RWEP/SD/20240326_3_datatransform/index.qmd

---
title: "Data Transform"
subtitle: 《区域水环境污染数据分析实践》<br>Data analysis practice of regional water environment pollution
author: 苏命、王为东<br>中国科学院大学资源与环境学院<br>中国科学院生态环境研究中心
date: today
lang: zh
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    toc-title: 大纲
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---

```{r}
#| echo: false
knitr::opts_chunk$set(echo = TRUE)
source("../../coding/_common.R")
library(nycflights13)
library(tidyverse)

```


## `tidyverse`风格数据分析总体流程

![](../../image/data-science/transform.png) 


## [dplyr cheatsheet](../../image/cheatsheet/data-transformation.pdf)


```{r}
#| echo: false
dwfun::ggsavep("../../image/cheatsheet/data-transformation.svg", loadit = TRUE)
```



## 查看数据

```{r}
flights
```


## 选择列

```{r}
#| results: false

flights |> 
  select(year, month, day)
```

## 选择列

```{r}
#| results: false

flights |> 
  select(year:day)
```


## 选择列

```{r}
flights |> 
select(3:5)
```

## 选择列

```{r}
flights |> 
  select(!year:day)
```

## 选择列

```{r}
flights |> 
  select(-(year:day))
```

## 选择列

```{r}
flights |> 
  select(where(is.character))
```

## 选择列

```{r}
flights |> 
  select(!where(is.character)) |>
  select(contains("_"))
```

## 选择列

```{r}
flights |> 
  select(tail_num = tailnum)
```

## 选择列

```{r}
flights |> 
  select(air_time, everything())
```


## 重命名

```{r}
flights |> 
  rename(tail_num = tailnum)
```

## 重命名

```{r}
flights |> 
  rename(年份 = 1) |>
  rename(月份 = 2)

```

## 重命名

```{r}
flights |> select(1:4) |> head(n = 3)
# 重命名
flights |> select(1:4) |> head(n = 3) |>
  rename_all(~c("c1", "c2", "c3", "c4"))
```

## 重命名

```{r}
flights |> select(1:4) |> head(n = 3)
# 重命名
flights |> select(1:4) |> head(n = 3) |>
  rename_all(toupper)
```


## 重命名

```{r}
flights |> select(1:4) |> head(n = 3)
# 重命名
flights |> select(1:4) |> head(n = 3) |>
  rename_all(~paste0(toupper(.), "_NEW"))
```


## 练习

将含有下划线的列名中的下划线去掉。


```{r}
flights |> select(1:4) |> head(n = 3)
```


## 练习

将`airqualitydf`中列名的单位信息去除（前5列）。


```{r}
airqualitydf <- readxl::read_xlsx("../../data/airquality.xlsx", sheet = 2)
airqualitydf |> select(1:5)
```



## `filter`

```{r}
flights |> 
  filter(dep_delay > 120)
```

## filter 练习

Flights that departed on January 1.

```{r}
#| echo: false
flights |> 
  filter(month == 1 & day == 1)
```

## filter 练习


Select flights that departed in January or February

```{r}
#| echo: false
flights |> 
  filter(month %in% c(1, 2))
```

## filter 练习

```{r}
jan1 <- flights |> 
  filter(month == 1 & day == 1)
```

## filter

```{r}
#| error: true
#| eval: false

flights |> 
  filter(month = 1)
```

## filter

```{r}
flights |> 
  filter(month == 1 | 2)
```

## 排序

```{r}
flights |> 
  arrange(year, month, day, dep_time)
```

## 排序

```{r}
flights |> 
  arrange(desc(dep_delay))
```

## slice

```{r}
flights |> head(n = 5)
flights |> slice(1:5)
```

## slice

```{r}
flights |> 
  slice_max(dep_delay, n = 5)
```

## slice

```{r}
flights |> 
  slice_min(dep_delay, prop = 0.005)
```

## 排序练习

根据`origin`、`dest`、`air_time`倒序排序。

```{r}
#| echo: false
flights |> 
  arrange(origin, dest, desc(air_time)) |>
  select(origin, dest, air_time, everything())
```


## 去重

```{r}
# Remove duplicate rows, if any
flights |> 
  distinct()
```

## 去重

```{r}
# Find all unique origin and destination pairs
flights |> 
  distinct(origin, dest)
```

## 去重

```{r}
flights |> 
  distinct(origin, dest, .keep_all = TRUE)
```

## 计数

```{r}
flights |>
  count(origin, dest, sort = TRUE)
```


## 计数-练习

统计每月的航班数量。

```{r}
#| echo: false
flights |>
  count(year, month, sort = TRUE)
```


