tabglm_svy: Generate Summary Tables of Fitted Generalized Linear Models...

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

Description

This function takes an object returned from the svyglm function and generates a clean summary table for a statistical report. Similar to tabglm, but for survey data. Relies heavily on the 'survey' package [1, 2].

Usage

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tabglm.svy(svyglmfit, latex = FALSE, xlabels = NULL, ci.beta = TRUE, inference = "wald.t",
           decimals = 2, p.decimals = c(2, 3), p.cuts = 0.01, p.lowerbound = 0.001, 
           p.leading0 = TRUE, p.avoid1 = FALSE, basic.form = FALSE, intercept = TRUE, 
           n = FALSE, events = FALSE, greek.beta = FALSE, binary.compress = TRUE, 
           bold.colnames = TRUE, bold.varnames = FALSE, bold.varlevels = FALSE, 
           predictor.colname = "Variable", print.html = FALSE, 
           html.filename = "table1.html")

Arguments

svyglmfit

An object returned from svyglm function call [1,2].

latex

If TRUE, object returned is formatted for printing in LaTeX using xtable [3]; if FALSE, formatted for copy-and-pasting from RStudio into a word processor.

xlabels

Optional character vector to label the x variables and their levels. If unspecified, the function uses the variable names and values themselves.

ci.beta

If TRUE, the table returned will include a column for Wald 95% confidence interval for the regression coefficients.

inference

If "wald.t", confidence intervals and p-values are based on t distributions with degrees of freedom given by svyglmfit$df.residual; if "wald.z", confidence intervals and p-values are based on z distributions.

decimals

Number of decimal places for numeric values in the table (except p-values).

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.

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).

basic.form

If TRUE, there is no attempt to neatly format factor variables and their levels, and the table returned is very similar to what you see when you run summary(glmfit).

intercept

If FALSE, the table returned will not include a row for the intercept.

n

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

events

If TRUE, the table returned will include a column for number of events observed. Only meaningful when the outcome variable is binary.

greek.beta

If TRUE, column headings refer to regression parameters as Greek letter beta rather than Beta. Only used when latex input is set to TRUE.

binary.compress

If TRUE, only one row of the table is dedicated to parameter estimates for each binary factor predictor. If FALSE, the table displays separate rows for the variable name and the two levels for each binary factor predictor, much like the presentation for factor variables with more than two levels.

bold.colnames

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

bold.varnames

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

bold.varlevels

If TRUE, levels of each factor variable are printed in bold font. Only applies if latex = TRUE and there is at least one factor variable included as a predictor.

predictor.colname

Character string with desired column heading for the column of predictors.

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

The function should work well with categorical predictors (factors), provided they are not ordered. For ordered factors, just convert to unordered before creating the svyglm object to pass to tabglm.svy. Note that you can define the levels of an unordered factor to control, which dictates which level is used as the reference group in regression models. For example, suppose a factor variable x takes values "low", "medium", and "high". If you write x = factor(x = x, levels = c("low", "medium", "high")), then you can run levels(x) to see that the levels are now arranged "low", "medium", "high". It is still a regular factor, but now if you use x as a predictor in a call to svyglm, "low" will be the reference group.

Interaction and polynomial terms are compatible with tabglm.svy. If interaction terms are included, the table will be formatted a little differently. Basically including an interaction is equivalent to setting basic.form to TRUE. All variable names and levels will be exactly as they appear when you run summary(svyglmfit), where svyglmfit is the object returned from a call to svyglm.

Value

A character matrix that summarizes the fitted generalized linear model. If latex is set to TRUE, the character matrix will be formatted for inserting into a Markdown/Sweave/knitr report using the xtable package [3].

Note

While tabglm.svy should work with any object generated by a call to svyglm, not all possibilities have been tested. Therefore in general I recommend always doing a quick check that the table created by tabglm.svy matches the information in the svyglm object itself.

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 [4]. 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. Lumley T (2012). survey: analysis of complex survey samples. R package version 3.28-2, https://cran.r-project.org/package=survey.

2. Lumley T (2014). Analysis of complex survey samples. Journal of Statistical Software 9(1): 1-19.

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

4. 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

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

Examples

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