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Population: Manage a patient population

Population.Rd

The Population class stores subject-level data and manages enrollment and dropout times for each subject.

Use set_enrolled() and set_dropped() to assign enrollment and dropout times to random subsets of subjects.

See also

Trial for multi-arm simulations, Timer for managing timepoints.

Population, Trial.

Population, Trial.

Population.

Public fields

name

character Unique identifier for the population.

data

data.frame Subject-level data frame with columns:

  • id integer

  • arm character

  • readout_time numeric

  • data numeric

  • may contain more columns

enrolled

numeric Vector of enrollment times for each subject.

dropped

numeric Vector of dropout times for each subject.

n

integer Number of unique subjects in the population.

n_readouts

integer Number of readout_times in the population.

Methods

Public methods

Method new()

Create a new Population instance.

Usage

Population$new(
  name,
  data = NULL,
  enrolled = NULL,
  dropped = NULL,
  n = NULL,
  n_readouts = NULL
)

Arguments

name

character Unique identifier for the population.

data

data.frame with columns: id, arm, readout_time, data, and optionally more columns.

enrolled

numeric Optional enrollment times (auto-initialized if NULL).

dropped

numeric Optional dropout times (auto-initialized if NULL).

n

integer Auto-computed from data (optional).

n_readouts

integer Auto-computed from data (optional).

Returns

A new Population instance.

Examples

Population$new(name = "Intervention", data = vector_to_dataframe(rnorm(5)))

Method set_enrolled()

Mark subjects as enrolled at a given time.

Enrollment applies only to unenrolled subjects (NA).

Usage

Population$set_enrolled(n, time)

Arguments

n

integer Number of subjects to enroll.

time

numeric Enrollment time.

Examples

pop <- Population$new("Test", vector_to_dataframe(rnorm(10)))
pop$set_enrolled(n = 4, time = 2)

Method set_dropped()

Mark subjects as dropped at a given time.

Dropout applies only to enrolled, not-yet-dropped subjects.

Usage

Population$set_dropped(n, time)

Arguments

n

integer Number of subjects to drop.

time

numeric Dropout time.

Examples

pop <- Population$new("Test", vector_to_dataframe(rnorm(10)))
pop$set_enrolled(n = 5, time = 1)
pop$set_dropped(n = 2, time = 3)

Method set_data()

Replace underlying subject data and reset enrollment/dropout status.

Usage

Population$set_data(data)

Arguments

data

data.frame with columns: id, data, arm, readout_time, and optionally more columns.

Examples

pop <- Population$new("ResetDemo", vector_to_dataframe(rnorm(5)))
pop$set_data(
  data.frame(
    id = 1:8,
    data = rnorm(8),
    arm = "ResetDemo",
    readout_time = 0
  )
)

Method clone()

The objects of this class are cloneable with this method.

Usage

Population$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

# Basic example: vector input
pop <- Population$new(name = "Control", data = vector_to_dataframe(rnorm(10)))

pop$n # number of subjects
#> [1] 10
head(pop$data) # generated subject-level data
#>   id         data readout_time     arm
#> 1  1 -1.400043517            0 Control
#> 2  2  0.255317055            0 Control
#> 3  3 -2.437263611            0 Control
#> 4  4 -0.005571287            0 Control
#> 5  5  0.621552721            0 Control
#> 6  6  1.148411606            0 Control

# Set enrollment for 5 subjects at time = 1
pop$set_enrolled(n = 5, time = 1)

# Drop 2 subjects at time = 3
pop$set_dropped(n = 2, time = 3)

# Reset underlying data
pop$set_data(vector_to_dataframe(rnorm(8)))


## ------------------------------------------------
## Method `Population$new`
## ------------------------------------------------

Population$new(name = "Intervention", data = vector_to_dataframe(rnorm(5)))
#> <Population>
#>   Public:
#>     clone: function (deep = FALSE) 
#>     data: data.frame
#>     dropped: NA NA NA NA NA
#>     enrolled: NA NA NA NA NA
#>     initialize: function (name, data = NULL, enrolled = NULL, dropped = NULL, 
#>     n: 5
#>     n_readouts: 1
#>     name: Intervention
#>     set_data: function (data) 
#>     set_dropped: function (n, time) 
#>     set_enrolled: function (n, time) 

## ------------------------------------------------
## Method `Population$set_enrolled`
## ------------------------------------------------

pop <- Population$new("Test", vector_to_dataframe(rnorm(10)))
pop$set_enrolled(n = 4, time = 2)

## ------------------------------------------------
## Method `Population$set_dropped`
## ------------------------------------------------

pop <- Population$new("Test", vector_to_dataframe(rnorm(10)))
pop$set_enrolled(n = 5, time = 1)
pop$set_dropped(n = 2, time = 3)

## ------------------------------------------------
## Method `Population$set_data`
## ------------------------------------------------

pop <- Population$new("ResetDemo", vector_to_dataframe(rnorm(5)))
pop$set_data(
  data.frame(
    id = 1:8,
    data = rnorm(8),
    arm = "ResetDemo",
    readout_time = 0
  )
)