Changes to package DoE.base

This package is under development. Although substantial progress has been made, 
many parts are still considered experimental. Suggestions and bug reports are very welcome. 

Most immiment next steps for this package:
- extension of available orthogonal arrays for function oa.design 

17/09/2009, Version 0.9-2
- added meaningful title to showData display (was always undesign(dataframe))
- corrected a link in documentation for lm.design

14/09/2009, Version 0.9-2
- add.response now converts the name of a numeric variable to a valid R name. This 
  solves issues with using add.response indirectly when applying it with a calculated response. 
- oa.design and fac.design now also convert factor names to valid R names using make.names
- param.design now converts given response names to valid R names.

11/09/2009, Version 0.9-1
- changed message to cat in print and summary
- added function SN for signal-to-noise ratio 
  (target only, since other versions are not scale invariant)
- added generic, default and design method for showData (in support of RcmdrPlugin.DoE)

07/09/09, Version 0.9
- export function contr.FrF2 
- fixed bugs in oa.design and fac.design for factor.names as an unnamed list 
  for cases with nfactors unspecified 
- made all experimental factors for function fac.design R factors per default 
  (previously, numeric 2-level experimental factors were exported as numerics)
- created method for aggregate for aggregating related response columns for the wide 
  designs (useful for repeated measurements and parameter designs)
- made contrasts option of function qua.design more user-friendly
- added function change.contr to change contrasts for design objects 
  even more user-friendly than with qua.design
- made function formula.design (method for function formula) a serious function that 
  covers the currently available design types for packages DoE.base, FrF2 and DoE.wrapper
- added a generic, a default and a class design method for function lm,
  the class design method of which does default analyses and adds the class lm.design 
  to the output object
- added a summary method for class lm.design that adds a class summary.lm.design 
  to a standard output object from summary.lm
- added print methods for classes lm.design and summary.lm.design in order to
  make sure that automatic changes to the data body (like 
  omission of center points or aggregation) cannot go unnoticed
- added function iscube (identical to the one in package FrF2) as an internal function  
  in support of lm.design
- bug fix: [.design generated a warning for logical i 
- bug fix: repeat.only element of design.info of wide format repeated measurement designs 
  was TRUE, which led to inconsistent behavior (fixed in function reptowide)

24/08/09, Version 0.8
- updated qua.design to also be able to make quantitative designs qualitative (except lhs designs), 
  fixed several bugs in qua.design, added a test file, and tidied the code
- made functions fac.design and oa.design tolerate factor.names to be an unnamed list
- bug fix: plot.design did not work, if design.info had a quantitative element with all entries NA
- removed bug for add.response, if some but not all response values are NA and replace=FALSE
Thanks to Matthias Burger for initiating the following improvements:
- exported function origin and added a usage example (was unintentionally internal before)
- eliminated instances of partial argument matching in function html.data.frame
- use functions comment and comment<- from package base and do not define special function here
- fixed installation note regarding global binding of result
- improved markup in Rd files


17/08/2009, Version 0.7
- added function plot.design for allowing to deviate from plot.design 
  in package graphics as appropriate
- splitted documentation for class design into documentation of class itself 
  with direct accessor functions on the one hand and methods for the class 
  on the other hand
- generalized function des.recode to be usable within FrF2 as well in place of the 
  previously existing internal function within FrF2; 
  made the function visible rather than internal
- bug fix: explicitly disabled qua.design for designs with center points for the time being
  (it is intended (but not trivial) to allow switching away from quantitative later)

12/08/2009, Version 0.6-1
- added further design types to designs for which run.order is displayed
  (for upcoming version of FrF2)
- bugfix: function design.info refused to assign correct design info element 
  to blocked designs

