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Revision 413 - Directory Listing
Modified Tue Apr 15 20:07:50 2014 UTC (4 years, 10 months ago) by gsimpson
fix bug in AUC calculation; bump to 0.13-5

Revision 412 - Directory Listing
Modified Fri Feb 14 23:07:08 2014 UTC (5 years ago) by gsimpson
the progressbar was resetting between repeats of k-fold CV

Revision 411 - Directory Listing
Modified Fri Feb 14 23:00:39 2014 UTC (5 years ago) by gsimpson
document r410

Revision 410 - Directory Listing
Modified Fri Feb 14 22:58:40 2014 UTC (5 years ago) by gsimpson
ChiSquare function wasn't returning the list it generated

Revision 409 - Directory Listing
Modified Fri Feb 14 22:52:27 2014 UTC (5 years ago) by gsimpson
minor documentation tweak

Revision 408 - Directory Listing
Modified Fri Feb 14 22:43:03 2014 UTC (5 years ago) by gsimpson
two further changes that should have gone with r407; documentation tweaked for performance()

Revision 407 - Directory Listing
Modified Fri Feb 14 22:40:45 2014 UTC (5 years ago) by gsimpson
adds a performance method for crossval objects.

Revision 406 - Directory Listing
Modified Fri Feb 14 19:27:27 2014 UTC (5 years ago) by gsimpson
predict.pcr was setting ncomp incorrectly if not specified by the user.

Revision 405 - Directory Listing
Modified Thu Feb 13 22:26:44 2014 UTC (5 years ago) by gsimpson
fix several bugs in crossval method for pcr() fits

Revision 404 - Directory Listing
Modified Tue Feb 11 20:04:31 2014 UTC (5 years ago) by gsimpson
Enhancements to timetrack; new points and predict methods; plot method enhanced; new example; bump to 0.13-3; update reference materials for checks.

Revision 403 - Directory Listing
Modified Tue Feb 11 18:10:37 2014 UTC (5 years ago) by gsimpson
remove redundant code to set a default value for method argument

Revision 402 - Directory Listing
Modified Tue Feb 11 18:10:06 2014 UTC (5 years ago) by gsimpson
now invisibly returns the ordination object

Revision 401 - Directory Listing
Modified Tue Feb 11 17:42:54 2014 UTC (5 years ago) by gsimpson
clean up (remove) some commented code chunks

Revision 400 - Directory Listing
Modified Thu Jan 2 05:28:49 2014 UTC (5 years, 1 month ago) by gsimpson
use dev.hold and dev.flush in plotting calls when plotit = TRUE

Revision 399 - Directory Listing
Modified Tue Dec 31 05:27:26 2013 UTC (5 years, 1 month ago) by gsimpson
Update plot3d.prcurve to use the data and ordination stored in the fitted prcurve object.

Revision 398 - Directory Listing
Modified Sun Dec 22 05:23:44 2013 UTC (5 years, 1 month ago) by gsimpson
add a fitted method for prcurve

Revision 397 - Directory Listing
Modified Sun Dec 22 02:03:02 2013 UTC (5 years, 1 month ago) by gsimpson
add first pass at a predict method for principal curves

Revision 396 - Directory Listing
Modified Mon Dec 16 18:58:00 2013 UTC (5 years, 2 months ago) by gsimpson
bump to 0.13-0 for development

Revision 395 - Directory Listing
Modified Mon Dec 16 18:55:09 2013 UTC (5 years, 2 months ago) by gsimpson
remove the use of analogue:::; hangover from development

Revision 394 - Directory Listing
Modified Sat Dec 14 02:28:57 2013 UTC (5 years, 2 months ago) by gsimpson
wrap up the 0.12-0 release for CRAN & submit

Revision 393 - Directory Listing
Modified Fri Dec 13 21:08:43 2013 UTC (5 years, 2 months ago) by gsimpson
add a NEWS.Rd file containing highlights on the upcoming 0.12-0 release

Revision 392 - Directory Listing
Modified Fri Dec 13 05:35:20 2013 UTC (5 years, 2 months ago) by gsimpson
prepare for 0.12-0 release; update reference material, bump to 0.11-99

Revision 391 - Directory Listing
Modified Fri Dec 13 04:08:51 2013 UTC (5 years, 2 months ago) by gsimpson
update the package documentation page

Revision 390 - Directory Listing
Modified Wed Dec 11 14:22:59 2013 UTC (5 years, 2 months ago) by gsimpson
remove the stupid test file the R-forge people polluted my source tree with

Revision 389 - Directory Listing
Modified Wed Dec 11 05:19:36 2013 UTC (5 years, 2 months ago) by gsimpson
document changes to predict and crossval methods for class "pcr"

Revision 388 - Directory Listing
Modified Wed Dec 11 05:11:28 2013 UTC (5 years, 2 months ago) by gsimpson
updated CV methods

Revision 387 - Directory Listing
Modified Wed Nov 27 15:45:48 2013 UTC (5 years, 2 months ago) by mpacala
triggering rebuild


Revision 386 - Directory Listing
Modified Wed Oct 9 04:37:21 2013 UTC (5 years, 4 months ago) by gsimpson
LOO CV was incorrectly averaging over PCR components

Revision 385 - Directory Listing
Modified Wed Oct 9 04:32:05 2013 UTC (5 years, 4 months ago) by gsimpson
new reference material

Revision 384 - Directory Listing
Modified Wed Oct 9 04:30:57 2013 UTC (5 years, 4 months ago) by gsimpson
document predict.pcr

Revision 383 - Directory Listing
Modified Wed Oct 9 04:29:50 2013 UTC (5 years, 4 months ago) by gsimpson
argument n.boot renamed to nboot; needed to subset transformation object to get at transformed data

Revision 382 - Directory Listing
Modified Wed Oct 9 02:49:41 2013 UTC (5 years, 4 months ago) by gsimpson
fix typo in object name

Revision 381 - Directory Listing
Modified Wed Oct 9 02:42:44 2013 UTC (5 years, 4 months ago) by gsimpson
predict.pcr now applies the transformation

Revision 380 - Directory Listing
Modified Tue Oct 8 05:21:32 2013 UTC (5 years, 4 months ago) by gsimpson
zap small values in printed output in vector case; update the example reference material

Revision 379 - Directory Listing
Modified Mon Oct 7 22:58:47 2013 UTC (5 years, 4 months ago) by gsimpson
update affiliation

Revision 378 - Directory Listing
Modified Mon Oct 7 22:58:25 2013 UTC (5 years, 4 months ago) by gsimpson
must not copy the reference outputs when checking --as-cran

Revision 377 - Directory Listing
Modified Mon Oct 7 02:36:50 2013 UTC (5 years, 4 months ago) by gsimpson
Update reference output for Example checks

Revision 376 - Directory Listing
Modified Mon Oct 7 02:36:01 2013 UTC (5 years, 4 months ago) by gsimpson
document some recent changes

Revision 375 - Directory Listing
Modified Mon Oct 7 02:32:59 2013 UTC (5 years, 4 months ago) by gsimpson
some minor edits to update details on C versions of dissimilarities and development dstage

Revision 374 - Directory Listing
Modified Mon Oct 7 00:17:24 2013 UTC (5 years, 4 months ago) by gsimpson
fix a minor typo in code applied to Kendall Dij in the x and y case

Revision 373 - Directory Listing
Modified Mon Oct 7 00:16:29 2013 UTC (5 years, 4 months ago) by gsimpson
now checks all dissimilarity methods in x-only and x and y cases

Revision 372 - Directory Listing
Modified Mon Oct 7 00:09:14 2013 UTC (5 years, 4 months ago) by gsimpson
fixes a bug in oldDistance() with Kendalls coef in the only-x case

Revision 371 - Directory Listing
Modified Sun Oct 6 22:48:37 2013 UTC (5 years, 4 months ago) by gsimpson
now Gowers mixed coef also works for case of supplied x and y

Revision 370 - Directory Listing
Modified Sun Oct 6 20:40:32 2013 UTC (5 years, 4 months ago) by gsimpson
a little tidying

Revision 369 - Directory Listing
Modified Sun Oct 6 20:32:05 2013 UTC (5 years, 4 months ago) by gsimpson
Gowers mixed coef now implemented for the x-only case

Revision 368 - Directory Listing
Modified Sat Oct 5 21:11:52 2013 UTC (5 years, 4 months ago) by gsimpson
bump to 0.11-6; new distance function using compiled C code; cleanup old attempts to interface the C code

Revision 367 - Directory Listing
Modified Sat Oct 5 21:10:47 2013 UTC (5 years, 4 months ago) by gsimpson
add tests

Revision 366 - Directory Listing
Modified Sat Oct 5 21:09:53 2013 UTC (5 years, 4 months ago) by gsimpson
name some more chunks

Revision 365 - Directory Listing
Modified Tue Oct 1 05:26:32 2013 UTC (5 years, 4 months ago) by gsimpson
remove a redundant line of code

Revision 364 - Directory Listing
Modified Tue Oct 1 05:24:36 2013 UTC (5 years, 4 months ago) by gsimpson
rearrange some of the code, simplify

