Log of /trunk/R

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Revision 197 - Directory Listing
Modified Thu Oct 15 16:07:21 2009 UTC (5 weeks, 4 days ago) by dupontct

reindented and cleaned up datadist.s

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Revision 196 - Directory Listing
Modified Thu Oct 1 16:33:05 2009 UTC (7 weeks, 4 days ago) by dupontct

reindented lrm.fit.s

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Revision 195 - Directory Listing
Modified Thu Oct 1 16:26:32 2009 UTC (7 weeks, 4 days ago) by dupontct

reindented lrm.s

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Revision 194 - Directory Listing
Modified Thu Oct 1 15:45:56 2009 UTC (7 weeks, 4 days ago) by dupontct

reindented predict.Design.s

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Revision 193 - Directory Listing
Modified Thu Oct 1 15:43:51 2009 UTC (7 weeks, 4 days ago) by dupontct

reindented predict.lrm.s

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Revision 190 - Directory Listing
Modified Mon Sep 14 21:34:36 2009 UTC (2 months, 1 week ago) by dupontct

Fixed mismatch on Varcov method function calls added missing tree packages to sugest list, fixed problems with Rd files

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Revision 171 - Directory Listing
Modified Mon Sep 14 15:27:27 2009 UTC (2 months, 1 week ago) by dupontct

merged changes from release_2.2 into trunk and added version bump from 2.2-0 to 2.3-0

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Revision 169 - Directory Listing
Modified Thu Sep 3 13:31:48 2009 UTC (2 months, 2 weeks ago) by harrelfe

prettied up a bit

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Revision 168 - Directory Listing
Modified Thu Sep 3 13:28:52 2009 UTC (2 months, 2 weeks ago) by harrelfe

added Varcov*, survfit.km->survfitKM

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Revision 166 - Directory Listing
Modified Thu Sep 3 13:14:44 2009 UTC (2 months, 2 weeks ago) by harrelfe

removed

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Revision 164 - Directory Listing
Modified Mon Aug 31 20:06:18 2009 UTC (2 months, 3 weeks ago) by dupontct

Stuff to make Design pass R check; fix bug in nomogram where it doesn't name elements of the returned object

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Revision 163 - Directory Listing
Modified Fri Aug 7 13:07:42 2009 UTC (3 months, 2 weeks ago) by harrelfe

fixed problem of non-alignment of row names if NAs were removed in which.influence.  Thanks to  Maria Melguizo <MSMelguizocastro@uams.edu> for finding the problem and providing a fix.

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Revision 162 - Directory Listing
Modified Mon Jul 27 23:24:29 2009 UTC (3 months, 3 weeks ago) by harrelfe

removed nmiss logic now in Design()
(done also for cphnew.s which is not added yet to repository)

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Revision 161 - Directory Listing
Modified Mon Jul 27 23:20:24 2009 UTC (3 months, 3 weeks ago) by harrelfe

Used newer R eval.parent function for evaluating model.frame
Used more streamlined way of passing only appropriate arguments to model.frame
Removed nmiss logic as now in Design()

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Revision 160 - Directory Listing
Modified Mon Jul 27 23:19:08 2009 UTC (3 months, 3 weeks ago) by harrelfe

removed nmiss logic as now in Design()

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Revision 159 - Directory Listing
Modified Mon Jul 27 23:18:37 2009 UTC (3 months, 3 weeks ago) by harrelfe

Logic for renaming terms in nmiss object created by na.delete moved into Design instead of duplicating it in all the fitting functions.

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Revision 158 - Directory Listing
Modified Sun Jul 26 15:05:48 2009 UTC (3 months, 4 weeks ago) by harrelfe

added nice printing of summary of NAs

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Revision 157 - Directory Listing
Modified Sat Jul 25 14:53:44 2009 UTC (3 months, 4 weeks ago) by harrelfe

used new RqFit

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Revision 156 - Directory Listing
Modified Sat Jul 25 14:53:25 2009 UTC (3 months, 4 weeks ago) by harrelfe

created a fitter creation function to expedite bootcov, validate, etc.  Is a model for the future.

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Revision 155 - Directory Listing
Modified Fri Jul 24 23:27:57 2009 UTC (4 months ago) by harrelfe

minor formatting improvement

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Revision 152 - Directory Listing
Modified Fri Jul 24 23:07:37 2009 UTC (4 months ago) by harrelfe

added new Design fitting function for quantile regression, i.e., version of rq in quantreg package

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Revision 151 - Directory Listing
Modified Fri Jul 24 23:06:27 2009 UTC (4 months ago) by harrelfe

added support for new function Rq for quantile regression

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Revision 150 - Directory Listing
Modified Fri Jul 24 23:04:22 2009 UTC (4 months ago) by harrelfe

look for fit$fitted.values in addition to fit$fitted

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Revision 147 - Directory Listing
Modified Mon Jul 6 19:57:24 2009 UTC (4 months, 2 weeks ago) by harrelfe

added type='joint' and arguments tol, jointonly

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Revision 145 - Directory Listing
Modified Mon Jun 29 20:30:42 2009 UTC (4 months, 3 weeks ago) by harrelfe

one more if(pr) but check the print at iteration zero - saw dups over reps

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Revision 144 - Directory Listing
Modified Mon Jun 29 20:08:16 2009 UTC (4 months, 3 weeks ago) by harrelfe

forgot to respect if(pr) in a few places

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Revision 143 - Directory Listing
Modified Mon Jun 29 19:09:43 2009 UTC (4 months, 3 weeks ago) by harrelfe

removed failure=2 from survreg.control as new version no longer supports

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Revision 142 - Directory Listing
Modified Mon Jun 29 19:09:28 2009 UTC (4 months, 3 weeks ago) by harrelfe

removed failure=2 from survreg.control as new version no longer supports

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Revision 141 - Directory Listing
Modified Thu Jun 25 21:09:03 2009 UTC (4 months, 4 weeks ago) by harrelfe

fixed bug: pr instead of !pr

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Revision 137 - Directory Listing
Modified Fri May 8 20:08:35 2009 UTC (6 months, 2 weeks ago) by dupontct

  * Fixed compatablity issues with survival in corperated survival C code into repository to prevent reacurace of problem.
  * version bump.

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Revision 136 - Directory Listing
Modified Sat May 2 18:24:50 2009 UTC (6 months, 3 weeks ago) by harrelfe

added ties=mean to approx() to avoid warnings

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Revision 135 - Directory Listing
Modified Tue Apr 28 17:33:22 2009 UTC (6 months, 3 weeks ago) by dupontct

indented summary.survfit.s

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Revision 134 - Directory Listing
Modified Wed Apr 22 20:03:21 2009 UTC (7 months ago) by dupontct

   * man/summary.survfit.Rd: Indented file
   * DESCRIPTION: Bumped version
   * R/cph.s R/survfit.cph.s: changed list elements with paritial names to full name of the element. 
   

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Revision 132 - Directory Listing
Modified Fri Apr 17 14:04:11 2009 UTC (7 months, 1 week ago) by harrelfe

fixed bug resulting in n=0 if no strata; prettied code; removed print() and str()

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Revision 131 - Directory Listing
Modified Thu Apr 16 13:30:17 2009 UTC (7 months, 1 week ago) by dupontct

fixed binary incompatablity with survival 2.35.2 C function agsurv2: added weight argument to C function call.  Removed restrictions on providing weights to the survfit.cph and survfit.cph.null functions.

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Revision 130 - Directory Listing
Modified Mon Mar 30 02:35:35 2009 UTC (7 months, 3 weeks ago) by harrelfe

used new Hmisc survfit.km

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Revision 129 - Directory Listing
Modified Mon Mar 30 02:35:16 2009 UTC (7 months, 3 weeks ago) by harrelfe

used new Hmisc survfit.km

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Revision 128 - Directory Listing
Modified Mon Mar 30 02:34:55 2009 UTC (7 months, 3 weeks ago) by harrelfe

used new Hmisc survfit.km for val.surv

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Revision 127 - Directory Listing
Modified Mon Mar 30 02:31:59 2009 UTC (7 months, 3 weeks ago) by harrelfe

used new survfit.km in Hmisc

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Revision 125 - Directory Listing
Modified Fri Dec 26 20:47:05 2008 UTC (10 months, 3 weeks ago) by dupontct

Alterations required to make new version of Design pass CRAN package check.

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Revision 124 - Directory Listing
Modified Thu Dec 18 03:03:40 2008 UTC (11 months ago) by harrelfe

corrected error in line type to step function

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Revision 123 - Directory Listing
Modified Wed Dec 17 00:14:41 2008 UTC (11 months, 1 week ago) by harrelfe

corrected bug in new function

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Revision 121 - Directory Listing
Modified Tue Dec 16 22:46:28 2008 UTC (11 months, 1 week ago) by harrelfe

new function survdiffplot for plotting difference of two Kaplan-Meier 
curves with shaded or banded region for confidence interval of the 
difference

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Revision 119 - Directory Listing
Modified Mon Sep 8 22:48:17 2008 UTC (14 months, 2 weeks ago) by harrelfe

Changed to use ordinary ols (not MLE) if all penalty or penalty.matrix terms are zero.  Affects 
sigma.

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Revision 117 - Directory Listing
Modified Sun Aug 31 14:27:41 2008 UTC (14 months, 3 weeks ago) by harrelfe

Passed col to 3-d plotting functions.

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Revision 116 - Directory Listing
Modified Tue Aug 12 15:45:07 2008 UTC (15 months, 1 week ago) by harrelfe

fixed plot.anova.Design to not plot tests of doubly nonlinear 
interactions

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Revision 114 - Directory Listing
Modified Tue Apr 29 12:55:28 2008 UTC (18 months, 3 weeks ago) by harrelfe

Removed debugging prn( ) statement; fixed bug with latest R related to sorting a NULL in rel[[nam]]; changed col.grid to expect a 1- or 2-vector to be consistent with R and gray(c(.8,.9)).

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Revision 113 - Directory Listing
Modified Sun Jan 6 17:20:17 2008 UTC (22 months, 2 weeks ago) by harrelfe

suppressed test of nonlinearity if all terms are nonlinear; makes it work with options(rcspc=TRUE); neatened code

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Revision 111 - Directory Listing
Modified Sun Jan 6 17:00:02 2008 UTC (22 months, 2 weeks ago) by harrelfe

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Revision 110 - Directory Listing
Modified Sun Jan 6 16:55:42 2008 UTC (22 months, 2 weeks ago) by harrelfe

let rcs use system option rcspc to invoke pc=TRUE to rcspline.eval

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Revision 109 - Directory Listing
Modified Mon Dec 31 21:51:46 2007 UTC (22 months, 3 weeks ago) by harrelfe

added cex.subtitles argument to plot.calibrate

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Revision 107 - Directory Listing
Modified Sat Oct 20 18:36:10 2007 UTC (2 years, 1 month ago) by harrelfe

fixed bug where related predictors were being addressed by integer subscripts (and one was out of range) rather than names

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Revision 106 - Directory Listing
Modified Sat Oct 20 18:35:14 2007 UTC (2 years, 1 month ago) by harrelfe

improved addressing of units for plotmath by using names rather than integer subscripts

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Revision 105 - Directory Listing
Modified Sat Oct 20 18:33:46 2007 UTC (2 years, 1 month ago) by harrelfe

enhanced related.predictors to include names attribute for returned list, with names of predictor

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Revision 103 - Directory Listing
Modified Fri Sep 21 19:43:54 2007 UTC (2 years, 2 months ago) by harrelfe

added scat1d.opts argument to plot.calibrate.default

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Revision 101 - Directory Listing
Modified Tue Aug 28 13:01:58 2007 UTC (2 years, 2 months ago) by harrelfe

removed str( ) commands; fixed bug in calls to seq(coefficients) which should have been seq(along=...)

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Revision 99 - Directory Listing
Modified Fri Jul 27 22:44:16 2007 UTC (2 years, 3 months ago) by harrelfe

added forceLines argument to force line plot for discrete numeric predictor

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Revision 98 - Directory Listing
Modified Fri Jun 22 22:52:38 2007 UTC (2 years, 5 months ago) by harrelfe

made cluster() work; uses changes in Design; assumes only a single cluster variable

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Revision 97 - Directory Listing
Modified Fri Jun 22 22:51:56 2007 UTC (2 years, 5 months ago) by harrelfe

makde Design() recognize cluster() for cph, return cluster variable (assume to be only one) as a cluster attribute of the object; improved formatting

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Revision 92 - Directory Listing
Modified Thu Jun 14 16:44:20 2007 UTC (2 years, 5 months ago) by dupontct

Added fixes as provided by Prof. Ripley

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Revision 91 - Directory Listing
Modified Wed Jun 13 19:02:15 2007 UTC (2 years, 5 months ago) by dupontct

Fixed various problems with validate.cph, predab.resample, and
calibrate.cph.  

Fixed missing \item in Overview.Rd.

Fixed syntax error in bootcov.Rd.

Added \dots argument to useage in predict.lrm.Rd

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Revision 90 - Directory Listing
Modified Tue Jun 5 16:00:53 2007 UTC (2 years, 5 months ago) by dupontct

tabbified Design.trans.s changed calls to storage.mode(x) <- "single" to "double"

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Revision 89 - Directory Listing
Modified Wed May 23 22:43:10 2007 UTC (2 years, 6 months ago) by harrelfe

fixed bug - R no longer lets you assign a class attribute of 'factor'

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Revision 88 - Directory Listing
Modified Mon May 7 19:53:37 2007 UTC (2 years, 6 months ago) by harrelfe

added abbrev implementation for method="dotplot", cleaned up code, changed !is.null() to length().

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Revision 86 - Directory Listing
Modified Fri May 4 18:38:43 2007 UTC (2 years, 6 months ago) by harrelfe

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Revision 84 - Directory Listing
Modified Thu May 3 20:52:33 2007 UTC (2 years, 6 months ago) by harrelfe

added function Mean.lrm for numeric ordinal response variables

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Revision 83 - Directory Listing
Modified Tue Mar 27 22:18:39 2007 UTC (2 years, 7 months ago) by harrelfe

ran headings through latexTranslate to handle underscores in response variable names

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Revision 81 - Directory Listing
Modified Tue Mar 20 16:41:43 2007 UTC (2 years, 8 months ago) by harrelfe

ran variable names through latexTranslate for latex methods, to handle underscores in variable names

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Revision 79 - Directory Listing
Modified Fri Feb 23 00:44:59 2007 UTC (2 years, 9 months ago) by harrelfe

improved source code formatting

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Revision 78 - Directory Listing
Modified Tue Jan 2 16:57:04 2007 UTC (2 years, 10 months ago) by harrelfe

used terms(terms object) instead of terms(formula attribute of terms object)

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Revision 77 - Directory Listing
Modified Tue Jan 2 16:56:15 2007 UTC (2 years, 10 months ago) by harrelfe

quit checking length of objects if individual=TRUE

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Revision 76 - Directory Listing
Modified Mon Nov 27 15:26:25 2006 UTC (2 years, 11 months ago) by harrelfe

added topcats argument, factored code

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Revision 73 - Directory Listing
Modified Wed Nov 22 21:58:21 2006 UTC (3 years ago) by harrelfe

added code to automatically change a categorical predictor to a binary one (whether or not it equals the modal category)

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Revision 72 - Directory Listing
Modified Sun Oct 29 14:47:58 2006 UTC (3 years ago) by harrelfe

Changed printing of iteration progress to overwrite the iteration number

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Revision 71 - Directory Listing
Modified Sun Oct 29 14:07:38 2006 UTC (3 years ago) by harrelfe

generalized rcs function to allow user to specify zero knots to use the identify function (linear)

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Revision 70 - Directory Listing
Modified Mon Oct 2 18:57:43 2006 UTC (3 years, 1 month ago) by dupontct

added data arg to terms call.

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Revision 69 - Directory Listing
Modified Thu Sep 7 02:26:37 2006 UTC (3 years, 2 months ago) by harrelfe

solve was used in a couple of places where solvet should have been used, so that eps argument could be honored

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Revision 67 - Directory Listing
Modified Tue Jul 4 15:28:35 2006 UTC (3 years, 4 months ago) by harrelfe

removed prn command

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Revision 66 - Directory Listing
Modified Tue Jul 4 15:27:14 2006 UTC (3 years, 4 months ago) by harrelfe

similar fix for names for frequency of missings as just done for lrm

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Revision 65 - Directory Listing
Modified Tue Jul 4 15:02:17 2006 UTC (3 years, 4 months ago) by harrelfe

fixed bug in renaming of nact$nmiss vector when weights present

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Revision 64 - Directory Listing
Modified Fri Apr 28 14:52:07 2006 UTC (3 years, 6 months ago) by dupontct

   * reindented cph.s summary.survfit.s and survfit.cph.s
   * fixed namespace issue with Design and survival.

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Revision 63 - Directory Listing
Modified Mon Apr 10 14:00:34 2006 UTC (3 years, 7 months ago) by harrelfe

added stat argument to bootcov to allow bootstrapping of a single element from the stats vector returned by the fitting function (e.g. to bootstrap ROC areas)

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Revision 61 - Directory Listing
Modified Mon Feb 13 16:01:19 2006 UTC (3 years, 9 months ago) by dupontct

fixed ldots naming error

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Revision 59 - Directory Listing
Modified Fri Jan 6 15:07:45 2006 UTC (3 years, 10 months ago) by dupontct

removed lower.tail=TRUE from pf and pchisq functions

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Revision 58 - Directory Listing
Modified Fri Jan 6 14:26:52 2006 UTC (3 years, 10 months ago) by dupontct

Changed to prevent P values less the 1e-15 from being trunkated to zero.
Also tabiffied the anova.Design.s file.

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Revision 57 - Directory Listing
Modified Thu Jan 5 16:31:47 2006 UTC (3 years, 10 months ago) by dupontct

Tabbified and corrected error in running both cluster and strata

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Revision 56 - Directory Listing
Modified Thu Dec 1 15:34:03 2005 UTC (3 years, 11 months ago) by dupontct

removed cox.zph doc entry

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Revision 55 - Directory Listing
Modified Thu Dec 1 15:32:53 2005 UTC (3 years, 11 months ago) by dupontct

fixed minor syntax error

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Revision 54 - Directory Listing
Modified Thu Dec 1 15:18:09 2005 UTC (3 years, 11 months ago) by dupontct

Made cox.zph a Splus version 4 only function

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Revision 53 - Directory Listing
Modified Mon Sep 19 20:20:06 2005 UTC (4 years, 2 months ago) by dupontct

tabified plot.Design.s

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Revision 50 - Directory Listing
Modified Mon Aug 29 23:04:11 2005 UTC (4 years, 2 months ago) by harrelfe

Fixed old bug when elements.to.delete has length > 1

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Revision 49 - Directory Listing
Modified Thu Aug 25 15:26:26 2005 UTC (4 years, 2 months ago) by dupontct

Removed References to function print.matrix() to print.default().

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Revision 48 - Directory Listing
Modified Thu Jul 28 17:24:55 2005 UTC (4 years, 3 months ago) by dupontct

Added csv.get.Rd and removed modreg requirement.  Fixed some Rd files

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Revision 47 - Directory Listing
Modified Sun Jun 26 21:43:56 2005 UTC (4 years, 4 months ago) by harrelfe

Stop if weights specified with no covariables.  Fixed major bugs in calculation of R2, sigma, variance matrix when weights are given.  Thanks: henric.nilsson@statisticon.se.

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Revision 46 - Directory Listing
Modified Tue Jun 7 19:54:20 2005 UTC (4 years, 5 months ago) by dupontct

Fixed variable name mismatch in Varcov.pphsm

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Revision 45 - Directory Listing
Modified Tue Jun 7 16:49:11 2005 UTC (4 years, 5 months ago) by dupontct

Tabified

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Revision 44 - Directory Listing
Modified Tue Jun 7 16:42:44 2005 UTC (4 years, 5 months ago) by dupontct

Tabified

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Revision 43 - Directory Listing
Modified Tue Jun 7 16:19:18 2005 UTC (4 years, 5 months ago) by dupontct

Added Varcov.pphsm that says that it is not implemented.

