gjamIIEplot: Plots indirect effects and interactions for gjam data

In dbystrova/GJAM_clust: Generalized Joint Attribute Modeling

Description

Using the object returned by gjamIIEplot generates a plot for a response variable.

Usage

  gjamIIEplot(fit, response, effectMu, effectSd = NULL, 
              ylim = NULL, col='black', legLoc = 'topleft', cex = 1)

Arguments

fit	object from gjamIIE.
response	name of a column in fit$y to plot.
effectMu	character vector of mean effects to plot, can include 'main','int','direct','ind'.
effectSd	character vector can include all or some of effectMu.
ylim	vector of two values defines vertical axis range.
col	vector of colors for barplot.
legLoc	character for legend location.
cex	font size.

Details

For plotting direct effects, interactions, and indirect effects from an object fit generated by gjamIIE. The character vector supplied as effectMu can include main effects ('main'), interactions ('int'), main effects plus interactions ('direct'), and/or indirect effects ('ind'). The list effectSd draws 0.95 predictive intervals for all or some of the effects listed in effectMu. Bars are contributions of each effect to the response.

For factors, effects are plotted relative to the mean over all factor levels.

Author(s)

James S Clark, [e-mail]

References

Clark, J.S., D. Nemergut, B. Seyednasrollah, P. Turner, and S. Zhang. 2017. Generalized joint attribute modeling for biodiversity analysis: Median-zero, multivariate, multifarious data. Ecological Monographs 87, 34-56.

See Also

gjamIIE generates output for gjamIIEplot

A more detailed vignette is can be obtained with:

browseVignettes('gjam')

web site 'http://sites.nicholas.duke.edu/clarklab/code/'.

Examples

## Not run: 
sim <- gjamSimData(S = 10, Q = 6, typeNames = 'OC')
ml  <- list(ng = 50, burnin = 5, typeNames = sim$typeNames)
out <- gjam(sim$formula, sim$xdata, sim$ydata, modelList = ml)

xvector <- colMeans(out$inputs$x)  #predict at mean values for data
xvector[1] <- 1

fit <- gjamIIE(out, xvector)

gjamIIEplot(fit, response = 'S1', effectMu = c('main','ind'), 
            effectSd = c('main','ind'), legLoc = 'topleft')

## End(Not run)

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