Join Keys

Overview

The teal.data package provides a way to define primary keys for a dataset and establish relationships with other datasets.

Each dataset joining keys can be characterized by:

Columns constituting the primary key;
Foreign/merge keys, analogous to SQL foreign keys.

Typically, an application developer specifies these keys manually. However, for datasets following the ADaM standard, teal.data can automatically assign keys using the default_cdisc_join_keys object. Refer to the section “Joining Keys with ADaM Datasets” for details on using this object to select specific datasets.

Uses of `join_keys` class in teal applications

The primary function of the join_keys class in teal applications is to facilitate the seamless merging of datasets using teal.transform.

Additionally, it plays a role in the data filtering using the Filter Panel in a teal application. The filters applied to a (parent) dataset are also applied to their children.

Anatomy of `join_keys`

The join_keys object contains information about the foreign/primary keys of multiple datasets. Each key is represented by a pair of datasets (by name reference) and a named character vector that encodes the column name mapping between the two datasets. In addition, a foreign key may also contain a parent-child attribute that is used in the “Filter Panel” as we mentioned above.

A new join keys can be created as an empty object, or by defining an initial set of primary and foreign keys.

That initial object can be extended by adding/modifying/removing keys and by establishing parent-child relationships between datasets.

`join_keys(...)`: Join Keys Constructor / Getter / Setter

Convenient function that is used both as the constructor and as the getter for join_keys objects.

As the Getter it is used to retrieve the joining keys that are contained in other objects, such as a teal_data object.

As the Constructor it is used to specify a collection of multiple individual keys (via join_key function described below).

`join_key(dataset_1, dataset_2, key, parent)`: Single Join Key Constructor

Specifies a primary key or a relationship between two datasets.

dataset_1, dataset_2: names of the datasets (if dataset_2 is the same as dataset_1 or is omitted, it creates a primary key);
key: named character vector of column name mapping between datasets (unnamed vector assumes column names between datasets are the same);
directed (optional): flag that indicates whether there is a parent-child directed relationship between dataset_2 to dataset_1 (latter as a parent).

Note that join keys are assumed to be symmetric, i.e., join_key("ds1", "ds2", c("ds1_col" = "ds2_col")) establishes a relationship from “x” to “y” and vice versa.

By default, the new joining key will set the dataset_1 as the parent.

Example & Output

library(teal.data)
jk <- join_keys(
  join_key("ds1", keys = "col_1"), # ds1: [col_1]
  join_key("ds2", keys = c("col_1", "col_2")), # ds2: [col_1, col_2]
  join_key("ds3", keys = c("col_1", "col_3")), # ds3: [col_1, col_3]
  join_key("ds1", "ds2", keys = "col_1"), # ds1 <-- ds2
  join_key("ds1", "ds3", keys = "col_1"), # ds1 <-- ds3
  join_key("ds4", "ds5", keys = c("col_4" = "col_5"), directed = FALSE) # ds4 <--> ds5
)

# The parent-child relationships are created automatically (unless 'parent' parameter is "none")
jk

Output of `print(jk)`	Output annotation
`## A join_keys object containing foreign keys between 3 datasets:`	Title
`## ds1: [col_1]`	Primary keys <dataset name>: [<primary_keys>]
`## <-- ds2: [col_1]`	Foreign keys (arrow `<--` denotes `ds1` is the parent of `ds2`)
`## <-- ds3: [col_1]`
`## ds2: [col_1, col_2]`
`## --> ds1: [col_1]`	arrow `-->` denotes `ds2` is a child of `ds1`
`## --* (implicit via parent with): ds3`	Implicit relationship between `ds2` & `ds3` (given that they share common keys with same parent)
`## ds3: [col_1, col_3]`
`## --> ds1: [col_1]`
`## --* (implicit via parent with): ds2`
`## ds4: [no primary keys]`
`## <-> ds5: [col_5]`	Foreign keys (arrow `<->` denotes no parent definition between datasets)
`## ds5: [no primary keys]`
`## <-> ds4: [col_4]`

Accessing and Modifying keys

The subset operator with 2 indices (x[i, j]) is used to retrieve the primary/foreign keys. Both indices must be a string denoting the dataset name.

