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Merged
osenan merged 45 commits into from
May 18, 2026
Merged

Unify picks feature branch: default parameters #1533

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8569fcf
fix: conf_values simplified as they are indirectly used
averissimo May 14, 2026
3ea7db6
fix: remove arg_name
averissimo May 14, 2026
c1de7d4
fix: remove assertion and adds migration
averissimo May 14, 2026
d22c24a
docs: update
averissimo May 14, 2026
f46da8e
revert some of the parameters
averissimo May 14, 2026
8979231
Apply suggestion from @averissimo
averissimo May 15, 2026
3740ad7
pr: feedback from @osenan
averissimo May 15, 2026
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Apply suggestion from @osenan
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e592e50
pr: feedback from @osenan
averissimo May 15, 2026
7592e8f
Merge branch '279-interactive_variables@main' into default_values@279…
averissimo May 15, 2026
a968f6f
pr: feedback from @osenan
averissimo May 15, 2026
4b23cc8
pr: feedback from @osenan
averissimo May 15, 2026
0075ecd
pr: feedback from @osenan
averissimo May 15, 2026
267084a
Merge remote-tracking branch 'origin/default_values@279-interactive_v…
averissimo May 15, 2026
9f01cfd
Merge branch '279-interactive_variables@main' into default_values2@27…
averissimo May 15, 2026
f6f4068
fix: revert default parameters in module
averissimo May 15, 2026
f1b67a4
fix: revert default parameters in module
averissimo May 15, 2026
8eb76bd
fix: revert default parameters in module
averissimo May 15, 2026
9d2ce61
fix: revert default parameters in module
averissimo May 15, 2026
e2c245a
fix: revert default parameters in module
averissimo May 15, 2026
23c709a
fix: revert default parameters in module
averissimo May 15, 2026
df3ecda
fix: revert default parameters in module
averissimo May 15, 2026
690fc28
fix: revert default parameters in module
averissimo May 15, 2026
7735fa5
fix: revert default parameters in module
averissimo May 15, 2026
5cd0633
fix: revert default parameters in module
averissimo May 15, 2026
aa6276c
fix: revert default parameters in module
averissimo May 15, 2026
14ab2b8
fix: revert default parameters in module
averissimo May 15, 2026
0a7e41c
fix: revert default parameters in module
averissimo May 15, 2026
3f7d25d
fix: revert default parameters in module
averissimo May 15, 2026
8aff817
fix: revert default parameters in module
averissimo May 15, 2026
4418b84
fix: revert default parameters in module
averissimo May 15, 2026
d089218
change tte to single method without dispatch
averissimo May 15, 2026
318d1f9
Merge branch '279-interactive_variables@main' into default_values2@27…
averissimo May 15, 2026
bf56ad1
docs: update
averissimo May 15, 2026
db7907c
fix: adds missing prefixes
averissimo May 15, 2026
79be8b0
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
github-actions[bot] May 15, 2026
3dc5e0f
Merge branch '279-interactive_variables@main' into default_values2@27…
averissimo May 15, 2026
95aa810
fix: tm_g_ci
averissimo May 15, 2026
4d8838f
fix: linter
averissimo May 15, 2026
4ace382
fix: styler
averissimo May 15, 2026
bafc60e
fix: tests
averissimo May 15, 2026
c45c3f2
[skip roxygen] [skip vbump] Roxygen Man Pages Auto Update
github-actions[bot] May 15, 2026
8992b85
fix: values with multiple = FALSE
averissimo May 15, 2026
3e3863c
docs: update
averissimo May 15, 2026
96aeaa5
fix: fix R cmd check
osenan May 18, 2026
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4 changes: 0 additions & 4 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,6 @@ S3method(tm_g_barchart_simple,picks)
S3method(tm_g_ci,default)
S3method(tm_g_ci,picks)
S3method(tm_g_ci,variables)
S3method(tm_t_tte,default)
S3method(tm_t_tte,list)
S3method(tm_t_tte,picks)
S3method(tm_t_tte,variables)
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export(add_expr)
export(as_num)
export(bracket_expr)
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66 changes: 9 additions & 57 deletions R/tm_g_ci_picks.R
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Expand Up @@ -2,44 +2,12 @@
#' (use [`tm_g_ci.variables()`] to pass [`teal.picks::variables()`] objects; they are wrapped into \code{picks}).
#' @export
tm_g_ci.picks <- function(label,
x_var = teal.picks::picks(
teal.picks::datasets("ADSL"),
teal.picks::variables(
choices = c("ARMCD", "BMRKR2"),
selected = "ARMCD",
multiple = FALSE
)
),
y_var = teal.picks::picks(
teal.picks::datasets("ADLB"),
teal.picks::variables(
choices = c("AVAL", "CHG", "CHG2"),
selected = "AVAL",
multiple = FALSE
)
),
color = teal.picks::picks(
teal.picks::datasets("ADSL"),
teal.picks::variables(
choices = c("SEX", "STRATA1", "STRATA2"),
selected = "STRATA1",
multiple = FALSE
)
),
x_var,
y_var,
color,

