3  Wrangling dates-time data

NSC-R Tidy Tuesday February 2022

Author

Alex Trinidad

Published

February 22, 2022

3.1 Introduction

The dataset for this Tidy Tuesday is about animal rescues! Alex Trinidad explores the temporal trends of animal rescues using lubridate package (Grolemund & Wickham, 2011) (Trinidad, n.d.)

3.2 Load packages and data

Install TT package (if necessary)

install.packages("tidytuesdayR")
install.packages("tidyverse")
library(tidyverse)
library(lubridate)
library(tidytuesdayR)

Download data.

mydatalist <- tidytuesdayR::tt_load("2021-06-29")

    Downloading file 1 of 1: `animal_rescues.csv`

Data as tbl

mydata <- mydatalist$animal_rescues

3.3 Explore the data

glimpse(mydata)
Rows: 7,544
Columns: 31
$ incident_number               <dbl> 139091, 275091, 2075091, 2872091, 355309~
$ date_time_of_call             <chr> "01/01/2009 03:01", "01/01/2009 08:51", ~
$ cal_year                      <dbl> 2009, 2009, 2009, 2009, 2009, 2009, 2009~
$ fin_year                      <chr> "2008/09", "2008/09", "2008/09", "2008/0~
$ type_of_incident              <chr> "Special Service", "Special Service", "S~
$ pump_count                    <chr> "1", "1", "1", "1", "1", "1", "1", "1", ~
$ pump_hours_total              <chr> "2", "1", "1", "1", "1", "1", "1", "1", ~
$ hourly_notional_cost          <dbl> 255, 255, 255, 255, 255, 255, 255, 255, ~
$ incident_notional_cost        <chr> "510", "255", "255", "255", "255", "255"~
$ final_description             <chr> "Redacted", "Redacted", "Redacted", "Red~
$ animal_group_parent           <chr> "Dog", "Fox", "Dog", "Horse", "Rabbit", ~
$ originof_call                 <chr> "Person (land line)", "Person (land line~
$ property_type                 <chr> "House - single occupancy", "Railings", ~
$ property_category             <chr> "Dwelling", "Outdoor Structure", "Outdoo~
$ special_service_type_category <chr> "Other animal assistance", "Other animal~
$ special_service_type          <chr> "Animal assistance involving livestock -~
$ ward_code                     <chr> "E05011467", "E05000169", "E05000558", "~
$ ward                          <chr> "Crystal Palace & Upper Norwood", "Woods~
$ borough_code                  <chr> "E09000008", "E09000008", "E09000029", "~
$ borough                       <chr> "Croydon", "Croydon", "Sutton", "Hilling~
$ stn_ground_name               <chr> "Norbury", "Woodside", "Wallington", "Ru~
$ uprn                          <chr> "NULL", "NULL", "NULL", "1.00021E+11", "~
$ street                        <chr> "Waddington Way", "Grasmere Road", "Mill~
$ usrn                          <chr> "20500146", "NULL", "NULL", "21401484", ~
$ postcode_district             <chr> "SE19", "SE25", "SM5", "UB9", "RM3", "RM~
$ easting_m                     <chr> "NULL", "534785", "528041", "504689", "N~
$ northing_m                    <chr> "NULL", "167546", "164923", "190685", "N~
$ easting_rounded               <dbl> 532350, 534750, 528050, 504650, 554650, ~
$ northing_rounded              <dbl> 170050, 167550, 164950, 190650, 192350, ~
$ latitude                      <chr> "NULL", "51.39095371", "51.36894086", "5~
$ longitude                     <chr> "NULL", "-0.064166887", "-0.161985191", ~

Do we have missing data?

summary(mydata)
 incident_number     date_time_of_call     cal_year      fin_year        
 Min.   :     4149   Length:7544        Min.   :2009   Length:7544       
 1st Qu.: 49306118   Class :character   1st Qu.:2012   Class :character  
 Median : 89438626   Mode  :character   Median :2015   Mode  :character  
 Mean   : 91854662                      Mean   :2015                     
 3rd Qu.:131567118                      3rd Qu.:2018                     
 Max.   :233284091                      Max.   :2021                     
 NA's   :3478                                                            
 type_of_incident    pump_count        pump_hours_total   hourly_notional_cost
 Length:7544        Length:7544        Length:7544        Min.   :255.0       
 Class :character   Class :character   Class :character   1st Qu.:260.0       
 Mode  :character   Mode  :character   Mode  :character   Median :298.0       
                                                          Mean   :301.3       
                                                          3rd Qu.:333.0       
                                                          Max.   :352.0       
                                                                              
 incident_notional_cost final_description  animal_group_parent
 Length:7544            Length:7544        Length:7544        
 Class :character       Class :character   Class :character   
 Mode  :character       Mode  :character   Mode  :character   
                                                              
