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Merge Lookup Table with Source Dataset

Source: R/derive_merged.R
derive_vars_merged_lookup.Rd

Merge user-defined lookup table with the input dataset. Optionally print a list of records from the input dataset that do not have corresponding mapping from the lookup table.

Usage

derive_vars_merged_lookup(
  dataset,
  dataset_add,
  by_vars,
  order = NULL,
  new_vars = NULL,
  mode = NULL,
  filter_add = NULL,
  check_type = "warning",
  duplicate_msg = NULL,
  print_not_mapped = TRUE
)

Arguments

dataset

Input dataset

The variables specified by the by_vars argument are expected to be in the dataset.

dataset_add

Lookup table

The variables specified by the by_vars argument are expected.

by_vars

Grouping variables

The input dataset and the selected observations from the additional dataset are merged by the specified variables.

Variables can be renamed by naming the element, i.e. by_vars = exprs(<name in input dataset> = <name in additional dataset>), similar to the dplyr joins.

Permitted Values: list of variables created by exprs() e.g. exprs(USUBJID, VISIT)

order

Sort order

If the argument is set to a non-null value, for each by group the first or last observation from the additional dataset is selected with respect to the specified order.

Variables defined by the new_vars argument can be used in the sort order.

For handling of NAs in sorting variables see Sort Order.

Permitted Values: list of expressions created by exprs(), e.g., exprs(ADT, desc(AVAL)) or NULL

new_vars

Variables to add

The specified variables from the additional dataset are added to the output dataset. Variables can be renamed by naming the element, i.e., new_vars = exprs(<new name> = <old name>).

For example new_vars = exprs(var1, var2) adds variables var1 and var2 from dataset_add to the input dataset.

And new_vars = exprs(var1, new_var2 = old_var2) takes var1 and old_var2 from dataset_add and adds them to the input dataset renaming old_var2 to new_var2.

Values of the added variables can be modified by specifying an expression. For example, new_vars = LASTRSP = exprs(str_to_upper(AVALC)) adds the variable LASTRSP to the dataset and sets it to the upper case value of AVALC.

If the argument is not specified or set to NULL, all variables from the additional dataset (dataset_add) are added.

Permitted Values: list of variables or named expressions created by exprs()

mode

Selection mode

Determines if the first or last observation is selected. If the order argument is specified, mode must be non-null.

If the order argument is not specified, the mode argument is ignored.

Permitted Values: "first", "last", NULL

filter_add

Filter for additional dataset (dataset_add)

Only observations fulfilling the specified condition are taken into account for merging. If the argument is not specified, all observations are considered.

Variables defined by the new_vars argument can be used in the filter condition.

Permitted Values: a condition

check_type

Check uniqueness?

If "warning" or "error" is specified, the specified message is issued if the observations of the (restricted) additional dataset are not unique with respect to the by variables and the order.

Permitted Values: "none", "warning", "error"

duplicate_msg

Message of unique check

If the uniqueness check fails, the specified message is displayed.

Default:

paste("Dataset `dataset_add` contains duplicate records with respect to",
      enumerate(vars2chr(by_vars)))

print_not_mapped

Print a list of unique by_vars values that do not have corresponding records from the lookup table?

Default: TRUE

Permitted Values: TRUE, FALSE

Value

The output dataset contains all observations and variables of the input dataset, and add the variables specified in new_vars from the lookup table specified in dataset_add. Optionally prints a list of unique by_vars values that do not have corresponding records from the lookup table (by specifying print_not_mapped = TRUE).

See also

General Derivation Functions for all ADaMs that returns variable appended to dataset: derive_var_extreme_flag(), derive_var_joined_exist_flag(), derive_var_merged_ef_msrc(), derive_var_merged_exist_flag(), derive_var_merged_summary(), derive_var_obs_number(), derive_var_relative_flag(), derive_vars_computed(), derive_vars_joined(), derive_vars_merged(), derive_vars_transposed()

