#数据集来源http://spamassassin.apache.org/publiccorpus/

#加载数据

library(tm)
library(ggplot2)
data.path<-'F:\\dataguru\\ML_for_Hackers\\ML_for_Hackers-master\\03-Classification\\data\\'
easyham.path<-paste(data.path,'easy_ham\\',sep='')

#读取文件的函数msg.full,返回一个向量,每一个元素都是邮件中的一行

msg.full <- function(path)
{
con <- file(path, open = "rt", encoding = "latin1")
msg <- readLines(con)
close(con)
return(msg)
}

#用正则表达式提取发件人地址,总是在From:后面,有些用<括起来>,有些没有

#参数是一封邮件向量,每一个元素就是邮件的一行

get.from <- function(msg.vec)
{

#查找所有有From:的行
from <- msg.vec[grepl("From: ", msg.vec)]

#按[":等符号进行拆分
from <- strsplit(from, '[":<> ]')[[1]]

#忽略空元素
from <- from[which(from != "" & from != " ")]

#取出带@的邮件地址的那一部分并返回
return(from[grepl("@", from)][1])
}

#提取主题

get.subject <- function(msg.vec)
{
subj <- msg.vec[grepl("Subject: ", msg.vec)]
if(length(subj) > 0)
{
return(strsplit(subj, "Subject: ")[[1]][2])
}
else
{
return("")
}
}

#读取正文,正文总是在第一个空行后面

get.msg <- function(msg.vec)
{
msg <- msg.vec[seq(which(msg.vec == "")[1] + 1, length(msg.vec), 1)]
return(paste(msg, collapse = "\n"))
}

#读取日期

get.date <- function(msg.vec)
{

#只保留以Date:开头的,也有其他开头的日期并不是我们要的
date.grep <- grepl("^Date: ", msg.vec)
date.grep <- which(date.grep == TRUE)

#邮件中的某一行也可能以Date:开头,因此只返回邮件第一行以Date:开头的
date <- msg.vec[date.grep[1]]

#冒号和+,冒号和-之间是我们要的日期
date <- strsplit(date, "\\+|\\-|: ")[[1]][2]

#以下gsub是把开头和结尾的空白字符去掉
date <- gsub("^\\s+|\\s+$", "", date)

#语料库中的标准日期格式只有25个字符,后面的可以全部不要
return(strtrim(date, 25))
}

#抽取4个特征，发件人地址，接收日期，主题，邮件正文

parse.email <- function(path)
{
full.msg <- msg.full(path)
date <- get.date(full.msg)
from <- get.from(full.msg)
subj <- get.subject(full.msg)
msg <- get.msg(full.msg)
return(c(date, from, subj, msg, path))
}

#开始处理文档吧

easyham.docs <- dir(easyham.path)
easyham.docs <- easyham.docs[which(easyham.docs != "cmds")]

#一个LIST,共2500个元素,每一个元素是一封邮件,分别包含时间,发件人,主题,正文,路径
easyham.parse <- lapply(easyham.docs,
function(p) parse.email(file.path(easyham.path, p)))

# Convert raw data from list to data frame
ehparse.matrix <- do.call(rbind, easyham.parse)
allparse.df <- data.frame(ehparse.matrix, stringsAsFactors = FALSE)
names(allparse.df) <- c("Date", "From.EMail", "Subject", "Message", "Path")

#allparse.df数据框,共2500行,每行一个邮件

#把日期处理成统一格式

#有两种格式

#Web,04 Dec 2002 11:36:32

#04 Dec 2002 11:36:32

#strptime的返回结果,能转则返回datetime类型,不能则返回NA

date.converter <- function(dates, pattern1, pattern2)
{
pattern1.convert <- strptime(dates, pattern1)
pattern2.convert <- strptime(dates, pattern2)
pattern1.convert[is.na(pattern1.convert)] <- pattern2.convert[is.na(pattern1.convert)]
return(pattern1.convert)
}

pattern1 <- "%a, %d %b %Y %H:%M:%S"
pattern2 <- "%d %b %Y %H:%M:%S"