                                                              
                                                              
                                                              
 originof_call      property_type      property_category 
 Length:7544        Length:7544        Length:7544       
 Class :character   Class :character   Class :character  
 Mode  :character   Mode  :character   Mode  :character  
                                                         
                                                         
                                                         
                                                         
 special_service_type_category special_service_type  ward_code        
 Length:7544                   Length:7544          Length:7544       
 Class :character              Class :character     Class :character  
 Mode  :character              Mode  :character     Mode  :character  
                                                                      
                                                                      
                                                                      
                                                                      
     ward           borough_code         borough          stn_ground_name   
 Length:7544        Length:7544        Length:7544        Length:7544       
 Class :character   Class :character   Class :character   Class :character  
 Mode  :character   Mode  :character   Mode  :character   Mode  :character  
                                                                            
                                                                            
                                                                            
                                                                            
     uprn              street              usrn           postcode_district 
 Length:7544        Length:7544        Length:7544        Length:7544       
 Class :character   Class :character   Class :character   Class :character  
 Mode  :character   Mode  :character   Mode  :character   Mode  :character  
                                                                            
                                                                            
                                                                            
                                                                            
  easting_m          northing_m        easting_rounded  northing_rounded
 Length:7544        Length:7544        Min.   :500050   Min.   :157050  
 Class :character   Class :character   1st Qu.:524750   1st Qu.:175150  
 Mode  :character   Mode  :character   Median :531650   Median :181250  
                                       Mean   :531243   Mean   :180725  
                                       3rd Qu.:537750   3rd Qu.:186750  
                                       Max.   :571350   Max.   :200750  
                                                                        
   latitude          longitude        
 Length:7544        Length:7544       
 Class :character   Class :character  
 Mode  :character   Mode  :character  
                                      
                                      
                                      
                                      

Create a unique ID

mydata <- mydata |> 
  arrange(cal_year) |> 
  mutate(uid = paste0(seq(1:n()), LETTERS, letters))

Are there any duplicated?

table(duplicated(mydata$uid))

FALSE 
 7544 

Select variables of interest.

mydataselection <- mydata |> 
  select(uid, date_time_of_call, type_of_incident, animal_group_parent, borough_code)

Show me the frequencies of different types of animal.

myfreq <- mydataselection |> 
  group_by(animal_group_parent) |> 
  summarise(freq = n()) |> 
  arrange(-freq)
myfreq
# A tibble: 28 x 2
   animal_group_parent               freq
   <chr>                            <int>
 1 Cat                               3649
 2 Bird                              1530
 3 Dog                               1194
 4 Fox                                349
 5 Horse                              193
 6 Unknown - Domestic Animal Or Pet   191
 7 Deer                               130
 8 Unknown - Wild Animal               89
 9 Squirrel                            65
10 Unknown - Heavy Livestock Animal    49
# ... with 18 more rows

Remove unkonwn type of animals from the dataset.

mydataselection <- mydataselection |> 
  filter(!grepl("Unknown", animal_group_parent))
myfreq <- mydataselection |> 
  group_by(animal_group_parent) |> 
  summarise(freq = n()) |> 
  arrange(-freq)

Merging the cat counts.

mydataselection$animal_group_parent <- recode(mydataselection$animal_group_parent,
                                              "cat" = "Cat")

Another way to do this (Nick van Doormaal suggestion).

mydataselection$animal_group_parent <- tolower(mydataselection$animal_group_parent)

3.4 Working with Date-Time Data

Now we are ready to work with Data-Time Data. We want to separate the date in year, month, day, hour….

