The htmlTable, forestplot, Gmisc, and Greg packages contain useful functions for graphics, tables etc that I’ve created/adapted for my own research. Gmisc was published on CRAN 2014-02-02, and as the
forestplot (prev. known as
forestplot2) have grown these have moved into separate packages. Some of the regression still needs some more testing before going on CRAN and these are in the Greg-package.
News since version >1.0
htmlTable() has moved as of 1.0 to a separate package in December 2014. The Gmisc will depend on this new package and the change should have minimal impact on user experience. There are plenty of new features and a few API-changes that may be good to be aware of (although the old API will work for 1-2 years only with warnings):
- rowname -> rnames
- headings -> header
- halign -> align.header
- cgroup.just -> align.cgroup
- rgroupCSSstyle -> css.rgroup
- rgroupCSSseparator -> css.rgroup.sep
- tspannerCSSstyle -> css.tspanner
- tspannerCSSseparator -> css.tspanner.sep
- rgroup.padding -> padding.rgroup
- rowlabel.pos -> pos.rowlabel
- caption.loc -> pos.caption
- altcol -> col.rgroup
- tableCSSclass -> css.table.class
The htmlTable-package is all about generating pretty tables, you can find some examples from my blog-posts below:
- Introducing the htmlTable-package
- Tables from R into Word
- Fast-track publishing using knitr: table mania
forestplot() has moved as of 1.0 to a separate package in December 2014. The Gmisc will have a deprecated call but the link between the package will be removed in the future (2016?). There are plenty of new features and a few API-changes that may be good to be aware of (although the old API will work for 1-2 years only with warnings):
- legend.* -> legend_args and takes input from
- confintNormalFn -> fn.ci_norm
- confintSummaryFn -> fn.ci_sum
- legendMarkerFn -> fn.legend
- main -> Title
The package also contains a vignette that you may want to look into:
The Gmisc package 1.0 was releast in December 2014 on CRAN. Apart from minor API-changes there is the new
mergeDesc() that I recommend looking into. Compiling a descriptive table has never been easier.
The Greg package is still in 1.0 development and may take some time before maturity. You can still download and play around with the new version by specifying the
ref="v1.0" as below:
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# If you haven't installed devtools before, # now is the time by uncommenting next line: # install.packages("devtools") # Install the Greg package using: devtools::install_github("gforge/Greg")
As CRAN limits the update frequency to 1-2 months you can download the most recent package from GitHub. You can download them using the
devtools package and downloading the develop branch:
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# If you haven't installed devtools before, # now is the time by uncommenting next line: # install.packages("devtools") # Install the htmlTable package using: devtools::install_github("gforge/htmlTable", ref="develop") # Install the forestplot package using: devtools::install_github("gforge/forestplot", ref="develop") # Install the Gmisc package using: devtools::install_github("gforge/Gmisc", ref="develop")
Writing documentation is hard and any suggestions are greatly appreciated. Try also to check that the output makes sense as bug-hunting is a difficult and endless task. If you want to suggest some changes, please use the GitHub-version as it has all the roxygen documentation and all my comments.
Some of the neat Gmisc functions that you will find are:
- getDescriptionsStatsBy – for generating a table 1 this is a very useful function that makes this much easier.
- transitionPlot – for generating a transition plot
- bezierArrowSmpl/bezierArrowSmplGradient – nicer alternatives to the default bezier arrow.
And the Greg-package contains among other things:
- printCrudeAndAdjusted – a useful function for generating a table with a models crude and adjusted estimates.
- plotHR – this is based upon r-forge Reinhard Seifert’s plotHR function. The function allows multiple models to be plotted on top of eachother, when used together with transparency (the alpha channel of the rgb) it is very convenient for comparing different subgroups, time-spans or adjusted/unadjusted regressions.
I hope you find the packages as useful as I do. And in case you were wondering – Yes, the Gmisc name is a ripoff from Frank Harrell’s useful Hmisc-package.