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strengejackestrengejacke
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Merge branch 'main' into bf-docs-and-methods
2 parents b22cc52 + 4e25713 commit d8df31f

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-37
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12 files changed

+49
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lines changed

‎.github/workflows/format-suggest.yaml‎

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Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@ jobs:
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pull-requests: write
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steps:
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- uses: actions/checkout@v5
31+
- uses: actions/checkout@v6
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with:
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ref: ${{ github.event.pull_request.head.sha }}
3434

‎DESCRIPTION‎

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Original file line numberDiff line numberDiff line change
@@ -66,8 +66,8 @@ Description: Provides utilities to describe posterior
6666
Depends:
6767
R (>= 3.6)
6868
Imports:
69-
insight (>= 1.4.2),
70-
datawizard (>= 1.2.0),
69+
insight (>= 1.4.3),
70+
datawizard (>= 1.3.0),
7171
graphics,
7272
methods,
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stats,

‎R/bci.R‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -102,7 +102,7 @@ bci.bamlss <- function(x,
102102
component = "all",
103103
verbose = TRUE,
104104
...) {
105-
d <- insight::get_parameters(x, component = component)
105+
d <- insight::get_parameters(x, component = component, verbose = verbose)
106106
dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = "bci")
107107
attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
108108
dat
@@ -111,7 +111,7 @@ bci.bamlss <- function(x,
111111

112112
#' @export
113113
bci.bcplm <- function(x, ci = 0.95, verbose = TRUE, ...) {
114-
d <- insight::get_parameters(x)
114+
d <- insight::get_parameters(x, verbose = verbose)
115115
dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = "bci")
116116
attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
117117
dat
@@ -169,7 +169,7 @@ bci.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
169169

170170
#' @export
171171
bci.emmGrid <- function(x, ci = 0.95, verbose = TRUE, ...) {
172-
xdf <- insight::get_parameters(x)
172+
xdf <- insight::get_parameters(x, verbose = verbose)
173173
dat <- bci(xdf, ci = ci, verbose = verbose, ...)
174174
dat <- .append_datagrid(dat, x, long = length(ci) > 1L)
175175
attr(dat, "object_name") <- insight::safe_deparse_symbol(substitute(x))
@@ -208,7 +208,8 @@ bci.stanreg <- function(x,
208208
x,
209209
effects = effects,
210210
component = component,
211-
parameters = parameters
211+
parameters = parameters,
212+
verbose = verbose
212213
),
213214
ci = ci,
214215
verbose = verbose,
@@ -249,7 +250,8 @@ bci.brmsfit <- function(x,
249250
x,
250251
effects = effects,
251252
component = component,
252-
parameters = parameters
253+
parameters = parameters,
254+
verbose = verbose
253255
),
254256
ci = ci,
255257
verbose = verbose,

‎R/ci.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -364,7 +364,7 @@ ci.bamlss <- function(x,
364364
verbose = TRUE,
365365
...) {
366366
ci(
367-
insight::get_parameters(x, component = component),
367+
insight::get_parameters(x, component = component, verbose = verbose),
368368
ci = ci,
369369
method = method,
370370
verbose = verbose,

‎R/equivalence_test.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -222,7 +222,7 @@ equivalence_test.rvar <- equivalence_test.draws
222222

223223
#' @export
224224
equivalence_test.emmGrid <- function(x, range = "default", ci = 0.95, verbose = TRUE, ...) {
225-
xdf <- insight::get_parameters(x)
225+
xdf <- insight::get_parameters(x, verbose = verbose)
226226
out <- equivalence_test(xdf, range = range, ci = ci, verbose = verbose, ...)
227227
out <- .append_datagrid(out, x)
228228
attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))

‎R/eti.R‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -124,7 +124,7 @@ eti.mcmc <- function(x, ci = 0.95, verbose = TRUE, ...) {
124124

