simcpfa: Simulate Data for Classification with Parallel Factor...

In cpfa: Classification with Parallel Factor Analysis

Simulate Data for Classification with Parallel Factor Analysis

Description

Simulates a two-way matrix, three-way array, or four-way array; and simulates a set of class labels that are related to the simulated matrix or array through one mode of that matrix or array. Data matrix or array is simulated using one of the following component models without constraints: Parafac, Parafac2, or PCA. Weights for mode weight matrices can be drawn from 12 common probability distributions. Alternatively, custom weights can be provided for any mode.

Usage

simcpfa(arraydim = NULL, model = "parafac", nfac = 2, nclass = 2, 
        smethod = "logistic", nreps = 100, onreps = 10, props = NULL,
        corresp = NULL, meanpred = NULL, modes = 3, corrpred = NULL, 
        pf2num = NULL, Amat = NULL, Bmat = NULL, Cmat = NULL, Dmat = NULL, 
        Gmat = NULL, Emat = NULL, technical = list())

Arguments

arraydim	Numeric vector containing the number of dimensions for each mode of the simulated data matrix or array. Must contain integers greater than or equal to 2. Defaults to c(10, 100) for modes = 2; to c(10, 10, 100) for modes = 3; and to c(10, 10, 10, 100) for modes = 4.
model	Character specifying the model to use for simulating the data array. Must be 'parafac', 'parafac2', or 'pca'.
nfac	Number of components in the component model. Must be an integer greater than or equal to 1.
nclass	Number of classes in simulated class labels. Must be an integer greater than or equal to 2.
smethod	Simulation method, either "logistic" or "eigende". The former implements an iterative Monte Carlo rejection sampling method based on the generalized linear model (slower). The latter uses a multivariate normal distribution and constructs a joint covariance matrix, employing a eigendecomposition and assuming class labels arise from discretizing continuous latent variables (faster).
nreps	Number of replications for simulating class labels for a given set of classification mode component weights.
onreps	Number of replications for simulating a set of classification mode component weights.
props	Target proportions for simulated class labels in output 'y'. Defaults to equal proportions across classes.
corresp	Numeric vector of target correlations between simulated class labels and columns of the classification mode component weight matrix. Must have length equal to 'nfac'. Defaults to 0.5 for all components.
meanpred	Numeric vector of means used to generate the classification mode component weights. Must be real numbers. Operates as the mean vector parameterizing a multivariate normal distribution from which classification mode component weights are generated. Length must be equal to input nfac. Defaults to a vector of zeros.
modes	Single integer of 2, 3, or 4, indicating whether to simulate a two-way matrix, three-way array, or four-way array, respectively.
corrpred	A positive definite correlation matrix containing the target correlations for the classification mode component weights. Must have number of rows and columns equal to input 'nfac'. Operates as the covariance matrix parameterizing a multivariate normal distribution from which classification mode component weights are generated. Defaults to a correlation matrix with 1 on the diagonal and 0.2 on the off-diagonals.
pf2num	When model = 'parafac2', number of rows for each simulated matrix in the list of matrices Amat. Replaces the first element of input arraydim because, for the Parafac2 model, the number of rows in each simulated matrix can vary. If not specified when model = 'parafac2', defaults to rep(c((nfac + 1), (nfac + 2), (nfac + 3)), length.out = arraydim[modes]).
Amat	When model = 'parafac', a matrix of A mode weights with number of rows equal to the first element of input 'arraydim' and with number of columns equal to input 'nfac'. When model = 'parafac2', a list with length equal to the last element of input 'arraydim', where each list element contains a matrix with number of rows of at least 2 and with number of columns equal to input 'nfac'. When provided, replaces a simulated Amat. When model = 'pca', a matrix of loadings with number of rows equal to the second element of input 'arraydim' and with number of columns equal to input 'nfac'.
Bmat	A matrix of B mode weights with number of rows equal to the second element of input 'arraydim' and with number of columns equal to the input 'nfac'. When provided, replaces a simulated Bmat. When model = 'pca', a matrix of scores with number of rows equal to the first element of input 'arraydim' and with number of columns equal to input 'nfac'. If provided when modes = 2, onreps is reduced to one when smethod is logistic.
Cmat	A matrix of C mode weights with number of rows equal to the third element of input 'arraydim' and with number of columns equal to the input 'nfac'. When provided, replaces a simulated Cmat when modes = 4. When modes = 3, replaces the simulated classification mode weight matrix. If provided when modes = 3, onreps is reduced to one when smethod is logistic. When modes is 2, this argument is ignored.
Dmat	A matrix of D mode weights with number of rows equal to the fourth element of input 'arraydim' and with number of columns equal to the input 'nfac'. When modes = 4, replaces the simulated classification mode weight matrix. When modes is 2 or 3, this argument is ignored. If provided when modes = 4, onreps is reduced to one when smethod is logistic.
Gmat	When model = 'parafac2', a matrix of G mode weights with number of rows equal to input 'nfac' and with number of columns equal to input 'nfac'. When provided, replaces a simulated Gmat.
Emat	When model = 'parafac', a 3-way or 4-way array containing noise to be added to the corresponding elements in the simulated data array. Error array dimensions must be equal to the values contained in arraydim. When model = 'parafac2', a list containing either matrices (i.e., when modes = 3) or three-way arrays (i.e., when modes = 4) whose elements contain noise to be added to corresponding elements in the simulated data array. When provided, replaces a simulated Emat. When model = 'pca', a matrix whose elements contain noise to be added to corresponding elements in the simulated data matrix. When provided, replaces a simulated Emat.
technical	List containing arguments related to distributions from which to simulate data. When specified, must contain one or more of the following: distA List containing arguments specifying the distribution from which deviates are drawn for A mode weights contained in Amat. Defaults to standard normal distribution when not specified. See Details section for additional information on acceptable arguments. distB List containing arguments specifying the distribution from which deviates are drawn for B mode weights contained in Bmat. Defaults to standard normal distribution when not specified. See Details section for additional information on acceptable arguments. Ignored if model = 'pca'. distC For when modes = '4', list containing arguments specifying the distribution from which deviates are drawn for C mode weights contained in Cmat. Defaults to standard normal distribution when not specified. See Details section for additional information on acceptable arguments. Ignored when modes = 3. distG For when model = 'parafac2', list containing arguments specifying the distribution from which deviates are drawn for G weights contained in Gmat. Defaults to standard normal distribution when not specified. See Details section for additional information on acceptable arguments. distE List containing arguments specifying the distribution from which deviates are drawn for error contained in Emat. Defaults to standard normal distribution when not specified. See Details section for additional information on acceptable arguments.

