Author: Andrew Parnell
Title: Stable Isotope Analysis in R
Description: This package takes data on organism isotopes and fits a Bayesian model to their dietary habits based upon a Gaussian likelihood with a mixture dirichlet-distributed prior on the mean.
Diff between siar versions 3.1 dated 2008-05-19 and 3.2 dated 2008-06-12
DESCRIPTION | 6 +++--- NAMESPACE | 2 +- R/siarhdrs.R | 26 +++++++++++++++++--------- R/siarhistograms.R | 14 ++++++++++++-- R/siarmatrixplot.R | 12 +++++++++++- R/siarmcmcdirichlet.R | 18 ++++++++++++++++-- R/siarmenu.R | 2 +- R/siarsolomcmc.r |only R/siarsolomultigrouprun.r |only R/siarsolosinglegrouprun.r |only man/siar-package.Rd | 4 ++-- man/siarsolomcmc.Rd |only man/siarsolomultigrouprun.Rd |only man/siarsolosinglegrouprun.Rd |only src/siarsolomcmcv3.c |only 15 files changed, 63 insertions(+), 21 deletions(-)
Author: Ken Beath
Diff between randomLCA versions 0.1-4 dated 2008-05-27 and 0.3-2 dated 2008-06-12
Title: Random Effects Latent Class Analysis
Description: Fits random effects latent class models, as well as standard latent class models.
randomLCA-0.1-4/randomLCA/._DESCRIPTION |only
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randomLCA-0.1-4/randomLCA/R/._fit.adapt.random2.randomLCA.R |only
randomLCA-0.1-4/randomLCA/R/._fit.adapt.random2byclass.randomLCA.R |only
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randomLCA-0.1-4/randomLCA/R/fit.randombyclass.randomLCA.R |only
randomLCA-0.1-4/randomLCA/inst/._NEWS |only
randomLCA-0.1-4/randomLCA/inst/doc/._randomLCA-example.Rnw |only
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randomLCA-0.1-4/randomLCA/man/._uterinecarcinoma.Rd |only
randomLCA-0.3-2/randomLCA/DESCRIPTION | 6
randomLCA-0.3-2/randomLCA/NAMESPACE | 1
randomLCA-0.3-2/randomLCA/R/fit.adapt.random.randomLCA.R | 106 +----
randomLCA-0.3-2/randomLCA/R/fit.adapt.randombyclass.randomLCA.R | 95 +---
randomLCA-0.3-2/randomLCA/R/fit.fixed.randomLCA.R | 142 +++----
randomLCA-0.3-2/randomLCA/R/randomLCA.R | 26 -
randomLCA-0.3-2/randomLCA/inst/NEWS | 19
randomLCA-0.3-2/randomLCA/inst/doc/randomLCA-example.Rnw | 202 +++-------
randomLCA-0.3-2/randomLCA/inst/doc/randomLCA-example.pdf |binary
randomLCA-0.3-2/randomLCA/man/dentistry.Rd | 4
randomLCA-0.3-2/randomLCA/man/randomLCA.Rd | 5
randomLCA-0.3-2/randomLCA/src |only
53 files changed, 229 insertions(+), 377 deletions(-)
Author: Reinhard Harter, Kurt Hornik and Stefan Theussl
Title: Symphony in R
Description: An R interface to the SYMPHONY MILP solver (version 5.1.8).
Diff between Rsymphony versions 0.1-4 dated 2008-03-06 and 0.1-5 dated 2008-06-12
DESCRIPTION | 8 R/sparse.R | 10 R/symphony.R | 161 configure | 4 man/Rsymphony_solve.Rd | 23 src/Makevars.in | 3 src/SYMPHONY/BuildTools/Makemain.inc | 25 src/SYMPHONY/BuildTools/coin.m4 | 332 src/SYMPHONY/BuildTools/commit_new_release | 4 src/SYMPHONY/BuildTools/compile_f2c/compile_f2c | 21 src/SYMPHONY/BuildTools/headers/configall_system_msc.h | 10 src/SYMPHONY/BuildTools/prepare_new_release | 10 src/SYMPHONY/Cgl/Makefile.am | 11 src/SYMPHONY/Cgl/Makefile.in | 42 src/SYMPHONY/Cgl/configure | 372 src/SYMPHONY/Cgl/configure.ac | 6 src/SYMPHONY/Cgl/examples/Makefile.in | 8 src/SYMPHONY/Cgl/src/CglAllDifferent/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglAllDifferent/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglClique/CglClique.cpp | 61 src/SYMPHONY/Cgl/src/CglClique/CglClique.hpp | 47 src/SYMPHONY/Cgl/src/CglClique/CglCliqueTest.cpp | 1 src/SYMPHONY/Cgl/src/CglClique/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglClique/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglCutGenerator.cpp | 6 src/SYMPHONY/Cgl/src/CglDuplicateRow/CglDuplicateRow.cpp | 28 src/SYMPHONY/Cgl/src/CglDuplicateRow/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglDuplicateRow/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglFlowCover/CglFlowCover.cpp | 26 src/SYMPHONY/Cgl/src/CglFlowCover/CglFlowCover.hpp | 4 src/SYMPHONY/Cgl/src/CglFlowCover/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglFlowCover/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglGomory/CglGomory.cpp | 60 src/SYMPHONY/Cgl/src/CglGomory/CglGomory.hpp | 12 src/SYMPHONY/Cgl/src/CglGomory/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglGomory/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglKnapsackCover/CglKnapsackCover.cpp | 37 src/SYMPHONY/Cgl/src/CglKnapsackCover/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglKnapsackCover/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglLandP/CglLandPSimplex.cpp | 2 src/SYMPHONY/Cgl/src/CglLandP/Makefile.am | 5 src/SYMPHONY/Cgl/src/CglLandP/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglLiftAndProject/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglLiftAndProject/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglMixedIntegerRounding/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglMixedIntegerRounding/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglMixedIntegerRounding2/CglMixedIntegerRounding2.cpp | 32 src/SYMPHONY/Cgl/src/CglMixedIntegerRounding2/CglMixedIntegerRounding2.hpp | 6 src/SYMPHONY/Cgl/src/CglMixedIntegerRounding2/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglMixedIntegerRounding2/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglOddHole/CglOddHole.cpp | 18 src/SYMPHONY/Cgl/src/CglOddHole/CglOddHole.hpp | 2 src/SYMPHONY/Cgl/src/CglOddHole/CglOddHoleTest.cpp | 4 src/SYMPHONY/Cgl/src/CglOddHole/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglOddHole/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglPreProcess/CglPreProcess.cpp | 1192 ++ src/SYMPHONY/Cgl/src/CglPreProcess/CglPreProcess.hpp | 2 src/SYMPHONY/Cgl/src/CglPreProcess/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglPreProcess/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglProbing/CglProbing.cpp | 454 src/SYMPHONY/Cgl/src/CglProbing/CglProbing.hpp | 3 src/SYMPHONY/Cgl/src/CglProbing/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglProbing/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglRedSplit/CglRedSplitTest.cpp | 1 src/SYMPHONY/Cgl/src/CglRedSplit/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglRedSplit/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglResidualCapacity/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglResidualCapacity/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglSimpleRounding/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglSimpleRounding/Makefile.in | 50 src/SYMPHONY/Cgl/src/CglStored.cpp | 175 src/SYMPHONY/Cgl/src/CglStored.hpp | 6 src/SYMPHONY/Cgl/src/CglTreeInfo.cpp | 1156 ++ src/SYMPHONY/Cgl/src/CglTreeInfo.hpp | 35 src/SYMPHONY/Cgl/src/CglTwomir/Makefile.am | 7 src/SYMPHONY/Cgl/src/CglTwomir/Makefile.in | 50 src/SYMPHONY/Cgl/src/Makefile.am | 11 src/SYMPHONY/Cgl/src/Makefile.in | 54 src/SYMPHONY/Cgl/test/Makefile.am | 2 src/SYMPHONY/Cgl/test/Makefile.in | 9 src/SYMPHONY/Clp/MSVisualStudio/v7/libClp/libClp.vcproj | 18 src/SYMPHONY/Clp/Makefile.am | 11 src/SYMPHONY/Clp/Makefile.in | 36 src/SYMPHONY/Clp/configure | 348 src/SYMPHONY/Clp/configure.ac | 4 src/SYMPHONY/Clp/examples/Makefile.in | 7 src/SYMPHONY/Clp/examples/addRows.cpp | 62 src/SYMPHONY/Clp/examples/g.tiny |only src/SYMPHONY/Clp/examples/gparm.tiny |only src/SYMPHONY/Clp/examples/myPdco.cpp |only src/SYMPHONY/Clp/examples/myPdco.hpp |only src/SYMPHONY/Clp/examples/pdco.cpp |only src/SYMPHONY/Clp/src/CbcOrClpParam.cpp | 235 src/SYMPHONY/Clp/src/CbcOrClpParam.hpp | 24 src/SYMPHONY/Clp/src/ClpDualRowSteepest.cpp | 45 src/SYMPHONY/Clp/src/ClpFactorization.cpp | 1297 ++ src/SYMPHONY/Clp/src/ClpFactorization.hpp | 188 src/SYMPHONY/Clp/src/ClpHelperFunctions.cpp | 1 src/SYMPHONY/Clp/src/ClpInterior.cpp | 8 src/SYMPHONY/Clp/src/ClpInterior.hpp | 1 src/SYMPHONY/Clp/src/ClpLsqr.cpp |only src/SYMPHONY/Clp/src/ClpLsqr.hpp |only src/SYMPHONY/Clp/src/ClpMain.cpp | 4 src/SYMPHONY/Clp/src/ClpMatrixBase.hpp | 2 src/SYMPHONY/Clp/src/ClpModel.cpp | 541 - src/SYMPHONY/Clp/src/ClpModel.hpp | 77 src/SYMPHONY/Clp/src/ClpNode.cpp |only src/SYMPHONY/Clp/src/ClpNode.hpp |only src/SYMPHONY/Clp/src/ClpPackedMatrix.cpp | 231 src/SYMPHONY/Clp/src/ClpPackedMatrix.hpp | 9 src/SYMPHONY/Clp/src/ClpPdco.cpp |only src/SYMPHONY/Clp/src/ClpPdco.hpp |only src/SYMPHONY/Clp/src/ClpPdcoBase.cpp |only src/SYMPHONY/Clp/src/ClpPdcoBase.hpp |only src/SYMPHONY/Clp/src/ClpPrimalColumnSteepest.cpp | 12 src/SYMPHONY/Clp/src/ClpSimplex.cpp | 1421 +- src/SYMPHONY/Clp/src/ClpSimplex.hpp | 175 src/SYMPHONY/Clp/src/ClpSimplexDual.cpp | 111 src/SYMPHONY/Clp/src/ClpSimplexNonlinear.cpp | 8 src/SYMPHONY/Clp/src/ClpSimplexOther.cpp | 406 src/SYMPHONY/Clp/src/ClpSimplexOther.hpp | 13 src/SYMPHONY/Clp/src/ClpSimplexPrimal.cpp | 44 src/SYMPHONY/Clp/src/ClpSolve.cpp | 490 src/SYMPHONY/Clp/src/ClpSolve.hpp | 118 src/SYMPHONY/Clp/src/IdiSolve.cpp | 21 src/SYMPHONY/Clp/src/Idiot.cpp | 5 src/SYMPHONY/Clp/src/Idiot.hpp | 3 src/SYMPHONY/Clp/src/Makefile.am | 18 src/SYMPHONY/Clp/src/Makefile.in | 75 src/SYMPHONY/Clp/src/unitTest.cpp | 1 src/SYMPHONY/Clp/test/Makefile.in | 3 src/SYMPHONY/CoinUtils/INSTALL |only src/SYMPHONY/CoinUtils/MSVisualStudio/v6/CoinUtils.dsw |only src/SYMPHONY/CoinUtils/MSVisualStudio/v6/CoinUtils.opt |only src/SYMPHONY/CoinUtils/MSVisualStudio/v6/libCoinUtils/libCoinUtils.dsp | 8 src/SYMPHONY/CoinUtils/MSVisualStudio/v7/CoinUtils.sln |only src/SYMPHONY/CoinUtils/MSVisualStudio/v7/CoinUtils.suo |only src/SYMPHONY/CoinUtils/MSVisualStudio/v7/libCoinUtils/libCoinUtils.vcproj | 22 src/SYMPHONY/CoinUtils/MSVisualStudio/v7/unitTestCoinUtils/unitTestCoinUtils.vcproj | 1 src/SYMPHONY/CoinUtils/MSVisualStudio/v8/CoinUtils.sln |only src/SYMPHONY/CoinUtils/MSVisualStudio/v8/CoinUtils.suo |only src/SYMPHONY/CoinUtils/MSVisualStudio/v8/libCoinUtils/libCoinUtils.vcproj | 16 src/SYMPHONY/CoinUtils/Makefile.am | 11 src/SYMPHONY/CoinUtils/Makefile.in | 39 src/SYMPHONY/CoinUtils/README |only src/SYMPHONY/CoinUtils/configure | 1105 +- src/SYMPHONY/CoinUtils/configure.ac | 79 src/SYMPHONY/CoinUtils/inc/config_coinutils.h.in | 12 src/SYMPHONY/CoinUtils/src/CoinAlloc.cpp |only src/SYMPHONY/CoinUtils/src/CoinAlloc.hpp |only src/SYMPHONY/CoinUtils/src/CoinBuild.cpp | 1 src/SYMPHONY/CoinUtils/src/CoinDenseFactorization.cpp |only src/SYMPHONY/CoinUtils/src/CoinDenseFactorization.hpp |only src/SYMPHONY/CoinUtils/src/CoinDenseVector.hpp | 1 src/SYMPHONY/CoinUtils/src/CoinError.hpp | 2 src/SYMPHONY/CoinUtils/src/CoinFactorization.hpp | 109 src/SYMPHONY/CoinUtils/src/CoinFactorization1.cpp | 13 src/SYMPHONY/CoinUtils/src/CoinFactorization3.cpp | 12 src/SYMPHONY/CoinUtils/src/CoinFactorization4.cpp | 40 src/SYMPHONY/CoinUtils/src/CoinFileIO.cpp | 20 src/SYMPHONY/CoinUtils/src/CoinFinite.hpp | 1 src/SYMPHONY/CoinUtils/src/CoinHelperFunctions.hpp | 202 src/SYMPHONY/CoinUtils/src/CoinLpIO.cpp | 7 src/SYMPHONY/CoinUtils/src/CoinLpIO.hpp | 3 src/SYMPHONY/CoinUtils/src/CoinMessageHandler.hpp | 4 src/SYMPHONY/CoinUtils/src/CoinModelUseful.cpp | 1 src/SYMPHONY/CoinUtils/src/CoinModelUseful2.cpp | 6 src/SYMPHONY/CoinUtils/src/CoinMpsIO.cpp | 1 src/SYMPHONY/CoinUtils/src/CoinPackedMatrix.cpp | 237 src/SYMPHONY/CoinUtils/src/CoinPackedMatrix.hpp | 16 src/SYMPHONY/CoinUtils/src/CoinPackedVector.cpp | 28 src/SYMPHONY/CoinUtils/src/CoinPackedVector.hpp | 21 src/SYMPHONY/CoinUtils/src/CoinPackedVectorBase.cpp | 17 src/SYMPHONY/CoinUtils/src/CoinPackedVectorBase.hpp | 19 src/SYMPHONY/CoinUtils/src/CoinPresolveSingleton.cpp | 28 src/SYMPHONY/CoinUtils/src/CoinPresolveTighten.cpp | 28 src/SYMPHONY/CoinUtils/src/CoinPresolveTripleton.cpp | 15 src/SYMPHONY/CoinUtils/src/CoinSearchTree.cpp | 53 src/SYMPHONY/CoinUtils/src/CoinSearchTree.hpp | 159 src/SYMPHONY/CoinUtils/src/CoinSignal.hpp | 7 src/SYMPHONY/CoinUtils/src/CoinSort.hpp | 132 src/SYMPHONY/CoinUtils/src/CoinTime.hpp | 63 src/SYMPHONY/CoinUtils/src/CoinTypes.hpp | 1 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src/SYMPHONY/Osi/src/OsiXpr/Makefile.in | 52 src/SYMPHONY/Osi/test/Makefile.in | 9 src/SYMPHONY/Osi/test/OsiDylpSolverInterfaceTest.cpp | 299 src/SYMPHONY/Osi/test/OsiRowCutTest.cpp | 2 src/SYMPHONY/Osi/test/OsiSolverInterfaceTest.cpp | 799 + src/SYMPHONY/Osi/test/unitTest.cpp | 77 src/SYMPHONY/README | 2 src/SYMPHONY/SYMPHONY/Applications/CNRP/Makefile | 129 src/SYMPHONY/SYMPHONY/Applications/CNRP/Makefile.in | 125 src/SYMPHONY/SYMPHONY/Applications/CNRP/include/cnrp_cg.h | 2 src/SYMPHONY/SYMPHONY/Applications/CNRP/include/cnrp_cg_params.h | 2 src/SYMPHONY/SYMPHONY/Applications/CNRP/include/cnrp_common_types.h | 2 src/SYMPHONY/SYMPHONY/Applications/CNRP/include/cnrp_const.h | 2 src/SYMPHONY/SYMPHONY/Applications/CNRP/include/cnrp_cp.h | 2 src/SYMPHONY/SYMPHONY/Applications/CNRP/include/cnrp_cp_params.h | 2 src/SYMPHONY/SYMPHONY/Applications/CNRP/include/cnrp_dg.h | 2 src/SYMPHONY/SYMPHONY/Applications/CNRP/include/cnrp_dg_functions.h | 2 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2 src/SYMPHONY/SYMPHONY/Applications/MPP/Makefile | 79 src/SYMPHONY/SYMPHONY/Applications/MPP/Makefile.in | 75 src/SYMPHONY/SYMPHONY/Applications/MPP/include/mpp.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/Makefile | 88 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/Makefile.in | 84 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_cg.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_cg_clique.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_cg_functions.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_cg_params.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_common.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_constants.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_lp.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_lp_functions.h | 2 src/SYMPHONY/SYMPHONY/Applications/SPP+CUTS/include/spp_lp_params.h | 2 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src/SYMPHONY/SYMPHONY/Applications/VRP/include/compute_cost.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/network.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/small_graph.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_cg.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_cg_params.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_common_types.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_cp.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_dg.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_dg_functions.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_io.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_lp.