所有作品合集传送门： Tidy Tuesday
2018 年合集传送门： 2018
Global Mortality
What do people die from?
在过去的几个世纪里，世界发生了很大的变化–这就是《我们的世界》的数据所显示的。然而，有一件事在这种转变中一直保持不变：我们都必须在某个时候死亡。然而，随着生活水平的提高、医疗保健的进步和生活方式的改变，死亡的原因正在发生变化。
在这篇博客中，我们试图回答 “人们死于什么？”，首先看一下全球死因的数据，然后选择国家层面的例子。
世界各地的主要死因仍有很大差异，因此，也可以选择了一些国家，以突出这种异质性。
本次示例通过一些可视化方式来展示这些信息。
plotly包是一个基于浏览器的交互式图表库，建立在开源的 JavaScript 图表库 plotly.js 上。
1. 一些环境设置
# 设置为国内镜像, 方便快速安装模块
options("repos" = c(CRAN = "https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
2. 设置工作路径
wkdir <- '/home/user/R_workdir/TidyTuesday/2018/2018-04-16_Global_Mortality/src-e'
setwd(wkdir)
3. 加载 R 包
library(scales)
library(tidyverse)
library(glue)
library(plotly)
library(ggpubr)
library(showtext)
# 在 Ubuntu 系统上测试的, 不加这个我画出来的汉字会乱码 ~
showtext_auto()
4. 加载数据
df_input <- readxl::read_excel("../data/global_mortality.xlsx")
# 简要查看数据内容
glimpse(df_input)
## Rows: 6,156
## Columns: 35
## $ country <chr> "Afghanistan", "Afghanistan…
## $ country_code <chr> "AFG", "AFG", "AFG", "AFG",…
## $ year <dbl> 1990, 1991, 1992, 1993, 199…
## $ `Cardiovascular diseases (%)` <dbl> 17.61040, 17.80181, 18.3868…
## $ `Cancers (%)` <dbl> 4.025975, 4.054145, 4.17395…
## $ `Respiratory diseases (%)` <dbl> 2.106626, 2.134176, 2.20829…
## $ `Diabetes (%)` <dbl> 3.832555, 3.822228, 3.90012…
## $ `Dementia (%)` <dbl> 0.5314287, 0.5324973, 0.540…
## $ `Lower respiratory infections (%)` <dbl> 10.886362, 10.356968, 10.09…
## $ `Neonatal deaths (%)` <dbl> 9.184653, 8.938897, 8.84138…
## $ `Diarrheal diseases (%)` <dbl> 2.497141, 2.572228, 2.70774…
## $ `Road accidents (%)` <dbl> 3.715944, 3.729142, 3.81635…
## $ `Liver disease (%)` <dbl> 0.8369093, 0.8455159, 0.874…
## $ `Tuberculosis (%)` <dbl> 5.877075, 5.891704, 6.03466…
## $ `Kidney disease (%)` <dbl> 1.680611, 1.671115, 1.70098…
## $ `Digestive diseases (%)` <dbl> 1.058771, 1.049322, 1.06288…
## $ `HIV/AIDS (%)` <dbl> 0.01301948, 0.01451458, 0.0…
## $ `Suicide (%)` <dbl> 0.4366105, 0.4422802, 0.456…
## $ `Malaria (%)` <dbl> 0.4488863, 0.4550191, 0.460…
## $ `Homicide (%)` <dbl> 1.287020, 1.290991, 1.32616…
## $ `Nutritional deficialbert (%)` <dbl> 0.3505045, 0.3432123, 0.345…
## $ `Meningitis (%)` <dbl> 3.037603, 2.903202, 2.84064…
## $ `Protein-energy malnutrition (%)` <dbl> 0.3297599, 0.3221711, 0.323…
## $ `Drowning (%)` <dbl> 0.9838624, 0.9545860, 0.951…
## $ `Maternal deaths (%)` <dbl> 1.769213, 1.749264, 1.76424…
## $ `Parkinson disease (%)` <dbl> 0.02515859, 0.02545063, 0.0…
## $ `Alcohol disorders (%)` <dbl> 0.02899828, 0.02917152, 0.0…
## $ `Intestinal albertious diseases (%)` <dbl> 0.1833303, 0.1781074, 0.176…
## $ `Drug disorders (%)` <dbl> 0.04120540, 0.04203340, 0.0…
## $ `Hepatitis (%)` <dbl> 0.1387378, 0.1350081, 0.134…
## $ `Fire (%)` <dbl> 0.1741567, 0.1706712, 0.171…
## $ `Heat-related (hot and cold exposure) (%)` <dbl> 0.1378229, 0.1348266, 0.139…
## $ `Natural disasters (%)` <dbl> 0.00000000, 0.79760256, 0.3…
## $ `Conflict (%)` <dbl> 0.932, 2.044, 2.408, NA, 4.…
## $ `Terrorism (%)` <dbl> 0.007, 0.040, 0.027, NA, 0.…
# 检查数据的列名
colnames(df_input)
## [1] "country"
## [2] "country_code"
## [3] "year"
## [4] "Cardiovascular diseases (%)"
## [5] "Cancers (%)"
## [6] "Respiratory diseases (%)"
## [7] "Diabetes (%)"
## [8] "Dementia (%)"
## [9] "Lower respiratory infections (%)"
## [10] "Neonatal deaths (%)"
## [11] "Diarrheal diseases (%)"
## [12] "Road accidents (%)"
## [13] "Liver disease (%)"
## [14] "Tuberculosis (%)"
## [15] "Kidney disease (%)"
## [16] "Digestive diseases (%)"
## [17] "HIV/AIDS (%)"
## [18] "Suicide (%)"
## [19] "Malaria (%)"
## [20] "Homicide (%)"
## [21] "Nutritional deficiencies (%)"
## [22] "Meningitis (%)"
## [23] "Protein-energy malalberton (%)"
## [24] "Drowning (%)"
## [25] "Maternal deaths (%)"
## [26] "Parkinson disease (%)"
## [27] "Alcohol disorders (%)"
## [28] "Intestinal infectious diseases (%)"
## [29] "Drug disorders (%)"
## [30] "Hepatitis (%)"
## [31] "Fire (%)"
## [32] "Heat-related (hot and cold exposure) (%)"
## [33] "Natural disasters (%)"
## [34] "Conflict (%)"
## [35] "Terrorism (%)"
5. 数据预处理
df_tidy = df_input %>%
# pivot_longer() 从宽数据透视到长数据转换
pivot_longer(names_to = "Cause", cols = contains("%"), values_to = "Percent") %>%
# 建议使用 dplyr::mutate 形式调用函数, 不然容易与 plyr 中的函数冲突 (因为我自己就报错了...)
dplyr::mutate(
Percent = Percent/100,
Cause = str_trim(str_to_title(sub(" [(]%[)]", "", Cause)))
)
# 删除缺失值的观测
df_tidy <- na.omit(df_tidy)
# 简要查看数据内容
glimpse(df_tidy)
## Rows: 167,808
## Columns: 5
## $ country <chr> "Afghanistan", "Afghanistan", "Afghanistan", "Afghanistan…
## $ country_code <chr> "AFG", "AFG", "AFG", "AFG", "AFG", "AFG", "AFG", "AFG", "…
## $ year <dbl> 1990, 1990, 1990, 1990, 1990, 1990, 1990, 1990, 1990, 199…
## $ Cause <chr> "Cardiovascular Diseases", "Cancers", "Respiratory Albert…
## $ Percent <dbl> 0.1761039712, 0.0402597540, 0.0210662613, 0.0383255475, 0…
6. 利用 ggplot2 绘图
# 以中国地区的数据为例画图
# 从中挑选一些需要关注的点
Country = "China"
Diseases = c('Cardiovascular Diseases', 'Cancers', 'Diabetes', 'Suicide', 'Homicide', 'Neonatal Deaths', 'Tuberculosis')
line.plot = df_tidy %>% filter(Cause %in% Diseases, country == Country)
gg <- line.plot %>% ggplot(aes(year, Percent, col = Cause,
text = paste("年份:", year, "\n致死因素: ", Cause, "\n百分比:", round(Percent, 4)*100, "%")))
# geom_line() 添加折线图
gg <- gg + geom_line(aes(lty = Cause, group = 1), lwd = 0.8)
gg <- gg + scale_x_continuous(breaks = seq(1990, 2018, by = 5), limits = c(1989, 2019))
gg <- gg + scale_y_continuous(labels = percent_format())
