plotpath function

Function to plot spatial SEM results for individual paths

A function to plot unstandardized path coefficients across lag distances. The default is to plot all directed paths with standard error bars, and greyed bars to indicate nonsignificant paths (z>0.05). A range of options are available to change the paths plotted, to add trendlines, and to alter the look of the plots.

plotpath(spatial_model_results, path.type = "directed", selectpath = "none selected",
        add.line = "none", add.error = T, pcut = 0.05, pch = 16, 
        lwd = 2, lty = 1,cex.main=1.2)

Arguments

• spatial_model_results: a list object produced by function runModels
• path.type: An option to select the paths to be plotted. "directed" = only directed paths plotted; "undirected" = only undirected correlations plotted; "both" = all paths plotted; "user" = allows user to specify particular paths and a particular order for plotting. Argument selectpath must also be provided with path.type="user"
• selectpath: An option to select specific paths for plotting. Usage is as follows: selectpath==c(5,18,16,23,29) where values refer to path numbers. Path numbers can be obtained using spatial_model_results[[2]]
• add.line: Options for plotting a fit line. "none" indicates no line; "step" plots straight line segments between points; "smooth" plots a smoothed curve fit using function lowess
• add.error: Should standard error bars be added for each path coefficient
• pcut: p-value cutoff above which points with non significant p-values are shaded grey. Set pcut=1 to have all points black.
• pch: Selects plotting symbols
• lwd: Sets trendline width
• lty: Sets trendline format
• cex.main: Sets plot title font

References

Lamb, E. G., K. Mengersen, K. J. Stewart, U. Attanayake, and S. D. Siciliano. 2014. Spatially explicit structural equation modeling. Ecology 95 :2434-2442.

Rosseel, Y. 2012 lavaan: an R package for structural equation modeling. Journal of Statistical Software 48 :1-36.

Author(s)

Eric Lamb

See Also

sem, make.covar, runModels, modelsummary, plotmodelfit, gam.path

Examples

#data=truelove
#distancematrix<-calc.dist(truelove)
#Truelove_bins<-make.bin(distancematrix,type="ALL",p.dist=20)
#binsize<-Truelove_bins[1][[1]] #truelove lowland bin sizes
#binname<-Truelove_bins[2][[1]] #truelove lowland bin names

#covariances<-make.covar(truelove,distancematrix,binsize,binname)
#covariances

# path model for the truelove dataset
#spatial_model<-'
#       Gram ~ Moisture
#       N_Fix ~ Bryoph + Lich + SoilCrust
#       SoilCrust ~ Bryoph + Lich + Gram + Shrubs + Forbs       
#       Bryoph ~ Gram + Shrubs + Forbs + Moisture
#       Lich ~ Moisture + Forbs + Gram + Shrubs + Bryoph
#       Forbs ~ Moisture
#       Gram ~~ Forbs
#       Shrubs ~ Moisture       
#       Gram ~~ Shrubs
#       Shrubs ~~ Forbs
#       '
#
#results<-runModels(spatial_model,covariances)

#The above script produces the sesem object stored as truelove_results

data=truelove_results

plotpath(truelove_results)
truelove_results[[2]]# list of path names
plotpath(truelove_results,path.type="user",selectpath=c(5,7,8))