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Engine Functions

Source: R/engine_functions.R
engine_functions.Rd

Functions currently supported by the C++ TMB engine for constructing expressions for defining model simulations.

Details

The quickest way to experiment with these functions is to use the engine_eval function, as in the following example that calculates a force of infection.

engine_eval(~ beta * I / N
  , beta = 0.25
  , I = 1e3
  , N = 1e7
)

To produce a simulation using these engine functions, one may use simple_sims.

simple_sims(
  iteration_exprs = list(x ~ x - 0.9 * x),
  time_steps = 5,
  mats = list(x = 1)
)

Elementwise Binary Operators

Elementwise binary operators take two matrix-valued arguments and apply a binary operator (e.g. +, *) to each set of corresponding elements, and return the corresponding matrix-valued output containing the resulting elements. What does 'corresponding' mean? If the two matrix-valued arguments have the same shape (same number of rows and columns), then two elements correspond if they occur in the same row and column position in the two matrices. If the two matrices are not of the same shape but there is one row and/or one column in either matrix, then the singleton rows and columns are recycled sufficiently many times so that they match the shape of the other matrix. If after recycling singleton rows and columns the matrices are still of different shape, then an error is thrown and the matrices are said to be incompatible.

Functions

  • x + y

  • x - y

  • x * y

  • x / y

  • x ^ y

Arguments

  • x – Any matrix with dimensions compatible with y.

  • y – Any matrix with dimensions compatible with x.

Return

  • A matrix with the binary operator applied elementwise after any necessary recycling of rows and/or columns.

Examples

engine_eval(~ 1 + 2)
engine_eval(~ y * z, y = 1:3, z = matrix(1:6, 3, 2))
engine_eval(~ 1 / (1 - y), y = 1/4)

Unary Elementwise Math

Functions

  • log(x) – Natural logarithm

  • exp(x) – Exponential function

  • cos(x) – Cosine function

  • proportions(x, limit, eps) – matrix of x / sum(x) or rep(limit, length(x)) if sum(x) < eps

Arguments

  • x – Any matrix

  • limit – numeric value to return elementwise from proportions if sum(x) < eps

  • eps – numeric tolerance for sum(x)

Return

  • A matrix with the same dimensions as x, with the unary function applied elementwise.

Examples

engine_eval(~ log(y), y = c(2, 0.5))

Integer Sequences

Functions

  • from:to – Inclusive and ordered sequence of integers between two bounds.

  • seq(from, length, by) – Ordered sequence of integers with equal spacing between adjacent values.

Arguments

  • from – Scalar integer giving the first integer in the sequence.

  • to – Scalar integer giving the last integer in the sequence.

  • length – Number of integers in the sequence.

  • by – Scalar giving the difference between adjacent values in the sequence.

Return

  • Column vector with a sequence of integers.

Details

The colon operator works much like the base R version :. It takes two scalar-valued integers and returns a column vector with all integers between the two inputs.

The seq function is a little different from the base R default, seq, in that it allows the user precise control over the length of the output through the length argument. The base R function gives the user this option, but not as the default.

Examples

engine_eval(~ 1:10)
engine_eval(~ seq(1, 10, 2))

Replicate Elements

Functions

  • rep(x, times) – Replicate a column vector a number of times, by repeatedly stacking it on top of itself.

  • rep_each – Not yet developed.

  • rep_length – Not yet developed.

Arguments

  • x – A scalar-valued variable to repeat.

  • times – A scalar-valued integer variable giving the number of times to repeat x.

Return

  • Column vector with times copies of x stacked on top of each other.

Examples

engine_eval(~ rep(1, 10))

Matrix Multiplication

Functions

  • x %*% y – Standard matrix multiplication.

  • x %x% y – Kronecker product

Arguments

  • x – A matrix. For the standard product, x must have as many columns as y has rows.

  • y – A matrix. For standard product, y must have as many rows as x has columns.

Return

  • The matrix product of x and y.

Examples

engine_eval(~ (1:10) %*% t(1:10))
engine_eval(~ (1:10) %x% t(1:10))

Parenthesis

The order of operations can be enforced in the usual way with round parentheses, (.

Reshaping and Combining Matrices

Functions

  • c(...) – Stack columns of arguments into a single column vector.

  • cbind(...) – Create a matrix containing all of the columns of a group of matrices with the same number of rows.

  • rbind(...) – Create a matrix containing all of the rows of a group of matrices with the same number of columns.

  • matrix(x, rows, cols) – Reshape a matrix to have rows rows and cols columns. The input x must have rows * cols elements.