125125
#' @export
126126
eti.bamlss <- function(x, ci = 0.95, component = "all", verbose = TRUE, ...) {
127-
d <- insight::get_parameters(x, component = component)
127+
d <- insight::get_parameters(x, component = component, verbose = verbose)
128128
dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = "eti")
129129
attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
130130
dat
@@ -133,7 +133,7 @@ eti.bamlss <- function(x, ci = 0.95, component = "all", verbose = TRUE, ...) {
133133

134134
#' @export
135135
eti.bcplm <- function(x, ci = 0.95, verbose = TRUE, ...) {
136-
d <- insight::get_parameters(x)
136+
d <- insight::get_parameters(x, verbose = verbose)
137137
dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = "eti")
138138
attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
139139
dat
@@ -191,7 +191,7 @@ eti.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
191191

192192
#' @export
193193
eti.emmGrid <- function(x, ci = 0.95, verbose = TRUE, ...) {
194-
xdf <- insight::get_parameters(x)
194+
xdf <- insight::get_parameters(x, verbose = verbose)
195195
dat <- eti(xdf, ci = ci, verbose = verbose, ...)
196196
dat <- .append_datagrid(dat, x, long = length(ci) > 1L)
197197
attr(dat, "object_name") <- insight::safe_deparse_symbol(substitute(x))
@@ -232,7 +232,8 @@ eti.stanreg <- function(x,
232232
x,
233233
effects = effects,
234234
component = component,
235-
parameters = parameters
235+
parameters = parameters,
236+
verbose = verbose
236237
),
237238
ci = ci,
238239
verbose = verbose,
@@ -272,7 +273,8 @@ eti.brmsfit <- function(x,
272273
x,
273274
effects = effects,
274275
component = component,
275-
parameters = parameters
276+
parameters = parameters,
277+
verbose = verbose
276278
),
277279
ci = ci,
278280
verbose = verbose,

‎R/hdi.R‎

Lines changed: 7 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -240,7 +240,7 @@ hdi.bamlss <- function(x,
240240
verbose = TRUE,
241241
...) {
242242
ci_fun <- .check_ci_fun(list(...))
243-
d <- insight::get_parameters(x, component = component)
243+
d <- insight::get_parameters(x, component = component, verbose = verbose)
244244
dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = ci_fun)
245245
dat <- .add_clean_parameters_attribute(dat, x)
246246
attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
@@ -261,7 +261,7 @@ hdi.mcmc <- function(x, ci = 0.95, verbose = TRUE, ...) {
261261
#' @export
262262
hdi.bcplm <- function(x, ci = 0.95, verbose = TRUE, ...) {
263263
ci_fun <- .check_ci_fun(list(...))
264-
d <- insight::get_parameters(x)
264+
d <- insight::get_parameters(x, verbose = verbose)
265265
dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = ci_fun)
266266
attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
267267
dat
@@ -321,7 +321,7 @@ hdi.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
321321

322322
#' @export
323323
hdi.emmGrid <- function(x, ci = 0.95, verbose = TRUE, ...) {
324-
xdf <- insight::get_parameters(x)
324+
xdf <- insight::get_parameters(x, verbose = verbose)
325325
out <- hdi(xdf, ci = ci, verbose = verbose, ...)
326326
out <- .append_datagrid(out, x, long = length(ci) > 1L)
327327
attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
@@ -363,7 +363,8 @@ hdi.stanreg <- function(x,
363363
x,
364364
effects = effects,
365365
component = component,
366-
parameters = parameters
366+
parameters = parameters,
367+
verbose = verbose
367368
),
368369
ci = ci,
369370
verbose = verbose,
@@ -406,7 +407,8 @@ hdi.brmsfit <- function(x,
406407
x,
407408
effects = effects,
408409
component = component,
409-
parameters = parameters
410+
parameters = parameters,
411+
verbose = verbose
410412
),
411413
ci = ci,
412414
verbose = verbose,

‎R/p_rope.R‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -75,7 +75,7 @@ p_rope.rvar <- p_rope.draws
7575

