--- a
+++ b/main.R
@@ -0,0 +1,140 @@
+Get_PubMed_Data <- function(topic, start_date, end_date, return_count) {
+  require(RISmed)
+  
+  search_query <- EUtilsSummary(topic, retmax=return_count, mindate=start_date,maxdate=end_date)
+  summary(search_query)
+  # see the ids of our returned query
+  QueryId(search_query)
+  # get actual data from PubMed
+  records<- EUtilsGet(search_query)
+  class(records)
+  # store it
+  pubmed_data <- data.frame('Title'=ArticleTitle(records),'Abstract'=AbstractText(records))
+  head(pubmed_data,1)
+  pubmed_data$Title <- as.character(pubmed_data$Title)
+  pubmed_data$Abstract <- as.character(pubmed_data$Abstract)
+  pubmed_data$Abstract <- gsub(",", " ", pubmed_data$Abstract, fixed = TRUE)
+  
+  return (pubmed_data)
+}
+
+medical_corpus <- Get_PubMed_Data('cardiology', 2013, 2015, 1500)
+dim(medical_corpus)
+head(medical_corpus)
+
+Text_To_Clean_Sentences <- function(text_blob) {
+  # swap all sentence ends with code 'ootoo'
+  text_blob <- gsub(pattern=';|\\.|!|\\?', x=text_blob, replacement='ootoo')
+  
+  # remove all non-alpha text (numbers etc)
+  text_blob <- gsub(pattern="[^[:alpha:]]", x=text_blob, replacement = ' ')
+  
+  # force all characters to lower case
+  text_blob <- tolower(text_blob)
+  
+  # remove any small words {size} or {min,max}
+  text_blob <- gsub(pattern="\\W*\\b\\w{1,2}\\b", x=text_blob, replacement=' ')
+  
+  # remove contiguous spaces
+  text_blob <- gsub(pattern="\\s+", x=text_blob, replacement=' ')
+  
+  # split sentences by split code
+  sentence_vector <- unlist(strsplit(x=text_blob, split='ootoo',fixed = TRUE))
+  return (sentence_vector)
+}
+
+corpus_sentences <- Text_To_Clean_Sentences(paste(medical_corpus$Abstract, collapse=" "))
+
+
+test_sentence <- "this is a big sentence"
+
+library(ngram)
+ng_2 <- ngram(test_sentence , n=2)
+print(ng_2)
+
+Trim <- function( x ) {
+  gsub("(^[[:space:]]+|[[:space:]]+$)", "", x)
+}
+
+
+Get_Ngrams <- function(sentence_splits, ngram_size=2) {
+  ngrams <- c()
+  for (sentence in sentence_splits) {
+    sentence <- Trim(sentence)
+    if ((nchar(sentence) > 0) && (sapply(gregexpr("\\W+", sentence), length) >= ngram_size)) {
+      ngs <- ngram(sentence , n=ngram_size)
+      ngrams <- c(ngrams, get.ngrams(ngs))
+    }
+  }
+  return (ngrams)
+}
+
+n2 <- Get_Ngrams(corpus_sentences, ngram_size=2)
+n3 <- Get_Ngrams(corpus_sentences, ngram_size=3)
+n4 <- Get_Ngrams(corpus_sentences, ngram_size=4)
+n5 <- Get_Ngrams(corpus_sentences, ngram_size=5)
+
+# consolidate all n-gram vectors into one
+n_all <- c(n2, n3, n4, n5)
+
+# save the n-grams in the same folder as your shiny code
+write.csv(n_all, "c:\\cordova\\pubmed_cardiology_ngrams.csv", row.names=FALSE)
+
+head(n_all)
+length(n_all)
+
+# notice the trailing space at end to avoid picking last word
+word <- 'infection '
+
+matches <- c()
+for (sentence in n_all) {
+  # find exact match with double backslash and escape
+  if (grepl(paste0('\\<',word), sentence)) {
+    print(sentence)
+    matches <- c(matches, sentence)
+  }
+}
+
+# find highest probability word
+precision_match <- c()
+for (a_match in matches) {
+  # how many spaces in from of search word
+  precision_match <- c(precision_match,nchar(strsplit(x = a_match, split = word)[[1]][[1]]))
+}
+
+# use highest number and a random of highest for multiples
+best_matched_sentence <- sample(matches[precision_match == max(precision_match)],size = 1)
+
+print(best_matched_sentence)
+
+# notice the trailing space at end to avoid picking last word
+word <- 'infection '
+
+matches <- c()
+for (sentence in n_all) {
+  # find exact match with double backslash and escape
+  if (grepl(paste0('\\<',word), sentence)) {
+    print(sentence)
+    matches <- c(matches, sentence)
+  }
+}
+
+# find highest probability word
+precision_match <- c()
+for (a_match in matches) {
+  # how many spaces in from of search word
+  precision_match <- c(precision_match,nchar(strsplit(x = a_match, split = word)[[1]][[1]]))
+}
+
+# use highest number and a random of highest for multiples
+best_matched_sentence <- sample(matches[precision_match == max(precision_match)],size = 1)
+
+print(best_matched_sentence)
+
+# split the best matching sentence by the search word
+best_match <- strsplit(x = best_matched_sentence, split = word)[[1]]
+# split second part by spaces and pick first word
+best_match <-  strsplit(x = best_match[[2]], split = " ")[[1]]
+best_match <- best_match[[1]]
+
+print(best_match)