![[Stable]](figures/lifecycle-stable.svg)
Functions to retrieve default settings for summary statistics and customize these settings.
Usage
summary_formats(type = "numeric", include_pval = FALSE)
summary_labels(type = "numeric", include_pval = FALSE)
summary_custom(
type = "numeric",
include_pval = FALSE,
stats_custom = NULL,
formats_custom = NULL,
labels_custom = NULL,
indent_mods_custom = NULL
)Arguments
- type
(
character)
choice of summary data type. Onlycountsandnumerictypes are currently supported.- include_pval
(
logical)
whether p-value should be included as a default statistic.- stats_custom
(
named vectorofcharacter)
vector of statistics to include if not the defaults. This argument overridesinclude_pvaland other custom value arguments such that only settings for these statistics will be returned.- formats_custom
(
named vectorofcharacter)
vector of custom statistics formats to use in place of the defaults defined insummary_formats(). Names should be a subset of the statistics defined instats_custom(or default statistics if this isNULL).- labels_custom
(
named vectorofcharacter)
vector of custom statistics labels to use in place of the defaults defined insummary_labels(). Names should be a subset of the statistics defined instats_custom(or default statistics if this isNULL).- indent_mods_custom
(
integerornamed vectorofinteger)
vector of custom indentation modifiers for statistics to use instead of the default of0Lfor all statistics. Names should be a subset of the statistics defined instats_custom(or default statistics if this isNULL). Alternatively, the same indentation modifier can be applied to all statistics by settingindent_mods_customto a single integer value.
Value
summary_formatsreturns a namedvectorof default statistic formats for the given data type.
summary_labelsreturns a namedvectorof default statistic labels for the given data type.
summary_customreturns alistof 4 named elements:stats,formats,labels, andindent_mods.
Functions
summary_formats(): Function to retrieve default formats for summary statistics. Returns format patterns for descriptive statistics which are understood byrtables.summary_labels(): Function to retrieve default labels for summary statistics. Returns labels of descriptive statistics which are understood byrtables.summary_custom(): Function to configure settings for default or custom summary statistics for a given data type. In addition to selecting a custom subset of statistics, the user can also set custom formats, labels, and indent modifiers for any of these statistics.
Examples
summary_formats()
#> n sum mean
#> "xx." "xx.x" "xx.x"
#> sd se mean_sd
#> "xx.x" "xx.x" "xx.x (xx.x)"
#> mean_se mean_ci mean_sei
#> "xx.x (xx.x)" "(xx.xx, xx.xx)" "(xx.xx, xx.xx)"
#> mean_sdi mean_pval median
#> "(xx.xx, xx.xx)" "xx.xx" "xx.x"
#> mad median_ci quantiles
#> "xx.x" "(xx.xx, xx.xx)" "xx.x - xx.x"
#> iqr range min
#> "xx.x" "xx.x - xx.x" "xx.x"
#> max median_range cv
#> "xx.x" "xx.x (xx.x - xx.x)" "xx.x"
#> geom_mean geom_mean_ci geom_cv
#> "xx.x" "(xx.xx, xx.xx)" "xx.x"
summary_formats(type = "count", include_pval = TRUE)
#> n sum mean
#> "xx." "xx.x" "xx.x"
#> sd se mean_sd
#> "xx.x" "xx.x" "xx.x (xx.x)"
#> mean_se mean_ci mean_sei
#> "xx.x (xx.x)" "(xx.xx, xx.xx)" "(xx.xx, xx.xx)"
#> mean_sdi mean_pval median
#> "(xx.xx, xx.xx)" "xx.xx" "xx.x"
#> mad median_ci quantiles
#> "xx.x" "(xx.xx, xx.xx)" "xx.x - xx.x"
#> iqr range min
#> "xx.x" "xx.x - xx.x" "xx.x"
#> max median_range cv
#> "xx.x" "xx.x (xx.x - xx.x)" "xx.x"
#> geom_mean geom_mean_ci geom_cv
#> "xx.x" "(xx.xx, xx.xx)" "xx.x"
#> pval
#> "x.xxxx | (<0.0001)"
summary_labels()
#> n sum
#> "n" "Sum"
#> mean sd
#> "Mean" "SD"
#> se mean_sd
#> "SE" "Mean (SD)"
#> mean_se mean_ci
#> "Mean (SE)" "Mean 95% CI"
#> mean_sei mean_sdi
#> "Mean -/+ 1xSE" "Mean -/+ 1xSD"
#> mean_pval median
#> "Mean p-value (H0: mean = 0)" "Median"