7676
#' @export
7777
p_rope.emmGrid <- function(x, range = "default", verbose = TRUE, ...) {
78-
xdf <- insight::get_parameters(x)
78+
xdf <- insight::get_parameters(x, verbose = verbose)
7979
out <- p_rope(xdf, range = range, verbose = verbose)
8080
out <- .append_datagrid(out, x)
8181
attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))

‎R/rope.R‎

Lines changed: 9 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -344,7 +344,7 @@ rope.emmGrid <- function(x,
344344
complement = FALSE,
345345
verbose = TRUE,
346346
...) {
347-
xdf <- insight::get_parameters(x)
347+
xdf <- insight::get_parameters(x, verbose = verbose)
348348
dat <- rope(
349349
xdf,
350350
range = range,
@@ -405,7 +405,7 @@ rope.BFBayesFactor <- function(x,
405405
range <- rope_range(x, verbose = verbose)
406406
}
407407
out <- rope(
408-
insight::get_parameters(x),
408+
insight::get_parameters(x, verbose = verbose),
409409
range = range,
410410
ci = ci,
411411
ci_method = ci_method,
@@ -476,7 +476,7 @@ rope.bcplm <- function(x,
476476
verbose = TRUE,
477477
...) {
478478
out <- rope(
479-
insight::get_parameters(x),
479+
insight::get_parameters(x, verbose = verbose),
480480
range = range,
481481
ci = ci,
482482
ci_method = ci_method,
@@ -528,7 +528,8 @@ rope.stanreg <- function(x,
528528
x,
529529
effects = effects,
530530
component = component,
531-
parameters = parameters
531+
parameters = parameters,
532+
verbose = verbose
532533
),
533534
range = range,
534535
ci = ci,
@@ -612,6 +613,7 @@ rope.brmsfit <- function(x,
612613
effects = effects,
613614
component = component,
614615
parameters = parameters,
616+
verbose = verbose,
615617
...
616618
),
617619
range = range[[dv_item]],
@@ -639,7 +641,7 @@ rope.brmsfit <- function(x,
639641
)
640642
} else {
641643
rope_data <- rope(
642-
insight::get_parameters(x, effects = effects, component = component, parameters = parameters),
644+
insight::get_parameters(x, effects = effects, component = component, parameters = parameters, verbose = verbose),
643645
range = range,
644646
ci = ci,
645647
ci_method = ci_method,
@@ -676,7 +678,7 @@ rope.sim.merMod <- function(x,
676678
}
677679

678680
rope_list <- lapply(c("fixed", "random"), function(.x) {
679-
parms <- insight::get_parameters(x, effects = .x, parameters = parameters)
681+
parms <- insight::get_parameters(x, effects = .x, parameters = parameters, verbose = verbose)
680682

681683
getropedata <- .prepare_rope_df(parms, range, ci, ci_method, complement, verbose)
682684
tmp <- getropedata$tmp
@@ -745,7 +747,7 @@ rope.sim <- function(x,
745747
insight::format_error("`range` should be 'default' or a vector of 2 numeric values (e.g., c(-0.1, 0.1)).")
746748
}
747749

748-
parms <- insight::get_parameters(x, parameters = parameters)
750+
parms <- insight::get_parameters(x, parameters = parameters, verbose = verbose)
749751
getropedata <- .prepare_rope_df(parms, range, ci, ci_method, complement, verbose)
750752

751753
dat <- getropedata$tmp

‎R/si.R‎

Lines changed: 7 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -181,10 +181,13 @@ si.predictions <- si.emmGrid
181181

182182

183183
#' @export
184-
si.stanfit <- si.stanreg
185-
186-
#' @export
187-
si.CmdStanFit <- si.stanreg
184+
si.stanfit <- function(posterior, prior = NULL, BF = 1, verbose = TRUE, effects = "fixed", ...) {
185+
out <- si(insight::get_parameters(posterior, effects = effects, verbose = verbose),
186+
prior = prior, BF = BF, verbose = verbose
187+
)
188+
attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(posterior))
189+
out
190+
}
188191

189192

190193
#' @rdname si

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