## 计算新变量

```{r}
flights |> 
  mutate(
    gain = dep_delay - arr_delay,
    speed = distance / air_time * 60
  )
```

## 计算新变量

```{r}
flights |> 
  mutate(
    gain = dep_delay - arr_delay,
    speed = distance / air_time * 60,
    .before = 1
  )
```

## 计算新变量

```{r}
flights |> 
  mutate(
    gain = dep_delay - arr_delay,
    speed = distance / air_time * 60,
    .after = day
  )
```

## 计算新变量

```{r}
flights |> 
  mutate(
    gain = dep_delay - arr_delay,
    hours = air_time / 60,
    gain_per_hour = gain / hours,
    .keep = "used"
  )
```




## 列排序

```{r}
flights |> 
  relocate(time_hour, air_time)
```

## 列排序

```{r}
#| results: false

flights |> 
  relocate(year:dep_time, .after = time_hour)
flights |> 
  relocate(starts_with("arr"), .before = dep_time)
flights |> 
  select(starts_with("arr"), everything())
```


## 练习

计算目的地为IAH，按飞行速度排序的表格，保留year:day, `dep_time`, carrier, flight与speed列。

```{r}
flights |> 
  filter(dest == "IAH") |> 
  mutate(speed = distance / air_time * 60) |> 
  select(year:day, dep_time, carrier, flight, speed) |> 
  arrange(desc(speed))
```

## 练习

计算目的地为IAH，按飞行速度排序的表格，保留year:day, `dep_time`, carrier, flight与speed列。

```{r}
#| results: false

flights1 <- filter(flights, dest == "IAH")
flights2 <- mutate(flights1, speed = distance / air_time * 60)
flights3 <- select(flights2, year:day, dep_time, carrier, flight, speed)
arrange(flights3, desc(speed))
```

## 练习

计算目的地为IAH，按飞行速度排序的表格，保留year:day, `dep_time`, carrier, flight与speed列。

```{r}
flights |> 
  filter(dest == "IAH") |> 
  mutate(speed = distance / air_time * 60) |> 
  select(year:day, dep_time, carrier, flight, speed) |> 
  arrange(desc(speed))
```


## 分组统计

```{r}

library(tidyverse)

mtcars %>% 
  group_by(cyl) %>%
  summarize(n = n())
```

## 分组统计

```{r}
flights |> 
  group_by(month)
```

## 分组统计

```{r}
flights |> 
  group_by(month) |> 
  summarize(
    avg_delay = mean(dep_delay)
  )
```

## 分组统计

```{r}
flights |> 
  group_by(month) |> 
  summarize(
    avg_delay = mean(dep_delay, na.rm = TRUE)
  )
```

## 分组统计

```{r}
flights |> 
  group_by(month) |> 
  summarize(
    avg_delay = mean(dep_delay, na.rm = TRUE), 
    n = n()
  )
```

## 分组统计

```{r}
flights |> 
  group_by(dest) |> 
  slice_max(arr_delay, n = 1) |>
  relocate(dest)
```

## 分组统计

```{r}

flights |>
  filter(dest == "IAH") |> 
  group_by(year, month, day) |> 
  summarize(
    arr_delay = mean(arr_delay, na.rm = TRUE)
  )
```


## 分组

```{r}
daily <- flights |>  
  group_by(year, month, day)
daily
```

## 分组统计

```{r}
daily_flights <- daily |> 
  summarize(n = n())
```

## 分组统计

```{r}
#| results: false

daily_flights <- daily |> 
  summarize(
    n = n(), 
    .groups = "drop_last"
  )
```



## 删除分组

```{r}
daily |> ungroup()
```

## 删除分组

```{r}
daily |> 
  ungroup() |>
  summarize(
    avg_delay = mean(dep_delay, na.rm = TRUE), 
    flights = n()
  )
```

## 分组统计

```{r}
flights |> 
  summarize(
    delay = mean(dep_delay, na.rm = TRUE), 
    n = n(),
    .by = month
  )
```

## 分组统计

```{r}
flights |> 
  summarize(
    delay = mean(dep_delay, na.rm = TRUE), 
    n = n(),
    .by = c(origin, dest)
  )
```



