Title: Automatic Generation of Exams in R
Diff between exams versions 1.9-4 dated 2013-03-15 and 1.9-5 dated 2013-06-04
Description: Sweave-based automatic generation of exams including
multiple-choice questions and arithmetic problems. Exams can be
produced in various formats, including PDF, HTML, Moodle XML,
QTI 1.2 (for OLAT).
Author: Achim Zeileis [aut, cre], Bettina Gruen [aut], Friedrich Leisch
[aut], Nikolaus Umlauf [aut]
Maintainer: Achim Zeileis
DESCRIPTION | 8
MD5 | 81 +++---
NAMESPACE | 3
NEWS | 43 +++
R/exams.R | 16 +
R/exams2html.R | 27 +-
R/exams2lops.R | 4
R/exams2moodle.R | 150 ++++++++---
R/exams2pdf.R | 41 ++-
R/exams2qti12.R | 175 +++++++++++--
R/exams_eval.R |only
R/exams_skeleton.R |only
R/read_exercise.R | 10
R/read_metainfo.R | 21 +
R/search_files.R |only
R/transformers.R | 1
R/xexams.R | 7
inst/doc/exams.R |only
inst/doc/exams.Rnw | 47 ++-
inst/doc/exams.pdf |binary
inst/doc/exams2.R |only
inst/doc/exams2.Rnw | 548 ++++++++++++++++++++++++++++++-------------
inst/doc/exams2.pdf |binary
inst/exercises/boxhist.Rnw | 14 -
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inst/exercises/currency1.Rnw |only
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inst/exercises/function.Rnw |only
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inst/tex/oexam.tex |only
inst/tex/osolution.tex |only
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inst/tex/solution.tex | 18 -
inst/xml/plain.html | 6
inst/xml/plain8.html |only
inst/xml/plain9.html |only
inst/xml/qti12.xml | 24 -
man/exams.Rd | 2
man/exams2html.Rd | 19 +
man/exams2lops.Rd | 3
man/exams2moodle.Rd | 17 +
man/exams2pdf.Rd | 3
man/exams2qti12.Rd | 38 +-
man/exams_eval.Rd |only
man/exams_skeleton.Rd |only
tests |only
vignettes/exams.Rnw | 47 ++-
vignettes/exams.bib | 112 +++++---
vignettes/exams2.Rnw | 548 ++++++++++++++++++++++++++++++-------------
51 files changed, 1457 insertions(+), 594 deletions(-)
Title: An R client for interacting with the White House's "We The
People" petition API.
Diff between wethepeople versions 0.4 dated 2013-05-01 and 0.5 dated 2013-06-04
Description: Implements an R client for the We The People petitions
API. The client supports loading petitions, signatures, and
users. Additionally, the package includes petition and
signature data samples. There are also several functions for
analyzing and visualizing the data. Term frequency calculations
and word clouds are supported using the tm and wordcloud
package, respectively. Petition and issue summary plots are
also implemented using the ggplot2 package. For additional
information about the We The People project, see
https://petitions.whitehouse.gov. Note that the API limits
requests to 10/second. For bulk data loading, please use the
data dump provided by the White House:
https://petitions.whitehouse.gov/developers
Author: Yoni Ben-Meshulam
Maintainer: Yoni Ben-Meshulam
wethepeople-0.4/wethepeople/R/WeThePeopleClient.r |only
wethepeople-0.4/wethepeople/man/WeThePeopleClient.Rd |only
wethepeople-0.5/wethepeople/DESCRIPTION | 20 +++--
wethepeople-0.5/wethepeople/MD5 | 34 +++++-----
wethepeople-0.5/wethepeople/NAMESPACE | 3
wethepeople-0.5/wethepeople/NEWS | 6 +
wethepeople-0.5/wethepeople/R/WeThePeopleAPIClient.r |only