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_lp_params.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_macros.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_master_functions.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_messages.h | 2 src/SYMPHONY/SYMPHONY/Applications/VRP/include/vrp_types.h | 2 src/SYMPHONY/SYMPHONY/Doc/Walkthrough.tex | 2 src/SYMPHONY/SYMPHONY/Doc/biblio.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-API.tex | 6 src/SYMPHONY/SYMPHONY/Doc/man-SYMPHONY.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-background.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-callable.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-cg.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-cp.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-design.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-dg.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-intro.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-lp.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-param.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man-start.tex | 4 src/SYMPHONY/SYMPHONY/Doc/man-tm.tex | 2 src/SYMPHONY/SYMPHONY/Doc/man.tex | 6 src/SYMPHONY/SYMPHONY/Examples/Makefile | 226 src/SYMPHONY/SYMPHONY/Examples/Makefile.in |only src/SYMPHONY/SYMPHONY/Examples/bicriteria.c | 2 src/SYMPHONY/SYMPHONY/Examples/milp.c | 28 src/SYMPHONY/SYMPHONY/Examples/milp2.c | 26 src/SYMPHONY/SYMPHONY/Examples/milpOsi.c | 2 src/SYMPHONY/SYMPHONY/Examples/milpOsi2.c | 2 src/SYMPHONY/SYMPHONY/Examples/sensitivity.c | 7 src/SYMPHONY/SYMPHONY/Examples/warm_start1.c | 20 src/SYMPHONY/SYMPHONY/Examples/warm_start2.c | 5 src/SYMPHONY/SYMPHONY/Examples/warm_start3.c | 15 src/SYMPHONY/SYMPHONY/Makefile.am | 9 src/SYMPHONY/SYMPHONY/Makefile.in | 54 src/SYMPHONY/SYMPHONY/README | 12 src/SYMPHONY/SYMPHONY/configure | 370 src/SYMPHONY/SYMPHONY/configure.ac | 10 src/SYMPHONY/SYMPHONY/include/sym_cg.h | 2 src/SYMPHONY/SYMPHONY/include/sym_cg_params.h | 2 src/SYMPHONY/SYMPHONY/include/sym_cg_u.h | 2 src/SYMPHONY/SYMPHONY/include/sym_constants.h | 12 src/SYMPHONY/SYMPHONY/include/sym_cp.h | 2 src/SYMPHONY/SYMPHONY/include/sym_cp_params.h | 2 src/SYMPHONY/SYMPHONY/include/sym_cp_u.h | 2 src/SYMPHONY/SYMPHONY/include/sym_dg.h | 2 src/SYMPHONY/SYMPHONY/include/sym_dg_params.h | 2 src/SYMPHONY/SYMPHONY/include/sym_dg_u.h | 2 src/SYMPHONY/SYMPHONY/include/sym_lp.h | 2 src/SYMPHONY/SYMPHONY/include/sym_lp_params.h | 22 src/SYMPHONY/SYMPHONY/include/sym_lp_solver.h | 18 src/SYMPHONY/SYMPHONY/include/sym_lp_u.h | 2 src/SYMPHONY/SYMPHONY/include/sym_macros.h | 2 src/SYMPHONY/SYMPHONY/include/sym_master.h | 2 src/SYMPHONY/SYMPHONY/include/sym_master_params.h | 2 src/SYMPHONY/SYMPHONY/include/sym_master_u.h | 2 src/SYMPHONY/SYMPHONY/include/sym_messages.h | 2 src/SYMPHONY/SYMPHONY/include/sym_pack_array.h | 2 src/SYMPHONY/SYMPHONY/include/sym_pack_cut.h | 2 src/SYMPHONY/SYMPHONY/include/sym_proccomm.h | 2 src/SYMPHONY/SYMPHONY/include/sym_proto.h | 2 src/SYMPHONY/SYMPHONY/include/sym_qsort.h | 2 src/SYMPHONY/SYMPHONY/include/sym_return_values.h | 2 src/SYMPHONY/SYMPHONY/include/sym_timemeas.h | 2 src/SYMPHONY/SYMPHONY/include/sym_tm.h | 4 src/SYMPHONY/SYMPHONY/include/sym_tm_params.h | 2 src/SYMPHONY/SYMPHONY/include/sym_types.h | 2 src/SYMPHONY/SYMPHONY/src/Common/pack_array.c | 2 src/SYMPHONY/SYMPHONY/src/Common/pack_cut.c | 2 src/SYMPHONY/SYMPHONY/src/Common/proccomm.c | 2 src/SYMPHONY/SYMPHONY/src/Common/sym_qsort.c | 2 src/SYMPHONY/SYMPHONY/src/Common/timemeas.c | 2 src/SYMPHONY/SYMPHONY/src/CutGen/cg_func.c | 2 src/SYMPHONY/SYMPHONY/src/CutGen/cg_proccomm.c | 2 src/SYMPHONY/SYMPHONY/src/CutGen/cg_wrapper.c | 2 src/SYMPHONY/SYMPHONY/src/CutGen/cut_gen.c | 2 src/SYMPHONY/SYMPHONY/src/CutPool/cp_func.c | 2 src/SYMPHONY/SYMPHONY/src/CutPool/cp_proccomm.c | 2 src/SYMPHONY/SYMPHONY/src/CutPool/cp_wrapper.c | 2 src/SYMPHONY/SYMPHONY/src/CutPool/cut_pool.c | 2 src/SYMPHONY/SYMPHONY/src/DrawGraph/draw_graph.c | 2 src/SYMPHONY/SYMPHONY/src/DrawGraph/tester.c | 2 src/SYMPHONY/SYMPHONY/src/LP/lp.c | 2 src/SYMPHONY/SYMPHONY/src/LP/lp_branch.c | 28 src/SYMPHONY/SYMPHONY/src/LP/lp_free.c | 11 src/SYMPHONY/SYMPHONY/src/LP/lp_genfunc.c | 3 src/SYMPHONY/SYMPHONY/src/LP/lp_proccomm.c | 2 src/SYMPHONY/SYMPHONY/src/LP/lp_pseudo_branch.c | 2 src/SYMPHONY/SYMPHONY/src/LP/lp_rowfunc.c | 2 src/SYMPHONY/SYMPHONY/src/LP/lp_solver.c | 765 + src/SYMPHONY/SYMPHONY/src/LP/lp_varfunc.c | 2 src/SYMPHONY/SYMPHONY/src/LP/lp_wrapper.c | 248 src/SYMPHONY/SYMPHONY/src/Makefile.am | 13 src/SYMPHONY/SYMPHONY/src/Makefile.in | 55 src/SYMPHONY/SYMPHONY/src/Master/main.c | 47 src/SYMPHONY/SYMPHONY/src/Master/master.c | 143 src/SYMPHONY/SYMPHONY/src/Master/master_func.c | 91 src/SYMPHONY/SYMPHONY/src/Master/master_io.c | 11 src/SYMPHONY/SYMPHONY/src/Master/master_wrapper.c | 90 src/SYMPHONY/SYMPHONY/src/TreeManager/tm_func.c | 81 src/SYMPHONY/SYMPHONY/src/TreeManager/tm_proccomm.c | 2 src/SYMPHONY/SYMPHONY/src/TreeManager/treemanager.c | 2 src/SYMPHONY/SYMPHONY/test/Makefile.in | 7 src/SYMPHONY/SYMPHONY/test/OsiSolverInterfaceTest.cpp | 647 + src/SYMPHONY/SYMPHONY/test/unitTestSym.cpp | 2 src/SYMPHONY/ThirdParty/Blas |only src/SYMPHONY/ThirdParty/Glpk/INSTALL.Glpk | 14 src/SYMPHONY/ThirdParty/Glpk/Makefile.am | 15 src/SYMPHONY/ThirdParty/Glpk/Makefile.in | 134 src/SYMPHONY/ThirdParty/Glpk/configure | 352 src/SYMPHONY/ThirdParty/Glpk/configure.ac | 18 src/SYMPHONY/ThirdParty/Glpk/get.Glpk | 6 src/SYMPHONY/ThirdParty/Glpk/glpk.patch |only src/SYMPHONY/ThirdParty/Lapack |only src/SYMPHONY/configure | 416 src/SYMPHONY/configure.ac | 8 458 files changed, 23073 insertions(+), 8301 deletions(-)
Author: Stig Mortensen
Diff between PSM versions 0.7 dated 2008-06-10 and 0.8 dated 2008-06-12
Title: Non-Linear Mixed-Effects modelling using Stochastic Differential Equations.
Description: This package provides functions for estimation of linear and non-linear mixed-effects models using stochastic differential equations. Moreover it provides functions for finding smoothed estimates of model states and for simulation. The package allows for any multivariate non-linear time-variant model to be specified, and it also handels multidimentional input, co-variates, missing observations and specification of dosage regimen.
DESCRIPTION | 6 +++---
inst/doc/PSM.Rnw | 40 ++++++++++++++++++++++++++++++++++++++--
inst/doc/PSM.pdf |binary
man/PSM.estimate.Rd | 1 -
man/PSM.simulate.Rd | 1 -
man/PSM.smooth.Rd | 1 -
6 files changed, 41 insertions(+), 8 deletions(-)
Author: Jae. H. Kim
Title: Bootstrap Prediction Intervals and Bias-Corrected Forecasting
Description: Bias-Corrected Forecasting and Bootstrap Prediction Intervals for Autoregressive Time Series
Diff between BootPR versions 0.55 dated 2008-04-20 and 0.56 dated 2008-06-12
DESCRIPTION | 6 +++--- R/Boot.PI.R | 2 +- R/BootAfterBoot.PI.R | 2 +- R/BootAfterBootT.PI.R | 2 +- R/BootT.PI.R | 2 +- R/LS.AR.R | 9 ++++----- R/OLS.AR.R | 15 ++++++++++++--- R/OLS.ART.R | 16 +++++++++++++--- R/adjust2.R | 3 +++ R/mainf.R |only man/LS.AR.Rd | 6 ++++-- 11 files changed, 43 insertions(+), 20 deletions(-)
Author: Andrew Balemi, James Curran, Brant Deppa, Mike Forster, Michael Maia, Chris Wild
Title: Stats 20x
Description: Stats 20x functions.
