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No auto fmt alternative #1

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62e111f
no_auto_fmt
iaugusty Oct 7, 2025
d1ee483
format to analyze
iaugusty Oct 7, 2025
83a251c
format to analyze count functions
iaugusty Oct 7, 2025
6e450eb
format to analyze other functions
iaugusty Oct 7, 2025
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6 changes: 4 additions & 2 deletions R/abnormal.R
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Original file line number Diff line number Diff line change
Expand Up @@ -216,7 +216,8 @@ count_abnormal <- function(lyt,
.stat_names = NULL,
.formats = list(fraction = format_fraction),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Process standard extra arguments
extra_args <- list(".stats" = .stats)
if (!is.null(.stat_names)) extra_args[[".stat_names"]] <- .stat_names
Expand All @@ -243,6 +244,7 @@ count_abnormal <- function(lyt,
nested = nested,
extra_args = extra_args,
show_labels = "hidden",
table_names = table_names
table_names = table_names,
format = format
)
}
6 changes: 4 additions & 2 deletions R/abnormal_by_baseline.R
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Original file line number Diff line number Diff line change
Expand Up @@ -233,7 +233,8 @@ count_abnormal_by_baseline <- function(lyt,
.stat_names = NULL,
.formats = list(fraction = format_fraction),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
checkmate::assert_character(abnormal, len = length(table_names), names = "named")
checkmate::assert_string(var)

Expand Down Expand Up @@ -266,7 +267,8 @@ count_abnormal_by_baseline <- function(lyt,
nested = nested,
extra_args = extra_args,
show_labels = "visible",
table_names = table_names[i]
table_names = table_names[i],
format = format
)
}

Expand Down
6 changes: 4 additions & 2 deletions R/abnormal_by_marked.R
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Expand Up @@ -273,7 +273,8 @@ count_abnormal_by_marked <- function(lyt,
.stat_names = NULL,
.formats = list(count_fraction = format_count_fraction),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
checkmate::assert_string(var)

# Process standard extra arguments
Expand All @@ -299,6 +300,7 @@ count_abnormal_by_marked <- function(lyt,
na_str = na_str,
nested = nested,
extra_args = extra_args,
show_labels = "hidden"
show_labels = "hidden",
format = format
)
}
6 changes: 4 additions & 2 deletions R/abnormal_by_worst_grade.R
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Expand Up @@ -209,7 +209,8 @@ count_abnormal_by_worst_grade <- function(lyt,
.stat_names = NULL,
.formats = list(count_fraction = format_count_fraction),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Process standard extra arguments
extra_args <- list(".stats" = .stats)
if (!is.null(.stat_names)) extra_args[[".stat_names"]] <- .stat_names
Expand All @@ -233,7 +234,8 @@ count_abnormal_by_worst_grade <- function(lyt,
na_str = na_str,
nested = nested,
extra_args = extra_args,
show_labels = "hidden"
show_labels = "hidden",
format = format
)
}

Expand Down
6 changes: 4 additions & 2 deletions R/abnormal_lab_worsen_by_baseline.R
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Expand Up @@ -197,7 +197,8 @@ count_abnormal_lab_worsen_by_baseline <- function(lyt,
.stat_names = NULL,
.formats = list(fraction = format_fraction),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
checkmate::assert_string(var)

# Deprecated argument warning
Expand Down Expand Up @@ -231,7 +232,8 @@ count_abnormal_lab_worsen_by_baseline <- function(lyt,
na_str = na_str,
nested = nested,
extra_args = extra_args,
show_labels = "hidden"
show_labels = "hidden",
format = format
)
}

Expand Down
6 changes: 4 additions & 2 deletions R/analyze_variables.R
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Expand Up @@ -762,7 +762,8 @@ analyze_vars <- function(lyt,
.stat_names = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Depending on main functions
extra_args <- list(
"na_rm" = na_rm,
Expand Down Expand Up @@ -796,6 +797,7 @@ analyze_vars <- function(lyt,
extra_args = extra_args,
show_labels = show_labels,
table_names = table_names,
section_div = section_div
section_div = section_div,
format = format
)
}
6 changes: 4 additions & 2 deletions R/count_cumulative.R
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Expand Up @@ -255,7 +255,8 @@ count_cumulative <- function(lyt,
.stat_names = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = format) {
# Depending on main functions
extra_args <- list(
"na_rm" = na_rm,
Expand Down Expand Up @@ -290,6 +291,7 @@ count_cumulative <- function(lyt,
var_labels = var_labels,
show_labels = show_labels,
nested = nested,
extra_args = extra_args
extra_args = extra_args,
format = format
)
}
6 changes: 4 additions & 2 deletions R/count_missed_doses.R
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Expand Up @@ -193,7 +193,8 @@ count_missed_doses <- function(lyt,
.stat_names = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Depending on main functions
extra_args <- list(
"na_rm" = na_rm,
Expand Down Expand Up @@ -226,6 +227,7 @@ count_missed_doses <- function(lyt,
var_labels = var_labels,
show_labels = show_labels,
nested = nested,
extra_args = extra_args
extra_args = extra_args,
format = format
)
}
6 changes: 4 additions & 2 deletions R/count_occurrences.R
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Original file line number Diff line number Diff line change
Expand Up @@ -253,7 +253,8 @@ count_occurrences <- function(lyt,
.stat_names = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
checkmate::assert_flag(riskdiff)
afun <- if (isFALSE(riskdiff)) a_count_occurrences else afun_riskdiff