## 练习

```{r}
df <- tibble(
  x = 1:5,
  y = c("a", "b", "a", "a", "b"),
  z = c("K", "K", "L", "L", "K")
)
df
```

```{r}
#| eval: false
    
df |> arrange(y)
```

## 练习

```{r}
#| echo: false
df
```

```{r}
#| eval: false
df |>
  group_by(y) |>
  summarize(mean_x = mean(x))
```

## 练习

```{r}
#| echo: false
df
```
```{r}
#| eval: false
    
df |>
  group_by(y, z) |>
  summarize(mean_x = mean(x))
```

## 练习

```{r}
#| echo: false
df
```
```{r}
#| eval: false
    
df |>
  group_by(y, z) |>
  summarize(mean_x = mean(x), .groups = "drop")
```

## 练习

```{r}
#| echo: false
df
```

```{r}
#| eval: false
df |>
  group_by(y, z) |>
  summarize(mean_x = mean(x))

df |>
  group_by(y, z) |>
  mutate(mean_x = mean(x))
```




## 练习

- 计算不同采样点的平均CO浓度、最大CO浓度、最小CO浓度、中位数CO浓度（`CO_mg/m3`）。
- 计算各小时全国的平均CO浓度、最大CO浓度、最小CO浓度、中位数CO浓度（`CO_mg/m3`）。
- 计算不同采样点各小时的平均CO浓度、最大CO浓度、最小CO浓度、中位数CO浓度（`CO_mg/m3`）。
- 计算各采样点中CO浓度小于全国平均CO浓度的占比。
- 找出全国各采样点中CO浓度小于全国平均CO浓度的占比最高的10个采样点。

```{r}
airqualitydf <- readxl::read_xlsx("../../data/airquality.xlsx",
  sheet = 2)
```


## 练习

按月统计dep_delay最大的3个航班的航班号（flight），用逗号连接。

```{r}
#| echo: false
flights |>
  group_by(year, month) |>
  slice_max(dep_delay, n = 3) |>
  summarize(flight = paste(paste0(carrier, flight), collapse = ", ")) |>
knitr::kable()
```




## 数据变形示意图

```{r}
billboard
knitr::include_graphics("../../image/tidy-data/variables.png", dpi = 270)
```

## 数据变形

```{r}
billboard |> 
  pivot_longer(
    cols = starts_with("wk"), 
    names_to = "week", 
    values_to = "rank",
    values_drop_na = TRUE
  )
```

## 数据变形

```{r}
billboard_longer <- billboard |> 
  pivot_longer(
    cols = starts_with("wk"), 
    names_to = "week", 
    values_to = "rank",
    values_drop_na = TRUE
  ) |> 
  mutate(
    week = parse_number(week)
  )
billboard_longer
```


## 练习


```{r}
#| echo: false
df <- tribble(
  ~id,  ~bp1, ~bp2,
   "A",  100,  120,
   "B",  140,  115,
   "C",  120,  125
)
df
```

将以上数据(`df`)转换为如下形式。

```{r}
#| echo: false
df |> 
  pivot_longer(
    cols = bp1:bp2,
    names_to = "measurement",
    values_to = "value"
  )
```

## 练习

请转换如下`iris`数据。

```{r}
#| echo: false
as_tibble(head(iris, n = 3))
cat("转为如下形式：")
iris |>
  pivot_longer(cols = c(Sepal.Length,
    Sepal.Width,
    Petal.Length,
    Petal.Width),
    names_to = "flower_attr",
    values_to = "attr_value") |>
  head()
```




## 数据变形示意图2

```{r}
who2
knitr::include_graphics("../../image/tidy-data/multiple-names.png", dpi = 270)
```


## 数据变形

```{r}
who2 |> 
  pivot_longer(
    cols = !(country:year),
    names_to = c("diagnosis", "gender", "age"), 
    names_sep = "_",
    values_to = "count"
  )
```


## 数据变形示意图

```{r}
household
knitr::include_graphics("../../image/tidy-data/names-and-values.png", dpi = 270)
```

## 数据变形

```{r}
household |> 
  pivot_longer(
    cols = !family, 
    names_to = c(".value", "child"), 
    names_sep = "_", 
    values_drop_na = TRUE
  )
```