Revision 363 - Directory Listing
Modified Tue Oct 1 03:17:41 2013 UTC (5 years, 4 months ago) by gsimpson
name some chunks

Revision 362 - Directory Listing
Modified Tue Oct 1 03:06:43 2013 UTC (5 years, 4 months ago) by gsimpson
wa warns of species contain zero info

Revision 361 - Directory Listing
Modified Mon Sep 30 16:19:05 2013 UTC (5 years, 4 months ago) by gsimpson
document r360

Revision 360 - Directory Listing
Modified Mon Sep 30 16:06:04 2013 UTC (5 years, 4 months ago) by gsimpson
allow logical vectors for which

Revision 359 - Directory Listing
Modified Mon Aug 26 21:59:58 2013 UTC (5 years, 5 months ago) by gsimpson
adds BugReports and NeedsCompilation

Revision 358 - Directory Listing
Modified Mon Aug 26 20:53:18 2013 UTC (5 years, 5 months ago) by gsimpson
add alias for distanceX()

Revision 357 - Directory Listing
Modified Mon Aug 26 19:28:28 2013 UTC (5 years, 5 months ago) by gsimpson
add Authors@R field

Revision 356 - Directory Listing
Modified Mon Aug 26 18:06:24 2013 UTC (5 years, 5 months ago) by gsimpson
stop R CMD check complaining about :::, even in comments

Revision 355 - Directory Listing
Modified Sat Aug 24 21:02:08 2013 UTC (5 years, 5 months ago) by gsimpson
slim down Depends

Revision 354 - Directory Listing
Modified Sat Aug 24 21:00:05 2013 UTC (5 years, 5 months ago) by gsimpson
tweak

Revision 353 - Directory Listing
Modified Sat Aug 24 20:59:01 2013 UTC (5 years, 5 months ago) by gsimpson
was using ::: when I didn't need to

Revision 352 - Directory Listing
Modified Sat Jul 27 03:28:52 2013 UTC (5 years, 6 months ago) by gsimpson
fix to the plot drawn via plotit = TRUE

Revision 351 - Directory Listing
Modified Thu Jul 25 16:55:27 2013 UTC (5 years, 6 months ago) by gsimpson
fix warning, and dropping of empty dimensions

Revision 350 - Directory Listing
Modified Sun Jul 21 22:50:59 2013 UTC (5 years, 6 months ago) by gsimpson
improvements to plot and lines methods following addition of components ordination and data to object returned from prcurve

Revision 349 - Directory Listing
Modified Sun Jul 21 20:50:38 2013 UTC (5 years, 6 months ago) by gsimpson
add a residuals method for prcurve; changes to prcurve as a result

Revision 348 - Directory Listing
Modified Sat Jul 20 21:42:03 2013 UTC (5 years, 6 months ago) by gsimpson
update example test output following r347

Revision 347 - Directory Listing
Modified Sat Jul 20 21:41:14 2013 UTC (5 years, 6 months ago) by gsimpson
stop the smoothGAM example from running as it is too slow at the moment

Revision 346 - Directory Listing
Modified Sat Jul 20 21:08:46 2013 UTC (5 years, 6 months ago) by gsimpson
updated test checks

Revision 345 - Directory Listing
Modified Sat Jul 20 21:00:38 2013 UTC (5 years, 6 months ago) by gsimpson
streamline some of the examples

Revision 344 - Directory Listing
Modified Sat Jul 20 20:59:03 2013 UTC (5 years, 6 months ago) by gsimpson
documenta changes in prcurve's printed output and addition of smoothGAM

Revision 343 - Directory Listing
Modified Sat Jul 20 20:31:00 2013 UTC (5 years, 6 months ago) by gsimpson
Update example test output

Revision 342 - Directory Listing
Modified Sat Jul 20 20:30:28 2013 UTC (5 years, 6 months ago) by gsimpson
add smoothGAM as a plugin for prcurve; rearrange documentation for plugins separate from main prcurve function

Revision 341 - Directory Listing
Modified Sat Jul 20 20:28:38 2013 UTC (5 years, 6 months ago) by gsimpson
shorten some of the labels in printed output

Revision 340 - Directory Listing
Modified Sat Jul 20 04:51:46 2013 UTC (5 years, 6 months ago) by gsimpson
minor formatting tweaks

Revision 339 - Directory Listing
Modified Fri Jul 19 22:39:58 2013 UTC (5 years, 7 months ago) by gsimpson
add plot3d method for prcurve

Revision 338 - Directory Listing
Modified Fri Jul 19 22:38:44 2013 UTC (5 years, 7 months ago) by gsimpson
fixing the mess I made of arguments in which methods

Revision 337 - Directory Listing
Modified Mon Jul 15 04:33:44 2013 UTC (5 years, 7 months ago) by gsimpson
push updated documentation to fix check issues

Revision 336 - Directory Listing
Modified Thu Jul 11 22:34:19 2013 UTC (5 years, 7 months ago) by gsimpson
add option to use Firth's bias reduced method for logistic regression. Bump to 0.11-4 and adds brglm to Imports

Revision 335 - Directory Listing
Modified Thu Jul 11 20:32:56 2013 UTC (5 years, 7 months ago) by gsimpson
adds 'na.rm = FALSE' argument to chooseTaxa

Revision 334 - Directory Listing
Modified Tue Jun 4 03:04:16 2013 UTC (5 years, 8 months ago) by gsimpson
minor code reformatting

Revision 333 - Directory Listing
Modified Tue Jun 4 03:03:27 2013 UTC (5 years, 8 months ago) by gsimpson
add some new things and reformat

Revision 332 - Directory Listing
Modified Tue Jun 4 03:02:25 2013 UTC (5 years, 8 months ago) by gsimpson
add some extra label handling code

Revision 331 - Directory Listing
Modified Wed May 22 14:53:45 2013 UTC (5 years, 8 months ago) by gsimpson
update examples to latest current dev release checks

Revision 330 - Directory Listing
Modified Wed May 22 14:53:00 2013 UTC (5 years, 8 months ago) by gsimpson
adds rankDC and plot methods

Revision 329 - Directory Listing
Modified Mon May 13 05:39:43 2013 UTC (5 years, 9 months ago) by gsimpson
updated for sppResponse and plot.sppResponse

Revision 328 - Directory Listing
Modified Mon May 13 05:39:07 2013 UTC (5 years, 9 months ago) by gsimpson
document sppResponse

Revision 327 - Directory Listing
Modified Mon May 13 05:11:39 2013 UTC (5 years, 9 months ago) by gsimpson
add plot method for sppResponse

Revision 326 - Directory Listing
Modified Mon May 13 05:06:44 2013 UTC (5 years, 9 months ago) by gsimpson
add sppResponse

Revision 325 - Directory Listing
Modified Mon May 13 05:02:27 2013 UTC (5 years, 9 months ago) by gsimpson
preserve the names on 'lambda' when returning it as a matrix

Revision 324 - Directory Listing
Modified Mon May 13 05:02:01 2013 UTC (5 years, 9 months ago) by gsimpson
preserve the names on 'lambda' when returning it as a matrix

Revision 323 - Directory Listing
Modified Mon May 13 04:56:03 2013 UTC (5 years, 9 months ago) by gsimpson
add 'value' argument

Revision 322 - Directory Listing
Modified Mon May 13 04:55:07 2013 UTC (5 years, 9 months ago) by gsimpson
fix typo in arguments

Revision 321 - Directory Listing
Modified Fri May 10 19:06:15 2013 UTC (5 years, 9 months ago) by gsimpson
add variables names to the smooths component

Revision 320 - Directory Listing
Modified Thu May 9 20:29:06 2013 UTC (5 years, 9 months ago) by gsimpson
adds scores.prcurve and a bug fix to predict.wa

Revision 319 - Directory Listing
Modified Mon Apr 8 04:48:18 2013 UTC (5 years, 10 months ago) by gsimpson
add analog.distance; distance() gains extra attribute as result.

Revision 318 - Directory Listing
Modified Fri Mar 22 16:23:14 2013 UTC (5 years, 10 months ago) by gsimpson
update the test example output in light of r317

Revision 317 - Directory Listing
Modified Fri Mar 22 16:19:58 2013 UTC (5 years, 10 months ago) by gsimpson
minor improvements to fitted and scores methods for timetrack

Revision 316 - Directory Listing
Modified Fri Mar 22 05:59:32 2013 UTC (5 years, 10 months ago) by gsimpson
add a proper formula implementation in timetrack; adds a scores method; change argument name in fitted method

Revision 315 - Directory Listing
Modified Thu Mar 21 22:11:50 2013 UTC (5 years, 10 months ago) by gsimpson
first commit of the new C code for dissimilarities and the R interface distanceX()

Revision 314 - Directory Listing
Modified Thu Mar 21 22:07:02 2013 UTC (5 years, 10 months ago) by gsimpson
allow 'lc' scores in plot.timetrack

Revision 313 - Directory Listing
Modified Thu Mar 21 22:04:39 2013 UTC (5 years, 10 months ago) by gsimpson
squash distance2()

Revision 312 - Directory Listing
Modified Thu Mar 21 22:04:00 2013 UTC (5 years, 10 months ago) by gsimpson
bump to 0.11-2

Revision 311 - Directory Listing
Modified Thu Mar 21 15:23:12 2013 UTC (5 years, 10 months ago) by gsimpson
document r309-310

Revision 310 - Directory Listing
Modified Thu Mar 21 15:22:51 2013 UTC (5 years, 10 months ago) by gsimpson
updated maintainer email address

Revision 309 - Directory Listing
Modified Thu Mar 21 15:22:33 2013 UTC (5 years, 10 months ago) by gsimpson
fix uninitialise variable and minor tweka

Revision 308 - Directory Listing
Modified Mon Mar 18 05:14:48 2013 UTC (5 years, 11 months ago) by gsimpson
prcurve now returns a 'smooths' component, a list of smoothers, one per variable.

