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Quick Wraps for Reproducible Reports

Source: R/qwraps2-package.R
qwraps2-package.Rd

qwraps2 is a collection of helper functions for authoring reproducible analysis reports. The package focuses on formatted summary statistics, summary tables, regression-result formatting, and ggplot2-based plots.

Details

Several wrappers for ggplot2-style graphics are provided, including receiver operating characteristic curves, precision-recall curves, Bland-Altman plots, autocorrelation plots, and Kaplan-Meier plots. These functions include qroc, qprc, qacf, qblandaltman, and qkmplot.

Other functions quickly generate meaningful character strings for reporting results in .Rnw, .Rmd, or similar report files.

Vignettes

Options

There are several options which can be set via options and will be used via getOption. The following lists, in alphabetical order the different options which are available and what they control.

  • getOption("qwraps2_alpha", 0.05) significance level, used for generating (1 - getOption("qwraps2_alpha", 0.05)) * 100% confidence intervals, and determining significance for p-value < getOption("qwraps2_alpha", 0.05).

  • getOption("qwraps2_frmt_digits", 2) Number of digits to the right of the decimal point for any value other than p-values.

  • getOption("qwraps2_frmtp_case", "upper") set to either 'upper' or 'lower' for the case of the 'P' for reporting p-values.

  • getOption("qwraps2_frmtp_digits", 4) Number of digits to the right of the decimal point to report p-values too. If log10(p-value) < getOption("qwraps2_frmtp_digits", 4) then the output will be "P < 0.01", to however many digits are correct. Other options control other parts of the output p-value format.

  • getOption("qwraps2_frmtp_leading0", TRUE) to display or not to display the leading zero in p-values, i.e., if TRUE p-values are reported as 0.02 versus when FALSE p-values are reported as .02.

  • getOption("qwraps2_journal", "default") if a journal has specific formatting for p-values or other statistics, this option will control the output. Many other options are ignored if this is any other than default. Check the GitHub wiki, or this file, for current lists of implemented journal style methods.

  • getOption("qwraps2_markup", "latex") value set to 'latex' or to 'markdown'. Output is formatted to meet requirements of either markup language.

Journals with predefined formatting

  • Obstetrics & Gynecology

    • https://www.editorialmanager.com/ong/default.aspx

    • options(qwraps2_journal = "obstetrics_gynecology")

    • P-value formatting as of April 2015:

      Express P values to no more than three decimal places.

      Based on observations of published work, leading 0 will be omitted.

  • Pediatric Dentistry:

    • https://www.aapd.org/publications/

    • options(qwraps2_journal = "pediatric_dentistry")

    • P-value formatting as of March 2015.

      If P > .01, the actual value for P should be expressed to 2 digits. Non-significant values should not be expressed as "NS" whether or not P is significant, unless rounding a significant P-value expressed to 3 digits would make it non-significant (i.e., P=.049, not P=.05). If P<.01, it should be expressed to 3 digits (e.g., P=.003, not P<.05). Actual P-values should be expressed unless P<.001, in which case they should be so designated.

See also

Useful links:

Author

Maintainer: Peter DeWitt dewittpe@gmail.com (ORCID)

Authors:

Other contributors: