Title: Sparse and Dense Matrix Classes and Methods
Diff between Matrix versions 1.1-4 dated 2014-06-15 and 1.1-5 dated 2015-01-18
Description: Classes and methods for dense and sparse matrices and
operations on them using LAPACK and SuiteSparse.
Author: Douglas Bates
Maintainer: Martin Maechler
Matrix-1.1-4/Matrix/po/R-en@quot.po |only
Matrix-1.1-4/Matrix/po/en@quot.po |only
Matrix-1.1-5/Matrix/ChangeLog | 13
Matrix-1.1-5/Matrix/DESCRIPTION | 8
Matrix-1.1-5/Matrix/MD5 | 209 ++++++------
Matrix-1.1-5/Matrix/NAMESPACE | 12
Matrix-1.1-5/Matrix/R/AllClass.R | 42 +-
Matrix-1.1-5/Matrix/R/AllGeneric.R | 2
Matrix-1.1-5/Matrix/R/Auxiliaries.R | 172 +++++++--
Matrix-1.1-5/Matrix/R/Csparse.R | 111 ++----
Matrix-1.1-5/Matrix/R/Math.R |only
Matrix-1.1-5/Matrix/R/Matrix.R | 105 ------
Matrix-1.1-5/Matrix/R/Ops.R | 29 -
Matrix-1.1-5/Matrix/R/Summary.R |only
Matrix-1.1-5/Matrix/R/associations.R |only
Matrix-1.1-5/Matrix/R/colSums.R | 28 +
Matrix-1.1-5/Matrix/R/dMatrix.R | 97 -----
Matrix-1.1-5/Matrix/R/ddenseMatrix.R | 15
Matrix-1.1-5/Matrix/R/denseMatrix.R | 10
Matrix-1.1-5/Matrix/R/dgCMatrix.R | 30 +
Matrix-1.1-5/Matrix/R/dgTMatrix.R | 2
Matrix-1.1-5/Matrix/R/dgeMatrix.R | 22 -
Matrix-1.1-5/Matrix/R/diagMatrix.R | 87 ++--
Matrix-1.1-5/Matrix/R/dspMatrix.R | 24 -
Matrix-1.1-5/Matrix/R/dsparseMatrix.R | 5
Matrix-1.1-5/Matrix/R/dsyMatrix.R | 70 ++--
Matrix-1.1-5/Matrix/R/dtpMatrix.R | 9
Matrix-1.1-5/Matrix/R/dtrMatrix.R | 4
Matrix-1.1-5/Matrix/R/lMatrix.R | 10
Matrix-1.1-5/Matrix/R/ldenseMatrix.R | 84 +---
Matrix-1.1-5/Matrix/R/lsparseMatrix.R | 17
Matrix-1.1-5/Matrix/R/ndenseMatrix.R | 69 +--
Matrix-1.1-5/Matrix/R/nsparseMatrix.R | 32 -
Matrix-1.1-5/Matrix/R/products.R | 59 ++-
Matrix-1.1-5/Matrix/R/sparseMatrix.R | 21 -
Matrix-1.1-5/Matrix/R/sparseVector.R | 52 --
Matrix-1.1-5/Matrix/R/symmetricMatrix.R | 24 -
Matrix-1.1-5/Matrix/R/triangularMatrix.R | 11
Matrix-1.1-5/Matrix/R/zzz.R | 7
Matrix-1.1-5/Matrix/TODO | 23 -
Matrix-1.1-5/Matrix/build |only
Matrix-1.1-5/Matrix/inst/doc/Comparisons.R |only
Matrix-1.1-5/Matrix/inst/doc/Comparisons.Rnw |only
Matrix-1.1-5/Matrix/inst/doc/Design-issues.R |only
Matrix-1.1-5/Matrix/inst/doc/Design-issues.Rnw |only
Matrix-1.1-5/Matrix/inst/doc/Intro2Matrix.R |only
Matrix-1.1-5/Matrix/inst/doc/Intro2Matrix.Rnw |only
Matrix-1.1-5/Matrix/inst/doc/Introduction.R |only
Matrix-1.1-5/Matrix/inst/doc/Introduction.Rnw |only
Matrix-1.1-5/Matrix/inst/doc/sparseModels.R |only
Matrix-1.1-5/Matrix/inst/doc/sparseModels.Rnw |only
Matrix-1.1-5/Matrix/inst/po/de/LC_MESSAGES/Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/de/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/en@quot/LC_MESSAGES/Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/en@quot/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/fr/LC_MESSAGES/Matrix.mo |only
Matrix-1.1-5/Matrix/inst/po/fr/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/pl/LC_MESSAGES/Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/po/pl/LC_MESSAGES/R-Matrix.mo |binary
Matrix-1.1-5/Matrix/inst/test-tools-1.R | 15
Matrix-1.1-5/Matrix/inst/test-tools-Matrix.R | 4
Matrix-1.1-5/Matrix/man/Matrix-class.Rd | 1
Matrix-1.1-5/Matrix/man/band.Rd | 3
Matrix-1.1-5/Matrix/man/colSums.Rd | 6
Matrix-1.1-5/Matrix/man/diagonalMatrix-class.Rd | 7
Matrix-1.1-5/Matrix/man/dtCMatrix-class.Rd | 19 -
Matrix-1.1-5/Matrix/man/forceSymmetric.Rd | 26 -
Matrix-1.1-5/Matrix/man/invPerm.Rd | 4
Matrix-1.1-5/Matrix/man/isTriangular.Rd | 15
Matrix-1.1-5/Matrix/man/ldenseMatrix-class.Rd | 1
Matrix-1.1-5/Matrix/man/matrix-products.Rd | 19 -
Matrix-1.1-5/Matrix/man/ndenseMatrix-class.Rd | 1
Matrix-1.1-5/Matrix/man/sparseMatrix.Rd | 21 -
Matrix-1.1-5/Matrix/man/sparseVector-class.Rd | 9
Matrix-1.1-5/Matrix/man/symmpart.Rd | 21 -
Matrix-1.1-5/Matrix/man/triangularMatrix-class.Rd | 4
Matrix-1.1-5/Matrix/po/Matrix.pot | 194 +++++------
Matrix-1.1-5/Matrix/po/R-Matrix.pot | 42 +-
Matrix-1.1-5/Matrix/po/R-de.po | 57 ++-
Matrix-1.1-5/Matrix/po/R-fr.po | 59 ++-
Matrix-1.1-5/Matrix/po/R-pl.po | 76 +++-
Matrix-1.1-5/Matrix/po/T |only
Matrix-1.1-5/Matrix/po/de.po | 193 +++++------
Matrix-1.1-5/Matrix/po/fr.po | 193 +++++------
Matrix-1.1-5/Matrix/po/pl.po | 193 +++++------
Matrix-1.1-5/Matrix/src/CHMfactor.c | 10
Matrix-1.1-5/Matrix/src/Csparse.c | 99 ++++-
Matrix-1.1-5/Matrix/src/Csparse.h | 2
Matrix-1.1-5/Matrix/src/Mutils.c | 35 +-
Matrix-1.1-5/Matrix/src/Mutils.h | 21 -
Matrix-1.1-5/Matrix/src/chm_common.c | 10
Matrix-1.1-5/Matrix/src/chm_common.h | 2
Matrix-1.1-5/Matrix/src/cs.c | 14
Matrix-1.1-5/Matrix/src/cs.h | 3
Matrix-1.1-5/Matrix/src/cs_utils.c | 2
Matrix-1.1-5/Matrix/src/dense.c | 118 +++---
Matrix-1.1-5/Matrix/src/dgCMatrix.c | 36 +-
Matrix-1.1-5/Matrix/src/dgeMatrix.c | 171 +++++----
Matrix-1.1-5/Matrix/src/dpoMatrix.c | 10
Matrix-1.1-5/Matrix/src/dsCMatrix.c | 16
Matrix-1.1-5/Matrix/src/dsyMatrix.c | 6