Revision 307 - Directory Listing
Modified Mon Mar 18 02:44:49 2013 UTC (5 years, 11 months ago) by gsimpson
Document recent changes...

Revision 306 - Directory Listing
Modified Mon Mar 18 02:43:57 2013 UTC (5 years, 11 months ago) by gsimpson
update namespace due to recent additions to pkg, 'grid' moved to Imports, bump to 0.11-1

Revision 305 - Directory Listing
Modified Mon Mar 18 02:42:26 2013 UTC (5 years, 11 months ago) by gsimpson
fix a silly bug in prcurve method, removes 'order' argument

Revision 304 - Directory Listing
Modified Mon Mar 18 02:41:22 2013 UTC (5 years, 11 months ago) by gsimpson
adds a scores method for class 'prcurve'

Revision 303 - Directory Listing
Modified Mon Mar 18 02:40:39 2013 UTC (5 years, 11 months ago) by gsimpson
add lines.prcurve, modify arguments to plot.prcurve

Revision 302 - Directory Listing
Modified Wed Jan 16 22:06:10 2013 UTC (6 years, 1 month ago) by gsimpson
Update the reference output following changes in r300 and r301

Revision 301 - Directory Listing
Modified Wed Jan 16 20:49:39 2013 UTC (6 years, 1 month ago) by gsimpson
reduce precision in test only during wa example

Revision 300 - Directory Listing
Modified Wed Jan 16 20:45:19 2013 UTC (6 years, 1 month ago) by gsimpson
move MASS and mgcv from Depends: to Imports: and update namespace directives accordingly

Revision 299 - Directory Listing
Modified Wed Jan 16 12:16:01 2013 UTC (6 years, 1 month ago) by gsimpson
pass in digits to the print method

Revision 298 - Directory Listing
Modified Wed Jan 16 12:15:36 2013 UTC (6 years, 1 month ago) by gsimpson
user-friendly improvements to timetrack; move to 0.11-0 for development

Revision 297 - Directory Listing
Modified Thu Jan 3 12:29:41 2013 UTC (6 years, 1 month ago) by gsimpson
no need to hide this as it works and checks in examples will help in finishing this one off without breaking things

Revision 296 - Directory Listing
Modified Thu Jan 3 12:24:13 2013 UTC (6 years, 1 month ago) by gsimpson
document the distance function

Revision 295 - Directory Listing
Modified Thu Jan 3 12:18:29 2013 UTC (6 years, 1 month ago) by gsimpson
adds a class and computes LOO estimates as rowMeans

Revision 294 - Directory Listing
Modified Thu Jan 3 12:07:56 2013 UTC (6 years, 1 month ago) by gsimpson
adds a new version of distance that calls C code

Revision 293 - Directory Listing
Modified Thu Jan 3 12:06:00 2013 UTC (6 years, 1 month ago) by gsimpson
sync up working copy of distxy

Revision 292 - Directory Listing
Modified Thu Jan 3 12:04:29 2013 UTC (6 years, 1 month ago) by gsimpson
set ordinal data handling to be same as nominal for time being

Revision 291 - Directory Listing
Modified Thu Jan 3 11:53:27 2013 UTC (6 years, 1 month ago) by gsimpson
undo inclusion of distance3 info as that is not ready for prime time yet

Revision 290 - Directory Listing
Modified Wed Jan 2 14:10:44 2013 UTC (6 years, 1 month ago) by gsimpson
set up 0.10-0 release for CRAN

Revision 289 - Directory Listing
Modified Sun Dec 23 19:12:15 2012 UTC (6 years, 1 month ago) by gsimpson
document r288

Revision 288 - Directory Listing
Modified Sun Dec 23 19:09:43 2012 UTC (6 years, 1 month ago) by gsimpson
left over code from pre-NAMESPACE loading of compiled code

Revision 287 - Directory Listing
Modified Sun Sep 9 11:42:42 2012 UTC (6 years, 5 months ago) by gsimpson
properly sort out the weighted standard deviation, plus adds print method and new computation function to avoid repeating code. Allows a weighted or unweighted SD to be used.

Revision 286 - Directory Listing
Modified Fri Sep 7 22:47:59 2012 UTC (6 years, 5 months ago) by gsimpson
weighted variance calc assumed weights summed to 1

Revision 285 - Directory Listing
Modified Wed Aug 15 14:14:50 2012 UTC (6 years, 6 months ago) by gsimpson
fix bug when plotting single model

Revision 284 - Directory Listing
Modified Wed Aug 1 21:56:07 2012 UTC (6 years, 6 months ago) by gsimpson
register predict.pcr S3 method

Revision 283 - Directory Listing
Modified Wed Aug 1 21:55:13 2012 UTC (6 years, 6 months ago) by gsimpson
adds a crossval method for pcr(); basic, not complete

Revision 282 - Directory Listing
Modified Wed Aug 1 21:54:51 2012 UTC (6 years, 6 months ago) by gsimpson
register crossval.pcr S3 method

Revision 281 - Directory Listing
Modified Wed Aug 1 21:53:45 2012 UTC (6 years, 6 months ago) by gsimpson
updates to reflect methods split out, plus updates to use fitPCR

Revision 280 - Directory Listing
Modified Wed Aug 1 21:53:13 2012 UTC (6 years, 6 months ago) by gsimpson
internal function wrapping key PCR matrix algebra

Revision 279 - Directory Listing
Modified Wed Aug 1 21:52:17 2012 UTC (6 years, 6 months ago) by gsimpson
missed one of the existing pcr methods

Revision 278 - Directory Listing
Modified Wed Aug 1 21:51:39 2012 UTC (6 years, 6 months ago) by gsimpson
change the way PCR transformation functions return objects

Revision 277 - Directory Listing
Modified Wed Aug 1 21:50:44 2012 UTC (6 years, 6 months ago) by gsimpson
split wa method out into own file

Revision 276 - Directory Listing
Modified Wed Aug 1 21:49:45 2012 UTC (6 years, 6 months ago) by gsimpson
Split out methods into their own files

Revision 275 - Directory Listing
Modified Mon Jul 30 19:29:19 2012 UTC (6 years, 6 months ago) by gsimpson
break out crossval wa method into own file

Revision 274 - Directory Listing
Modified Sun Jul 29 09:39:31 2012 UTC (6 years, 6 months ago) by gsimpson
add short form for caterpillarPlot

Revision 273 - Directory Listing
Modified Sat Jul 28 22:03:25 2012 UTC (6 years, 6 months ago) by gsimpson
adds print.prcurve, tweaks to caterpillaPlot and Stratiplot, don't repeat example(wa); bump to 0.9-9.

Revision 272 - Directory Listing
Modified Wed Jul 25 14:58:07 2012 UTC (6 years, 6 months ago) by gsimpson
change lwd for type = 'h' to give thicker bars and draw these use lineend = 'butt' so they display more accurately and without the unsightly round ends

Revision 271 - Directory Listing
Modified Wed Jul 25 12:21:57 2012 UTC (6 years, 6 months ago) by gsimpson
fix NA-handling issue in Stratiplot.default, bump to 0.9-7, fix example .Rout.save

Revision 270 - Directory Listing
Modified Tue Jul 24 20:04:43 2012 UTC (6 years, 6 months ago) by gsimpson
updates to caterpillarPlot

Revision 269 - Directory Listing
Modified Wed May 16 12:14:17 2012 UTC (6 years, 9 months ago) by gsimpson
fix a typo in the vignette

Revision 268 - Directory Listing
Modified Sun May 6 20:30:48 2012 UTC (6 years, 9 months ago) by gsimpson
fix Stratiplot.formula to pass 'NA's through to lattice; bump to 0.9-5

Revision 267 - Directory Listing
Modified Fri May 4 13:10:44 2012 UTC (6 years, 9 months ago) by gsimpson
add predict and fitted methods for 'logitreg'. Required a number of changes to logitreg() and associated methods. Bump to 0.9-4.

