nicetable: Lisa's Summary Table Function
In lisaerein/nicetable: This function creates a nice summary table

View source: R/nicetable.R

nicetable

R Documentation

Lisa's Summary Table Function

Description

This function creates a nice looking summary table. It returns a dataframe and prints an html table by default for use in R markdown documents.

Usage

nicetable(
  df,
  covs,
  type,
  labels = NA,
  by = NA,
  bylab = NA,
  warnmissby = FALSE,
  allcol = TRUE,
  alllab = NA,
  orderfreq = FALSE,
  percent = 2,
  perc.dec = 1,
  stats = c("mean_sd", "median_q1q3", "minmax"),
  cont.dec = 2,
  dispmiss = TRUE,
  dispN = FALSE,
  tests = NA,
  exact = FALSE,
  pval.dec = 3,
  testcol = TRUE,
  pvalcol = TRUE,
  mingroup = 0,
  mincell = 0,
  paired = FALSE,
  altp = NA,
  fisher.test.workspace = 2e+05,
  kable = TRUE,
  htmlTable = FALSE,
  use_flextable = FALSE,
  htmltitle = "",
  caption = "",
  color = "#EEEEEE",
  byref = TRUE
)

Arguments

`df`	Dataset, a dataframe object (REQUIRED).
`covs`	Character vector of variable names to include in table (REQUIRED).
`type`	Numeric vector indicating variable type for each covariate: 1 for continuous and 2 for categorical (REQUIRED).
`labels`	Labels for covariates. Default = NA, variable names will be used.
`by`	Variable name (character) to stratify by. Defaults to NA, no stratifying variable and no tests.
`bylab`	Label (character) for stratification variable to use in warning statement. Default is NA.
`warnmissby`	Indicator (logical) to warn user of missing values in stratification variable. Default = FALSE.
`allcol`	Indicator (logical) to diplay the "All Data" column. Default = TRUE.
`alllab`	Character label for "All" column. Default = "All (N = )".
`orderfreq`	Indicator (logical) to order (non-factor) categorical variables by descending frequency. Ordered factor variables will retain original ordering. Default = FALSE.
`percent`	Should row or column percents be used: 2 for row and 1 for column percents. Default is row percentages (2).
`perc.dec`	Number of decimal places for percentages (categorcal variables). Default = 1.
`stats`	Statistics to display for continuous variables, a character vector of the following options (Default = mean_sd, median_q1q3, minmax): mean, sd, median, iqr, q1, q3, q1q3, min, max, minmax, range, sem, mean_sd, mean_sem, median_iqr, median_range, median_q1q3, median_minmax.
`cont.dec`	Number of decimal placess for continuous variable summary stats (mean, median, sd, iqr, etc.). Default = 2.
`dispmiss`	Indicator (logical) to display number of missing values. Default = TRUE.
`dispN`	Indicator (logical) to display number of non-missing values. Default = FALSE.
`tests`	Character vector of tests to calculate p-values. If only one is entered it will apply to all variables. If NA (default), no tests will be done. Parametric ("p": T-test, Chi-squared, Anova, etc.), Non-Parametric ("np": Rank-sum, Fisher's exact, Kruskal-Wallis, etc.), T-test ("ttest"), Wilcoxon/Mann-Whitney Rank-sum ("ranksum"), Chi-squared ("chisq"), Fisher's Exact test ("fe"), Anova ("anova"), and Kruskal-Wallis ("kw") are currently supported.
`exact`	Logical indicator to use exact version of Wilcoxon rank-sum test (using coin package). Default = FALSE.
`pval.dec`	Number of decimal places for p-values. Default = 3.
`testcol`	Indicator (logical) to display column with statistical test names. Default = TRUE.
`pvalcol`	Indicator (logical) to display column with p-values. Default = TRUE.
`mingroup`	Minimum non-missing group size required to report p-value (0 by default to report all p-values).
`mincell`	Minimum non-missing cell size required to report p-value (0 by default to report all p-values).
`paired`	Indicator (logical) to use a test for paired data (only available for ttest and ranksum). Default = FALSE.
`altp`	Numeric vector for alternative p-values to use (default is NA, use regular p-values).
`fisher.test.workspace`	Number. Use this to change the default workspace for fisher.test if desired. Default = 200000.
`kable`	Indicator (logical) to use kable to display table. Default = TRUE.
`htmlTable`	Indicator (logical) to use htmlTable package to display table instead of kable Default = FALSE.
`use_flextable`	Indicator (logical) to use flextable package to display table. Default = FALSE.
`htmltitle`	Character label for htmlTable variable names column. Default = " ".
`caption`	Character title for htmlTable or kable table. Default = " ".
`color`	Character Hex color to use for htmlTable striping. Default = "#EEEEEE" (light grey).
`byref`	Indicator (logical) to include reference "by" category column be included (default = TRUE).