Extra parameters

Grouped simulation

It is quite common that values of the column are strongly related to the groups defined by the other column values.

Some of the examples may be the age of death that may differ between males and females.

In order to allow simulating values based on groups designed by the other columns, group_by parameter was introduced.

Let’s see the below schema structure:

# schema-patient.yml
public:
  tables:
    patient:
      columns:
        treatment_id:
          type: varchar
          formula: !expr paste0(patient_id, line_number)
        patient_id:
          type: char(8)
        line_number: 
          type: smallint
        gender:
          type: char(1)
          values: [F, M]
        biomarker:
          type: numeric
          range: [0, 1]

Let’s simulate the data using the below definition:

sch <- schema_source(system.file("extdata", "schema-patient.yml", package = "DataFakeR"))
sch <- schema_simulate(sch)
schema_get_table(sch, "patient")
#> # A tibble: 10 × 5
#>    treatment_id   patient_id line_number gender biomarker
#>    <chr>          <chr>            <int> <chr>      <dbl>
#>  1 OoVtwCbu-16802 OoVtwCbu        -16802 M          0.600
#>  2 cXxXjdFu11013  cXxXjdFu         11013 M          0.333
#>  3 MCRxukhz-5398  MCRxukhz         -5398 F          0.489
#>  4 ikcePHyu18886  ikcePHyu         18886 M          0.954
#>  5 jpBYnLQM-26027 jpBYnLQM        -26027 M          0.483
#>  6 HVVTHHMY-4267  HVVTHHMY         -4267 F          0.890
#>  7 NsCWpGdK31781  NsCWpGdK         31781 F          0.914
#>  8 GnuTiETO25758  GnuTiETO         25758 M          0.609
#>  9 qXqqpWng25327  qXqqpWng         25327 F          0.411
#> 10 kAYLTfSF-21296 kAYLTfSF        -21296 F          0.147

Now we’d like to extend the definition following the below rules:

For each patient_id we usually want to have more than one row (it allows us to analyze the patient in multiple treatment stages).
For each patient_id, lineid is the sequence starting from 1 to the number of patient rows.
gender should be unique for each patient_id value.
biomarker value should mean = 0.5 for females and mean = 0.6 for males.

Rule no 1

Let’s start with condition 1. We may simply achieve this by providing possible patient_id values with unique number less than target number of rows.

# schema-patient_2.yml
public:
  tables:
    patient:
      columns:
        treatment_id:
          type: varchar
          formula: !expr paste0(patient_id, line_number)
        patient_id:
          type: char(8)
          values: [PTNT01ID, PTNT02ID, PTNT03ID]
        line_number: 
          type: smallint
        gender:
          type: char(1)
          values: [F, M]
        biomarker:
          type: numeric
          range: [0, 1]

Let’s simulate the data using the below definition:

sch <- schema_update_source(sch, file = system.file("extdata", "schema-patient_2.yml", package = "DataFakeR"))
sch <- schema_simulate(sch)
schema_get_table(sch, "patient")
#> # A tibble: 10 × 5
#>    treatment_id   patient_id line_number gender biomarker
#>    <chr>          <chr>            <int> <chr>      <dbl>
#>  1 PTNT02ID-8554  PTNT02ID         -8554 M         0.843 
#>  2 PTNT03ID31733  PTNT03ID         31733 M         0.231 
#>  3 PTNT01ID-22662 PTNT01ID        -22662 M         0.239 
#>  4 PTNT02ID-26801 PTNT02ID        -26801 M         0.0767
#>  5 PTNT02ID-23468 PTNT02ID        -23468 M         0.246 
#>  6 PTNT03ID12452  PTNT03ID         12452 F         0.732 
#>  7 PTNT02ID7815   PTNT02ID          7815 M         0.847 
#>  8 PTNT01ID25650  PTNT01ID         25650 M         0.498 
#>  9 PTNT03ID11337  PTNT03ID         11337 M         0.388 
#> 10 PTNT03ID15536  PTNT03ID         15536 F         0.246

Rule no 2

Now, we’d like to make sure line_id is a sequence 1:n, where n is the number of rows for each patient.

If we define line_number formula as !expr 1:dplyr::n(), the resulting column would be a sequence 1:n where n is the number of table rows. There is an obvious need to apply grouping by patient_id.

How can we achieve this in DataFakeR?

It is enough to add group_by: patient_id parameter to line_number.

Let’s see it in action:

# schema-patient_3.yml
public:
  tables:
    patient:
      columns:
        treatment_id:
          type: varchar
          formula: !expr paste0(patient_id, line_number)
        patient_id:
          type: char(8)
          values: [PTNT01ID, PTNT02ID, PTNT03ID]
        line_number: 
          type: smallint
          group_by: patient_id
          formula: !expr 1:dplyr::n()
        gender:
          type: char(1)
          values: [F, M]
        biomarker:
          type: numeric
          range: [0, 1]

Looking at the dependency graph:

sch <- schema_update_source(sch, file = system.file("extdata", "schema-patient_3.yml", package = "DataFakeR"))
schema_plot_deps(sch, "patient")

we can see, DataFakeR detected dependency between patient_id and line_numer column.

line_number was also created according to our needs:

sch <- schema_simulate(sch)
schema_get_table(sch, "patient")
#> # A tibble: 10 × 5
#>    treatment_id patient_id line_number gender biomarker
#>    <chr>        <chr>            <int> <chr>      <dbl>
#>  1 PTNT03ID1    PTNT03ID             1 F         0.974 
#>  2 PTNT02ID1    PTNT02ID             1 F         0.760 
#>  3 PTNT02ID2    PTNT02ID             2 M         0.887 
#>  4 PTNT02ID3    PTNT02ID             3 M         0.222 
#>  5 PTNT01ID1    PTNT01ID             1 F         0.270 
#>  6 PTNT02ID4    PTNT02ID             4 M         0.607 
#>  7 PTNT02ID5    PTNT02ID             5 F         0.340 
#>  8 PTNT02ID6    PTNT02ID             6 M         0.757 
#>  9 PTNT01ID2    PTNT01ID             2 M         0.0748
#> 10 PTNT02ID7    PTNT02ID             7 M         0.891

Rule no 3

Now let’s assure gender is unique for each patient.

To achieve this, we’ll have to group by patient_id and sample one value from c("F", "M) and repeat this with desired number of rows.

We may again use the formula, but for the sake of the example we’ll define custom restricted method.

The method will be executed whenever singular: true parameter is provided to the column.

# schema-patient_4.yml
public:
  tables:
    patient:
      columns:
        treatment_id:
          type: varchar
          formula: !expr paste0(patient_id, line_number)
        patient_id:
          type: char(8)
          values: [PTNT01ID, PTNT02ID, PTNT03ID]
        line_number: 
          type: smallint
          group_by: patient_id
          formula: !expr 1:dplyr::n()
        gender:
          type: char(1)
          values: [F, M]
          singular: true
          group_by: patient_id
        biomarker:
          type: numeric
          range: [0, 1]

The method definition:

singular_vals <- function(n, values, singular, ...) {

  if (!missing(singular) && isTRUE(singular)) {
    val <- sample(values, 1)
    return(rep(val, n))
  }

  return(NULL)
}

and add it to schema options:

my_opts = set_faker_opts(
  opt_simul_restricted_character = opt_simul_restricted_character(
    singular = singular_vals
  )
)

Now we can start simulation:

sch <- schema_update_source(
  sch, 
  file = system.file("extdata", "schema-patient_4.yml", package = "DataFakeR"),
  my_opts
)
sch <- schema_simulate(sch)
schema_get_table(sch, "patient")
#> # A tibble: 10 × 5
#>    treatment_id patient_id line_number gender biomarker
#>    <chr>        <chr>            <int> <chr>      <dbl>
#>  1 PTNT01ID1    PTNT01ID             1 M        0.716  
#>  2 PTNT02ID1    PTNT02ID             1 M        0.595  
#>  3 PTNT02ID2    PTNT02ID             2 M        0.0432 
#>  4 PTNT01ID2    PTNT01ID             2 M        0.449  
#>  5 PTNT01ID3    PTNT01ID             3 M        0.639  
#>  6 PTNT02ID3    PTNT02ID             3 M        0.801  
#>  7 PTNT02ID4    PTNT02ID             4 M        0.542  
#>  8 PTNT02ID5    PTNT02ID             5 M        0.882  
#>  9 PTNT03ID1    PTNT03ID             1 M        0.00679
#> 10 PTNT01ID4    PTNT01ID             4 M        0.447

Voila!

Rule no 4

We’d like to sample from normal distribution with a specific mean dependent on the gender value.

Again we have a few options here. The simplest one would be to group biomarker by gender and use:

formula: ifelse(gender == "F", rnorm(dplyr::n(), 0.5, 0.01), rnorm(dplyr::n(), 0.6, 0.01))

but we’ll do it using a special method instead.

