tabfreq: Generate Frequency Tables for Statistical Reports

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

View source: R/tabfreq.R

Description

This function creates an I-by-J frequency table and summarizes the results in a clean table for a statistical report.

Usage

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tabfreq(x, y, latex = FALSE, xlevels = NULL, yname = NULL, ylevels = NULL, 
        quantiles = NULL, quantile.vals = FALSE, cell = "n", parenth = NULL, 
        text.label = NULL, parenth.sep = "-", test = "chi", decimals = NULL, 
        p.include = TRUE, p.decimals = c(2, 3), p.cuts = 0.01, p.lowerbound = 0.001, 
        p.leading0 = TRUE, p.avoid1 = FALSE, overall.column = TRUE, n.column = FALSE, 
        n.headings = TRUE, compress = FALSE, compress.val = NULL, bold.colnames = TRUE, 
        bold.varnames = FALSE, bold.varlevels = FALSE, variable.colname = "Variable",
        print.html = FALSE, html.filename = "table1.html")

Arguments

x

Vector of values indicating group membership for columns of IxJ table.

y

Vector of values indicating group membership for rows of IxJ table.

latex

If TRUE, object returned is formatted for printing in LaTeX using xtable [1]; if FALSE, formatted for copy-and-pasting from RStudio into a word processor.

xlevels

Optional character vector to label the levels of x, used in the column headings. If unspecified, the function uses the values that x takes on.

yname

Optional label for the y (row) variable. If unspecified, variable name of y is used.

ylevels

Optional character vector to label the levels of y. If unspecified, the function uses the values that y takes on. Note that levels of y will be listed in the order that they appear when you run table(y, x).

quantiles

If specified, function compares distribution of the y variable across quantiles of the x variable. For example, if x contains continuous BMI values and y is race, setting quantiles to 3 would result in the distribution of race being compared across tertiles of BMI.

quantile.vals

If TRUE, labels for x show quantile number and corresponding range of the x variable. For example, Q1 [0.00, 0.25). If FALSE, labels for quantiles just show quantile number (e.g. Q1). Only used if xlevels is not specified.

cell

Controls what value is placed in each cell of the table. Possible choices are "n" for counts, "tot.percent" for table percentage, "col.percent" for column percentage, "row.percent" for row percentage, "tot.prop" for table proportion, "col.prop" for column proportion, "row.prop" for row proportion, "n/totn" for count/total counts, "n/coln" for count/column count, and "n/rown" for count/row count.

parenth

Controls what values (if any) are placed in parentheses after the values in each cell. By default, if cell is "n", "n/totn", "n/coln", or "n/rown" then the corresponding percentage is shown in parentheses; if cell is "tot.percent", "col.percent", "row.percent", "tot.prop", "col.prop", or "row.prop" then a 95% confidence interval for the requested percentage of proportion is shown in parentheses. Possible values are "none", "se" (for standard error of requested percentage or proportion based on cell), "ci" (for 95% confidence interval for requested percentage of proportion based on cell), "tot.percent", "col.percent", "row.percent", "tot.prop", "col.prop", and "row.prop".

text.label

Optional text to put after the y variable name, identifying what cell values and parentheses indicate in the table. If unspecified, function uses default labels based on cell and parenth settings. Set to "none" for no text labels.

parenth.sep

Optional character specifying the separator between lower and upper bound of confidence interval (when requested). Usually either "-" or ", "" depending on user preference.

test

Controls test for association between x and y. Use "chi" for Pearson's chi-squared test, which is valid only in large samples; "fisher" for Fisher's exact test, which is valid in small or large samples; "z" for z test without continuity correction; or "z.continuity" for z test with continuity correction. "z" and "z.continuity" can only be used if x and y are binary.

decimals

Number of decimal places for values in table (no decimals are used for counts). If unspecified, function uses 1 decimal for percentages and 3 decimals for proportions.

p.include

If FALSE, statistical test is not performed and p-value is not returned.

p.decimals

Number of decimal places for p-values. If a vector is provided rather than a single value, number of decimal places will depend on what range the p-value lies in. See p.cuts input.

p.cuts

Cut-point(s) to control number of decimal places used for p-values. For example, by default p.cuts is 0.1 and p.decimals is c(2, 3). This means that p-values in the range [0.1, 1] will be printed to two decimal places, while p-values in the range [0, 0.1) will be printed to three decimal places.

p.lowerbound

Controls cut-point at which p-values are no longer printed as their value, but rather <lowerbound. For example, by default p.lowerbound is 0.001. Under this setting, p-values less than 0.001 are printed as <0.001.

p.leading0

If TRUE, p-values are printed with 0 before decimal place; if FALSE, the leading 0 is omitted.

p.avoid1

If TRUE, p-values rounded to 1 are not printed as 1, but as >0.99 (or similarly depending on values for p.decimals and p.cuts).

