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Package options

Source: R/surveytable.R
surveytable-options.Rd

This article is for more advanced users. Typical users, see set_opts() and show_opts() to set and show certain options.

Details

To view all available options, use show_options(). Below is a description of some noteworthy options.

Printing using various table-making packages

The tabulation functions return objects of class surveytable_table (for a single table) or surveytable_list (for multiple tables, which is just a list of surveytable_table objects). A surveytable_table object is just a data.frame with the following attributes: title, footer, and num, which is the index of columns that should be formatted as a number.

Naturally, these objects can be printed using a variety of packages. surveytable ships with the ability to use huxtable, gt, or kableExtra. See the output argument of set_opts().

You can supply custom code to use another table-making package or to use one of these table-making packages, but in a different way. The two relevant options are surveytable.output_object and surveytable.output_print.

surveytable.output_object is the name of a function with the following arguments: x and ..., where x is a surveytable_table object. This function returns an object from a table-making package, for example, it returns a gt object. Be sure that this package is installed.

surveytable.output_print is the name of a function with the following arguments: x and ..., where x is an object returned by the surveytable.output_object function. The surveytable.output_print function prints this object.

For an example of how this works, see the internal functions surveytable:::.as_object_huxtable and surveytable:::.print_huxtable.

Low-precision estimates

Optionally, all of the tabulation functions can identify low-precision estimates. Turn on this functionality using any of the following: set_opts(lpe = TRUE), set_opts(mode = "nchs"), set_survey(*, mode = "nchs"), or options(surveytable.find_lpe = TRUE).

By default, low-precision estimates are identified using National Center for Health Statistics (NCHS) algorithms. However, this can be changed, as described below.

Here is a description of the options related to the identification of low-precision estimates.

  • surveytable.find_lpe: should the tabulation functions look for low-precision estimates? You can change this directly with options() or with either set_opts() or set_survey().

  • surveytable.lpe_n, surveytable.lpe_counts, surveytable.lpe_percents: names of 3 functions.

The argument for surveytable.lpe_n is a vector of the number of observations for each level of the variable.

The argument for surveytable.lpe_counts is a data frame with count-related estimates. Specifically, the data frame has the following variables:

  • x: point estimates of counts

  • s: SE

  • ll, ul: CI

  • samp.size: effective sample size

  • counts: actual sample size

  • degf: degrees of freedom

The argument for surveytable.lpe_percents is a data frame with percent-related estimates. Specifically, the data frame has the following variables:

  • Proportion: point estimates of proportions (between 0 and 1)

  • SE: SE

  • LL, UL: CI

  • n numerator: the number of observations for which the variable is TRUE

  • n denominator: the total number of observations

Each of these functions must return a list with the following elements:

  • id: the name of the algorithm used, such as "NCHS presentation standards"

  • flags: a vector. For each level of the variable, short codes indicating the presence of low-precision estimates.

  • has.flag: a vector of short codes that are present in flags.

  • descriptions: a named vector. The names must be the short codes, the values are the longer descriptions.

For example, if a variable has 3 levels, flags might be c("", "A1 A2", ""). This indicates that for the first and third level, nothing was found, whereas for the second level, two different things were found, indicated by short codes A1 and A2. In this case, has.flag = c("A1", "A2"), descriptions = c(A1 = "A1: something", A2 = "A2: something else").

See also

Useful links:

Other options: set_opts(), set_survey(), show_options()

Author

Maintainer: Alex Strashny AStrashny@cdc.gov (ORCID)