@m7pr m7pr May 15, 2026

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At some point I though that for S3 dispatches for teal.picks we will just provide teal.picks default.
No idea if this is a good approach or if it's even possible to guess proper defaults, so maybe we can revert back to empty values

@averissimo averissimo May 15, 2026

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I guess picks should the default then, I'll make the change there

@m7pr m7pr May 15, 2026

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thanks!

@averissimo averissimo May 15, 2026

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Done, please review @m7pr

@averissimo averissimo May 15, 2026

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Note: can you update the documentation field on event_desc_var I'm not in the context on why wasreferencing an internal implementation

stat = c("mean", "median"),
paramcd = teal.picks::values(
choices = c("ALT", "CRP", "IGA"),
selected = "ALT",
multiple = FALSE
),
avisit = teal.picks::values(
choices = c(
"SCREENING", "BASELINE", "WEEK 1 DAY 8", "WEEK 2 DAY 15",
"WEEK 3 DAY 22", "WEEK 4 DAY 29", "WEEK 5 DAY 36"
),
selected = "SCREENING",
multiple = FALSE
),
paramcd,
avisit,
conf_level = teal.picks::values(c(0.95, 0.9, 0.8), 0.95),
plot_height = c(700L, 200L, 2000L),
plot_width = NULL,
Expand Down Expand Up @@ -105,27 +73,11 @@
#' @describeIn tm_g_ci teal.picks encodings via \code{variables} (recommended entry point).
#' @export
tm_g_ci.variables <- function(label,
x_var = teal.picks::variables(
choices = c("ARMCD", "BMRKR2"),
selected = "ARMCD",
multiple = FALSE
),
y_var = teal.picks::variables(
choices = c("AVAL", "CHG", "CHG2"),
selected = "AVAL",
multiple = FALSE
),
color = teal.picks::variables(
choices = c("SEX", "STRATA1", "STRATA2"),
selected = "STRATA1",
multiple = FALSE
),
x_var,
y_var,
color,
stat = c("mean", "median"),
paramcd = teal.picks::values(
choices = c("ALT", "CRP", "IGA"),
selected = "ALT",
multiple = FALSE
),
paramcd = NULL,
avisit = teal.picks::values(
choices = c(
"SCREENING", "BASELINE", "WEEK 1 DAY 8", "WEEK 2 DAY 15",
Expand Down Expand Up @@ -162,7 +114,7 @@
}

#' @keywords internal
ui_g_ci.picks <- function(id,

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file=R/tm_g_ci_picks.R,line=117,col=1,[object_name_linter] Variable and function name style should match snake_case, symbols, ANL, ADaM or column_names.
x_var_picks,
y_var_picks,
paramcd_picks,
Expand Down Expand Up @@ -220,7 +172,7 @@
}