  • t(x) – Standard matrix transpose.

Arguments

  • ... – Any number of dimensionally consistent matrices. The definition of dimensionally consistent depends on the function.

  • x – Can be any matrix for t, but for matrix it must have rows * cols elements.

  • rows – Scalar integer giving the number of rows in the output.

  • cols – Scalar integer giving the number of columns in the output.

Return

  • A combined or reshaped matrix.

Details

Any number of column vectors can be combined into a bigger column vector.

Column and row vectors of the same length can be combined using the cbind and rbind functions respectively

The matrix function can be used to redefine the numbers of rows and columns to use for arranging the values of a matrix. It works similarly to the base R matrix function in that it takes the same arguments. On the other hand, this function differs substantially from the base R version in that it must be filled by column and there is no byrow option.

Matrices can be transposed with the usual function, t.

Examples

engine_eval(~ c(a, b, c), a = 1, b = 10:13, c = matrix(20:25, 3, 2))
engine_eval(~ cbind(a, 10 + a), a = 0:3)
engine_eval(~ rbind(a, 10 + a), a = t(0:3))
engine_eval(~ matrix(1:12, 4, 3))
engine_eval(~ t(1:3))

Matrix Diagonals

Functions

  • to_diag(x) – Create a diagonal matrix by setting the diagonal to a column vector, x.

  • from_diag(x) – Extract the diagonal from a matrix, x, and return the diagonal as a column vector.

Arguments

  • x – Any matrix (for from_diag) or a column vector (for to_diag). It is common to assume that x is square for from_diag but this is not required.

Return

  • to_diag(x) – Diagonal matrix with x on the diagonal.

  • from_diag(x) – Column vector containing the diagonal of x. A value is considered to be on the diagonal if it has a row index equal to the column index.

Details

The to_diag function can be used to produce a diagonal matrix by setting a column vector equal to the desired diagonal. The from_diag does (almost) the opposite, which is to get a column vector containing the diagonal of an existing matrix.

Examples

engine_eval(~from_diag(matrix(1:9, 3, 3)))
engine_eval(~to_diag(from_diag(matrix(1:9, 3, 3))))
engine_eval(~from_diag(to_diag(from_diag(matrix(1:9, 3, 3)))))

Summarizing Matrix Values

Functions

  • sum(...) – Sum all of the elements of all of the matrices passed to ....

  • col_sums(x) – Row vector containing the sums of each column.

  • row_sums(x) – Column vector containing the sums of each row.

  • group_sums(x, f, n) – Column vector containing the sums of groups of elements in x. The groups are determined by the integers in f and the order of the sums in the output is determined by these integers.

Arguments

  • ... – Any number of matrices of any shape.

  • x – A matrix of any dimensions, except for group_sums that expects x to be a column vector.

  • f – A column vector the same length as x containing integers between 0 and m-1, given m unique groups. Elements of f refer to the indices of x that will be grouped and summed.

  • n – A column vector of length m. If f does not contain group k in [0, m-1], group_sums skips this group and the output at index k+1 is n[k+1].

Return

  • A matrix containing sums of subsets of the inputs.

Details

The row_sums and col_sums are similar to the base R rowSums and colSums functions, but with slightly different behaviour. In particular, the row_sums function returns a column vector and the col_sums function returns a row vector. If a specific shape is required then the transpose t function must be explicitly used.

Examples

x = 1
y = 1:3
A = matrix(1:12, 4, 3)
engine_eval(~ sum(y), y = y)
engine_eval(~ sum(x, y, A), x = x, y = y, A = A)
engine_eval(~ col_sums(A), A = A)
engine_eval(~ row_sums(A), A = A)
engine_eval(~ group_sums(x, f, n), x = 1:10, f = rep(0:3, 1:4), n = c(1:4))

Extracting Matrix Elements

Functions

Arguments

  • x – Any matrix.

  • i – An integer column vector (for [) or integer scalar (for block) containing the indices of the rows to extract (for [) or the index of the first row to extract (for block).

  • j – An integer column vector (for [) or integer scalar (for block) containing the indices of the columns to extract (for [) or the index of the first column to extract (for block).

  • n – Number of rows in the block to return.

  • m – Number of columns in the block to return.

Return

  • A matrix containing a subset of the rows and columns in x.

Details

Note that zero-based indexing is used so the first row/column gets index, 0, etc.

Examples

engine_eval(~ A[c(3, 1, 2), 2], A = matrix(1:12, 4, 3))
engine_eval(~ block(x,i,j,n,m), x = matrix(1:12, 4, 3), i=1, j=1, n=2, m=2)

Accessing Past Values in the Simulation History

For matrices with their simulation history saved, it is possible to bind the rows or columns of past versions of such matrices into a single matrix.

