NEWS.md

qwraps2 0.6.1

• bug fix in qroc - use geom_path instead of geom_line
• extend return section of confusion_matrix to fix CRAN NOTE

qwraps2 0.6.0

General Improvements

• Unit testing is done in base R, moved away from testthat.
• Updating roxygen dependencies to correctly document the package.
• Extend documentation and testing of set_diff
• The default value for conf_int in qacf has been modified from 0.05 to 1 - getOption("qwraps2_alpha", 0.05)
• ggplot2_extract_legend is now and S3 method
• qable 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)
• vignettes have been renamed to have a consistent "qwraps2-" structure.
• summary_table has it's own vignette.

New Features

• 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

User Visible Changes

• 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.

Deprecated / Removed

• 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

qwraps2 0.5.2

Bug Fixes

• Correct error in summary table cbind (#104)

qwraps2 0.5.1

Bug Fixes

• Correct error in output of bootstrapped results for confusion matrices (#102)

qwraps2 0.5.0

New Features

• 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")

• A data set pefr for peak expiratory flow rate data from Martin and Altman (1986) has been added to the package. Documentation of the data set is found in the vignette("qwraps2-data-sets")

• Examples, and extended details, for graphics have been added to new vignette vignette("qwraps2-graphics")

Bug Fixes

• Scoping issue (#85) in the confusion matrix call
• Long object names passed to summary_table no longer generate an error (#90)

Improvements

• confusion matrix returns additional statistics (#87)

  • F1
  • MCC

• ... 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.

qwraps2 0.4.2

New Features

• 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.

qwraps2 0.4.1

Comment out a test due to the change in random number generating for sample. (#72)

qwraps2 0.4.0

New Features

• rbind.qwraps2_summary_table (#55, #56)
• formatting options for package names and urls to CRAN, gitlab, and github. (#68)

Improvements:

• cbind.qwrap2_summary_table check attributes of objects to be combined together. (#56)
• Added example to vignette to address the use 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.

Deprecation

• 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.

qwraps2 0.3.0

New Features

• 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.

Improvements:

• 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)

Bug Fixes

• Factor levels as characters in summary_table (#48)

• qkmplot works for intercept only models (#38)

qwraps2 0.2.4

New Features

• frmtci.data.frame method added.
• for the 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.

Bug Fixes:

• frmtci.matrix using the est arg correctly

Improvements

• extended documentation and examples for summary_table

qwraps2 0.2.3

New features

• qacf plot (#11)
• ll an improved version of ls()
• rtitle option added to qable (#35)

Bug Fixes:

• perc_n reports the strings in the correct order.

Improvements:

• Extended documentation for qable
• Minor edits and extensions to the summary-statistics vignette.

qwraps2 0.2.2

New Features:

• summary_table and tab_summary added (#33)
• New vignette vignette("summary-statistics, package = "qwraps2")

Bug Fixes:

• boot strapped statistics in confusion matrices

qwraps 0.2.1

New Features:

• logit and invlogit functions added. Using Rcpp so they are fast.

Bug Fixes:

• format is correctly passed from qwraps2::qable to knitr::kable's format argument.

qwraps 0.2.0

This is a long over due version bump. Many new features and bug fixes have been made since 0.1.0.

Bug Fixes:

• confusion_matrix produces the correct confusion matrix. Prior version could transpose the result.
• gmean_sd displays the correct geometric standard deviation

Improvements

• mean_sd and gmean_sd have better show_n handling.

New Features

• 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 added

qwraps 0.1.4

Bug Fixes:

• confusion_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.

qwraps 0.1.3

New features

• gmean_sd returns the geometric mean and standard deviation

Notable Changes

• The confusion_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.

qwraps 0.1.2

New features

• methods for finding the sensitivity and specificity of confusion matrices (contingency tables) added.
• 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 symbol
• n_perc0 added in 0.1.1.9004 sets defaults which may be preferred for tables.
• qkmplot for plotting Kaplan Meier curves
• qable creates knitr::kable tables with row groups and names similar to hmisc::latex or htmlTable::htmlTable.

qwraps 0.1.1

Pushed to CRAN on 20 April 2015.

New features

• extract_fstat extracts the F-statistic from lm
• extract_fpvalue extracts and formats the omnibus F-test p-value from lm
• P-value formatting for Obstetrics & Gynecology

New vignettes

• none

Minor improvements

• Set R dependence to 3.0.2 to match the dependence noted for dplyr
• Default setting for the qwraps2_frmtp_digits is 4 instead of 2.
• Spelling and grammar fixes in documentation (#21)

Bug fixes

• mean_sd passes the digits option to frmt correctly (#20)

qwraps2 0.1

Initial release.