wethepeople-0.5/wethepeople/R/WeThePeopleMySQLClient.r |only
wethepeople-0.5/wethepeople/R/petition_term_document_matrix.r | 1
wethepeople-0.5/wethepeople/R/plot_issues_over_time.r | 4 -
wethepeople-0.5/wethepeople/R/plot_issues_pending_response.r | 4 -
wethepeople-0.5/wethepeople/R/plot_signatures_by_time_of_day.r | 2
wethepeople-0.5/wethepeople/R/plot_status_by_creation.r | 4 -
wethepeople-0.5/wethepeople/R/wethepeople-package.r | 15 ++--
wethepeople-0.5/wethepeople/README.md | 4 -
wethepeople-0.5/wethepeople/data/petitions.RData |binary
wethepeople-0.5/wethepeople/man/WeThePeopleAPIClient.Rd |only
wethepeople-0.5/wethepeople/man/WeThePeopleMySQLClient.Rd |only
wethepeople-0.5/wethepeople/man/petition_term_document_matrix.Rd | 1
wethepeople-0.5/wethepeople/man/plot_signatures_by_time_of_day.Rd | 4 -
wethepeople-0.5/wethepeople/man/wethepeople.Rd | 12 ++-
21 files changed, 69 insertions(+), 45 deletions(-)
Title: Differentially private regularized logistic regression
Diff between PrivateLR versions 1.0-21 dated 2012-03-23 and 1.1-69 dated 2013-06-04
Description: Differentially private regularized logistic regression
Author: Staal A. Vinterbo
Maintainer: Staal A. Vinterbo
DESCRIPTION | 9 -
MD5 | 8
NAMESPACE | 4
R/dplr.r | 514 +++++++++++++++++++++++++++++++++++++++++++++---------------
man/dplr.Rd | 121 +++++++++++---
5 files changed, 497 insertions(+), 159 deletions(-)
Title: netClass: An R Package for Network-Based Biomarker Discovery
Diff between netClass versions 1.0 dated 2013-05-30 and 1.1 dated 2013-06-04
Description: netClass is an R package for network-based feature (gene)
selection for biomarkers discovery via integrating biological
information. This package adapts the following 5 algorithms
for classifying and predicting gene expression data using prior
knowledge: 1) average gene expression of pathway (aep); 2)
pathway activities classification (PAC); 3) Hub network
Classification (hubc); 4) filter via top ranked genes (FrSVM);
5) smoothed t-statistic (stSVM).
Author: Yupeng Cun
Maintainer: Yupeng Cun
DESCRIPTION | 30 +++++++++++++++---------------
MD5 | 14 +++++++-------
R/FrSVM.R | 11 ++++-------
R/averageExpressionPathwaySVM.R | 11 ++++-------
R/hubNetworkAnalysisCV.R | 12 +++++-------
R/pacCV.R | 17 ++++++-----------
R/stSVM.R | 12 ++++--------
man/netClass-package.Rd | 2 +-
8 files changed, 46 insertions(+), 63 deletions(-)
Title: Estimation and simulation of CARMA(p,q)
Diff between ctarma versions 0.1.4 dated 2013-02-07 and 0.1.5 dated 2013-06-04
Description: Estimation and simulation of CARMA(p,q),
continuous-time-autoregressive-moving-average models
Author: Helgi Tomasson
Maintainer: Helgi Tomasson
DESCRIPTION | 9 ++++----
MD5 | 14 ++++++-------
NEWS | 8 ++++++-
man/carma.covm.rd | 2 -
man/carma.var.lspectrum.rd | 14 +++++++++----
src/blas.f | 30 ++++++++++++++---------------
src/fftest.f | 46 ++++++++++++++++++++++-----------------------
src/zexpm.f | 32 +++++++++++++++----------------
8 files changed, 84 insertions(+), 71 deletions(-)
Title: adegenet: an R package for the exploratory analysis of genetic
and genomic data.
Diff between adegenet versions 1.3-8 dated 2013-05-15 and 1.3-9 dated 2013-06-04
Description: Classes and functions for genetic data analysis within the
multivariate framework.