Revision 266 - Directory Listing
Modified Fri Apr 20 14:13:14 2012 UTC (6 years, 9 months ago) by gsimpson
add monotonic deshrinking to wa()

Revision 265 - Directory Listing
Modified Fri Apr 20 14:12:38 2012 UTC (6 years, 9 months ago) by gsimpson
run the example and set a seed

Revision 264 - Directory Listing
Modified Wed Apr 18 20:30:39 2012 UTC (6 years, 10 months ago) by gsimpson
Silly bug in splitSample, constrain the while loop too

Revision 263 - Directory Listing
Modified Mon Apr 16 21:32:09 2012 UTC (6 years, 10 months ago) by gsimpson
add replacement by mean tolerance for small tolerances in WA models

Revision 262 - Directory Listing
Modified Fri Apr 13 22:46:53 2012 UTC (6 years, 10 months ago) by gsimpson
adds splitSample function

Revision 261 - Directory Listing
Modified Tue Apr 10 22:15:02 2012 UTC (6 years, 10 months ago) by gsimpson
make caterpillarPlot an S3 generic with default, data.frame, and wa methods

Revision 260 - Directory Listing
Modified Thu Apr 5 21:48:31 2012 UTC (6 years, 10 months ago) by gsimpson
add caterpillarPlot and bump to 0.9-0

Revision 259 - Directory Listing
Modified Tue Apr 3 20:07:27 2012 UTC (6 years, 10 months ago) by gsimpson
remove static vignette pdf

Revision 258 - Directory Listing
Modified Tue Apr 3 20:01:40 2012 UTC (6 years, 10 months ago) by gsimpson
update changelog and bump version to 0.8-2

Revision 257 - Directory Listing
Modified Tue Apr 3 19:59:57 2012 UTC (6 years, 10 months ago) by gsimpson
move vignettes from inst/doc to vignettes

Revision 256 - Directory Listing
Modified Tue Apr 3 19:49:54 2012 UTC (6 years, 10 months ago) by gsimpson
fix the remainin .Internal calls following release of .colSums etc in R 2.15

Revision 255 - Directory Listing
Modified Tue Apr 3 19:48:36 2012 UTC (6 years, 10 months ago) by gsimpson
delete jss.bst from inst/doc as per check request; this is now part of R

Revision 254 - Directory Listing
Modified Mon Feb 20 12:45:42 2012 UTC (6 years, 11 months ago) by gsimpson
always generate a list of close analogues; original code could simplify to an array in some circumstances

Revision 253 - Directory Listing
Modified Thu Feb 9 12:57:17 2012 UTC (7 years ago) by gsimpson
update example checking master

Revision 252 - Directory Listing
Modified Thu Feb 9 12:43:26 2012 UTC (7 years ago) by gsimpson
update to 0.8-1

Revision 251 - Directory Listing
Modified Thu Feb 9 12:41:40 2012 UTC (7 years ago) by gsimpson
replace .Internal(sample(...)) usage with sample.int()

Revision 250 - Directory Listing
Modified Wed Jan 11 14:29:38 2012 UTC (7 years, 1 month ago) by gsimpson
package ready for 0.8-0 release

Revision 249 - Directory Listing
Modified Wed Jan 11 12:22:25 2012 UTC (7 years, 1 month ago) by gsimpson
initial stab at a simpler CCA-only engine

Revision 248 - Directory Listing
Modified Tue Nov 8 14:55:51 2011 UTC (7 years, 3 months ago) by gsimpson
fix typo bug in choosTaxa for type = 'OR'

Revision 247 - Directory Listing
Modified Fri Nov 4 16:27:17 2011 UTC (7 years, 3 months ago) by gsimpson
separate out the code for MIXED dissimilarity into one that replicates current distance and one that i can use to add extensions for handling ordinal data better.

Revision 246 - Directory Listing
Modified Fri Nov 4 16:26:15 2011 UTC (7 years, 3 months ago) by gsimpson
minor clean-up in rdaFit

Revision 245 - Directory Listing
Modified Fri Nov 4 16:24:13 2011 UTC (7 years, 3 months ago) by gsimpson
add kmax argument to mat(), which requires ahcnages to some internal functions. Bump to 0.7-7.

Revision 244 - Directory Listing
Modified Mon Oct 24 13:59:14 2011 UTC (7 years, 3 months ago) by gsimpson
add ability to control number of grid lines drawn in panel.Stratiplot

Revision 243 - Directory Listing
Modified Sat Oct 8 09:28:41 2011 UTC (7 years, 4 months ago) by gsimpson
fix broken absolute data types in Stratiplot

Revision 242 - Directory Listing
Modified Tue Sep 20 09:09:04 2011 UTC (7 years, 4 months ago) by gsimpson
remove the testing 'analogue:::' prefixes

Revision 241 - Directory Listing
Modified Sun Sep 18 20:51:03 2011 UTC (7 years, 5 months ago) by gsimpson
adds Telford and Birks (2011) weighted correlation test of reconstructions.

Revision 240 - Directory Listing
Modified Sun Sep 11 18:10:14 2011 UTC (7 years, 5 months ago) by gsimpson
start on a new function to replace distance that uses compiled code, most functionality works, with main exception being a compiled code version of gower's coefficient

Revision 239 - Directory Listing
Modified Sun Sep 11 18:07:33 2011 UTC (7 years, 5 months ago) by gsimpson
fix warning on CRAN on one system, start new code for expanded gower's method

Revision 238 - Directory Listing
Modified Fri Aug 26 16:45:10 2011 UTC (7 years, 5 months ago) by gsimpson
slightly better title

Revision 237 - Directory Listing
Modified Fri Aug 26 14:37:12 2011 UTC (7 years, 5 months ago) by gsimpson
update examples test because of version bump

Revision 236 - Directory Listing
Modified Fri Aug 26 14:28:39 2011 UTC (7 years, 5 months ago) by gsimpson
bump to 0.7-4

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Modified Fri Aug 26 13:32:26 2011 UTC (7 years, 5 months ago) by jarioksa
update (but where is coreData?)

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Modified Thu Aug 25 06:22:51 2011 UTC (7 years, 5 months ago) by jarioksa
relax: vegan_1.17-12 also has a NAMESPACE and exports everything

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Modified Wed Aug 24 19:53:40 2011 UTC (7 years, 5 months ago) by gsimpson
typo in link

Revision 232 - Directory Listing
Modified Tue Aug 23 08:50:13 2011 UTC (7 years, 5 months ago) by gsimpson
document recent changes in changelog

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Modified Tue Aug 23 08:49:56 2011 UTC (7 years, 5 months ago) by gsimpson
bump to 0.7-4

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Modified Tue Aug 23 08:49:26 2011 UTC (7 years, 5 months ago) by gsimpson
adds a name space

Revision 229 - Directory Listing
Modified Tue Aug 23 08:48:37 2011 UTC (7 years, 5 months ago) by gsimpson
Adds a variance explained generic and methods

Revision 228 - Directory Listing
Modified Tue Aug 23 08:47:53 2011 UTC (7 years, 5 months ago) by gsimpson
Adds gradientDist()

Revision 227 - Directory Listing
Modified Tue Aug 23 08:47:13 2011 UTC (7 years, 5 months ago) by gsimpson
tweaks to distance()

Revision 226 - Directory Listing
Modified Tue Aug 23 08:44:33 2011 UTC (7 years, 5 months ago) by gsimpson
fix the S3 method defs for tolerance() as the generic is now in vegan

Revision 225 - Directory Listing
Modified Tue Aug 23 08:43:33 2011 UTC (7 years, 5 months ago) by gsimpson
extend the print method to handle performance methods that return a matrix of measures (i.e. a set of performance statistics for each axis in PCR)

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Modified Tue Aug 23 08:41:48 2011 UTC (7 years, 5 months ago) by gsimpson
add principal components regression

Revision 223 - Directory Listing
Modified Mon May 30 21:26:07 2011 UTC (7 years, 8 months ago) by gsimpson
add pcr() for principal components regression, bump to 0.7-2

Revision 222 - Directory Listing
Modified Fri May 27 09:44:50 2011 UTC (7 years, 8 months ago) by gsimpson
document r221

Revision 221 - Directory Listing
Modified Fri May 27 09:42:57 2011 UTC (7 years, 8 months ago) by gsimpson
add a tests directory with a saved copy of output from running the examples

Revision 220 - Directory Listing
Modified Fri May 27 09:23:44 2011 UTC (7 years, 8 months ago) by gsimpson
minor tweak might mean this runs faster, was growing an object in a loop

Revision 219 - Directory Listing
Modified Fri May 27 09:22:39 2011 UTC (7 years, 8 months ago) by gsimpson
adds crossval()

Revision 218 - Directory Listing
Modified Tue May 24 09:03:53 2011 UTC (7 years, 8 months ago) by gsimpson
final tweaks to man page for prcurve didn't get saved in file updated by r217

Revision 217 - Directory Listing
Modified Tue May 24 08:47:38 2011 UTC (7 years, 8 months ago) by gsimpson
add final version 1 of principal curve fitting code and documentation

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Modified Mon Mar 28 19:37:50 2011 UTC (7 years, 10 months ago) by gsimpson
compressed analogue vignette

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Modified Sat Mar 26 19:52:41 2011 UTC (7 years, 10 months ago) by gsimpson
Example tweaks knock 3+ seconds off package check timings

Revision 214 - Directory Listing
Modified Sat Mar 26 19:20:32 2011 UTC (7 years, 10 months ago) by gsimpson
Fixes NA or NaN optima issue

