Should dummy variables be allowed to correlate (R code & data provided)
tl;dr: What is the difference between a regression model that allows its dummy variables to be correlated and one that doesn't do so? For example, how does that affect Standard Error of the regression coefficients (coefs)? In my reproducible SEM ( structural equation model ) modelA below, imagine I remove the Group_HI ~~ 0*Group_MT (denoting correlation bet. two dummies is 0 ) altogether leading to modelB . What is the difference between a model that uses Group_HI ~~ 0*Group_MT ( modelA ) and one that doesn't include anything to describe the relation between Group_HI and Group_MT ( modelB )? Specifically, it seems modelB produces Standard Errors for coefs that are closer to those given by a MANOVA: summary(lm(cbind(MP,SE)~Group,data=d)) Response MP : Estimate Std. Error t value Pr(>|t|) (Intercept) 4.6667 0.6150 7.588 8.19e-10 *** GroupHI 3.1833 0.8136 3.913 0.000281 *** ## This SE GroupMT 6.7451 0.8438 7.994 1.95e-10 *** ## This SE Response SE : Estimate Std. Error t value Pr(>|t|) (Intercept) 4.2000 0.3378 12.432 But modelA produces Standard Errors for coefs that are closer to those given by: stacked_DVs |t|) DVMP 4.666667 0.4961705 9.405370 2.364383e-15 DVSE 4.200000 0.4961705 8.464833 2.559422e-13 GroupHI 3.183333 0.6563718 4.849893 4.648941e-06 ## This SE GroupMT 6.745098 0.6807403 9.908475 1.912183e-16 ## This SE Reproducible data and R code: library(tidyverse); library(fastDummies) ; library(lavaan) d |z|) MP ~ Group_HI 3.183 0.659 4.830 0.000 ## This SE SE ~ Group_HI…