make.table: Make Summary Table

Description Usage Arguments Value Note Author(s) See Also Examples

View source: R/Table1.R

Description

This function produces summary statistics for categeorical and continuous variables and combines the results into a data frame for plain text, HTML, or LaTeX output, serving as a wrapper to apply vectorized inputs to cat.var and cont.var. The input dataset must be cleaned (e.g. blank cells and NaNs replaced with NAs).

Usage

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make.table(dat, cat.varlist, cat.header, cat.rownames, cat.ptype,
cont.varlist, cont.header, cont.ptype, strat, cat.rmstat, cont.rmstat,
dec, pname, colnames, output, vspace, varorder, stripe, stripe.col, header.style,
factor.style, stat.style, nowrap, caption, footer, tspanner, n.tspanner,
cgroup, n.cgroup, col.columns)

Arguments

dat

Clean data frame input of all variables used for the summary table.

cat.varlist

Vector of categorical variable names. Optional; defaults to NULL.

cat.header

Ordered vector of short descriptions for each categorical variable. Optional; defaults to variable names.

cat.rownames

Ordered list of vectors providing row names for each level of each vector found in cat.varlist. Optional; defaults to the coded value of each level.

cat.ptype

Ordered vector of tests requested to add p-values to table for categorical variables. Optional; defaults to no p-values. See stat.col for a complete list of options.

cont.varlist

Vector of continuous variable names. Optional; defaults to NULL.

cont.header

Ordered vector of short descriptions for each continuous variable. Optional; defaults to variable name.

cont.ptype

Ordered vector of tests requested to add p-values to table for continuous variables. Optional; defaults to no p-values. See stat.col for a complete list of options.

strat

Vector of one or more stratifying variables. Optional; defaults to no stratification.

cat.rmstat

Ordered list of vectors of statistics that should be removed from respective final summaries of categorical variables.

cont.rmstat

Ordered list of vectors of statistics that should be removed from respective final summaries of continuous variables.

dec

Integer value indicating the number of decimal places to be printed for each summary statistic. Optional; defaults to 2.

pname

Logical indicator for whether to print statistical test used beneath each p-value. Optional; defaults to TRUE.

colnames

Ordered vector of column names for the table. Optional; defaults to levels of stratifying variable(s) with an overall summary column.

output

Choice of formatted table output: "html", "latex", or "plain". Optional; defaults to plain text printed to the console.

vspace

TRUE for additional vertical whitespace between variables (default). Optional.

varorder

Order of variables in the outputted table. Defaults to "data", or the order of variables in the inputted dataset. Alternatively, variables may be presented alphabetically using the "abc" option. Optional.

stripe

HTML output only: logical indicator for whether to zebra stripe every other variable in the table. Optional; defaults to TRUE.

stripe.col

HTML output only: hex color code to be used for zebra striping the table. Optional; defaults to a light gray, #F7F7F7.

header.style

Variable name style: "plain", "bold", "italic", or "bolditalic". Optional; defaults to "bold".

factor.style

Variable factor levels style: "plain", "bold", "italic", or "bolditalic". Optional; defaults to "bold".

stat.style

Summary statistic style: "plain", "bold", "italic", or "bolditalic". Optional; defaults to "plain".

nowrap

HTML output only: option to prevent text wrapping of long lines to the table output. Useful for generating wide tables with knitr. Optional; defaults to TRUE.

caption

Table caption. Optional; no default.

footer

Table footer. Optional; no default.

tspanner

HTML output only: Rowwise table spanner, passed to htmlTable. Optional; see ?htmlTable for default information.

n.tspanner

HTML output only: Vector of rows in each table spanner, passed to htmlTable. Optional; see ?htmlTable for default information.

cgroup

HTML output only: Column group headers, passed to htmlTable. Optional; see ?htmlTable for default information.

n.cgroup

HTML output only: Vector of columns under each group header, passed to htmlTable. Optional; see ?htmlTable for default information.

col.columns

HTML output only: Vector of column colors, passed to htmlTable. Optional; defaults to "none".

Value

Returns a table of summary statistics for specified categorical and continuous variables in the requested output format. The plain text default returns a formatted data frame to the console.

Note

A few miscellaneous notes:

Table output to HTML and LaTeX require the package dependencies htmlTable and xtable

If missing values occur in stratifying variables (strat =), then the observations with missings will be removed from the table, and a comment will be printed indicating the total number removed. If multiple stratifying variables are provided, look to the console for a summary of total missing observations for each variable.

Author(s)

Erica Wozniak

See Also

Table1 quick.table cat.var cont.var stat.col out.plain out.latex out.html

Examples

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library(survival)

# Example with non-HTML options
make.table(dat   = pbc,
    cat.varlist  = c('stage', 'sex'),
    cat.header   = c('Stage', 'Sex'),
    cat.rownames = list(c('I', 'II', 'III', 'IV'), c('Male', 'Female')),
    cat.ptype    = c('fisher', 'fisher'),   
    cont.varlist = c('bili', 'copper'),
    cont.header  = c('Bilirubin', 'Urine copper'),
    cont.ptype   = c('wilcox', 'wilcox'), 
    strat        = c('trt'),
    # Remove row percents from all categorical variables (list is recycled)
    cat.rmstat   = list('row'),
    # Remove missing, min/max from bili and no summary stats from copper
    cont.rmstat  = list(c('miss', 'minmax'), 'None'),
    colnames     = c('', 'D-penicillamine', 'Placebo', 'Overall', 'p-value')
    )
    
# Example with HTML options
library(htmlTable)
make.table(dat   = pbc,
    cat.varlist  = c('stage', 'sex'),
    cat.header   = c('Stage', 'Sex'),
    cat.rownames = list(c('I', 'II', 'III', 'IV'), c('Male', 'Female')),
    cat.ptype    = c('fisher', 'fisher'),   
    cont.varlist = c('bili', 'copper'),
    cont.header  = c('Bilirubin', 'Urine copper'),
    cont.ptype   = c('wilcox', 'wilcox'), 
    strat        = c('trt'),
    cat.rmstat   = list('row'),
    colnames     = c('', 'D-penicillamine', 'Placebo', 'Overall', 'p-value'),
    output       = 'html',   
    # Check out \url{www.color-hex.com}
    stripe.col = '#f4dfd0'
    )

emwozniak/Table1 documentation built on May 13, 2017, 6:06 p.m.