Title: Visualization of regression models
Diff between visreg versions 1.2-1 dated 2013-02-21 and 2.0-0 dated 2013-05-23
Description: Provides convenient interface for constructing plots to
visualize the fit of regression models arising from a wide
variety of models in R (lm, glm, coxph, rlm, gam, locfit, etc.)
Author: Patrick Breheny, Woodrow Burchett
Maintainer: Patrick Breheny
visreg-1.2-1/visreg/WISHLIST |only
visreg-1.2-1/visreg/tests/visreg-effect.R |only
visreg-2.0-0/visreg/DESCRIPTION | 8
visreg-2.0-0/visreg/FAQ.md | 20 -
visreg-2.0-0/visreg/MD5 | 71 ++-
visreg-2.0-0/visreg/NEWS | 25 +
visreg-2.0-0/visreg/R/Response.R | 14
visreg-2.0-0/visreg/R/Terms.R | 17
visreg-2.0-0/visreg/R/factorAxis.R | 30 -
visreg-2.0-0/visreg/R/factorPlot.R | 57 +-
visreg-2.0-0/visreg/R/getXY.R | 15
visreg-2.0-0/visreg/R/pal.R |only
visreg-2.0-0/visreg/R/printCond.R |only
visreg-2.0-0/visreg/R/removeFormulaFormatting.R | 1
visreg-2.0-0/visreg/R/setupCond.R | 76 +--
visreg-2.0-0/visreg/R/setupD.R | 14
visreg-2.0-0/visreg/R/setupF.R | 24 -
visreg-2.0-0/visreg/R/setupV.R |only
visreg-2.0-0/visreg/R/setupV2.R |only
visreg-2.0-0/visreg/R/setupX.R | 38 +
visreg-2.0-0/visreg/R/subsetV.R |only
visreg-2.0-0/visreg/R/toplegend.R |only
visreg-2.0-0/visreg/R/visreg.R | 55 +-
visreg-2.0-0/visreg/R/visreg2d.R | 128 ++----
visreg-2.0-0/visreg/R/visregFactorPanel.R | 26 -
visreg-2.0-0/visreg/R/visregLatticePlot.R | 105 +----
visreg-2.0-0/visreg/R/visregOverlayPlot.R |only
visreg-2.0-0/visreg/R/visregPanel.R | 21 -
visreg-2.0-0/visreg/R/visregPlot.R | 97 ++---
visreg-2.0-0/visreg/man/visreg-package.Rd | 76 +--
visreg-2.0-0/visreg/man/visreg.Rd | 462 ++++++++++++++----------
visreg-2.0-0/visreg/man/visreg2d.Rd | 209 ++++++----
visreg-2.0-0/visreg/tests/missing-data.R | 65 ++-
visreg-2.0-0/visreg/tests/visreg-contrast.R |only
visreg-2.0-0/visreg/tests/visreg-coxph.R | 6
visreg-2.0-0/visreg/tests/visreg-glm.R | 19
visreg-2.0-0/visreg/tests/visreg-interactions.R | 65 ++-
visreg-2.0-0/visreg/tests/visreg-lm.R | 62 +--
visreg-2.0-0/visreg/tests/visreg-mlm.R | 19
visreg-2.0-0/visreg/tests/visreg2d-glm.R | 43 +-
visreg-2.0-0/visreg/tests/visreg2d-lm.R | 108 ++---
visreg-2.0-0/visreg/to-do.txt |only
42 files changed, 1090 insertions(+), 886 deletions(-)
Title: Relational Class Analysis
Diff between RCA versions 1.3.2 dated 2013-04-03 and 1.4 dated 2013-05-23
Description: Relational Class Analysis (RCA) is a method for detecting
heterogeneity in attitudinal data. (as described in Goldberg
A., 2011, Am. J. Soc, 116(5)) . src/ also contains the source
files of igraph-C which was written by Gabor.
Author: Amir Goldberg
Maintainer: Yuan Wang
RCA-1.3.2/RCA/src/igraph-R |only
RCA-1.4/RCA/DESCRIPTION | 17
RCA-1.4/RCA/MD5 | 643 +++++++++++++++++---
RCA-1.4/RCA/R/RCA.R | 3
RCA-1.4/RCA/man/RCA-package.Rd | 30
RCA-1.4/RCA/man/RCA.Rd | 62 +
RCA-1.4/RCA/man/Result.Rd | 39 -
RCA-1.4/RCA/man/SampleInputMatrix.Rd | 14
RCA-1.4/RCA/matrix.pmt |only
RCA-1.4/RCA/src/Color.cpp |only
RCA-1.4/RCA/src/Color.h |only
RCA-1.4/RCA/src/DensityGrid.cpp |only
RCA-1.4/RCA/src/DensityGrid.h |only
RCA-1.4/RCA/src/DensityGrid_3d.cpp |only
RCA-1.4/RCA/src/DensityGrid_3d.h |only
RCA-1.4/RCA/src/Light.cpp |only
RCA-1.4/RCA/src/Light.h |only
RCA-1.4/RCA/src/Makevars | 13
RCA-1.4/RCA/src/Makevars.win | 11
RCA-1.4/RCA/src/NetDataTypes.cpp |only
RCA-1.4/RCA/src/NetDataTypes.h |only
RCA-1.4/RCA/src/NetRoutines.cpp |only
RCA-1.4/RCA/src/NetRoutines.h |only
RCA-1.4/RCA/src/Point.cpp |only
RCA-1.4/RCA/src/Point.h |only
RCA-1.4/RCA/src/RCAlib.c | 36 -
RCA-1.4/RCA/src/RIgraphRay.cpp |only
RCA-1.4/RCA/src/Ray.cpp |only
RCA-1.4/RCA/src/Ray.h |only
RCA-1.4/RCA/src/RayTracer.cpp |only
RCA-1.4/RCA/src/RayTracer.h |only
RCA-1.4/RCA/src/RayVector.cpp |only
RCA-1.4/RCA/src/RayVector.h |only
RCA-1.4/RCA/src/Shape.cpp |only
RCA-1.4/RCA/src/Shape.h |only
RCA-1.4/RCA/src/Sphere.cpp |only
RCA-1.4/RCA/src/Sphere.h |only
RCA-1.4/RCA/src/Triangle.cpp |only
RCA-1.4/RCA/src/Triangle.h |only
RCA-1.4/RCA/src/amd_1.c |only
RCA-1.4/RCA/src/amd_2.c |only
RCA-1.4/RCA/src/amd_aat.c |only
RCA-1.4/RCA/src/amd_control.c |only
RCA-1.4/RCA/src/amd_defaults.c |only
RCA-1.4/RCA/src/amd_dump.c |only
RCA-1.4/RCA/src/amd_info.c |only
RCA-1.4/RCA/src/amd_order.c |only
RCA-1.4/RCA/src/amd_post_tree.c |only
RCA-1.4/RCA/src/amd_postorder.c |only
RCA-1.4/RCA/src/amd_preprocess.c |only
RCA-1.4/RCA/src/amd_valid.c |only
RCA-1.4/RCA/src/arpack.c |only
RCA-1.4/RCA/src/atlas-edges.h |only
RCA-1.4/RCA/src/atlas.c |only
RCA-1.4/RCA/src/attributes.c |only
RCA-1.4/RCA/src/autom4te.cache |only
RCA-1.4/RCA/src/basic_query.c |only
RCA-1.4/RCA/src/bfgs.c |only
RCA-1.4/RCA/src/bigint.c |only
RCA-1.4/RCA/src/bigint.h |only
RCA-1.4/RCA/src/bignum.c |only
RCA-1.4/RCA/src/bignum.h |only
RCA-1.4/RCA/src/bipartite.c |only
RCA-1.4/RCA/src/blas.c |only
RCA-1.4/RCA/src/bliss.cc |only
RCA-1.4/RCA/src/bliss_bignum.h |only
RCA-1.4/RCA/src/bliss_defs.h |only
RCA-1.4/RCA/src/bliss_eqrefhash.cc |only
RCA-1.4/RCA/src/bliss_eqrefhash.h |only
RCA-1.4/RCA/src/bliss_graph.cc |only
RCA-1.4/RCA/src/bliss_graph.h |only
RCA-1.4/RCA/src/bliss_heap.cc |only
RCA-1.4/RCA/src/bliss_heap.h |only
RCA-1.4/RCA/src/bliss_kqueue.h |only
RCA-1.4/RCA/src/bliss_kstack.h |only
RCA-1.4/RCA/src/bliss_orbit.cc |only
RCA-1.4/RCA/src/bliss_orbit.h |only
RCA-1.4/RCA/src/bliss_partition.cc |only
RCA-1.4/RCA/src/bliss_partition.h |only
RCA-1.4/RCA/src/bliss_timer.cc |only
RCA-1.4/RCA/src/bliss_timer.h |only
RCA-1.4/RCA/src/bliss_utils.cc |only
RCA-1.4/RCA/src/bliss_utils.h |only
RCA-1.4/RCA/src/cattributes.c |only
RCA-1.4/RCA/src/centrality.c |only
RCA-1.4/RCA/src/cliques.c |only
RCA-1.4/RCA/src/clustertool.cpp |only
RCA-1.4/RCA/src/cocitation.c |only
RCA-1.4/RCA/src/cohesive_blocks.c |only
RCA-1.4/RCA/src/colamd.c |only
RCA-1.4/RCA/src/community.c |only
RCA-1.4/RCA/src/complex.c |only
RCA-1.4/RCA/src/components.c |only
RCA-1.4/RCA/src/config.h |only
RCA-1.4/RCA/src/conversion.c |only
RCA-1.4/RCA/src/cores.c |only
RCA-1.4/RCA/src/cs |only
RCA-1.4/RCA/src/cs_add.c |only
RCA-1.4/RCA/src/cs_amd.c |only
RCA-1.4/RCA/src/cs_chol.c |only
RCA-1.4/RCA/src/cs_cholsol.c |only
RCA-1.4/RCA/src/cs_compress.c |only
RCA-1.4/RCA/src/cs_counts.c |only
RCA-1.4/RCA/src/cs_cumsum.c |only
RCA-1.4/RCA/src/cs_dfs.c |only
RCA-1.4/RCA/src/cs_dmperm.c |only
RCA-1.4/RCA/src/cs_droptol.c |only
RCA-1.4/RCA/src/cs_dropzeros.c |only
RCA-1.4/RCA/src/cs_dupl.c |only
RCA-1.4/RCA/src/cs_entry.c |only
RCA-1.4/RCA/src/cs_ereach.c |only
RCA-1.4/RCA/src/cs_etree.c |only
RCA-1.4/RCA/src/cs_fkeep.c |only
RCA-1.4/RCA/src/cs_gaxpy.c |only
RCA-1.4/RCA/src/cs_happly.c |only
RCA-1.4/RCA/src/cs_house.c |only
RCA-1.4/RCA/src/cs_ipvec.c |only
RCA-1.4/RCA/src/cs_leaf.c |only