#以下一句是我补充的,可能是操作系统问题,导致strptime返回值永远是NA,加上以下一句就不会

Sys.setlocale("LC_TIME", "C");

allparse.df$Date <- date.converter(allparse.df$Date, pattern1, pattern2)

allparse.df$Subject <- tolower(allparse.df$Subject)
allparse.df$From.EMail <- tolower(allparse.df$From.EMail)

#按时间顺序排,存入priority.df

#with将操作限制在数据框
priority.df <- allparse.df[with(allparse.df, order(Date)), ]

#分成两半,一半作训练集,剩下的作测试集,共1250条数据,包括日期,发件人,主题,正文,路径
priority.train <- priority.df[1:(round(nrow(priority.df) / 2)), ]

#以下注释掉的是书上的,不可用会出错,不知道怎么改

#from.weight<-ddply(priority.train,.(From.EMail),summarise,Freq=length(Subject))

#melt要加载reshape2包,计算每个发件人的次数

#with(priority.train, table(From.EMail))可以统计priority.train中From.EMail的频数

#melt转化为数据框并为频数加了列名

#from.weight就是发件人的发件频数

from.weight <- melt(with(priority.train, table(From.EMail)), value.name="Freq")

#排个序

from.weight <- from.weight[with(from.weight, order(Freq)), ]

#画个图，只取频数>6的画图，共52条，纵轴是X，横轴是Y

from.ex <- subset(from.weight, Freq > 6)

from.scales <- ggplot(from.ex) +
geom_rect(aes(xmin = 1:nrow(from.ex) - 0.5,
xmax = 1:nrow(from.ex) + 0.5,
ymin = 0,
ymax = Freq,
fill = "lightgrey",
color = "darkblue")) +
scale_x_continuous(breaks = 1:nrow(from.ex), labels = from.ex$From.EMail) +
coord_flip() +
scale_fill_manual(values = c("lightgrey" = "lightgrey"), guide = "none") +
scale_color_manual(values = c("darkblue" = "darkblue"), guide = "none") +
ylab("Number of Emails Received (truncated at 6)") +
xlab("Sender Address") +
theme_bw() +
theme(axis.text.y = element_text(size = 5, hjust = 1))

#如上图排名第一那位发太多了,会导致权重产生偏移,需要用Log加权策略,让特征数值关系不那么极端

#有自然对数,以e为底

#有常用对数,以10为底

#画个图对比一下

from.weight <- transform(from.weight,Weight = log(Freq + 1),log10Weight = log10(Freq + 1))

#from.weight共346行,数据框,两列,发件人,频数

from.rescaled <- ggplot(from.weight, aes(x = 1:nrow(from.weight))) +
geom_line(aes(y = Weight, linetype = "ln")) +
geom_line(aes(y = log10Weight, linetype = "log10")) +
geom_line(aes(y = Freq, linetype = "Absolute")) +
scale_linetype_manual(values = c("ln" = 1,
"log10" = 2,
"Absolute" = 3),
name = "Scaling") +
xlab("") +
ylab("Number of emails Receieved") +
theme_bw() +
theme(axis.text.y = element_blank(), axis.text.x = element_blank())

#变换后,曲线平缓了,常用对数变换程度更大,而自然对数变换还是保留了一些差异性,因此采用自然对数

#线程,用户和发件方来回回复邮件称为一个线程,以下函数用于查找线程,结果两列，是发件人及主题

find.threads <- function(email.df)
{
response.threads <- strsplit(email.df$Subject, "re: ")

#如果用re:分割后什么都没有,说明是初始线程,不是回复的邮件
is.thread <- sapply(response.threads,
function(subj) ifelse(subj[1] == "", TRUE, FALSE))

threads <- response.threads[is.thread]
senders <- email.df$From.EMail[is.thread]

#下面一句，万一主题中还有re:被分割了，那么再把它连起来拼回去
threads <- sapply(threads,function(t) paste(t[2:length(t)], collapse = "re: "))
return(cbind(senders,threads))
}

