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Merged
sfcheung merged 1 commit into from
Jun 3, 2026
Merged

Add the option to compute df internally #83

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8 changes: 8 additions & 0 deletions R/fit_many.R
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Original file line number Diff line number Diff line change
Expand Up @@ -350,6 +350,7 @@ fit_many <- function(model_list,
MoreArgs = list(fit_i = fit_i),
SIMPLIFY = TRUE)
if (is.null(original)) {
# Can use "fitMeasures" because sem_out is always a fitted object
sem_out_df <- as.numeric(lavaan::fitMeasures(sem_out, "df"))
# change_list <- sapply(fit_list,
# function(x) sem_out_df - as.numeric(lavaan::fitMeasures(x, fit.measures = "df")))
Expand Down Expand Up @@ -389,6 +390,7 @@ lavaan_to_sem_outs <- function(x,
} else {
if (original %in% names(x)) {
i_original <- match(original, names(x))
# Can use "fitMeasures" because sem_out is always a fitted object
change_list <- sapply(x,
function(x) as.numeric(lavaan::fitMeasures(x, fit.measures = "df")))
df_original <- change_list[i_original]
Expand All @@ -415,6 +417,7 @@ lavaan_to_sem_outs <- function(x,
fit_many_get_df <- function(fit,
model,
fit_i) {
# Can try "fitMeasures" because sem_out is always a fitted object
out <- tryCatch(lavaan::fitMeasures(fit, fit.measures = "df"),
error = function(e) e)
if (!inherits(out, "error")) {
Expand All @@ -426,6 +429,11 @@ fit_many_get_df <- function(fit,
warn = FALSE)))
out <- tryCatch(lavaan::fitMeasures(fit1, fit.measures = "df"),
error = function(e) e)
if (!inherits(out, "error")) {
return(as.numeric(out))
}
# Last resort
out <- lavaan_df(lavaan::parameterTable(fit))
if (!inherits(out, "error")) {
return(as.numeric(out))
}
Expand Down
56 changes: 39 additions & 17 deletions R/get_add.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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", TRUE)
if (length(x_free) > 0) {
x_free_str <- par_names(pars_list = x_free)
p_to_add <- sapply(x_free, paste0, collapse = "")
Expand All @@ -434,40 +435,37 @@ gen_pt_add <- function(x, pt, sem_out, from = NA) {
object = sem_out,
model = pt,
add = x_free_str,
do.fit = TRUE,
do.fit = do_fit,
optim.force.converged = TRUE,
control = list(max.iter = 1)
)
# sem_out_update <- lavaan::update(sem_out,
# pt,
# add = x_free_str,
# do.fit = TRUE,
# optim.force.converged = TRUE,
# control = list(max.iter = 1))
pt_update <- lavaan::parameterTable(sem_out_update)
pt_update$se <- NA
pt_update_df <- unname(lavaan::fitMeasures(sem_out_update,
fit.measures = "df"))
if (do_fit) {
pt_update_df <- unname(lavaan::fitMeasures(sem_out_update,
fit.measures = "df"))
} else {
pt_update_df <- lavaan_df(sem_out_update)
}
} else {
x_free_str <- NULL
p_to_add <- NULL
sem_out_update <- auto_ram(
FUN = lavaan::update,
object = sem_out,
model = pt,
do.fit = TRUE,
do.fit = do_fit,
optim.force.converged = TRUE,
control = list(max.iter = 1)
)
# sem_out_update <- lavaan::update(sem_out,
# pt,
# do.fit = TRUE,
# optim.force.converged = TRUE,
# control = list(max.iter = 1))
pt_update <- lavaan::parameterTable(sem_out_update)
pt_update$se <- NA
pt_update_df <- unname(lavaan::fitMeasures(sem_out_update,
fit.measures = "df"))
if (do_fit) {
pt_update_df <- unname(lavaan::fitMeasures(sem_out_update,
fit.measures = "df"))
} else {
pt_update_df <- lavaan_df(sem_out_update)
}
}
attr(pt_update, "parameters_added") <- p_to_add
attr(pt_update, "parameters_added_str") <- x_free_str
Expand All @@ -477,8 +475,32 @@ gen_pt_add <- function(x, pt, sem_out, from = NA) {
attr(pt_update, "constraints_released") <- x_constr_pars
attr(pt_update, "constraints_released_list") <- x_constr_out
attr(pt_update, "from") <- from
# Can use "fitMeasures" because sem_out is always a fitted object
attr(pt_update, "df_expected") <- unname(lavaan::fitMeasures(sem_out, "df")) -
length(x)
attr(pt_update, "df_actual") <- pt_update_df
pt_update
}

