I am trying to run a Vuong test using the vuong() function from pscl to compare two lmer() models that use the same data. However, each time I run it, I get the following error message:
> vuong(mod1, mod2)
Error: $ operator not defined for this S4 class
I have tried restarting R and updating my packages, but I still get the same error.
These are the packages I have loaded:
# ---- Load libraries ----
library(ggplot2)
library(pscl)
library(lmtest)
library(lme4)
library(car)
And this is the R version I am running:
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252 LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C LC_TIME=English_Canada.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] car_3.0-11 carData_3.0-4 lme4_1.1-27 Matrix_1.2-18 lmtest_0.9-38 zoo_1.8-9 pscl_1.5.5 ggplot2_3.3.5
loaded via a namespace (and not attached):
[1] tidyselect_1.1.1 purrr_0.3.4 splines_4.0.2 haven_2.4.3 lattice_0.20-41 colorspace_2.0-2
[7] vctrs_0.3.8 generics_0.1.0 mgcv_1.8-31 utf8_1.2.2 rlang_0.4.11 nloptr_1.2.2.2
[13] pillar_1.6.3 foreign_0.8-80 glue_1.4.2 withr_2.4.2 DBI_1.1.1 readxl_1.3.1
[19] lifecycle_1.0.1 munsell_0.5.0 gtable_0.3.0 cellranger_1.1.0 zip_2.2.0 labeling_0.4.2
[25] rio_0.5.27 forcats_0.5.1 curl_4.3.2 fansi_0.5.0 Rcpp_1.0.6 scales_1.1.1
[31] abind_1.4-5 farver_2.1.0 digest_0.6.28 hms_1.1.1 stringi_1.7.4 openxlsx_4.2.4
[37] dplyr_1.0.7 grid_4.0.2 tools_4.0.2 magrittr_2.0.1 tibble_3.1.4 crayon_1.4.1
[43] pkgconfig_2.0.3 MASS_7.3-51.6 ellipsis_0.3.2 data.table_1.14.2 assertthat_0.2.1 minqa_1.2.4
[49] R6_2.5.1 boot_1.3-25 nlme_3.1-148 compiler_4.0.2
Is there an issue with the packages I have loaded that would cause this function to not work? Or is there some other solution I could try to fix this?
I've also tried running other model types (e.g. lm instear of lmer) but all combinations return the same error, so I don't suspect it's something with the data and/or model.
Any help would be appreciated!
As you discovered, pscl::vuong doesn't work with lmer models.
There is a nonnest package with a vuongtest function. From the example in that help page:
## Supplying custom vcov function
require(lme4)
require(merDeriv)
fm1 <- lmer(Reaction ~ Days + (Days | Subject), sleepstudy, REML=FALSE)
fm2 <- lmer(Reaction ~ Days + (Days || Subject), sleepstudy, REML=FALSE)
vcl <- function(obj) vcov(obj, full=TRUE)
vuongtest(fm1, fm2, vc1=vcl, vc2=vcl, nested=TRUE)