Examples

library(dplyr, warn.conflicts = FALSE)
vs <- tribble(
  ~STUDYID,  ~DOMAIN,  ~USUBJID,        ~VISIT, ~VSTESTCD,       ~VSTEST,
  "PILOT01",    "VS", "01-1028",   "SCREENING",  "HEIGHT",      "Height",
  "PILOT01",    "VS", "01-1028",   "SCREENING",    "TEMP", "Temperature",
  "PILOT01",    "VS", "01-1028",    "BASELINE",    "TEMP", "Temperature",
  "PILOT01",    "VS", "01-1028",      "WEEK 4",    "TEMP", "Temperature",
  "PILOT01",    "VS", "01-1028", "SCREENING 1",  "WEIGHT",      "Weight",
  "PILOT01",    "VS", "01-1028",    "BASELINE",  "WEIGHT",      "Weight",
  "PILOT01",    "VS", "01-1028",      "WEEK 4",  "WEIGHT",      "Weight",
  "PILOT01",    "VS", "04-1325",   "SCREENING",  "HEIGHT",      "Height",
  "PILOT01",    "VS", "04-1325",   "SCREENING",    "TEMP", "Temperature",
  "PILOT01",    "VS", "04-1325",    "BASELINE",    "TEMP", "Temperature",
  "PILOT01",    "VS", "04-1325",      "WEEK 4",    "TEMP", "Temperature",
  "PILOT01",    "VS", "04-1325", "SCREENING 1",  "WEIGHT",      "Weight",
  "PILOT01",    "VS", "04-1325",    "BASELINE",  "WEIGHT",      "Weight",
  "PILOT01",    "VS", "04-1325",      "WEEK 4",  "WEIGHT",      "Weight",
  "PILOT01",    "VS", "10-1027",   "SCREENING",  "HEIGHT",      "Height",
  "PILOT01",    "VS", "10-1027",   "SCREENING",    "TEMP", "Temperature",
  "PILOT01",    "VS", "10-1027",    "BASELINE",    "TEMP", "Temperature",
  "PILOT01",    "VS", "10-1027",      "WEEK 4",    "TEMP", "Temperature",
  "PILOT01",    "VS", "10-1027", "SCREENING 1",  "WEIGHT",      "Weight",
  "PILOT01",    "VS", "10-1027",    "BASELINE",  "WEIGHT",      "Weight",
  "PILOT01",    "VS", "10-1027",      "WEEK 4",  "WEIGHT",      "Weight"
)

param_lookup <- tribble(
  ~VSTESTCD,                 ~VSTEST, ~PARAMCD,                       ~PARAM,
  "SYSBP", "Systolic Blood Pressure",  "SYSBP", "Syst Blood Pressure (mmHg)",
  "WEIGHT",                 "Weight", "WEIGHT",                "Weight (kg)",
  "HEIGHT",                 "Height", "HEIGHT",                "Height (cm)",
  "TEMP",              "Temperature",   "TEMP",            "Temperature (C)",
  "MAP",    "Mean Arterial Pressure",    "MAP",   "Mean Art Pressure (mmHg)",
  "BMI",           "Body Mass Index",    "BMI",    "Body Mass Index(kg/m^2)",
  "BSA",         "Body Surface Area",    "BSA",     "Body Surface Area(m^2)"
)

derive_vars_merged_lookup(
  dataset = vs,
  dataset_add = param_lookup,
  by_vars = exprs(VSTESTCD),
  new_vars = exprs(PARAMCD, PARAM),
  print_not_mapped = TRUE
)
#> All `VSTESTCD` are mapped.
#> # A tibble: 21 × 8
#>    STUDYID DOMAIN USUBJID VISIT       VSTESTCD VSTEST      PARAMCD PARAM        
#>    <chr>   <chr>  <chr>   <chr>       <chr>    <chr>       <chr>   <chr>        
#>  1 PILOT01 VS     01-1028 SCREENING   HEIGHT   Height      HEIGHT  Height (cm)  
#>  2 PILOT01 VS     01-1028 SCREENING   TEMP     Temperature TEMP    Temperature …
#>  3 PILOT01 VS     01-1028 BASELINE    TEMP     Temperature TEMP    Temperature …
#>  4 PILOT01 VS     01-1028 WEEK 4      TEMP     Temperature TEMP    Temperature …
#>  5 PILOT01 VS     01-1028 SCREENING 1 WEIGHT   Weight      WEIGHT  Weight (kg)  
#>  6 PILOT01 VS     01-1028 BASELINE    WEIGHT   Weight      WEIGHT  Weight (kg)  
#>  7 PILOT01 VS     01-1028 WEEK 4      WEIGHT   Weight      WEIGHT  Weight (kg)  
#>  8 PILOT01 VS     04-1325 SCREENING   HEIGHT   Height      HEIGHT  Height (cm)  
#>  9 PILOT01 VS     04-1325 SCREENING   TEMP     Temperature TEMP    Temperature …
#> 10 PILOT01 VS     04-1325 BASELINE    TEMP     Temperature TEMP    Temperature …
#> # ℹ 11 more rows