overall.column

If FALSE, column showing distribution of y in full sample is suppressed.

n.column

If TRUE, the table will have a column for sample size.

n.headings

If TRUE, the table will indicate the sample size overall and in each group in parentheses after the column headings.

compress

If y has only two levels, setting compress to TRUE will produce a single row rather than two rows. For example, if y is sex with 0 for female, 1 for male, and cell = "n" and parenth = "col.pecent", setting compress = TRUE will return a table with n (percent) for males only. If FALSE, the table would show n (percent) for both males and females, which is somewhat redundant.

compress.val

When x and y are both binary, and compress is TRUE, compress.val can be used to specify which level of the y variable should be shown. For example, if x is sex and y is obesity status with levels "Obese" and "Not Obese", setting compress to TRUE and compress.val to "Not Obese" would result in the table comparing the proportions of subjects that are not obese by sex.

bold.colnames

If TRUE, column headings are printed in bold font. Only applies if latex = TRUE.

bold.varnames

If TRUE, variable name in the first column of the table is printed in bold font. Only applies if latex = TRUE.

bold.varlevels

If TRUE, levels of the y variable are printed in bold font. Only applies if latex = TRUE.

variable.colname

Character string with desired heading for first column of table, which shows the y variable name and levels.

print.html

If TRUE, function prints a .html file to the current working directory.

html.filename

Character string indicating the name of the .html file that gets printed if print.html is set to TRUE.

Details

NA

Value

A character matrix with the requested frequency table. If latex is set to TRUE, the character matrix will be formatted for inserting into a Markdown/Sweave/knitr report using the xtable package [1].

Note

If you wish to paste your tables into Word, you can use either of these approaches:

1. Use the write.cb function in the Kmisc package [2]. If your table is stored in a character matrix named table1, use write.cb(table1) to copy the table to your clipboard. Paste the result into Word, then highlight the text and go to Insert - Table - Convert Text to Table... OK.

2. Set the print.html input to TRUE. This will result in a .html file writing to your current working directory. When you open this file, you will see a nice looking table that you can copy and paste into Word. You can control the name of this file with the html.filename input.

If you wish to use LaTeX, R Markdown, knitr, Sweave, etc., please see the package vignette for examples. In most cases, you have to set the latex input to TRUE and then use the xtable package [1].

If you have suggestions for additional options or features, or if you would like some help using any function in the package tab, please e-mail me at [email protected] Thanks!

Author(s)

Dane R. Van Domelen

References

1. Dahl DB (2013). xtable: Export tables to LaTeX or HTML. R package version 1.7-1, https://cran.r-project.org/package=xtable.

2. Kevin Ushey (2013). Kmisc: Kevin Miscellaneous. R package version 0.5.0. https://CRAN.R-project.org/package=Kmisc.

Acknowledgment: This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE-0940903.

See Also

tabmeans, tabmedians, tabmulti, tabglm, tabcox, tabgee, tabfreq.svy, tabmeans.svy, tabmedians.svy, tabmulti.svy, tabglm.svy

Examples

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# Load in sample dataset d and drop rows with missing values
data(d)
d <- d[complete.cases(d), ]

# Compare sex distribution by group, with group as column variable
freqtable1 <- tabfreq(x = d$Group, y = d$Sex)

# Same comparison, but compress table to show Female row only, show percent (SE) rather
# than n (percent), and suppress (n = ) from column headings
freqtable2 <- tabfreq(x = d$Group, y = d$Sex, compress = TRUE, compress.val = "Female",
                      cell = "col.percent", parenth = "se", n.headings = FALSE)

# Compare sex distribution by race, suppressing (n = ) from column headings and 
# showing percent (95% CI) rather than n (percent)
freqtable3 <- tabfreq(x = d$Race, y = d$Sex, n.headings = FALSE, cell = "col.percent")

# Use rbind to create single table comparing sex and race in control vs. treatment group
freqtable4 <- rbind(tabfreq(x = d$Group, y = d$Sex), tabfreq(x = d$Group, y = d$Race))
                            
# A (usually) faster way to make the above table is to call the the tabmulti function
freqtable5 <- tabmulti(dataset = d, xvarname = "Group", yvarnames = c("Sex", "Race"))
                        
# freqtable4 and freqtable5 are equivalent
all(freqtable4 == freqtable5)

# To move freqtable1 into Word, run write.cb(freqtable1) to copy the table onto your
# clipboard. Paste into Word, highlight the table and go to Insert - Table - Convert Text 
# to Table... OK. Alternatively, if you set print.html to TRUE, the function will write 
# a html file named html.filename to your current working directory. You can open this 
# file, copy the table, and paste it into Word.

tab documentation built on May 31, 2017, 5:05 a.m.