# Using the jk object defined in "Anatomy of Join Keys"
jk

## A join_keys object containing foreign keys between 5 datasets:
## ds1: [col_1]
##   <-- ds2: [col_1]
##   <-- ds3: [col_1]
## ds2: [col_1, col_2]
##   --> ds1: [col_1]
##   --* (implicit via parent with): ds3
## ds3: [col_1, col_3]
##   --> ds1: [col_1]
##   --* (implicit via parent with): ds2
## ds4: [no primary keys]
##   <-> ds5: [col_5]
## ds5: [no primary keys]
##   <-> ds4: [col_4]

# Getting primary key of "ds1"
jk["ds1", "ds1"]

##   col_1 
## "col_1"

# Getting foreign keys between "ds4" and "ds5"
jk["ds4", "ds5"]

##   col_4 
## "col_5"

Note that there is a symmetry in the keys between ds4 and ds5 relationship:

jk["ds5", "ds4"]

##   col_5 
## "col_4"

jk["ds5", "ds4"]

##   col_5 
## "col_4"

When only 1 argument is used this operator will return a join_keys object that is filtered accordingly.

# Using the jk object defined in "Anatomy of Join Keys"
jk

## A join_keys object containing foreign keys between 5 datasets:
## ds1: [col_1]
##   <-- ds2: [col_1]
##   <-- ds3: [col_1]
## ds2: [col_1, col_2]
##   --> ds1: [col_1]
##   --* (implicit via parent with): ds3
## ds3: [col_1, col_3]
##   --> ds1: [col_1]
##   --* (implicit via parent with): ds2
## ds4: [no primary keys]
##   <-> ds5: [col_5]
## ds5: [no primary keys]
##   <-> ds4: [col_4]

# Getting primary key of "ds1"
jk["ds1", "ds1"]

##   col_1 
## "col_1"

# Getting keys of "ds1" and "ds2"
jk[c("ds1", "ds2")]

## A join_keys object containing foreign keys between 2 datasets:
## ds1: [col_1]
##   <-- ds2: [col_1]
## ds2: [col_1, col_2]
##   --> ds1: [col_1]

Modifying or adding a key uses the same notation with the assignment operator <-. A symmetric relationship will be created automatically, where the parent (by default) will be the dataset defined in the first index. Assigning NULL value will delete the relationship.

# Adding a new ds5 <-- ds1 key
jk["ds1", "ds5"] <- "a_column"

# Removing an existing key
jk["ds4", "ds5"] <- NULL

Merging Join Keys

The combining of multiple joining keys is achieved using the c() generic function, which generates a symmetric and valid join_keys object. When encountering identical relationship pairs, this operation retains the last occurrence of the pair within the specified argument order.

For added convenience, the function also accommodates join_key_set objects created through the join_key function. These objects can be provided as the initial argument or in any other position as needed.

jk1 <- join_keys(join_key("ds1", "ds1", "col_1"))
jk2 <- join_keys(join_key("ds2", "ds2", "col_1"), join_key("ds1", "ds2", "col_1"))

# Merging
c(jk1, jk2)

## A join_keys object containing foreign keys between 2 datasets:
## ds1: [col_1]
##   <-- ds2: [col_1]
## ds2: [col_1]
##   --> ds1: [col_1]

# Keeping last occurence
c(jk1, jk2, join_keys(join_key("ds2", "ds2", "col_2"), join_key("ds1", "ds2", c("col_1" = "col_2"))))

## A join_keys object containing foreign keys between 2 datasets:
## ds1: [col_1]
##   <-- ds2: [col_2]
## ds2: [col_2]
##   --> ds1: [col_1]

# Merges join_key and join_key_set objects (from join_key function)
c(jk1, join_key("ds3", "ds3", "col_3"))

## A join_keys object containing foreign keys between 2 datasets:
## ds1: [col_1]
## ds3: [col_3]

Join Keys Relationships

There are 2 types of relationships encoded with joining keys that are described in the following sections. The primary and foreign keys are created explicitly using the constructor for individual keys (join_key).

Additionally, the join_keys object infers implicit relationships when two datasets share foreign keys to a parent dataset, but not between themselves. These implicit relationships are available just like another foreign key and can be used to merge datasets, despite not being defined by the user.

Primary Key with `teal_data`

When using the teal_data function, the simplest method to define the join keys is to use the join_keys argument. We can specify the column(s) of the dataset that (together) uniquely identify rows in the dataset.

library(teal.data)

td_pk <- within(
  teal_data(),
  ds1 <- transform(iris, id = seq_len(nrow(iris)))
)
datanames(td_pk) <- "ds1"

join_keys(td_pk) <- join_keys(join_key("ds1", keys = "id"))

join_keys(td_pk)

## A join_keys object containing foreign keys between 1 datasets:
## ds1: [id]

We can extend the previous example and define primary keys for multiple datasets:

td_pk <- within(
  td_pk,
  {
    ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2))
    ds3 <- data.frame(V = 5:14, N = 4)
  }
)
datanames(td_pk) <- c(datanames(td_pk), "ds2", "ds3")

join_keys(td_pk)["ds2", "ds2"] <- c("V", "W")
join_keys(td_pk)["ds3", "ds3"] <- c("V", "W")

join_keys(td_pk)

## A join_keys object containing foreign keys between 3 datasets:
## ds1: [id]
## ds2: [V, W]
## ds3: [V, W]

Foreign Keys with `teal_data`

When passing multiple datasets to the teal_data function, dataset relationships are set using join_keys and join_key functions, which then can be used to merge datasets together within teal apps. For users familiar with SQL database schema, these relationships are symmetric and not as strict as SQL foreign key relationships as teal does not validate whether the values defined as foreign key columns are present in the table.

