set_diff
conf_int
in qacf
has been modified from 0.05
to 1 - getOption("qwraps2_alpha", 0.05)
ggplot2_extract_legend
is now and S3 methodqable
is now and S3 method and has gained a new argument kable_args
to make it clear what values are used by qable
and which are passed to knitr::kable
(#84)summary_table
has gained two arguments, qable_args
and kable_args
to help with passing through arguments and being able to use the features of knitr::kable (#84)summary_table
has it’s own vignette.mean_se
to provide the mean and standard error of the mean in the same format as the mean_sd
function.
Add Precision-Recall curve, qprc
, to complement ROC, qroc
.
Add quick “restricted mean survival time,” qrmst
method.
Binary Operators:
%s%
for “adding” strings together, e.g., "A" %s% "B" %s% "C"
is equivalent to paste0("A", "B", "C")
add append
argument to frmt
qable
has been modified to return a character matrix with the S3 class qwraps2_qable
. A print
method has been added as a wrapper to knitr::kable
to generate the table with the wanted markup. This change will allow end users to modify the matrix generated by qable
and print the markup results with ease. This will be particularly useful when using summary_table
and added bespoke p-values to the rows in a “table 1.”
spin_comments
returns TRUE
or FALSE
with the notes on the matching/mismatched comments as an attribute of the return object.
Extend the S3 methods provided for qroc_build_data_frame
Potentially breaking Change confusion_matrix
has been undergone a major refactor. If nothing else, the return object is now a data.frame with more output than before. The inputs are hopefully easier for end users as well. This change includes the addition of the function auc
and major refactor of qroc
and qprc
.
summary_table_042
and tab_summary
, the tidyverse versions of summary table that had been deprecated have been removed from the package. (#96)
qroc_build_data_frame
as been deprecated in favor of auc
set_diff
spin_comments
- a tool to identify opening and closing pairs of comments in a .R file expected to go through knitr::spin. Built to help resolve the “comments must be put in pair of start and end delimiters” error that can be thrown by knitr::spin.mtcars2
is a fully documented data set provided as part of the qwraps2 package.summary_table
has a by
argument and supports summaries by more than one variable.
The example data set mtcars2
is now exported as part of the package. The construction of this data set is documented in a new vignette, vignette("qwraps2-data-sets")
pefr
for peak expiratory flow rate data from Martin and Altman
vignette("qwraps2-data-sets")
Examples, and extended details, for graphics have been added to new vignette vignette("qwraps2-graphics")
summary_table
no longer generate an error (#90)...
passes values arguments to stats::predict
via qroc
and qroc_build_data_frame
reduced the use of non-base R, specifically tidyverse and magrittr, within the base code of qwraps2. Focus on base R methods instead. This will, hopefully, improve long term stability of the package and reduce warnings and error generated by an ever changing tidyverse api. This includes a by
argument (#100), and other notes related to #96, #98, and #71.
deprecated the transform argument in mean_ci
– to easy to have bad results come out of that option. Think about the delta method.
If the a variable in a data.frame has an attributed called “label” then that label will be used in the rgroup for qsummary
and summary_table
, (#74)
backtick
is provided as a work around for a knitr::spin
issue. The function wraps text in backticks so that backticks do not need to be explicitly used in a .R file expected to be spun to .Rmd.
Comment out a test due to the change in random number generating for sample
. (#72)
rbind.qwraps2_summary_table
(#55, #56)cbind.qwrap2_summary_table
check attributes of objects to be combined together. (#56)tab_summary
with more than one variable, e.g., in a sapply
call. (#53)qsummary
will return the first (min) and last (max) for variables where inherit(var, "Date")
is TRUE
.tab_summary
has been deprecated, use qsummary
instead. A warning message will be given to the user at this time. tab_summary
will be removed completely in a later version.
create_pkg
has been deprecated and removed from the package. The function was going to need a massive rewrite to deal with changes to devtools and usethis. Effectively, the function would no longer work and this deprecation is just being pragmatic.
Added lazyload_cache_dir
and lazyload_cache_labels
for (lazy)loading of cached chunks. Very useful for loading cached knitr
code chunks into an interactive R session.
Added traprule
for a quick way to integrate a numeric vector
Added create_pkg
: a wrapper about devtools::create
with more defaults that I prefer.
Added a file_check
(#50) to check for read access and optionally md5sum of files.
Added a pkg_check
(#51) to check if a list of packages are available.
Added functions for geometric mean, variance, and standard deviation. (#52) See the summary-statistics vignette for details.
Extended the documentation for logit
and invlogit
to reference bases R methods.
Added to the examples for summary_table
showing how to add a caption to a LaTeX table (#39)
step ribbon used in qkmplot
(#45)
Factor levels as characters in summary_table
(#48)
qkmplot
works for intercept only models (#38)
frmtci.data.frame
method added.tab_summary
methods to new arguments: n_perc_args
and envir
. The former gives the end user control over the formatting options passed to n_perc
and the latter controls the environment
associated with the generated formulae.frmtci.matrix
using the est
arg correctlysummary_table
qacf
plot (#11)ll
an improved version of ls()
rtitle
option added to qable
(#35)perc_n
reports the strings in the correct order.qable
summary_table
and tab_summary
added (#33)vignette("summary-statistics, package = "qwraps2")
logit
and invlogit
functions added. Using Rcpp so they are fast.format
is correctly passed from qwraps2::qable
to knitr::kable
’s format
argument.This is a long over due version bump. Many new features and bug fixes have been made since 0.1.0.
confusion_matrix
produces the correct confusion matrix. Prior version could transpose the result.gmean_sd
displays the correct geometric standard deviationmean_sd
and gmean_sd
have better show_n
handling.print.confusion_matrix
provides more detail to make it clear which variable is the Truth and which is the Prediction.ggplot2_extract_legend
added (#6)show_n
functionality for median_iqr
implemented. (closes #24)frmtci
added (#32)mean_ci
addedconfusion_matrix.formula
no longer uses named columns. The function only worked when called from confusion_matrix.default
. Fix allows the function to be used as intended.gmean_sd
returns the geometric mean and standard deviationconfusion_matrix
method has been modified. Please read the documentation. If you used version 0.1.2 these changes will affect your work. The confusion_matrix
is now an S3 generic.median_iqr
returns a formatted string with the median and IQR of a data vector.perc_n
similar to the n_perc
but returns a string of the form p% (n = N)
.n_perc
has option to suppress the percent symboln_perc0
added in 0.1.1.9004 sets defaults which may be preferred for tables.qkmplot
for plotting Kaplan Meier curvesqable
creates knitr::kable
tables with row groups and names similar to hmisc::latex
or htmlTable::htmlTable
.Pushed to CRAN on 20 April 2015.
extract_fstat
extracts the F-statistic from lm
extract_fpvalue
extracts and formats the omnibus F-test p-value from lm
mean_sd
passes the digits
option to frmt
correctly (#20)Initial release.