Revision 213 - Directory Listing
Modified Sat Mar 26 19:18:54 2011 UTC (7 years, 10 months ago) by gsimpson
Some sapply() tweaks

Revision 212 - Directory Listing
Modified Mon Mar 14 14:39:28 2011 UTC (7 years, 11 months ago) by gsimpson
provides waFit, updates wa and documents the new fitting function workhorse

Revision 211 - Directory Listing
Modified Mon Mar 14 14:37:48 2011 UTC (7 years, 11 months ago) by gsimpson
rename wa.fit to waFit to avoid silly S3 methodness

Revision 210 - Directory Listing
Modified Sun Mar 13 22:32:15 2011 UTC (7 years, 11 months ago) by gsimpson
adds new function wa.fit, used in wa.default

Revision 209 - Directory Listing
Modified Fri Jan 28 23:35:42 2011 UTC (8 years ago) by gsimpson
Document r207 and r208 in ChangeLog

Revision 208 - Directory Listing
Modified Fri Jan 28 23:34:04 2011 UTC (8 years ago) by gsimpson
remove some of the example that was commented out and that should have been deleted as part of r207

Revision 207 - Directory Listing
Modified Fri Jan 28 23:32:36 2011 UTC (8 years ago) by gsimpson
reductions in check times thorugh streamlined examples to use Imbrie and Kipp

Revision 206 - Directory Listing
Modified Fri Jan 28 23:24:42 2011 UTC (8 years ago) by gsimpson
fix bugs in bootstrap and k-fold CV, plus silly stop criterion in fixUpTol

Revision 205 - Directory Listing
Modified Fri Jan 28 23:18:11 2011 UTC (8 years ago) by gsimpson
fix NOTE during package check

Revision 204 - Directory Listing
Modified Fri Jan 28 18:36:16 2011 UTC (8 years ago) by gsimpson
Update compression on data sets

Revision 203 - Directory Listing
Modified Thu Jan 13 16:33:52 2011 UTC (8 years, 1 month ago) by gsimpson
Stratiplot gains ability to handle absolute data

Revision 202 - Directory Listing
Modified Thu Jan 13 16:06:23 2011 UTC (8 years, 1 month ago) by gsimpson
documentation for changes in r200

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Modified Thu Jan 13 15:56:45 2011 UTC (8 years, 1 month ago) by gsimpson
document r200

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Modified Thu Jan 13 15:54:06 2011 UTC (8 years, 1 month ago) by gsimpson
adds cma methods for mat and predict.mat objects

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Modified Thu Jan 13 15:52:33 2011 UTC (8 years, 1 month ago) by gsimpson
document r198

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Modified Thu Jan 13 15:51:11 2011 UTC (8 years, 1 month ago) by gsimpson
some NA reslience added to a couple of coefficients

Revision 197 - Directory Listing
Modified Wed Sep 29 19:09:33 2010 UTC (8 years, 4 months ago) by gsimpson
swap examples to use the imbrie & kipp data which results in an 8-second reduction in package check times

Revision 196 - Directory Listing
Modified Wed Sep 29 17:32:33 2010 UTC (8 years, 4 months ago) by gsimpson
simplify the 'data()' calls - load all data in one call

Revision 195 - Directory Listing
Modified Wed Sep 29 17:31:50 2010 UTC (8 years, 4 months ago) by gsimpson
fix joining in residLen - should have been a left join

Revision 194 - Directory Listing
Modified Wed Sep 29 16:45:12 2010 UTC (8 years, 4 months ago) by gsimpson
Adds ability to draw a zone legend on the right of the plot

Revision 193 - Directory Listing
Modified Wed Sep 29 15:56:24 2010 UTC (8 years, 4 months ago) by gsimpson
improve the replacement of missing values

Revision 192 - Directory Listing
Modified Wed Sep 22 16:23:26 2010 UTC (8 years, 4 months ago) by gsimpson
The pollen data are not all of the same type, warning section added

Revision 191 - Directory Listing
Modified Fri Jul 9 20:55:57 2010 UTC (8 years, 7 months ago) by gsimpson
fix bug in ylim processing

Revision 190 - Directory Listing
Modified Sun Jul 4 19:04:18 2010 UTC (8 years, 7 months ago) by gsimpson
update citation file to auto generate the date in the text version.

Revision 189 - Directory Listing
Modified Sun Jul 4 17:46:22 2010 UTC (8 years, 7 months ago) by gsimpson
add prcurve and timetrack plus associated functions. bump to 0.7-0 to prepare for release.

Revision 188 - Directory Listing
Modified Sun Jul 4 12:30:26 2010 UTC (8 years, 7 months ago) by gsimpson
A bit more documentation on adding zone markers.

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Modified Sun Jul 4 12:16:55 2010 UTC (8 years, 7 months ago) by gsimpson
Add's handling of drawing zone markers to panels on stratigraphic plots.

Revision 186 - Directory Listing
Modified Sun Jul 4 11:21:42 2010 UTC (8 years, 7 months ago) by gsimpson
document new 'topPad' argument to Stratiplot.default

Revision 185 - Directory Listing
Modified Fri Jul 2 23:02:22 2010 UTC (8 years, 7 months ago) by gsimpson
update for Abernethy and edit texisting text, fix typos etc.

Revision 184 - Directory Listing
Modified Fri Jul 2 22:19:32 2010 UTC (8 years, 7 months ago) by gsimpson
more fixes to names-preservation in Stratiplot formula

Revision 183 - Directory Listing
Modified Fri Jul 2 16:36:12 2010 UTC (8 years, 7 months ago) by gsimpson
fixes to Stratiplot ylims, y-axis padding and variable labels when 'strip = FALSE'

Revision 182 - Directory Listing
Modified Tue Jun 29 12:34:40 2010 UTC (8 years, 7 months ago) by gsimpson
bump to 0.6-26, adds abernethy data and changes to dependencies, Stratiplot.formula and chooseTaxa

Revision 181 - Directory Listing
Modified Tue Jun 29 12:29:17 2010 UTC (8 years, 7 months ago) by gsimpson
Don't allow 'names' to be checked when building data frame to be passed to Stratiplot.default

Revision 180 - Directory Listing
Modified Tue Jun 29 12:28:35 2010 UTC (8 years, 7 months ago) by gsimpson
Explicitly preserve column and row names

Revision 179 - Directory Listing
Modified Tue Jun 29 12:28:07 2010 UTC (8 years, 7 months ago) by gsimpson
prematurely added princurve as a dependency

Revision 178 - Directory Listing
Modified Mon Jun 28 17:25:39 2010 UTC (8 years, 7 months ago) by gsimpson
add function chooseTaxa and document, bump package version

Revision 177 - Directory Listing
Modified Wed Jun 23 20:53:54 2010 UTC (8 years, 7 months ago) by gsimpson
fix handling ylim in Stratiplot so it works more intuitively

Revision 176 - Directory Listing
Modified Sat May 29 15:16:23 2010 UTC (8 years, 8 months ago) by gsimpson
Fixing typo in ChangeLog

Revision 175 - Directory Listing
Modified Sat May 29 15:14:02 2010 UTC (8 years, 8 months ago) by gsimpson
minor tidying in the C code

Revision 173 - Directory Listing
Modified Wed May 26 22:15:27 2010 UTC (8 years, 8 months ago) by gsimpson
document package dependency on grid

Revision 172 - Directory Listing
Modified Wed May 26 22:14:28 2010 UTC (8 years, 8 months ago) by gsimpson
variable labels plotted as axis labels not strips by default, new argument 'strip', both in Stratiplot.default

Revision 171 - Directory Listing
Modified Wed May 19 17:36:09 2010 UTC (8 years, 9 months ago) by gsimpson
fix the warnings from Grid about inappropriate colour format - silly bug in code not using the  of the trellis settings for the reference line

Revision 170 - Directory Listing
Modified Wed May 19 17:30:44 2010 UTC (8 years, 9 months ago) by gsimpson
Minor tweak to way panel.Stratiplot is called from Stratiplot; now uses the name of the function

Revision 169 - Directory Listing
Modified Wed May 19 17:29:15 2010 UTC (8 years, 9 months ago) by gsimpson
More reductions in package check timings

Revision 168 - Directory Listing
Modified Thu May 13 22:03:21 2010 UTC (8 years, 9 months ago) by gsimpson
fix plot.roc resetting plotting region at end of plotting when not needed

Revision 167 - Directory Listing
Modified Fri Apr 23 14:43:04 2010 UTC (8 years, 9 months ago) by gsimpson
changed definition of residuals in WA and change ordering of axes in plot.wa method to match

Revision 166 - Directory Listing
Modified Fri Apr 23 14:40:30 2010 UTC (8 years, 9 months ago) by gsimpson
useN argument/object being created in wrong place meant it was not available for other CV methods than LOO

Revision 165 - Directory Listing
Modified Fri Apr 23 14:37:48 2010 UTC (8 years, 9 months ago) by gsimpson
Large reductions in package check timings as now using Imbrie and Kipp for examples

