)))

    }

    l <- cbind(l, rep(0, times = nrow(l)))

    names(l)[ncol(l)] <- "wc"

    for (i in 1:nrow(l)) {

      l[i,ncol(l)] <- length(grep("IGNORE", l[i,]))

    }

    row1 <- unlist(strsplit(unlist(strsplit(b[which.max(l$wc),1], "[^[:alnum:]<>=./]")), "(?=[<>=./])", perl = TRUE))

    l <- l[1:(ncol(l)-1)]

    d <- as.data.frame(matrix(.Machine$double.xmax, ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)

    listo <- rep(.Machine$double.xmax, times = nrow(l))

    results <- rep('IGNORE', times = ncol(l))

    n <- 1

    k <- 1

    g <- 1

    p <- 0

    s <- 1

    check <- 0

    ignorecheck <- 0

    switch01 <- 0

    while (n <= length(row1)) {

      while (k <= length(row1)) {

        p <- 0 

        if (n > 0) {

          if (k > 0) {

            for (i in 1:nrow(l)) {

              if (i > 0) {

                for (v in 1:ncol(l)) {

                  for (w in 1:ncol(l)) {  

                    if (s == 1) {  

                      if ( ((paste(l[i, v:w], collapse = ' ')) == (paste(row1[n:k], collapse = ' '))) ){

                        if (w < listo[i]) {  

                          p <- p + 1

                          listo[i] <- w

                          if (n == 1 & v > 1) {

                            check <- check + 1

                          }

                        }

                      }

                    }else {

                      if ( ((paste(l[i, v:w], collapse = ' ')) == (paste(row1[n:k], collapse = ' '))) ){

                        if (v > d[i,s-1]) {

                          if (w < listo[i]) {

                            p <- p + 1

                            listo[i] <- w

                          }

                        }

                      }

                    } 

                  } 

                }

              }    

            }

          }

        }

        if (p >= nrow(b)) {

          results[g] <- paste(row1[n:k], collapse = ' ')

          if (k == length(row1)) {

            n <- k

          }

          if (k < length(row1)) {

            k <- k + 1

          }

          d[,s] <- listo

          listo <- rep(.Machine$double.xmax, times = nrow(l))

          ignorecheck <- ignorecheck + 1

          switch01 <- 1

        }

        if ((p < nrow(b))) {

          if (n < length(row1)) {

            if (switch01 == 0) {

              n <- k + 1

              k <- n

            }

            if (switch01 == 1) {

              n <- k

            }

            g <- g + 2

            if (d[1,s] != .Machine$double.xmax) {

              s <- s + 1

            }

            listo <- rep(.Machine$double.xmax, times = nrow(l))

            switch01 <- 0 

          }

        }

        if (n == length(row1)) {

          n <- n + 1

          k <- k + 1

        }

      }

    }

    if (ignorecheck > 0) {

      results <- unlist(strsplit(results, " "))

      results <- as.data.frame((results))

      results <- cbind(results, rep("f", times = nrow(results)))

      colnames(results)[ncol(results)] <- "tf"

      results[] <- lapply(results, as.character)

      results <- results[complete.cases(results),]

      for (i in 2:nrow(results)) {

        if (results[i,1] == "IGNORE") {

          if (results[i,1] == results[(i-1),1]) {

            results[i,2] <- "t"

          }

        }

      }

      igcheck <- 0

      results <- subset(results, tf == "f")  

      results <- as.data.frame(results[,-(ncol(results))])

      colnames(results)[1] <- "Template"

      results <- as.character(results[,1])

      if (length(results) < ncol(l)) {

        for (i in (length(results)+1):(ncol(l))) {

          results[i] <- "IGNORE"

          igcheck <- 1

        }

      }

      if (check > 0) {

        results <- c("IGNORE", results)

