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change all defaults for debugging purposes #1470

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2 changes: 1 addition & 1 deletion R/count_values.R
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Expand Up @@ -185,7 +185,7 @@ count_values <- function(lyt,
table_names = vars,
.stats = "count_fraction",
.stat_names = NULL,
.formats = c(count_fraction = "xx (xx.xx%)", count = "xx"),
.formats = c(count_fraction = "xx (xx.x%)", count = "xx"),
.labels = c(count_fraction = paste(values, collapse = ", ")),
.indent_mods = NULL) {
# Process standard extra arguments
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2 changes: 1 addition & 1 deletion R/estimate_multinomial_rsp.R
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Expand Up @@ -204,7 +204,7 @@ estimate_multinomial_response <- function(lyt,
table_names = var,
.stats = "prop_ci",
.stat_names = NULL,
.formats = list(prop_ci = "(xx.xx, xx.xx)"),
.formats = list(prop_ci = "(xx.x, xx.x)"),
.labels = NULL,
.indent_mods = NULL) {
# Process standard extra arguments
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2 changes: 1 addition & 1 deletion R/incidence_rate.R
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Expand Up @@ -234,7 +234,7 @@ estimate_incidence_rate <- function(lyt,
table_names = vars,
.stats = c("person_years", "n_events", "rate", "rate_ci"),
.stat_names = NULL,
.formats = list(rate = "xx.xx", rate_ci = "(xx.xx, xx.xx)"),
.formats = list(rate = "xx.x", rate_ci = "(xx.x, xx.x)"),
.labels = NULL,
.indent_mods = NULL) {
# Process standard extra arguments
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8 changes: 4 additions & 4 deletions R/logistic_regression.R
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Expand Up @@ -339,12 +339,12 @@ logistic_summary_by_flag <- function(flag_var, na_str = default_na_str(), .inden
checkmate::assert_string(flag_var)
function(lyt) {
cfun_list <- list(
df = cfun_by_flag("df", flag_var, format = "xx.", .indent_mods = .indent_mods),
estimate = cfun_by_flag("estimate", flag_var, format = "xx.xxx", .indent_mods = .indent_mods),
std_error = cfun_by_flag("std_error", flag_var, format = "xx.xxx", .indent_mods = .indent_mods),
df = cfun_by_flag("df", flag_var, format = "xx.x", .indent_mods = .indent_mods),
estimate = cfun_by_flag("estimate", flag_var, format = "xx.xx", .indent_mods = .indent_mods),
std_error = cfun_by_flag("std_error", flag_var, format = "xx.xx", .indent_mods = .indent_mods),
odds_ratio = cfun_by_flag("odds_ratio", flag_var, format = ">999.99", .indent_mods = .indent_mods),
ci = cfun_by_flag("ci", flag_var, format = format_extreme_values_ci(2L), .indent_mods = .indent_mods),
pvalue = cfun_by_flag("pvalue", flag_var, format = "x.xxxx | (<0.0001)", .indent_mods = .indent_mods)
pvalue = cfun_by_flag("pvalue", flag_var, format = "x.xxx | (<0.0001)", .indent_mods = .indent_mods)
