--- a
+++ b/scripts/AllClinTrialRun(NOTWORKING).R
@@ -0,0 +1,85 @@
+library("tm")
+library("SnowballC")
+library("ggplot2")
+library("wordcloud")
+library("stringi")
+
+setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads")
+
+thingcsv <- read.csv("allInclusionExclusionBulletPoint.csv", encoding = "latin1")
+thingcsv <- as.data.frame(thingcsv[,4])
+thingcsv[] <- lapply(thingcsv, as.character)
+for (l in 1:nrow(thingcsv)) {
+  thingcsv[l,] <- stringi::stri_trans_general(thingcsv[l,], "latin-ascii")
+}
+setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads/ClusterSentAllCTFinal2")
+n <- 1
+for (i in 1:nrow(thingcsv)) {
+  if (!is.na(thingcsv[i,1])) {
+    if (thingcsv[i,1] != "" & thingcsv[i,1] != "#NAME?" & thingcsv[i,1] != "All") {
+      n <- as.character(n)
+      str <- paste("allsent", n, ".txt", sep = "")
+      write.table(as.data.frame(thingcsv[i,1]),file = str, row.names = F, col.names = F)
+      n <- as.numeric(n)
+      n <- n + 1
+    }
+  }
+}
+
+
+allsentdocs <- Corpus(DirSource("/afs/athena.mit.edu/user/w/i/williame/Downloads/ClusterSentAllCTFinal2"))
+writeLines(as.character(allsentdocs[[25]]))
+
+allsentdocs <- tm_map(allsentdocs,content_transformer(tolower))
+toSpace <- content_transformer(function(x, pattern) { return (gsub(pattern, " ", x))})
+allsentdocs <- tm_map(allsentdocs, toSpace, '"')
+allsentdocs <- tm_map(allsentdocs, removeWords, stopwords("english"))
+allsentdocs <- tm_map(allsentdocs, stripWhitespace)
+allsentdocs <- tm_map(allsentdocs,stemDocument)
+allsentdtm <- DocumentTermMatrix(allsentdocs)
+allsentm <- as.matrix(allsentdtm)
+rownames(allsentm) <- paste(substring(rownames(allsentm),1,3),rep("..",nrow(allsentm)), substring(rownames(allsentm), nchar(rownames(allsentm))-12,nchar(rownames(allsentm))-4))
+allsentd <- dist(allsentm)
+setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads")
+write.csv(as.matrix(allsentd), file ="distmatclusterallsentfinal2.csv")
+allsentgroups <- hclust(allsentd,method="ward.D")
+allsentgroupsplot <- as.dendrogram(allsentgroups)
+
+plot(allsentgroups, hang=-1)
+par(mfrow=c(3,1))
+
+plot(allsentgroupsplot, main="Main")
+plot(cut(allsentgroupsplot, h=4000)$upper, 
+     main="Upper tree of cut at h=1000")
+plot(cut(allsentgroupsplot, h=4000)$lower[[2]], 
+     main="Second branch of lower tree with cut at h=3000")
+library("ggplot2")
+library("ggdendro")
+
+ggdendrogram(allsentgroups)
+allsentdata <- dendro_data(allsentgroupsplot, type = "rectangle")
+head(allsentdata$labels)
+
+allsentdatalabel<- allsentdata[["labels"]][["label"]]
+
+allsentdatalabeldf <- as.data.frame(allsentdatalabel)
+allsentdatalabeldf <- as.data.frame(cbind(allsentdatalabeldf, rep("n/a", times = nrow(allsentdatalabeldf))))
+gsuballsen <- function(x) {gsub("all .. ", "", x)} #this might not be right
+allsentdatalabeldf$allsentdatalabel <- lapply(allsentdatalabeldf$allsentdatalabel, gsuballsen)
+setwd("C:/Users/AI/Downloads/ClusterSentAllCTFinal2")
+colnames(allsentdatalabeldf)[c(1,2)] <- c("file", "text")
+allsentdatalabeldf[] <- lapply(allsentdatalabeldf, as.character)
+for (i in 1:nrow(allsentdatalabeldf)) {
+  allsentdatalabeldf[i,2] <- as.character(read.table(paste(allsentdatalabeldf[i,1],".txt",sep=""), header = F)[1,1])
+  
+} 
+
+setwd("/afs/athena.mit.edu/user/w/i/williame/Downloads")
+
+write.csv(allsentdatalabeldf, file = "allsentclusterresultsclean.csv")
+
+
+pdf("pdfgraphallsentfinal2.pdf", width=40, height=15)
+plot(allsentgroups, hang=-1)
+dev.off()
+