Functions

  • rbind_lag(x, lag, t_min) – Bind the rows of versions of x that were recorded at the end of all simulation iterations corresponding to time lags given by integers in lag.

  • rbind_time(x, t, t_min) – Bind the rows of versions of x that were recorded at the end of all simulation iterations corresponding to integers in t.

  • cbind_lag(x, lag, t_min) – Bind the columns of versions of x that were recorded at the end of all simulation iterations corresponding to time lags given by integers in lag. (TODO – cbind_lag is not developed yet)

  • cbind_time(x, t, t_min) – Bind the columns of versions of x that were recorded at the end of all simulation iterations corresponding to integers in t. (TODO – cbind_lag is not developed yet)

Arguments

  • x – Any matrix with saved history such that the number of columns (for rbind_*) or rows (for cbind_*) does not change throughout the simulation.

  • lag – Integer vector giving numbers of time steps before the current step to obtain past values of x.

  • t – Integer vector giving time steps at which to obtain past values of x.

  • t_min – Integer giving the minimum time step that is allowed to be accessed. All time-steps in t or implied by lag that are before t_min are ignored.

Return

  • A matrix containing values of x from past times.

Time Indexing

Get or update the index of the current or lagged time step or the index of the current time group. A time group is a contiguous set of time steps defined by two change points.

Functions

  • time_step(lag): Get the time-step associated with a particular lag from the current time-step. If the lagged time-step is less than zero, the function returns zero.

  • time_group(index, change_points): Update the index associated with the current time group. The current group is defined by the minimum of all elements of change_points that are greater than the current time step. The time group index is the index associated with this element. Please see the examples below, they are easier to understand than this explanation.

  • time_var(x, change_points): An improvement to time_group. Returns values in x at time steps in change_points, return value remains constant between change_points.

Arguments

  • x: Column vector representing a time series. time_var will return the value of x corresponding to element in change_points that contains the current time.

  • lag: Number of time-steps to look back for the time-step to return.

  • change_points: Increasing column vector of time steps giving the lower bound of each time group.

Return

A 1-by-1 matrix with the time-step lag steps ago, or with zero if t+1 < lag

Examples

simple_sims(
  iteration_exprs = list(x ~ time_step(0)),
  time_steps = 10,
  mats = list(x = empty_matrix)
)
sims = simple_sims(
  iteration_exprs = list(
    j ~ time_group(j, change_points),
    time_varying_parameter ~ time_variation_schedule[j]
  ),
  mats = list(
    j = 0,
    change_points = c(0, 4, 7),
    time_variation_schedule = c(42, pi, sqrt(2)),
    time_varying_parameter = empty_matrix
  ),
  time_steps = 10,
)
set.seed(1L)
change_points = c(0,2,5)
x_val = rnorm(length(change_points))
simple_sims(
    iteration_exprs = list(x ~ time_var(x_val,change_points))
  , int_vecs = list(change_points = change_points)
  , mats = list(x = empty_matrix, x_val=x_val)
  , time_steps = 10
)

Convolution

One may take the convolution of each element in a matrix, x, over simulation time using a kernel, k. There are two arguments of this function.

Functions

  • convolution(x, k)

Arguments

  • x – The matrix containing elements to be convolved.

  • k – A column vector giving the convolution kernel.

Return

A matrix the same size as x but with the convolutions, \(y_{ij}\), of each element, \(x_{ij}\), given by the following.

$$y_{ij} = \sum_{\tau = 0} x_{ij}(t-\tau) k(\tau)$$

unless \(t < \tau\), in which case,

$$y_{ij} = $$

where \(y_{ij}\) is the convolution, \(x_{ij}(t)\) is the value of \(x_{ij}\) at time step, \(t\), \(k(\tau)\) is the value of the kernel at lag, \(\tau\), and \(\lambda\) is the length of the kernel.

Details

If any empty matrices are encountered when looking back in time, they are treated as matrices with all zeros. Similarly, any matrices encounte of x

Clamp

Smoothly clamp the elements of a matrix so that they do not get closer to 0 than a tolerance, eps, with a default of 1e-12. The output of the clamp function is as follows.

Functions

  • clamp(x, eps)

Arguments

  • x : A matrix with elements that should remain positive.

  • eps : A small positive number giving the theoretical minimum of the elements in the returned matrix.

Probability Densities

All probability densities have the same first two arguments.