RCA-1.4/RCA/src/cs_load.c |only
RCA-1.4/RCA/src/cs_lsolve.c |only
RCA-1.4/RCA/src/cs_ltsolve.c |only
RCA-1.4/RCA/src/cs_lu.c |only
RCA-1.4/RCA/src/cs_lusol.c |only
RCA-1.4/RCA/src/cs_malloc.c |only
RCA-1.4/RCA/src/cs_maxtrans.c |only
RCA-1.4/RCA/src/cs_multiply.c |only
RCA-1.4/RCA/src/cs_norm.c |only
RCA-1.4/RCA/src/cs_permute.c |only
RCA-1.4/RCA/src/cs_pinv.c |only
RCA-1.4/RCA/src/cs_post.c |only
RCA-1.4/RCA/src/cs_print.c |only
RCA-1.4/RCA/src/cs_pvec.c |only
RCA-1.4/RCA/src/cs_qr.c |only
RCA-1.4/RCA/src/cs_qrsol.c |only
RCA-1.4/RCA/src/cs_randperm.c |only
RCA-1.4/RCA/src/cs_reach.c |only
RCA-1.4/RCA/src/cs_scatter.c |only
RCA-1.4/RCA/src/cs_scc.c |only
RCA-1.4/RCA/src/cs_schol.c |only
RCA-1.4/RCA/src/cs_spsolve.c |only
RCA-1.4/RCA/src/cs_sqr.c |only
RCA-1.4/RCA/src/cs_symperm.c |only
RCA-1.4/RCA/src/cs_tdfs.c |only
RCA-1.4/RCA/src/cs_transpose.c |only
RCA-1.4/RCA/src/cs_updown.c |only
RCA-1.4/RCA/src/cs_usolve.c |only
RCA-1.4/RCA/src/cs_util.c |only
RCA-1.4/RCA/src/cs_utsolve.c |only
RCA-1.4/RCA/src/debug.h |only
RCA-1.4/RCA/src/decomposition.c |only
RCA-1.4/RCA/src/dgetv0.f |only
RCA-1.4/RCA/src/distances.c |only
RCA-1.4/RCA/src/dlaqrb.f |only
RCA-1.4/RCA/src/dmout.f |only
RCA-1.4/RCA/src/dnaitr.f |only
RCA-1.4/RCA/src/dnapps.f |only
RCA-1.4/RCA/src/dnaup2.f |only
RCA-1.4/RCA/src/dnaupd.f |only
RCA-1.4/RCA/src/dnconv.f |only
RCA-1.4/RCA/src/dneigh.f |only
RCA-1.4/RCA/src/dneupd.f |only
RCA-1.4/RCA/src/dngets.f |only
RCA-1.4/RCA/src/drl_Node.h |only
RCA-1.4/RCA/src/drl_Node_3d.h |only
RCA-1.4/RCA/src/drl_graph.cpp |only
RCA-1.4/RCA/src/drl_graph.h |only
RCA-1.4/RCA/src/drl_graph_3d.cpp |only
RCA-1.4/RCA/src/drl_graph_3d.h |only
RCA-1.4/RCA/src/drl_layout.cpp |only
RCA-1.4/RCA/src/drl_layout.h |only
RCA-1.4/RCA/src/drl_layout_3d.cpp |only
RCA-1.4/RCA/src/drl_layout_3d.h |only
RCA-1.4/RCA/src/drl_parse.cpp |only
RCA-1.4/RCA/src/drl_parse.h |only
RCA-1.4/RCA/src/dsaitr.f |only
RCA-1.4/RCA/src/dsapps.f |only
RCA-1.4/RCA/src/dsaup2.f |only
RCA-1.4/RCA/src/dsaupd.f |only
RCA-1.4/RCA/src/dsconv.f |only
RCA-1.4/RCA/src/dseigt.f |only
RCA-1.4/RCA/src/dsesrt.f |only
RCA-1.4/RCA/src/dseupd.f |only
RCA-1.4/RCA/src/dsgets.f |only
RCA-1.4/RCA/src/dsortc.f |only
RCA-1.4/RCA/src/dsortr.f |only
RCA-1.4/RCA/src/dstatn.f |only
RCA-1.4/RCA/src/dstats.f |only
RCA-1.4/RCA/src/dstqrb.f |only
RCA-1.4/RCA/src/dvout.f |only
RCA-1.4/RCA/src/eigen.c |only
RCA-1.4/RCA/src/error.c |only
RCA-1.4/RCA/src/evolver_cit.c |only
RCA-1.4/RCA/src/f2c.h |only
RCA-1.4/RCA/src/f2c_dummy.c |only
RCA-1.4/RCA/src/fast_community.c |only
RCA-1.4/RCA/src/feedback_arc_set.c |only
RCA-1.4/RCA/src/flow.c |only
RCA-1.4/RCA/src/foreign-dl-header.h |only
RCA-1.4/RCA/src/foreign-dl-lexer.c |only
RCA-1.4/RCA/src/foreign-dl-parser.c |only
RCA-1.4/RCA/src/foreign-dl-parser.h |only
RCA-1.4/RCA/src/foreign-gml-header.h |only
RCA-1.4/RCA/src/foreign-gml-lexer.c |only
RCA-1.4/RCA/src/foreign-gml-parser.c |only
RCA-1.4/RCA/src/foreign-gml-parser.h |only
RCA-1.4/RCA/src/foreign-graphml.c |only
RCA-1.4/RCA/src/foreign-lgl-header.h |only
RCA-1.4/RCA/src/foreign-lgl-lexer.c |only
RCA-1.4/RCA/src/foreign-lgl-parser.c |only
RCA-1.4/RCA/src/foreign-lgl-parser.h |only
RCA-1.4/RCA/src/foreign-ncol-header.h |only
RCA-1.4/RCA/src/foreign-ncol-lexer.c |only
RCA-1.4/RCA/src/foreign-ncol-parser.c |only
RCA-1.4/RCA/src/foreign-ncol-parser.h |only
RCA-1.4/RCA/src/foreign-pajek-header.h |only
RCA-1.4/RCA/src/foreign-pajek-lexer.c |only
RCA-1.4/RCA/src/foreign-pajek-parser.c |only
RCA-1.4/RCA/src/foreign-pajek-parser.h |only
RCA-1.4/RCA/src/foreign.c |only
RCA-1.4/RCA/src/forestfire.c |only
RCA-1.4/RCA/src/fortran_intrinsics.c |only
RCA-1.4/RCA/src/games.c |only
RCA-1.4/RCA/src/gengraph_box_list.cpp |only
RCA-1.4/RCA/src/gengraph_box_list.h |only
RCA-1.4/RCA/src/gengraph_definitions.h |only
RCA-1.4/RCA/src/gengraph_degree_sequence.cpp |only
RCA-1.4/RCA/src/gengraph_degree_sequence.h |only
RCA-1.4/RCA/src/gengraph_graph_molloy_hash.cpp |only
RCA-1.4/RCA/src/gengraph_graph_molloy_hash.h |only
RCA-1.4/RCA/src/gengraph_graph_molloy_optimized.cpp |only
RCA-1.4/RCA/src/gengraph_graph_molloy_optimized.h |only
RCA-1.4/RCA/src/gengraph_hash.h |only
RCA-1.4/RCA/src/gengraph_header.h |only
RCA-1.4/RCA/src/gengraph_mr-connected.cpp |only
RCA-1.4/RCA/src/gengraph_powerlaw.cpp |only
RCA-1.4/RCA/src/gengraph_powerlaw.h |only
RCA-1.4/RCA/src/gengraph_qsort.h |only
RCA-1.4/RCA/src/gengraph_random.cpp |only
RCA-1.4/RCA/src/gengraph_random.h |only
RCA-1.4/RCA/src/gengraph_vertex_cover.h |only
RCA-1.4/RCA/src/glpapi01.c |only
RCA-1.4/RCA/src/glpapi02.c |only
RCA-1.4/RCA/src/glpapi03.c |only
RCA-1.4/RCA/src/glpapi04.c |only
RCA-1.4/RCA/src/glpapi05.c |only
RCA-1.4/RCA/src/glpapi06.c |only
RCA-1.4/RCA/src/glpapi07.c |only
RCA-1.4/RCA/src/glpapi08.c |only
RCA-1.4/RCA/src/glpapi09.c |only
RCA-1.4/RCA/src/glpapi10.c |only
RCA-1.4/RCA/src/glpapi11.c |only
RCA-1.4/RCA/src/glpapi12.c |only
RCA-1.4/RCA/src/glpapi13.c |only
RCA-1.4/RCA/src/glpapi14.c |only
RCA-1.4/RCA/src/glpapi15.c |only
RCA-1.4/RCA/src/glpapi16.c |only
RCA-1.4/RCA/src/glpapi17.c |only
RCA-1.4/RCA/src/glpapi18.c |only
RCA-1.4/RCA/src/glpapi19.c |only
RCA-1.4/RCA/src/glpavl.c |only
RCA-1.4/RCA/src/glpbfd.c |only
RCA-1.4/RCA/src/glpbfx.c |only
RCA-1.4/RCA/src/glpcpx.c |only
RCA-1.4/RCA/src/glpdmp.c |only
RCA-1.4/RCA/src/glpdmx.c |only
RCA-1.4/RCA/src/glpenv01.c |only
RCA-1.4/RCA/src/glpenv02.c |only
RCA-1.4/RCA/src/glpenv03.c |only
RCA-1.4/RCA/src/glpenv04.c |only
RCA-1.4/RCA/src/glpenv05.c |only
RCA-1.4/RCA/src/glpenv06.c |only
RCA-1.4/RCA/src/glpenv07.c |only
RCA-1.4/RCA/src/glpenv08.c |only
RCA-1.4/RCA/src/glpfhv.c |only
RCA-1.4/RCA/src/glpgmp.c |only
RCA-1.4/RCA/src/glphbm.c |only
RCA-1.4/RCA/src/glpini01.c |only
RCA-1.4/RCA/src/glpini02.c |only
RCA-1.4/RCA/src/glpios01.c |only
RCA-1.4/RCA/src/glpios02.c |only
RCA-1.4/RCA/src/glpios03.c |only
RCA-1.4/RCA/src/glpios04.c |only
RCA-1.4/RCA/src/glpios05.c |only
RCA-1.4/RCA/src/glpios06.c |only
RCA-1.4/RCA/src/glpios07.c |only
RCA-1.4/RCA/src/glpios08.c |only
RCA-1.4/RCA/src/glpios09.c |only
RCA-1.4/RCA/src/glpios10.c |only
RCA-1.4/RCA/src/glpios11.c |only
RCA-1.4/RCA/src/glpios12.c |only
RCA-1.4/RCA/src/glpipm.c |only
RCA-1.4/RCA/src/glpk |only
RCA-1.4/RCA/src/glpk_support.c |only
RCA-1.4/RCA/src/glplib01.c |only
RCA-1.4/RCA/src/glplib02.c |only
RCA-1.4/RCA/src/glplib03.c |only
RCA-1.4/RCA/src/glplpf.c |only
RCA-1.4/RCA/src/glplpx01.c |only
RCA-1.4/RCA/src/glplpx02.c |only
RCA-1.4/RCA/src/glplpx03.c |only
RCA-1.4/RCA/src/glpluf.c |only
RCA-1.4/RCA/src/glplux.c |only
RCA-1.4/RCA/src/glpmat.c |only
RCA-1.4/RCA/src/glpmpl01.c |only
RCA-1.4/RCA/src/glpmpl02.c |only
RCA-1.4/RCA/src/glpmpl03.c |only
RCA-1.4/RCA/src/glpmpl04.c |only
RCA-1.4/RCA/src/glpmpl05.c |only
RCA-1.4/RCA/src/glpmpl06.c |only
RCA-1.4/RCA/src/glpmps.c |only
RCA-1.4/RCA/src/glpnet01.c |only
RCA-1.4/RCA/src/glpnet02.c |only
RCA-1.4/RCA/src/glpnet03.c |only
RCA-1.4/RCA/src/glpnet04.c |only
RCA-1.4/RCA/src/glpnet05.c |only
RCA-1.4/RCA/src/glpnet06.c |only
RCA-1.4/RCA/src/glpnet07.c |only
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RCA-1.4/RCA/src/revolver_grow.c |only
RCA-1.4/RCA/src/revolver_ml_cit.c |only
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RCA-1.4/RCA/src/scg_approximate_methods.c |only
RCA-1.4/RCA/src/scg_exact_scg.c |only
RCA-1.4/RCA/src/scg_headers.h |only
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RCA-1.4/RCA/src/type_indexededgelist.c |only
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RCA-1.4/RCA/src/unit_limiter.cpp |only
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522 files changed, 701 insertions(+), 167 deletions(-)
Title: SNP-set (Sequence) Kernel Association Test
Diff between SKAT versions 0.83 dated 2013-05-09 and 0.90 dated 2013-05-23
Description: Kernel based SNP set test
Author: Seunggeun Lee, Larisa Miropolsky and Micheal Wu
Maintainer: Seunggeun (Shawn) Lee
DESCRIPTION | 9 ++++----
MD5 | 19 +++++++++--------
NAMESPACE | 3 +-
R/Joint_CommonRare.R |only
R/Main.R | 3 +-
R/Null_Model.R | 5 ++--
inst/doc/Example_bped.zip |only
inst/doc/SKAT.Rnw | 40 ++++++++++++++++++++++++++++++++++--
inst/doc/SKAT.pdf |binary
man/SKAT.rd | 2 -
man/SKAT_CommonRare.rd |only
man/SKAT_Null_Model_MomentAdjust.rd | 3 +-
12 files changed, 64 insertions(+), 20 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Diff between MALDIquant versions 1.6 dated 2013-03-01 and 1.7 dated 2013-05-23
Description: MALDIquant provides a complete analysis pipeline for
MALDI-TOF and other mass spectrometry data. Distinctive
features include baseline subtraction methods such as TopHat or
SNIP, peak alignment using warping functions, handling of
replicated measurements as well as allowing spectra with
different resolutions.
Author: Sebastian Gibb [aut, cre], Korbinian Strimmer [ths]
Maintainer: Sebastian Gibb
MALDIquant-1.6/MALDIquant/LICENSE |only
MALDIquant-1.6/MALDIquant/R/isValidHalfWindowSize.R |only
MALDIquant-1.6/MALDIquant/R/movingAverage-functions.R |only
MALDIquant-1.6/MALDIquant/inst/tests/test_movingAverage-functions.R |only
MALDIquant-1.6/MALDIquant/src/morphologicalFilters.h |only
MALDIquant-1.7/MALDIquant/DESCRIPTION | 18
MALDIquant-1.7/MALDIquant/MD5 | 122 +--
MALDIquant-1.7/MALDIquant/NAMESPACE | 3
MALDIquant-1.7/MALDIquant/NEWS | 379 +++++++---
MALDIquant-1.7/MALDIquant/R/AllGenerics.R | 4
MALDIquant-1.7/MALDIquant/R/binPeaks-functions.R | 20
MALDIquant-1.7/MALDIquant/R/determineWarpingFunctions-functions.R | 9
MALDIquant-1.7/MALDIquant/R/doByLabels-functions.R | 7
MALDIquant-1.7/MALDIquant/R/estimateBaseline-functions.R | 42 -
MALDIquant-1.7/MALDIquant/R/estimateBaseline-methods.R | 2
MALDIquant-1.7/MALDIquant/R/estimateNoise-methods.R | 2
MALDIquant-1.7/MALDIquant/R/filterPeaks-functions.R | 54 +
MALDIquant-1.7/MALDIquant/R/grouper-functions.R | 6
MALDIquant-1.7/MALDIquant/R/iplot-functions.R | 58 +
MALDIquant-1.7/MALDIquant/R/irregular-functions.R |only
MALDIquant-1.7/MALDIquant/R/isEmpty-methods.R | 11
MALDIquant-1.7/MALDIquant/R/isFunctionList-functions.R | 5
MALDIquant-1.7/MALDIquant/R/isMassObjectList-functions.R | 18
MALDIquant-1.7/MALDIquant/R/isRegular-methods.R |only
MALDIquant-1.7/MALDIquant/R/isValidHalfWindowSize-functions.R |only
MALDIquant-1.7/MALDIquant/R/localMaxima-functions.R | 8
MALDIquant-1.7/MALDIquant/R/memoryUsage-functions.R |only
MALDIquant-1.7/MALDIquant/R/merge-functions.R | 50 +
MALDIquant-1.7/MALDIquant/R/morphologicalFilter-functions.R | 28
MALDIquant-1.7/MALDIquant/R/onAttach.R | 5
MALDIquant-1.7/MALDIquant/R/plot-methods.R | 8
MALDIquant-1.7/MALDIquant/R/show-functions.R | 2
MALDIquant-1.7/MALDIquant/R/show-methods.R | 18
MALDIquant-1.7/MALDIquant/R/smoothingFilters-functions.R |only
MALDIquant-1.7/MALDIquant/R/totalIonCurrent-methods.R | 10
MALDIquant-1.7/MALDIquant/R/valid-methods.R | 12
MALDIquant-1.7/MALDIquant/demo/warping.R | 8
MALDIquant-1.7/MALDIquant/demo/workflow.R | 40 -
MALDIquant-1.7/MALDIquant/inst/tests/test_calibrate-methods.R | 2
MALDIquant-1.7/MALDIquant/inst/tests/test_doByLabel-functions.R | 23
MALDIquant-1.7/MALDIquant/inst/tests/test_estimateBaseline-methods.R | 43 -
MALDIquant-1.7/MALDIquant/inst/tests/test_filterPeaks-functions.R | 18
MALDIquant-1.7/MALDIquant/inst/tests/test_irregular-functions.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_isEmpty-methods.R | 21
MALDIquant-1.7/MALDIquant/inst/tests/test_isRegular-methods.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_merge-functions.R | 13
MALDIquant-1.7/MALDIquant/inst/tests/test_morphologicalFilter-functions.R | 19
MALDIquant-1.7/MALDIquant/inst/tests/test_removeBaseline-methods.R | 6
MALDIquant-1.7/MALDIquant/inst/tests/test_show-methods.R | 9
MALDIquant-1.7/MALDIquant/inst/tests/test_smoothingFilters-functions.R |only
MALDIquant-1.7/MALDIquant/inst/tests/test_totalIonCurrent-methods.R | 11
MALDIquant-1.7/MALDIquant/inst/tests/test_transformIntensity-methods.R | 6
MALDIquant-1.7/MALDIquant/man/AbstractMassObject-class.Rd | 3
MALDIquant-1.7/MALDIquant/man/MALDIquant-internal.Rd | 7
MALDIquant-1.7/MALDIquant/man/MALDIquant-package.Rd | 8
MALDIquant-1.7/MALDIquant/man/MassSpectrum-class.Rd | 7
MALDIquant-1.7/MALDIquant/man/calibrate-methods.Rd | 2
MALDIquant-1.7/MALDIquant/man/estimateBaselineSnip-functions.Rd | 20
MALDIquant-1.7/MALDIquant/man/estimateBaselineTopHat-functions.Rd | 2
MALDIquant-1.7/MALDIquant/man/estimateNoiseMad-functions.Rd | 1
MALDIquant-1.7/MALDIquant/man/filterPeaks-functions.Rd | 34
MALDIquant-1.7/MALDIquant/man/iplot-methods.Rd | 11
MALDIquant-1.7/MALDIquant/man/movingAverage-functions.Rd | 20
MALDIquant-1.7/MALDIquant/man/savitzkyGolay-functions.Rd |only
MALDIquant-1.7/MALDIquant/src/MALDIquant.h |only
MALDIquant-1.7/MALDIquant/src/init.c |only
MALDIquant-1.7/MALDIquant/src/localMaxima.c | 75 +
MALDIquant-1.7/MALDIquant/src/lowerConvexHull.c | 78 +-
MALDIquant-1.7/MALDIquant/src/morphologicalFilters.c | 178 ++++
MALDIquant-1.7/MALDIquant/src/snip.c | 98 +-
70 files changed, 1161 insertions(+), 503 deletions(-)
Title: R package for parallelized mRMR ensemble feature selection
Diff between mRMRe versions 2.0.0 dated 2013-04-16 and 2.0.2 dated 2013-05-23
Description: This package contains a set of function to compute mutual
information matrices from continuous, categorical and survival
variables. It also contains function to perform feature
selection with mRMR and a new ensemble mRMR technique.
