CRAN Recipes: DPLYR, Stringr, Lubridate, and RegEx in R

© The Author(s), under exclusive license to APress Media, LLC, part of Springer Nature 2021

W. YarberryCRAN Recipeshttps://doi.org/10.1007/978-1-4842-6876-6_1

1. DPLYR

William Yarberry¹  

(1)

Kingwood, TX, USA

DPLYR is one of my favorite R packages. Its logical and consistent rules replace the older, motley collection of syntactically inconsistent packages and functions. It’s like a Swiss Army knife in the woods—don’t leave home without it.

Most of the book’s code examples use built-in R datasets or toy dataframe hard-coded into the program. For practice, you should substitute your own data when running the snippets of code.

1.1 Filter Commands

The filter command is used to eliminate rows (records) you do not want. The following commands use built-in datasets as the input dataframe. The dataset mtcars is used in the following. The output shows cars with six cylinders only.

Note

The following shown libraries will be used in all code unless otherwise noted. DPLYR is included in the mega-package tidyverse.

1.1.1 Single-Condition Filter

library(tidyverse)

data(mtcars)

#select only cars with six cylinders

six.cyl.only <- filter(mtcars, cyl == 6)

six.cyl.only

##                 mpg cyl  disp  hp drat    wt  qsec vs am gear carb

## Mazda RX4      21.0   6 160.0 110 3.90 2.620 16.46  0  1    4    4

## Mazda RX4 Wag  21.0   6 160.0 110 3.90 2.875 17.02  0  1    4    4

## Hornet 4 Drive 21.4   6 258.0 110 3.08 3.215 19.44  1  0    3    1

## Valiant        18.1   6 225.0 105 2.76 3.460 20.22  1  0    3    1

## Merc 280       19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4

## Merc 280C      17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4

## Ferrari Dino   19.7   6 145.0 175 3.62 2.770 15.50  0  1    5    6

In the filter command, equals is a double equals sign ==.

1.1.2 Multiple-Condition Filter

Filter the dataset mtcars for both six cylinders and 110 horsepower:

six.cylinders.and.110.horse.power <- filter(mtcars, cyl == 6,

 hp == 110)

six.cylinders.and.110.horse.power

##                 mpg cyl disp  hp drat    wt  qsec vs am gear carb

## Mazda RX4      21.0   6  160 110 3.90 2.620 16.46  0  1    4    4

## Mazda RX4 Wag  21.0   6  160 110 3.90 2.875 17.02  0  1    4    4

## Hornet 4 Drive 21.4   6  258 110 3.08 3.215 19.44  1  0    3    1

1.1.3 OR Logic for Filtering

You can use as many OR symbols (pipe |) as needed.

Filter based on the OR logical operator:

gear.eq.4.or.more.than.8 <- filter(mtcars, gear == 4|cyl > 6)