## 查看数据

```{r}
cms_patient_experience
```

## 查看数据

```{r}
cms_patient_experience |> 
  distinct(measure_cd, measure_title)
```

## 数据变形（变宽）

```{r}
cms_patient_experience |> 
  pivot_wider(
    names_from = measure_cd,
    values_from = prf_rate
  )
```

## 数据变形（变宽）

```{r}
cms_patient_experience |> 
  pivot_wider(
    id_cols = starts_with("org"),
    names_from = measure_cd,
    values_from = prf_rate
  )
```

## 练习

```{r}
df <- tribble(
  ~id, ~measurement, ~value,
  "A",        "bp1",    100,
  "B",        "bp1",    140,
  "B",        "bp2",    115, 
  "A",        "bp2",    120,
  "A",        "bp3",    105
)
```


变形成如下形式：


```{r}
#| echo: false
df |> 
  pivot_wider(
    names_from = measurement,
    values_from = value
  )
```


## 练习：变宽

```{r}
df <- tribble(
  ~id, ~measurement, ~value,
  "A",        "bp1",    100,
  "A",        "bp1",    102,
  "A",        "bp2",    120,
  "B",        "bp1",    140, 
  "B",        "bp2",    115
)
```

## 练习

```{r}
df |>
  pivot_wider(
    names_from = measurement,
    values_from = value
  )
```

## 练习

```{r}
df |> 
  group_by(id, measurement) |> 
  summarize(n = n(), .groups = "drop") |> 
  filter(n > 1)
```


## nest，套嵌数据框

```{r}
#| echo: false
df <- tibble(x = c(1, 1, 1, 2, 2, 3), y = 1:6, z = 6:1)
df
```

```{r}
df %>% nest(data = c(y, z))
```

## nest，套嵌数据框

Specify variables to nest by (rather than variables to nest) using `.by`

```{r}
df %>% nest(.by = x)
```


## nest，套嵌数据框

In this case, since `...` isn't used you can specify the resulting column name with `.key`

```{r}
df %>% nest(.by = x, .key = "cols")
```


## nest，套嵌数据框

Use tidyselect syntax and helpers, just like in `dplyr::select()`

```{r}
df %>% nest(data = any_of(c("y", "z")))
```

## nest，套嵌数据框

`...` and `.by` can be used together to drop columns you no longer need,
or to include the columns you are nesting by in the inner data frame too.
This drops `z`:

```{r}
df %>% nest(data = y, .by = x)
```

## nest，套嵌数据框

This includes `x` in the inner data frame:

```{r}
df %>% nest(data = everything(), .by = x)
```

## nest，套嵌数据框

Multiple nesting structures can be specified at once

```{r}
iris %>%
  nest(petal = starts_with("Petal"), sepal = starts_with("Sepal"))
```


## nest，套嵌数据框

```{r}
iris %>%
  nest(width = contains("Width"), length = contains("Length"))
```


## nest，套嵌数据框

Nesting a grouped data frame nests all variables apart from the group vars

```{r}
fish_encounters
fish_encounters %>%
  dplyr::group_by(fish) %>%
  nest()
```

## nest，套嵌数据框

That is similar to `nest(.by = )`, except here the result isn't grouped

```{r}
fish_encounters %>%
  nest(.by = fish)
```

## nest，套嵌数据框

Nesting is often useful for creating per group models

```{r}
mtcars %>%
  nest(.by = cyl) %>%
  dplyr::mutate(models = lapply(data, function(df) lm(mpg ~ wt, data = df)))
```


## 练习

```{r}
#| echo: false
(airqualitydf <- readxl::read_xlsx("../../data/airquality.xlsx",
  sheet = 2))
```

```{r}
airqualitydf
airqualitynestdf <- airqualitydf |>
  nest(sitedf = -site)
```

## `nest`与`group_by`联用

```{r}
#| echo: false
iris %>%
  group_by(Species) %>%
  nest(.key = "spdf")
```

## unnest

```{r}
airqualitynestdf |> unnest(sitedf)
```



## `purrr`包

- map()：依次应用一元函数到一个序列的每个元素上，基本等同 lapply()
- map2()：依次应用二元函数到两个序列的每对元素上
- pmap()：应用多元函数到多个序列的每组元素上，可以实现对数据框逐行迭代
- map 系列默认返回列表型，可根据想要的返回类型添加后缀：_int, _dbl, _lgl, _chr, _df, 甚至可以接着对返回的数据框df做行/列合并：_dfr, _dfc
- 如果只想要函数依次作用的过程，而不需要返回结果，改用 walk 系列即可
- 所应用的函数，有 purrr公式风格简写（匿名函数），支持一元，二元，多元函数
- purrr 包中的其它有用函数

