所有作品合集传送门： Tidy Tuesday
2018 年合集传送门： 2018
Global Mortality
Tidy Tuesday 在 GitHub 上的传送地址： **Thomas Mock (2022). Tidy Tuesday: A weekly data project aimed at the R ecosystem.** [https://github.com/rfordatascience/tidytuesday](https://github.com/rfordatascience/tidytuesday)
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。
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-a'
setwd(wkdir)
3. 加载 R 包
library(tidyverse)
library(ggbump)
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 deficiencies (%)` <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 infectious 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 malnutrition (%)"
## [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 %>%
# 从宽数据透视到长数据转换
pivot_longer(cols = 4:35, names_to = "cause", values_to = "percent") %>%
# 筛选数据
filter(country == "World") %>%
group_by(year) %>%
# 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(rank = min_rank(desc(percent))) %>%
ungroup() %>%
dplyr::mutate(cause = str_remove(cause, "[[:space:]]\\(%\\)"),
color_albert = case_when(cause == "HIV/AIDS" ~ "HIV/AIDS",
cause == "Conflict" ~ "冲突",
cause == "Malaria" ~ "疟疾",
cause == "Natural disasters" ~ "自然灾害",
cause == "Cancers" ~ "癌症",
cause == "Diabetes" ~ "糖尿病",
cause == "Dementia" ~ "精神错乱",
TRUE ~ "其他因素"))
df_plot.one <- df_tidy %>% filter(color_albert == "其他因素")
df_plot.two <- df_tidy %>% filter(color_albert != "其他因素")
# 删除缺失值的观测
df_tidy <- na.omit(df_tidy)
df_plot.one <- na.omit(df_plot.one)
df_plot.two <- na.omit(df_plot.two)
# 简要查看数据内容
glimpse(df_tidy)
## Rows: 862
## Columns: 7
## $ country <chr> "World", "World", "World", "World", "World", "World", "Wo…
## $ country_code <chr> "OWID_WRL", "OWID_WRL", "OWID_WRL", "OWID_WRL", "OWID_WRL…
## $ year <dbl> 1990, 1990, 1990, 1990, 1990, 1990, 1990, 1990, 1990, 199…
## $ cause <chr> "Cardiovascular diseases", "Cancers", "Respiratory diseas…
## $ percent <dbl> 26.5037427, 12.2480991, 7.0684616, 3.4360712, 2.0611337, …
## $ rank <int> 1, 2, 3, 8, 10, 4, 5, 6, 9, 12, 7, 15, 11, 22, 13, 14, 21…
## $ color_albert <chr> "其他因素", "癌症", "其他因素", "糖尿病", "精神错乱", "其…
6. 利用 ggplot2 绘图
# PS: 方便讲解, 我这里进行了拆解, 具体使用时可以组合在一起
gg <- ggplot(df_plot.one, aes(year, rank, group = cause))
# geom_bump() 可以用来绘制凹凸图 (bump charts)
gg <- gg + geom_bump(size = 0.7, alpha = 0.7, color = "grey")
# geom_point() 绘制散点图
gg <- gg + geom_point(size = 1.5, color = "grey")
gg <- gg + geom_text(data = df_plot.one %>% filter(year == 1990), aes(x = 1989, y = rank, label = rank),
hjust = 1,
size = 3)
gg <- gg + geom_text(data = df_plot.one %>% filter(year == 2016), aes(x = 2016.2, y = rank, label = cause),
hjust = 0,
size = 3)
gg <- gg + geom_bump(data = df_plot.two, aes(year, rank, group = cause, colour = color_albert), size = 1)
gg <- gg + geom_point(data = df_plot.two, aes(year, rank, group = cause, colour = color_albert), size = 1.8)
gg <- gg + geom_text(data = df_plot.two %>% filter(year == 1990), aes(x = 1989, y = rank, label = rank),