Revision 164 - Directory Listing
Modified Mon Apr 19 17:49:45 2010 UTC (8 years, 10 months ago) by gsimpson
summary.predict.mat was incorrectly extracting the MAT model estimates for the training set

Revision 163 - Directory Listing
Modified Tue Mar 9 12:19:32 2010 UTC (8 years, 11 months ago) by gsimpson
new argument abline.lty in plot.bayesF

Revision 162 - Directory Listing
Modified Tue Mar 9 12:18:08 2010 UTC (8 years, 11 months ago) by gsimpson
new argument abline.lty in plot.roc

Revision 161 - Directory Listing
Modified Mon Mar 8 19:19:00 2010 UTC (8 years, 11 months ago) by gsimpson
lty.quantile now used in plot.minDC

Revision 160 - Directory Listing
Modified Tue Mar 2 15:47:59 2010 UTC (8 years, 11 months ago) by gsimpson
add more flexible handling of line types in plot.roc

Revision 159 - Directory Listing
Modified Tue Mar 2 08:30:14 2010 UTC (8 years, 11 months ago) by gsimpson
fix bug in generation of points on ROC curve where we evaluate other statistics

Revision 158 - Directory Listing
Modified Fri Jan 22 19:02:48 2010 UTC (9 years ago) by gsimpson
Tidying WA code to match R standards for indenting

Revision 157 - Directory Listing
Modified Mon Jan 18 19:04:17 2010 UTC (9 years, 1 month ago) by gsimpson
fix passing tolerance-related arguments from formula to default method in wa and correct a bug in argument matching within fixUpTol

Revision 156 - Directory Listing
Modified Sat Jan 16 16:53:24 2010 UTC (9 years, 1 month ago) by gsimpson
tidying code in wa.R

Revision 155 - Directory Listing
Modified Sat Jan 16 13:50:40 2010 UTC (9 years, 1 month ago) by gsimpson
rootroot transformation was same as cuberoot from r140

Revision 154 - Directory Listing
Modified Tue Nov 3 20:46:19 2009 UTC (9 years, 3 months ago) by gsimpson
bug fix in tran.formula allows pass R CMD check with R 2.10.0

Revision 153 - Directory Listing
Modified Mon Nov 2 09:45:33 2009 UTC (9 years, 3 months ago) by gsimpson
Silly typo in C code distx and distxy made them non ISO C-compliant.

Revision 152 - Directory Listing
Modified Wed Oct 14 20:45:33 2009 UTC (9 years, 4 months ago) by gsimpson
Bump version and updated ChangeLog reflecting r150-151

Revision 151 - Directory Listing
Modified Wed Oct 14 20:44:54 2009 UTC (9 years, 4 months ago) by gsimpson
erroneous links to panel.Loess in lattice package causing warnings in R 2.10-0 beta

Revision 150 - Directory Listing
Modified Wed Oct 14 20:43:47 2009 UTC (9 years, 4 months ago) by gsimpson
Stratiplot not respecting sort variable in some situations

Revision 149 - Directory Listing
Modified Sun Aug 16 17:42:23 2009 UTC (9 years, 6 months ago) by gsimpson
Add check of r148 to example in join.Rd

Revision 148 - Directory Listing
Modified Sun Aug 16 17:30:58 2009 UTC (9 years, 6 months ago) by gsimpson
Selection of columns incorrect in leftJoin internal fun

Revision 147 - Directory Listing
Modified Sun Aug 16 13:19:38 2009 UTC (9 years, 6 months ago) by gsimpson
adds inner join to 'join'.

Revision 146 - Directory Listing
Modified Sun Aug 16 11:52:47 2009 UTC (9 years, 6 months ago) by gsimpson
adds left join to 'join' and new argument to supply the value using in replacing missing values.

Revision 145 - Directory Listing
Modified Sat Aug 15 21:25:23 2009 UTC (9 years, 6 months ago) by gsimpson
Additions to Stratiplot to implement reversing the y-axis and sorting of the plotted variables, by WA of depth/time or a supplied variable.

Revision 144 - Directory Listing
Modified Sat Aug 15 21:17:25 2009 UTC (9 years, 6 months ago) by gsimpson
Changelog and version bump for r143

Revision 143 - Directory Listing
Modified Sat Aug 15 16:52:56 2009 UTC (9 years, 6 months ago) by gsimpson
deshrinking of predictions not respecting the type of deshrinking used to fit the WA model

Revision 142 - Directory Listing
Modified Sun Aug 9 23:31:23 2009 UTC (9 years, 6 months ago) by gsimpson
implements thinning in roc for large problems.

Revision 141 - Directory Listing
Modified Sun Aug 9 10:36:32 2009 UTC (9 years, 6 months ago) by gsimpson
new formula method for tran()

Revision 140 - Directory Listing
Modified Sun Jul 19 18:57:31 2009 UTC (9 years, 7 months ago) by gsimpson
more robust cube root and rootroot transformations

Revision 139 - Directory Listing
Modified Sun Jun 14 12:12:21 2009 UTC (9 years, 8 months ago) by gsimpson
minor documentation fixes

Revision 138 - Directory Listing
Modified Fri Jun 12 15:47:08 2009 UTC (9 years, 8 months ago) by gsimpson
add power, 4th root, log ratio and row centring methods to tran()

Revision 137 - Directory Listing
Modified Wed Jun 10 09:06:21 2009 UTC (9 years, 8 months ago) by gsimpson
Bootstrap CV now handles tol dw WA models in predict.wa (and hence bootstrap.wa).

Revision 136 - Directory Listing
Modified Tue Jun 9 21:17:01 2009 UTC (9 years, 8 months ago) by gsimpson
Updated and improved deshrinking mechanism for wa() and predict.wa()

Revision 135 - Directory Listing
Modified Mon Jun 8 22:11:35 2009 UTC (9 years, 8 months ago) by gsimpson
C code in WATpred plus changes to predict.wa and wa to make use of the new C code

Revision 134 - Directory Listing
Modified Mon Jun 8 19:23:50 2009 UTC (9 years, 8 months ago) by gsimpson
'tran' now uses data.matrix to convert input data to matrix.

Revision 133 - Directory Listing
Modified Sun Jun 7 13:34:37 2009 UTC (9 years, 8 months ago) by gsimpson
Incremental improvements in wa() and predict.wa() for tolerance down-weighting models. LOO CV now works with tol.dw = TRUE; code tidied a lot to re-use new internal utility functions. New C code for internal utility function w.tol().

Revision 130 - Directory Listing
Modified Fri May 29 22:39:57 2009 UTC (9 years, 8 months ago) by gsimpson
Update ChangeLog for r129

Revision 129 - Directory Listing
Modified Fri May 29 22:30:12 2009 UTC (9 years, 8 months ago) by gsimpson
wa now uses WApred and WATpred and returns 'options.tol', a list containing the tolerance tweaking options.
Updated the Rd file.

Revision 128 - Directory Listing
Modified Fri May 29 22:23:07 2009 UTC (9 years, 8 months ago) by gsimpson
Forgot to bump the version number...

Revision 127 - Directory Listing
Modified Fri May 29 22:19:39 2009 UTC (9 years, 8 months ago) by gsimpson
Clarified what happens to small tolerances by default

Revision 126 - Directory Listing
Modified Wed May 27 22:33:50 2009 UTC (9 years, 8 months ago) by gsimpson
predict.wa now works for tol DW WA models if no CV is used

Revision 125 - Directory Listing
Modified Tue May 5 21:13:46 2009 UTC (9 years, 9 months ago) by gsimpson
Update ChangeLog to reflect r124

Revision 124 - Directory Listing
Modified Tue May 5 21:11:55 2009 UTC (9 years, 9 months ago) by gsimpson
Updated CITATION file

Revision 123 - Directory Listing
Modified Sun Apr 26 14:09:48 2009 UTC (9 years, 9 months ago) by gsimpson
Update ChangeLog to reflect r122

Revision 122 - Directory Listing
Modified Sun Apr 26 14:06:22 2009 UTC (9 years, 9 months ago) by gsimpson
Adds stdError() to compute weighted standard deviations of environment values for the k-closest analogues in MAT models.

Revision 121 - Directory Listing
Modified Sun Apr 26 14:05:22 2009 UTC (9 years, 9 months ago) by gsimpson
Update getK.Rd to reflect r119

Revision 120 - Directory Listing
Modified Sun Apr 26 13:13:48 2009 UTC (9 years, 9 months ago) by gsimpson
Update ChangeLog to reflect r119

Revision 119 - Directory Listing
Modified Sun Apr 26 13:12:28 2009 UTC (9 years, 9 months ago) by gsimpson
new getK method for predict.mat

Revision 118 - Directory Listing
Modified Sun Apr 26 10:56:06 2009 UTC (9 years, 9 months ago) by gsimpson
predict.mat returns the dissimilarity betwen training set samples and 'newdata' samples;
Updated the help page for predict.mat to document new feature, plus some features previously undocumented in returned object;

Revision 117 - Directory Listing
Modified Sun Apr 26 09:17:26 2009 UTC (9 years, 9 months ago) by gsimpson
Update ChangeLog to reflect changes in r116

Revision 116 - Directory Listing
Modified Sun Apr 26 09:12:54 2009 UTC (9 years, 9 months ago) by gsimpson
residLen, no longer generic,
internal functions in residLen exposed externally and documented;
new plot methods for residLen objects.

