src_mysql: Connect to mysql/mariadb.

In sctyner/dplyr050: A Grammar of Data Manipulation

Description

Use src_mysql to connect to an existing mysql or mariadb database, and tbl to connect to tables within that database. If you are running a local mysqlql database, leave all parameters set as their defaults to connect. If you're connecting to a remote database, ask your database administrator for the values of these variables.

Usage

src_mysql(dbname, host = NULL, port = 0L, user = "root", password = "",
  ...)

## S3 method for class 'src_mysql'
tbl(src, from, ...)

Arguments

dbname	Database name
host, port	Host name and port number of database
user, password	User name and password. Rather than supplying a username and password here, it's better to save them in my.cnf, as described in MySQL. In that case, supply NULL to both user and password.
...	for the src, other arguments passed on to the underlying database connector, dbConnect. For the tbl, included for compatibility with the generic, but otherwise ignored.
src	a mysql src created with src_mysql.
from	Either a string giving the name of table in database, or sql described a derived table or compound join.

Debugging

To see exactly what SQL is being sent to the database, you see show_query and explain.

Grouping

Typically you will create a grouped data table is to call the group_by method on a mysql tbl: this will take care of capturing the unevalated expressions for you.

For best performance, the database should have an index on the variables that you are grouping by. Use explain to check that the database is using the indexes that you expect.

Output

All data manipulation on SQL tbls are lazy: they will not actually run the query or retrieve the data unless you ask for it: they all return a new tbl_sql object. Use compute to run the query and save the results in a temporary in the database, or use collect to retrieve the results to R.

Note that do is not lazy since it must pull the data into R. It returns a tbl_df or grouped_df, with one column for each grouping variable, and one list column that contains the results of the operation. do never simplifies its output.

Query principles

This section attempts to lay out the principles governing the generation of SQL queries from the manipulation verbs. The basic principle is that a sequence of operations should return the same value (modulo class) regardless of where the data is stored.

• arrange(arrange(df, x), y) should be equivalent to arrange(df, y, x)

• select(select(df, a:x), n:o) should be equivalent to select(df, n:o)

• mutate(mutate(df, x2 = x * 2), y2 = y * 2) should be equivalent to mutate(df, x2 = x * 2, y2 = y * 2)

• filter(filter(df, x == 1), y == 2) should be equivalent to filter(df, x == 1, y == 2)

• summarise should return the summarised output with one level of grouping peeled off.

Examples

## Not run: 
# Connection basics ---------------------------------------------------------
# To connect to a database first create a src:
my_db <- src_mysql(host = "blah.com", user = "hadley",
  password = "pass")
# Then reference a tbl within that src
my_tbl <- tbl(my_db, "my_table")

## End(Not run)

# Here we'll use the Lahman database: to create your own local copy,
# create a local database called "lahman", or tell lahman_mysql() how to
# a database that you can write to

if (!has_lahman("postgres") && has_lahman("mysql")) {
lahman_m <- lahman_mysql()
# Methods -------------------------------------------------------------------
batting <- tbl(lahman_m, "Batting")
dim(batting)
colnames(batting)
head(batting)

# Data manipulation verbs ---------------------------------------------------
filter(batting, yearID > 2005, G > 130)
select(batting, playerID:lgID)
arrange(batting, playerID, desc(yearID))
summarise(batting, G = mean(G), n = n())
mutate(batting, rbi2 = 1.0 * R / AB)

# note that all operations are lazy: they don't do anything until you
# request the data, either by `print()`ing it (which shows the first ten
# rows), by looking at the `head()`, or `collect()` the results locally.

system.time(recent <- filter(batting, yearID > 2010))
system.time(collect(recent))

# Group by operations -------------------------------------------------------
# To perform operations by group, create a grouped object with group_by
players <- group_by(batting, playerID)
group_size(players)

# MySQL doesn't support windowed functions, which means that only
# grouped summaries are really useful:
summarise(players, mean_g = mean(G), best_ab = max(AB))

# When you group by multiple level, each summarise peels off one level
per_year <- group_by(batting, playerID, yearID)
stints <- summarise(per_year, stints = max(stint))
filter(ungroup(stints), stints > 3)
summarise(stints, max(stints))

# Joins ---------------------------------------------------------------------
player_info <- select(tbl(lahman_m, "Master"), playerID,
  birthYear)
hof <- select(filter(tbl(lahman_m, "HallOfFame"), inducted == "Y"),
 playerID, votedBy, category)

# Match players and their hall of fame data
inner_join(player_info, hof)
# Keep all players, match hof data where available
left_join(player_info, hof)
# Find only players in hof
semi_join(player_info, hof)
# Find players not in hof
anti_join(player_info, hof)

# Arbitrary SQL -------------------------------------------------------------
# You can also provide sql as is, using the sql function:
batting2008 <- tbl(lahman_m,
  sql("SELECT * FROM Batting WHERE YearID = 2008"))
batting2008
}

sctyner/dplyr050 documentation built on May 17, 2019, 2:22 p.m.