#threads.matrix共755行,这是初始线程,共两列,发件人,主题

threads.matrix <- find.threads(priority.train)

#给初始线程发件人赋权重,结果是数据框共三列发件Email，频次及权重，参数第一列是发件人，第二列是主题

email.thread <- function(threads.matrix)
{

#threads.matrix初始线程矩阵，只有两列,列1是发件人,列2是主题
senders <- threads.matrix[, 1]

#table，计算发件人频数，结果是一个table
senders.freq <- table(senders)

#结果转矩阵，矩阵有三个列，分别是发件人，频数及权重。这个矩阵每一行都有名字，就是发件人
senders.matrix <- cbind(names(senders.freq),
senders.freq,
log(senders.freq + 1))
senders.df <- data.frame(senders.matrix, stringsAsFactors=FALSE)

#将矩阵的行名字换成行号
row.names(senders.df) <- 1:nrow(senders.df)
names(senders.df) <- c("From.EMail", "Freq", "Weight")
senders.df$Freq <- as.numeric(senders.df$Freq)
senders.df$Weight <- as.numeric(senders.df$Weight)
return(senders.df)
}

#计算线程活跃度，参数thread是一个初始线程，email.df是所有电子邮件，包含了5个特征

#返回线程的活跃度，时间间隔及权重，意思在活跃度相同的情况下，来回时间短的信件更重要

#只要初始线程同名就全部一起计算，不管发件人是谁

thread.counts <- function(thread, email.df)
{
#获取该初始线程连接所有回复的所有时间
thread.times <- email.df$Date[which(email.df$Subject == thread |email.df$Subject == paste("re:", thread))]

#freq表明该线程活跃度
freq <- length(thread.times)
min.time <- min(thread.times)
max.time <- max(thread.times)

#计算最早和最晚时间来往的间隔
time.span <- as.numeric(difftime(max.time, min.time, units = "secs"))

#活跃度是1
if(freq < 2)
{
return(c(NA, NA, NA))
}
else
{

#活跃度>=2
trans.weight <- freq / time.span

#为了保证值是正的，所以加了10保证肯定能得到正值
log.trans.weight <- 10 + log(trans.weight, base = 10)
return(c(freq, time.span, log.trans.weight))
}
}

#senders.df共233条记录，是初始线程中的发件*重，包括发件人，活跃度及权重

#from.weight共346条记录，是所有发件*重，包括发件人，活跃度及权重，还有一个试验用的常用对数权重(讲解常用对数和自然对数用的,后面代码实验并不用这个列)

senders.df <- email.thread(threads.matrix)

#参数一是线程矩阵(发件人,主题),参数2是Email权重(发件人,权重)，返回矩阵，线程名，频次，间隔及权重

get.threads <- function(threads.matrix, email.df)
{

#unique好像是去重，按主题去重，不管发件人是谁

#语料库中，有好几个不同的邮箱发来主题一模一样的邮件
threads <- unique(threads.matrix[, 2])
thread.counts <- lapply(threads,function(t) thread.counts(t, email.df))
thread.matrix <- do.call(rbind, thread.counts)
return(cbind(threads, thread.matrix))
}

#thread.weights是线程，频次，时间间隔及权重

thread.weights <- get.threads(threads.matrix, priority.train)

thread.weights <- data.frame(thread.weights, stringsAsFactors = FALSE)
names(thread.weights) <- c("Thread", "Freq", "Response", "Weight")
thread.weights$Freq <- as.numeric(thread.weights$Freq)
thread.weights$Response <- as.numeric(thread.weights$Response)
thread.weights$Weight <- as.numeric(thread.weights$Weight)

#以下，频次不是空的，完全没回复过，频次为空，有回复过频次不为空

#从254条降到176条
thread.weights <- subset(thread.weights, is.na(thread.weights$Freq) == FALSE)