Revision 109 - Directory Listing
Modified Mon Apr 13 20:40:25 2009 UTC (9 years, 10 months ago) by gsimpson
add squared residual length code

Revision 108 - Directory Listing
Modified Mon Apr 6 17:54:54 2009 UTC (9 years, 10 months ago) by gsimpson
fix bug in distance method kendall; was using min not pmin on input vectors x and y

Revision 107 - Directory Listing
Modified Fri Apr 3 19:33:15 2009 UTC (9 years, 10 months ago) by gsimpson
as.data.frame methods for optima/tolerance and bump version to 0.6-7

Revision 99 - Directory Listing
Modified Sun Mar 1 18:12:04 2009 UTC (9 years, 11 months ago) by gsimpson
correct last missing link in Rd files on Windows

Revision 98 - Directory Listing
Modified Sat Feb 28 09:14:45 2009 UTC (9 years, 11 months ago) by gsimpson
Get \link's correct for Windows builds

Revision 97 - Directory Listing
Modified Wed Feb 25 11:51:53 2009 UTC (9 years, 11 months ago) by gsimpson
tweaked changelog ready for release to CRAN

Revision 95 - Directory Listing
Modified Mon Feb 23 14:28:12 2009 UTC (9 years, 11 months ago) by gsimpson
tweaked URLs in CITATION

Revision 94 - Directory Listing
Modified Mon Feb 23 10:31:28 2009 UTC (9 years, 11 months ago) by gsimpson
added URL to CITATION

Revision 93 - Directory Listing
Modified Fri Feb 20 10:23:17 2009 UTC (9 years, 11 months ago) by gsimpson
Updated citation information for the package

Revision 92 - Directory Listing
Modified Thu Feb 19 09:22:02 2009 UTC (9 years, 11 months ago) by gsimpson
Remove wacalib option for dealing with missing tolerances in WA. Steve Juggins informs me this was just buggy and need not be replicated.

Revision 91 - Directory Listing
Modified Wed Feb 11 20:17:15 2009 UTC (10 years ago) by gsimpson
forgot to add \alias entries for print.optima and print.tolerance

Revision 90 - Directory Listing
Modified Tue Feb 10 18:35:32 2009 UTC (10 years ago) by gsimpson
add head and tail methods for class 'join'

Revision 89 - Directory Listing
Modified Sat Feb 7 12:56:59 2009 UTC (10 years ago) by gsimpson
new print methods for optima and tolerance; additional attributes are now returned.

Revision 88 - Directory Listing
Modified Fri Feb 6 19:37:25 2009 UTC (10 years ago) by gsimpson
bump package version to 0.6-5 and update ChangeLog to reflect r85:87

Revision 87 - Directory Listing
Modified Fri Feb 6 19:36:45 2009 UTC (10 years ago) by gsimpson
new user visible functions for computing WA optima and tolerances

Revision 86 - Directory Listing
Modified Fri Feb 6 19:35:47 2009 UTC (10 years ago) by gsimpson
add new internal functions mentioned in r85

Revision 85 - Directory Listing
Modified Fri Feb 6 19:34:39 2009 UTC (10 years ago) by gsimpson
add tolerance downweighting to wa(), includes some new internal functions

Revision 84 - Directory Listing
Modified Fri Jan 23 18:21:23 2009 UTC (10 years ago) by jarioksa
wa: warns users that tol.dw is not yet implemented (bug report #287)

Revision 83 - Directory Listing
Modified Fri Jan 23 13:08:22 2009 UTC (10 years ago) by gsimpson
updates to bayesF and roc

Revision 82 - Directory Listing
Modified Fri Jan 23 12:59:00 2009 UTC (10 years ago) by gsimpson
Document fact that tol.dw is ignored in wa

Revision 81 - Directory Listing
Modified Thu Jan 22 08:43:32 2009 UTC (10 years ago) by gsimpson
roc() now stores the location of the maximal point on the ROC curve

Revision 80 - Directory Listing
Modified Wed Jan 21 16:54:53 2009 UTC (10 years ago) by gsimpson
modified degrees of freedom in confidence interval calculation

Revision 79 - Directory Listing
Modified Wed Jan 21 10:52:43 2009 UTC (10 years ago) by gsimpson
Updated THANKS to include reference to NAMPD

Revision 78 - Directory Listing
Modified Tue Jan 20 21:01:05 2009 UTC (10 years ago) by gsimpson
Add North American Modern Pollen Database datasets

Revision 77 - Directory Listing
Modified Tue Jan 20 21:00:19 2009 UTC (10 years ago) by gsimpson
PDF rebuilt

Revision 76 - Directory Listing
Modified Tue Jan 20 00:03:15 2009 UTC (10 years ago) by gsimpson
Update changelog to reflect r74:75

Revision 75 - Directory Listing
Modified Mon Jan 19 21:58:31 2009 UTC (10 years ago) by gsimpson
prettying the plots by drawing things in better order and adding box() calls

Revision 74 - Directory Listing
Modified Mon Jan 19 21:57:30 2009 UTC (10 years ago) by gsimpson
reordering the returned individual roc objects in 

Revision 73 - Directory Listing
Modified Tue Jan 13 18:46:12 2009 UTC (10 years, 1 month ago) by gsimpson
Add addition of MASS to dependencies to ChangeLog

Revision 72 - Directory Listing
Modified Tue Jan 13 18:38:46 2009 UTC (10 years, 1 month ago) by gsimpson
New function logitreg() and associated code

Revision 71 - Directory Listing
Modified Sun Jan 11 12:36:29 2009 UTC (10 years, 1 month ago) by gsimpson
strange missing links error in windows checker on R-forge - just checking...

Revision 70 - Directory Listing
Modified Fri Jan 9 19:07:06 2009 UTC (10 years, 1 month ago) by gsimpson
changes to class of objects returned by distance

Revision 69 - Directory Listing
Modified Fri Jan 9 18:30:43 2009 UTC (10 years, 1 month ago) by gsimpson
bump to 0.6-3 and fix-ups to distance and tweak to dissimilarities

Revision 68 - Directory Listing
Modified Fri Jan 9 17:33:12 2009 UTC (10 years, 1 month ago) by gsimpson
stop analog() changing 'x' and 'y' which messes up factor handling in distance()

Revision 67 - Directory Listing
Modified Fri Jan 9 14:30:13 2009 UTC (10 years, 1 month ago) by gsimpson
Tweaked documentation and markup for bootstrap and summary.bootstrap objects

Revision 66 - Directory Listing
Modified Fri Jan 9 14:09:42 2009 UTC (10 years, 1 month ago) by gsimpson
Fixes for nested lists in summary.bootstrap.mat that were causing check warnings with the new Rd parse in 2.9.0-to-be

Revision 65 - Directory Listing
Modified Fri Jan 9 13:22:47 2009 UTC (10 years, 1 month ago) by gsimpson
Tweak to markup in Rd for Stratiplot

Revision 64 - Directory Listing
Modified Thu Jan 1 23:10:25 2009 UTC (10 years, 1 month ago) by gsimpson
new function Stratiplot() and panel functions

Revision 63 - Directory Listing
Modified Tue Dec 23 20:58:15 2008 UTC (10 years, 1 month ago) by gsimpson
Documentation tweaks and examples to ImbrieKipp

Revision 62 - Directory Listing
Modified Tue Dec 23 18:33:32 2008 UTC (10 years, 1 month ago) by gsimpson
Fix wanring about 'freq' not being using in call to hist()

Revision 61 - Directory Listing
Modified Tue Dec 23 13:30:15 2008 UTC (10 years, 1 month ago) by gsimpson
Fixes to documentation bugs due to r58:59

Revision 60 - Directory Listing
Modified Tue Dec 23 13:19:09 2008 UTC (10 years, 1 month ago) by gsimpson
Altered DESCRIPTION and ChangeLog to reflect r59

Revision 59 - Directory Listing
Modified Tue Dec 23 13:18:17 2008 UTC (10 years, 1 month ago) by gsimpson
Changes to IK data sets

Revision 58 - Directory Listing
Modified Tue Dec 23 13:17:48 2008 UTC (10 years, 1 month ago) by gsimpson
Changes to IK data sets

Revision 57 - Directory Listing
Modified Mon Dec 15 16:33:40 2008 UTC (10 years, 2 months ago) by gsimpson
distance now returns method as attribute

Revision 55 - Directory Listing
Modified Wed Oct 22 13:20:06 2008 UTC (10 years, 3 months ago) by gsimpson
Added URL field to DESCRIPTION

Revision 50 - Directory Listing
Modified Sat Oct 11 15:59:32 2008 UTC (10 years, 4 months ago) by gsimpson
Typos in roc.Rd

Revision 49 - Directory Listing
Modified Sat Oct 11 12:26:54 2008 UTC (10 years, 4 months ago) by gsimpson
Added the Imbrie and Kipp data set

Revision 48 - Directory Listing
Modified Mon Oct 6 18:56:50 2008 UTC (10 years, 4 months ago) by gsimpson
plot.mcarlo now calculates y-axis limits from both histogram and KDE

Revision 47 - Directory Listing
Modified Mon Oct 6 15:52:52 2008 UTC (10 years, 4 months ago) by gsimpson
tran() now preserves object dimnames

Revision 46 - Directory Listing
Modified Wed Oct 1 08:14:36 2008 UTC (10 years, 4 months ago) by gsimpson
Forgot to comment out the library.dynam call in zzz.R

Revision 45 - Directory Listing
Modified Tue Sep 30 13:11:56 2008 UTC (10 years, 4 months ago) by gsimpson
mat() now passes '...' to distance()

Revision 44 - Directory Listing
Modified Tue Sep 30 12:09:55 2008 UTC (10 years, 4 months ago) by gsimpson
rebuilt vignette pdf for some reason?