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Revision 37 - Directory Listing
Modified Fri May 6 17:26:37 2005 UTC (4 years, 6 months ago) by dupontct

Fix for lrm bug 'No data for variable "blood.pressure"' error.

Removed line setting model.frame names to NULL.

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Revision 32 - Directory Listing
Modified Thu Apr 21 21:36:32 2005 UTC (4 years, 7 months ago) by harrelfe

Changed grep('*%ia%*',...) to '%ia%'

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Revision 28 - Directory Listing
Modified Thu Jan 20 04:24:30 2005 UTC (4 years, 10 months ago) by harrelfe

Added new argument vnames like nomogram but default is to use variable names.  Removed many old comments regarding changes and dates.

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Revision 27 - Directory Listing
Modified Thu Jan 20 03:58:10 2005 UTC (4 years, 10 months ago) by harrelfe

Fixed problem where values$x found when looking for values$x3 and x is continuous - required exact matching of variable names.

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Revision 26 - Directory Listing
Modified Wed Jan 5 00:26:38 2005 UTC (4 years, 10 months ago) by harrelfe

Prof Brian Ripley wrote:
For a while R has been using old GNU regex code that was tolerant of
mistakes, but to allow internationalization we are moving to current
code (that works like modern GNU grep).  This has caught out your packages.
In most cases I think you want fixed = TRUE as you did not mean a regexp
at all.

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Revision 24 - Directory Listing
Modified Sun Jan 2 17:36:10 2005 UTC (4 years, 10 months ago) by harrelfe

latex.anova.Design was ignoring dec.P if any P-values tiny

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Revision 22 - Directory Listing
Modified Sun Jan 2 00:23:15 2005 UTC (4 years, 10 months ago) by harrelfe

Fixed bug for R in which missing(which) was being updated.  Prevented X*beta from appearing.

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Revision 21 - Directory Listing
Modified Sat Jan 1 23:26:40 2005 UTC (4 years, 10 months ago) by harrelfe

Fixed bug in argu in des.args.  An unlabeled factor involved in %ia% was causing comparison with "" with an out-of-bounds element.

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Revision 17 - Directory Listing
Modified Wed Sep 1 18:13:21 2004 UTC (5 years, 2 months ago) by harrelfe

Looked for terms in one additional place

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Revision 15 - Directory Listing
Modified Sun Jul 11 14:39:08 2004 UTC (5 years, 4 months ago) by harrelfe

Remove verbose argument from .First.lib since R does not pass this.  Instead sense system option Hverbose.  If not specified or FALSE will suppress information messages.

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Revision 13 - Directory Listing
Modified Thu Jun 3 11:40:18 2004 UTC (5 years, 5 months ago) by harrelfe

Remove debugging code that had resulted in returning a character string rather than a true function.

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Revision 11 - Directory Listing
Modified Tue Jun 1 02:27:32 2004 UTC (5 years, 5 months ago) by harrelfe

Renamed First.lib.s AFirst.lib.s to make sure will put in front of package source file.

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Revision 9 - Directory Listing
Modified Thu May 27 21:17:01 2004 UTC (5 years, 5 months ago) by harrelfe

Fixed calls to axis to use cex.axis instead of cex for R.  Thanks: Xi <xz3@duke.edu>.

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Revision 7 - Directory Listing
Modified Mon May 24 13:01:12 2004 UTC (5 years, 6 months ago) by harrelfe

Removed prn() used in debugging

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Revision 5 - Directory Listing
Modified Fri May 21 19:53:42 2004 UTC (5 years, 6 months ago) by harrelfe

added perspArgs

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Revision 2 - Directory Listing
Added Wed Apr 21 15:21:55 2004 UTC (5 years, 7 months ago) by hornerjr

Initial revision