11/08/2009, Version 0.6
- further restricted the designs to be treatable by function cross.design 
  (splitplot and combined designs excluded, wide version designs excluded, 
  designs with response.names excluded);
  this should not limit reasonable use much and greatly reduces the number 
  of cases to be distinguished
- improved the design.info content for designs output by function cross.design, 
  particularly the generators element (in case of FrF2.generator designs), but also 
  for the elements generating.oa, origin, residual.df, clear, res3, map, nlevels 
  (the last two are set to NULL and replaced by elements cross.map and cross.nlevels 
  respectively)
- modified the type of designs output by function paramtowide to be the type of the 
  inner array design suffixed by .paramwide
- modified the design.info for wide parameter designs to refer to the inner array 
  only (the outer array is usually the noise array that is aggregated over in various 
  ways for analysis purposes)
- modified summary.design (printing of response for wide format designs) 
- added function qua.design for switching between quantitative and qualitative factors 
  and choosing contrasts for qualitative factors (limited freedom of choice for contrasts!)
- documentation bug fix: nruns in oa.design gives the *minimum* number of runs


31/07/2009 Version 0.5
- changed R version to R-2.8.0 or newer (extractor for class design does not work 
  with earlier versions)
- added function print.design for printing useful information along with the design
- added function summary.design for providing key information from design.info in 
  convenient format
  (will be developed further and may still change)
- added functions reptowide and reptolong to reshape the experiment for 
  repeated measurements (repeat.only=TRUE) between wide and long shape;
  still experimental when applied to non-standard designs
- added function cross.design for crossing designs, 
  algorithm modified from function direct.sum from package conf.design
- added function param.design for creating Taguchi style inner/outer array designs, 
  and function paramtowide for setting these to wide format
- added type all to export.design so that both csv and html can be output at the same time; 
  meant for non-Excel users who want to work with csv file but nevertheless need the legend from 
  html file
- new function add.response to combine exported design with externally input response data;
  this is still somewhat experimental
- extended extractor method for designs to allow limited replication possibilities
- added modification step to creator attribute of designs modified by extraction
- removed intercept column from desnum attribute for designs created with 
  fac.design or oa.design or modified with factor.names
- bug fix: there were unintended names attached to the selected.columns element in design.info;
  these were not always correct and have now been removed
- bug fix: [.design did not always work correctly if j was not specified
- bug fix: run.no.in.std.order for run.order attribute of functions fac.design 
  and oa.design was previously made unique (by uniqueness of row.names for data frames); 
  corrected to yield the run numbers only
- bug fix: renamed randomized to randomize in functions oa.design and fac.design, 
  in line with package FrF2, and adjusted documentation accordingly

15/07/2009   Version 0.4-1
- bug fix in function fix.design: error checking for changed factors 
  had a bug and stopped perfectly legal edits from being stored.


13/07/2009   Version 0.4
- all experimental factors are now R-factors, even if they are numeric
- export.design can now also export the R workspace only, without csv or html
- bugfix: export.design did not correctly check replacing of files in case of 
  capital letters in file names
- modified export.design to handle factor labels with blanks from (future) GUI 
  package RcmdrPlugin.DoE
- added S3 generic for fix with default and design method
- extended design.info for output objects from function oa.design to include nruns, 
  nfactors and nlevels
- improved documentation of class design and the respective parts of the value 
  sections of functions oa.design and fac.design
- included function contr.FrF2 and constant Yates from package FrF2 
  (not exported; also remain in package FrF2)

27/06/2009   Version 0.3
- added list element creator to design.info attributes of created designs
  and improved documentation of class design and its accessors
- bug fix in documentation to export.design and several other small changes 
  in documentation and package description
- substantially improved and extended documentation to function oa.design

26/05/2009   Version 0.2
- modified internal function html.data.frame, 
  so that top row of html file created by export.design 
  is only one row when file is opened in Excel 
  (changed top row formatting from <h3> to <b>)
- added options filename and replace to function export, 
  in order to protect users from inadvertent replacement of existing 
  files and to allow filenames different from design names
- moved documentation of constant Letters from oa.design.Rd 
  to Utilities.Rd