Diff between s20x versions 2.6.1.000 dated 2008-02-12 and 3.1-0 dated 2008-06-12
s20x-2.6.1.000/s20x/data/STATS20x.txt |only s20x-2.6.1.000/s20x/data/airpass.txt |only s20x-2.6.1.000/s20x/data/arousal.txt |only s20x-2.6.1.000/s20x/data/beer.txt |only s20x-2.6.1.000/s20x/data/bodim.txt |only s20x-2.6.1.000/s20x/data/bursary.01.txt |only s20x-2.6.1.000/s20x/data/camplake.txt |only s20x-2.6.1.000/s20x/data/computer.txt |only s20x-2.6.1.000/s20x/data/course.2way.txt |only s20x-2.6.1.000/s20x/data/crest.txt |only s20x-2.6.1.000/s20x/data/diamonds.txt |only s20x-2.6.1.000/s20x/data/fire.txt |only s20x-2.6.1.000/s20x/data/houseprices.txt |only s20x-2.6.1.000/s20x/data/incomes.txt |only s20x-2.6.1.000/s20x/data/la.rain.txt |only s20x-2.6.1.000/s20x/data/lakemary.txt |only s20x-2.6.1.000/s20x/data/mazda.txt |only s20x-2.6.1.000/s20x/data/mening.txt |only s20x-2.6.1.000/s20x/data/mergers.txt |only s20x-2.6.1.000/s20x/data/mozart.txt |only s20x-2.6.1.000/s20x/data/oyster.txt |only s20x-2.6.1.000/s20x/data/peru.txt |only s20x-2.6.1.000/s20x/data/soya.txt |only s20x-2.6.1.000/s20x/data/teach.methods.txt |only s20x-2.6.1.000/s20x/data/technitron.txt |only s20x-2.6.1.000/s20x/data/thyroid.txt |only s20x-2.6.1.000/s20x/data/zoo.txt |only s20x-2.6.1.000/s20x/man/STATS20x.Rd |only s20x-2.6.1.000/s20x/man/airpass.Rd |only s20x-2.6.1.000/s20x/man/arousal.Rd |only s20x-2.6.1.000/s20x/man/beer.Rd |only s20x-2.6.1.000/s20x/man/bodim.Rd |only s20x-2.6.1.000/s20x/man/bursary.01.Rd |only s20x-2.6.1.000/s20x/man/camplake.Rd |only s20x-2.6.1.000/s20x/man/computer.Rd |only s20x-2.6.1.000/s20x/man/course.2way.Rd |only s20x-2.6.1.000/s20x/man/crest.Rd |only s20x-2.6.1.000/s20x/man/diamonds.Rd |only s20x-2.6.1.000/s20x/man/fire.Rd |only s20x-2.6.1.000/s20x/man/houseprices.Rd |only s20x-2.6.1.000/s20x/man/incomes.Rd |only s20x-2.6.1.000/s20x/man/la.rain.Rd |only s20x-2.6.1.000/s20x/man/lakemary.Rd |only s20x-2.6.1.000/s20x/man/mazda.Rd |only s20x-2.6.1.000/s20x/man/mening.Rd |only s20x-2.6.1.000/s20x/man/mergers.Rd |only s20x-2.6.1.000/s20x/man/mozart.Rd |only s20x-2.6.1.000/s20x/man/oyster.Rd |only s20x-2.6.1.000/s20x/man/peru.Rd |only s20x-2.6.1.000/s20x/man/soya.Rd |only s20x-2.6.1.000/s20x/man/teach.methods.Rd |only s20x-2.6.1.000/s20x/man/technitron.Rd |only s20x-2.6.1.000/s20x/man/thyroid.Rd |only s20x-2.6.1.000/s20x/man/zoo.Rd |only s20x-3.1-0/s20x/DESCRIPTION | 10 - s20x-3.1-0/s20x/R/DEPRECATED.R | 21 ++- s20x-3.1-0/s20x/R/eovcheck.R |only s20x-3.1-0/s20x/R/levene.test.R | 19 ++- s20x-3.1-0/s20x/R/normcheck.R |only s20x-3.1-0/s20x/R/pairs20x.R | 5 s20x-3.1-0/s20x/R/predict20x.R | 26 ++-- s20x-3.1-0/s20x/R/rowdistr.r | 166 ++++++++++++++--------------- s20x-3.1-0/s20x/R/version.R |only s20x-3.1-0/s20x/data/airpass.df.txt |only s20x-3.1-0/s20x/data/arousal.df.txt |only s20x-3.1-0/s20x/data/beer.df.txt |only s20x-3.1-0/s20x/data/bodim.df.txt |only s20x-3.1-0/s20x/data/bursary.df.txt |only s20x-3.1-0/s20x/data/camplake.df.txt |only s20x-3.1-0/s20x/data/computer.df.txt |only s20x-3.1-0/s20x/data/course.df.txt |only s20x-3.1-0/s20x/data/diamonds.df.txt |only s20x-3.1-0/s20x/data/fire.df.txt |only s20x-3.1-0/s20x/data/houseprices.df.txt |only s20x-3.1-0/s20x/data/incomes.df.txt |only s20x-3.1-0/s20x/data/lakemary.df.txt |only s20x-3.1-0/s20x/data/larain.df.txt |only s20x-3.1-0/s20x/data/mazda.df.txt |only s20x-3.1-0/s20x/data/mening.df.txt |only s20x-3.1-0/s20x/data/mergers.df.txt |only s20x-3.1-0/s20x/data/mozart.df.txt |only s20x-3.1-0/s20x/data/oyster.df.txt |only