From 50e4f4e6e3a884eecc01e82f7d1eebc73e4dc0c6 Mon Sep 17 00:00:00 2001 From: Haziq Jamil Date: Fri, 21 Jun 2024 09:48:18 +0800 Subject: [PATCH] Changes to lavaan verbose handling --- R/30-inlavaan.R | 3 ++- README.Rmd | 4 ++-- README.md | 63 +++++++++++++++++++++++-------------------------- inst/demo.R | 2 +- 4 files changed, 35 insertions(+), 37 deletions(-) diff --git a/R/30-inlavaan.R b/R/30-inlavaan.R index de9deef..2465bc8 100644 --- a/R/30-inlavaan.R +++ b/R/30-inlavaan.R @@ -553,7 +553,8 @@ inlavaan <- function( lavoptions$llnsamp <- mcmcextra$data$llnsamp } - verbose <- lavoptions$verbose + verbose <- dotdotdot$verbose + if (length(verbose) == 0) verbose <- FALSE # redo estimation + vcov + test # 6. estimate free parameters diff --git a/README.Rmd b/README.Rmd index 3a3ef35..06a5dfc 100644 --- a/README.Rmd +++ b/README.Rmd @@ -73,7 +73,7 @@ pak::pak("haziqj/INLAvaan") A simple two-factor SEM with six observed, correlated Gaussian variables. Let $i=1,\dots,n$ index the subjects. -Conditional on the values of $k$th latent variable $\eta_{ki}$ for subject $i$, the six measurement model equations are +Conditional on the values of $k$-th latent variable $\eta_{ki}$ for subject $i$, the six measurement model equations are

@@ -313,7 +313,7 @@ res |> blavaan = res_blav_time, blavaan_vb = res_blavvb_time, INLAvaan = res_inla_time - ) |> + ) |> pivot_longer( cols = -n, names_to = "method", diff --git a/README.md b/README.md index 5795647..41f87df 100644 --- a/README.md +++ b/README.md @@ -58,7 +58,7 @@ pak::pak("haziqj/INLAvaan") A simple two-factor SEM with six observed, correlated Gaussian variables. Let $i=1,\dots,n$ index the subjects. Conditional on the -values of $k$th latent variable $\eta_{ki}$ for subject $i$, the six +values of $k$-th latent variable $\eta_{ki}$ for subject $i$, the six measurement model equations are
@@ -116,12 +116,12 @@ mod <- " dplyr::glimpse(dat) #> Rows: 10,000 #> Columns: 6 -#> $ y1 -1.26736639, -2.31884913, 1.71420679, 2.01369694, 1.37071214, -0.95… -#> $ y2 -1.3071645, -2.4263002, 1.9387949, 2.9101688, 1.7358113, -1.6660828… -#> $ y3 -2.2831840, -2.2597714, 2.3922723, 3.1412267, 2.1247038, -1.3562886… -#> $ y4 -0.18661779, -1.42605096, 2.49517728, -1.17149170, -1.01596946, 0.0… -#> $ y5 -0.6070868, -1.9211147, 2.9405287, -1.0167702, -0.4167566, -1.00124… -#> $ y6 -1.2278010, -2.2398984, 3.2180808, -1.8873268, -1.2123784, -0.60215… +#> $ y1 -1.21410027, 0.42781790, -1.23105577, 1.29706010, -0.14438098, -1.2… +#> $ y2 -1.084814450, 0.372560944, -1.142733592, 1.906949830, -0.013115768,… +#> $ y3 -1.7501130, 1.2281783, -0.9274464, 3.0957939, 