Author: Nicolas De Jay, Simon Papillon-Cavanagh, Catharina Olsen,
Gianluca Bontempi, Benjamin Haibe-Kains
Maintainer: Benjamin Haibe-Kains
.Rinstignore | 1 +
DESCRIPTION | 10 +++++-----
MD5 | 30 +++++++++++++++---------------
R/generics.R | 11 +++++++----
R/mRMRe.Data.R | 22 ++++++++++++++++++++++
R/mRMRe.Filter.R | 32 +++++++++++++++++++++++++-------
R/mRMRe.Network.R | 24 ++++++++++++++++++++++++
REVISIONS | 37 +++++++++++++++++++++++--------------
data/cgps.rda |binary
inst/doc/mRMRe.pdf |binary
man/mRMRe.Data-class.Rd | 2 +-
man/mRMRe.Filter-class.Rd | 23 ++++++++++++++---------
man/mim.Rd | 5 +++--
man/sampleStrata.Rd | 4 ++--
man/scores.Rd | 9 +++++++--
man/subsetData.Rd | 7 ++++---
src/exports.cpp | 4 ++--
17 files changed, 155 insertions(+), 66 deletions(-)
Title: Fitting finite mixture of scale mixture of skew-normal
distributions .
Diff between mixsmsn versions 1.0-7 dated 2013-05-02 and 1.0-8 dated 2013-05-23
Description: Functions to fit finite mixture of scale mixture of
skew-normal (FM-SMSN) distributions.
Author: Marcos Prates
Maintainer: Marcos Prates
ChangeLog | 10 ++++++++++
DESCRIPTION | 6 +++---
MD5 | 10 +++++-----
R/mixsmsn.R | 14 ++++++++------
R/smsn.mmix.R | 29 +++++++++++++++--------------
R/utils.multi.R | 20 ++++++++++----------
6 files changed, 51 insertions(+), 38 deletions(-)
Title: Network analysis and visualization
Diff between igraph versions 0.6.5-1 dated 2013-02-28 and 0.6.5-2 dated 2013-05-23
Description: Routines for simple graphs and network analysis. igraph
can handle large graphs very well and provides functions for
generating random and regular graphs, graph visualization,
centrality indices and much more.
Author: See AUTHORS file.
Maintainer: Gabor Csardi
igraph-0.6.5-1/igraph/LICENSE |only
igraph-0.6.5-2/igraph/DESCRIPTION | 8 +--
igraph-0.6.5-2/igraph/MD5 | 25 +++++----
igraph-0.6.5-2/igraph/NEWS | 13 +++++
igraph-0.6.5-2/igraph/R/auto.R.in |only
igraph-0.6.5-2/igraph/configure | 25 ++++++---
igraph-0.6.5-2/igraph/configure.in | 5 +
igraph-0.6.5-2/igraph/man/graph.graphdb.Rd | 5 +
igraph-0.6.5-2/igraph/man/igraph.vertex.shapes.Rd | 5 +
igraph-0.6.5-2/igraph/src/Makevars |only
igraph-0.6.5-2/igraph/src/arpack.c | 48 +++++++++++++++++++
igraph-0.6.5-2/igraph/src/atlas.c | 2
igraph-0.6.5-2/igraph/src/config.h.in | 3 +
igraph-0.6.5-2/igraph/src/igraph_arpack_internal.h | 53 +++++++++++++++++++++
igraph-0.6.5-2/igraph/src/infomap.cc | 6 +-
15 files changed, 167 insertions(+), 31 deletions(-)
Title: Generalised Additive Models for Location Scale and Shape.
Diff between gamlss versions 4.2-0 dated 2012-09-29 and 4.2-4 dated 2013-05-23
Description: The library for fitting GAMLSS models.
Author: Mikis Stasinopoulos
Maintainer: Mikis Stasinopoulos
gamlss-4.2-0/gamlss/LICENSE |only
gamlss-4.2-0/gamlss/R/HistDist2-12-11.R |only
gamlss-4.2-0/gamlss/R/SUMMARY.R |only
gamlss-4.2-0/gamlss/R/findhyper.R |only
gamlss-4.2-0/gamlss/R/fitDist.R |only
gamlss-4.2-0/gamlss/R/gamlss.R |only
gamlss-4.2-0/gamlss/R/gamlssML-11-9-12.R |only
gamlss-4.2-0/gamlss/R/profterm_new_18_8_12.R |only
gamlss-4.2-0/gamlss/R/qstats-20-09-12.R |only
gamlss-4.2-0/gamlss/R/rqresplot.R |only
gamlss-4.2-0/gamlss/R/stepGAICall-18-03-10.R |only
gamlss-4.2-0/gamlss/R/vcov_gamlss.R |only
gamlss-4.2-0/gamlss/R/wp.R |only
gamlss-4.2-0/gamlss/inst/doc/LICENSE |only
gamlss-4.2-4/gamlss/DESCRIPTION | 21
gamlss-4.2-4/gamlss/MD5 | 88 +-
gamlss-4.2-4/gamlss/NAMESPACE | 4
gamlss-4.2-4/gamlss/R/HistDist-17-05-13.R |only
gamlss-4.2-4/gamlss/R/SUMMARY-26-03-13.R |only
gamlss-4.2-4/gamlss/R/acfResid.R |only
gamlss-4.2-4/gamlss/R/confint-gamlss-02-05-13.R |only
gamlss-4.2-4/gamlss/R/extra.R | 862 ++++++++++----------
gamlss-4.2-4/gamlss/R/findhyper-23-05-13.R |only
gamlss-4.2-4/gamlss/R/fitDist-17-05-13.R |only
gamlss-4.2-4/gamlss/R/gamlss-01-05-13.R |only
gamlss-4.2-4/gamlss/R/gamlssML-17-05-13.R |only
gamlss-4.2-4/gamlss/R/gen-Likelihood-22-03-13.R |only
gamlss-4.2-4/gamlss/R/histSmo-6-03-12.R | 8
gamlss-4.2-4/gamlss/R/lms-23-5-13.r |only
gamlss-4.2-4/gamlss/R/lms.r | 51 -
gamlss-4.2-4/gamlss/R/par_plot-21-5-13.R |only
gamlss-4.2-4/gamlss/R/par_plot.R | 1026 ++++++++++++------------
gamlss-4.2-4/gamlss/R/pb_19-04-2012.R | 1
gamlss-4.2-4/gamlss/R/profterm_18_05_13.R |only
gamlss-4.2-4/gamlss/R/qstats-29-12-12.R |only
gamlss-4.2-4/gamlss/R/rqres.R | 126 +-
gamlss-4.2-4/gamlss/R/rqresplot17-10-12.R |only
gamlss-4.2-4/gamlss/R/stepGAICall-23-05-13.R |only
gamlss-4.2-4/gamlss/R/term-plot.R | 460 +++++-----
gamlss-4.2-4/gamlss/R/vcoc-gamlss-22-03-13.R |only
gamlss-4.2-4/gamlss/R/wp-18-5-13.R |only
gamlss-4.2-4/gamlss/inst/doc/NEWS.txt | 38
gamlss-4.2-4/gamlss/man/IC.Rd | 6
gamlss-4.2-4/gamlss/man/Q.stats.Rd | 26
gamlss-4.2-4/gamlss/man/Rsq.Rd |only
gamlss-4.2-4/gamlss/man/acfResid.Rd |only
gamlss-4.2-4/gamlss/man/calibration.Rd | 3
gamlss-4.2-4/gamlss/man/centiles.pred.Rd | 204 ++--
gamlss-4.2-4/gamlss/man/findhyper.Rd | 187 ++--
gamlss-4.2-4/gamlss/man/gen.likelihood.Rd |only
gamlss-4.2-4/gamlss/man/histDist.Rd | 142 +--
gamlss-4.2-4/gamlss/man/histSmo.Rd | 251 ++---
gamlss-4.2-4/gamlss/man/lms.Rd | 31
gamlss-4.2-4/gamlss/man/par.plot.Rd | 113 +-
gamlss-4.2-4/gamlss/man/prof.dev.Rd | 115 +-
gamlss-4.2-4/gamlss/man/prof.term.Rd | 17
gamlss-4.2-4/gamlss/man/ps.Rd | 373 ++++----
gamlss-4.2-4/gamlss/man/random.Rd | 6
gamlss-4.2-4/gamlss/man/rqres.plot.Rd | 128 +-
gamlss-4.2-4/gamlss/man/stepGAIC.Rd | 498 +++++------
gamlss-4.2-4/gamlss/man/term.plot.Rd | 166 +--
gamlss-4.2-4/gamlss/man/wp.Rd | 190 ++--
62 files changed, 2663 insertions(+), 2478 deletions(-)
Title: Fast hierarchical clustering routines for R and Python
Diff between fastcluster versions 1.1.10 dated 2013-05-23 and 1.1.11 dated 2013-05-23
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical,
agglomerative clustering routines. Part of the functionality is
designed as drop-in replacement for existing routines:
“linkage” in the SciPy package “scipy.cluster.hierarchy”,
“hclust” in R's “stats” package, and the “flashClust” package.