#' @keywords internal
srv_g_ci.picks <- function(id,

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file=R/tm_g_ci_picks.R,line=175,col=1,[object_name_linter] Variable and function name style should match snake_case, symbols, ANL, ADaM or column_names.
data,
x_dataname,
y_dataname,
Expand Down
2 changes: 1 addition & 1 deletion R/tm_g_forest_rsp.R
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Expand Up @@ -343,7 +343,7 @@ tm_g_forest_rsp <- function(label,
arm_var,
arm_ref_comp = NULL,
paramcd,
aval_var = teal.picks::variables("AVALC", fixed = TRUE),
aval_var = teal.picks::variables("AVALC", "AVALC", fixed = TRUE),
subgroup_var,
strata_var,
stats = c("n_tot", "n", "n_rsp", "prop", "or", "ci"),
Expand Down
6 changes: 3 additions & 3 deletions R/tm_g_forest_tte.R
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Expand Up @@ -326,12 +326,12 @@ tm_g_forest_tte <- function(label,
subgroup_var,
paramcd,
strata_var,
aval_var = teal.picks::variables("AVAL", fixed = TRUE),
cnsr_var = teal.picks::variables("CNSR", fixed = TRUE),
aval_var = teal.picks::variables("AVAL", "AVAL", fixed = TRUE),
cnsr_var = teal.picks::variables("CNSR", "CNSR", fixed = TRUE),
stats = c("n_tot_events", "n_events", "median", "hr", "ci"),
riskdiff = NULL,
conf_level = teal.picks::values(c(0.95, 0.9, 0.8), 0.95),
time_unit_var = teal.picks::variables("AVALU", fixed = TRUE),
time_unit_var = teal.picks::variables("AVALU", "AVALU", fixed = TRUE),
fixed_symbol_size = TRUE,
plot_height = c(500L, 200L, 2000L),
plot_width = c(1500L, 800L, 3000L),
Expand Down
10 changes: 5 additions & 5 deletions R/tm_g_ipp.R
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Expand Up @@ -265,11 +265,11 @@ tm_g_ipp <- function(label,
parentname = "ADSL",
arm_var,
paramcd,
id_var = teal.picks::variables("USUBJID", fixed = TRUE),
visit_var = teal.picks::variables("AVISIT", fixed = TRUE),
aval_var = teal.picks::variables("AVAL", fixed = TRUE),
avalu_var = teal.picks::variables("AVALU", fixed = TRUE),
baseline_var = teal.picks::variables("BASE", fixed = TRUE),
id_var = teal.picks::variables("USUBJID", "USUBJID", fixed = TRUE),
visit_var = teal.picks::variables("AVISIT", "AVISIT", fixed = TRUE),
aval_var = teal.picks::variables("AVAL", "AVAL", fixed = TRUE),
avalu_var = teal.picks::variables("AVALU", "AVALU", fixed = TRUE),
baseline_var = teal.picks::variables("BASE", "BASE", fixed = TRUE),
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add_baseline_hline = FALSE,
separate_by_obs = FALSE,
suppress_legend = FALSE,
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12 changes: 5 additions & 7 deletions R/tm_g_lineplot.R
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Expand Up @@ -299,18 +299,16 @@ tm_g_lineplot <- function(label,
strata = lifecycle::deprecated(),
group_var = teal.picks::variables(
choices = c("ARM", "ARMCD", "ACTARMCD"),
selected = "ARM",
multiple = FALSE
selected = "ARM"
),
x = teal.picks::variables("AVISIT", fixed = TRUE),
x = teal.picks::variables("AVISIT", "AVISIT", fixed = TRUE),
y = teal.picks::variables(
choices = c("AVAL", "BASE", "CHG", "PCHG"),
selected = "AVAL",
multiple = FALSE
selected = "AVAL"
),
y_unit = teal.picks::variables("AVALU", fixed = TRUE),
y_unit = teal.picks::variables("AVALU", "AVALU", fixed = TRUE),
paramcd = teal.picks::picks(
teal.picks::variables("PARAMCD", fixed = TRUE),
teal.picks::variables("PARAMCD", "PARAMCD", fixed = TRUE),
teal.picks::values(
choices = c("ALT", "CRP", "IGA"),
selected = "ALT",
Expand Down
17 changes: 8 additions & 9 deletions R/tm_t_abnormality.R
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Expand Up @@ -361,10 +361,10 @@ tm_t_abnormality <- function(label,
by_vars,
grade,
abnormal = list(low = c("LOW", "LOW LOW"), high = c("HIGH", "HIGH HIGH")),
id_var = teal.picks::variables(choices = "USUBJID", fixed = TRUE),
baseline_var = teal.picks::variables(choices = "BNRIND", fixed = TRUE),
treatment_flag_var = teal.picks::variables(choices = "ONTRTFL", fixed = TRUE),
treatment_flag = teal.picks::values("Y", "Y", multiple = TRUE),
id_var = teal.picks::variables("USUBJID", "USUBJID", fixed = TRUE),
baseline_var = teal.picks::variables("BNRIND", "BNRIND", fixed = TRUE),
treatment_flag_var = teal.picks::variables("ONTRTFL", "ONTRTFL", fixed = TRUE),
treatment_flag = teal.picks::values("Y", "Y", fixed = TRUE),
add_total = TRUE,
total_label = default_total_label(),
exclude_base_abn = FALSE,
Expand All @@ -376,13 +376,15 @@ tm_t_abnormality <- function(label,
transformators = list(),
decorators = list()) {
message("Initializing tm_t_abnormality")

