Title: Using V-algorithm and Newton-Raphson Method to Obtain
Multiple-objective Optimal Design
Diff between VNM versions 2.0 dated 2014-10-31 and 4.0 dated 2015-02-09
Description: Using V-algorithm and Newton-Raphson method to obtain multiple-objective optimal design for estimating the shape of dose-response, the ED50 (the dose producing an effect midway between the expected responses at the extreme doses) and the MED (the minimum effective dose level) for the 2,3,4-parameter logistic models and for evaluating its efficiencies for the three objectives.
Author: Seung Won Hyun, Weng Kee Wong, and Yarong Yang
Maintainer: Yarong Yang
DESCRIPTION | 14 +++---
MD5 | 34 +++++++++-----
NAMESPACE | 14 +++++-
R/AllClasses.R |only
R/Deff.R | 109 +++++++++++++++++++++++++++++++++-------------
R/MOPT.R | 113 +++++++++++++++++++++++++++++++++++++-----------
R/S.Weight.R | 95 ++++++++++++++++++++++++++++------------
R/ceff1.R | 104 ++++++++++++++++++++++++++++++++------------
R/ceff2.R | 114 ++++++++++++++++++++++++++++++++++++-------------
R/plot-methods.R |only
R/summary-methods.R |only
man/Deff.Rd | 8 +--
man/MOPT.Rd | 10 ++--
man/OPT-class.Rd |only
man/PAR-class.Rd |only
man/S.Weight.Rd | 2
man/SW-class.Rd |only
man/VNM-package.Rd | 12 ++---
man/ceff1.Rd | 11 ++--
man/ceff2.Rd | 8 +--
man/plot-methods.Rd |only
man/summary-methods.Rd |only
22 files changed, 464 insertions(+), 184 deletions(-)
Title: Penalized Semiparametric Bayesian Cox Models with Shrinkage and
Grouping Priors
Diff between psbcGroup versions 1.0 dated 2013-04-05 and 1.1 dated 2015-02-09
Description: The package provides algorithms for fitting penalized semiparametric Bayesian Cox (PSBC) models with shrinkage and grouping priors.
Author: Kyu Ha Lee, Sounak Chakraborty, (Tony) Jianguo Sun
Maintainer: Kyu Ha Lee
DESCRIPTION | 17 ++++++++---------
MD5 | 18 +++++++++---------
NAMESPACE | 5 +++++
R/psbcEN.R | 1 -
R/psbcFL.R | 2 +-
R/psbcGL.R | 1 -
man/psbcEN.Rd | 22 +++++++++++++---------
man/psbcFL.Rd | 21 ++++++++++++---------
man/psbcGL.Rd | 25 +++++++++++++++----------
man/psbcGroup.Rd | 15 ++++++++-------
10 files changed, 71 insertions(+), 56 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Diff between nat versions 1.5.12 dated 2014-08-21 and 1.6.4 dated 2015-02-09
Description: NeuroAnatomy Toolbox (nat) is a reboot of the AnalysisSuite
(see https://github.com/jefferis/nat.as) bundle of R code that we have
been using for a number of years to analyse and visualise 3D biological
image data, especially traced neurons. The nat package is considerably
cleaner, properly documented and provides all of the core functionality of
nat.as / AnalysisSuite. nat can read and write 3D images in NRRD and Amira
formats and read surfaces in Amira's hxsurf format. Traced neurons can be
imported from and written to SWC and Amira LineSet and SkeletonGraph
formats. These data can then be visualised in 3D via rgl, manipulated
including applying calculated registrations, e.g. using the CMTK
registration suite, and analysed. The package also has a simple
representation for neurons that have been subjected to a 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the nat.nblast extension
package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis
nat-1.5.12/nat/man/amiralandmark-io.Rd |only
nat-1.5.12/nat/man/cmtklandmarks.Rd |only
nat-1.5.12/nat/tests/testthat/test-amiralandmarks-io.R |only
nat-1.6.4/nat/DESCRIPTION | 46 -
nat-1.6.4/nat/MD5 | 346 +++++-----
nat-1.6.4/nat/NAMESPACE | 38 -
nat-1.6.4/nat/NEWS | 70 ++
nat-1.6.4/nat/R/amiralandmarks-io.R | 129 +++
nat-1.6.4/nat/R/amiramesh-io.R | 72 +-
nat-1.6.4/nat/R/cmtk-reformat.R | 58 +
nat-1.6.4/nat/R/cmtk.R | 17