But, what variable type is the date in our data set?

glimpse(mydataselection)
Rows: 7,211
Columns: 5
$ uid                 <chr> "1Aa", "2Bb", "3Cc", "4Dd", "5Ee", "7Gg", "8Hh", "~
$ date_time_of_call   <chr> "01/01/2009 03:01", "01/01/2009 08:51", "04/01/200~
$ type_of_incident    <chr> "Special Service", "Special Service", "Special Ser~
$ animal_group_parent <chr> "dog", "fox", "dog", "horse", "rabbit", "dog", "do~
$ borough_code        <chr> "E09000008", "E09000008", "E09000029", "E09000017"~

If not “date” format, transform ir

mydatadate <- mydataselection |> 
  mutate(datetime = lubridate::as_datetime(date_time_of_call, 
                                   format = "%d/%m/%Y %H:%M"))
# # Non-lubridate Alternative
# mydatadate <- mydataselection |> 
#   mutate(datetime = strptime(date_time_of_call,
#                          format ="%d/%m/%Y %H:%M", 
#                          tz = "Europe/London"))
# OlsonNames() # function for for the tz

Create separate variables for day, month, year, hour, minute, and date.

mydatadate <- mydataselection |> 
  mutate(datetime = as_datetime(date_time_of_call,
                            format ="%d/%m/%Y %H:%M"),
         day = day(datetime),
         month = month(datetime),
         year = year(datetime),
         hour = hour(datetime),
         minute = minute(datetime),
         date = as_date(datetime))

head(mydatadate[, 6:12])
# A tibble: 6 x 7
  datetime              day month  year  hour minute date      
  <dttm>              <int> <dbl> <dbl> <int>  <int> <date>    
1 2009-01-01 03:01:00     1     1  2009     3      1 2009-01-01
2 2009-01-01 08:51:00     1     1  2009     8     51 2009-01-01
3 2009-01-04 10:07:00     4     1  2009    10      7 2009-01-04
4 2009-01-05 12:27:00     5     1  2009    12     27 2009-01-05
5 2009-01-06 15:23:00     6     1  2009    15     23 2009-01-06
6 2009-01-07 06:29:00     7     1  2009     6     29 2009-01-07

How many cases do we have now per day?

caseperday <- mydatadate |> 
  group_by(date) |> 
  summarise(resc_counts = n())

Plot trends of cases

ggplot(data = caseperday, 
       aes(
         x = date,
         y = resc_counts
       )) +
  geom_line()

Trends of cases

And how many cases do we have per year?

mydatadate |> 
  group_by(year) %>% 
  summarise(resc_counts = n()) |> 
  ggplot() +
  aes(
    x = year,
    y = resc_counts
  ) + 
  geom_line()

How many cases per year

Is there a rescue every day?

perday <- mydatadate |> 
          group_by(date) |> 
          summarise(resc_counts = n())

How many days are (more or less) in those years?

length(unique(mydatadate$year)) * 365
[1] 4745

How can I know the days that are missing? Create for this a data set with all the days

compdates <- data.frame(date = c(seq(ymd('2009-01-01'), 
                                     ymd('2021-12-31'), by = '1 day')))

How can I know the days that are missing? Create for this a data set with all the days

compdates <- data.frame(date = c(seq(ymd('2009-01-01'), 
                                     ymd('2021-12-31'), by = '1 day')))

Save missing dates

missingdates <- anti_join(compdates, perday)

Add missing dates to our data set.

fulldates <- rbind(perday, missingdates) #

This will give an error because we need the same arguments We need the same arguments

missingdates <- missingdates %>% 
  mutate(resc_counts = vector(mode = "numeric", length = length(.)))

Add now the missing dates to our data set

fulldates <- rbind(perday, missingdates)

Are any date duplicated?

table(duplicated(fulldates$date))

FALSE 
 4748 

Wim Bernasco’s suggestion instead of using anti_join() and rbind(), use left_join.

fulldates <- left_join(compdates, perday, by = "date") %>% 
  replace(is.na(.), 0)

Separate the date ymd

fulldates <- fulldates %>% 
  mutate(year = year(date),
         month = month(date),
         day = day(date))

What week of the year did it happen?

fulldates <- fulldates %>% 
  mutate(week = week(date))

What day of the week did it happen?

fulldates <- fulldates %>% 
  mutate(weekday = wday(date, label = TRUE))

4 Plotting results

Plot by week.

byweek <- fulldates %>% 
  group_by(year, week) %>% 
  summarise(resc_counts = sum(resc_counts))
ggplot(data = byweek) +
  geom_line(aes(x = week, y = resc_counts), size = 1) +
  facet_wrap(vars(year),scales = "free_x") 

Plot Trends by Type of Animal, so accounting the type of animals.

