qwraps2 is a collection of helpful functions when working on a varied collection of different analysis reports. There are two types of functions, helpful data summary functions, formatting results from regression models, and ggplot2 wrappers.
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.
getOptions("qwraps2_alpha", 0.05) significance level, used for
generating (1 - getOptions("qwraps2_alpha", 0.05)) * 100% confidence
intervals, and determining significance for p-value <
getOptions("qwraps2_alpha", 0.05).
getOptions("qwraps2_frmt_digits", 2) Number of digits to the
right of the decimal point for any value other than p-values.
getOptions("qwraps2_frmtp_case", "upper") set to either
'upper' or 'lower' for the case of the 'P' for reporting p-values.
getOptions("qwraps2_frmtp_digits", 4) Number of digits to the
right of the decimal point to report p-values too. If
log10(p-value) < getOptions("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.
getOptions("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.
getOptions("qwraps2_journal", "default") if a journal has
specific formating 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.
getOptions("qwraps2_markup", latex) value set to 'latex' or
to 'markdowm'. Output is formatted to meet requirements of either markup
language.
getOptions("qwraps2_style", "default") By setting this option
to a specific journal, p-values and other output, will be formatted to
meet journal requirements.
Obstetrics \& Gynecology
options(qwraps2_journal = "obstetrics_gynecology")
P-value formating 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:
options(qwraps2_journal = "pediatric_dentistry")
P-value formating 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 note P is significant, unless rounding a significant P-value expressed to 3 digits would make it non significant (ie P=.049, not P=.05). If P<.01, it should be express to 3 digits (eg, P=.003, not P<.05). Actual P-values should be expressed unless P<.001, in which case they should be so designated.
Several wrappers for ggplot2 style graphics, such as ROC, AUC,
Bland-Altman, and KM
plots are provided. Named as qroc, qacf,
qblandaltman and
qkmplot to pay homage to qplot form ggplot2 and
the standard names for such plots.
Other functions are used to quickly generate meaningful character strings for outputting results in .Rnw, .Rmd, or other similar functions.