Building data models from data frames with dm

dm allows you to create your own relational data models from local data frames. Once your data model is complete, you can deploy it a range of DBMSs using dm.

Creating a dm object from data frames

The example data set that we will be using is available through the nycflights13 package. The five tables that we are working with contain information about all flights that departed from the airports of New York to other destinations in the United States in 2013:

flights represents the trips taken by planes
airlines includes
- the names of transport organizations (name)
- their abbreviated codes (carrier)
airports indicates the ports of departure (origin) and of destination (dest)
weather contains meteorological information at each hour
planes describes characteristics of the aircraft

Once we’ve loaded {nycflights13}, the aforementioned tables are all in our work environment, ready to be accessed.

library(nycflights13)

airports

#> # A tibble: 1,458 x 8
#>    faa   name                    lat    lon   alt    tz dst   tzone        
#>    <chr> <chr>                 <dbl>  <dbl> <dbl> <dbl> <chr> <chr>        
#>  1 04G   Lansdowne Airport      41.1  -80.6  1044    -5 A     America/New_…
#>  2 06A   Moton Field Municipa…  32.5  -85.7   264    -6 A     America/Chic…
#>  3 06C   Schaumburg Regional    42.0  -88.1   801    -6 A     America/Chic…
#>  4 06N   Randall Airport        41.4  -74.4   523    -5 A     America/New_…
#>  5 09J   Jekyll Island Airport  31.1  -81.4    11    -5 A     America/New_…
#>  6 0A9   Elizabethton Municip…  36.4  -82.2  1593    -5 A     America/New_…
#>  7 0G6   Williams County Airp…  41.5  -84.5   730    -5 A     America/New_…
#>  8 0G7   Finger Lakes Regiona…  42.9  -76.8   492    -5 A     America/New_…
#>  9 0P2   Shoestring Aviation …  39.8  -76.6  1000    -5 U     America/New_…
#> 10 0S9   Jefferson County Intl  48.1 -123.    108    -8 A     America/Los_…
#> # … with 1,448 more rows

Your own data will probably not be available as an R package. Whatever format it is in, you will need to be able to load it as data frames into your R session. If the data is too large, consider using dm to connect to the database instead. See vignette("howto-dm-db") for details on using dm with databases.

Adding Tables

Our first step will be to tell dm which tables we want to work with and how they are connected. For that we can use dm(), passing in the table names as arguments.

library(dm)

flights_dm_no_keys <- dm(airlines, airports, flights, planes, weather)
flights_dm_no_keys

#> ── Metadata ───────────────────────────────────────────────────────────────
#> Tables: `airlines`, `airports`, `flights`, `planes`, `weather`
#> Columns: 53
#> Primary keys: 0
#> Foreign keys: 0

The as_dm() function is an alternative that works if you already have a list of tables.

A dm is a list

dm objects behave like lists with a user- and console-friendly print format. In fact, using a dm as a nicer list for organizing your data frames in your environment is an easy first step towards using dm and its data modeling functionality.

Member referencing, by subscript and by name, and list and slice manipulation functions work just as you would expect on a dm object.

names(flights_dm_no_keys)
#> [1] "airlines" "airports" "flights"  "planes"   "weather"
flights_dm_no_keys$airports

#> # A tibble: 1,458 x 8
#>    faa   name                    lat    lon   alt    tz dst   tzone        
#>    <chr> <chr>                 <dbl>  <dbl> <dbl> <dbl> <chr> <chr>        
#>  1 04G   Lansdowne Airport      41.1  -80.6  1044    -5 A     America/New_…
#>  2 06A   Moton Field Municipa…  32.5  -85.7   264    -6 A     America/Chic…
#>  3 06C   Schaumburg Regional    42.0  -88.1   801    -6 A     America/Chic…
#>  4 06N   Randall Airport        41.4  -74.4   523    -5 A     America/New_…
#>  5 09J   Jekyll Island Airport  31.1  -81.4    11    -5 A     America/New_…
#>  6 0A9   Elizabethton Municip…  36.4  -82.2  1593    -5 A     America/New_…
#>  7 0G6   Williams County Airp…  41.5  -84.5   730    -5 A     America/New_…
#>  8 0G7   Finger Lakes Regiona…  42.9  -76.8   492    -5 A     America/New_…
#>  9 0P2   Shoestring Aviation …  39.8  -76.6  1000    -5 U     America/New_…
#> 10 0S9   Jefferson County Intl  48.1 -123.    108    -8 A     America/Los_…
#> # … with 1,448 more rows

flights_dm_no_keys[c("airports", "flights")]

#> ── Metadata ───────────────────────────────────────────────────────────────
#> Tables: `airports`, `flights`
#> Columns: 27
#> Primary keys: 0
#> Foreign keys: 0

Defining Keys

Even though we now have a dm object that contains all our data, we have not specified how our five tables are connected. To do this we need to define primary keys and foreign keys on the tables.