)
summarize_row_groups(
lyt = lyt,
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10 changes: 5 additions & 5 deletions R/summarize_change.R
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Expand Up @@ -162,11 +162,11 @@ summarize_change <- function(lyt,
.stats = c("n", "mean_sd", "median", "range"),
.stat_names = NULL,
.formats = c(
mean_sd = "xx.xx (xx.xx)",
mean_se = "xx.xx (xx.xx)",
median = "xx.xx",
range = "xx.xx - xx.xx",
mean_pval = "xx.xx"
mean_sd = "xx.x (xx.x)",
mean_se = "xx.x (xx.x)",
median = "xx.x",
range = "xx.x - xx.x",
mean_pval = "xx.x"
),
.labels = NULL,
.indent_mods = NULL) {
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2 changes: 1 addition & 1 deletion R/summarize_coxreg.R
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Expand Up @@ -329,7 +329,7 @@ summarize_coxreg <- function(lyt,
common_var = "STUDYID",
.stats = c("n", "hr", "ci", "pval", "pval_inter"),
.formats = c(
n = "xx", hr = "xx.xx", ci = "(xx.xx, xx.xx)",
n = "xx", hr = "xx.x", ci = "(xx.xx, xx.xx)",
pval = "x.xxxx | (<0.0001)", pval_inter = "x.xxxx | (<0.0001)"
),
varlabels = NULL,
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2 changes: 1 addition & 1 deletion R/survival_timepoint.R
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Expand Up @@ -305,7 +305,7 @@ surv_timepoint <- function(lyt,
"rate_diff", "rate_diff_ci", "ztest_pval"
),
.stat_names = NULL,
.formats = list(rate_ci = "(xx.xx, xx.xx)"),
.formats = list(rate_ci = "(xx.x, xx.x)"),
.labels = NULL,
.indent_mods = if (method == "both") {
c(rate_diff = 1L, rate_diff_ci = 2L, ztest_pval = 2L)
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140 changes: 70 additions & 70 deletions R/utils_default_stats_formats_labels.R
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Expand Up @@ -608,82 +608,82 @@ tern_default_stats <- list(
#' @export
tern_default_formats <- c(
ci = list(format_extreme_values_ci(2L)),
count = "xx.",
count = "xx.x",
count_fraction = format_count_fraction,
count_fraction_fixed_dp = format_count_fraction_fixed_dp,
cv = "xx.x",
event_free_rate = "xx.xx",
cv = "xx.xx",
event_free_rate = "xx.xxx",
fraction = format_fraction_fixed_dp,
geom_cv = "xx.x",
geom_mean = "xx.x",
geom_mean_ci = "(xx.xx, xx.xx)",
geom_mean_ci_3d = "xx.xx (xx.xx - xx.xx)",
geom_mean_sd = "xx.x (xx.x)",
geom_sd = "xx.x",
geom_cv = "xx.xx",
geom_mean = "xx.xx",
geom_mean_ci = "(xx.x, xx.x)",
geom_mean_ci_3d = "xx.x (xx.x - xx.x)",
geom_mean_sd = "xx.xx (xx.xx)",
geom_sd = "xx.xx",
hr = list(format_extreme_values(2L)),
hr_ci = "(xx.xx, xx.xx)",
hr_ci_3d = "xx.xx (xx.xx - xx.xx)",
iqr = "xx.x",
lsmean = "xx.xx",
lsmean_diff = "xx.xx",
lsmean_diff_ci = "(xx.xx, xx.xx)",
mad = "xx.x",
max = "xx.x",
mean = "xx.x",
mean_ci = "(xx.xx, xx.xx)",
mean_ci_3d = "xx.xx (xx.xx - xx.xx)",
mean_pval = "x.xxxx | (<0.0001)",
mean_sd = "xx.x (xx.x)",
mean_sdi = "(xx.xx, xx.xx)",
mean_se = "xx.x (xx.x)",