arm_var <- migrate_choices_selected_to_variables(arm_var)
by_vars <- migrate_choices_selected_to_variables(by_vars)
by_vars <- migrate_choices_selected_to_variables(by_vars, multiple = TRUE)
grade <- migrate_choices_selected_to_variables(grade)
id_var <- migrate_choices_selected_to_variables(id_var)
baseline_var <- migrate_choices_selected_to_variables(baseline_var)
treatment_flag_var <- migrate_choices_selected_to_variables(treatment_flag_var)
treatment_flag <- migrate_choices_selected_to_values(treatment_flag)
treatment_flag <- migrate_choices_selected_to_values(treatment_flag, multiple = TRUE)

checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
Expand All @@ -408,9 +410,6 @@ tm_t_abnormality <- function(label,
treatment_flag
)

checkmate::assert_true(teal.picks::is_pick_multiple(by_vars$variables))
checkmate::assert_true(teal.picks::is_pick_multiple(treatment_flag_var$values))
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args <- as.list(environment())

module(
Expand Down
15 changes: 8 additions & 7 deletions R/tm_t_abnormality_by_worst_grade.R
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Expand Up @@ -333,15 +333,16 @@ tm_t_abnormality_by_worst_grade <- function(label, # nolint: object_length.
dataname,
parentname = "ADSL",
arm_var,
id_var = teal.picks::variables(choices = "USUBJID", fixed = TRUE),
id_var = teal.picks::variables("USUBJID", "USUBJID", fixed = TRUE),
paramcd,
atoxgr_var = teal.picks::variables(choices = "ATOXGR", fixed = TRUE),
worst_high_flag_var = teal.picks::variables("WGRHIFL", fixed = TRUE),
worst_low_flag_var = teal.picks::variables("WGRLOFL", fixed = TRUE),
worst_flag_indicator = teal.picks::values(
c("Y", "N", ""), "Y",
multiple = FALSE
atoxgr_var = teal.picks::variables("ATOXGR", "ATOXGR", fixed = TRUE),
worst_high_flag_var = teal.picks::variables(
"WGRHIFL", "WGRHIFL", fixed = TRUE
),
worst_low_flag_var = teal.picks::variables(
"WGRLOFL", "WGRLOFL", fixed = TRUE
),
worst_flag_indicator = teal.picks::values("Y", "Y", fixed = FALSE),
add_total = TRUE,
total_label = default_total_label(),
drop_arm_levels = TRUE,
Expand Down
4 changes: 2 additions & 2 deletions R/tm_t_coxreg.R
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Expand Up @@ -545,8 +545,8 @@ tm_t_coxreg <- function(label,
paramcd,
cov_var,
strata_var,
aval_var = variables(choices = "AVAL", fixed = TRUE),
cnsr_var = variables(choices = "CNSR", fixed = TRUE),