gear.eq.4.or.more.than.8

##                      mpg cyl  disp  hp drat    wt  qsec vs am gear carb

## Mazda RX4           21.0   6 160.0 110 3.90 2.620 16.46  0  1    4    4

## Mazda RX4 Wag       21.0   6 160.0 110 3.90 2.875 17.02  0  1    4    4

## Datsun 710          22.8   4 108.0  93 3.85 2.320 18.61  1  1    4    1

## Hornet Sportabout   18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2

## Duster 360          14.3   8 360.0 245 3.21 3.570 15.84  0  0    3    4

## Merc 240D           24.4   4 146.7  62 3.69 3.190 20.00  1  0    4    2

## Merc 230            22.8   4 140.8  95 3.92 3.150 22.90  1  0    4    2

## Merc 280            19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4

## Merc 280C           17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4

## Merc 450SE          16.4   8 275.8 180 3.07 4.070 17.40  0  0    3    3

## Merc 450SL          17.3   8 275.8 180 3.07 3.730 17.60  0  0    3    3

## Merc 450SLC         15.2   8 275.8 180 3.07 3.780 18.00  0  0    3    3

## Cadillac Fleetwood  10.4   8 472.0 205 2.93 5.250 17.98  0  0    3    4

## Lincoln Continental 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3    4

## Chrysler Imperial   14.7   8 440.0 230 3.23 5.345 17.42  0  0    3    4

## Fiat 128            32.4   4  78.7  66 4.08 2.200 19.47  1  1    4    1

## Honda Civic         30.4   4  75.7  52 4.93 1.615 18.52  1  1    4    2

## Toyota Corolla      33.9   4  71.1  65 4.22 1.835 19.90  1  1    4    1

## Dodge Challenger    15.5   8 318.0 150 2.76 3.520 16.87  0  0    3    2

## AMC Javelin         15.2   8 304.0 150 3.15 3.435 17.30  0  0    3    2

## Camaro Z28          13.3   8 350.0 245 3.73 3.840 15.41  0  0    3    4

## Pontiac Firebird    19.2   8 400.0 175 3.08 3.845 17.05  0  0    3    2

## Fiat X1-9           27.3   4  79.0  66 4.08 1.935 18.90  1  1    4    1

## Ford Pantera L      15.8   8 351.0 264 4.22 3.170 14.50  0  1    5    4

## Maserati Bora       15.0   8 301.0 335 3.54 3.570 14.60  0  1    5    8

## Volvo 142E          21.4   4 121.0 109 4.11 2.780 18.60  1  1    4    2

1.1.4 Filter by Minimums, Maximums, and Other Numeric Criteria

The output shows, as one would expect, a single row with the smallest engine displacement:

smallest.engine.displacement <- filter(mtcars, disp ==

     min(disp))

smallest.engine.displacement

##                 mpg cyl disp hp drat    wt qsec vs am gear carb

## Toyota Corolla 33.9   4 71.1 65 4.22 1.835 19.9  1  1    4    1

Filter with conditions separated by commas:

data(ChickWeight)

chick.subset <- filter(ChickWeight, Time < 3, weight > 53)

chick.subset

##   weight Time Chick Diet

## 1     55    2    22    2

## 2     55    2    40    3

## 3     55    2    43    4

## 4     54    2    50    4

1.1.5 Filter Out Missing Values (NAs) for a Specific Column

The built-in dataset airquality has a missing value in the fifth row of the first column (Ozone):

data(airquality)

head(airquality,10) #before filter

##    Ozone Solar.R Wind Temp Month Day

## 1     41     190  7.4   67     5   1

## 2     36     118  8.0   72     5   2

## 3     12     149 12.6   74     5   3

## 4     18     313 11.5   62     5   4

## 5     NA      NA 14.3   56     5   5

## 6     28      NA 14.9   66     5   6

## 7     23     299  8.6   65     5   7

## 8     19      99 13.8   59     5   8

## 9      8      19 20.1   61     5   9

## 10    NA     194  8.6   69     5  10

Remove any row with missing values in the Ozone column:

no.missing.ozone = filter(airquality, !is.na(Ozone))

head(no.missing.ozone,8) #after filter

##   Ozone Solar.R Wind Temp Month Day

## 1    41     190  7.4   67     5   1

## 2    36     118  8.0   72     5   2

## 3    12     149 12.6   74     5   3

## 4    18     313 11.5   62     5   4

## 5    28      NA 14.9   66     5   6

## 6    23     299  8.6   65     5   7

## 7    19      99 13.8   59     5   8

## 8     8      19 20.1   61     5   9

Note that although the row with NA for Ozone has been eliminated, the row with an NA for Solar.R is still there.

1.1.6 Filter Rows with NAs Anywhere in the Dataset

Use complete.cases() to remove any rows containing an NA in any column:

airqual.no.NA.anywhere <- filter(airquality[1:10,],

  complete.cases(airquality[1:10,]))

airqual.no.NA.anywhere

##   Ozone Solar.R Wind Temp Month Day

## 1    41     190  7.4   67     5   1

## 2    36     118  8.0   72     5   2

## 3    12     149 12.6   74     5   3

## 4    18     313 11.5   62     5   4

## 5    23     299  8.6   65     5   7

## 6    19      99 13.8   59     5   8

## 7     8      19 20.1   61     5   9

1.1.7 Filter by %in%

%in% is a powerful operator, providing a convenient shorthand for including/excluding specified values:

data(iris)

table(iris$Species) #counts of species in the dataset

##

##     setosa versicolor  virginica

##         50         50         50

iris.two.species <- filter(iris,

Species %in% c(setosa, virginica))

table(iris.two.species$Species)

##

##     setosa versicolor  virginica

##         50          0         50

Show the number of rows before and after filtering:

nrow(iris); nrow(iris.two.species)

## [1] 150

## [1] 100

1.1.8 Filter for Ozone > 29 and Include Only Three Columns

data(airquality)

airqual.3.columns <- filter(airquality, Ozone > 29)[,1:3]

head(airqual.3.columns)