For example:

library(teal.data)

td_fk <- within(
  teal_data(),
  {
    ds1 <- data.frame(X = 1:10, Y = 21:30, Z = 1:10)
    ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2))
    ds3 <- data.frame(V = 5:14, N = 4)
  }
)
datanames(td_fk) <- c("ds1", "ds2", "ds3")

join_keys(td_fk) <- join_keys(
  # Primary keys
  join_key("ds1", keys = c("X")),
  join_key("ds2", keys = c("V", "W")),
  join_key("ds3", keys = c("V")),
  # Foreign keys
  join_key("ds1", "ds2", c("X" = "W")),
  join_key("ds2", "ds3", c("V" = "V"))
)

join_keys(td_fk)

## A join_keys object containing foreign keys between 3 datasets:
## ds1: [X]
##   <-- ds2: [W]
## ds2: [V, W]
##   --> ds1: [X]
##   <-- ds3: [V]
## ds3: [V]
##   --> ds2: [V]

Implicit Relationships

Two datasets that share common foreign keys to the same parent dataset have an implicit relationship between them that is modeled and accessible in joining keys.

This is a special relationship that is inferred from existing foreign keys. It does not need to be explicitly defined but it can be accessed and overwritten just as any other foreign key.

These implicit relationships can be used to merge 2 datasets together, just as if they were defined manually.

library(teal.data)

td <- within(
  teal_data(),
  {
    ds1 <- data.frame(X = 1:10, Y = 21:30, Z = 1:10)
    ds2 <- data.frame(W = 10:1, V = 5:14, M = rep(1:5, 2))
    ds3 <- data.frame(V = 5:14, N = 4)
    ds4 <- data.frame(V = 5:14, R = rnorm(10))
  }
)
datanames(td) <- c("ds1", "ds2", "ds3", "ds4")

join_keys(td) <- join_keys(
  # Primary keys
  join_key("ds1", keys = c("X")),
  join_key("ds2", keys = c("V", "W")),
  join_key("ds3", keys = c("V")),
  join_key("ds4", keys = c("V")),
  # Foreign keys
  join_key("ds1", "ds2", c("X" = "W")),
  join_key("ds2", "ds3", c("V" = "V")),
  join_key("ds1", "ds4", c("X" = "B"))
)

join_keys(td)

## A join_keys object containing foreign keys between 4 datasets:
## ds1: [X]
##   <-- ds2: [W]
##   <-- ds4: [B]
## ds2: [V, W]
##   --> ds1: [X]
##   <-- ds3: [V]
##   --* (implicit via parent with): ds4
## ds3: [V]
##   --> ds2: [V]
## ds4: [V]
##   --> ds1: [X]
##   --* (implicit via parent with): ds2

join_keys(td)["ds2", "ds4"]

##   W 
## "B"

Note that the definition above contains no join_key for "ds2" <-> "ds4"

Join Keys in ADaM Datasets

teal.data provides a set of default join keys (primary and foreign) for datasets named according to the ADaM standard. They are stored in default_cdisc_join_keys.

names(default_cdisc_join_keys) |> sort()

##  [1] "ADAE"     "ADAETTE"  "ADCM"     "ADCSSRS"  "ADDV"     "ADEG"    
##  [7] "ADEQ5D5L" "ADEX"     "ADHY"     "ADLB"     "ADMH"     "ADQLQC"  
## [13] "ADQS"     "ADRS"     "ADSAFTTE" "ADSL"     "ADSUB"    "ADTTE"   
## [19] "ADVS"

When not all default keys are required users can select a smaller set of datasets by subsetting (for example: default_cdisc_join_keys[c("ADSL", "ADTTE")]). Please note, that for every element that is selected, its parent will also be returned (if it has one) as well as any pair-wise relationships in the resulting selection.