aval_var = variables(choices = "AVAL", "AVAL", fixed = TRUE),
cnsr_var = variables(choices = "CNSR", "CNSR", fixed = TRUE),
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Outdated
multivariate = TRUE,
na_level = tern::default_na_str(),
conf_level = teal.picks::values(c(0.95, 0.9, 0.8), 0.95),
Expand Down
4 changes: 2 additions & 2 deletions R/tm_t_events_patyear.R
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Expand Up @@ -310,8 +310,8 @@ tm_t_events_patyear <- function(label,
arm_var,
events_var,
paramcd,
aval_var = variables(choices = "AVAL", fixed = TRUE),
avalu_var = variables(choices = "AVALU", fixed = TRUE),
aval_var = variables("AVAL", "AVAL", fixed = TRUE),
avalu_var = variables("AVALU", "AVALU", fixed = TRUE),
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Outdated
add_total = TRUE,
total_label = default_total_label(),
na_level = tern::default_na_str(),
Expand Down
10 changes: 6 additions & 4 deletions R/tm_t_events_summary.R
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Expand Up @@ -640,10 +640,10 @@ tm_t_events_summary <- function(label,
arm_var,
flag_var_anl = NULL,
flag_var_aesi = NULL,
dthfl_var = variables(choices = "DTHFL", fixed = TRUE),
dcsreas_var = variables(choices = "DCSREAS", fixed = TRUE),
llt = variables(choices = "AEDECOD", fixed = TRUE),
aeseq_var = variables(choices = "AESEQ", fixed = TRUE),
dthfl_var = teal.picks::variables("DTHFL", "DTHFL", fixed = TRUE),
dcsreas_var = teal.picks::variables("DCSREAS", "DCSREAS", fixed = TRUE),
llt = teal.picks::variables("AEDECOD", "AEDECOD", fixed = TRUE),
aeseq_var = teal.picks::variables("AESEQ", "AESEQ", fixed = TRUE),
add_total = TRUE,
total_label = default_total_label(),
na_level = tern::default_na_str(),
Expand All @@ -658,13 +658,15 @@ tm_t_events_summary <- function(label,
transformators = list(),
decorators = list()) {
message("Initializing tm_t_events_summary")

arm_var <- migrate_choices_selected_to_variables(arm_var)
flag_var_anl <- migrate_choices_selected_to_variables(flag_var_anl, null.ok = TRUE)
flag_var_aesi <- migrate_choices_selected_to_variables(flag_var_aesi, null.ok = TRUE)
dthfl_var <- migrate_choices_selected_to_variables(dthfl_var)
dcsreas_var <- migrate_choices_selected_to_variables(dcsreas_var)
llt <- migrate_choices_selected_to_variables(llt)
aeseq_var <- migrate_choices_selected_to_variables(aeseq_var)

