Reconsider color schemes, update leftover sempaths to Diagrammer, remove pca arrows from initial section, others as needed.

Especially in resources section.

Known:

• workshop.zip
• limitSEM footnote in SEM chapter

in measures of reliability section

Clean up Model Comparison Example to hide code

update due to FA workshop notes, specifically change the multiple factors example, some of the notation in pca, and wording elsewhere.

https://cran.r-project.org/web/packages/PLmixed/vignettes/PLmixed_intro.html

Minor change to core fa function broke one example, though functionality is left to use the old method. Perhaps change that example from Harman.5 to a more realistic data set.

The parallel process depiction leaves out intercept/slope correlations that would probably be included in models. Also would be good to show the equivalence as multivariate random effect model via brms.

For example, update the main model as:

mainModel = "
i1 =~ 1*y11 + 1*y12 + 1*y13 + 1*y14
s1 =~ 0*y11 + 1*y12 + 2*y13 + 3*y14


i2 =~ 1*y21 + 1*y22 + 1*y23 + 1*y24
s2 =~ 0*y21 + 1*y22 + 2*y23 + 3*y24

s1 ~ i2
s2 ~ i1

i1 ~~ s1
i2 ~~ s2
"

And for brms

library(tidyverse)

library(brms)

head(d2)
d = left_join(d1, d2)

form = bf(y1 ~ time + (1 + time | p | Subject)) +
  bf(y2 ~ time + (1 + time | p | Subject))

mod = brm(form, data = d, cores=4)      

summary(mod)

For identity you will have to fix variances in lavaan or model sigma by time for brms.

In factor analysis section, transpose W in X = ZW and perhaps introduce component score part in pca section to make link clearer.

Add some detail as well as a plan of action for model assessment generally/more explicitly.

Borked footnote for limitSEM (was missing caret). Fixed in Rmd but not published.

Currently lacks the graphical model.

Given that the exact same yaml works in every other document, I don't see what there is to fix. But revisit this at some point.

Add section on topic models

topic model plots should have three distinct colors

move bobfrom title page and just leave R img as with other docs.