default_cdisc_join_keys

## A join_keys object containing foreign keys between 19 datasets:
## ADSL: [STUDYID, USUBJID]
##   <-- ADAE: [STUDYID, USUBJID]
##   <-- ADEG: [STUDYID, USUBJID]
##   <-- ADTTE: [STUDYID, USUBJID]
##   <-- ADAETTE: [STUDYID, USUBJID]
##   <-- ADCM: [STUDYID, USUBJID]
##   <-- ADEX: [STUDYID, USUBJID]
##   <-- ADLB: [STUDYID, USUBJID]
##   <-- ADMH: [STUDYID, USUBJID]
##   <-- ADQS: [STUDYID, USUBJID]
##   <-- ADRS: [STUDYID, USUBJID]
##   <-- ADSAFTTE: [STUDYID, USUBJID]
##   <-- ADVS: [STUDYID, USUBJID]
##   <-- ADDV: [STUDYID, USUBJID]
##   <-- ADSUB: [STUDYID, USUBJID]
##   <-- ADHY: [STUDYID, USUBJID]
##   <-- ADQLQC: [STUDYID, USUBJID]
##   <-- ADCSSRS: [STUDYID, USUBJID]
##   <-- ADEQ5D5L: [STUDYID, USUBJID]
## ADAE: [STUDYID, USUBJID, ASTDTM, AETERM, AESEQ]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADEG: [STUDYID, USUBJID, PARAMCD, AVISIT]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADTTE: [STUDYID, USUBJID, PARAMCD]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADAETTE: [STUDYID, USUBJID, PARAMCD]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADCM: [STUDYID, USUBJID, ASTDTM, CMSEQ, ATC1CD, ATC2CD, ATC3CD, ATC4CD]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADEX: [STUDYID, USUBJID, PARCAT1, PARAMCD, AVISITN, ASTDTM, EXSEQ]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADLB: [STUDYID, USUBJID, PARAMCD, AVISIT]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADMH: [STUDYID, USUBJID, ASTDTM, MHSEQ]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADQS: [STUDYID, USUBJID, PARAMCD, AVISIT]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADRS: [STUDYID, USUBJID, PARAMCD, AVISIT]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADSAFTTE: [STUDYID, USUBJID, PARAMCD]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADVS: [STUDYID, USUBJID, PARAMCD, AVISIT]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADDV: [STUDYID, USUBJID, ASTDT, DVTERM, DVSEQ]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADSUB, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADSUB: [STUDYID, USUBJID, PARAMCD, AVISITN, ADTM, SRCSEQ]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADHY, ADQLQC, ADCSSRS, ADEQ5D5L
## ADHY: [STUDYID, USUBJID, PARAMCD, AVISITN, ADTM, SRCSEQ]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADQLQC, ADCSSRS, ADEQ5D5L
## ADQLQC: [STUDYID, USUBJID, PARCAT1N, PARAMCD, BASETYPE, AVISITN, ATPTN, ADTM, QSSEQ]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADCSSRS, ADEQ5D5L
## ADCSSRS: [STUDYID, USUBJID, PARAMCD, BASETYPE, AVISITN, DTYPE, ADTM]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADEQ5D5L
## ADEQ5D5L: [STUDYID, USUBJID, PARCAT1N, PARAMCD, BASETYPE, AVISITN, ATPTN, ADTM, QSSEQ]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADAE, ADEG, ADTTE, ADAETTE, ADCM, ADEX, ADLB, ADMH, ADQS, ADRS, ADSAFTTE, ADVS, ADDV, ADSUB, ADHY, ADQLQC, ADCSSRS

default_cdisc_join_keys["ADSL"]

## A join_keys object containing foreign keys between 1 datasets:
## ADSL: [STUDYID, USUBJID]

default_cdisc_join_keys["ADTTE"]

## A join_keys object containing foreign keys between 2 datasets:
## ADSL: [STUDYID, USUBJID]
##   <-- ADTTE: [STUDYID, USUBJID]
## ADTTE: [STUDYID, USUBJID, PARAMCD]
##   --> ADSL: [STUDYID, USUBJID]

default_cdisc_join_keys[c("ADSL", "ADTTE", "ADRS")]

## A join_keys object containing foreign keys between 3 datasets:
## ADSL: [STUDYID, USUBJID]
##   <-- ADTTE: [STUDYID, USUBJID]
##   <-- ADRS: [STUDYID, USUBJID]
## ADTTE: [STUDYID, USUBJID, PARAMCD]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADRS
## ADRS: [STUDYID, USUBJID, PARAMCD, AVISIT]
##   --> ADSL: [STUDYID, USUBJID]
##   --* (implicit via parent with): ADTTE

NEST CoreDev

Overview

Uses of join_keys class in teal applications

Anatomy of join_keys

join_keys(...): Join Keys Constructor / Getter / Setter

join_key(dataset_1, dataset_2, key, parent): Single Join Key Constructor