#' @noRd
lavaan_df <- function(
object
) {
# Adapted from lavaan:::lav_model_test()
pt <- lavaan::parameterTable(object)
df <- lavaan::lav_partable_df(pt)
slotModel <- object@Model
if (!slotModel@cin.simple.only &&
(nrow(slotModel@con.jac) > 0L)) {
ceq_idx <- attr(slotModel@con.jac, "ceq.idx")
if (length(ceq_idx) > 0L) {
neq <- qr(slotModel@con.jac[ceq_idx, , drop = FALSE])$rank
df <- df + neq
}
} else if (slotModel@ceq.simple.only) {
ndat <- lavaan::lav_partable_ndat(pt)
npar <- sum(pt$free > 0)
df <- ndat - npar
}
df
}
24 changes: 10 additions & 14 deletions R/get_drop.R
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Original file line number Diff line number Diff line change
Expand Up @@ -176,6 +176,7 @@ get_drop <- function(sem_out,
}
)
sets_to_gen <- unlist(sets_to_gen, recursive = FALSE)
# Can use "fitMeasures" because sem_out is always a fitted object
df0 <- lavaan::fitMeasures(sem_out, "df")
if (progress) {
cat("\nGenerate", length(sets_to_gen), "more restrictive model(s):\n")
Expand Down Expand Up @@ -231,11 +232,12 @@ 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,
model = pt,
do.fit = TRUE,
do.fit = do_fit,
optim.force.converged = TRUE,
warn = FALSE,
se = "none",
Expand All @@ -245,25 +247,19 @@ gen_pt_drop <- function(x, pt, to, source_df = NA, sem_out) {
check.vcov = FALSE,
control = list(max.iter = 1))
)
# suppressWarnings(sem_out_update <- lavaan::update(sem_out,
# pt,
# do.fit = TRUE,
# optim.force.converged = TRUE,
# warn = FALSE,
# se = "none",
# baseline = FALSE,
# check.start = FALSE,
# check.post = FALSE,
# check.vcov = FALSE,
# control = list(max.iter = 1)))
pt_update <- lavaan::parameterTable(sem_out_update)
if (do_fit) {
pt_update_df <- unname(lavaan::fitMeasures(sem_out_update,
fit.measures = "df"))
} else {
pt_update_df <- lavaan_df(sem_out_update)
}
attr(pt_update, "parameters_dropped") <- p_to_drop
attr(pt_update, "parameters_dropped_list") <- p_to_drop_out
attr(pt_update, "ids_dropped") <- x
attr(pt_update, "to") <- to
attr(pt_update, "df_expected") <- unname(source_df) +
length(x)
attr(pt_update, "df_actual") <- unname(lavaan::fitMeasures(sem_out_update,
fit.measures = "df"))
attr(pt_update, "df_actual") <- pt_update_df
pt_update
}
2 changes: 2 additions & 0 deletions R/helpers3_for_model_graph.R
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Expand Up @@ -102,6 +102,7 @@ models_network2 <- function(object,
if (!all(converged)) {
stop("One or more models did not converge.")
}
# Can use "fitMeasures" because sem_out is always a fitted object
if (inherits(object, "model_set")) {
if (!is.null(object$model_df)) {
model_dfs <- object$model_df
Expand Down Expand Up @@ -189,6 +190,7 @@ x_net_y <- function(x,
chk <- check_x_net_y(x, y,
ignore_fixed_x = FALSE)
}
# Can use "fitMeasures" because sem_out is always a fitted object
if (is.null(x_df)) {
x_df <- lavaan::fitMeasures(x, fit.measures = "df")
}
Expand Down
1 change: 1 addition & 0 deletions R/helpers4_for_model_graph.R
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Expand Up @@ -10,6 +10,7 @@ layer_by_df <- function(g,
if (!all(model_set_out$converged)) {
stop("Not all models converged.")
} else {
# Can use "fitMeasures" because sem_out is always a fitted object
model_dfs <- sapply(model_set_out$fit,
lavaan::fitMeasures,
fit.measures = "df")
Expand Down
1 change: 1 addition & 0 deletions R/print.model_set.R
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Original file line number Diff line number Diff line change
Expand Up @@ -140,6 +140,7 @@ print.model_set <- function(x,
if (!is.null(x$model_df)) {
model_df_tmp <- x$model_df
} else {
# Can use "fitMeasures" because sem_out is always a fitted object
model_df_tmp <- sapply(x$fit, lavaan::fitMeasures,
fit.measures = "df")
}
Expand Down
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