nat-1.6.4/nat/R/cmtk_io.R | 91 +-
nat-1.6.4/nat/R/dotprops.R | 14
nat-1.6.4/nat/R/hxsurf.R | 5
nat-1.6.4/nat/R/im3d.R | 99 ++
nat-1.6.4/nat/R/nat-package.R | 4
nat-1.6.4/nat/R/ndigest.R | 12
nat-1.6.4/nat/R/neuron-io-amira.R | 28
nat-1.6.4/nat/R/neuron-io-fiji.R |only
nat-1.6.4/nat/R/neuron-io-neuroml.R |only
nat-1.6.4/nat/R/neuron-io.R | 284 ++++++--
nat-1.6.4/nat/R/neuron-plot.R | 21
nat-1.6.4/nat/R/neuron.R | 228 +++---
nat-1.6.4/nat/R/neuronlist.R | 225 +++++-
nat-1.6.4/nat/R/neuronlist_sets.R |only
nat-1.6.4/nat/R/ngraph.R | 85 +-
nat-1.6.4/nat/R/nrrd-io.R | 20
nat-1.6.4/nat/R/seglist.R | 46 -
nat-1.6.4/nat/R/vaa3draw-io.R | 40 -
nat-1.6.4/nat/R/xform.R | 53 +
nat-1.6.4/nat/R/xformimage.R |only
nat-1.6.4/nat/R/xformpoints.R | 8
nat-1.6.4/nat/R/zzz.R | 39 +
nat-1.6.4/nat/README.md | 5
nat-1.6.4/nat/man/Cell07PNs.Rd | 3
nat-1.6.4/nat/man/affmat2cmtkparams.Rd | 3
nat-1.6.4/nat/man/all.equal.dotprops.Rd | 3
nat-1.6.4/nat/man/all.equal.im3d.Rd | 21
nat-1.6.4/nat/man/all.equal.neuron.Rd | 31
nat-1.6.4/nat/man/amiramesh-io.Rd | 5
nat-1.6.4/nat/man/amiratype.Rd | 5
nat-1.6.4/nat/man/as.im3d.Rd | 36 -
nat-1.6.4/nat/man/as.mesh3d.Rd | 3
nat-1.6.4/nat/man/as.neuronlist.Rd | 5
nat-1.6.4/nat/man/as.neuronlist.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/boundingbox.Rd | 31
nat-1.6.4/nat/man/c.neuronlist.Rd | 3
nat-1.6.4/nat/man/clampmax.Rd | 3
nat-1.6.4/nat/man/cmtk.bindir.Rd | 5
nat-1.6.4/nat/man/cmtk.call.Rd | 5
nat-1.6.4/nat/man/cmtk.dof2mat.Rd | 3
nat-1.6.4/nat/man/cmtk.extract_affine.Rd |only
nat-1.6.4/nat/man/cmtk.mat2dof.Rd | 3
nat-1.6.4/nat/man/cmtk.reformatx.Rd | 42 -
nat-1.6.4/nat/man/cmtk.statistics.Rd | 3
nat-1.6.4/nat/man/cmtk.targetvolume.Rd | 18
nat-1.6.4/nat/man/cmtk.version.Rd | 3
nat-1.6.4/nat/man/cmtkparams2affmat.Rd | 11
nat-1.6.4/nat/man/cmtkreg.Rd | 3
nat-1.6.4/nat/man/cmtkreglist.Rd | 10
nat-1.6.4/nat/man/coord2ind.Rd | 3
nat-1.6.4/nat/man/dotprops-arithmetic.Rd | 3
nat-1.6.4/nat/man/dotprops.Rd | 21
nat-1.6.4/nat/man/fileformats.Rd | 71 +-
nat-1.6.4/nat/man/find.neuron.Rd | 8
nat-1.6.4/nat/man/find.soma.Rd |only
nat-1.6.4/nat/man/flip.Rd | 3
nat-1.6.4/nat/man/graph.nodes.Rd | 3
nat-1.6.4/nat/man/im3d-coords.Rd | 6
nat-1.6.4/nat/man/im3d-io.Rd | 15
nat-1.6.4/nat/man/im3d.Rd | 6
nat-1.6.4/nat/man/image.im3d.Rd | 27
nat-1.6.4/nat/man/imexpand.grid.Rd | 6
nat-1.6.4/nat/man/imscalebar.Rd | 3
nat-1.6.4/nat/man/imslice.Rd | 6
nat-1.6.4/nat/man/ind2coord.Rd | 3
nat-1.6.4/nat/man/intersect.Rd |only
nat-1.6.4/nat/man/is.amiramesh.Rd | 17
nat-1.6.4/nat/man/is.fijitraces.Rd |only
nat-1.6.4/nat/man/is.neuroml.Rd |only
nat-1.6.4/nat/man/is.neuronlist.Rd | 3
nat-1.6.4/nat/man/is.nrrd.Rd | 10
nat-1.6.4/nat/man/is.swc.Rd |only
nat-1.6.4/nat/man/is.vaa3draw.Rd | 11
nat-1.6.4/nat/man/kcs20.Rd | 3
nat-1.6.4/nat/man/materials.Rd | 3
nat-1.6.4/nat/man/mirror.Rd | 3
nat-1.6.4/nat/man/nat-internal.Rd | 3
nat-1.6.4/nat/man/nat-package.Rd | 10
nat-1.6.4/nat/man/ndigest.Rd | 16
nat-1.6.4/nat/man/neuron-arithmetic.Rd | 3
nat-1.6.4/nat/man/neuron.Rd | 13
nat-1.6.4/nat/man/neuronlist-arithmetic.Rd | 3
nat-1.6.4/nat/man/neuronlist-dataframe-methods.Rd | 15
nat-1.6.4/nat/man/neuronlist.Rd | 3
nat-1.6.4/nat/man/neuronlistfh.Rd | 9
nat-1.6.4/nat/man/ngraph.Rd | 81 +-
nat-1.6.4/nat/man/nlapply.Rd | 10
nat-1.6.4/nat/man/nlscan.Rd |only
nat-1.6.4/nat/man/nopen3d.Rd | 3
nat-1.6.4/nat/man/normalise_swc.Rd |only
nat-1.6.4/nat/man/npop3d.Rd | 3
nat-1.6.4/nat/man/nrrd.voxdims.Rd | 3
nat-1.6.4/nat/man/origin.Rd | 6
nat-1.6.4/nat/man/pan3d.Rd | 3
nat-1.6.4/nat/man/plot.neuron.Rd | 3
nat-1.6.4/nat/man/plot.neuronlist.Rd | 18
nat-1.6.4/nat/man/plot3d.boundingbox.Rd | 3
nat-1.6.4/nat/man/plot3d.dotprops.Rd | 3