##   Ozone Solar.R Wind

## 1    41     190  7.4

## 2    36     118  8.0

## 3    34     307 12.0

## 4    30     322 11.5

## 5    32      92 12.0

## 6    45     252 14.9

1.1.9 Filter by Total Frequency of a Value Across All Rows

This logic uses group_by to enable counting of rows based on number of gears. After the counts of gears are made, then only those rows whose total counts exceed ten are included in the output. All you want to see here are records that have at least 11 rows with a specific number of gears in the car. The filter is driven solely by frequency of occurrence. Your question may be phrased as just show me records where common gear configurations occur. Five gears are not nearly as common as three and four, so in the filtered dataframe, they are omitted. In the following first table, there are 15 records with a car having three gears, 12 records for four gears, and five records for five gears. After applying the filter and creating a new dataframe, there are no records having five gears:

table(mtcars$gear)

##

##  3  4  5

## 15 12  5

more.frequent.no.of.gears <- mtcars %>%

  group_by(gear) %>%

  filter(n() > 10)  #

table(more.frequent.no.of.gears$gear)

##

##  3  4

## 15 12

Additional criteria can be added to the filter by including a requirement that the horsepower be less than 105:

more.frequent.no.of.gears.and.low.horsepower <- mtcars %>%

group_by(gear) %>%

  filter(n() > 10, hp < 105)

  table(more.frequent.no.of.gears.and.low.horsepower$gear)

##

## 3 4

## 1 7

1.1.10 Filter by Column Name Using starts with

In this code, records are selected where the column name starts with an S:

names(iris)  #show the column names

## [1] Sepal.Length Sepal.Width  Petal.Length Petal.Width  Species

iris.display <- iris %>% dplyr::select(starts_with(S))

head(iris.display)  #use head to reduce number of rows output

##   Sepal.Length Sepal.Width Species

## 1          5.1         3.5  setosa

## 2          4.9         3.0  setosa

## 3          4.7         3.2  setosa

## 4          4.6         3.1  setosa

## 5          5.0         3.6  setosa

## 6          5.4         3.9  setosa

1.1.11 Filter Rows: Columns Meet Criteria (filter_at)

Use filter_at to find rows which meet some criteria such as maximum:

new.mtcars <- mtcars %>% filter_at(vars(cyl, hp),

   all_vars(. == max(.)))

new.mtcars

##               mpg cyl disp  hp drat   wt qsec vs am gear carb

## Maserati Bora  15   8  301 335 3.54 3.57 14.6  0  1    5    8

Note that only one car, the Maserati Bora, had both the maximum number of cylinders and the maximum horsepower for each column, respectively.

Another example dataset comes from Suzan Baert’s blog (https://suzan.rbind.io/2018/02/dplyr-tutorial-3/#filter-at), using sleep study research.

Load the msleep dataframe from the package ggplot2:

msleep <- ggplot2::msleep

msleep

## # A tibble: 83 x 11

##    name  genus vore  order conservation sleep_total sleep_rem sleep_cycle awake

##                        

##  1 Chee~ Acin~ carni Carn~ lc             12.1    NA       NA      11.9

##  2 Owl ~ Aotus omni  Prim~            17      1.8      NA      7

##  3 Moun~ Aplo~ herbi Rode~ nt             14.4    2.4      NA      9.6

##  4 Grea~ Blar~ omni  Sori~ lc             14.9    2.3      0.133   9.1

##  5 Cow   Bos   herbi Arti~ domesticated   4       0.7      0.667   20

##  6 Thre~ Brad~ herbi Pilo~            14.4    2.2      0.767   9.6

##  7 Nort~ Call~ carni Carn~ vu             8.7     1.4      0.383   15.3

##  8 Vesp~ Calo~   Rode~            7       NA       NA      17

##  9 Dog   Canis carni Carn~ domesticated   10.1    2.9      0.333   13.9

## 10 Roe ~ Capr~ herbi Arti~ lc             3       NA       NA      21

## # ... with 73 more rows, and 2 more variables: brainwt , bodywt

msleep.over.5 <- msleep %>%

  select(name, sleep_total:sleep_rem, brainwt:bodywt) %>%

  filter_at(vars(contains(sleep)), all_vars(.>5))

msleep.over.5

## # A tibble: 2 x 5

##   name                 sleep_total sleep_rem brainwt bodywt

##                                    

## 1 Thick-tailed opposum        19.4     6.6      NA      0.37

## 2 Giant armadillo             18.1     6.1      0.081   60

For the preceding code, ignore the select statement for the moment (covered later). The filter_at function says to look at only variables containing the word sleep. Within those variables (in this case, two of them), filter for any values greater than 5. The . means any variable with sleep in the name. Only two rows met the criteria for the filter in this case.