Author: Thibaut Jombart, Ismail Ahmed, Federico Calboli, Anne Cori,
Tobias Erik Reiners, Peter Solymos
Maintainer: Thibaut Jombart
adegenet-1.3-8/adegenet/TODO |only
adegenet-1.3-9/adegenet/DESCRIPTION | 15 +-
adegenet-1.3-9/adegenet/MD5 | 112 ++++++++--------
adegenet-1.3-9/adegenet/NAMESPACE | 24 +--
adegenet-1.3-9/adegenet/R/SNPbin.R | 12 -
adegenet-1.3-9/adegenet/R/auxil.R | 24 ++-
adegenet-1.3-9/adegenet/R/dapc.R | 107 ++++++++++++---
adegenet-1.3-9/adegenet/R/find.clust.R | 22 +--
adegenet-1.3-9/adegenet/R/gengraph.R | 12 -
adegenet-1.3-9/adegenet/R/glFunctions.R | 34 ++--
adegenet-1.3-9/adegenet/R/glHandle.R | 10 -
adegenet-1.3-9/adegenet/R/glSim.R | 2
adegenet-1.3-9/adegenet/R/gstat.randtest.R | 1
adegenet-1.3-9/adegenet/R/haploGen.R | 8 -
adegenet-1.3-9/adegenet/R/import.R | 33 ++--
adegenet-1.3-9/adegenet/R/monmonier.R | 2
adegenet-1.3-9/adegenet/R/mutations.R | 2
adegenet-1.3-9/adegenet/R/seqTrack.R | 2
adegenet-1.3-9/adegenet/R/sequences.R | 1
adegenet-1.3-9/adegenet/R/setAs.R | 4
adegenet-1.3-9/adegenet/R/spca.R | 6
adegenet-1.3-9/adegenet/R/spca.rtests.R | 4
adegenet-1.3-9/adegenet/R/xvalDapc.R |only
adegenet-1.3-9/adegenet/data/H3N2.RData |binary
adegenet-1.3-9/adegenet/data/dapcIllus.RData |binary
adegenet-1.3-9/adegenet/data/datalist | 2
adegenet-1.3-9/adegenet/data/eHGDP.RData |binary
adegenet-1.3-9/adegenet/data/microbov.RData |binary
adegenet-1.3-9/adegenet/data/nancycats.RData |binary
adegenet-1.3-9/adegenet/data/rupica.RData |binary
adegenet-1.3-9/adegenet/data/sim2pop.RData |binary
adegenet-1.3-9/adegenet/data/spcaIllus.RData |binary
adegenet-1.3-9/adegenet/inst/doc/adegenet-genomics.R | 34 ++--
adegenet-1.3-9/adegenet/inst/doc/adegenet-genomics.Rnw | 38 ++---
adegenet-1.3-9/adegenet/inst/doc/adegenet-genomics.pdf |binary
adegenet-1.3-9/adegenet/inst/doc/adegenet-spca.R | 92 ++++++-------
adegenet-1.3-9/adegenet/inst/doc/adegenet-spca.Rnw | 2
adegenet-1.3-9/adegenet/inst/doc/adegenet-spca.pdf |binary
adegenet-1.3-9/adegenet/man/adegenet.package.Rd | 7 -
adegenet-1.3-9/adegenet/man/auxil.Rd | 26 ++-
adegenet-1.3-9/adegenet/man/dapc.Rd | 32 +---
adegenet-1.3-9/adegenet/man/dapcGraphics.Rd | 4
adegenet-1.3-9/adegenet/man/dapcIllus.Rd | 2
adegenet-1.3-9/adegenet/man/fasta2genlight.Rd | 17 +-
adegenet-1.3-9/adegenet/man/glAux.Rd | 8 -
adegenet-1.3-9/adegenet/man/glPca.Rd | 24 +--
adegenet-1.3-9/adegenet/man/monmonier.Rd | 2
adegenet-1.3-9/adegenet/man/nancycats.Rd | 3
adegenet-1.3-9/adegenet/man/read.PLINK.Rd | 21 ---
adegenet-1.3-9/adegenet/man/read.snp.Rd | 22 ---
adegenet-1.3-9/adegenet/man/seploc.Rd | 8 -
adegenet-1.3-9/adegenet/man/xvalDapc.Rd |only
adegenet-1.3-9/adegenet/vignettes/adegenet-genomics.Rnw | 38 ++---
adegenet-1.3-9/adegenet/vignettes/adegenet-spca.Rnw | 2
adegenet-1.3-9/adegenet/vignettes/base-045.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-068.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-070.pdf |only
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adegenet-1.3-9/adegenet/vignettes/base-088.pdf |only
adegenet-1.3-9/adegenet/vignettes/base-104.pdf |only
63 files changed, 434 insertions(+), 387 deletions(-)
Title: The R-to-MOSEK Optimization Interface
Diff between Rmosek versions 1.2.4 dated 2012-09-04 and 1.2.5 dated 2013-06-04
Description: An interface to the MOSEK optimization library designed to
solve large-scale mathematical optimization problems. Supports
linear, quadratic and second order cone optimization
with/without integer variables, in addition to the more general
separable convex problems. Trial and free academic licenses
available at http://www.mosek.com.