nat-1.6.4/nat/man/plot3d.hxsurf.Rd | 3
nat-1.6.4/nat/man/plot3d.neuron.Rd | 10
nat-1.6.4/nat/man/plot3d.neuronlist.Rd | 18
nat-1.6.4/nat/man/pointsinside.Rd | 3
nat-1.6.4/nat/man/potential_synapses.Rd | 11
nat-1.6.4/nat/man/projection.Rd | 6
nat-1.6.4/nat/man/prune.Rd | 3
nat-1.6.4/nat/man/read.cmtk.Rd | 7
nat-1.6.4/nat/man/read.cmtkreg.Rd | 10
nat-1.6.4/nat/man/read.hxsurf.Rd | 10
nat-1.6.4/nat/man/read.landmarks.Rd |only
nat-1.6.4/nat/man/read.morphml.Rd |only
nat-1.6.4/nat/man/read.neuron.Rd | 39 +
nat-1.6.4/nat/man/read.neuron.fiji.Rd |only
nat-1.6.4/nat/man/read.neuron.neuroml.Rd |only
nat-1.6.4/nat/man/read.neuron.swc.Rd | 6
nat-1.6.4/nat/man/read.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/read.neurons.Rd | 26
nat-1.6.4/nat/man/read.nrrd.Rd | 7
nat-1.6.4/nat/man/read.vaa3draw.Rd | 3
nat-1.6.4/nat/man/remotesync.Rd | 7
nat-1.6.4/nat/man/resample.Rd | 20
nat-1.6.4/nat/man/rootpoints.Rd | 3
nat-1.6.4/nat/man/scale.dotprops.Rd | 3
nat-1.6.4/nat/man/scale.neuron.Rd | 3
nat-1.6.4/nat/man/seglengths.Rd | 3
nat-1.6.4/nat/man/seglist.Rd | 3
nat-1.6.4/nat/man/seglist2swc.Rd | 39 -
nat-1.6.4/nat/man/segmentgraph.Rd | 3
nat-1.6.4/nat/man/setdiff.Rd |only
nat-1.6.4/nat/man/spine.Rd | 16
nat-1.6.4/nat/man/sub-.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/sub2ind.Rd | 3
nat-1.6.4/nat/man/subset.dotprops.Rd | 3
nat-1.6.4/nat/man/subset.hxsurf.Rd | 3
nat-1.6.4/nat/man/subset.neuronlist.Rd | 3
nat-1.6.4/nat/man/threshold.Rd | 10
nat-1.6.4/nat/man/union.Rd |only
nat-1.6.4/nat/man/unmask.Rd | 12
nat-1.6.4/nat/man/voxdims.Rd | 6
nat-1.6.4/nat/man/write.amiramesh.Rd | 13
nat-1.6.4/nat/man/write.cmtk.Rd | 7
nat-1.6.4/nat/man/write.cmtkreg.Rd | 7
nat-1.6.4/nat/man/write.hxsurf.Rd | 5
nat-1.6.4/nat/man/write.neuron.Rd | 14
nat-1.6.4/nat/man/write.neuronlistfh.Rd | 3
nat-1.6.4/nat/man/write.neurons.Rd | 41 -
nat-1.6.4/nat/man/write.nrrd.Rd | 3
nat-1.6.4/nat/man/xform.Rd | 29
nat-1.6.4/nat/man/xformimage.Rd |only
nat-1.6.4/nat/man/xformpoints.Rd | 3
nat-1.6.4/nat/man/xyzmatrix.Rd | 3
nat-1.6.4/nat/tests/testthat/test-.neuron-io-remote-nocran.R |only
nat-1.6.4/nat/tests/testthat/test-amiramesh-io.R | 23
nat-1.6.4/nat/tests/testthat/test-cmtk-reformat.R | 29
nat-1.6.4/nat/tests/testthat/test-cmtk.R | 1
nat-1.6.4/nat/tests/testthat/test-hxsurf.R | 7
nat-1.6.4/nat/tests/testthat/test-im3d.R | 16
nat-1.6.4/nat/tests/testthat/test-landmarks-io.R |only
nat-1.6.4/nat/tests/testthat/test-ndigest.R | 3
nat-1.6.4/nat/tests/testthat/test-neuroml-io.R |only
nat-1.6.4/nat/tests/testthat/test-neuron-fiji-io.R |only
nat-1.6.4/nat/tests/testthat/test-neuron-io.R | 63 +
nat-1.6.4/nat/tests/testthat/test-neuron.R | 33
nat-1.6.4/nat/tests/testthat/test-neuronlist.R | 34
nat-1.6.4/nat/tests/testthat/test-ngraph.R | 23
nat-1.6.4/nat/tests/testthat/test-nrrd-io.R | 10
nat-1.6.4/nat/tests/testthat/test-seglist.R | 7
nat-1.6.4/nat/tests/testthat/test-xform.R | 22
nat-1.6.4/nat/tests/testthat/test-xformimage.R |only
nat-1.6.4/nat/tests/testthat/testdata/amira/landmarks.am |only
nat-1.6.4/nat/tests/testthat/testdata/landmarks |only
nat-1.6.4/nat/tests/testthat/testdata/neuroml |only
nat-1.6.4/nat/tests/testthat/testdata/neuroml2 |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/MultiplePathsJoinedToMainPath.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/SequentiallyBranchingTrace.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/SinglePath.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/fitted.traces |only
nat-1.6.4/nat/tests/testthat/testdata/neuron/unfitted.swc |only
nat-1.6.4/nat/tests/testthat/testdata/nrrd/FCWB_2um_mask.nrrd |only
nat-1.6.4/nat/tests/testthat/testdata/nrrd/JFRC2-444_mask.nrrd |only
