Sometimes it's possible to get someone to download a snapshot into a .csv for you, but this is generally not desirable as the iteration speed is very slow.
In this chapter, you'll first learn the basics of the DBI package: how to use it to connect to a database and how to retrieve data by executing an SQL query.
**SQL**, short for **s**tructured **q**uery **l**anguage, is the lingua franca of databases, and is an important language for you to learn as a data scientist.
However, we're not going to start with SQL, but instead we'll teach you dbplyr, which can convert your dplyr code to the equivalent SQL.
We'll use that as way to teach you some of the most important features of SQL.
You won't become a SQL master by the end of the chapter, but you will be able to identify the most important components and understand what they do.
The main focus of this chapter, is working with data that already exists, data that someone else has collected in a database for you, as this represents the most common case.
But as we go along, we will point out a few tips and tricks for getting your own data into a database.
- You'll always use DBI (**d**ata**b**ase **i**nterface), provides a set of generic functions that perform connect to the database, upload data, run queries, and so on.
If you can't find a specific package for your DBMS, you can usually use the generic odbc package instead.
This uses the widespread ODBC standard.
odbc requires a little more setup because you'll also need to install and configure an ODBC driver.
Concretely, to create a database connection using `DBI::dbConnect()`.
The first argument specifies the DBMS and the second and subsequent arguments describe where the database lives and any credentials that you'll need to access it.
The following code shows are few typical examples:
If you want to use duckdb for a real data analysis project[^import-databases-1], you'll also need to supply the `dbdir` argument to tell duckdb where to store the database files.
Assuming you're using a project (Chapter -@sec-workflow-scripts-projects)), it's reasonable to store it in the `duckdb` directory of the current project:
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = "duckdb")
```
duckdb is a high-performance database that's designed very much with the needs of the data scientist in mind, and the developers very much understand R and the types of real problems that R users face.
As you'll see in this chapter, it's really easy to get started with but it can also handle very large datasets.
Notice something important with the diamonds dataset: the `cut`, `color`, and `clarity` columns were originally ordered factors, but now they're regular factors.
This particularly case isn't very important since ordered factors are barely different to regular factors, but it's good to know that the way that the database represents data can be slightly different to the way R represents data.
In this case, we're actually quite lucky because most databases don't support factors at all and would've converted the column to a string.
Again, not that important, because most of the time you'll be working with data that lives in a database, but good to be aware of if you're storing your own data into a database.
Generally you can expect numbers, strings, dates, and date-times to convert just fine, but other types may not.
-->
```
In real life, it's rare that you'll use `dbReadTable()` because the whole reason you're using a database is that there's too much data to fit in a data frame, and you want to use the database to bring back only a subset of the rows and columns.
We won't discuss it further here, but if you're dealing with very large datasets it's possible to deal with a "page" of data at a time by using `dbSendQuery()` to get a "result set" which you can page through by calling `dbFetch()` until `dbHasCompleted()` returns `TRUE`.
There are lots of other functions in DBI that you might find useful if you're managing your own data (like `dbWriteTable()` which we used in @sec-load-data), but we're going to skip past them in the interests of staying focused on working with data that already lives in a database.
Now that you've learned the low-level basics for connecting to a database and running a query, we're going to switch it up a bit and learn a bit about dbplyr.
dbplyr is a dplyr **backend**, which means that you write the dplyr code that you're already familiar with and dbplyr translates it to run in a different way, in this case to SQL.
This object is **lazy**; when you use dplyr verbs on it, dplyr doesn't do any work: it just records the sequence of operations that you want to perform and only performs them when needed.
You can tell this object represents a database query because it prints the DBMS name at the top, and while it tells you the number of columns, it typically it won't tell you the number of rows.
This is because finding the total number of rows usually requires executing the complete query, something we're trying to avoid.
You can see the SQL the dbplyr generates by a dbplyr query by calling `show_query()`:
It's an introduction to SQL designed specifically for the needs of data scientists, and includes examples of the sort of highly interconnected data you're likely to encounter in real organizations.