checkmate::assert_string(label)
checkmate::assert_string(dataname)
checkmate::assert_string(parentname)
Expand Down
8 changes: 4 additions & 4 deletions R/tm_t_exposure.R
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Expand Up @@ -318,12 +318,12 @@ tm_t_exposure <- function(label,
parentname = "ADSL",
row_by_var,
col_by_var,
paramcd = variables(choices = "PARAMCD"),
paramcd = teal.picks::variables("PARAMCD"),
paramcd_label = "PARAM",
id_var = variables(choices = "USUBJID", fixed = TRUE),
id_var = teal.picks::variables("USUBJID", "USUBJID", fixed = TRUE),
parcat,
aval_var = variables(choices = "AVAL", fixed = TRUE),
avalu_var = variables(choices = "AVALU", fixed = TRUE),
aval_var = teal.picks::variables("AVAL", "AVAL", fixed = TRUE),
avalu_var = teal.picks::variables("AVALU", "AVALU", fixed = TRUE),
add_total,
total_label = default_total_label(),
add_total_row = TRUE,
Expand Down
2 changes: 1 addition & 1 deletion R/tm_t_logistic.R
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Expand Up @@ -296,7 +296,7 @@ tm_t_logistic <- function(label,
arm_ref_comp = NULL,
paramcd,
cov_var = NULL,
avalc_var = teal.picks::variables("AVALC", fixed = TRUE),
avalc_var = teal.picks::variables("AVALC", "AVALC", fixed = TRUE),
conf_level = teal.picks::values(c(0.95, 0.9, 0.8), 0.95),
pre_output = NULL,
post_output = NULL,
Expand Down
4 changes: 2 additions & 2 deletions R/tm_t_shift_by_arm.R
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Expand Up @@ -270,8 +270,8 @@ tm_t_shift_by_arm <- function(label,
aval_var,
base_var = lifecycle::deprecated(),
baseline_var,
treatment_flag_var = variables(choices = "ONTRTFL"),
treatment_flag = teal.picks::values(c("Y", "N", ""), "Y", multiple = FALSE),
treatment_flag_var = teal.picks::variables("ONTRTFL", "ONTRTFL"),
treatment_flag = teal.picks::values("Y", "Y", fixed = TRUE),
useNA = c("ifany", "no"), # nolint: object_name.
na_level = tern::default_na_str(),
add_total = FALSE,
Expand Down
6 changes: 3 additions & 3 deletions R/tm_t_shift_by_arm_by_worst.R
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Expand Up @@ -193,13 +193,13 @@
#' variable for analysis range indicator.
#' @param baseline_var ([teal.picks::variables()]; legacy `teal.transform` objects are deprecated but still accepted)\cr
#' variable for baseline reference range indicator.
#' @param worst_flag_var ([teal.picks::variables()]; legacy `teal.transform` objects are deprecated but still accepted)\cr

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file=R/tm_t_shift_by_arm_by_worst.R,line=196,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 122 characters.
#' variable for the worst post-baseline flag.
#' @param worst_flag ([teal.picks::values()]; legacy `teal.transform::choices_selected()` is deprecated but still accepted)\cr

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file=R/tm_t_shift_by_arm_by_worst.R,line=198,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 126 characters.
#' value matching `worst_flag_var` for worst post-baseline records (commonly `"Y"`).
#' @param treatment_flag_var ([teal.picks::variables()]; legacy `teal.transform` objects are deprecated but still accepted)\cr

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file=R/tm_t_shift_by_arm_by_worst.R,line=200,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 126 characters.
#' variable for on-treatment flag.
#' @param treatment_flag ([teal.picks::values()]; legacy `teal.transform::choices_selected()` is deprecated but still accepted)\cr

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file=R/tm_t_shift_by_arm_by_worst.R,line=202,col=121,[line_length_linter] Lines should not be more than 120 characters. This line is 130 characters.
#' value matching `treatment_flag_var` for on-treatment records (default `"Y"`).
#'
#' @inherit module_arguments return
Expand Down Expand Up @@ -255,7 +255,7 @@
#' choices = c("WORS01FL", "WORS02FL"),
#' selected = "WORS02FL"
#' ),
#' worst_flag = values(c("Y", "N", ""), "Y", multiple = FALSE),
#' worst_flag = values("Y", "Y", fixed = TRUE),
#' aval_var = variables(choices = c("AVALC", "ANRIND"), selected = "ANRIND"),
#' baseline_var = variables(choices = c("BASEC", "BNRIND"), selected = "BNRIND"),
#' useNA = "ifany"
Expand All @@ -277,8 +277,8 @@
baseline_var,
worst_flag_var,
worst_flag,
treatment_flag_var = variables(choices = "ONTRTFL"),
treatment_flag = teal.picks::values(c("Y", "N", ""), "Y", multiple = FALSE),
treatment_flag_var = teal.picks::variables("ONTRTFL", "ONTRTFL"),
treatment_flag = teal.picks::values("Y", "Y", fixed = TRUE),
useNA = c("ifany", "no"), # nolint: object_name.
na_level = tern::default_na_str(),
add_total = FALSE,
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