190 files changed, 2452 insertions(+), 1044 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Diff between letsR versions 1.0 dated 2014-05-19 and 2.0 dated 2015-02-09
Description: Includes R functions for handling and analyzing geographic data, mainly
species' geographic distributions (in ESRI shapefile format) and
environmental variables (in raster format), as well as species' information
related to their description (e.g. taxonomy and year of description) and
conservation status (e.g. category of threat, population trend) as provided
by the IUCN's RedList database. The package includes functions to create
presence-absence matrices based on species distributions and user-defined
grid systems, from which several other functions could be applied to
generate, for example, species richness rasters and maps, and geographical
midpoints of species. In addition, it provides a function to create spatial
correlograms of variables, based on the Moran's I index, under the
equiprobable or equidistant criterion to define distance classes.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela
letsR-1.0/letsR/R/Data_PAM.R |only
letsR-1.0/letsR/R/Data_Phyllomedusa.R |only
letsR-1.0/letsR/R/Data_temp.R |only
letsR-1.0/letsR/R/lets.correl.R |only
letsR-1.0/letsR/R/lets_cont.R |only
letsR-1.0/letsR/R/lets_iun_habitats.R |only
letsR-1.0/letsR/man/letsR.Rd |only
letsR-2.0/letsR/DESCRIPTION | 16 -
letsR-2.0/letsR/MD5 | 116 ++++++-----
letsR-2.0/letsR/NAMESPACE | 20 +-
letsR-2.0/letsR/R/Data_iucn.R | 32 +++
letsR-2.0/letsR/R/letsR-package.R | 12 -
letsR-2.0/letsR/R/lets_addpoly.R | 74 ++++---
letsR-2.0/letsR/R/lets_addvar.R | 8
letsR-2.0/letsR/R/lets_classvar.R |only
letsR-2.0/letsR/R/lets_correl.R |only
letsR-2.0/letsR/R/lets_distmat.R |only
letsR-2.0/letsR/R/lets_field.R | 19 +
letsR-2.0/letsR/R/lets_gridirizer.R |only
letsR-2.0/letsR/R/lets_iucn.R | 7
letsR-2.0/letsR/R/lets_iucn_habitats.R |only
letsR-2.0/letsR/R/lets_iucn_historic.R | 7
letsR-2.0/letsR/R/lets_iucncont.R |only
letsR-2.0/letsR/R/lets_maplizer.R | 8
letsR-2.0/letsR/R/lets_midpoint.R | 12 -
letsR-2.0/letsR/R/lets_overlap.R |only
letsR-2.0/letsR/R/lets_pamcrop.R |only
letsR-2.0/letsR/R/lets_presab.R | 188 +++++++++++++------
letsR-2.0/letsR/R/lets_presab_birds.R | 145 ++++++++++----
letsR-2.0/letsR/R/lets_presab_points.R |only
letsR-2.0/letsR/R/lets_rangesize.R |only
letsR-2.0/letsR/R/lets_shpfilter.R | 4
letsR-2.0/letsR/R/lets_summaryze.R |only
letsR-2.0/letsR/R/plot_PresenceAbsence.R | 14 -
letsR-2.0/letsR/R/print_PresenceAbsence.R | 2
letsR-2.0/letsR/R/print_summary_PresenceAbsence.R | 4
letsR-2.0/letsR/R/removecells.R | 2
letsR-2.0/letsR/R/removesp.R | 2
letsR-2.0/letsR/R/summary_PresenceAbsence.R | 2
letsR-2.0/letsR/R/unicas.R | 2
letsR-2.0/letsR/README.md | 41 ++--
letsR-2.0/letsR/data/temp.rda |binary
letsR-2.0/letsR/man/PAM.Rd | 8
letsR-2.0/letsR/man/Phyllomedusa.Rd | 9
letsR-2.0/letsR/man/iucn.Rd | 7
letsR-2.0/letsR/man/lets.addpoly.Rd | 23 +-
letsR-2.0/letsR/man/lets.addvar.Rd | 21 +-
letsR-2.0/letsR/man/lets.classvar.Rd |only
letsR-2.0/letsR/man/lets.correl.Rd | 39 +--
letsR-2.0/letsR/man/lets.distmat.Rd |only
letsR-2.0/letsR/man/lets.field.Rd | 37 +--
letsR-2.0/letsR/man/lets.gridirizer.Rd |only
letsR-2.0/letsR/man/lets.iucn.Rd | 26 +-
letsR-2.0/letsR/man/lets.iucn.ha.Rd | 23 +-
letsR-2.0/letsR/man/lets.iucn.his.Rd | 27 +-
letsR-2.0/letsR/man/lets.iucncont.Rd | 19 +
letsR-2.0/letsR/man/lets.maplizer.Rd | 22 +-
letsR-2.0/letsR/man/lets.midpoint.Rd | 19 -
letsR-2.0/letsR/man/lets.overlap.Rd |only
letsR-2.0/letsR/man/lets.pamcrop.Rd |only
letsR-2.0/letsR/man/lets.presab.Rd | 136 +++++--------