s20x-3.1-0/s20x/data/peru.df.txt |only s20x-3.1-0/s20x/data/soya.df.txt |only s20x-3.1-0/s20x/data/teach.df.txt |only s20x-3.1-0/s20x/data/technitron.df.txt |only s20x-3.1-0/s20x/data/thyroid.df.txt |only s20x-3.1-0/s20x/data/toothpaste.df.txt |only s20x-3.1-0/s20x/data/zoo.df.txt |only s20x-3.1-0/s20x/demo/cs1.r | 27 ++-- s20x-3.1-0/s20x/demo/cs11.r | 9 - s20x-3.1-0/s20x/demo/cs12.r | 6 - s20x-3.1-0/s20x/demo/cs13.r | 8 - s20x-3.1-0/s20x/demo/cs14.r | 8 - s20x-3.1-0/s20x/demo/cs2.r | 7 - s20x-3.1-0/s20x/demo/cs21.r | 5 s20x-3.1-0/s20x/demo/cs22.r | 4 s20x-3.1-0/s20x/demo/cs23.r | 4 s20x-3.1-0/s20x/demo/cs24.r | 5 s20x-3.1-0/s20x/demo/cs25.r | 5 s20x-3.1-0/s20x/demo/cs28.r | 5 s20x-3.1-0/s20x/demo/cs29.r | 6 - s20x-3.1-0/s20x/demo/cs3.r | 4 s20x-3.1-0/s20x/demo/cs30.r | 5 s20x-3.1-0/s20x/demo/cs31.r | 5 s20x-3.1-0/s20x/demo/cs32.r | 7 - s20x-3.1-0/s20x/demo/cs33.r | 7 - s20x-3.1-0/s20x/demo/cs34.r | 4 s20x-3.1-0/s20x/demo/cs4.r | 8 - s20x-3.1-0/s20x/demo/cs5.r | 5 s20x-3.1-0/s20x/demo/cs8.r | 7 - s20x-3.1-0/s20x/man/airpass.df.Rd |only s20x-3.1-0/s20x/man/arousal.df.Rd |only s20x-3.1-0/s20x/man/autocor.plot.Rd | 6 - s20x-3.1-0/s20x/man/beer.df.Rd |only s20x-3.1-0/s20x/man/bodim.df.Rd |only s20x-3.1-0/s20x/man/boxqq.Rd | 6 - s20x-3.1-0/s20x/man/bursary.df.Rd |only s20x-3.1-0/s20x/man/camplake.df.Rd |only s20x-3.1-0/s20x/man/ci.reg.Rd | 8 - s20x-3.1-0/s20x/man/computer.df.Rd |only s20x-3.1-0/s20x/man/cooks.20x.Rd | 6 - s20x-3.1-0/s20x/man/course.df.Rd |only s20x-3.1-0/s20x/man/crosstabs.20x.Rd | 6 - s20x-3.1-0/s20x/man/diamonds.df.Rd |only s20x-3.1-0/s20x/man/eovcheck.Rd |only s20x-3.1-0/s20x/man/estimate.contrasts.Rd | 6 - s20x-3.1-0/s20x/man/fire.df.Rd |only s20x-3.1-0/s20x/man/freq1way.Rd | 8 - s20x-3.1-0/s20x/man/houseprices.df.Rd |only s20x-3.1-0/s20x/man/incomes.df.Rd |only s20x-3.1-0/s20x/man/interaction.20x.Rd | 6 - s20x-3.1-0/s20x/man/lakemary.df.Rd |only s20x-3.1-0/s20x/man/larain.df.Rd |only s20x-3.1-0/s20x/man/layout.20x.Rd | 6 - s20x-3.1-0/s20x/man/levene.test.Rd | 28 ++-- s20x-3.1-0/s20x/man/mazda.df.Rd |only s20x-3.1-0/s20x/man/mening.df.Rd |only s20x-3.1-0/s20x/man/mergers.df.Rd |only s20x-3.1-0/s20x/man/mozart.df.Rd |only s20x-3.1-0/s20x/man/multiple.comp.Rd | 6 - s20x-3.1-0/s20x/man/normcheck.Rd |only s20x-3.1-0/s20x/man/numerical.summary.Rd | 12 +- s20x-3.1-0/s20x/man/oneway.plot.Rd | 10 - s20x-3.1-0/s20x/man/oyster.df.Rd |only s20x-3.1-0/s20x/man/pairs20x.Rd | 15 +- s20x-3.1-0/s20x/man/peru.df.Rd |only s20x-3.1-0/s20x/man/predict20x.Rd | 17 +- s20x-3.1-0/s20x/man/resid.plot.Rd | 13 +- s20x-3.1-0/s20x/man/rowdistr.Rd | 7 - s20x-3.1-0/s20x/man/skewness.Rd | 6 - s20x-3.1-0/s20x/man/soya.df.Rd |only s20x-3.1-0/s20x/man/stripqq.Rd | 5 s20x-3.1-0/s20x/man/summary1way.Rd | 4 s20x-3.1-0/s20x/man/summary2way.Rd | 13 +- s20x-3.1-0/s20x/man/teach.df.Rd |only s20x-3.1-0/s20x/man/technitron.df.Rd |only s20x-3.1-0/s20x/man/thyroid.df.Rd |only s20x-3.1-0/s20x/man/toothpaste.df.Rd |only s20x-3.1-0/s20x/man/trendscatter.Rd | 12 +- s20x-3.1-0/s20x/man/version.Rd |only s20x-3.1-0/s20x/man/zoo.df.Rd |only 162 files changed, 314 insertions(+), 290 deletions(-)
Author: Rolf Turner
Diff between Iso versions 0.0-4 dated 2008-03-07 and 0.0-5 dated 2008-06-12
Title: Functions to perform isotonic regression.
Description: Does linear order and unimodal order isotonic regression.
DESCRIPTION | 6 +++---
R/pava.R | 15 ++++++++++++---
R/pava.sa.R | 13 +++++++++++--
man/pava.Rd | 23 +++++++++++++++++------
4 files changed, 43 insertions(+), 14 deletions(-)