It provides the same functionality with the benefit of a much
faster implementation. Moreover, there are memory-saving
routines for clustering of vector data, which go beyond what
the existing packages provide. For information on how to
install the Python files, see the file INSTALL in the source
distribution.
Author: Daniel Müllner, http://math.stanford.edu/~muellner
Maintainer: Daniel Müllner
DESCRIPTION | 8 ++++----
INSTALL | 2 +-
MD5 | 20 ++++++++++----------
NEWS | 7 +++++--
README | 38 +++++++++++++++++++-------------------
inst/doc/fastcluster.Rtex | 4 ++--
inst/doc/fastcluster.pdf |binary
python/fastcluster.py | 2 +-
src/fastcluster.cpp | 15 +++++++++------
src/fastcluster_R.cpp | 12 +++++++++---
src/fastcluster_python.cpp | 4 ++++
11 files changed, 64 insertions(+), 48 deletions(-)
Title: R Interface to C API of IBM ILOG CPLEX
Diff between cplexAPI versions 1.2.6 dated 2013-01-23 and 1.2.9 dated 2013-05-23
Description: R Interface to C API of IBM ILOG CPLEX, depends on IBM
ILOG CPLEX (>= 12.1)
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 9 +-
MD5 | 34 +++++----
NAMESPACE | 5 +
R/cplexAPI.R | 88 +++++++++++++++++++++++
R/cplexConst.R | 144 +++++++++++++++++++-------------------
configure | 18 ++--
configure.ac | 2
inst/NEWS.Rd | 28 +++++++
inst/c2r.map | 5 +
inst/doc/cplexAPI.R |only
inst/doc/cplexAPI.pdf |binary
man/copyOrderCPLEX.Rd |only
man/getMIPrelGapCPLEX.Rd |only
man/getOrderCPLEX.Rd |only
man/ordWriteCPLEX.Rd |only
man/readCopyOrderCPLEX.Rd |only
man/setIntParmCPLEX.Rd | 2
man/setStrParmCPLEX.Rd | 2
src/cplexAPI.c | 170 ++++++++++++++++++++++++++++++++++++++++++++++
src/cplexAPI.h | 15 ++++
src/init.c | 5 +
21 files changed, 424 insertions(+), 103 deletions(-)
Title: RMAWGEN (R Multi-site Auto-regressive Weather GENerator), a
package to generate daily time series of precipitation and
temperature from monthly mean values
Diff between RMAWGEN versions 1.2.5.4 dated 2013-04-24 and 1.2.5.5 dated 2013-05-23
Description: This package contains S3 and S4 functions for spatial
multi-site stochastic generation of daily time series of
temperature and precipitation. The implemented tools make use
of Vector AutoRegressive models (VARs). The VAR is calibrated
by daily instrumental "Gaussianized" time series and then works
with monthly time series as input.
Bugs/comments/questions/collaboration of any kind are warmly
welcome.
Author: Emanuele Cordano, Emanuele Eccel
Maintainer: Emanuele Cordano
DESCRIPTION | 13 -
MD5 | 164 +++++++++---------
R/ComprehensivePrecipitationGenerator.R | 47 +----
R/ComprehensiveTemperatureGenerator.R | 30 ++-
R/PrecipitationEndDay.R | 2
R/PrecipitationStartDay.R | 8
R/RMAWGEN-package.R | 8
R/VAR_mod.R | 2
R/WhereIs.R | 2
R/acvWGEN.R | 2
R/adddate.R | 2
R/addsuffixes.R | 4
R/arch_test.varest2.R | 4
R/continuity_ratio.R | 2
R/countNAs.R | 2
R/covariance.R | 6
R/extractTnFromAnomalies.R | 4
R/extractTxFromAnomalies.R | 2
R/extractdays.R | 2
R/extractmonths.R | 2
R/findDate.R | 12 +
R/generateTemperatureTimeseries.R | 12 -
R/getDailyMean.R | 2
R/getMonthlyMean.R | 6
R/getVARmodel.R | 16 -
R/is.monthly.climate.R | 6
R/normalizeGaussian.R | 4
R/normalizeGaussian_prec.R | 4
R/normalizeGaussian_sevaralstations.R | 6
R/normalizeGaussian_sevaralstations_prec.R | 4
R/plot.sample.R | 34 ++-
R/plotDailyClimate.R | 3
R/qqplot.lagged.R | 6
R/qqplotWGEN.R | 4
R/qqplot_RMAWGENts.R | 12 -
R/qqplotprecWGEN.R | 2
R/qqplotprecWGEN_seasonal.R | 2
R/removeNAs.R | 2
R/setWholeTemperatureGeneratorParameters.R | 12 -
R/splineInterpolateMonthlytoDaily.R | 4
R/splineInterpolateMonthlytoDailyforSeveralYears.R | 2
R/zc0_GPCAiteration.R | 4
man/ComprehensivePrecipitationGenerator.Rd | 21 +-
man/ComprehensiveTemperatureGenerator.Rd | 26 +-
man/GPCAiteration-class.Rd | 4
man/PrecipitationEndDay.Rd | 4
man/PrecipitationStartDay.Rd | 8
man/RMAWGEN-package.Rd | 18 -
man/VAR_mod.Rd | 2
man/WhereIs.Rd | 2
man/acvWGEN.Rd | 6
man/adddate.Rd | 4
man/addsuffixes.Rd | 7
man/arch_test.Rd | 10 -
man/continuity_ratio.Rd | 2
man/countNAs.Rd | 3
man/covariance.Rd | 6
man/extractTnFromAnomalies.Rd | 4
man/extractTxFromAnomalies.Rd | 4
man/extractdays.Rd | 2
man/extractmonths.Rd | 2
man/findDate.Rd | 11 -
man/generateTemperatureTimeseries.Rd | 19 --
man/getDailyMean.Rd | 9
man/getMonthlyMean.Rd | 16 -
man/getVARmodel.Rd | 17 -
man/is.monthly.climate.Rd | 8
man/normalizeGaussian.Rd | 4
man/normalizeGaussian_prec.Rd | 4
man/normalizeGaussian_severalstations.Rd | 12 -
man/normalizeGaussian_severalstations_prec.Rd | 4
man/plotDailyClimate.Rd | 8
man/plot_sample.Rd | 35 ++-
man/qqplot.lagged.Rd | 4
man/qqplotWGEN.Rd | 4
man/qqplot_RMAWGEN_Tx.Rd | 18 -
man/qqplotprecWGEN.Rd | 2
man/qqplotprecWGEN_seasonal.Rd | 2
man/removeNAs.Rd | 4
man/setComprehensiveTemperatureGeneratorParameters.Rd | 16 -
man/splineInterpolateMonthlytoDaily.Rd | 7
man/splineInterpolateMonthlytoDailyforSeveralYears.Rd | 2
man/trentino.Rd | 2
83 files changed, 436 insertions(+), 374 deletions(-)
Title: Handling missing values with/in multivariate data analysis
(principal component methods)
Diff between missMDA versions 1.7 dated 2013-03-30 and 1.7.1 dated 2013-05-23
Description: Imputation of incomplete continuous or categorical
datasets; Missing values are imputed with a principal component
analysis (PCA), a multiple correspondence analysis (MCA) model
or a multiple factor analysis (MFA) model; Perform multiple
imputation with and in PCA
Author: Francois Husson, Julie Josse
Maintainer: Francois Husson
DESCRIPTION | 8 +++----
MD5 | 18 +++++++--------
R/imputePCA.R | 2 -
R/plot.MIPCA.R | 9 +++----
man/MIPCA.Rd | 3 +-
man/imputeFAMD.Rd | 6 +++--
man/imputeMCA.Rd | 6 +++--
man/imputeMFA.Rd | 14 ++++++++----
man/plot.MIPCA.Rd | 2 +
missMDA-Ex.R | 61 +++++++++++++++++++++++++++++++++---------------------
10 files changed, 78 insertions(+), 51 deletions(-)
Title: Calculate generalized eigenvalues of a matrix pair
Diff between geigen versions 1.0 dated 2013-05-15 and 1.1 dated 2013-05-23
Description: Compute generalized eigenvalues and eigenvectors of a pair
of matrices, using routines from Lapack (dggev and zggev).
Compute the generalized Schur decomposition of a pair of
matrices using Lapack routines. In the latter case options for
ordering the generalized eigenvalues are provided.
