From 24809abf2786da48e57ea86d246f2ea51686f2c9 Mon Sep 17 00:00:00 2001
From: Weiting <weitinglin66@gmail.com>
Date: Mon, 15 Feb 2016 00:25:39 +0800
Subject: [PATCH] use xml package rewrite the code

---
 version2.R | 82 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 version2.R

diff --git a/version2.R b/version2.R
new file mode 100644
index 0000000..7bc003d
--- /dev/null
+++ b/version2.R
@@ -0,0 +1,82 @@
+#set working directory
+setwd("/Users/jasonlin/Documents/2016/2016 Practice/20160124")
+
+#loading package
+library(dplyr)
+library(ggplot2)
+library(reshape2)
+library(RCurl)
+library(XML)
+
+raw_data<-readLines("testlab.html",encoding = "BIG-5")
+raw_data<-iconv(raw_data,from ="BIG-5",to = "UTF-8")
+
+#seperate the data sheet
+pages<-grep("<table border",raw_data)
+#===============================
+pagecut<-function(pages,raw_data){
+  output<-list()
+  for( i in 1: length(pages)){
+    if(i < length(pages)){
+      a<-pages[i];b<-pages[(i+1)]-1
+      output[[i]]<-raw_data[a:b]
+    }else{
+      a<-pages[i]
+      output[[i]]<-raw_data[a:length(raw_data)]
+    }
+  }
+  return(output)
+}
+#============================
+#cut the data into 6 page with "<table"
+pages<-pagecut(pages,raw_data)
+#separate the 1st page's table into page1_table
+pages1<-grep("Date",pages[[1]])
+page1_table<-pagecut(pages1,pages[[1]])
+#use XML package
+index<-c(1,2,84:798)
+tables_test_index <- readHTMLTable(pages[[1]][index],encoding="UTF-8",as.data.frame = TRUE)
+#get the time 
+page_1_date_line<-grep("<tr><td",unlist(page1_table))
+time1_raw<-c(unlist(page1_table)[seq(3,(page_1_date_line-2),by=2)])
+#===============function:filter_chr(time1_raw) no.2  need
+filter_chr<-function(time1_raw){
+  for(i in 1:length(time1_raw)){
+    n<-regexpr("<tt>",time1_raw[i])+4
+    time1_raw[i]<-substring(time1_raw[i],n[1],n[1]+7)
+  }
+  return(time1_raw)}
+time1<-filter_chr(time1_raw)   ##the lab data time
+#name
+name_raw<-raw_data[grep("姓名",raw_data)[1]+2]
+name<-substring(name_raw,(regexpr("tt",name_raw)+3),(regexpr("tt",name_raw)+5))
+
+#patient_id
+id_raw<-raw_data[grep("病歷號",raw_data)[1]+2]
+id<-substring(id_raw,(regexpr("tt",id_raw)+3),(regexpr("tt",id_raw)+9))
+
+#gender
+gender_raw<-raw_data[grep("性別",raw_data)[1]+2]
+gender<-substring(gender_raw,(regexpr("tt",gender_raw)[1]+3),(regexpr("tt",gender_raw)[1]+3))
+#birthday
+birth_raw<-raw_data[grep("生日",raw_data)[1]+2]
+birth<-getlabname(birth_raw)
+#try 1
+names(tables_test_index)<-"table1"
+index_table<-c(2,seq(4,28,by=4))
+clean_test<-tables_test_index$table1[index_table]
+sapply(clean_test[,1],function(x){nchar(as.character(x))})>0 -> rule_out
+#remove the NA column
+clean_test<-clean_test[rule_out,]
+#remove duplicate data : normale plasma mean
+!duplicated(clean_test[,1],fromLast = TRUE)&!duplicated(clean_test[,1]) -> duplicat_index
+clean_test<-clean_test[duplicat_index,]
+row.names(clean_test)<-clean_test[,1]
+colnames(clean_test)[1]<-c("Lab_data")
+colnames(clean_test)[2:8]<-time1
+#
+clean_test
+clean_melt_test<-melt(clean_test,id.vars = "Lab_data")
+clean_melt_test$ID<-id
+clean_melt_test$BIRTH<-birth
+clean_melt_test$GENDER<-gender