Module 11: Apply it to your data 10

Import your data

data <- read.csv("../00_data/myData.csv")

Chapter 15

Create a factor

Modify factor order

SMTDAYS_by_TOTDAYS <- data %>%
    
    group_by(TOTDAYS) %>%
    summarise(
        avg_SMTDAYS = mean(TOTDAYS + SMTDAYS, na.rm = TRUE)
    ) 
SMTDAYS_by_TOTDAYS

## # A tibble: 57 × 2
##    TOTDAYS avg_SMTDAYS
##      <int>       <dbl>
##  1       0        1.75
##  2       1        1   
##  3       2        4   
##  4       3        5   
##  5       4        7.25
##  6       5        7.5 
##  7       6       10   
##  8       7       12.2 
##  9       8       13.2 
## 10       9       15.5 
## # ℹ 47 more rows

SMTDAYS_by_TOTDAYS %>%
  
  ggplot(aes(x = avg_SMTDAYS, y = TOTDAYS)) +
  geom_point() 

data %>%
    
    ggplot(aes(x = HOST_FACTOR, y = HOST)) +
    geom_point()

Modify factor levels

fct_recode

data %>% distinct(HOST_FACTOR)

##   HOST_FACTOR
## 1       China
## 2       Nepal
## 3       India

data %>%

mutate(HOST_FACTOR_rev = fct_recode(HOST_FACTOR, "Nepal" = "EVER")) %>%
  select(HOST_FACTOR, HOST_FACTOR_rev) %>%
    filter(HOST_FACTOR == "EVER")

## Warning: There was 1 warning in `mutate()`.
## ℹ In argument: `HOST_FACTOR_rev = fct_recode(HOST_FACTOR, Nepal = "EVER")`.
## Caused by warning:
## ! Unknown levels in `f`: EVER

## [1] HOST_FACTOR     HOST_FACTOR_rev
## <0 rows> (or 0-length row.names)

fct_collapse

data %>%
  mutate(HOST_FACTOR_col = fct_collapse(HOST_FACTOR,
                                        "Nepal" = c("EVER"))) %>%
  select(HOST_FACTOR, HOST_FACTOR_col) %>%
  filter(HOST_FACTOR == "EVER")

## Warning: There was 1 warning in `mutate()`.
## ℹ In argument: `HOST_FACTOR_col = fct_collapse(HOST_FACTOR, Nepal =
##   c("EVER"))`.
## Caused by warning:
## ! Unknown levels in `f`: EVER

## [1] HOST_FACTOR     HOST_FACTOR_col
## <0 rows> (or 0-length row.names)

fct_lump

data %>% count(HOST)

##   HOST   n
## 1    1 855
## 2    2  25
## 3    3   2

data %>% mutate(HOST_lump = fct_lump(f = "HOST")) %>% distinct(HOST_lump)

##   HOST_lump
## 1      HOST

Chapter 16

No need to do anything here.