letsR-2.0/letsR/man/lets.presab.birds.Rd | 117 +++--------
letsR-2.0/letsR/man/lets.presab.points.Rd |only
letsR-2.0/letsR/man/lets.rangesize.Rd |only
letsR-2.0/letsR/man/lets.shFilter.Rd | 50 ++---
letsR-2.0/letsR/man/lets.summarizer.Rd |only
letsR-2.0/letsR/man/lets.transf.Rd | 12 -
letsR-2.0/letsR/man/plot.PresenceAbsence.Rd | 17 -
letsR-2.0/letsR/man/print.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/print.summary.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/summary.PresenceAbsence.Rd | 7
letsR-2.0/letsR/man/temp.Rd | 11 -
72 files changed, 758 insertions(+), 623 deletions(-)
Title: K-Sample Rank Tests and their Combinations
Diff between kSamples versions 1.0 dated 2012-08-31 and 1.0.1 dated 2015-02-09
Description: Compares k samples using the Anderson-Darling test,
Kruskal-Wallis type tests with different rank score criteria,
and Steel's multiple comparison test. It computes asymptotic,
simulated or (limited) exact P-values, all valid under
randomization, with or without ties, or conditionally under
random sampling from populations, given the observed tie
pattern. Except for Steel's test it also combines these tests
across several blocks of samples. Also analyzed are 2 x t
contingency tables and their blocked combinations using the
Kruskal-Wallis criterion. Steel's test is inverted to provide
simultaneous confidence bounds for shift parameters. A
plotting function shows that asymptotic approximations for
small sample sizes provide only very limited utility when
comparing tail probabilities with those obtained via simulation
or exact calculations.
Author: Fritz Scholz [aut, cre],
Angie Zhu [aut]
Maintainer: Fritz Scholz
kSamples-1.0.1/kSamples/DESCRIPTION | 18 ++++++++++--------
kSamples-1.0.1/kSamples/MD5 | 9 ++++-----
kSamples-1.0.1/kSamples/NAMESPACE | 6 +++++-
kSamples-1.0.1/kSamples/R/qn.test.R | 2 +-
kSamples-1.0.1/kSamples/man/kSamples-package.Rd | 4 ++--
kSamples-1.0/kSamples/man/print.kSamples.Rd |only
6 files changed, 22 insertions(+), 17 deletions(-)
Title: Meta-Analysis of Diagnostic Test Accuracy when Reference Test is
Imperfect
Diff between HSROC versions 2.1.7 dated 2013-08-22 and 2.1.8 dated 2015-02-09
Description: Implements a model for joint meta-analysis of sensitivity and specificity of the diagnostic test under evaluation, while taking into account the possibly imperfect sensitivity and specificity of the reference test. This hierarchical model accounts for both within and between study variability. Estimation is carried out using a Bayesian approach, implemented via a Gibbs sampler. The model can be applied in situations where more than one reference test is used in the selected studies.
Author: Ian Schiller and Nandini Dendukuri
Maintainer: Ian Schiller
HSROC-2.1.7/HSROC/inst/doc/Tutorial.R |only
HSROC-2.1.8/HSROC/DESCRIPTION | 16 ++++++++--------
HSROC-2.1.8/HSROC/MD5 | 16 ++++++++--------
HSROC-2.1.8/HSROC/NAMESPACE | 2 +-
HSROC-2.1.8/HSROC/NEWS | 9 ++++++++-
HSROC-2.1.8/HSROC/R/HSROC-internal.R | 2 +-
HSROC-2.1.8/HSROC/build |only
HSROC-2.1.8/HSROC/data/In.house.rda |binary
HSROC-2.1.8/HSROC/data/MRI.rda |binary
HSROC-2.1.8/HSROC/inst/doc/Tutorial.pdf |binary
10 files changed, 26 insertions(+), 19 deletions(-)
Title: Redraw Base Graphics Using grid Graphics
Diff between gridGraphics versions 0.1-2 dated 2014-11-26 and 0.1-3 dated 2015-02-09
Description: Functions to convert a page of plots drawn with the
graphics package into identical output drawn with the grid package.
The result looks like the original graphics-based plot, but consists
of grid grobs and viewports that can then be manipulated with
grid functions (e.g., edit grobs and revisit viewports).
