tabler_stat: Description statistics 'tabler'
In raredd/rawr: rawr miscellaneous

tabler_stat

R Documentation

Description statistics `tabler`

Description

Wrapper function to create table of description statistics with optional tests of association.

Usage

tabler_stat(
  data,
  varname,
  byvar = NULL,
  digits = 0L,
  FUN = NULL,
  format_pval = TRUE,
  color_pval = TRUE,
  color_missing = TRUE,
  dagger = TRUE,
  color_cell_by = c("none", "value", "pct"),
  cell_color = palette()[1:2],
  confint = FALSE,
  survmedian = FALSE,
  survtime = FALSE,
  time = 0,
  include_na_in_prop = TRUE,
  iqr = FALSE,
  total = TRUE,
  continuous_fn = function(...) Gmisc::describeMedian(..., iqr = iqr),
  factor_fn = if (!include_na_in_prop) describeFactors else Gmisc::describeFactors,
  ...
)

Arguments

`data`	a matrix or data frame with variables `varname` and `byvar`
`varname`, `byvar`	the row and column variable, respectively
`digits`	number of digits past the decimal point to keep
`FUN`	a function performing the test of association between `varname` and `byvar`; `FALSE` will suppress the test but keep a column for p-values; `NA` will suppress the test and drop the column for p-values; or a character string; see details
`format_pval`	logical; if `TRUE`, p-values will be formatted using `pvalr`; alternatively, a function may by used which will be applied to each p-value
`color_pval`	logical; if `TRUE`, p-values will be colored by significance; see `color_pval`; alternatively, a vector of colors passed to `color_pval`)
`color_missing`	logical; if `TRUE`, rows summarizing missing values will be shown in light grey; alternatively, a color string can be used for a custom color
`dagger`	logical or a character string giving the character to associate with `FUN`; if `FALSE`, none are used; if `TRUE`, the defaults are used (`"*"` is used if `FUN` is given)
`color_cell_by`	apply a color gradient to each cell (for html output); one of `"none"` for no coloring, `"value"` to color by numeric summary (e.g., for continuous variables), or `"pct"` to color by proportions (e.g., for factors)
`cell_color`	a vector of colors used for `color_cell_by`
`confint`	logical or `varname`; if `TRUE` (or `varname`) rows will be formatted as confidence intervals; see `binconr`
`include_na_in_prop`	logical; if `TRUE` (default), the number of missing values is included when calculating proportions for factor levels; if `FALSE`, only non-missing levels count towards proportions
`iqr`	logical; if `TRUE`, the interquartile range is used instead of the full range (default) for continuous variables
`total`	logical; if `TRUE`, total column will be shown
`continuous_fn`, `factor_fn`	functions to describe continuous and factor-like variables (default is to show median and range for continuous); see `getDescriptionStatsBy`
`...`	additional arguments passed to `getDescriptionStatsBy`

Details

If FUN is FALSE, no test will be performed but a column for p-values will still be added; FUN = NA will prevent both the test from being performed and the column from being added to the output.

For FUN = NULL (default), the correct test will be guessed based on the row and column data. The current options are fisher.test, wilcox.test, and kruskal.test. If the row data is continuous, one of the latter two tests will be used based on the number of unique values in the column data.

For special cases, the function is not always guessed correctly (e.g., if the row data contains few unique values, a Fisher test may be used where not appropriate). One of the default tests can be given explicitly with a character string, one of "fisher", "wilcoxon", "ttest", "kruskal", "chisq", "anova", "cuzick", "jt", "ca", or "kw" (can be abbreviated).

If FUN is a function, it must take two vector arguments: the row variable vector, data$varname, and the column variable vector, data$byvar, in this order and return a numeric p-value only.

Value

A matrix with additional attributes:

`attr(,"FUN")`	the test passed to `FUN` or the test selected based on `varname` and `byvar` if `FUN = NULL`
`attr(,"p.value")`	the numeric p-value returned by `FUN`
`attr(,"fnames")`	a vector of the default `FUN` options with names to match the appropriate `dagger` character; see examples; if `FUN` is given, the function name will be added with a new dagger symbol (`"*"` by default or `dagger` if given)
`attr(,"tfoot")`	a footnote for the table using each dagger and corresponding test name

Examples

tabler_stat(mtcars, 'mpg', 'cyl')                 # picks kruskal-wallis
tabler_stat(mtcars, 'mpg', 'cyl', FUN = NA)       # no test, no p-value column
tabler_stat(mtcars, 'mpg', 'cyl', FUN = FALSE)    # no test, p-value column
tabler_stat(mtcars, 'mpg', 'cyl', FUN = 'fisher') # force fisher test
tabler_stat(mtcars, 'mpg', 'cyl', FUN = 'anova')  # force anova test

## use of a custom function - see ?rawr::cuzick.test
tabler_stat(mtcars, 'mpg', 'cyl',
  continuous_fn = Gmisc::describeMean,
  FUN = function(x, y)
    cuzick.test(x ~ y, data.frame(x, y))$p.value)

## "cuzick" is also an option for FUN
tabler_stat(mtcars, 'mpg', 'cyl', FUN = 'cuzick')


## typical usage
mt <- within(mtcars, {
  mpg[1:5] <- carb[1:5] <- drat[1:20] <- NA
  carb <- factor(carb, ordered = TRUE)
  cyl  <- factor(cyl)
})

tbl <- lapply(names(mt)[-10L], function(x)
  tabler_stat(mt, x, 'gear', percentage_sign = FALSE,
              color_cell_by = ifelse(is.factor(mt[, x]), 'pct', 'none'),
              continuous_fn = Gmisc::describeMean))

ht <- htmlTable::htmlTable(
  do.call('rbind', tbl),
  cgroup = c('', 'Gear', ''), n.cgroup = c(1, 3, 1),
  rgroup = names(mt)[-10L], n.rgroup = sapply(tbl, nrow),
  tfoot = toString(unique(unlist(strsplit(sapply(seq_along(tbl), function(ii)
    attr(tbl[[ii]], 'tfoot')), ', '))))
)
structure(ht, class = 'htmlTable')


## survival object (median, 95% CI, log-rank test)
library('survival')
mt <- within(mt, {
  surv <- Surv(wt, vs)
})
tabler_stat(mt, 'surv', 'gear')


## use the tabler_stat2 wrapper for convenience
tabler_stat2(mt, names(mt)[-10L], 'gear')

tabler_stat2(mt, names(mt)[-10L], 'gear', FUN = c(cyl = 'jt'))

mt$gear <- factor(mt$gear, ordered = TRUE)
tabler_stat2(mt, names(mt)[-10L], 'gear',
  format_pval = function(x) format.pval(x, digits = 3))

raredd/rawr documentation built on April 29, 2024, 10:29 a.m.