Nothing
plotSEMM_ci <- function(SEMLIdatapks, linesearch, lnty = 3, lncol = 1, deltaci=TRUE,
deltace=TRUE, bsci=TRUE, ninty_five = TRUE, include_title = TRUE,
use_fixed_value, cex = 1.5, ...) {
nf <- layout(matrix(c(1, 2), 2, 1, byrow = TRUE), c(4, 4), c(4, 1), TRUE)
par(mar=c(5,5,5,2))
if(use_fixed_value){
fixed_values <- SEMLIdatapks[nrow(SEMLIdatapks), ]
SEMLIdatapks <- SEMLIdatapks[-nrow(SEMLIdatapks), ]
}
dots <- list(...)
input <- dots$input
if(!is.null(input$xlab)) xlab <- input$xlab
if(!is.null(input$ylab)) ylab <- input$ylab
legend_location <- if(!is.null(input$legend_location)) input$legend_location else 'bottomleft'
if(legend_location == 'default') legend_location <- 'bottomleft'
#requires setup from plotSEMM_setup2
if(!SEMLIdatapks$setup2[1L])
stop('plotSEMM_ci requires a setup model that included the parameter ACOV matrix')
def.par <- par(no.readonly = TRUE)
pick <- SEMLIdatapks$agg_denEta1 > 0.02
SEMLIdatapks <- SEMLIdatapks[pick, ]
legendkeep <- c(TRUE, deltaci, deltace, bsci)
# plot(SEMLIdatapks$Eta1,SEMLIdatapks$y,type='n',xlab='Latent Predictor', ylab='Latent Outcome')
plot(SEMLIdatapks$Eta1, SEMLIdatapks$Eta2, type = "n", xlab = xlab, ylab = ylab,
cex.lab=cex, cex.axis=cex)
lines(SEMLIdatapks$Eta1, SEMLIdatapks$agg_pred, col = 1, lwd = 2)
if(deltaci){
points(SEMLIdatapks$Eta1, SEMLIdatapks$delta_CIlo, col = 2, lwd = 1, lty = 2)
points(SEMLIdatapks$Eta1, SEMLIdatapks$delta_CIhi, col = 2, lwd = 1, lty = 2)
}
if(deltace){
lines(SEMLIdatapks$Eta1, SEMLIdatapks$delta_CElo, col = 2, lwd = 2, lty = 2)
lines(SEMLIdatapks$Eta1, SEMLIdatapks$delta_CEhi, col = 2, lwd = 2, lty = 2)
}
if(bsci){
points(SEMLIdatapks$Eta1, SEMLIdatapks$bs_CIlo, col = 4, lwd = 1, lty = 3, pch = 4)
points(SEMLIdatapks$Eta1, SEMLIdatapks$bs_CIhi, col = 4, lwd = 1, lty = 3, pch = 4)
}
if(ninty_five){
legend = c("Aggregate Function", "Delta Method 95% Confidence Interval",
"Delta Method 95% Confidence Envelope",
"Bootstrap 95% Confidence Interval")[legendkeep]
} else {
legend = c("Aggregate Function", "Delta Method 90% Confidence Interval",
"Delta Method 90% Confidence Envelope",
"Bootstrap 90% Confidence Interval")[legendkeep]
}
lwd = c(2, 1, 2, 1)[legendkeep]
lty = c(1, 0, 2, 0) [legendkeep]
pch = c(NA, 1, NA, 4)[legendkeep]
col = c(1, 2, 2, 4)[legendkeep]
if(SEMLIdatapks$boot[1]){
lines(SEMLIdatapks$Eta1, SEMLIdatapks$bs_CElo, col = 4, lwd = 2, lty = 4, pch = 4)
lines(SEMLIdatapks$Eta1, SEMLIdatapks$bs_CEhi, col = 4, lwd = 2, lty = 4, pch = 4)
if(ninty_five) legend <- c(legend, 'Bootstrap 95% Confidence Envelope')
else legend <- c(legend, 'Bootstrap 90% Confidence Envelope')
lwd <- c(lwd, 2); lty <- c(lty, 4); pch = c(pch, NA); col = c(col, 4)
}
if(legend_location != 'none')
legend(legend_location, legend = legend, lwd = lwd, lty = lty,
pch = pch, col = col, bty = "n", cex=cex)
if(linesearch){
found <- FALSE
search <- attr(SEMLIdatapks, 'search')
if(length(search) && deltace){
found <- TRUE
nc <- ncol(search)
lines(c(search[1,1], search[1,nc]), c(search[2,1], search[2,nc]),
col = 'pink', lwd=3, lty=1)
}
if(SEMLIdatapks$boot[1]){
search <- attr(SEMLIdatapks, 'search.bs')
if(length(search)){
found <- TRUE
nc <- ncol(search)
lines(c(search[1,1], search[1,nc]), c(search[2,1], search[2,nc]),
col = 'lightblue', lwd=3, lty=1)
}
}
if(!found && include_title)
title('No Line was Found within the Confidence Envelope(s)', cex.main=cex*(4/3))
}
if(use_fixed_value){
#plot some text
percent <- '90%'
if(ninty_five) percent <- '95%'
# points(fixed_values$Eta1, (fixed_values$delta_CIlo + fixed_values$delta_CIhi)/2,
# col='purple', cex=1.5, pch=17)
par(mar = c(0, 0, 0, 0))
plot(c(0,5), c(0,5), axes=FALSE, frame.plot=FALSE, type='n', xlab='', ylab='')
txt <- paste0('Latent Predictor Value: ', fixed_values$Eta1)
txt <- c(txt, paste0('Predicted Latent Outcome Value: ',
round((fixed_values$delta_CIlo + fixed_values$delta_CIhi)/2, 4)))
if(deltaci)
txt <- c(txt, paste0(percent, ' Delta Method Wald-type Confidence Interval: (',
round(fixed_values$delta_CIlo, 3), ', ',
round(fixed_values$delta_CIhi, 3), ')'))
if(bsci)
txt <- c(txt, paste0(percent, ' Parametric Bootstrap Confidence Interval: (',
round(fixed_values$bs_CIlo, 3), ', ',
round(fixed_values$bs_CIhi, 3), ')'))
if(!deltaci && !bsci)
txt <- c(txt, paste0(percent, ' Confidence interval: NA NA (No method selected)'))
legend('topleft', legend=txt, cex=cex, bty='n')
}
}
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