The main issue we might have is how to access the group value from within the method. We shouldn’t be worried. DataFakeR automatically passes the value as a group_val parameter.

So let’s try it out.

Let’s define spec method named dep_sampl:

# schema-patient_5.yml
public:
  tables:
    patient:
      columns:
        treatment_id:
          type: varchar
          formula: !expr paste0(patient_id, line_number)
        patient_id:
          type: char(8)
          values: [PTNT01ID, PTNT02ID, PTNT03ID]
        line_number:
          type: smallint
          group_by: patient_id
          formula: !expr 1:dplyr::n()
        gender:
          type: char(1)
          values: [F, M]
          singular: true
          group_by: patient_id
        biomarker:
          type: numeric
          range: [0, 1]
          spec: dep_sampl
          group_by: gender

Inside function definition let’s add print line to see current group_key value:

dep_sampl <- function(n, group_val, range, ...) {
  print(group_val)
  if (group_val == "M") {
    pmax(pmin(rnorm(n, 0.6, 0.01), range[2]), range[1])
  } else {
    pmax(pmin(rnorm(n, 0.5, 0.01), range[2]), range[1])
  }
}

my_opts = set_faker_opts(
  opt_simul_spec_numeric = opt_simul_spec_numeric(
    dep_sampl = dep_sampl
  ),
  # don't forget option from previous case
  opt_simul_restricted_character = opt_simul_restricted_character(
    singular = singular_vals
  )
)

sch <- schema_update_source(
  sch, 
  file = system.file("extdata", "schema-patient_5.yml", package = "DataFakeR"), 
  my_opts
)
sch <- schema_simulate(sch)
#> [1] "M"
schema_get_table(sch, "patient")
#> # A tibble: 10 × 5
#>    treatment_id patient_id line_number gender biomarker
#>    <chr>        <chr>            <int> <chr>      <dbl>
#>  1 PTNT02ID1    PTNT02ID             1 M          0.602
#>  2 PTNT01ID1    PTNT01ID             1 M          0.587
#>  3 PTNT03ID1    PTNT03ID             1 M          0.589
#>  4 PTNT02ID2    PTNT02ID             2 M          0.599
#>  5 PTNT03ID2    PTNT03ID             2 M          0.603
#>  6 PTNT03ID3    PTNT03ID             3 M          0.600
#>  7 PTNT01ID2    PTNT01ID             2 M          0.600
#>  8 PTNT03ID4    PTNT03ID             4 M          0.599
#>  9 PTNT03ID5    PTNT03ID             5 M          0.594
#> 10 PTNT02ID3    PTNT02ID             3 M          0.608

This way we achieved assumed goal.

Ratio of NA values

Another extra parameter offered by DataFakeR is na_ratio. Na ratio allows to precise the ratio of how many NA values should the column have.

For each simulation method the final sample is modified by na_rand function, that replaces desired ratio of values with NAs. Default na_ratio value is 0.05 but can be easily overwritten by opt_default_ configuration, or passed directly in column definition.

Note Whenever column have defined not_null: true, na_rand doesn’t attach NA values to the sample.

Ratio of column values

The last extra parameter offered by DataFakeR is levels_ratio. Levels ratio allows to precise how many unique values should the column have.

For each simulation method (before the sample is modified by na_rand) the sample is modified by levels_rand function, that takes desired number of sample levels and resamples it using only provided levels. Default levels_ratio is 1 but can be easily overwritten by opt_default_ configuration, or passed directly in column definition.

Note Whenever column have defined unique: true or levels_ratio: 1, levels_rand doesn’t modify the sample.

Remaining parameters

There are a few parameters that can be configured to each column and be handled by all the simulation methods.

Such parameters are:

values - The parameter keeps possible values for the simulated column,
range - Two-length parameter storing minimum and maximum value for simulated column (numeric, integer and date only),
precision - Precision of numeric column values,
scale - Scale of numeric column values,
min_date, max_date - minimal and maximal values for simulating date columns (overwritten by range when specified),
format - Date format of min_date, max_date and range in case of date columns (%Y-%m-%d by default),
nchar - Maximum number of characters for simulating character column (10 by default).

Whenever any of the above parameters is defined as a parameter of column-type simulation method, such value can be used to get more accurate result respecting the configuration.

For example default character simulation method (simul_default_character) takes an advantage of nchar parameter, but special method for simulating names don’t (simul_spec_character_name).