Author: Berend Hasselman
Maintainer: Berend Hasselman
geigen-1.0/geigen/src/xdgg.f |only
geigen-1.1/geigen/DESCRIPTION | 8 ++--
geigen-1.1/geigen/MD5 | 41 ++++++++++++-----------
geigen-1.1/geigen/NAMESPACE | 2 -
geigen-1.1/geigen/NEWS | 9 +++++
geigen-1.1/geigen/R/geigen.R | 56 ++++++++++++++++++--------------
geigen-1.1/geigen/R/gqz.R | 47 ++++++++++++++++----------
geigen-1.1/geigen/src/xdgges.f | 35 ++++++++++++--------
geigen-1.1/geigen/src/xdggev.f |only
geigen-1.1/geigen/src/xzgges.f | 40 +++++++++++++---------
geigen-1.1/geigen/src/xzggev.f |only
geigen-1.1/geigen/tests/tgqz1.R | 7 ++++
geigen-1.1/geigen/tests/tgqz1.Rout | 18 ++++++++--
geigen-1.1/geigen/tests/tgqz1.Rout.save | 18 ++++++++--
geigen-1.1/geigen/tests/tgqz2.R | 12 +++---
geigen-1.1/geigen/tests/tgqz2.Rout | 14 ++++----
geigen-1.1/geigen/tests/tgqz2.Rout.save | 14 ++++----
geigen-1.1/geigen/tests/tgqz5.R | 8 ++++
geigen-1.1/geigen/tests/tgqz5.Rout | 15 +++++++-
geigen-1.1/geigen/tests/tgqz5.Rout.save | 15 +++++++-
geigen-1.1/geigen/tests/tgqz6.R | 18 +++++-----
geigen-1.1/geigen/tests/tgqz6.Rout | 20 +++++------
geigen-1.1/geigen/tests/tgqz6.Rout.save | 20 +++++------
23 files changed, 259 insertions(+), 158 deletions(-)
Title: Analyze Multinomial Processing Tree Models
Diff between MPTinR versions 1.0.1 dated 2013-02-07 and 1.1.8 dated 2013-05-23
Description: MPTinR provides a user-friendly way for the analysis of
multinomial processing tree (MPT) models (e.g., Riefer, D. M.,
and Batchelder, W. H. [1988]. Multinomial modeling and the
measurement of cognitive processes. Psychological Review, 95,
318-339) for single and multiple datasets. The main functions
perform model fitting and model selection. Model selection can
be done using AIC, BIC, or the Fisher Information Approximation
(FIA) a measure based on the Minimum Description Length (MDL)
framework. The model and restrictions can specified in external
files or within an R script in an intuitive syntax. The
'classical' .EQN file format for model files is also supported.
Besides MPTs, MPTinR can fit a wide variety of other cognitive
models such as SDT models (see fit.model). MPTinR supports
multicore fitting and FIA calculation using the snowfall
package. MPTinR can generate data generating from a model for
e.g., parametric bootstrap and plot predicted versus observed
data.
Author: Henrik Singmann, David Kellen, and Christian Mueller
Maintainer: Henrik Singmann
ChangeLog | 38 ++++++++++++++++++++++++
DESCRIPTION | 25 +++++++++-------
MD5 | 53 ++++++++++++++++++----------------
NAMESPACE | 1
NEWS | 35 ++++++++++++++++++++++
R/bmpt.fia.R | 75 ++++++++++++++++++++++---------------------------
R/fit.model.R | 6 +--
R/fit.mpt.R | 6 +--
R/fit.mptinr.R | 14 +++++++--
R/get.mpt.fia.R | 4 +-
R/make.eqn.R | 2 -
R/select.mpt.R | 3 +
data/d.broeder.rda |binary
data/rb.fig1.data.rda |binary
data/rb.fig2.data.rda |binary
man/MPTinR-package.Rd | 6 +--
man/bmpt.fia.Rd | 17 +++++++++--
man/fit.model.Rd | 15 ++++++---
man/fit.mpt.Rd | 45 +++++++++++++++++------------
man/fit.mpt.old.Rd | 6 +--
man/fit.mptinr.Rd | 9 +++--
man/gen.data.Rd | 15 ++++++---
man/get.mpt.fia.Rd | 13 +++++++-
man/prediction.plot.Rd | 44 +++++++++++++++++++---------
man/prepare.mpt.fia.Rd | 3 +
man/select.mpt.Rd | 10 ++++--
src |only
27 files changed, 297 insertions(+), 148 deletions(-)
Title: Pharmacometric tools for data preparation, modeling, simulation,
and reporting
Diff between metrumrg versions 5.45 dated 2013-05-01 and 5.49 dated 2013-05-23
Description: Pharmacometric tools for common data preparation tasks,
stratified bootstrap resampling of data sets, NONMEM control
stream creation/editing, NONMEM model execution, creation of
standard and user-defined diagnostic plots, execution and
summary of bootstrap and predictive check results,
implementation of simulations from posterior parameter
distributions, reporting of output tables and creation of
detailed analysis logs.
Author: Tim Bergsma, Bill Knebel, Leonid Gibiansky, Natalie Hsiang
Maintainer: Tim Bergsma
ChangeLog | 18 ++++++++++++
DESCRIPTION | 8 ++---
MD5 | 56 ++++++++++++++++++++--------------------
NAMESPACE | 10 +++----
R/cast.R | 1
R/first.R | 23 ++++------------
R/reapply.R | 10 +++++--
R/temporal.R | 12 ++++----
man/NONR.Rd | 3 +-
man/as.pxml.Rd | 22 +++++++--------
man/as.second.Rd | 6 ++++
man/c.temporal.Rd | 26 +++++++++---------
man/electronicAppendix.Rd | 9 +++++-
man/extensions.Rd | 7 ++++-
man/helpList.Rd | 10 +++----
man/index.Rd | 20 ++++++++++++--
man/inner.data.frame.Rd | 2 -
man/iterations.Rd | 64 +++++++++++++++++++++++-----------------------
man/lookup.Rd | 10 +++----
man/metrumrg-package.Rd | 4 +-
man/panel.hist.Rd | 3 +-
man/panel.stratify.Rd | 6 ++--
man/qsub.Rd | 3 +-
man/reapply.Rd | 14 +++++++---
man/runCommand.Rd | 6 ++--
man/runlog.Rd | 27 +++++++++++--------
man/temporal.Rd | 2 -
man/wikiparse.Rd | 15 ++++++++++
man/xyplot.ext.Rd | 22 +++++++--------
29 files changed, 249 insertions(+), 170 deletions(-)
Title: R Interface to C API of GLPK
Diff between glpkAPI versions 1.2.6 dated 2013-02-12 and 1.2.7 dated 2013-05-23
Description: R Interface to C API of GLPK, needs GLPK Version >= 4.42
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 9 +++---
MD5 | 25 ++++++++++--------
NAMESPACE | 2 +
R/glpkAPI.R | 46 +++++++++++++++++++++++++++++++++-
configure | 18 ++++++-------
configure.ac | 2 -
inst/NEWS.Rd | 10 +++++++
inst/doc/glpkAPI.R |only
inst/doc/glpkAPI.pdf |binary
man/setColsNamesGLPK.Rd |only
man/setRowsNamesGLPK.Rd |only
src/Makevars.win | 2 -
src/glpkAPI.c | 64 ++++++++++++++++++++++++++++++++++++++++++++++++
src/glpkAPI.h | 6 ++++
src/init.c | 2 +
15 files changed, 159 insertions(+), 27 deletions(-)
Title: R Interface to C API of COIN-OR Clp
Diff between clpAPI versions 1.2.2 dated 2013-01-16 and 1.2.3 dated 2013-05-23
Description: R Interface to C API of COIN-OR Clp, depends on COIN-OR
Clp Version >= 1.12.0
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 9 ++--
MD5 | 33 ++++++++-------
NAMESPACE | 8 +++
R/clpAPI.R | 77 +++++++++++++++++++++++++++++++++++
R/zzz.R | 5 +-
configure | 18 ++++----
configure.ac | 2
inst/NEWS.Rd | 10 ++++
inst/c2r.map | 5 ++
inst/doc/clpAPI.R |only
inst/doc/clpAPI.pdf |binary
man/copyNamesCLP.Rd |only
man/dropNamesCLP.Rd |only
man/lengthNamesCLP.Rd |only
man/loadProblemCLP.Rd | 4 +
man/versionCLP.Rd |only
src/clpAPI.c | 109 ++++++++++++++++++++++++++++++++++++++++++++++++++
src/clpAPI.h | 18 ++++++++
src/clpR.h | 1
src/init.c | 6 ++
20 files changed, 274 insertions(+), 31 deletions(-)
Title: Colocalisation tests of two genetic traits
Diff between coloc versions 1.11 dated 2013-01-25 and 2.0 dated 2013-05-23
Description: Performs the colocalisation tests described in Plagnol et
al (2009), Wallace et al (2013) and Giambartolomei et al
(2013).
Author: Chris Wallace, with contributions from Claudia Giambartolemei
Maintainer: Chris Wallace
coloc-1.11/coloc/R/plots.R |only
coloc-2.0/coloc/ChangeLog | 9
coloc-2.0/coloc/DESCRIPTION | 21 +-
coloc-2.0/coloc/MD5 | 40 ++-
coloc-2.0/coloc/NAMESPACE | 12 +
coloc-2.0/coloc/R/AllClasses.R | 86 ++++----
coloc-2.0/coloc/R/bma.R | 211 ++++++++++----------
coloc-2.0/coloc/R/claudia.R |only
coloc-2.0/coloc/R/coloc.test.R | 304 ++++++++++++++++--------------
coloc-2.0/coloc/R/pcs.R | 2
coloc-2.0/coloc/R/private.R |only
coloc-2.0/coloc/README.md |only
coloc-2.0/coloc/inst |only
coloc-2.0/coloc/man/Var.data.Rd |only
coloc-2.0/coloc/man/Var.data.cc.Rd |only
coloc-2.0/coloc/man/approx.bf.Rd |only
coloc-2.0/coloc/man/bf.Rd |only
coloc-2.0/coloc/man/coloc-class.Rd | 17 -
coloc-2.0/coloc/man/coloc.abf.Rd |only
coloc-2.0/coloc/man/coloc.abf.datasets.Rd |only
coloc-2.0/coloc/man/coloc.abf.snpStats.Rd |only
coloc-2.0/coloc/man/coloc.bma.Rd | 36 ++-
coloc-2.0/coloc/man/coloc.test.Rd | 92 ++-------
coloc-2.0/coloc/man/coloc.test.summary.Rd |only
coloc-2.0/coloc/man/eta.Rd | 39 +--
coloc-2.0/coloc/man/logdiff.Rd |only
coloc-2.0/coloc/man/logsum.Rd |only
27 files changed, 466 insertions(+), 403 deletions(-)
Title: Analyzing case-parent triad and/or case-control data with SNP
haplotypes
Diff between Haplin versions 5.2 dated 2013-05-02 and 5.3 dated 2013-05-23
Description: Haplin performs a genetic association analysis of
case-parent triad (trio) data with multiple markers. It can
also incorporate complete or incomplete control triads, for
instance independent control children. Estimation is based on
haplotypes, for instance SNP haplotypes, even though phase is
not known from the genetic data. Haplin estimates relative risk
(RR + conf.int.) and p-value associated with each haplotype. It
uses maximum likelihood estimation to make optimal use of data
from triads with missing genotypic data, for instance if some
SNPs has not been typed for some individuals. Haplin also
allows estimation of effects of maternal haplotypes and
parent-of-origin effects, particularly appropriate in perinatal
epidemiology. Haplin allows special models, like
X-inactivation, to be fitted on the X-chromosome.