Revision 43 - Directory Listing
Modified Tue Sep 30 12:09:21 2008 UTC (10 years, 4 months ago) by gsimpson
Updated TODO list a little

Revision 42 - Directory Listing
Modified Tue Sep 30 12:08:59 2008 UTC (10 years, 4 months ago) by gsimpson
Fix to make both types of plot in plot.mcarlo() work properly again.

Revision 41 - Directory Listing
Modified Tue Sep 30 08:46:57 2008 UTC (10 years, 4 months ago) by gsimpson
Major changes to roc and bayesF and related methods

Revision 40 - Directory Listing
Modified Mon Sep 29 16:41:28 2008 UTC (10 years, 4 months ago) by gsimpson
Added details of r38 and r39 to ChangeLog

Revision 39 - Directory Listing
Modified Mon Sep 29 16:37:46 2008 UTC (10 years, 4 months ago) by gsimpson
speed-up for summary.mat

Revision 38 - Directory Listing
Modified Mon Sep 29 16:33:17 2008 UTC (10 years, 4 months ago) by gsimpson
mat.default was converting to matrix too soon, plus speed-up for print.mat

Revision 37 - Directory Listing
Modified Sat Jul 26 11:46:41 2008 UTC (10 years, 6 months ago) by gsimpson
argument 'depths' was not being obeyed

Revision 36 - Directory Listing
Modified Sat Jul 19 11:55:56 2008 UTC (10 years, 7 months ago) by gsimpson
bump version number to 0.5-4

Revision 35 - Directory Listing
Modified Sat Jul 19 11:55:32 2008 UTC (10 years, 7 months ago) by gsimpson
Updated changelog reflecting r32, r33, r34

Revision 34 - Directory Listing
Modified Sat Jul 19 11:44:50 2008 UTC (10 years, 7 months ago) by gsimpson
New function fuse() for combining dissimilarities

Revision 33 - Directory Listing
Modified Sat Jul 19 11:42:56 2008 UTC (10 years, 7 months ago) by gsimpson
speed-up in calculating ranges/maximums in some dissimilarity measures

Revision 32 - Directory Listing
Modified Sat Jul 19 11:42:12 2008 UTC (10 years, 7 months ago) by gsimpson
startup message now uses packageStartupMessage()

Revision 31 - Directory Listing
Modified Sun Jun 15 15:02:22 2008 UTC (10 years, 8 months ago) by gsimpson
Constants 'a' and 'b' were being applied twice in the Log transformation

Revision 30 - Directory Listing
Modified Tue May 20 04:29:57 2008 UTC (10 years, 9 months ago) by jarioksa
doc update: typo, cross-references, JO as an co-author in predict.wa

Revision 29 - Directory Listing
Modified Mon May 19 19:36:37 2008 UTC (10 years, 9 months ago) by jarioksa
k-fold (nfold) CV for predict.wa

Revision 28 - Directory Listing
Modified Sun May 18 14:16:08 2008 UTC (10 years, 9 months ago) by gsimpson
fix r27 error in CITATION syntax

Revision 27 - Directory Listing
Modified Sun May 18 14:08:48 2008 UTC (10 years, 9 months ago) by gsimpson
Update CITATION to include Jari Oksanen as a package author.

Revision 26 - Directory Listing
Modified Sun May 18 13:59:41 2008 UTC (10 years, 9 months ago) by gsimpson
Adds new function tran() to perform common transformations and standardisations

Revision 25 - Directory Listing
Modified Fri May 2 16:18:11 2008 UTC (10 years, 9 months ago) by gsimpson
Updated changleog to reflect r24

Revision 24 - Directory Listing
Modified Sun Apr 27 22:29:41 2008 UTC (10 years, 9 months ago) by gsimpson
join() now checks for inheritance from class 'data.frame' for objects to join

Revision 23 - Directory Listing
Modified Thu Apr 24 08:15:52 2008 UTC (10 years, 9 months ago) by jarioksa
predict.wa learnt about new deshrinking options (and now bootstrap works with them)

Revision 22 - Directory Listing
Modified Thu Apr 24 07:52:42 2008 UTC (10 years, 9 months ago) by jarioksa
fix classical dehsrinking, add expanded and none as new deshrinking alternatives

Revision 21 - Directory Listing
Modified Tue Apr 22 12:51:31 2008 UTC (10 years, 9 months ago) by gsimpson
Fix problems with residuals, plot.mat now draws absolute bias stat, improvements in internal functions, Jari Oksanen joins the analogue team

Revision 20 - Directory Listing
Modified Tue Apr 22 11:46:50 2008 UTC (10 years, 9 months ago) by jarioksa
incidentally overwrote the pdf file in a previous commit: this should put things back like they were

Revision 19 - Directory Listing
Modified Tue Apr 22 08:41:14 2008 UTC (10 years, 9 months ago) by jarioksa
added internal function expand.deshrink to wait for a possible use

Revision 18 - Directory Listing
Modified Tue Apr 22 07:30:58 2008 UTC (10 years, 9 months ago) by jarioksa
wa residuals calculated as predicted - observed (reverses the sign from the previous version)

Revision 17 - Directory Listing
Modified Sat Apr 19 12:42:38 2008 UTC (10 years, 10 months ago) by gsimpson
predict.wa was not returning some attributes of the WA model

Revision 16 - Directory Listing
Modified Wed Apr 9 23:56:20 2008 UTC (10 years, 10 months ago) by gsimpson
Adding vignette based on jstatsoft paper

Revision 15 - Directory Listing
Modified Wed Apr 9 22:33:16 2008 UTC (10 years, 10 months ago) by gsimpson
Update DESCRIPTION

Revision 14 - Directory Listing
Modified Wed Apr 9 20:32:08 2008 UTC (10 years, 10 months ago) by gsimpson
Adds print methods for new functions

Revision 13 - Directory Listing
Modified Wed Apr 9 19:58:36 2008 UTC (10 years, 10 months ago) by gsimpson
Update the changelog to reflect 0.5-0 additions

Revision 12 - Directory Listing
Modified Wed Apr 9 19:46:20 2008 UTC (10 years, 10 months ago) by gsimpson
Add WA methods and support functions, bump version to 0.5-0

Revision 11 - Directory Listing
Modified Wed Apr 9 17:15:55 2008 UTC (10 years, 10 months ago) by gsimpson
Upped version to 0.5-0 ready to check-in the WA code

Revision 10 - Directory Listing
Modified Wed Apr 9 17:12:12 2008 UTC (10 years, 10 months ago) by gsimpson
Bugfix: plot.minDC not drawing axis correctly for the quantiles

Revision 9 - Directory Listing
Modified Wed Feb 13 18:41:02 2008 UTC (11 years ago) by gsimpson
Minor efficiency tweak to cummean in internal.R

Revision 8 - Directory Listing
Modified Mon Oct 15 20:18:59 2007 UTC (11 years, 4 months ago) by gsimpson
distance() is now generic with default and join methods

Revision 7 - Directory Listing
Modified Mon Oct 15 19:31:04 2007 UTC (11 years, 4 months ago) by gsimpson
join() now returns a classed object

Revision 6 - Directory Listing
Modified Mon Oct 15 18:59:16 2007 UTC (11 years, 4 months ago) by gsimpson
Changed Version: field in DESCRIPTION to match new standards in R2.6.0

Revision 5 - Directory Listing
Modified Sat Oct 13 18:39:55 2007 UTC (11 years, 4 months ago) by gsimpson
Fixed un-matched braces in Rd files

Revision 4 - Directory Listing
Modified Sat Oct 13 18:24:59 2007 UTC (11 years, 4 months ago) by gsimpson
fixes to join and distance for handling factors

Revision 3 - Directory Listing
Modified Sat Sep 15 18:35:14 2007 UTC (11 years, 5 months ago) by gsimpson
Documentation fixes - will eventually become version 0.4-3

Revision 2 - Directory Listing
Modified Fri Sep 14 17:34:35 2007 UTC (11 years, 5 months ago) by gsimpson
Checking in analogue_0.4-2 (CRAN version)

Revision 1 - Directory Listing
Added Mon Jun 25 10:38:44 2007 UTC (11 years, 7 months ago) by stefan7th
Email in Readme changed

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