## `purrr`包

- `map_chr(.x, .f)`: 返回字符型向量
- `map_lgl(.x, .f)`: 返回逻辑型向量
- `map_dbl(.x, .f)`: 返回实数型向量
- `map_int(.x, .f)`: 返回整数型向量
- `map_dfr(.x, .f)`: 返回数据框列表，再 bind_rows 按行合并为一个数据框
- `map_dfc(.x, .f)`: 返回数据框列表，再 bind_cols 按列合并为一个数据框


## `purrr`包-cheatsheet

```{r}
dwfun::ggsavep("../../image/cheatsheet/purrr.svg", loadit = TRUE)
```

[purrr](../../image/cheatsheet/purrr.pdf) 


## `purrr`包

生成从1到10的10组随机数，每组随机数个数为100，均值依次为1到10，标准差为1，并存储在数据框中。

```{r}
res <- list()
for (i in 1:10) {
  res[[i]] <- tibble(随机数 = rnorm(n = 100, mean = i, sd = 1))
}
res
  
```




## `purrr`包

生成从1到10的10组随机数，每组随机数个数为100，均值依次为1到10，标准差为1，并存储在数据框中。

```{r}
1:10 |>
purrr::map(~tibble(随机数 = rnorm(n = 100, mean = .x, sd = 1)))
```

## purrr

```{r}
library(purrr)
mtcars |> 
  split(mtcars$cyl) |>  # from base R
  map(\(df) lm(mpg ~ wt, data = df)) |> 
  map(summary) %>%
  map_dbl("r.squared")
```


## 练习：

计算每月最后一个周六的航班数：

```{r}
flights
```

## `tidyr` + `purrr`包

任务：展示不同城市间的大气指标散点图

```{r}
(airqualitydf <- readxl::read_xlsx("../../data/airquality.xlsx",
  sheet = 2))
```

## join

Perform left join

```{r}
(df1 <- data.frame(id = 1:5, value1 = letters[1:5]))
(df2 <- data.frame(id = c(2, 4, 6), value2 = LETTERS[1:3]))
left_join(df1, df2, by = "id")
```

## left join

Create sample data frames with non-matching rows

```{r}
(df1 <- data.frame(id = 1:5, value1 = letters[1:5]))
(df2 <- data.frame(id = c(2, 4, 6), value2 = LETTERS[1:3]))
left_join(df2, df1, by = "id")
```

## left join


Create sample data frames with multiple columns

```{r}
df1 <- data.frame(id1 = c(1, 2, 3), id2 = c("A", "B", "C"), value1 = letters[1:3])
df2 <- data.frame(id1 = c(2, 3, 4), id2 = c("B", "C", "D"), value2 = LETTERS[1:3])
# Perform left join
left_join(df1, df2, by = c("id1", "id2"))
```

## right join


```{r}
(df1 <- data.frame(id = 1:5, value1 = letters[1:5]))
(df2 <- data.frame(id = c(2, 4, 6), value2 = LETTERS[1:3]))

# Perform right join
right_join(df1, df2, by = "id")
```


## inner join

```{r}
# Create sample data frames
(df1 <- data.frame(id = 1:5, value1 = letters[1:5]))
(df2 <- data.frame(id = c(2, 4, 6), value2 = LETTERS[1:3]))
# Perform inner join
inner_join(df1, df2, by = "id")
```


## full join

```{r}
# Create sample data frames
(df1 <- data.frame(id = 1:5, value1 = letters[1:5]))
(df2 <- data.frame(id = c(2, 4, 6), value2 = LETTERS[1:3]))
# Perform inner join
full_join(df1, df2, by = "id")
```

## semi join

Create sample data frames

```{r}
(df1 <- data.frame(id = 1:5, value1 = letters[1:5]))
(df2 <- data.frame(id = c(2, 4, 6), value2 = LETTERS[1:3]))
# Perform semi join
semi_join(df1, df2, by = "id")
```


## 欢迎讨论！{.center}


`r rmdify::slideend(wechat = FALSE, type = "public", tel = FALSE, thislink = "https://drwater.rcees.ac.cn/course/public/RWEP/@PUB/SD/")`