Matrix-1.1-5/Matrix/src/dsyMatrix.h | 1
Matrix-1.1-5/Matrix/src/dtCMatrix.c | 37 +-
Matrix-1.1-5/Matrix/src/dtrMatrix.c | 11
Matrix-1.1-5/Matrix/src/dtrMatrix.h | 1
Matrix-1.1-5/Matrix/src/init.c | 4
Matrix-1.1-5/Matrix/src/t_Csparse_subassign.c | 8
Matrix-1.1-5/Matrix/tests/Simple.R | 64 +++
Matrix-1.1-5/Matrix/tests/factorizing.R | 6
Matrix-1.1-5/Matrix/tests/group-methods.R | 97 ++++-
Matrix-1.1-5/Matrix/tests/indexing.R | 27 +
Matrix-1.1-5/Matrix/tests/indexing.Rout.save | 57 ++-
Matrix-1.1-5/Matrix/tests/matprod.R | 97 +++++
Matrix-1.1-5/Matrix/tests/other-pkgs.R | 4
114 files changed, 2033 insertions(+), 1634 deletions(-)
Title: Rigorous - NIfTI+ANALYZE+AFNI Input / Output
Diff between oro.nifti versions 0.4.0 dated 2013-12-27 and 0.4.3 dated 2015-01-18
Description: Functions for the input/output and visualization of
medical imaging data that follow either the ANALYZE, NIfTI or AFNI
formats. This package is part of the Rigorous Analytics bundle.
Author: Brandon Whitcher, Volker Schmid and Andrew Thornton, with
contributions by Karsten Tabelow and Jon Clayden
Maintainer: Brandon Whitcher
oro.nifti-0.4.0/oro.nifti/R/oro2fmri.R |only
oro.nifti-0.4.0/oro.nifti/man/oro2fmri.Rd |only
oro.nifti-0.4.3/oro.nifti/DESCRIPTION | 10
oro.nifti-0.4.3/oro.nifti/LICENSE | 2
oro.nifti-0.4.3/oro.nifti/MD5 | 36 +-
oro.nifti-0.4.3/oro.nifti/NAMESPACE | 6
oro.nifti-0.4.3/oro.nifti/R/afniS4.R | 130 ++++++----
oro.nifti-0.4.3/oro.nifti/R/auditTrail.R | 98 +++----
oro.nifti-0.4.3/oro.nifti/R/niftiS4.R | 24 +
oro.nifti-0.4.3/oro.nifti/R/readS4.R | 31 +-
oro.nifti-0.4.3/oro.nifti/R/tim_colors.R | 4
oro.nifti-0.4.3/oro.nifti/build/vignette.rds |binary
oro.nifti-0.4.3/oro.nifti/inst/afni/TT_N27_EZ_LR+tlrc.BRIK.gz |only
oro.nifti-0.4.3/oro.nifti/inst/afni/TT_N27_EZ_LR+tlrc.HEAD |only
oro.nifti-0.4.3/oro.nifti/inst/doc/nifti.Rnw | 13 -
oro.nifti-0.4.3/oro.nifti/inst/doc/nifti.pdf |binary
oro.nifti-0.4.3/oro.nifti/man/descrip-methods.Rd | 2
oro.nifti-0.4.3/oro.nifti/man/q2R.Rd | 2
oro.nifti-0.4.3/oro.nifti/man/read_afni.Rd | 7
oro.nifti-0.4.3/oro.nifti/tests/Examples/oro.nifti-Ex.Rout.save | 25 +
oro.nifti-0.4.3/oro.nifti/vignettes/nifti.Rnw | 13 -
21 files changed, 233 insertions(+), 170 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Diff between ztable versions 0.1.2 dated 2015-01-03 and 0.1.3 dated 2015-01-18
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm or coxph objects.