      }

      seq <- as.data.frame(t(as.data.frame(results)))

      seq <- seq[,(1:(ncol(l)))]

      seq [] <- lapply(seq, as.character)

      l[] <- lapply(l, as.character)

      p <- list(as.character(print(seq[1,])))

      p <- as.data.frame(p)

      colnames(p)[1] <- "col1"

      p <- cbind(p, rep("f", times =nrow(p)))

      colnames(p)[2] <- "tf"

      p[,2] <- sapply(p[,2], as.character)

      for (i in 2:nrow(p)) {

        if ((trimws(p[i,1], which = "both")) == "IGNORE") {

          if (p[i,1] == p[(i-1),1])

            p[i,2] <- "t"

        }

      }

      p <- subset(p, tf == "f")

      p <- as.character(print(p[,1]))

      p <- paste(p,collapse=" ")

      w <- strsplit(p, "IGNORE")

      w <- as.data.frame(w[[1]])

      colnames(w)[1] <- "col1"

      w <- subset(w, col1 != " ")

      w <- subset(w, col1 != "")

      w <- as.character(w[,1])

      w <- gsub(" ","", w)

      non2 <- as.data.frame(matrix(0, ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)

      d2 <- as.data.frame(matrix("f", ncol = length(w), nrow = nrow(l)), stringsAsFactors = F)

      non2[] <- lapply(non2, as.numeric)

      g <- 1 

      for (j in 1:nrow(l)) {

        if (j > 0) {

          for (i in 1:length(w)) {

            if (i > 0) {

              for (k in 1:ncol(l)) {

                for (m in 1:ncol(l)) {

                  if ( (gsub(" ","",paste(l[j,k:m],collapse=" ")) == w[i]) & (d2[j,i] == "f") ){

                    d2[j,i] <- "t"

                    if (g == 1) {

                      non2[j, g] <- k

                      non2[j, g+1] <- m

                      g <- g + 2

                    }else if ((k > as.numeric(non2[j, (g-1)])) & (m > as.numeric(non2[j, (g-1)]))) {

                      non2[j, g] <- k

                      non2[j, g+1] <- m

                      g <- g + 2

                    }

                  }

                }

              }

            }

          }

        }

        g <- 1

      }

      non3 <- as.data.frame(matrix("IGNORE", ncol = ncol(l), nrow = nrow(l)), stringsAsFactors = F)

      g <- rep(1, times = nrow(non2))

      f <- 1

      for (m in 1:nrow(non2)) {

        q <- as.character(print(non2[m,]))

        q <- paste(q,collapse=" ")

        q <- unlist(strsplit(q, " "))

        x <- 1

        while (x <= length(q)) {

          if (q[x] == "0") {

            q <- q[-x]

          }else {

            x <- x + 1

          }

        }

        q <- list(q)

        q <- as.data.frame(q[[1]])

        colnames(q)[1] <- "col1"

        q <- subset(q, col1 != "")

        q[,1] <- sapply(q[,1], as.character)

        q[,1] <- sapply(q[,1], as.numeric)

        i <- 1

        while (i <= nrow(q)) {

          if (i == 1) { 

            if (as.numeric(q[i,1]-1) >=1) {

              non3[m,g[m]] <- paste(as.character(l[m,1:(as.numeric(q[i,1]-1))]), collapse = " ")

              g[m] <- g[m] + 1

            }else {

              g[m] <- 2

            }

          }

          if ((i %% 2 == 0) & (i != nrow(q)) & ((as.numeric(q[i+1,1]-1)) >= (as.numeric(q[i,1]+1)))) {

            non3[m,g[m]] <- paste(as.character(l[m,(as.numeric(q[i,1]+1)):(as.numeric(q[i+1,1]-1))]), collapse = " ")

            g[m] <- g[m] + 1

          }

          if ((i %% 2 == 0) & (i != nrow(q)) & ((as.numeric(q[i+1,1]-1)) < (as.numeric(q[i,1]+1)))) {

            g[m] <- g[m] + 1

          }

          if ((i %% 2 == 0) & (i == nrow(q)) & (as.numeric(q[i,1]+1) <= as.numeric(ncol(l)))) {

            non3[m,g[m]] <- paste(as.character(l[m,(as.numeric(q[i,1]+1)):(as.numeric(ncol(l)))]), collapse = " ")

            g[m] <- g[m] + 1

          }

          if (i < nrow(q)) {

            i <- i + 1

          }else {

            break

          }

        }

      }

      for (i in 1:ncol(seq)) {

        if (seq[1,i] == "IGNORE") {

          seq[1,i] <- "BLANK" 

