学习笔记1join point

setwd ("D:/study_data/shujuku/data-space")
install.packages('ggmap')
install.packages('dplyr')
install.packages('magrittr')
install.packages('data.table')
library(magrittr)
library(dplyr)
library(data.table)
source('function_year5.R')

# 各年龄层人口数据 --------------------------------------------------------------------
dirname <- dir("D:/data-space/GBD_population")
file <- paste0("D:/data-space/GBD_population/",dirname)
ages <- c("30 to 34", "35 to 39", "40 to 44", "45 to 49", "50 to 54", "55 to 59",        
          "60 to 64", "65 to 69", "70 to 74", "75 to 79", "80 to 84", "85 plus") 
var_name <- c("location_name","sex_name","year_id","age_group_id","age_group_name","val")

population  <-  as.data.frame(matrix(nrow=0,ncol=length(var_name))) 
names(population)=var_name
for (a in file) {
  data <- fread(a) %>% select(var_name) %>% 
    filter(location_name %in% 'China' & age_group_name %in% ages & sex_name %in% 'both')
  population <- rbind(population,data)
} 
population_n <- dcast(data = population[,-c(1:2)], age_group_id + age_group_name ~ year_id)
population_g <- function_year5(population_n, 1990, 2019, 2019) 
rownames(population_g) <- population_n$age_group_name

# 死亡数据 --------------------------------------------------------------------
OEC <- fread('OST.csv')
EC_incidence <- subset(OEC,age_name %in% ages  & 
                         sex_name== 'Both' &
                         metric_name == 'Number' &
                         cause_name == 'Osteoarthritis' &
                         measure_name == 'Incidence')[,c(7,8,13,14)]
EC_incidence_n <- dcast(data = EC_incidence, age_id + age_name ~ year)
EC_incidence_g <- function_year5(EC_incidence_n, 1990, 2019, 2019)
rownames(EC_incidence_g) <- EC_incidence_n$age_name
name <- intersect(population_n$age_group_name,EC_incidence_n$age_name)
population_g <- population_g[rownames(population_g) %in% name,]
EC_incidence_g <- EC_incidence_g[rownames(EC_incidence_g) %in% name,]
for (i in 1:(2*ncol(population_g))){
  if(i == 1){
    incidecen_population <-EC_incidence_g[,i] %>% as.data.frame()}
  else{
    if(i%%2==0){
      incidecen_population <- cbind(incidecen_population,population_g[,ceiling(i/2)])}
    else{
      incidecen_population <- cbind(incidecen_population,EC_incidence_g[,ceiling(i/2)])}
  }
}

# 二者取交集 -------------------------------------------------------------------
names(incidecen_population) <- rep(names(population_g),each=2)
write.table(incidecen_population,'web_ost.csv',row.names = F,col.names = F,sep = ',')

# joinpoint ---------------------------------------------------------------
library(ggplot2)