Author: "Keon-Woong Moon" [aut, cre]
Maintainer: "Keon-Woong Moon"
ztable-0.1.2/ztable/man/myhtmlHead.Rd |only
ztable-0.1.3/ztable/DESCRIPTION | 6
ztable-0.1.3/ztable/MD5 | 41
ztable-0.1.3/ztable/NEWS | 21
ztable-0.1.3/ztable/R/print.ztable.html.R | 285 -
ztable-0.1.3/ztable/R/ztable.R | 249
ztable-0.1.3/ztable/R/ztable2.R |only
ztable-0.1.3/ztable/R/zzz.R | 2
ztable-0.1.3/ztable/README.md | 3965 ++++++++++++--
ztable-0.1.3/ztable/inst/doc/ztable.R | 51
ztable-0.1.3/ztable/inst/doc/ztable.Rmd | 73
ztable-0.1.3/ztable/inst/doc/ztable.html | 7770 ++++++++++++++++++++--------
ztable-0.1.3/ztable/man/addCellColor.Rd |only
ztable-0.1.3/ztable/man/addColColor.Rd |only
ztable-0.1.3/ztable/man/addRowColor.Rd |only
ztable-0.1.3/ztable/man/addcgroup.Rd |only
ztable-0.1.3/ztable/man/addrgroup.Rd |only
ztable-0.1.3/ztable/man/cGroupSpan.Rd |only
ztable-0.1.3/ztable/man/caption2minipage.Rd |only
ztable-0.1.3/ztable/man/colGroupCount.Rd |only
ztable-0.1.3/ztable/man/getNewAlign.Rd |only
ztable-0.1.3/ztable/man/myhtmlStyle.Rd |only
ztable-0.1.3/ztable/man/printHTMLHead.Rd |only
ztable-0.1.3/ztable/man/printLatexHead.Rd |only
ztable-0.1.3/ztable/man/totalCol.Rd |only
ztable-0.1.3/ztable/man/update_ztable.Rd | 17
ztable-0.1.3/ztable/man/validColor2.Rd |only
ztable-0.1.3/ztable/man/ztable2viewer.Rd |only
ztable-0.1.3/ztable/man/ztable_sub.Rd | 21
ztable-0.1.3/ztable/vignettes/ztable.Rmd | 73
30 files changed, 9849 insertions(+), 2725 deletions(-)
Title: Fishery Stock Assessment by Generalized Depletion Models
Diff between CatDyn versions 1.0-5 dated 2014-04-10 and 1.0-6 dated 2015-01-18
Description: Using high-frequency or medium-frequency catch in biomass or numbers, fishing nominal effort, and mean body weight by time step, from one or two fishing fleets, estimate stock abundance, natural mortality rate, and fishing operational parameters. It includes methods for data organization, plotting standard exploratory and analytical plots, predictions, for 237 types of models of increasing complexity, and six likelihood models.
Author: Ruben H. Roa-Ureta
Maintainer: Ruben H. Roa-Ureta
DESCRIPTION | 12
MD5 | 48
NAMESPACE | 2
R/CatDyn-internal.R |77392 +++++++++++++++++++++++++++++++++++++++++++------
R/CatDynCor.R |only
R/CatDynFit.R |21588 ++++++++++++-
R/CatDynPred.R | 732
R/CatDynSum.R |only
R/as.CatDynData.R | 27
R/catdynexp_1.R | 2701 +
R/deltamethod.R | 6
R/plot.CatDynExp.R | 35
R/plot.CatDynMod.R | 33
data/gayhake.rda |only
data/lolgahi.rda |binary
data/twelver.rda |only
man/CatDyn-package.Rd | 34
man/CatDynCor.Rd |only
man/CatDynFit.Rd | 283
man/CatDynPred.Rd | 11
man/CatDynSum.Rd |only