Author: Henrik Alsing Friberg
Maintainer: Henrik Alsing Friberg
DESCRIPTION | 10 +++++++---
MD5 | 18 +++++++++---------
NEWS | 9 +++++++++
configure | 2 +-
configure.win | 6 +++---
inst/doc/userguide.pdf |binary
man/mosek_qptoprob.Rd | 11 +++++++++--
src/Rmosek.cc | 1 +
src/compatibility/pkgMatrixVersion.h | 2 +-
src/rmsk_obj_sexp.h | 2 +-
10 files changed, 41 insertions(+), 20 deletions(-)
Title: Varying stimulus coefficient fMRI models in R
Diff between RfmriVC versions 1.0 dated 2012-04-26 and 1.0.4 dated 2013-06-04
Description: A varying coefficient on the stimulus effect is introduced
into the voxelwise fMRI regression model. By this the effects
of the canonical hemodynamic response function are allowed to
vary with another variable, like for example time or a
vigilance parameter.
Author: Ludwig Bothmann, Stefanie Kalus
Maintainer: Stefanie Kalus
RfmriVC-1.0.4/RfmriVC/DESCRIPTION | 9 -
RfmriVC-1.0.4/RfmriVC/MD5 | 28 ++--
RfmriVC-1.0.4/RfmriVC/R/Fct_designmatrix.R | 2
RfmriVC-1.0.4/RfmriVC/R/RfmriVCConfig.R | 106 ++++++++++++++----
RfmriVC-1.0.4/RfmriVC/R/RfmriVCResults.R | 127 +++++++++++++++++++++-
RfmriVC-1.0.4/RfmriVC/R/calc.ImagePars.R |only
RfmriVC-1.0.4/RfmriVC/R/calcDeviceHeight.R |only
RfmriVC-1.0.4/RfmriVC/R/plotNifti.R |only
RfmriVC-1.0.4/RfmriVC/man/ConfigVC-class.Rd | 5
RfmriVC-1.0.4/RfmriVC/man/ConfigVC-setConfigVC.Rd | 7 -
RfmriVC-1.0.4/RfmriVC/man/ResultsVC-class.Rd | 8 +
RfmriVC-1.0.4/RfmriVC/man/ResultsVC-hrfHat.Rd | 3
RfmriVC-1.0.4/RfmriVC/man/ResultsVC-setters.Rd | 4
RfmriVC-1.0.4/RfmriVC/man/RfmriVC-internal.Rd | 2
RfmriVC-1.0.4/RfmriVC/man/RfmriVC-package.Rd | 9 +
RfmriVC-1.0.4/RfmriVC/man/RfmriVC-saveload.rd |only
RfmriVC-1.0.4/RfmriVC/man/calcDeviceHeight.Rd |only
RfmriVC-1.0.4/RfmriVC/man/plotNifti.Rd |only
RfmriVC-1.0/RfmriVC/.project |only
RfmriVC-1.0/RfmriVC/.settings |only
20 files changed, 260 insertions(+), 50 deletions(-)
Title: Time series costationarity determination
Diff between costat versions 2.1 dated 2012-11-27 and 2.2 dated 2013-06-04
Description: Contains functions that can determine whether a time
series is second-order stationary or not (and hence evidence
for locally stationarity). Given two non-stationary series
(i.e. locally stationary series) this package can then
discover time-varying linear combinations that are second-order
stationary.
Author: Guy Nason, Alessandro Cardinali
Maintainer: Guy Nason
costat-2.1/costat/NEWS |only
costat-2.2/costat/DESCRIPTION | 11 ++++++-----
costat-2.2/costat/MD5 | 4 ++--
costat-2.2/costat/inst |only
4 files changed, 8 insertions(+), 7 deletions(-)
Title: Generalized Diffusion Magnetic Resonance Imaging
Diff between gdimap versions 0.0-3 dated 2013-03-20 and 0.1-1 dated 2013-06-04
Description: Diffusion anisotropy has been used to characterize white
matter neuronal pathways in the human brain, and infer global
connectivity in the central nervous system. The package
implements algorithms to estimate and visualize the orientation
of neuronal pathways in model-free methods (q-space imaging
methods). For estimating fibre orientations two methods have
been implemented. One method implements fibre orientation
detection through local maxima extraction. A second more robust
method is based on directional statistical clustering of ODF
voxel data. Fibre orientations in multiple fibre voxels are
estimated using a mixture of von Mises-Fisher (vMF)
distributions. This statistical estimation procedure is used to
resolve crossing fibre configurations. Reconstruction of
orientation distribution function (ODF) profiles may be
performed using the standard generalized q-sampling imaging
(GQI) approach, Garyfallidis' GQI (GQI2) approach, or Aganj's
variant of the Q-ball imaging (CSA-QBI) approach. Procedures
for the visualization of RGB-maps, line-maps and glyph-maps of
real diffusion magnetic resonance imaging (dMRI) data-sets are
included in the package.