There are three other important clauses: `WHERE`, `ORDER BY`, and `GROUP BY`. `WHERE` and `ORDER BY` control which rows are included in the result and how they are ordered:
There are two important differences between dplyr verbs and SELECT clauses:
- SQL, unlike R, is **case** **insensitive** so you can write `select`, `SELECT`, or even `SeLeCt`. In this book we'll stick with the common convention of writing SQL keywords in uppercase to distinguish them from table or variables names.
- In SQL, order matters. Unlike dplyr, where you can call the verbs in whatever order makes the most sense to you, SQL clauses must come in a specific order: `SELECT`, `FROM`, `WHERE`, `GROUP BY`, `ORDER BY`. Confusingly, this order doesn't match how they are actually evaluated, which is `FROM`, `WHERE`, `GROUP BY`, `SELECT`, `ORDER BY`.
Note that every database uses a slightly different dialect of SQL.
For the vast majority of simple examples in this chapter, you won't see any differences.
But as you start to write more complex SQL you'll discover that what works on what database might not work on another.
Fortunately, dbplyr will take care a lot of this for you, as it automatically varies the SQL that it generates based on the database you're using.
It's not perfect, but if you discover the dbplyr creates SQL that works on one database but not another, please file an issue so we can try to make it better.
`SELECT` is the workhorse of SQL queries, and is equivalent to `select()`, `mutate()`, `rename()`, `relocate()`, and, as you'll learn in the next section, `summarize()`.
`select()`, `rename()`, and `relocate()` have very direct translations to `SELECT` as they affect where a column appears (if at all) along with its name:
So if you modify a column that you just created, dbplyr will need to create a subquery:
```{r}
diamonds_db |>
select(carat) |>
mutate(
carat2 = carat + 2,
carat3 = carat2 + 1
) |>
show_query()
```
A subquery is just a query that's nested inside of `FROM`, so instead of a table being used as the source, the new query is.
Another similar restriction is that `WHERE`, like `SELECT` can only operate on variables in `FROM`, so if you try and filter based on a variable that you just created, you'll need to create a subquery.
```{r}
diamonds_db |>
select(carat) |>
mutate(carat2 = carat + 2) |>
filter(carat2 > 1) |>
show_query()
```
Sometimes dbplyr uses a subquery where strictly speaking it's not necessary.
SQL joins are straightforward, but dbplyr's current translations are rather verbose (we're working on doing better in the future, so if you're lucky it'll be better by the time you're reading this):
Sometimes it's useful to perform a join or semi/anti join with data that you have locally.
How can you get that data into the database?
There are a few ways to do so.
You can set `copy = TRUE` to automatically copy.
There are two other ways that give you a little more control:
`copy_to()` --- this works very similarly to `DBI::dbWriteTable()` but returns a `tbl` so you don't need to create one after the fact.
By default this creates a temporary table, which will only be visible to the current connection (not to other people using the database), and will automatically be deleted when the connection finishes.
Most database will allow you to create temporary tables, even if you don't otherwise have write access to the data.
`copy_inline()` --- new in the latest version of db.
Rather than copying the data to the database, it builds SQL that generates the data inline.
It's useful if you don't have permission to create temporary tables, and is faster than `copy_to()` for small datasets.
dbplyr provides translation for other dplyr verbs like `distinct()`, `slice_*()`, and `intersect()`, and a growing selection of tidyr functions like `pivot_longer()` and `pivot_wider()`.
The easiest way to see the full set of what's currently available is to visit the dbplyr website: <https://dbplyr.tidyverse.org/reference/>.
So far we've focussed on the big picture of how dplyr verbs are translated in to `SELECT` clauses.
Now we're going to zoom in a little and talk about how individual R functions are translated, i.e. what happens when you use `mean(x)` in a `summarize()`?
The translation is certainly not perfect, and there are many R functions that aren't converted to SQL, but dbplyr does a surprisingly good job covering the functions that you'll use most of the time.
To explore these translations I'm going to make a couple of little helper functions that run a `summarise()` or `mutate()` and return the generated SQL.
