I fit a random slope and random intercept hlm using OpenMx and I am wondering how to get the latent values of the random slope and intercept. From what I can tell the issue is that the latent variables exist in second level so the function mxFactorScores does not know what to do but I am not sure In this example U_00 is my random intercept and U_01 is my random slope.
Here is code to simulate HLM data
library(dplyr)
library(tidyr)
library(OpenMx)
# Simulate Data -------------
J <- 100 #number of clusters
n_j <- 30#number of observations
gamma_00 <- 5
gamma_10 <- 3
mu_x <- 4
sim.dat <- data.frame(J_ID = 1:J) |>
mutate(U_0j = rnorm(J, mean = 0 , sd = 1),
U_1j = rnorm(J, mean = 0, sd = 1),
gamma_00 = gamma_00,
gamma_10 = gamma_10,
n_j = n_j) |>
rowwise() |>
mutate(X = list(rnorm(n_j, mu_x, sd = 1)),
R = list(rnorm(n_j, 0, sd = 1))) |>
unnest(cols = c(X, R)) |>
mutate(Y = gamma_00 + U_0j + (gamma_10 + U_1j) * X + R)
sim.dat.obs <- sim.dat|>
select(J_ID, X, Y) |>
mutate(J_ID = as.factor(J_ID))
Here is code for openmx
## J level (Teacher) --------
J_obs <- sim.dat.obs |>
select(J_ID) |>
distinct()
J_cluster_name <- "J_ID"
J_latent <- c("U_0", "U_1")
J_data <- mxData(J_obs, type = "raw",
primaryKey = J_cluster_name)
J_var <- mxPath(from = J_latent,
arrows = 2, values = 1,
connect = "single")
J_cov <- mxPath(from = J_latent,
arrows = 2, values = 0,
connect = "unique.bivariate",
free = FALSE)
J_model <- mxModel("Level_J", type = "RAM",
latentVars = J_latent,
J_data,
J_var,
J_cov)
## I level (Student) --------
I_obs <- mxData(sim.dat.obs, type = "raw")
I_manifest <- c("X", "Y")
I_means <- mxPath(from = "one",
to = c("X"),
labels = c("mu_x"),
value = 1)
I_var <- mxPath(from = c("X", "Y"),
labels = c("sd_x", "R_ysd"),
arrow = 2,
value = 1)
I_fixed <- mxPath(from = c("one","X"),
to = "Y",
value = 1,
labels = c("gamma_00", "gamma_10"))
I_randomslope <- mxPath(from = c("Level_J.U_1"),
to = c("Y"),
labels = c("data.X"),
free = FALSE,
joinKey = J_cluster_name)
I_randomint <- mxPath(from = c("Level_J.U_0"),
to = c("Y"),
value = 1,
free = FALSE,
joinKey = J_cluster_name)
I_model<- mxModel("Level_I", type = "RAM",
manifestVars = I_manifest,
J_model,
I_obs,
I_means,
I_var,
I_fixed,
I_randomslope,
I_randomint)
I.fit <- mxRun(I_model)
#> Running Level_I with 7 parameters
summary(I.fit)
#> Summary of Level_I
#>
#> free parameters:
#> name matrix row col Estimate Std.Error A
#> 1 gamma_10 A Y X 3.0702452 0.09300885
#> 2 sd_x S X X 0.9924763 0.02562636
#> 3 R_ysd S Y Y 1.0691329 0.02857744
#> 4 mu_x M 1 X 4.0054015 0.01818861
#> 5 gamma_00 M 1 Y 5.0011756 0.13307218
#> 6 Level_J.S[1,1] Level_J.S U_0 U_0 1.1217698 0.24712431 !
#> 7 Level_J.S[2,2] Level_J.S U_1 U_1 0.8267078 0.12055658
#>
#> Model Statistics:
#> | Parameters | Degrees of Freedom | Fit (-2lnL units)
#> Model: 7 5993 17907.01
#> Saturated: NA NA NA
#> Independence: NA NA NA
#> Number of observations/statistics: 3100/6000
#>
#> Information Criteria:
#> | df Penalty | Parameters Penalty | Sample-Size Adjusted
#> AIC: 5921.013 17921.01 17921.05
#> BIC: -30271.658 17963.29 17941.04
#> CFI: NA
#> TLI: 1 (also known as NNFI)
#> RMSEA: 0 [95% CI (NA, NA)]
#> Prob(RMSEA <= 0.05): NA
#> To get additional fit indices, see help(mxRefModels)
#> timestamp: 2024-05-03 20:11:30
#> Wall clock time: 9.318122 secs
#> optimizer: SLSQP
#> OpenMx version number: 2.21.8
#> Need help? See help(mxSummary)
Me trying the factor score function.
mxFactorScores(I.fit, "WeightedML")
#> Running Container with 0 parameters
#> Error in `[.data.frame`(got, , paste0(names(coef(fit)), "SE"), drop = FALSE): undefined columns selected
mxFactorScores(I.fit@submodels$Level_J, "WeightedML")
#> Error in mxEvalByName(model$expectation$M, model, compute = TRUE): 'name' argument must be a character argument
Created on 2024-05-03 with reprex v2.0.2
One work around I tried was to specify dummy latent variables which are the Level_J.U01 times one at the level 1 but the results were not cohort. Observations within a cluster had different values of U_01
I also asked the question on OpenMx forum: https://openmx.ssri.psu.edu/node/4909