Author: Paul Murrell [cre, aut]
Maintainer: Paul Murrell
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/par.R | 3 +++
inst/NEWS.Rd | 8 ++++++++
4 files changed, 18 insertions(+), 7 deletions(-)
Title: The Complex Multivariate Gaussian Distribution
Diff between cmvnorm versions 1.0 dated 2014-09-09 and 1.0-1 dated 2015-02-09
Description: Various utilities for the complex multivariate Gaussian distribution.
Author: Robin K. S. Hankin
Maintainer: Robin K. S. Hankin
DESCRIPTION | 10 -
MD5 | 16 -
build/vignette.rds |binary
inst/doc/complicator.R | 59 ++++--
inst/doc/complicator.Rnw | 374 ++++++++++++++++++++++++++---------------
inst/doc/complicator.pdf |binary
man/corr_complex.Rd | 65 +++++--
vignettes/complex_gaussian.bib | 48 +++++
vignettes/complicator.Rnw | 374 ++++++++++++++++++++++++++---------------
9 files changed, 641 insertions(+), 305 deletions(-)
Title: Semiparametric Bivariate Probit Modelling
Diff between SemiParBIVProbit versions 3.2-13.2 dated 2015-01-15 and 3.3 dated 2015-02-09
More information about SemiParBIVProbit at CRAN
Description: Routine for fitting bivariate models for binary responses with semiparametric predictors (including linear and nonlinear effects) in the presence of correlated error equations, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra
Maintainer: Giampiero Marra
ChangeLog | 6 +
DESCRIPTION | 8 -
MD5 | 82 +++++++++---------
NAMESPACE | 24 ++++-
R/AT.r | 119 +++++++++++++-------------
R/BCDF.r |only
R/BiCDF.r |only
R/LM.bpm.r | 22 ++--
R/S.m.r | 50 ++++-------
R/SemiParBIVProbit.fit.R | 8 -
R/SemiParBIVProbit.fit.post.r | 124 +++++++++++++++++----------
R/SemiParBIVProbit.fit1.R | 14 ++-
R/SemiParBIVProbit.r | 165 +++++++++++++++++++++++++++----------
R/adjCov.r | 10 +-
R/adjCovSD.r | 6 +
R/bprobgHs.r | 65 +++++++++++---
R/bprobgHsPL.r | 11 +-
R/bprobgHsPO.r | 60 ++++++++++---
R/bprobgHsSS.r | 95 ++++++++++++++-------
R/copgHs.r | 65 ++------------
R/est.prev.r | 6 +
R/gt.bpm.R | 2
R/pen.r | 90 ++++++++++++--------
R/penPL.r | 8 -
R/plot.SemiParBIVProbit.r | 11 +-
R/predict.SemiParBIVProbit.r | 14 ++-
R/print.SemiParBIVProbit.r | 47 ++++++----
R/print.summary.SemiParBIVProbit.r | 87 ++++++++++++-------
R/sem.checks.r | 2
R/startSS.r | 6 -
R/summary.SemiParBIVProbit.r | 150 +++++++++++++++++----------------
man/BCDF.Rd |only
man/BiCDF.Rd |only
man/LM.bpm.Rd | 5 -
man/S.m.Rd | 2
man/SemiParBIVProbit-package.Rd | 7 +
man/SemiParBIVProbit.Rd | 59 +++++++++----
man/SemiParBIVProbit.fit1.Rd | 2
man/SemiParBIVProbitObject.Rd | 11 +-
man/bprobgHs.Rd | 2
man/bprobgHsPL.Rd | 4
man/bprobgHsPO.Rd | 2
man/bprobgHsSS.Rd | 4
man/est.prev.Rd | 2
44 files changed, 880 insertions(+), 577 deletions(-)
Permanent link
Title: Optimal k-Means Clustering for One-Dimensional Data
Diff between Ckmeans.1d.dp versions 3.02 dated 2014-03-30 and 3.3.0 dated 2015-02-09
Description: A dynamic programming algorithm for optimal one-dimensional k-means clustering. The algorithm minimizes the sum of squares of within-cluster distances. As an alternative to the standard heuristic k-means algorithm, this algorithm guarantees optimality and repeatability.
Author: Joe Song and Haizhou Wang
Maintainer: Joe Song
DESCRIPTION | 13 +--
MD5 | 16 ++--
NAMESPACE | 3
NEWS |only
R/Ckmeans.1d.dp.R | 25 ++++--
inst/CITATION | 12 +--
man/Ckmeans.1d.dp.Rd | 29 ++++---
man/print.Ckmeans.1d.dp.Rd | 10 +-
src/Ckmeans.1d.dp.cpp | 178 +++++++++++++++------------------------------
tests |only
10 files changed, 124 insertions(+), 162 deletions(-)
Title: SNPs Enrichment Analysis
Diff between snpEnrichment versions 1.6.0 dated 2014-11-04 and 1.6.3 dated 2015-02-09
Description: Implements classes and methods for large scale SNP enrichment analysis (e.g. SNPs associated with genes expression in a GWAS signal).