man/as.CatDynData.Rd | 56
man/catdynexp_1.Rd | 30
man/gayhake.Rd |only
man/lolgahi.Rd | 11
man/plot.CatDynData.Rd | 2
man/plot.CatDynExp.Rd | 5
man/plot.CatDynMod.Rd | 5
man/twelver.Rd |only
29 files changed, 92131 insertions(+), 10882 deletions(-)
Title: Power Calculations for SNP Studies with Censored Outcomes
Diff between survSNP versions 0.21-7 dated 2013-12-12 and 0.23.2 dated 2015-01-18
Description: This package can be used to conduct asymptotic and empirical power and sample size calculations for SNP association studies with right censored time to event outcomes
Author: Kouros Owzar, Zhiguo Li, Nancy Cox, Sin-Ho Jung and Chanhee Yi
Maintainer: Kouros Owzar
survSNP-0.21-7/survSNP/configure.in |only
survSNP-0.23.2/survSNP/DESCRIPTION | 13
survSNP-0.23.2/survSNP/MD5 | 35 -
survSNP-0.23.2/survSNP/NAMESPACE | 1
survSNP-0.23.2/survSNP/R/sim.snp.expsurv.power.R | 83 +++-
survSNP-0.23.2/survSNP/R/sim.snp.expsurv.sctest.R | 22 -
survSNP-0.23.2/survSNP/R/surv.exp.gt.model.R | 18
survSNP-0.23.2/survSNP/R/survSNP.power.table.R | 8
survSNP-0.23.2/survSNP/build/vignette.rds |binary
survSNP-0.23.2/survSNP/cleanup | 6
survSNP-0.23.2/survSNP/configure | 369 ++++++++-----------
survSNP-0.23.2/survSNP/configure.ac |only
survSNP-0.23.2/survSNP/inst/CITATION |only
survSNP-0.23.2/survSNP/inst/doc/survSNP-knitr.R | 15
survSNP-0.23.2/survSNP/inst/doc/survSNP-knitr.pdf |binary
survSNP-0.23.2/survSNP/man/sim.snp.expsurv.sctest.Rd | 4
survSNP-0.23.2/survSNP/man/surv.exp.gt.model.Rd | 4
survSNP-0.23.2/survSNP/man/survSNP-package.Rd | 7
survSNP-0.23.2/survSNP/src/Makevars.in | 9
survSNP-0.23.2/survSNP/src/Makevars.win | 21 -
20 files changed, 304 insertions(+), 311 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Diff between EpiModel versions 1.1.2 dated 2014-12-01 and 1.1.3 dated 2015-01-18
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Li Wang [ctb]
Maintainer: Samuel Jenness
DESCRIPTION | 8 -
MD5 | 259 +++++++++++++++++++--------------------
NAMESPACE | 2
NEWS | 27 +++-
R/EpiModel-package.r | 4
R/as.data.frame.R | 22 +--
R/conc.microsim.R | 22 +--
R/control.R | 121 +++++++++---------
R/crosscheck.R | 59 +++-----
R/dcm.R | 6
R/dcm.mods.R | 8 -
R/get.R | 24 +--
R/icm.R | 6
R/icm.mod.init.R | 8 -
R/icm.mod.status.R | 8 -
R/icm.mod.vital.R | 8 -
R/icm.utils.R | 4
R/init.R | 44 +++---
R/merge.R | 15 +-
R/net.mod.init.R | 16 +-
R/net.mod.simnet.R | 18 +-
R/net.mod.status.R | 16 +-
R/net.mod.vital.R | 8 -
R/net.utils.R | 92 +++++++-------
R/netdx.R | 2
R/netest.R | 33 ++---
R/netsim.R | 63 ++-------
R/param.R | 60 ++++-----
R/plot.R | 88 ++++++-------
R/saveout.R | 22 +--
R/shiny.R | 2