Details

By selecting smethod = "logistic", the data array simulation consists of two steps. First, a Monte Carlo simulation is conducted to simulate class labels using a binomial logistic (i.e., in the binary case) or multinomial logistic (i.e., in the multiclass case) regression model. Specifically, columns of the classification mode weights matrix (e.g., Cmat when modes = 3) are generated from a multivariate normal distribution with mean vector meanpred and with covariance matrix corrpred. Values are then drawn randomly from a uniform or a normal distribution and serve as beta coefficients. A linear combination of these beta coefficients and the generated classification weights produces a linear systematic part, which is passed through the logistic function (i.e., the sigmoid) in the binary case or through the softmax function in the multiclass case. Resulting probabilities are used to assign class labels. The simulation repeats classification weights generation onreps times and repeats class label generation, within each onreps iteration, a total of nreps times. The generated class labels that correlate best with the generated classification weights (i.e., with correlations closest to corresp) are retained as the final class labels with corresponding final classification weights. An adaptive sampling technique is used during the simulation such that optimal beta coefficients from previous iterations are used to parameterize a normal distribution, from which new coefficients are drawn in subsequent iterations. Note that, if any simulation replicate produces a set of class labels where all labels are the same (i.e., have no variance), that replicate is discarded. Note also that onreps is ignored when the classification mode weight matrix (i.e., Bmat when modes = 2, Cmat when modes = 3, or Dmat when modes = 4) is provided; in this case, class labels are simulated with respect to the provided classification mode weight matrix.

Second, depending on the chosen model (i.e., Parafac, Parafac2, or PCA) specified via model, and depending on the number of modes specified via modes, component matrices are randomly generated for each mode of the data matrix or array. A data matrix or array is then constructed using a Parafac, Parafac2, or PCA structure from these weight matrices, including the generated classification mode weight matrix (i.e., Bmat, Cmat, or Dmat) from the first step. Alternatively, weight matrices can be provided to override random generation for any weight matrix with the exception of the classification mode. When provided, weight matrices are used to form the final data matrix or array. Finally, random noise is added to each value in the matrix or array. The resulting output is a synthetic data matrix or array paired, through one mode of that matrix or array, with a simulated binary or multiclass response.

Alternatively, by selecting smethod = "eigende", the function simulates component weights and a latent response variable simultaneously from a joint multivariate normal distribution using an eigendecomposition. The covariance structure is defined by corrpred and by a corrected version of corresp that accounts for the attenuation in correlation caused by discretizing the latent response. This continuous latent response vector is then discretized into class labels using quantile cuts defined by the cumulative sum of props. This method offers an efficient, non-iterative alternative that satisfies the target covariance structure without rejection sampling.

The technical argument controls the probability distributions used to simulate weights for different modes. Currently, technical is highly structured. In particular, technical must be provided as a named list whose elements must be one of 'distA', 'distB', 'distC', 'distG', or 'distE', with the last letter of each name designating a mode or, in the case of 'distE', designating error. Each element provided must itself be a list where the first inner list element is named 'dname', specifying the distribution to be used to generate weights for a given mode or for error. There are 12 'dname' options: 'normal', 'uniform', 'gamma', 'beta', 'binomial', 'poisson', 'exponential', 'geometric', 'negbinomial', 'hypergeo', 'lognormal', and 'cauchy'. Additional arguments can be added to each inner list to parameterize the probability distribution being used. These arguments can be one of the following, for each distribution allowed:

For dname = 'normal', allowed arguments are mean or sd (i.e., function rnorm is called).