Author: Mickael Canouil [aut, cre],
Loic Yengo [ctb]
Maintainer: Mickael Canouil
ChangeLog | 15 +++++++++++++++
DESCRIPTION | 16 ++++++++--------
MD5 | 12 ++++++------
R/Global.R | 2 +-
R/chromosome.R | 2 +-
R/enrichment.R | 7 ++++---
data/toyEnrichment.RData |binary
7 files changed, 35 insertions(+), 19 deletions(-)
Title: R Interface to the Pushbullet Messaging Service
Diff between RPushbullet versions 0.1.1 dated 2014-11-04 and 0.2.0 dated 2015-02-09
Description: An R interface to the Pushbullet messaging service which
provides fast and efficient notifications (and file transfer) between
computers, phones and tablets. An account has to be registered at the site
http://www.pushbullet.com site to obtain a (free) API key.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 51 +++++++++++++++++++++
DESCRIPTION | 20 ++++----
MD5 | 19 ++++---
NAMESPACE | 4 +
R/init.R | 99 ++++++++++++++++++++++++++---------------
R/pushes.R | 82 ++++++++++++++++++++++------------
README.md | 43 +++++++++++++++--
inst |only
man/pbGetDevices.Rd | 3 -
man/pbPost.Rd | 14 ++++-
tests/simpleTests.R | 125 ++++++++++++++++++++++++++++++++++++++++++++++++----
11 files changed, 359 insertions(+), 101 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Diff between openair versions 1.1-3 dated 2015-01-27 and 1.1-5 dated 2015-02-09
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw
DESCRIPTION | 14
MD5 | 83 ++--
NAMESPACE | 9
R/TaylorDiagram.R | 4
R/TheilSen.R | 10
R/aqStats.R | 303 ++++++--------
R/calcPercentile.R | 6
R/calendarPlot.R | 22 -
R/checkPrep.R | 27 -
R/conditionalEval.R | 14
R/conditionalQuantile.R | 6
R/cutData.R | 68 +--
R/importAURN.R | 2
R/importAURNCsv.R | 2
R/importAirbase.R | 2
R/importKCL.R | 14
R/importSAQN.R | 2
R/importTraj.R | 2
R/kernelExceed.R | 2
R/linearRelation.R | 20
R/modStats.R | 22 -
R/percentileRose.R | 20
R/polarAnnulus.R | 4
R/polarCluster.R | 2
R/polarFreq.R | 2
R/polarPlot.R | 977 +++++++++++++++++++++++------------------------
R/quickText.R | 9
R/scatterPlot.R | 104 ++---
R/smoothTrend.R | 8
R/summaryPlot.R | 33 +
R/timeAverage.R | 993 ++++++++++++++++++++++++------------------------
R/timePlot.R | 8
R/timeProp.R | 12
R/timeVariation.R | 56 +-
R/trajCluster.R | 4
R/trajLevel.R | 33 -
R/utilities.R | 113 +++--
R/windRose.R | 35 -
README.md | 12
man/aqStats.Rd | 5
man/scatterPlot.Rd | 4
src/Cquantile.cpp |only
src/rolling.cpp | 124 ++---
43 files changed, 1634 insertions(+), 1558 deletions(-)
Title: Generalized Method of Moments and Generalized Empirical
Likelihood
Diff between gmm versions 1.5-0 dated 2013-12-11 and 1.5-1 dated 2015-02-09
Description: It is a complete suite to estimate models based on moment
conditions. It includes the two step Generalized method of
moments (GMM) of Hansen(1982), the iterated GMM and continuous
updated estimator (CUE) of Hansen-Eaton-Yaron(1996) and several
methods that belong to the Generalized Empirical Likelihood
(GEL) family of estimators, as presented by Smith(1997),
Kitamura(1997), Newey-Smith(2004) and Anatolyev(2005).
Author: Pierre Chausse
Maintainer: Pierre Chausse
DESCRIPTION | 12 +++----
MD5 | 24 +++++++--------
NAMESPACE | 2 -
NEWS | 6 +++
R/Methods.gmm.R | 28 +++++++++++++----
R/getModel.R | 5 +--
R/gmm.R | 43 ++++++++++++++++++++-------
R/momentEstim.R | 21 ++++++-------
build/vignette.rds |binary
inst/doc/gmm_with_R.R | 74 ++++++++++++++++++++++++-----------------------
inst/doc/gmm_with_R.pdf |binary
inst/doc/gmm_with_R.rnw | 4 ++
vignettes/gmm_with_R.rnw | 4 ++
13 files changed, 138 insertions(+), 85 deletions(-)
Title: Dirichlet Regression in R
Diff between DirichletReg versions 0.6-1 dated 2014-12-10 and 0.6-2 dated 2015-02-09
Description: Implements Dirichlet regression models in R.
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier
DESCRIPTION | 15
MD5 | 32 -
NEWS | 9
R/plot_DRdata_3d.R | 2
R/sysdata.rda |binary
build/partial.rdb |binary
build/vignette.rds |binary
data/ArcticLake.RData |binary
data/BloodSamples.RData |binary
data/GlacialTills.RData |binary
data/ReadingSkills.RData |binary
data/Rocks.RData |binary
inst/CITATION | 5
inst/NEWS.Rd | 6
inst/NEWS.pdf |binary
inst/doc/DirichletReg-vig.R | 824 +++++++++++++++++++++---------------------
inst/doc/DirichletReg-vig.pdf |binary
17 files changed, 452 insertions(+), 441 deletions(-)
Title: Computation of Bayes Factors for Common Designs
Diff between BayesFactor versions 0.9.10-1 dated 2015-02-04 and 0.9.10-2 dated 2015-02-09
Description: A suite of functions for computing
various Bayes factors for simple designs, including contingency tables,
one- and two-sample designs, one-way designs, general ANOVA designs, and
linear regression.