size = 3.95,
hjust = 1,
color = 'red',
fontface = "bold")
gg <- gg + geom_text(data = df_plot.two %>% filter(year == 2016), aes(x = 2016.2, y = rank, label = cause),
size = 2.98,
hjust = 0,
color = 'red',
fontface = "bold")
# scale_color_manual() 采取的是手动赋值的方法, 也就是直接把颜色序列赋值给它的参数 value
gg <- gg + scale_color_manual(values = c("#F61220", "#201B2A", "#1A9623", "#D2691E", "#0C55E2", "#2E2D41", "#FFD700"))
# scale_y_reverse() 逆转坐标轴
gg <- gg + scale_y_reverse(breaks = 1:32, expand = c(0.01, 0.01))
gg <- gg + scale_x_continuous(breaks = seq(1990, 2016, by = 2), limits = c(1989, 2026))
gg <- gg + labs(title = "世界范围内的死亡原因",
subtitle = "历年死亡变化情况",
x = NULL,
y = NULL,
caption = "资料来源: Our World in Data · graph by 萤火之森")
# theme_minimal() 去坐标轴边框的最小化主题
gg <- gg + theme_minimal()
# 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(),
# axis.text.y Y-坐标轴文本
axis.text.y = element_blank(),
# plot.title 主标题
plot.title = element_text(hjust = 0.1, color = "black", size = 20, face = "bold"),
# plot.subtitle 次要标题
plot.subtitle = element_text(hjust = 0.1, color = "red", size = 12),
# plot.caption 说明文字
plot.caption = element_text(hjust = 0.85),
# legend.position 设置图例位置, "none" 表示不显示图例
legend.position = "none",
# plot.background 图片背景
plot.background = element_rect(fill = "white"))
7. 保存图片到 PDF 和 PNG
gg
filename = '20180416-A-01'
ggsave(filename = paste0(filename, ".pdf"), width = 9.2, height = 6.0, device = cairo_pdf)
ggsave(filename = paste0(filename, ".png"), width = 9.2, height = 6.0, dpi = 100, device = "png")
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 ggbump_0.1.0
## [5] forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10 purrr_0.3.4
## [9] readr_2.1.2 tidyr_1.2.1 tibble_3.1.8 ggplot2_3.3.6
## [13] tidyverse_1.3.2
##
## loaded via a namespace (and not attached):
## [1] lubridate_1.8.0 assertthat_0.2.1 digest_0.6.29
## [4] utf8_1.2.2 R6_2.5.1 cellranger_1.1.0
## [7] backports_1.4.1 reprex_2.0.2 evaluate_0.16
## [10] highr_0.9 httr_1.4.4 pillar_1.8.1
## [13] rlang_1.0.5 googlesheets4_1.0.1 readxl_1.4.1
## [16] rstudioapi_0.14 jquerylib_0.1.4 rmarkdown_2.16
## [19] textshaping_0.3.6 googledrive_2.0.0 munsell_0.5.0
## [22] broom_1.0.1 compiler_4.2.1 modelr_0.1.9
## [25] xfun_0.32 systemfonts_1.0.4 pkgconfig_2.0.3
## [28] htmltools_0.5.3 tidyselect_1.1.2 fansi_1.0.3
## [31] crayon_1.5.1 tzdb_0.3.0 dbplyr_2.2.1
## [34] withr_2.5.0 grid_4.2.1 jsonlite_1.8.0
## [37] gtable_0.3.1 lifecycle_1.0.1 DBI_1.1.3
## [40] magrittr_2.0.3 scales_1.2.1 cli_3.3.0
## [43] stringi_1.7.8 cachem_1.0.6 farver_2.1.1
## [46] fs_1.5.2 xml2_1.3.3 bslib_0.4.0
## [49] ragg_1.2.3 ellipsis_0.3.2 generics_0.1.3
## [52] vctrs_0.4.1 tools_4.2.1 glue_1.6.2
## [55] hms_1.1.2 fastmap_1.1.0 yaml_2.3.5
## [58] colorspace_2.0-3 gargle_1.2.1 rvest_1.0.3
## [61] knitr_1.40 haven_2.5.1 sass_0.4.2
测试数据
配套数据下载：global_mortality.xlsx
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