#term.counts算词频

term.counts <- function(term.vec, control)
{
vec.corpus <- Corpus(VectorSource(term.vec))
vec.tdm <- TermDocumentMatrix(vec.corpus, control = control)
return(rowSums(as.matrix(vec.tdm)))
}

thread.terms <- term.counts(thread.weights$Thread,
control = list(stopwords = TRUE))

#只留下词项
thread.terms <- names(thread.terms)

#计算包含了该词所有主题的权重均值，作为词频权重

term.weights <- sapply(thread.terms,
function(t) mean(thread.weights$Weight[grepl(t, thread.weights$Thread, fixed = TRUE)]))

#转数据框，把行名改成行号，因此得到一个词频权重矩阵，472条记录
term.weights <- data.frame(list(Term = names(term.weights),
Weight = term.weights),
stringsAsFactors = FALSE,
row.names = 1:length(term.weights))

# Finally, create weighting based on frequency of terms in email.
# Will be similar to SPAM detection, but in this case weighting
# high words that are particularly HAMMMY.

#正文算权重，19479条记录

msg.terms <- term.counts(priority.train$Message,
control = list(stopwords = TRUE,
removePunctuation = TRUE,
removeNumbers = TRUE))
msg.weights <- data.frame(list(Term = names(msg.terms),
Weight = log(msg.terms, base = 10)),
stringsAsFactors = FALSE,
row.names = 1:length(msg.terms))

#只留下权重大于0的，剩下11400条记录

msg.weights <- subset(msg.weights, Weight > 0)

#查询词项权重，True取正文权重，FALSE取主题权重？

get.weights <- function(search.term, weight.df, term = TRUE)
{
if(length(search.term) > 0)
{
if(term)
{
term.match <- match(names(search.term), weight.df$Term)
}
else
{
term.match <- match(search.term, weight.df$Thread)
}
match.weights <- weight.df$Weight[which(!is.na(term.match))]

#这里书上写>1，是书上写错了，给的代码是没错的
if(length(match.weights) < 1)
{
return(1)
}
else
{
return(mean(match.weights))
}
}
else
{
return(1)
}
}

#rank.message函数,在特征还未映射为一个权重值时执行权重查找,即主题和正文词项

#对目录path下的所有文件得出日期，发件人，主题，得分

rank.message <- function(path)
{

#抽取4个特征
msg <- parse.email(path)

#msg1是日期，msg2是发件人,msg3是主题,msg4是正文
# Weighting based on message author
#判断抽取特征是否出现在某个用于排序的权重数据框中,并赋上相应的权重
# First is just on the total frequency

#from.weight权重在0.69和3.82间
from <- ifelse(length(which(from.weight$From.EMail == msg[2])) > 0,
from.weight$Weight[which(from.weight$From.EMail == msg[2])],
1)
#senders.df权重在0.69和3.4之间
# Second is based on senders in threads, and threads themselves
thread.from <- ifelse(length(which(senders.df$From.EMail == msg[2])) > 0,
senders.df$Weight[which(senders.df$From.EMail == msg[2])],
1)
#下面是查一下是不是初始线程
subj <- strsplit(tolower(msg[3]), "re: ")
is.thread <- ifelse(subj[[1]][1] == "", TRUE, FALSE)

if(is.thread)
{

#如果是初始线程，去查询线程权重thread.weights，该权重值在4.4和8.5之间
activity <- get.weights(subj[[1]][2], thread.weights, term = FALSE)
}
else
{
activity <- 1
}

# Next, weight based on terms

# Weight based on terms in threads
thread.terms <- term.counts(msg[3], control = list(stopwords = TRUE))
thread.terms.weights <- get.weights(thread.terms, term.weights)

# Weight based terms in all messages
msg.terms <- term.counts(msg[4],
control = list(stopwords = TRUE,
removePunctuation = TRUE,
removeNumbers = TRUE))
msg.weights <- get.weights(msg.terms, msg.weights)

# Calculate rank by interacting all weights

#所有权重全部相乘
rank <- prod(from,
thread.from,
activity,
thread.terms.weights,
msg.weights)
#返回日期，发件人，主题，权重结果
return(c(msg[1], msg[2], msg[3], rank))
}