Author: Richard D. Morey [aut, cre],
Jeffrey N. Rouder [aut],
Tahira Jamil [ctb]
Maintainer: Richard D. Morey
DESCRIPTION | 10 +++++-----
MD5 | 20 ++++++++++----------
NEWS | 5 +++++
R/BayesFactorPCL-package.R | 3 +--
R/aaGenerics.R | 2 +-
build/vignette.rds |binary
inst/doc/compare_lme4.html | 14 +++++++-------
inst/doc/manual.html | 2 +-
inst/doc/priors.html | 2 +-
man/BayesFactor-package.Rd | 5 +----
man/grapes-termin-grapes.Rd | 4 ++--
11 files changed, 34 insertions(+), 33 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Diff between vardpoor versions 0.2.4 dated 2015-01-04 and 0.2.6 dated 2015-02-09
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow, 1953), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y.G.). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre], Martins Liberts [aut], Santa Ivanova [aut]
Maintainer: Juris Breidaks
DESCRIPTION | 12 ++++++------
MD5 | 26 +++++++++++++-------------
R/vardcros.R | 2 +-
R/vardom.R | 6 +++---
R/vardomh.R | 18 ++++++++++++------
R/variance_est.R | 2 +-
R/varpoord.R | 44 +++++++++++++++++++++++++-------------------
inst/CITATION | 4 ++--
inst/NEWS | 11 ++++++++++-
man/vardchanges.Rd | 2 +-
man/vardcros.Rd | 3 ++-
man/vardom.Rd | 2 +-
man/vardomh.Rd | 2 +-
man/vardpoor-package.Rd | 4 ++--
14 files changed, 80 insertions(+), 58 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Diff between excursions versions 2.0.6 dated 2015-02-02 and 2.0.16 dated 2015-02-09
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package.
Author: David Bolin
Maintainer: David Bolin
DESCRIPTION | 12 ++--
MD5 | 41 +++++++-------
NAMESPACE | 7 ++
R/geometry.R | 12 ++--
R/utils.R | 68 ++++++++++++++++++-----
man/continuous.Rd | 12 ++--
man/contourmap.colors.Rd | 4 -
man/contourmap.inla.Rd | 4 -
man/excursions.inla.Rd | 4 -
man/excursions.variances.Rd | 4 -
man/require.nowarnings.Rd |only
man/simconf.inla.Rd | 4 -
man/tricontour.Rd | 2
man/tricontourmap.Rd | 10 +--
src/Makevars | 6 --
src/integration.cpp | 78 +++++++++++++++++++++++++++
tests/testthat/helper-data.R | 6 --
tests/testthat/test.contourmap.R | 6 +-
tests/testthat/test.contourmap.inla.R | 2
tests/testthat/test.excursions.R | 97 ++++++++++++++++------------------
tests/testthat/test.excursions.inla.R | 2
tests/testthat/test.integration.R | 37 ++++++++----
22 files changed, 275 insertions(+), 143 deletions(-)
Title: Transcription Factor Binding Site Identification Tool
Diff between rtfbs versions 0.3.3 dated 2015-01-13 and 0.3.4 dated 2015-02-09
Description: RTFBS identifies and scores possible Transcription Factor
Binding Sites and allows for FDR analysis and pruning. It supports
splitting of sequences based on size or a specified GFF, grouping
by G+C content, and specification of Markov model order. The heavy
lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam
Siepel
Maintainer: Melissa Hubisz
DESCRIPTION | 10 -
MD5 | 20 +--
configure | 31 +++--
configure.ac | 8 -
inst/doc/vignette.pdf |binary
man/rtfbs-package.Rd | 8 -
src/Makevars.in | 108 +++++++++----------
src/Makevars.win | 108 +++++++++----------
src/fit_column.c | 14 ++
src/fit_feature.c | 4
src/maf.c | 274 +++++++++++++++++++++++++-------------------------
11 files changed, 302 insertions(+), 283 deletions(-)
Title: Local Average Response Functions for Instrumental Variable
Estimation of Treatment Effects
Diff between LARF versions 1.2 dated 2014-09-28 and 1.3 dated 2015-02-09
Description: Provides instrumental variable estimation of treatment effects when both the endogenous treatment and its instrument are binary. Applicable to both binary and continuous outcomes.
Author: Weihua An and Xuefu Wang, Indiana University Bloomington
Maintainer: Weihua An
DESCRIPTION | 8 +--
MD5 | 12 +++-
NAMESPACE | 7 ++
R/larf.R | 120 ++++++++++++++++++++++++++-----------------------
R/npse.R |only
man/Generate.Powers.Rd |only
man/cvlm.Rd |only
man/larf.Rd | 4 -
man/npse.Rd |only
9 files changed, 86 insertions(+), 65 deletions(-)