        }

      }

      non3 <- as.data.frame(t(non3))

      non3 <- cbind(non3, rep("f", times = nrow(non3)))

      colnames(non3)[ncol(non3)] <- "tf"

      non3[] <- lapply(non3, as.character)

      for (i in 1:nrow(non3)) {

        if (paste(as.character(print(non3[i,1:(ncol(non3)-1)])), collapse = " ") == paste(as.character(rep("IGNORE", times = ncol(non3)-1)), collapse = " ")) {

          non3[i,ncol(non3)] <- "t" 

        }

      }

      non3 <- subset(non3, tf == "f")  

      non3 <- non3[,-(ncol(non3))]

      non3 <- as.data.frame(t(non3))

      seq <- as.data.frame(t(seq))

      seq <- cbind(seq, rep("f", times = nrow(seq)))

      colnames(seq)[ncol(seq)] <- "tf"

      seq[] <- lapply(seq, as.character)

      for (i in 2:nrow(seq)) {

        if (seq[i,1] == "BLANK") {

          if (seq[i,1] == seq[(i-1),1]) {

            seq[i,2] <- "t"

          }

        }

      }

      if (seq[nrow(seq),1] == "BLANK") {

        if (igcheck == 1) {

          seq[nrow(seq),2] <- "t" 

        }

      }

      seq <- subset(seq, tf == "f")  

      seq <- as.data.frame(seq[,-(ncol(seq))])

      colnames(seq)[1] <- "Template"

      seq <- as.data.frame(t(seq))

      template <- seq

      fillins <- non3

      if (ncol(non3) > 0) {

        for (j in 1:ncol(fillins)) {

          fillinstest <- as.character(fillins[,j])

          for (i in 1:length(fillinstest)) {

            fillinstest[i] <- gsub("IGNORE", "", fillinstest[i])

          }

          fillins[,j] <- fillinstest

        }

        i <- 1

        while (i <=  ncol(fillins)) {

          fillins <- as.data.frame(cbind (fillins[,c(1:i)], rep(1, times = nrow(fillins)), fillins[,-c(1:i)]))

          i <- i+ 2

        }

        for (i in 1:ncol(fillins)) {

          if (i %% 2 == 0) {

            colnames(fillins)[i] <- "Frequency"

            fillins[,i] <- sapply(fillins[,i], as.character)

            fillins[,i] <- sapply(fillins[,i], as.numeric)

          }

        }

        for (i in 1:ncol(fillins)) {

          if (i %% 2 == 1) {

            colnames(fillins)[i] <- paste("Blank", (i+1)/2, collapse ="")

            fillins[,i] <- sapply(fillins[,i], as.character)

          }

        }

        for (j in 1:ncol(fillins)) {

          for (i in 1:nrow(fillins)) {

            if (j %% 2 == 1) {

              for (k in 1:i) {

                if (k < i) {

                  if (trimws(fillins[i, j], which = "both") == trimws(fillins[k,j], which = "both")) {

                    fillins[k, j+1] <- fillins[k, j+1] + 1

                    fillins[i, j] <- paste("IGNORE", i, collapse ="")

                    fillins[i, j + 1] <- 0 

                  }

                }

              }

            }

          }

        }

      }

    } else {

      template <- fillins <- as.data.frame(matrix("", ncol = 1, nrow = 1))

    }

    template <- cbindPad(template, b)

    fillins <- cbindPad(fillins, b)

    names(template)[ncol(template)] <- "Cluster Text"

    names(fillins)[ncol(fillins)] <- "Cluster Text"

    setwd("C:/Users/cloud/Downloads/PipelineTestRun5") 

    numbochar <- as.character(numbo)

    numbotempstr <- paste("template", numbochar, ".csv", sep = "")

    numbofillinsstr <- paste("fillins", numbochar, ".csv", sep = "")

    write.csv(template, file = numbotempstr, row.names = F)

    write.csv(fillins, file = numbofillinsstr, col.names = F)

  }

  numbo <- numbo + 1

}