Author: Hakon K. Gjessing
Maintainer: Hakon K. Gjessing
DESCRIPTION | 8 ++---
MD5 | 63 ++++++++++++++++++++--------------------
NAMESPACE | 1
R/convertPed.R | 2 -
R/f.Rplot.R | 4 +-
R/f.check.pars.R | 12 ++++---
R/f.data.R | 26 ++++++++--------
R/f.data.ready.R | 9 +----
R/f.get.data.R | 24 +++++++--------
R/f.get.marker.names.R |only
R/f.haptable.list.R | 13 +-------
R/f.plot.effects.R | 3 +
R/f.prep.data.R | 6 +--
R/f.read.data.R | 2 -
R/f.split.matrix.R | 4 +-
R/gwaaToHaplin.R | 4 +-
R/haplin.R | 14 +++-----
R/haplinSlide.R | 31 ++++++++++---------
R/haptable.default.R |only
R/haptable.haplin.R | 7 ++--
R/haptable.haplinSlide.R | 5 ---
R/haptable.haplinStrat.R | 2 -
R/lineByLine.R | 14 ++++----
R/plot.haplin.R | 37 ++++++++++++++---------
R/prepPed.R | 17 ++++++++--
R/print.summary.tri.glm.R | 4 +-
R/textlabel.R |only
R/toDataFrame.R | 19 +++++++-----
inst/doc/Haplin_data_format.pdf |binary
man/convertPed.Rd | 2 -
man/lineByLine.Rd | 16 +++++-----
man/plot.haptable.Rd | 6 ++-
man/prepPed.Rd | 3 +
man/snpPos.Rd | 5 +--
34 files changed, 193 insertions(+), 170 deletions(-)
Title: Flexible regression models for survival data.
Diff between timereg versions 1.7.5 dated 2013-05-02 and 1.7.6 dated 2013-05-23
Description: Programs for Martinussen and Scheike (2006), `Dynamic
Regression Models for Survival Data', Springer Verlag. Plus
more recent developments. Additive survival model,
semiparametric proportional odds model, cumulative residuals,
excess risk models and more. Flexible competing risks
regression including GOF-tests. Two-stage frailty modelling.
PLS for the additive risk model. Lasso in ahaz package.
Author: Thomas Scheike with contributions from Torben Martinussen and
Jeremy Silver
Maintainer: Thomas Scheike
DESCRIPTION | 8
MD5 | 40 -
R/Gprop-odds-subdist.r | 3
R/Gprop-odds.r | 2
R/clusterindex-reshape.r | 5
R/comprisk.r | 1032 +++++++++++++++++++++++------------------------
R/cox-aalen.r | 8
R/mgresid.r | 2
R/new.aalen.r | 3
R/new.cox-aalen.r | 19
R/new.pe-sasieni.r | 2
R/predict-timereg.r | 5
R/prop-odds-subdist.r | 3
R/prop-odds.r | 3
R/read-design.r | 6
R/two-stage-reg.r | 1
man/comp.risk.Rd | 27 -
man/cox.aalen.Rd | 20
src/aalen.c | 104 +++-
src/cox-aalen.c | 444 ++++++++++++++------
src/matrix.c | 11
21 files changed, 993 insertions(+), 755 deletions(-)
Title: Internal validation of forensic STR kits made easy with
strvalidator.
Diff between strvalidator versions 0.1 dated 2013-03-11 and 0.2.0 dated 2013-05-23
Description: strvalidator provide tools that make it easier to perform
an internal validation of a forensic short tandem repeat (STR)
kit for human identification. The tools are developed to
provide all necessary data to conform with the ENFSI guidelines
for internal validation. More information about each function
can be found in the respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson
strvalidator-0.1/strvalidator/R/addZvalue.r |only
strvalidator-0.1/strvalidator/R/addZygosity.r |only
strvalidator-0.1/strvalidator/R/calculateZvalue.r |only
strvalidator-0.1/strvalidator/R/calculateZygosity.r |only
strvalidator-0.1/strvalidator/R/importGM.r |only
strvalidator-0.1/strvalidator/man/addZvalue.Rd |only
strvalidator-0.1/strvalidator/man/addZygosity.Rd |only
strvalidator-0.1/strvalidator/man/calculateZvalue.Rd |only
strvalidator-0.1/strvalidator/man/calculateZygosity.Rd |only
strvalidator-0.1/strvalidator/man/importGM.Rd |only
strvalidator-0.2.0/strvalidator/DESCRIPTION | 19
strvalidator-0.2.0/strvalidator/MD5 | 130 +-
strvalidator-0.2.0/strvalidator/NAMESPACE | 4
strvalidator-0.2.0/strvalidator/NEWS | 16
strvalidator-0.2.0/strvalidator/R/addData.r | 183 ++-
strvalidator-0.2.0/strvalidator/R/addData_gui.r |only
strvalidator-0.2.0/strvalidator/R/addDye_gui.r |only
strvalidator-0.2.0/strvalidator/R/addKitInfo.r | 2
strvalidator-0.2.0/strvalidator/R/calculateBalance.r | 462 ++++++----
strvalidator-0.2.0/strvalidator/R/calculateBalance_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateDropout.r | 304 ++++--
strvalidator-0.2.0/strvalidator/R/calculateDropout_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateH.r | 114 +-
strvalidator-0.2.0/strvalidator/R/calculateH_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateHeterozygous.r |only
strvalidator-0.2.0/strvalidator/R/calculateHeterozygous_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateMean.r | 3
strvalidator-0.2.0/strvalidator/R/calculateStutter.r | 134 ++
strvalidator-0.2.0/strvalidator/R/calculateStutter_gui.r |only
strvalidator-0.2.0/strvalidator/R/calculateSummary.r | 2
strvalidator-0.2.0/strvalidator/R/checkSubset.r | 24
strvalidator-0.2.0/strvalidator/R/checkSubset_gui.r |only
strvalidator-0.2.0/strvalidator/R/combineRef.r | 2
strvalidator-0.2.0/strvalidator/R/concatenate_gui.r |only
strvalidator-0.2.0/strvalidator/R/countPeaks.r | 2
strvalidator-0.2.0/strvalidator/R/detectKit.r |only
strvalidator-0.2.0/strvalidator/R/editData_gui.r |only
strvalidator-0.2.0/strvalidator/R/filterProfile.r | 319 +++++-
strvalidator-0.2.0/strvalidator/R/filterProfile_gui.r |only
strvalidator-0.2.0/strvalidator/R/getKit.r | 142 ---
strvalidator-0.2.0/strvalidator/R/globals.R |only
strvalidator-0.2.0/strvalidator/R/guessProfile.r |only
strvalidator-0.2.0/strvalidator/R/guessProfile_gui.r |only
strvalidator-0.2.0/strvalidator/R/import.r |only
strvalidator-0.2.0/strvalidator/R/import_gui.r |only
strvalidator-0.2.0/strvalidator/R/listObjects.r |only
strvalidator-0.2.0/strvalidator/R/modelDropout_gui.r |only
strvalidator-0.2.0/strvalidator/R/plotBalance_gui.r |only
strvalidator-0.2.0/strvalidator/R/plotDropout_gui.r |only
strvalidator-0.2.0/strvalidator/R/plotStutter_gui.r |only
strvalidator-0.2.0/strvalidator/R/savePlot_gui.r |only
strvalidator-0.2.0/strvalidator/R/slim.r | 19
strvalidator-0.2.0/strvalidator/R/slim_gui.r |only
strvalidator-0.2.0/strvalidator/R/strvalidator-package.r | 43
strvalidator-0.2.0/strvalidator/R/strvalidator.r |only
strvalidator-0.2.0/strvalidator/R/trim.r | 49 -
strvalidator-0.2.0/strvalidator/R/trim_gui.r |only
strvalidator-0.2.0/strvalidator/data/ref2.RData |only
strvalidator-0.2.0/strvalidator/data/set2.RData |only
strvalidator-0.2.0/strvalidator/inst |only
strvalidator-0.2.0/strvalidator/man/addData.Rd | 14
strvalidator-0.2.0/strvalidator/man/addData_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/addDye_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateBalance.Rd | 54 -
strvalidator-0.2.0/strvalidator/man/calculateBalance_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateDropout.Rd | 5
strvalidator-0.2.0/strvalidator/man/calculateDropout_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateH.Rd | 28
strvalidator-0.2.0/strvalidator/man/calculateH_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateHeterozygous.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateHeterozygous_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/calculateStutter.Rd | 13
strvalidator-0.2.0/strvalidator/man/calculateStutter_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/checkSubset.Rd | 5
strvalidator-0.2.0/strvalidator/man/checkSubset_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/concatenate_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/detectKit.Rd |only
strvalidator-0.2.0/strvalidator/man/editData_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/filterProfile.Rd | 12
strvalidator-0.2.0/strvalidator/man/filterProfile_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/getKit.Rd | 7
strvalidator-0.2.0/strvalidator/man/guessProfile.Rd |only
strvalidator-0.2.0/strvalidator/man/guessProfile_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/import.Rd |only
strvalidator-0.2.0/strvalidator/man/import_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/listObjects.Rd |only
strvalidator-0.2.0/strvalidator/man/modelDropout_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/plotBalance_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/plotDropout_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/plotStutter_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/ref2.Rd |only
strvalidator-0.2.0/strvalidator/man/savePlot_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/set2.Rd |only
strvalidator-0.2.0/strvalidator/man/slim.Rd | 9
strvalidator-0.2.0/strvalidator/man/slim_gui.Rd |only
strvalidator-0.2.0/strvalidator/man/strvalidator-package.Rd | 15
strvalidator-0.2.0/strvalidator/man/strvalidator.Rd |only
strvalidator-0.2.0/strvalidator/man/trim.Rd | 9
strvalidator-0.2.0/strvalidator/man/trim_gui.Rd |only
99 files changed, 1502 insertions(+), 642 deletions(-)
Title: Spatio-Temporal Bayesian Modelling Using R
Diff between spTimer versions 0.6 dated 2013-03-01 and 0.7 dated 2013-05-23
Description: The package is able to fit, spatially predict and
temporally forecast large amounts of space-time data using [1]
Bayesian Gaussian Process (GP) Models, [2] Bayesian
Auto-Regressive (AR) Models, and [3] Bayesian Gaussian
Predictive Processes (GPP) based AR Models.