Author: Adelino Ferreira da Silva
Maintainer: Adelino Ferreira da Silva
gdimap-0.0-3/gdimap/inst/extdata/data_V1_gqi.nii.gz |only
gdimap-0.0-3/gdimap/inst/extdata/data_V2_gqi.nii.gz |only
gdimap-0.0-3/gdimap/inst/extdata/data_brain.nii.gz |only
gdimap-0.0-3/gdimap/inst/extdata/data_gfa_gqi.nii.gz |only
gdimap-0.0-3/gdimap/inst/extdata/dsi203_bmax4000.txt |only
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gdimap-0.0-3/gdimap/man/data_V2_gqi.Rd |only
gdimap-0.0-3/gdimap/man/data_brain.Rd |only
gdimap-0.0-3/gdimap/man/data_gfa_gqi.Rd |only
gdimap-0.0-3/gdimap/man/dsi203_bmax4000.Rd |only
gdimap-0.1-1/gdimap/DESCRIPTION | 38 +--
gdimap-0.1-1/gdimap/MD5 | 91 ++++----
gdimap-0.1-1/gdimap/NAMESPACE | 2
gdimap-0.1-1/gdimap/NEWS | 19 +
gdimap-0.1-1/gdimap/R/gdiutils.R | 22 +-
gdimap-0.1-1/gdimap/R/gqi.odfpeaklines.R | 31 +-
gdimap-0.1-1/gdimap/R/gqi.odfpeaks.R | 30 +-
gdimap-0.1-1/gdimap/R/gqi.odfvmf.R | 34 ++-
gdimap-0.1-1/gdimap/R/gqi.odfvmflines.R | 31 +-
gdimap-0.1-1/gdimap/R/gqi.odfvxgrid.R | 30 +-
gdimap-0.1-1/gdimap/R/readutils.R | 89 ++++++++
gdimap-0.1-1/gdimap/R/rgbvolmap.R | 29 +-
gdimap-0.1-1/gdimap/R/simul.fandtasia.R | 20 +
gdimap-0.1-1/gdimap/R/simul.simplefield.R | 28 +-
gdimap-0.1-1/gdimap/R/simulglyph.vmf.R | 70 +++++-
gdimap-0.1-1/gdimap/R/sph.odfpeaklines.R |only
gdimap-0.1-1/gdimap/R/sph.odfpeaks.R |only
gdimap-0.1-1/gdimap/R/sph.odfvmf.R |only
gdimap-0.1-1/gdimap/R/sph.odfvmflines.R |only
gdimap-0.1-1/gdimap/R/sph.odfvxgrid.R |only
gdimap-0.1-1/gdimap/R/sphutils.R |only
gdimap-0.1-1/gdimap/R/synthfiberss2z.R | 18 +
gdimap-0.1-1/gdimap/inst/extdata/btable.txt |only
gdimap-0.1-1/gdimap/inst/extdata/data.bvec | 206 -------------------
gdimap-0.1-1/gdimap/inst/extdata/data_V1.nii.gz |only
gdimap-0.1-1/gdimap/inst/extdata/data_V2.nii.gz |only
gdimap-0.1-1/gdimap/inst/extdata/data_gfa.nii.gz |only
gdimap-0.1-1/gdimap/man/btable.Rd |only
gdimap-0.1-1/gdimap/man/data.Rd | 9
gdimap-0.1-1/gdimap/man/data.bval.Rd | 6
gdimap-0.1-1/gdimap/man/data.bvec.Rd | 10
gdimap-0.1-1/gdimap/man/data_V1.Rd |only
gdimap-0.1-1/gdimap/man/data_V2.Rd |only
gdimap-0.1-1/gdimap/man/data_brain_mask.Rd | 9
gdimap-0.1-1/gdimap/man/data_gfa.Rd |only
gdimap-0.1-1/gdimap/man/gdimap-package.Rd | 60 +++++
gdimap-0.1-1/gdimap/man/gqi.odfpeaklines.Rd | 61 +----
gdimap-0.1-1/gdimap/man/gqi.odfpeaks.Rd | 46 +---
gdimap-0.1-1/gdimap/man/gqi.odfvmf.Rd | 51 +---
gdimap-0.1-1/gdimap/man/gqi.odfvmflines.Rd | 54 +---
gdimap-0.1-1/gdimap/man/gqi.odfvxgrid.Rd | 11 -
gdimap-0.1-1/gdimap/man/rgbvolmap.Rd | 2
gdimap-0.1-1/gdimap/man/simul.fandtasia.Rd | 5
gdimap-0.1-1/gdimap/man/simul.simplefield.Rd | 13 -
gdimap-0.1-1/gdimap/man/simulglyph.vmf.Rd | 75 ++++--
gdimap-0.1-1/gdimap/man/sph.odfpeaklines.Rd |only
gdimap-0.1-1/gdimap/man/sph.odfpeaks.Rd |only
gdimap-0.1-1/gdimap/man/sph.odfvmf.Rd |only
