plotpath {sesem} | R Documentation |
Function to plot spatial SEM results for individual paths
Description
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.
Usage
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 |
Author(s)
Eric Lamb
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.
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))