gg <- gg + labs(title = glue("死亡因素致死变化情况 中国 {Country}"),
subtitle = "历年死亡变化情况",
x ='年份',
y = '百分比 (%)')
# theme_classic2() 经典白色背景, L坐标系主体
gg <- gg + theme_classic2()
# theme() 实现对非数据元素的调整, 对结果进行进一步渲染, 使之更加美观
gg <- gg + theme(
# panel.grid.major 主网格线, 这一步表示删除主要网格线
panel.grid.major = element_blank(),
# panel.grid.minor 次网格线, 这一步表示删除次要网格线
panel.grid.minor = element_blank(),
# plot.title 主标题
plot.title = element_text(hjust = 0.1, color = "black", size = 20, face = "bold"),
# axis.text 坐标轴刻度文本
axis.text = element_text(hjust = 0.1, size = 12),
# plot.caption 说明文字
plot.caption = element_text(hjust = -0.85),
# legend.direction 设置图例的方向
legend.direction = "vertical",
# legend.position 设置图例位置
legend.position = "right")
7. 保存图片到 HTML
ggplotly(gg, tooltip = c("text"))
filename = '20180416-E-01'
htmlwidgets::saveWidget(ggplotly(gg, tooltip = c("text")), paste0(filename, ".html"))
8. session-info
sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.5 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] showtext_0.9-5 showtextdb_3.0 sysfonts_0.8.8 ggpubr_0.4.0
## [5] gridExtra_2.3 plotly_4.10.0 maps_3.4.0 glue_1.6.2
## [9] extrafont_0.18 tidytext_0.3.4 ggthemes_4.2.4 forcats_0.5.2
## [13] stringr_1.4.1 dplyr_1.0.10 purrr_0.3.4 readr_2.1.2
## [17] tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2
## [21] ggbump_0.1.0 scales_1.2.1
##
## loaded via a namespace (and not attached):
## [1] fs_1.5.2 lubridate_1.8.0 httr_1.4.4
## [4] SnowballC_0.7.0 tools_4.2.1 backports_1.4.1
## [7] bslib_0.4.0 utf8_1.2.2 R6_2.5.1
## [10] DBI_1.1.3 lazyeval_0.2.2 colorspace_2.0-3
## [13] withr_2.5.0 tidyselect_1.1.2 compiler_4.2.1
## [16] extrafontdb_1.0 cli_3.3.0 rvest_1.0.3
## [19] xml2_1.3.3 labeling_0.4.2 sass_0.4.2
## [22] digest_0.6.29 rmarkdown_2.16 pkgconfig_2.0.3
## [25] htmltools_0.5.3 dbplyr_2.2.1 fastmap_1.1.0
## [28] htmlwidgets_1.5.4 rlang_1.0.5 readxl_1.4.1
## [31] rstudioapi_0.14 farver_2.1.1 jquerylib_0.1.4
## [34] generics_0.1.3 jsonlite_1.8.0 crosstalk_1.2.0
## [37] tokenizers_0.2.3 car_3.1-0 googlesheets4_1.0.1
## [40] magrittr_2.0.3 Matrix_1.5-1 Rcpp_1.0.9
## [43] munsell_0.5.0 fansi_1.0.3 abind_1.4-5
## [46] lifecycle_1.0.1 stringi_1.7.8 yaml_2.3.5
## [49] carData_3.0-5 grid_4.2.1 crayon_1.5.1
## [52] lattice_0.20-45 haven_2.5.1 hms_1.1.2
## [55] knitr_1.40 pillar_1.8.1 ggsignif_0.6.3
## [58] reprex_2.0.2 evaluate_0.16 data.table_1.14.2
## [61] modelr_0.1.9 vctrs_0.4.1 tzdb_0.3.0
## [64] Rttf2pt1_1.3.10 cellranger_1.1.0 gtable_0.3.1
## [67] assertthat_0.2.1 cachem_1.0.6 xfun_0.32
## [70] broom_1.0.1 rstatix_0.7.0 janeaustenr_1.0.0
## [73] googledrive_2.0.0 viridisLite_0.4.1 gargle_1.2.1
## [76] ellipsis_0.3.2
测试数据
配套数据下载：global_mortality.xlsx
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