First cat

cat <- mydatadate %>% 
  filter(animal_group_parent == "cat") %>%  
  group_by(date, animal_group_parent) %>% 
  summarise(resc_counts = n())

mdatecat <- anti_join(compdates, cat)

fullcat <- rbind(cat, mdatecat) %>% 
  mutate(animal_group_parent = "cat") %>% 
  replace(is.na(.),0)

Dog now.

dog <- mydatadate %>% 
  filter(animal_group_parent == "dog") %>%  
  group_by(date, animal_group_parent) %>% 
  summarise(resc_counts = n())

mdatedog <- anti_join(compdates, dog)

fulldog <- rbind(dog, mdatedog) %>% 
  mutate(animal_group_parent = "dog") %>% 
  replace(is.na(.),0)

Bird now.

bird <- mydatadate %>% 
  filter(animal_group_parent == "bird") %>%  
  group_by(date, animal_group_parent) %>% 
  summarise(resc_counts = n())

mdatebird <- anti_join(compdates, bird)

fullbird <- rbind(bird, mdatebird) %>% 
  mutate(animal_group_parent = "bird") %>% 
  replace(is.na(.),0)

Three datasets together.

myfulldata <- rbind(fullcat,fulldog, fullbird)

Dates by components

myfulldata <- myfulldata %>% 
  mutate(day = day(date),
         month = month(date, label = TRUE),
         year = year(date),
         week = week(date),
         weekday = wday(date, label = TRUE))

By day of the week

bywday <- myfulldata %>% 
  group_by(year, weekday, animal_group_parent) %>% 
  summarise(resc_counts = sum(resc_counts))

What levels are in weekday?

levels(bywday$weekday)
[1] "zo" "ma" "di" "wo" "do" "vr" "za"

Order these levels.

levelorder <- c("Mon", "Tue", "Wed", "Thu", "Fri", "Sat", "Sun")
ggplot(data = bywday) +
  geom_line(aes(x = factor(weekday, level = levelorder), 
                y = resc_counts, 
                group = animal_group_parent, 
                color = animal_group_parent), size = 1) +
  facet_wrap(vars(year), scales = "free_x")+
  labs(
    title = "Animal Rescue per Weekday",
    x = "Weekday",
    y = "Count of Rescues",
    color = "Animal"
  )

By week of the year

myfulldata <- myfulldata %>% 
  mutate(weekyear = paste0(week,month,day))
byweek <- myfulldata %>% 
  group_by(year, weekyear, animal_group_parent) %>% 
  summarise(resc_counts = sum(resc_counts))

Plot it.

ggplot(data = byweek) +
  geom_line(aes(x = weekyear, 
                y = resc_counts, 
                group = animal_group_parent, 
                color = animal_group_parent), size = 1) +
  facet_wrap(vars(year), scales = "free_x") +
  labs(
    title = "Animal Rescue per Week",
    x = "Week",
    y = "Count of Rescues",
    color = "Animal"
  )

By month of the year

bymonth <- myfulldata %>% 
  group_by(year, month, animal_group_parent) %>% 
  summarise(resc_counts = sum(resc_counts))
ggplot(data = bymonth) +
  geom_line(aes(x = month, 
                y = resc_counts, 
                group = animal_group_parent, 
                color = animal_group_parent), size = 1) +
  facet_wrap(vars(year), scales = "free_x") +
  labs(
    title = "Animal Rescue per Month",
    x = "Month",
    y = "Count of Rescues",
    color = "Animal"
  )

By year

byyear <- myfulldata %>% 
  group_by(year,animal_group_parent) %>% 
  summarise(resc_counts = sum(resc_counts))
ggplot(data = byyear) +
  geom_line(aes(x = year, 
                y = resc_counts, 
                group = animal_group_parent, 
                color = animal_group_parent), size = 1) +
  labs(
    title = "Animal Rescue per Year",
    x = "Year",
    y = "Count of Rescues",
    color = "Animal"
  )

5 References

Trinidad, A. (n.d.). NSC-R Workshops: NSC-R Tidy Tuesday. NSCR. Retrieved from https://nscrweb.netlify.app/posts/2022-02-22-nsc-r-tidy-tuesday/