  • observed

  • simulated

The simulated argument gives a matrix of means for the observed values at which the densities are being evaluated. Additional arguments are other distributional parameters such as the standard deviation or dispersion parameter. All densities are given as log-densities, so if you would like the density itself you must pass the result through the exp function.

If the simulated matrix or the additional parameter matrices have either a single row or single column, these singleton rows and columns are repeated to match the number of rows and columns in the observed matrix. This feature allows one to do things like specify a single common mean for several values.

Functions

  • dpois(observed, simulated) – Log of the Poisson density based on this dpois TMB function.

  • dnbinom(observed, simulated, over_dispersion) – Log of the negative binomial density based on this dnbinom TMB function. To get the variance that this function requires we use this expression, simulated + simulated^2/over_dispersion, following p.165 in this book

  • dnorm(observed, simulated, standard_deviation) – Log of the normal density based on this dnorm TMB function.

Arguments

  • observed – Matrix of observed values at which the density is being evaluated.

  • simulated – Matrix of distributional means, with singleton rows and columns recycled to match the numbers of rows and columns in observed.

  • over_dispersion – Over-dispersion parameter given by (simulated/standard_deviation)^2 - simulated).

  • standard_deviation – Standard deviation parameter.

Pseudo-Random Number Generators

All random number generator functions have mean as the first argument. Subsequent arguments give additional distributional parameters. Singleton rows and columns in the matrices passed to the additional distributional parameters are recycled so that all arguments have the same number of rows and columns. All functions return a matrix the same shape as mean but with pseudo-random numbers deviating from each mean in the mean matrix.

Functions

  • rpois(mean) – Pseudo-random Poisson distributed values.

  • rnbinom(mean, over_dispersion) – Pseudo-random negative binomially distributed values.

  • rnorm(mean, standard_deviation) – Pseudo-random normal values.

Arguments

  • mean – Matrix of means about which to simulate pseudo-random variation.

  • over_dispersion – Matrix of over-dispersion parameters given by (simulated/standard_deviation)^2 - simulated).

  • standard_deviation – Matrix of standard deviation parameters.

Assign

Assign values to a subset of the elements in a matrix.

Functions

  • assign(x, i, j, v)

Arguments

  • x – Matrix with elements that are to be updated by the values in v.

  • i – Column vector of row indices pointing to the elements of x to be updated. These indices are paired with those in v. If the length of i does not equal that of v, then it must have a single index that gets paired with every element of v. Indices are zero-based, i=0 corresponds to the first row.

  • j – Column vector of column indices pointing to the elements of x to be updated. These indices are paired with those in v. If the length of j does not equal that of v, then it must have a single index that gets paired with every element of v. Indices are zero-based, j=0 corresponds to the first column.

  • v – Column vector of values to replace elements of x at locations given by i and j.

Return

The assign function is not called for its return value, which is an empty_matrix, but rather to modify x but replacing some of its components with those in v.

Examples

x = matrix(1:12, 3, 4)
engine_eval(~ x + 1, x = x)
engine_eval(~ x + 1, x = x, .matrix_to_return = "x")
engine_eval(~ assign(x, 2, 1, 100), x = x, .matrix_to_return = "x")
engine_eval(~ assign(x
  , c(2, 1, 0)
  , 0
  , c(100, 1000, 10000)
), x = x, .matrix_to_return = "x")

Unpack

Unpack elements of a matrix into smaller matrices.

Functions

  • unpack(x, ...)

Arguments

  • x – Matrix with elements to be distributed to the matrices passed through ....

  • ... – Matrices with elements to be replaced by the values of elements in x in column-major order. These matrices must be named matrices and not computed on the fly using expressions. Note that even subsetting (e.g. unpack(x, y[0], y[3])) counts as an expression. This use-case would require the assign function assign(y, c(0, 3), 0, x).

Return

The unpack function is not called for its return value, which is an empty_matrix, but rather to modify the matrices in ... by replacing at least some of its components with those in x.

Examples

Here we fill a matrix with integers from 1 to 12 and then unpack them one-at-a-time into two column vectors, x and y. By returning y we see the integers after the first three were used up by x.

engine_eval(~unpack(matrix(1:12, 3, 4), x, y)
  , x = rep(0, 3)
  , y = rep(1, 5)
  , .matrix_to_return = "y"
)

Print out the value of a matrix.

Functions

  • print(x)

Arguments

  • x – Name of a matrix in the model.

Return

An empty_matrix.

Examples

simple_sims(
     list(dummy ~ print(x), x ~ x / 2)
   , time_steps = 10
   , mats = list(x = 2)
)