Comprehensive data analysis software, and the name "cg" stands for "compare groups." Its genesis and evolution are driven by common needs to compare administrations, conditions, etc. in medicine research and development. The current version provides comparisons of unpaired samples, i.e. a linear model with one factor of at least two levels. It also provides comparisons of two paired samples. Good data graphs, modern statistical methods, and useful displays of results are emphasized.
Fixed missing requirements of digits argument in the comparisonsGraph method for OneFactor and PairedDifference objects. The main error appeared when graphing the min and max digits range of "differences". This discovery happened when data was fit and analyzed in its original scale. The default logarithmic scale case was unaffected since the min and max "percent/ratio difference" numbers does not need the missing digits= argument.
Fixed an oversight to check that if the refgrp= argument is used in a comparisonsTable call for a OneFactorFit object, then the type= argument needs to be also set to "allgroupstocontrol." Thanks again to Vince Pileggi for reporting these bugs.
Corrected placement of warning message in samplesizeGraph() calls when the calculated sample sizes are greater than a specified threshold (default 1000). This placement is based on the largest.empty() function in Frank Harrell's Hmisc package.
Fixed a graph render error where logscale=FALSE was not specified in setting up x-axis ticks for the comparisonsGraph() method for cgOneFactorComparisonsTable objects when the endpoint is analyzed in the original (not transformed) scale. Thanks to Vince Pileggi for reporting the error.
Revised Authors fields in documentation to reflect creator, contributor roles, etc. with the recent syntax enhancements.
deprecated an internal, non-exported function validDataFormat(); replaced by validArgMatch()
Reformatted this file to conform to R special requirements. Thanks go to Hadley Wickam and his http://adv-r.had.co.nz/Documenting-packages.html link to clarify that for me.
Added paired samples methods and functions, with a base label "PairedDifference".
Removed specific arguments in these generics: comparisonsTable, samplesizeTable, and samplesizeGraph. The arguments included: mcadjust, contrastmatrix, device, and refgrp. All of these have no meaning for the PairedDifference methods, so to use the same generics as used for the OneFactor methods, these are now callable through the dots arguments.
Revised Depends and Imports configurations to align with CRAN checks.
Corrected numerous typographical errors in the help files.
Refined use of the Hmisc::largest.empty function to avoid warning of "Foreign function call with �PACKAGE� argument in a different package"
Added CITATION file since a Journal of Statistical Software article on the manuscript is due to soon be published in 2013.
Changed name of this file from CHANGES to NEWS and placed it in the /inst subdirectory.
Corrected DESCRIPTION file to have only 1 maintainer, and corrected package help file to reflect the right version.
No functional changes from 0-9.4
Discovered and fixed bug of stamp that notes the graph symbols used for boxplot() method
Dependency on R 2.14.0 and VGAM 0.8.6 or greater was tested and clarified after finding CRAN warnings.
Cleaned up plotting of one-factor group level names on the x-axis when they are rotated, by making sure there is clear whitespace between the right end of each group name label and the x-axis.
Cleaned up bad mixing of base graphics and grid/lattice functions in cgDevice(), which did not allow file output graphics devices to work properly.
Fixed bug in print method of cgOneFactorComparisonsTable object when addpct=TRUE is specified for comparison of groups on untransformed data. Thanks to Journal of Statistics (JSS) anonymous reviewer of submitted paper of cg package for reporting this bug.
For output from the comparisonsTable method, the label "geomean" is used in place for "mean" to make clear that geometric means are displayed. Thanks to JSS anonymous reviewer for remarks that led to the decision of this label change.
Added simple print and summary methods for the cgOneFactorFit object, again thanks to a suggestion of a JSS reviewer.
Changed calls of VGAM:::cnormal1 to VGAM:::cennormal1 due to rename in VGAM package when version 0.8-3 was released 17 June 2011.
Since VGAM 0-8.3 would not load in R 2.11 in my Windows installation, the cg package now requires >= R 2.12.0 and VGAM >= 0.8-3.
Removed duplication of author and maintained email address contact in the DESCRIPTION FILE.
Switched to more conventional package number versioning (from initial release 0.9.0 (on 20 December 2010) to 0.9-1 .
No functional changes were made in the package in this release.
Added this CHANGES file.