#> mad median_ci
#> "Median Absolute Deviation" "Median 95% CI"
#> quantiles iqr
#> "25% and 75%-ile" "IQR"
#> range min
#> "Min - Max" "Minimum"
#> max median_range
#> "Maximum" "Median (Min - Max)"
#> cv geom_mean
#> "CV (%)" "Geometric Mean"
#> geom_mean_ci geom_cv
#> "Geometric Mean 95% CI" "CV % Geometric Mean"
summary_labels(type = "count", include_pval = TRUE)
#> n sum
#> "n" "Sum"
#> mean sd
#> "Mean" "SD"
#> se mean_sd
#> "SE" "Mean (SD)"
#> mean_se mean_ci
#> "Mean (SE)" "Mean 95% CI"
#> mean_sei mean_sdi
#> "Mean -/+ 1xSE" "Mean -/+ 1xSD"
#> mean_pval median
#> "Mean p-value (H0: mean = 0)" "Median"
#> mad median_ci
#> "Median Absolute Deviation" "Median 95% CI"
#> quantiles iqr
#> "25% and 75%-ile" "IQR"
#> range min
#> "Min - Max" "Minimum"
#> max median_range
#> "Maximum" "Median (Min - Max)"
#> cv geom_mean
#> "CV (%)" "Geometric Mean"
#> geom_mean_ci geom_cv
#> "Geometric Mean 95% CI" "CV % Geometric Mean"
#> pval
#> "p-value (t-test)"
summary_custom()
#> $stats
#> [1] "n" "sum" "mean" "sd" "se"
#> [6] "mean_sd" "mean_se" "mean_ci" "mean_sei" "mean_sdi"
#> [11] "mean_pval" "median" "mad" "median_ci" "quantiles"
#> [16] "iqr" "range" "min" "max" "median_range"
#> [21] "cv" "geom_mean" "geom_mean_ci" "geom_cv"
#>
#> $formats
#> n sum mean
#> "xx." "xx.x" "xx.x"
#> sd se mean_sd
#> "xx.x" "xx.x" "xx.x (xx.x)"
#> mean_se mean_ci mean_sei
#> "xx.x (xx.x)" "(xx.xx, xx.xx)" "(xx.xx, xx.xx)"
#> mean_sdi mean_pval median
#> "(xx.xx, xx.xx)" "xx.xx" "xx.x"
#> mad median_ci quantiles
#> "xx.x" "(xx.xx, xx.xx)" "xx.x - xx.x"
#> iqr range min
#> "xx.x" "xx.x - xx.x" "xx.x"
#> max median_range cv
#> "xx.x" "xx.x (xx.x - xx.x)" "xx.x"
#> geom_mean geom_mean_ci geom_cv
#> "xx.x" "(xx.xx, xx.xx)" "xx.x"
#>
#> $labels
#> n sum
#> "n" "Sum"
#> mean sd
#> "Mean" "SD"
#> se mean_sd
#> "SE" "Mean (SD)"
#> mean_se mean_ci
#> "Mean (SE)" "Mean 95% CI"
#> mean_sei mean_sdi
#> "Mean -/+ 1xSE" "Mean -/+ 1xSD"
#> mean_pval median
#> "Mean p-value (H0: mean = 0)" "Median"
#> mad median_ci
#> "Median Absolute Deviation" "Median 95% CI"
#> quantiles iqr
#> "25% and 75%-ile" "IQR"
#> range min
#> "Min - Max" "Minimum"
#> max median_range
#> "Maximum" "Median (Min - Max)"
#> cv geom_mean
#> "CV (%)" "Geometric Mean"
#> geom_mean_ci geom_cv
#> "Geometric Mean 95% CI" "CV % Geometric Mean"
#>
#> $indent_mods
#> n sum mean sd se mean_sd
#> 0 0 0 0 0 0
#> mean_se mean_ci mean_sei mean_sdi mean_pval median
#> 0 0 0 0 0 0
#> mad median_ci quantiles iqr range min
#> 0 0 0 0 0 0
#> max median_range cv geom_mean geom_mean_ci geom_cv
#> 0 0 0 0 0 0
#>
summary_custom(type = "counts", include_pval = TRUE)
#> $stats
#> [1] "n" "count" "count_fraction" "n_blq"
#> [5] "pval"
#>
#> $formats
#> $formats$n
#> [1] "xx."
#>
#> $formats$count
#> [1] "xx."
#>
#> $formats$count_fraction
#> function(x, ...) {
#> attr(x, "label") <- NULL
#>
#> if (any(is.na(x))) {
#> return("NA")
#> }
#>
#> checkmate::assert_vector(x)
#> checkmate::assert_integerish(x[1])
#> assert_proportion_value(x[2], include_boundaries = TRUE)
#>
#> result <- if (x[1] == 0) {
#> "0"
#> } else {
#> paste0(x[1], " (", round(x[2] * 100, 1), "%)")
#> }
#>
#> return(result)
#> }
#> <environment: namespace:tern>
#>
#> $formats$n_blq
#> [1] "xx."
#>
#> $formats$pval
#> [1] "x.xxxx | (<0.0001)"
#>
#>
#> $labels
#> n count
#> "n" "count"
#> count_fraction n_blq
#> "count_fraction" "n_blq"
#> pval
#> "p-value (chi-squared test)"
#>
#> $indent_mods
#> n count count_fraction n_blq pval
#> 0 0 0 0 0
#>
summary_custom(
include_pval = TRUE, stats_custom = c("n", "mean", "sd", "pval"),
labels_custom = c(sd = "Std. Dev."), indent_mods_custom = 3L
)
#> $stats
#> [1] "n" "mean" "sd" "pval"
#>
#> $formats
#> n mean sd
#> "xx." "xx.x" "xx.x"
#> pval
#> "x.xxxx | (<0.0001)"
#>
#> $labels
#> n mean sd pval
#> "n" "Mean" "Std. Dev." "p-value (t-test)"
#>
#> $indent_mods
#> n mean sd pval
#> 3 3 3 3
#>