1.2 Arrange (Sort)

Arrange, the sorting function, is as old as the alphabet. Based on the defined ASCII order, it rearranges a dataframe or vector in a sequence defined as either ascending or descending. Sort keys are defined as primary, secondary, and so on.

Load the msleep dataframe from the package ggplot2:

msleep <- ggplot2::msleep

msleep[,1:4]

## # A tibble: 83 x 4

##    name                       genus       vore  order

##                                 

##  1 Cheetah                    Acinonyx    carni Carnivora

##  2 Owl monkey                 Aotus       omni  Primates

##  3 Mountain beaver            Aplodontia  herbi Rodentia

##  4 Greater short-tailed shrew Blarina     omni  Soricomorpha

##  5 Cow                        Bos         herbi Artiodactyla

##  6 Three-toed sloth           Bradypus    herbi Pilosa

##  7 Northern fur seal          Callorhinus carni Carnivora

##  8 Vesper mouse               Calomys       Rodentia

##  9 Dog                        Canis       carni Carnivora

## 10 Roe deer                   Capreolus   herbi Artiodactyla

## # ... with 73 more rows

1.2.1 Ascending

animal.name.sequence <- arrange(msleep, vore, order)

animal.name.sequence[,1:4]

## # A tibble: 83 x 4

##    name              genus        vore  order

##                         

##  1 Cheetah           Acinonyx     carni Carnivora

##  2 Northern fur seal Callorhinus  carni Carnivora

##  3 Dog               Canis        carni Carnivora

##  4 Domestic cat      Felis        carni Carnivora

##  5 Gray seal         Halichoerus carni Carnivora

##  6 Tiger             Panthera     carni Carnivora

##  7 Jaguar            Panthera     carni Carnivora

##  8 Lion              Panthera     carni Carnivora

##  9 Caspian seal      Phoca        carni Carnivora

## 10 Genet             Genetta      carni Carnivora

## # ... with 73 more rows

1.2.2 Descending

animal.name.sequence.desc <- arrange(msleep, vore, desc(order))

head(animal.name.sequence.desc[,1:4])

## # A tibble: 6 x 4

##   name                       genus         vore  order

##                                  

## 1 Northern grasshopper mouse Onychomys     carni Rodentia

## 2 Slow loris                 Nyctibeus     carni Primates

## 3 Thick-tailed opposum       Lutreolina    carni Didelphimorphia

## 4 Long-nosed armadillo       Dasypus       carni Cingulata

## 5 Pilot whale                Globicephalus carni Cetacea

## 6 Common porpoise            Phocoena      carni Cetacea

In section Mutate, you’ll see how a variable can be created on the fly and then used in the same statement for sorting.

1.3 Rename

Rename allows you to change the name of one or more columns. It is a convenience function and changes no data.

Rename one or more columns in a dataset:

names(iris)

## [1] Sepal.Length Sepal.Width  Petal.Length Petal.Width  Species

Show new column names:

renamed.iris <- rename(iris, width.of.petals = Petal.Width,

various.plants.and.animals = Species)

names(renamed.iris)

## [1] Sepal.Length               Sepal.Width

## [3] Petal.Length               width.of.petals

## [5] various.plants.and.animals

1.4 Mutate

Mutate adds new variables to a dataframe. It requires the original dataframe as the first argument and then arguments to create new variables as the remaining arguments. The following example adds the natural log of length and weight to the dataframe created earlier that contains just the length and weight variables.

Add a new, calculated variable to a dataframe:

data(ChickWeight)

ChickWeight[1:2,]  #first two rows

##   weight Time Chick Diet

## 1     42    0     1    1

## 2     51    2     1    1

First two rows, with new field added:

Chickweight.with.log <- mutate(ChickWeight,

log.of.weight = log10(weight))

Chickweight.with.log[1:2,]

##   weight Time Chick Diet log.of.weight

## 1     42    0     1    1      1.623249

## 2     51    2     1    1      1.707570

1.4.1 mutate_all to Add New Fields All