Primary keys and foreign keys are how relational database tables are linked with each other. A primary key is a column that has a unique value for each row within a table. A foreign key is a column containing the primary key for a row in another table.¹ Foreign keys act as cross references between tables. They specify the relationships that gives us the relational database. For more information on keys and a crash course on databases, see vignette("howto-dm-theory").

Primary Keys

dm offers dm_enum_pk_candidates() to identify viable primary keys, and dm_add_pk() to add them.

dm_enum_pk_candidates(
  dm = flights_dm_no_keys,
  table = planes
)

#> # A tibble: 9 x 3
#>   columns     candidate why                                                
#>   <keys>      <lgl>     <chr>                                              
#> 1 tailnum     TRUE      ""                                                 
#> 2 engine      FALSE     "has duplicate values: 4 Cycle, Reciprocating, Tur…
#> 3 engines     FALSE     "has duplicate values: 1, 2, 3, 4"                 
#> 4 manufactur… FALSE     "has duplicate values: AIRBUS, AIRBUS INDUSTRIE, A…
#> 5 model       FALSE     "has duplicate values: 717-200, 737-301, 737-3G7, …
#> 6 seats       FALSE     "has duplicate values: 2, 4, 5, 6, 7, …"           
#> 7 speed       FALSE     "has duplicate values: 90, 105, 162, 432, NA"      
#> 8 type        FALSE     "has duplicate values: Fixed wing multi engine, Fi…
#> 9 year        FALSE     "has duplicate values: 1959, 1963, 1975, 1976, 197…

Now, we add the primary keys that we have identified:

flights_dm_only_pks <-
  flights_dm_no_keys %>%
  dm_add_pk(table = airlines, columns = carrier) %>%
  dm_add_pk(airports, faa) %>%
  dm_add_pk(planes, tailnum)
flights_dm_only_pks

#> ── Metadata ───────────────────────────────────────────────────────────────
#> Tables: `airlines`, `airports`, `flights`, `planes`, `weather`
#> Columns: 53
#> Primary keys: 3
#> Foreign keys: 0

Note that we demonstrate both named and positional arguments above.

Foreign Keys

To define how our tables are related, we use dm_add_fk() to add foreign keys. In calling dm_add_fk() the table argument is the table that needs a foreign key to link it to a second table. ref_table is the table to be linked to and it needs a primary key already defined for it.

dm_enum_fk_candidates(
  dm = flights_dm_only_pks,
  table = flights,
  ref_table = airlines
)

#> # A tibble: 19 x 3
#>    columns      candidate why                                              
#>    <keys>       <lgl>     <chr>                                            
#>  1 carrier      TRUE      ""                                               
#>  2 tailnum      FALSE     "334264 entries (99.3%) of `flights$tailnum` not…
#>  3 dest         FALSE     "336776 entries (100%) of `flights$dest` not in …
#>  4 origin       FALSE     "336776 entries (100%) of `flights$origin` not i…
#>  5 air_time     FALSE     "Can't join on `x$value` x `y$value` because of …
#>  6 arr_delay    FALSE     "Can't join on `x$value` x `y$value` because of …
#>  7 arr_time     FALSE     "Can't join on `x$value` x `y$value` because of …
#>  8 day          FALSE     "Can't join on `x$value` x `y$value` because of …
#>  9 dep_delay    FALSE     "Can't join on `x$value` x `y$value` because of …
#> 10 dep_time     FALSE     "Can't join on `x$value` x `y$value` because of …
#> 11 distance     FALSE     "Can't join on `x$value` x `y$value` because of …
#> 12 flight       FALSE     "Can't join on `x$value` x `y$value` because of …
#> 13 hour         FALSE     "Can't join on `x$value` x `y$value` because of …
#> 14 minute       FALSE     "Can't join on `x$value` x `y$value` because of …
#> 15 month        FALSE     "Can't join on `x$value` x `y$value` because of …
#> 16 sched_arr_t… FALSE     "Can't join on `x$value` x `y$value` because of …
#> 17 sched_dep_t… FALSE     "Can't join on `x$value` x `y$value` because of …
#> 18 time_hour    FALSE     "Can't join on `x$value` x `y$value` because of …
#> 19 year         FALSE     "Can't join on `x$value` x `y$value` because of …