0.7869644, -1.1736760… +#> $ y4 1.83828191, 0.92323072, 0.68456209, 1.88557378, -0.71608409, -0.519… +#> $ y5 1.32807356, 0.62454411, 1.26304139, 2.50170072, -0.82536783, -1.213… +#> $ y6 1.47070238, 1.36488688, 1.74260694, 2.89753599, -0.51635709, -0.748… ``` To fit this model using `{INLAvaan}`, use the familiar `{lavaan}` @@ -349,14 +349,14 @@ sessioninfo::session_info(info = "all") #> ─ Session info ─────────────────────────────────────────────────────────────── #> setting value #> version R version 4.4.0 (2024-04-24) -#> os macOS Sonoma 14.4.1 +#> os macOS Sonoma 14.5 #> system aarch64, darwin20 #> ui X11 #> language (EN) #> collate en_US.UTF-8 #> ctype en_US.UTF-8 -#> tz Asia/Riyadh -#> date 2024-05-30 +#> tz Asia/Brunei +#> date 2024-06-21 #> pandoc 3.2 @ /opt/homebrew/bin/ (via rmarkdown) #> #> ─ Packages ─────────────────────────────────────────────────────────────────── @@ -366,7 +366,7 @@ sessioninfo::session_info(info = "all") #> backports 1.5.0 2024-05-23 [1] CRAN (R 4.4.0) #> base64enc 0.1-3 2015-07-28 [1] CRAN (R 4.4.0) #> bayesplot 1.11.1 2024-02-15 [1] CRAN (R 4.4.0) -#> blavaan * 0.5-4 2024-04-15 [1] CRAN (R 4.4.0) +#> blavaan * 0.5-5 2024-06-09 [1] CRAN (R 4.4.0) #> boot 1.3-30 2024-02-26 [1] CRAN (R 4.4.0) #> carData 3.0-5 2022-01-06 [1] CRAN (R 4.4.0) #> checkmate 2.3.1 2023-12-04 [1] CRAN (R 4.4.0) @@ -382,22 +382,21 @@ sessioninfo::session_info(info = "all") #> corpcor 1.6.10 2021-09-16 [1] CRAN (R 4.4.0) #> curl 5.2.1 2024-03-01 [1] CRAN (R 4.4.0) #> data.table 1.15.4 2024-03-30 [1] CRAN (R 4.4.0) -#> DBI 1.2.2 2024-02-16 [1] CRAN (R 4.4.0) -#> Deriv 4.1.3 2021-02-24 [1] CRAN (R 4.4.0) +#> DBI 1.2.3 2024-06-02 [1] CRAN (R 4.4.0) #> digest 0.6.35 2024-03-11 [1] CRAN (R 4.4.0) #> dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0) #> e1071 1.7-14 2023-12-06 [1] CRAN (R 4.4.0) -#> evaluate 0.23 2023-11-01 [1] CRAN (R 4.4.0) +#> evaluate 0.24.0 2024-06-10 [1] CRAN (R 4.4.0) #> fansi 1.0.6 2023-12-08 [1] CRAN (R 4.4.0) #> farver 2.1.2 2024-05-13 [1] CRAN (R 4.4.0) #> fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0) #> fBasics 4032.96 2023-11-03 [1] CRAN (R 4.4.0) #> fdrtool 1.2.17 2021-11-13 [1] CRAN (R 4.4.0) -#> fmesher 0.1.5 2023-12-20 [1] CRAN (R 4.4.0) +#> fmesher 0.1.6 2024-06-14 [1] CRAN (R 4.4.0) #> forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.4.0) #> foreign 0.8-86 2023-11-28 [1] CRAN (R 4.4.0) #> Formula 1.2-5 2023-02-24 [1] CRAN (R 4.4.0) -#> future * 1.33.2 2024-03-26 [1] CRAN (R 4.4.0) +#> future 1.33.2 2024-03-26 [1] CRAN (R 4.4.0) #> future.apply 1.11.2 2024-03-28 [1] CRAN (R 