From f5d39d9cadad2439d4bb41f961f40348c40259c6 Mon Sep 17 00:00:00 2001 From: Shu Fai Cheung Date: Wed, 3 Jun 2026 21:26:13 +0800 Subject: [PATCH 1/5] Disable baseline --- R/get_add.R | 2 ++ 1 file changed, 2 insertions(+) diff --git a/R/get_add.R b/R/get_add.R index 5390e9b..ee6ff8e 100644 --- a/R/get_add.R +++ b/R/get_add.R @@ -436,6 +436,7 @@ gen_pt_add <- function(x, pt, sem_out, from = NA) { model = pt, add = x_free_str, do.fit = do_fit, + baseline = FALSE, optim.force.converged = TRUE, control = list(max.iter = 1) ) @@ -455,6 +456,7 @@ gen_pt_add <- function(x, pt, sem_out, from = NA) { object = sem_out, model = pt, do.fit = do_fit, + baseline = FALSE, optim.force.converged = TRUE, control = list(max.iter = 1) ) From 26da895e1377436ba7f43b855c7beb698920ecc5 Mon Sep 17 00:00:00 2001 From: Shu Fai Cheung Date: Wed, 3 Jun 2026 21:52:19 +0800 Subject: [PATCH 2/5] Disable more options tests and checks passed. --- R/get_add.R | 16 ++++++++++++++++ R/get_drop.R | 5 +++++ 2 files changed, 21 insertions(+) diff --git a/R/get_add.R b/R/get_add.R index ee6ff8e..2fe5ed7 100644 --- a/R/get_add.R +++ b/R/get_add.R @@ -437,6 +437,14 @@ gen_pt_add <- function(x, pt, sem_out, from = NA) { add = x_free_str, do.fit = do_fit, baseline = FALSE, + h1 = FALSE, + implied = FALSE, + check.vcov = FALSE, + check.start = FALSE, + check.sigma.pd = FALSE, + check.gradient = FALSE, + check.post = FALSE, + samplestats = do_fit, optim.force.converged = TRUE, control = list(max.iter = 1) ) @@ -457,6 +465,14 @@ gen_pt_add <- function(x, pt, sem_out, from = NA) { model = pt, do.fit = do_fit, baseline = FALSE, + h1 = FALSE, + implied = FALSE, + check.vcov = FALSE, + check.start = FALSE, + check.sigma.pd = FALSE, + check.gradient = FALSE, + check.post = FALSE, + samplestats = do_fit, optim.force.converged = TRUE, control = list(max.iter = 1) ) diff --git a/R/get_drop.R b/R/get_drop.R index 85386f2..b9c163b 100644 --- a/R/get_drop.R +++ b/R/get_drop.R @@ -245,6 +245,11 @@ gen_pt_drop <- function(x, pt, to, source_df = NA, sem_out) { check.start = FALSE, check.post = FALSE, check.vcov = FALSE, + h1 = FALSE, + implied = FALSE, + check.sigma.pd = FALSE, + check.gradient = FALSE, + samplestats = do_fit, control = list(max.iter = 1)) ) pt_update <- lavaan::parameterTable(sem_out_update) From f2f9a13e982fdbb9469373c292dfab6dfeb0410f Mon Sep 17 00:00:00 2001 From: Shu Fai Cheung Date: Wed, 3 Jun 2026 21:52:45 +0800 Subject: [PATCH 3/5] modelbpp.do_fit default to FALSE tests and checks passed. --- R/get_add.R | 1 - R/get_drop.R | 1 - 2 files changed, 2 deletions(-) diff --git a/R/get_add.R b/R/get_add.R index 2fe5ed7..76467b6 100644 --- a/R/get_add.R +++ b/R/get_add.R @@ -426,7 +426,6 @@ gen_pt_add <- function(x, pt, sem_out, from = NA) { x_constr_out <- NULL } # Add free parameters - do_fit <- getOption("modelbpp.do_fit", TRUE) if (length(x_free) > 0) { x_free_str <- par_names(pars_list = x_free) p_to_add <- sapply(x_free, paste0, collapse = "") diff --git a/R/get_drop.R b/R/get_drop.R index b9c163b..871700a 100644 --- a/R/get_drop.R +++ b/R/get_drop.R @@ -232,7 +232,6 @@ gen_pt_drop <- function(x, pt, to, source_df = NA, sem_out) { p_to_drop_out <- lapply(x, function(x) { c(lhs = pt[x, "lhs"], op = pt[x, "op"], rhs = pt[x, "rhs"]) }) - do_fit <- getOption("modelbpp.do_fit", TRUE) suppressWarnings(sem_out_update <- auto_ram( FUN = lavaan::update, object = sem_out, From 9c89a1f6bfba824e7dea31284f5fa26d69bac19e Mon Sep 17 00:00:00 2001 From: Shu Fai Cheung Date: Wed, 3 Jun 2026 21:53:30 +0800 Subject: [PATCH 4/5] Add the lines forgot to add in the previous commit --- R/get_add.R | 1 + R/get_drop.R | 1 + 2 files changed, 2 insertions(+) diff --git a/R/get_add.R b/R/get_add.R index 76467b6..c176e32 100644 --- a/R/get_add.R +++ b/R/get_add.R @@ -426,6 +426,7 @@ gen_pt_add <- function(x, pt, sem_out, from = NA) { x_constr_out <- NULL } # Add free parameters + do_fit <- getOption("modelbpp.do_fit", FALSE) if (length(x_free) > 0) { x_free_str <- par_names(pars_list = x_free) p_to_add <- sapply(x_free, paste0, collapse = "") diff --git a/R/get_drop.R b/R/get_drop.R index 871700a..cd6738e 100644 --- a/R/get_drop.R +++ b/R/get_drop.R @@ -232,6 +232,7 @@ gen_pt_drop <- function(x, pt, to, source_df = NA, sem_out) { p_to_drop_out <- lapply(x, function(x) { c(lhs = pt[x, "lhs"], op = pt[x, "op"], rhs = pt[x, "rhs"]) }) + do_fit <- getOption("modelbpp.do_fit", FALSE) suppressWarnings(sem_out_update <- auto_ram( FUN = lavaan::update, object = sem_out, From 1f77bdee2dc6cd572939957bc89c627e4ebfd2a4 Mon Sep 17 00:00:00 2001 From: Shu Fai Cheung Date: Wed, 3 Jun 2026 21:58:28 +0800 Subject: [PATCH 5/5] Bump the version to 0.3.0.3 --- DESCRIPTION | 2 +- NEWS.md | 12 ++++++++---- README.md | 2 +- 3 files changed, 10 insertions(+), 6 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ba88ef1..9979cd7 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: modelbpp Title: Model BIC Posterior Probability -Version: 0.3.0.2 +Version: 0.3.0.3 Authors@R: c(person(given = "Shu Fai", family = "Cheung", diff --git a/NEWS.md b/NEWS.md index b3963a8..2a36e04 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# modelbpp 0.3.0.2 +# modelbpp 0.3.0.3 ## Miscellaneous @@ -8,13 +8,17 @@ (0.3.0.1) - If the option `modelbpp.do_fit` is set - to `FALSE`, a parameter table will not + to `FALSE` or not set, a parameter table will not be fitted to get the model *df*, leading to faster search. If this options is - set to `TRUE` or is not set, then the + set to `TRUE`, then the parameter table will be fitted as in 0.3.0.2 or older version. - (0.3.0.2) + (0.3.0.2, 0.3.0.3) + +- Disabled more options to make the search + faster. + (0.3.0.3) - Depends on R 4.1.0 or later now. (0.3.0.2) diff --git a/README.md b/README.md index b19fb4e..0969214 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ # modelbpp: Model BIC Posterior Probability -(Version 0.3.0.2 updated on 2026-05-30, [release history](https://sfcheung.github.io/modelbpp/news/index.html)) +(Version 0.3.0.3 updated on 2026-06-03, [release history](https://sfcheung.github.io/modelbpp/news/index.html)) This package is for assessing model uncertainty in structural equation modeling (SEM) by the BIC posterior