Expand Down Expand Up @@ -285,7 +286,8 @@ count_occurrences <- function(lyt,
extra_args = extra_args,
var_labels = var_labels,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
}

Expand Down
6 changes: 4 additions & 2 deletions R/count_occurrences_by_grade.R
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Expand Up @@ -377,7 +377,8 @@ count_occurrences_by_grade <- function(lyt,
.stat_names = NULL,
.formats = list(count_fraction = format_count_fraction_fixed_dp),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
checkmate::assert_flag(riskdiff)
afun <- if (isFALSE(riskdiff)) a_count_occurrences_by_grade else afun_riskdiff

Expand Down Expand Up @@ -409,7 +410,8 @@ count_occurrences_by_grade <- function(lyt,
extra_args = extra_args,
var_labels = var_labels,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
}

Expand Down
6 changes: 4 additions & 2 deletions R/count_patients_with_event.R
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Expand Up @@ -211,7 +211,8 @@ count_patients_with_event <- function(lyt,
.stat_names = NULL,
.formats = list(count_fraction = format_count_fraction_fixed_dp),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
checkmate::assert_flag(riskdiff)
afun <- if (isFALSE(riskdiff)) a_count_patients_with_event else afun_riskdiff

Expand Down Expand Up @@ -242,6 +243,7 @@ count_patients_with_event <- function(lyt,
nested = nested,
extra_args = extra_args,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
}
6 changes: 4 additions & 2 deletions R/count_patients_with_flags.R
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Original file line number Diff line number Diff line change
Expand Up @@ -225,7 +225,8 @@ count_patients_with_flags <- function(lyt,
.stat_names = NULL,
.formats = list(count_fraction = format_count_fraction_fixed_dp),
.indent_mods = NULL,
.labels = NULL) {
.labels = NULL,
format = NULL) {
checkmate::assert_flag(riskdiff)
afun <- if (isFALSE(riskdiff)) a_count_patients_with_flags else afun_riskdiff

Expand Down Expand Up @@ -257,6 +258,7 @@ count_patients_with_flags <- function(lyt,
extra_args = extra_args,
var_labels = var_labels,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
}
6 changes: 4 additions & 2 deletions R/count_values.R
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Expand Up @@ -187,7 +187,8 @@ count_values <- function(lyt,
.stat_names = NULL,
.formats = c(count_fraction = "xx (xx.xx%)", count = "xx"),
.labels = c(count_fraction = paste(values, collapse = ", ")),
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Process standard extra arguments
extra_args <- list(".stats" = .stats)
if (!is.null(.stat_names)) extra_args[[".stat_names"]] <- .stat_names
Expand All @@ -214,6 +215,7 @@ count_values <- function(lyt,
nested = nested,
extra_args = extra_args,
show_labels = ifelse(length(vars) > 1, "visible", "hidden"),
table_names = table_names
table_names = table_names,
format = format
)
}
6 changes: 4 additions & 2 deletions R/estimate_multinomial_rsp.R
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Expand Up @@ -206,7 +206,8 @@ estimate_multinomial_response <- function(lyt,
.stat_names = NULL,
.formats = list(prop_ci = "(xx.xx, xx.xx)"),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Process standard extra arguments
extra_args <- list(".stats" = .stats)
if (!is.null(.stat_names)) extra_args[[".stat_names"]] <- .stat_names
Expand All @@ -232,6 +233,7 @@ estimate_multinomial_response <- function(lyt,
nested = nested,
extra_args = extra_args,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
}
6 changes: 4 additions & 2 deletions R/estimate_proportion.R
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Expand Up @@ -249,7 +249,8 @@ estimate_proportion <- function(lyt,
.stat_names = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Process standard extra arguments
extra_args <- list(".stats" = .stats)
if (!is.null(.stat_names)) extra_args[[".stat_names"]] <- .stat_names
Expand Down Expand Up @@ -277,7 +278,8 @@ estimate_proportion <- function(lyt,
nested = nested,
extra_args = extra_args,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
}