R/summary.R | 30 ++--
R/test.R | 6
R/utils.R | 17 +-
R/verbose.R | 22 +--
inst/doc/Intro.R | 4
inst/doc/Intro.Rmd | 22 ++-
inst/doc/Intro.html | 269 ++++++++++-------------------------------
man/EpiModel-package.Rd | 7 -
man/as.data.frame.dcm.Rd | 13 +
man/as.data.frame.icm.Rd | 15 +-
man/bipvals.Rd | 3
man/births.icm.Rd | 7 -
man/births.net.Rd | 7 -
man/brewer_ramp.Rd | 7 -
man/check_bip_degdist.Rd | 3
man/color_tea.Rd | 23 +--
man/comp_plot.Rd | 13 +
man/conc_microsim.Rd | 25 +--
man/control.dcm.Rd | 3
man/control.icm.Rd | 35 ++---
man/control.net.Rd | 102 ++++++++-------
man/copy_toall_attr.Rd | 9 -
man/crosscheck.dcm.Rd | 9 -
man/crosscheck.icm.Rd | 9 -
man/crosscheck.net.Rd | 11 -
man/dcm.Rd | 9 -
man/dcm.mods.Rd | 11 -
man/deaths.icm.Rd | 7 -
man/deaths.net.Rd | 7 -
man/deleteAttr.Rd | 3
man/discord_edgelist.Rd | 11 -
man/dissolution_coefs.Rd | 9 -
man/edgelist_censor.Rd | 5
man/edgelist_meanage.Rd | 7 -
man/edges_correct.Rd | 7 -
man/epiweb.Rd | 5
man/get_args.Rd | 5
man/get_attr_prop.Rd | 9 -
man/get_formula_terms.Rd | 5
man/get_network.Rd | 13 +
man/get_nwparam.Rd | 7 -
man/get_nwstats.Rd | 9 -
man/get_prev.icm.Rd | 7 -
man/get_prev.net.Rd | 7 -
man/get_sims.Rd | 3
man/get_transmat.Rd | 7 -
man/icm.Rd | 9 -
man/idmode.Rd | 7 -
man/infection.icm.Rd | 7 -
man/infection.net.Rd | 7 -
man/init.dcm.Rd | 17 +-
man/init.icm.Rd | 19 +-
man/init.net.Rd | 17 +-
man/init_pids.Rd | 7 -
man/init_status.icm.Rd | 5
man/init_status.net.Rd | 5
man/initialize.icm.Rd | 9 -
man/initialize.net.Rd | 13 +
man/mcat.Rd | 5
man/merge.icm.Rd | 9 -
man/merge.netsim.Rd | 10 +
man/modeids.Rd | 7 -
man/modules.icm.Rd | 3
man/modules.net.Rd | 3
man/netdx.Rd | 3
man/netest.Rd | 27 ++--
man/netsim.Rd | 11 -
man/netsim_parallel.Rd | 5
man/node_active.Rd | 13 +
man/param.dcm.Rd | 35 ++---
man/param.icm.Rd | 35 ++---
man/param.net.Rd | 31 ++--
man/plot.conc_microsim.Rd | 3
man/plot.dcm.Rd | 31 ++--
man/plot.icm.Rd | 45 +++---
man/plot.netdx.Rd | 3
man/plot.netsim.Rd | 3
man/recovery.icm.Rd | 7 -
man/recovery.net.Rd | 7 -
man/resim_nets.Rd | 7 -
man/saveout.dcm.Rd | 13 +
man/saveout.icm.Rd | 9 -
man/saveout.net.Rd | 9 -
man/sim_nets.Rd | 13 +
man/split_bip.Rd | 17 +-
man/ssample.Rd | 7 -
man/summary.dcm.Rd | 13 +
man/summary.icm.Rd | 11 -
man/summary.netest.Rd | 7 -
man/summary.netsim.Rd | 11 -
man/test_icm.Rd | 5
man/test_net.Rd | 5
man/transco.Rd | 9 -
man/update_nwattr.Rd | 13 +
man/verbose.dcm.Rd | 9 -
man/verbose.icm.Rd | 11 -
man/verbose.net.Rd | 11 -
tests/testthat/test-newnet.R | 14 ++
tests/testthat/test-parallel.R |only
vignettes/Intro.Rmd | 22 ++-
131 files changed, 1269 insertions(+), 1264 deletions(-)