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## ----setup, include=FALSE, message=FALSE--------------------------------------
knitr::opts_chunk$set(echo = TRUE,
fig.width=7, fig.height=6,
tidy.opts=list(width.cutoff=100), tidy=TRUE, comment=NA)
require(regmed)
## ---- medsim------------------------------------------------------------------
data(medsim)
## ---- filtermediate-----------------------------------------------------------
dat.filter <- regmed.prefilter(x[,1], med, y[,1], k=10)
colnames(dat.filter$mediator)
## ----set_grid-----------------------------------------------------------------
lambda.grid <- seq(from=.4, to=.01, by=-.05)
x1 <- dat.filter$x
y1 <- dat.filter$y
med <- dat.filter$mediator
fit.grid <- regmed.grid(x1, med, y1, lambda.grid, frac.lasso=.8)
## ---- methodsgrid-------------------------------------------------------------
print(fit.grid)
plot.regmed.grid(fit.grid)
## ---- fitbest-----------------------------------------------------------------
fit.best <- regmed.grid.bestfit(fit.grid)
summary(fit.best)
## ---- singlefit---------------------------------------------------------------
fit.single <- regmed.fit(x1, med, y1, lambda=0.3, frac.lasso=.8)
summary(fit.single)
## ----edges--------------------------------------------------------------------
edges.med <- regmed.edges(fit.best, type="mediators")
plot.regmed.edges(edges.med)
edges.any <- regmed.edges(fit.best, type="any")
plot.regmed.edges(edges.any)
## ---- setuplavaan-------------------------------------------------------------
dat <- regmed.lavaan.dat(x1, med, y1)
mod.best <- regmed.lavaan.model(edges.med, fit.best)
mod.any <- regmed.lavaan.model(edges.any, fit.best)
## ---- fitlavaan---------------------------------------------------------------
fit.lav.med <- lavaan:::sem(model=mod.best, data=dat)
summary.lavaan(fit.lav.med)
fit.lav.any <- lavaan:::sem(model=mod.any, data=dat)
summary.lavaan(fit.lav.any)
## ----mvfit_grid---------------------------------------------------------------
fit.grid <- mvregmed.grid(x, med, y, lambda.grid)
summary(fit.grid)
## ----plot_mvgrid--------------------------------------------------------------
plot(fit.grid)
## ----mvfit_best---------------------------------------------------------------
mvfit.best <- mvregmed.grid.bestfit(fit.grid)
## ----mvfit_summary------------------------------------------------------------
summary(mvfit.best)
mvedges <- mvregmed.edges(mvfit.best)
plot(mvedges)
## ----fit_mvregmed-------------------------------------------------------------
mvfit <- mvregmed.fit(x, med, y, lambda=0.4)
summary.mvregmed(mvfit, eps=0.01)
## ----plot_mvedges1------------------------------------------------------------
## get vertices and edges of graph
mvfit.edges <- mvregmed.edges(mvfit.best, eps=5e-2)
plot.mvregmed.edges(mvfit.edges,
x.color="palegreen",y.color="palevioletred",med.color="skyblue",
v.size=20, seed=3)
## ----plot_mvedges2------------------------------------------------------------
gr <- regmed:::mvregmed.graph.attributes(mvfit.edges, x.color ="limegreen",
y.color="palevioletred",
med.color="royalblue", v.size=40)
set.seed(3);
plot(gr$gr, vertex.size=gr$vsize, vertex.color=gr$vcol,
vertex.label.font=2,vertex.label.color="black",
vertex.label.cex=.5,
edge.arrow.mode=">",edge.arrow.size=.3)
## ----lavaanmv-----------------------------------------------------------------
mvmod <- mvregmed.lavaan.model(mvfit.edges, mvfit.best)
mvdat <- mvregmed.lavaan.dat(x, med, y)
mvfit.lavaan <- lavaan:::sem(model=mvmod, data=mvdat)
summary.lavaan(mvfit.lavaan)
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