healthdb (version 0.5.0)

fetch_var: Get variables from multiple tables with common ID columns

Description

This function fetches variables from different tables that linked by common IDs. It calls dplyr::left_join() multiple times with various source tables (y argument of the join) to gather variables. It is not meant to replace left_join() but simplify syntax for the situation that you started off a table of study sample and wanted to gather covariates from different sources linked by common client IDs, which is often the case when working with healthcare databases. Caution: this function is intended for one-to-one joins only because it could be problematic when we do not know which source caused a one-to-many join and changed the number of rows. For data.frame input, an error will be given when one-to-many joins were detected. However, such checking could be an expensive operation on remote source. Therefore, for database input, the result will not be checked.

Usage

fetch_var(data, keys, linkage, ...)

Value

A data.frame or remote table containing all original columns of x and new variables matched from other tables based on the specified linkage.

Arguments

data

A data.frame or remote table (tbl_sql) which must be an object and not from a pipe. It would be used as the x argument in left_join().

keys

A vector of quoted/unquoted variable names, or 'tidyselect' expression (see dplyr::select()). These variables must be present in data and would be used as the by argument in left_join(). The y tables must have a subset of these if not all.

linkage

A list of formulas in the form of "from_tab ~ get_vars|by_keys":

• source table on the left-hand-side

• variables on the right-hand-side

• If a source table does not have all the variables in keys, use "|" on RHS to specify the subset of keys to be used.

For example, given keys has 3 variables, list( y1 ~ tidyselect_expr1, y2 ~ tidyselect_expr2|key1 + key2)

meaning:

1. from table y1 get variables picked by the tidyselect expression matching on all 3 keys;

2. from table y2 get variables matching on only key1 and key2.

...

Additional arguments, e.g., copy = TRUE, passing to left_join().

Examples

# make toy data
size <- 30
n <- 10
df1 <- data.frame(
  id = sample(1:n, size = size, replace = TRUE),
  service_dt = sample(seq(as.Date("2020-01-01"), as.Date("2022-01-31"), by = 1),
    size = size
  )
) %>%
  dplyr::mutate(year = lubridate::year(service_dt))
df2 <- data.frame(
  id = rep(1:n, size / n), year = rep(2020:2022, each = n),
  status_1 = sample(0:1, size = size, replace = TRUE),
  status_2 = sample(0:1, size = size, replace = TRUE)
)
df3 <- data.frame(id = 1:n, sex = sample(c("F", "M"), size = n, replace = TRUE))

# simple joins
# note that for left_join(df1, df2), boths keys have to be used,
# otherwise, error as the relation would not be one-to-one
fetch_var(df1,
  keys = c(id, year),
  linkage = list(
    df2 ~ starts_with("s"), # match both keys without '|'
    df3 ~ sex | id
  ) # match by id only; otherwise failed because df3 has no year
)

# example if some y is remote
# make df2 as database table
db2 <- dbplyr::tbl_memdb(df2)

fetch_var(df1,
  keys = c(id, year),
  linkage = list(
    db2 ~ starts_with("s"),
    df3 ~ sex | id
  ),
  copy = TRUE # pass to left_join for forced collection of remote table
)