gjamSimData: Simulated data for gjam analysis

In dbystrova/GJAM_clust: Generalized Joint Attribute Modeling

Description

Simulates data for analysis by gjam.

Usage

  gjamSimData(n = 1000, S = 10, Q = 5, x = NULL, nmiss = 0, typeNames, effort = NULL)

Arguments

n	Sample size
S	Number of response variables (columns) in y, typically less than n
Q	Number of predictors (columns) in design matrix x << n
x	design matrix, if supplied n and Q will be set to nrow(x) and ncol(x), respectively
nmiss	Number of missing values to in x << n
typeNames	Character vector of data types, see Details
effort	List containing 'columns' specifying columns to which effort applies, and 'values', a length-n vector of effort per observation.

Details

Generates simulated data and parameters for analysis by gjam. Because both parameters and data are stochastic, not all simulations will give good results.

typeNames can be 'PA' (presenceAbsence), 'CA' (continuous), 'DA' (discrete), 'FC' (fractional composition), 'CC' (count composition), 'OC' (ordinal counts), and 'CAT' (categorical levels). If more than one 'CAT' is included, each defines a multilevel categorical reponse. One additional type, 'CON' (continuous), is not censored at zero by default.

If defined as a single character value typeNames applies to all columns in y. If not, typeNames is length-S character vector, identifying each response by column in y. If a column 'CAT' is included, a random number of levels will be generated, a, b, c, ....

A more detailed vignette is can be obtained with:

browseVignettes('gjam')

website 'http://sites.nicholas.duke.edu/clarklab/code/'.

Value

formula	R formula for model, e.g., ~ x1 + x2
xdata	data.frame includes columns for predictors in the design matrix
ydata	data.frame for the simulated response
y	response as a n by S matrix as assembled in gjam.
w	n by S latent states
typeY	vector of data types corresponding to columns in y, see Details
typeNames	vector of data types corresponding to columns in ydata
trueValues	list containing true parameter values beta (regression coefficients), sigma (covariance matrix), corSpec (correlation matrix corresponding to sigma), and cuts (partition matrix for ordinal data).
effort	see Arguments.

Author(s)

James S Clark, [e-mail]

References

Clark, J.S., D. Nemergut, B. Seyednasrollah, P. Turner, and S. Zhang. 2016. Generalized joint attribute modeling for biodiversity analysis: Median-zero, multivariate, multifarious data. Ecological Monographs 87, 34-56.

See Also

gjam

Examples

## Not run: 
## ordinal data, show true parameter values
sim <- gjamSimData(S = 5, typeNames = 'OC')  
sim$ydata[1:5,]                              # example data
sim$trueValues$cuts                          # simulated partition
sim$trueValues$beta                          # coefficient matrix

## continuous data censored at zero, note latent w for obs y = 0
sim <- gjamSimData(n = 5, S = 5, typeNames = 'CA')  
sim$w
sim$y

## continuous and discrete data
types <- c(rep('DA',5), rep('CA',4))
sim   <- gjamSimData(n = 10, S = length(types), Q = 4, typeNames = types)
sim$typeNames
sim$ydata
                             
## composition count data  
sim <- gjamSimData(n = 10, S = 8, typeNames = 'CC')
totalCount <- rowSums(sim$ydata)
cbind(sim$ydata, totalCount)  # data with sample effort

## multiple categorical responses - compare matrix y and data.frqme ydata
types <- rep('CAT',2)
sim   <- gjamSimData(S = length(types), typeNames = types)
head(sim$ydata)
head(sim$y)

## discrete abundance, heterogeneous effort 
S   <- 5
n   <- 1000
ef  <- list( columns = 1:S, values = round(runif(n,.5,5),1) )
sim <- gjamSimData(n, S, typeNames = 'DA', effort = ef)
sim$effort$values[1:20]

## combinations of scales, partition only for 'OC' columns
types <- c('OC','OC','OC','CC','CC','CC','CC','CC','CA','CA','PA','PA')
sim   <- gjamSimData(S = length(types), typeNames = types)
sim$typeNames                           
head(sim$ydata)
sim$trueValues$cuts

## End(Not run)

dbystrova/GJAM_clust documentation built on Sept. 15, 2020, 5:46 p.m.