Expand Down
3 changes: 3 additions & 0 deletions R/formatting_functions.R
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Expand Up @@ -565,6 +565,9 @@ count_decimalplaces <- function(dec) {
#'
#' @keywords internal
apply_auto_formatting <- function(.formats, x_stats, .df_row, .var) {
if (inherits(.formats, "no_auto_fmt")){
return(NULL)
}
is_auto_fmt <- vapply(.formats, function(ii) is.character(ii) && ii == "auto", logical(1))
if (any(is_auto_fmt)) {
auto_stats <- x_stats[is_auto_fmt]
Expand Down
6 changes: 4 additions & 2 deletions R/incidence_rate.R
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Expand Up @@ -236,7 +236,8 @@ estimate_incidence_rate <- function(lyt,
.stat_names = NULL,
.formats = list(rate = "xx.xx", rate_ci = "(xx.xx, xx.xx)"),
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Process standard extra arguments
extra_args <- list(".stats" = .stats)
if (!is.null(.stat_names)) extra_args[[".stat_names"]] <- .stat_names
Expand Down Expand Up @@ -264,7 +265,8 @@ estimate_incidence_rate <- function(lyt,
nested = nested,
extra_args = extra_args,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
} else {
summarize_row_groups(
Expand Down
6 changes: 4 additions & 2 deletions R/odds_ratio.R
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Expand Up @@ -264,7 +264,8 @@ estimate_odds_ratio <- function(lyt,
.stat_names = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = NULL) {
.indent_mods = NULL,
format = NULL) {
# Process standard extra arguments
extra_args <- list(".stats" = .stats)
if (!is.null(.stat_names)) extra_args[[".stat_names"]] <- .stat_names
Expand Down Expand Up @@ -292,7 +293,8 @@ estimate_odds_ratio <- function(lyt,
extra_args = extra_args,
var_labels = var_labels,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
}

Expand Down
6 changes: 4 additions & 2 deletions R/prop_diff.R
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Expand Up @@ -283,7 +283,8 @@ estimate_proportion_diff <- function(lyt,
.stat_names = NULL,
.formats = c(diff = "xx.x", diff_ci = "(xx.x, xx.x)"),
.labels = NULL,
.indent_mods = c(diff = 0L, diff_ci = 1L)) {
.indent_mods = c(diff = 0L, diff_ci = 1L),
format = NULL) {
# Depending on main functions
extra_args <- list(
"na_rm" = na_rm,
Expand Down Expand Up @@ -320,7 +321,8 @@ estimate_proportion_diff <- function(lyt,
extra_args = extra_args,
show_labels = show_labels,
table_names = table_names,
section_div = section_div
section_div = section_div,
format = format
)
}

Expand Down
6 changes: 4 additions & 2 deletions R/prop_diff_test.R
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Expand Up @@ -236,7 +236,8 @@ test_proportion_diff <- function(lyt,
.stat_names = NULL,
.formats = c(pval = "x.xxxx | (<0.0001)"),
.labels = NULL,
.indent_mods = c(pval = 1L)) {
.indent_mods = c(pval = 1L),
format = NULL) {
# Depending on main functions
extra_args <- list(
"na_rm" = na_rm,
Expand Down Expand Up @@ -271,7 +272,8 @@ test_proportion_diff <- function(lyt,
extra_args = extra_args,
show_labels = show_labels,
table_names = table_names,
section_div = section_div
section_div = section_div,
format = format
)
}

Expand Down
6 changes: 4 additions & 2 deletions R/summarize_ancova.R
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Expand Up @@ -321,7 +321,8 @@ summarize_ancova <- function(lyt,
.stat_names = NULL,
.formats = NULL,
.labels = NULL,
.indent_mods = list("lsmean_diff_ci" = 1L, "pval" = 1L)) {
.indent_mods = list("lsmean_diff_ci" = 1L, "pval" = 1L),
format = NULL) {
# Process standard extra arguments
extra_args <- list(".stats" = .stats)
if (!is.null(.stat_names)) extra_args[[".stat_names"]] <- .stat_names
Expand Down Expand Up @@ -351,6 +352,7 @@ summarize_ancova <- function(lyt,
extra_args = extra_args,
var_labels = var_labels,
show_labels = show_labels,
table_names = table_names
table_names = table_names,
format = format
)
}
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