4.4.0) #> generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0) #> ggplot2 * 3.5.1 2024-04-23 [1] CRAN (R 4.4.0) @@ -409,33 +408,32 @@ sessioninfo::session_info(info = "all") #> gtable 0.3.5 2024-04-22 [1] CRAN (R 4.4.0) #> gtools 3.9.5 2023-11-20 [1] CRAN (R 4.4.0) #> highr 0.11 2024-05-26 [1] CRAN (R 4.4.0) -#> Hmisc 5.1-2 2024-03-11 [1] CRAN (R 4.4.0) +#> Hmisc 5.1-3 2024-05-28 [1] CRAN (R 4.4.0) #> hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0) #> htmlTable 2.4.2 2023-10-29 [1] CRAN (R 4.4.0) #> htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0) #> htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.4.0) #> igraph 2.0.3 2024-03-13 [1] CRAN (R 4.4.0) -#> INLA 24.05.27-2 2024-05-27 [1] local -#> INLAvaan * 0.1.0.9012 2024-05-30 [1] local +#> INLA 24.06.04 2024-06-03 [1] local +#> INLAvaan * 0.1.0.9013 2024-05-31 [1] local #> inline 0.3.19 2021-05-31 [1] CRAN (R 4.4.0) #> jpeg 0.1-10 2022-11-29 [1] CRAN (R 4.4.0) #> jsonlite 1.8.8 2023-12-04 [1] CRAN (R 4.4.0) -#> KernSmooth 2.23-22 2023-07-10 [1] CRAN (R 4.4.0) -#> knitr 1.46 2024-04-06 [1] CRAN (R 4.4.0) +#> KernSmooth 2.23-24 2024-05-17 [1] CRAN (R 4.4.0) +#> knitr 1.47 2024-05-29 [1] CRAN (R 4.4.0) #> kutils 1.73 2023-09-17 [1] CRAN (R 4.4.0) #> labeling 0.4.3 2023-08-29 [1] CRAN (R 4.4.0) #> lattice 0.22-6 2024-03-20 [1] CRAN (R 4.4.0) -#> lavaan * 0.6-17 2023-12-20 [1] CRAN (R 4.4.0) +#> lavaan * 0.6-18 2024-06-07 [1] CRAN (R 4.4.0) #> lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0) #> lisrelToR 0.3 2024-02-07 [1] CRAN (R 4.4.0) #> listenv 0.9.1 2024-01-29 [1] CRAN (R 4.4.0) -#> lme4 1.1-35.3 2024-04-16 [1] CRAN (R 4.4.0) +#> lme4 1.1-35.4 2024-06-19 [1] CRAN (R 4.4.0) #> loo 2.7.0 2024-02-24 [1] CRAN (R 4.4.0) #> lubridate * 1.9.3 2023-09-27 [1] CRAN (R 4.4.0) #> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0) -#> MASS 7.3-60.2 2024-04-24 [1] local +#> MASS 7.3-61 2024-06-13 [1] CRAN (R 4.4.0) #> Matrix 1.7-0 2024-03-22 [1] CRAN (R 4.4.0) -#> MatrixModels 0.5-3 2023-11-06 [1] CRAN (R 4.4.0) #> matrixStats 1.3.0 2024-04-11 [1] CRAN (R 4.4.0) #> mgcv 1.9-1 2023-12-21 [1] CRAN (R 4.4.0) #> mi 1.1 2022-06-06 [1] CRAN (R 4.4.0) @@ -444,8 +442,8 @@ sessioninfo::session_info(info = "all") #> modeest 2.4.0 2019-11-18 [1] CRAN (R 4.4.0) #> munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0) #> mvtnorm 1.2-5 2024-05-21 [1] CRAN (R 4.4.0) -#> nlme 3.1-164 2023-11-27 [1] CRAN (R 4.4.0) -#> nloptr 2.0.3 2022-05-26 [1] CRAN (R 4.4.0) +#> nlme 3.1-165 2024-06-06 [1] CRAN (R 4.4.0) +#> nloptr 2.1.0 2024-06-19 [1] CRAN (R 4.4.0) #> nnet 7.3-19 2023-05-03 [1] CRAN (R 4.4.0) #> nonnest2 0.5-7 2024-05-06 [1] CRAN (R 