#训练集路径和测试集路径

train.paths <- priority.df$Path[1:(round(nrow(priority.df) / 2))]
test.paths <- priority.df$Path[((round(nrow(priority.df) / 2)) + 1):nrow(priority.df)]

# Now, create a full-featured training set.

#去训练
train.ranks <- suppressWarnings(lapply(train.paths, rank.message))
train.ranks.matrix <- do.call(rbind, train.ranks)
train.ranks.matrix <- cbind(train.paths, train.ranks.matrix, "TRAINING")
train.ranks.df <- data.frame(train.ranks.matrix, stringsAsFactors = FALSE)
names(train.ranks.df) <- c("Message", "Date", "From", "Subj", "Rank", "Type")
train.ranks.df$Rank <- as.numeric(train.ranks.df$Rank)

# Set the priority threshold to the median of all ranks weights

#训练结果中取个中位数作为阈值
priority.threshold <- median(train.ranks.df$Rank)

# Visualize the results to locate threshold
threshold.plot <- ggplot(train.ranks.df, aes(x = Rank)) +
stat_density(aes(fill="darkred")) +
geom_vline(xintercept = priority.threshold, linetype = 2) +
scale_fill_manual(values = c("darkred" = "darkred"), guide = "none") +
theme_bw()
print(threshold.plot)

#下图，虚线是阈值，排序结果是明显的重尾分布，表示算法不错，左边是低于阈值的，右边是高于阈值的

#斜率向下倾斜的都优先推荐了，表示结果不错

# Classify as priority, or not，以中位数分类，1表示优先
train.ranks.df$Priority <- ifelse(train.ranks.df$Rank >= priority.threshold, 1, 0)

#去测试集运行一下，使用训练集得出来的阈值来划分

test.ranks <- suppressWarnings(lapply(test.paths,rank.message))
test.ranks.matrix <- do.call(rbind, test.ranks)
test.ranks.matrix <- cbind(test.paths, test.ranks.matrix, "TESTING")
test.ranks.df <- data.frame(test.ranks.matrix, stringsAsFactors = FALSE)
names(test.ranks.df) <- c("Message","Date","From","Subj","Rank","Type")
test.ranks.df$Rank <- as.numeric(test.ranks.df$Rank)
test.ranks.df$Priority <- ifelse(test.ranks.df$Rank >= priority.threshold, 1, 0)

# Finally, we combine the data sets.

#把训练集和测试集合并一下
final.df <- rbind(train.ranks.df, test.ranks.df)

#日期统一一下
final.df$Date <- date.converter(final.df$Date, pattern1, pattern2)

#rev是反转，本来是时间升序，倒过来时间降序
final.df <- final.df[rev(with(final.df, order(Date))), ]

# Save final data set and plot results.
write.csv(final.df, file.path("data", "final_df.csv"), row.names = FALSE)

#最终结果画图

testing.plot <- ggplot(subset(final.df, Type == "TRAINING"), aes(x = Rank)) +
stat_density(aes(fill = Type, alpha = 0.65)) +
stat_density(data = subset(final.df, Type == "TESTING"),
aes(fill = Type, alpha = 0.65)) +
geom_vline(xintercept = priority.threshold, linetype = 2) +
scale_alpha(guide = "none") +
scale_fill_manual(values = c("TRAINING" = "darkred", "TESTING" = "darkblue")) +
theme_bw()

print(testing.plot)

#测试数据分布尾部密度更高，说明更多邮件的优先级排序值不高。

#测试数据没训练数据平滑，说明测试数据包含了很多没出现在训练数据中的特征，这些特征没得到匹配，就被忽略了

#结果不算太糟，测试数据中处于阈值右侧的密度数量还比较合理，说明还能找到重要的邮件推荐。

#这个结果是无法评估量化，不可能去问收件人效果如何。

#书上列出的表表明效果不错，测试集中有些邮件被推荐到了前40位