For dname = 'uniform', allowed arguments are min or max (i.e., function runif is called).

For dname = 'gamma', allowed arguments are shape or scale (i.e., function rgamma is called).

For dname = 'beta', allowed arguments are shape1 or shape2 (i.e., function rbeta is called).

For dname = 'binomial', allowed arguments are size or prob (i.e., function rbinom is called).

For dname = 'poisson', allowed argument is lambda (i.e., function rpois is called).

For dname = 'exponential', allowed argument is rate (i.e., function rexp is called).

For dname = 'geometric', allowed argument is prob (i.e., function rgeom is called).

For dname = 'negbinomial', allowed arguments are size or prob (i.e., function rnbinom is called).

For dname = 'hypergeo', allowed arguments are m, n, or k (i.e., function rhyper is called).

For dname = 'lognormal', allowed arguments are meanlog or sdlog (i.e., function rlnorm is called).

For dname = 'cauchy', allowed arguments are location or scale (i.e., function rcauchy is called).

Note that if a weight matrix and technical information are both provided for a given mode (or for error), the weight matrix is used while technical information is ignored. See Examples below for an example of how to set up technical.

Value

X	Simulated data matrix or array with dimensions specified by arraydim and, when model = 'parafac2', also by pf2num. When model = 'parafac', X is an object of class 'array'. When model = 'parafac2', X is an object of class 'list'. When model = 'pca', X is an object of class 'matrix'.
y	Simulated class labels provided as an object of class 'factor'. When model = 'parafac' or model = 'parafac2', the number of labels is equal to the last element of arraydim. When model = 'pca', the number of labels is equal to the first element of arraydim.
model	Character value indicating the component model that was used to simulate the data matrix or array.
Amat	Simulated A mode weights. When model = 'parafac', output is a matrix with number of rows equal to the first element of arraydim and with number of columns equal to the number of components nfac. When model = 'parafac2', output is a list of matrices with number of rows for each matrix equal to those specified by pf2num and with number of columns equal to nfac. When model = 'pca', output is a matrix with number of rows equal to the second element of arraydim. If Amat was supplied, returns original Amat instead of a simulated Amat.
Bmat	Simulated B mode weights provided as a matrix with number of rows equal to the second element of arraydim and with number of columns equal to the number of components nfac. When model = 'pca', output is a matrix with number of rows equal to the first element of arraydim. If Bmat was supplied, returns original Bmat instead of a simulated Bmat.
Cmat	Simulated C mode weights provided as a matrix with number of rows equal to the third element of arraydim and with number of columns equal to the number of components nfac. If Cmat was supplied when modes = 4, returns original Cmat instead of a simulated Cmat. Not provided when modes = 2.
Dmat	Simulated D mode weights provided when modes = 4. Output is a matrix with number of rows equal to the fourth element of arraydim and with number of columns equal to the number of components nfac. Not provided when modes = 2 or when modes = 3.
Gmat	Simulated G weights provided when model = 'parafac2'. Provided as a matrix with number of rows and columns equal to nfac. If Gmat was supplied, returns original Gmat instead of a simulated Gmat.
Emat	Error matrix, array, or list containing noise added to corresponding elements of simulated data matrix or array. Output has dimensions specified by arraydim and, when model = 'parafac2', also by pf2num. When model = 'parafac', Emat is an object of class 'array'. When model = 'parafac2', Emat is an object of class 'list'. When model = 'pca', Emat is an object of class 'matrix'.

Author(s)

Matthew Asisgress <[e-mail]>

References

See help file for function cpfa for a list of references.

Examples

########## Parafac2 example with 4-way array and multiclass response ##########
## Not run: 
# set seed for reproducibility
set.seed(5)

# define list of arguments specifying distributions for A and G weights
techlist <- list(distA = list(dname = "poisson", 
                              lambda = 3),                 # for A weights
                 distG = list(dname = "gamma", shape = 2, 
                              scale = 4))                  # for G weights

# define target correlation matrix for columns of D mode weights matrix
cormat <- matrix(c(1, .6, .6, .6, 1, .6, .6, .6, 1), nrow = 3, ncol = 3)

# simulate a four-way ragged array connected to a response
data <- simcpfa(arraydim = c(10, 11, 12, 100), model = "parafac2", nfac = 3, 
                nclass = 3, nreps = 1e2, onreps = 10, corresp = rep(.6, 3), 
                meanpred = rep(2, 3), modes = 4, corrpred = cormat,
                technical = techlist, smethod = "eigende")
                
# examine correlations among columns of classification mode matrix Dmat
cor(data$Dmat)

# examine correlations between columns of classification mode matrix Dmat and
# simulated class labels
yproc <- as.numeric(data$y) - 1
cor(data$Dmat, yproc)

## End(Not run)

cpfa documentation built on March 30, 2026, 1:06 a.m.