Having chosen a column from the successful candidates provided by dm_enum_fk_candidates(), we use the dm_add_fk() function to establish the foreign key linking the tables. In the second call to dm_add_fk() we complete the process for the flights and airlines tables that we started above. The carrier column in the airlines table will be added as the foreign key in flights.

flights_dm_all_keys <-
  flights_dm_only_pks %>%
  dm_add_fk(table = flights, columns = tailnum, ref_table = planes) %>%
  dm_add_fk(flights, carrier, airlines) %>%
  dm_add_fk(flights, origin, airports)
flights_dm_all_keys

#> ── Metadata ───────────────────────────────────────────────────────────────
#> Tables: `airlines`, `airports`, `flights`, `planes`, `weather`
#> Columns: 53
#> Primary keys: 3
#> Foreign keys: 3

Having created the required primary and foreign keys to link all the tables together, we now have a relational data model we can work with.

Visualization

Visualizing a data model is a quick and easy way to verify that we have successfully created the model we were aiming for. We can use dm_draw() at any stage of the process to generate a visual representation of the tables and the links between them:

flights_dm_no_keys %>%
  dm_draw(rankdir = "TB", view_type = "all")


flights_dm_no_keys %>%
  dm_add_pk(airlines, carrier) %>%
  dm_draw()


flights_dm_only_pks %>%
  dm_add_fk(flights, tailnum, planes) %>%
  dm_draw()


flights_dm_all_keys %>%
  dm_draw()

Integrity Checks

As well as checking our data model visually, dm can examine the constraints we have created by the addition of keys and verify that they are sensible.

flights_dm_no_keys %>%
  dm_examine_constraints()

#> ℹ No constraints defined.


flights_dm_only_pks %>%
  dm_examine_constraints()

#> ℹ All constraints satisfied.


flights_dm_all_keys %>%
  dm_examine_constraints()

#> ! Unsatisfied constraints:

#> ● Table `flights`: foreign key tailnum into table `planes`: 50094 entries (14.9%) of `flights$tailnum` not in `planes$tailnum`: N725MQ (575), N722MQ (513), N723MQ (507), N713MQ (483), N735MQ (396), …

The results are presented in a human-readable form, and available as a tibble for programmatic inspection.

Programming

Helper functions are available to access details on keys and check results.

dm_get_all_pks() returns a data frame with our primary keys:

flights_dm_only_pks %>%
  dm_get_all_pks()

#> # A tibble: 3 x 2
#>   table    pk_col 
#>   <chr>    <keys> 
#> 1 airlines carrier
#> 2 airports faa    
#> 3 planes   tailnum

A data frame of foreign keys is retrieved with dm_get_all_fks():

flights_dm_all_keys %>%
  dm_get_all_pks()

#> # A tibble: 3 x 2
#>   table    pk_col 
#>   <chr>    <keys> 
#> 1 airlines carrier
#> 2 airports faa    
#> 3 planes   tailnum

We can use tibble::as_tibble() on the result of dm_examine_constraints() to programmatically inspect which constraints are not satisfied:

flights_dm_all_keys %>%
  dm_examine_constraints() %>%
  tibble::as_tibble()

#> # A tibble: 6 x 6
#>   table   kind  columns ref_table is_key problem                           
#>   <chr>   <chr> <keys>  <chr>     <lgl>  <chr>                             
#> 1 flights FK    tailnum planes    FALSE  "50094 entries (14.9%) of `flight…
#> 2 airlin… PK    carrier NA        TRUE   ""                                
#> 3 airpor… PK    faa     NA        TRUE   ""                                
#> 4 planes  PK    tailnum NA        TRUE   ""                                
#> 5 flights FK    carrier airlines  TRUE   ""                                
#> 6 flights FK    origin  airports  TRUE   ""

Support for compound keys (consisting of multiple columns) is planned.↩︎

Create a dm object from data frames

2020-07-29