mean_sei = "(xx.xx, xx.xx)",
median = "xx.x",
median_ci = "(xx.xx, xx.xx)",
median_ci_3d = "xx.xx (xx.xx - xx.xx)",
median_range = "xx.x (xx.x - xx.x)",
min = "xx.x",
n = "xx.",
n_blq = "xx.",
n_events = "xx",
n_patients = "xx (xx.x%)",
n_prop = "xx (xx.x%)",
n_rate = "xx (xx.x)",
n_rsp = "xx",
n_tot = "xx",
n_tot_events = "xx",
n_unique = "xx",
nonunique = "xx",
hr_ci = "(xx.x, xx.x)",
hr_ci_3d = "xx.x (xx.x - xx.x)",
iqr = "xx.xx",
lsmean = "xx.x",
lsmean_diff = "xx.x",
lsmean_diff_ci = "(xx.x, xx.x)",
mad = "xx.xx",
max = "xx.xx",
mean = "xx.xx",
mean_ci = "(xx.x, xx.x)",
mean_ci_3d = "xx.x (xx.x - xx.x)",
mean_pval = "x.xxx | (<0.0001)",
mean_sd = "xx.xx (xx.xx)",
mean_sdi = "(xx.x, xx.x)",
mean_se = "xx.xx (xx.xx)",
mean_sei = "(xx.x, xx.x)",
median = "xx.xx",
median_ci = "(xx.x, xx.x)",
median_ci_3d = "xx.x (xx.x - xx.x)",
median_range = "xx.xx (xx.xx - xx.xx)",
min = "xx.xx",
n = "xx.x",
n_blq = "xx.x",
n_events = "xx.x",
n_patients = "xx.x (xx.xx%)",
n_prop = "xx (xx.xx%)",
n_rate = "xx (xx.xx)",
n_rsp = "xx.x",
n_tot = "xx.x",
n_tot_events = "xx.x",
n_unique = "xx.x",
nonunique = "xx.x",
or = list(format_extreme_values(2L)),
or_ci = "xx.xx (xx.xx - xx.xx)",
person_years = "xx.x",
prop = "xx.x%",
prop_ci = "(xx.x, xx.x)",
pt_at_risk = "xx",
pval = "x.xxxx | (<0.0001)",
pvalue = "x.xxxx | (<0.0001)",
pval_counts = "x.xxxx | (<0.0001)",
quantiles = "xx.x - xx.x",
quantiles_lower = "xx.xx (xx.xx - xx.xx)",
quantiles_upper = "xx.xx (xx.xx - xx.xx)",
range = "xx.x - xx.x",
range_censor = "xx.x to xx.x",
range_event = "xx.x to xx.x",
rate = "xx.xxxx",
rate_ci = "(xx.xxxx, xx.xxxx)",
rate_diff = "xx.xx",
rate_diff_ci = "(xx.xx, xx.xx)",
rate_diff_ci_3d = format_xx("xx.xx (xx.xx, xx.xx)"),
rate_ratio = "xx.xxxx",
rate_ratio_ci = "(xx.xxxx, xx.xxxx)",
rate_se = "xx.xx",
riskdiff = "xx.x (xx.x - xx.x)",
sd = "xx.x",
se = "xx.x",
sum = "xx.x",
sum_exposure = "xx",
or_ci = "xx.x (xx.x - xx.x)",
person_years = "xx.xx",
prop = "xx.xx%",
prop_ci = "(xx.xx, xx.xx)",
pt_at_risk = "xx.x",
pval = "x.xxx | (<0.0001)",
pvalue = "x.xxx | (<0.0001)",
pval_counts = "x.xxx | (<0.0001)",
quantiles = "xx.xx - xx.xx",
quantiles_lower = "xx.x (xx.x - xx.x)",
quantiles_upper = "xx.x (xx.x - xx.x)",
range = "xx.xx - xx.xx",
range_censor = "xx.xx to xx.xx",
range_event = "xx.xx to xx.xx",
rate = "xx.xxx",
rate_ci = "(xx.xxx, xx.xxx)",
rate_diff = "xx.x",
rate_diff_ci = "(xx.x, xx.x)",
rate_diff_ci_3d = format_xx("xx.x (xx.x, xx.x)"),
rate_ratio = "xx.xxx",
rate_ratio_ci = "(xx.xxx, xx.xxx)",
rate_se = "xx.x",
riskdiff = "xx.xx (xx.xx - xx.xx)",
sd = "xx.xx",
se = "xx.xx",
sum = "xx.xx",
sum_exposure = "xx.x",
unique = format_count_fraction_fixed_dp,
unique_count = "xx",
ztest_pval = "x.xxxx | (<0.0001)"
unique_count = "xx.x",
ztest_pval = "x.xxx | (<0.0001)"
)

# tern_default_labels ----------------------------------------------------------
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