Author: K. Shuvo Bakar & Sujit K. Sahu
Maintainer: Khandoker Shuvo Bakar
spTimer-0.6/spTimer/man/DataFit.Rd |only
spTimer-0.6/spTimer/man/DataFitFore.Rd |only
spTimer-0.6/spTimer/man/DataValFore.Rd |only
spTimer-0.6/spTimer/man/DataValPred.Rd |only
spTimer-0.7/spTimer/DESCRIPTION | 14 ++--
spTimer-0.7/spTimer/MD5 | 43 +++++-------
spTimer-0.7/spTimer/R/spAR.r | 24 ++-----
spTimer-0.7/spTimer/R/spGP.r | 24 ++-----
spTimer-0.7/spTimer/R/spGPP.r | 68 ++------------------
spTimer-0.7/spTimer/R/spTfnc.R | 44 ++++++-------
spTimer-0.7/spTimer/R/spTimer.R | 10 ++
spTimer-0.7/spTimer/R/useful_commands.R | 76 +++++++++++++++++-----
spTimer-0.7/spTimer/man/NYdata.Rd | 88 ++++++++++++++++++++------
spTimer-0.7/spTimer/man/as.forecast.object.Rd |only
spTimer-0.7/spTimer/man/predict.spT.Rd | 20 +++++
spTimer-0.7/spTimer/man/spT.Gibbs.Rd | 31 +++++----
spTimer-0.7/spTimer/man/spT.initials.Rd | 2
spTimer-0.7/spTimer/man/spT.priors.Rd | 2
spTimer-0.7/spTimer/man/spT.validation.Rd | 6 -
spTimer-0.7/spTimer/man/spTimer-internal.Rd | 1
spTimer-0.7/spTimer/man/spTimer-package.Rd | 13 ++-
spTimer-0.7/spTimer/man/summary.spT.Rd | 12 ++-
spTimer-0.7/spTimer/src/equation_xb_ar.c | 39 ++++++++---
spTimer-0.7/spTimer/src/mathematics.c | 4 -
spTimer-0.7/spTimer/src/randgenerator.c | 3
25 files changed, 305 insertions(+), 219 deletions(-)
Title: Simulation of the forensic DNA process
Diff between pcrsim versions 0.1 dated 2013-04-06 and 0.1.1 dated 2013-05-23
Description: pcrsim is a package for simulating the forensic DNA
process. pcrsim() opens up a graphical user interface which
allow the user to enter parameters required for the simulation.
Once calibrated the program can be used to: reduce the
laboratory work needed for validation of new STR kits, help
develop methods for interpretation of DNA evidence, etc. This
is a first version which is still experimental and under
development.
Author: Oskar Hansson
Maintainer: Oskar Hansson
DESCRIPTION | 8 ++++----
MD5 | 20 +++++++++++---------
NEWS | 5 +++++
R/findScaling.r |only
R/generateEPG.r | 5 -----
R/generateEPGgui.r | 6 +++---
R/pcrsim.r | 15 ++++++++++-----
R/simPCR.r | 18 ++++++++++--------
R/simulateprofile.r | 31 +++++++++++++++++--------------
man/findScaling.Rd |only
man/simPCR.Rd | 2 +-
man/simulateProfile.Rd | 7 +++++--
12 files changed, 66 insertions(+), 51 deletions(-)
Title: Miscellaneous Functions from M. Kohl
Diff between MKmisc versions 0.93 dated 2013-02-17 and 0.94 dated 2013-05-23
Description: Miscellaneous Functions from M. Kohl
Author: Matthias Kohl
Maintainer: Matthias Kohl
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++++------
NAMESPACE | 2 ++
NEWS | 11 +++++++++++
R/stringDist.R | 17 ++++++++++++-----
R/stringSim.R |only
R/traceBack.R |only
man/heatmapCol.Rd | 6 ++++--
man/stringDist.Rd | 16 ++++++++++------
man/stringSim.Rd |only
man/traceBack.Rd |only
11 files changed, 53 insertions(+), 23 deletions(-)
Title: Citations for knitr markdown files
Diff between knitcitations versions 0.4-4 dated 2013-03-18 and 0.4-7 dated 2013-05-23
Description: knitcitations provides the ability to create dynamic
citations in which the bibliographic information is pulled from
the web rather than having to be entered into a local database
such as bibtex ahead of time. Knitcitations is primarily aimed
at authoring in the R markdown format, and can provide outputs
for web-based authoring such as linked text and tooltips over
inline citations. Cite using a DOI, URL, or bibtex file key.
See the package URL for details.
Author: Carl Boettiger [aut, cre]
Maintainer: Carl Boettiger
DESCRIPTION | 9 ++++---
MD5 | 58 +++++++++++++++++++++++++-------------------------
NEWS | 45 +++++++++++++++++++++++++++++++-------
R/bibliography.R | 36 +++++++++++++++++++++++--------
R/cite.R | 9 +++++--
R/cite_options.R | 7 ++++--
R/citep.R | 23 ++++++++++++++-----
R/citet.R | 48 +++++++++++++++++++++++++++++++----------
R/create_bibkey.R | 11 ++++++---
R/formatref.R | 4 ++-
R/functiontable.R | 9 ++++---
R/init_knitbib.R | 6 +++--
R/inline_formats.R | 34 +++++++++++++++++++----------
R/print_html.R |only
R/print_markdown.R | 16 ++++++++-----
R/print_rdfa.R | 14 +++++++++---
R/read.bibtex.R | 2 -
R/write.bibtex.R | 28 ++++++++++++++----------
R/write_cache.R | 9 +++++--
man/bib_format.Rd | 3 +-
man/bibliography.Rd | 12 ++++++----
man/cite_options.Rd | 4 +--
man/citep.Rd | 10 +++++++-
man/citet.Rd | 4 ++-
man/functiontable.Rd | 8 +++---
man/print_html.Rd |only
man/print_markdown.Rd | 10 ++++++--
man/print_rdfa.Rd | 3 +-
man/unique_inline.Rd | 2 -
man/write.bibtex.Rd | 6 +++--
man/write_cache.Rd | 2 -
31 files changed, 293 insertions(+), 139 deletions(-)
Title: Fast hierarchical clustering routines for R and Python
Diff between fastcluster versions 1.1.9 dated 2013-03-17 and 1.1.10 dated 2013-05-23
Description: This is a two-in-one package which provides interfaces to
both R and Python. It implements fast hierarchical,
agglomerative clustering routines. Part of the functionality is
designed as drop-in replacement for existing routines:
“linkage” in the SciPy package “scipy.cluster.hierarchy”,
“hclust” in R's “stats” package, and the “flashClust” package.
It provides the same functionality with the benefit of a much
faster implementation. Moreover, there are memory-saving
routines for clustering of vector data, which go beyond what
the existing packages provide. For information on how to
install the Python files, see the file INSTALL in the source
distribution.
Author: Daniel Müllner, http://math.stanford.edu/~muellner
Maintainer: Daniel Müllner
DESCRIPTION | 16 +--
MD5 | 24 ++---
NEWS | 13 ++
inst/CITATION | 25 +++--
inst/doc/fastcluster.Rtex | 8 +
inst/doc/fastcluster.pdf |binary
man/fastcluster.Rd | 2
python/fastcluster.py | 4
python/setup.py | 13 ++
src/Makevars | 2
src/fastcluster.cpp | 200 ++++++++++++++++++++++++++++++++++-------
src/fastcluster_R.cpp | 132 ++++++++++++++++++++++-----
src/fastcluster_python.cpp | 215 +++++++++++++++++++++++++++++++++++++++++----
13 files changed, 540 insertions(+), 114 deletions(-)
Title: Differential Co-expression Analysis and Differential Regulation
Analysis of Gene Expression Microarray Data
Diff between DCGL versions 2.0 dated 2013-03-28 and 2.0.1 dated 2013-05-23
Description: Functions for 1) gene filtration; 2) link filtration; 3)
differential co-expression analysis: DCG (Differential
Coexpressed Gene) identification and DCL (Differentially
Coexpressed Link) identification; and 4) differential
regulation analysis: DRG (Differential Regulated Gene)
identification, DRL (Differential Regulated Link)
identification, DRL visualization and regulator ranking.
Author: Jing Yang, Hui Yu, Bao-Hong Liu
Maintainer: Bao-Hong Liu
DESCRIPTION | 10 +++++-----
MD5 | 26 +++++++++++++-------------
R/DCGL.r | 4 ++--
doc/DCGL_2.0.pdf |binary
man/ASC.Rd | 5 +++--
man/DCGL-package.Rd | 47 +++++++++++++++++++++++++++++++----------------
man/DCe.Rd | 18 ++++++++++++++----
man/DCp.Rd | 20 +++++++++++++++-----
man/DCsum.Rd | 6 ++++--
man/DRplot.Rd | 23 ++++++++++++++++-------
man/DRrank.Rd | 23 +++++++++++++++--------
man/DRsort.Rd | 17 ++++++++++++-----
man/LRC.Rd | 2 +-
man/qLinkfilter.Rd | 10 ++++++++--
14 files changed, 139 insertions(+), 72 deletions(-)