4.4.0) #> OpenMx 2.21.11 2023-11-28 [1] CRAN (R 4.4.0) @@ -463,13 +461,13 @@ sessioninfo::session_info(info = "all") #> purrr * 1.0.2 2023-08-10 [1] CRAN (R 4.4.0) #> qgraph 1.9.8 2023-11-03 [1] CRAN (R 4.4.0) #> quadprog 1.5-8 2019-11-20 [1] CRAN (R 4.4.0) -#> QuickJSR 1.1.3 2024-01-31 [1] CRAN (R 4.4.0) +#> QuickJSR 1.2.2 2024-06-07 [1] CRAN (R 4.4.0) #> R6 2.5.1 2021-08-19 [1] CRAN (R 4.4.0) #> Rcpp * 1.0.12 2024-01-09 [1] CRAN (R 4.4.0) #> RcppParallel 5.1.7 2023-02-27 [1] CRAN (R 4.4.0) #> readr * 2.1.5 2024-01-10 [1] CRAN (R 4.4.0) #> reshape2 1.4.4 2020-04-09 [1] CRAN (R 4.4.0) -#> rlang 1.1.3 2024-01-10 [1] CRAN (R 4.4.0) +#> rlang 1.1.4 2024-06-04 [1] CRAN (R 4.4.0) #> rmarkdown 2.27 2024-05-17 [1] CRAN (R 4.4.0) #> rmutil 1.1.10 2022-10-27 [1] CRAN (R 4.4.0) #> rockchalk 1.8.157 2022-08-06 [1] CRAN (R 4.4.0) @@ -477,7 +475,6 @@ sessioninfo::session_info(info = "all") #> rstan 2.32.6 2024-03-05 [1] CRAN (R 4.4.0) #> rstantools 2.4.0 2024-01-31 [1] CRAN (R 4.4.0) #> rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.4.0) -#> runjags 2.2.2-4 2024-03-10 [1] CRAN (R 4.4.0) #> sandwich 3.1-0 2023-12-11 [1] CRAN (R 4.4.0) #> scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0) #> sem 3.1-15 2022-04-10 [1] CRAN (R 4.4.0) @@ -489,7 +486,7 @@ sessioninfo::session_info(info = "all") #> spatial 7.3-17 2023-07-20 [1] CRAN (R 4.4.0) #> stable 1.1.6 2022-03-02 [1] CRAN (R 4.4.0) #> stabledist 0.7-1 2016-09-12 [1] CRAN (R 4.4.0) -#> StanHeaders 2.32.8 2024-05-21 [1] CRAN (R 4.4.0) +#> StanHeaders 2.32.9 2024-05-29 [1] CRAN (R 4.4.0) #> statip 0.2.3 2019-11-17 [1] CRAN (R 4.4.0) #> stringi 1.8.4 2024-05-06 [1] CRAN (R 4.4.0) #> stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.4.0) @@ -507,7 +504,7 @@ sessioninfo::session_info(info = "all") #> V8 4.4.2 2024-02-15 [1] CRAN (R 4.4.0) #> vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0) #> withr 3.0.0 2024-01-16 [1] CRAN (R 4.4.0) -#> xfun 0.44 2024-05-15 [1] CRAN (R 4.4.0) +#> xfun 0.45 2024-06-16 [1] CRAN (R 4.4.0) #> XML 3.99-0.16.1 2024-01-22 [1] CRAN (R 4.4.0) #> xml2 1.3.6 2023-12-04 [1] CRAN (R 4.4.0) #> xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0) @@ -526,7 +523,7 @@ sessioninfo::session_info(info = "all") #> jpeg 9.5 #> tiff LIBTIFF, Version 4.5.0 #> tcl 8.6.13 -#> curl 8.4.0 +#> curl 8.6.0 #> zlib 1.2.12 #> bzlib 1.0.8, 13-Jul-2019 #> xz 5.4.4 diff --git a/inst/demo.R b/inst/demo.R index 0b2d175..cad0fe4 100644 --- a/inst/demo.R +++ b/inst/demo.R @@ -23,7 +23,7 @@ fit <- isem( meanstructure = FALSE, verbose = TRUE, # std.lv = TRUE, - stop_at_jagtrans = TRUE + stop_at_jagtrans = FALSE ) tmp <- fit