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gdimap-0.1-1/gdimap/man/sph.odfvxgrid.Rd |only
gdimap-0.1-1/gdimap/man/synthfiberss2z.Rd | 11 -
61 files changed, 639 insertions(+), 572 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-19 1.1
2011-11-25 1.0
Title: Statistical methods to model and adjust for bias in
meta-analysis
Diff between copas versions 0.6-5 dated 2012-03-20 and 0.7-0 dated 2013-06-04
Description: Copas selection model.
Author: James Carpenter
Maintainer: Guido Schwarzer
COPYRIGHT | 2 +-
DESCRIPTION | 9 +++++----
MD5 | 22 ++++++++++++----------
NAMESPACE | 3 +++
NEWS | 28 +++++++++++++++++++++++++++-
R/copas-interal.R |only
R/copas.R | 9 +++++++++
R/crtitle.R |only
R/print.copas.R | 11 ++++++++---
R/print.summary.copas.R | 11 +++++++----
R/summary.copas.R | 6 ++++++
man/copas.Rd | 4 ++++
man/print.copas.Rd | 14 ++++++++++----
13 files changed, 92 insertions(+), 27 deletions(-)
Title: EasyABC: performing efficient approximate Bayesian computation
sampling schemes
Diff between EasyABC versions 1.2 dated 2013-02-27 and 1.2.2 dated 2013-06-04
Description: The package EasyABC enables to launch a series of
simulations of a computer code from the R platform, and to
retrieve the simulation outputs in an appropriate format for
post-processing treatments. Four sequential sampling schemes
and three coupled-to-MCMC schemes are implemented.
Author: Franck Jabot, Thierry Faure, Nicolas Dumoullin
Maintainer: Nicolas Dumoulin
CHANGELOG | 14 +++++++++++
DESCRIPTION | 12 ++++-----
MD5 | 25 ++++++++++----------
R/binary_model.R | 3 +-
R/binary_model_cluster.R | 3 +-
inst/doc/EasyABC.R |only
inst/doc/EasyABC.pdf |binary
man/ABC_mcmc.Rd | 41 ++++++++++++++++++++++-----------
man/ABC_rejection.Rd | 54 +++++++++++++++++++++++++++++---------------
man/ABC_sequential.Rd | 36 +++++++++++++++++++----------
man/EasyABC-package.Rd | 4 +--
man/binary_model.Rd | 3 +-
man/binary_model_cluster.Rd | 9 ++++---
src/trait_model_rc.cpp | 2 -
14 files changed, 136 insertions(+), 70 deletions(-)
Title: Efficient meta analysis for the SKAT test
Diff between skatMeta versions 1.3.1 dated 2013-04-01 and 1.4.3 dated 2013-06-04
Description: Computes necessary information to meta analyze SKAT
statistics in each individual cohort, and then performs the
meta analysis.
Author: Arend Voorman, Jennifer Brody, Thomas Lumley
Maintainer: Arend Voorman
DESCRIPTION | 10 -
MD5 | 44 +++++---
NAMESPACE | 2
R/burdenMeta.R | 211 ++++++++++++++++++++---------------------
R/cohortAdjust.R |only
R/pchisqsum2.R |only
R/singlesnpMeta.R | 215 +++++++++++++++++++++---------------------
R/skatCohort.R | 230 +++++++++++++++++++++++----------------------
R/skatCoxCohort.R | 220 +++++++++++++++++++++++--------------------
R/skatFamCohort.R | 257 ++++++++++++++++++++++++++-------------------------
R/skatMeta.R | 227 ++++++++++++++++++++++-----------------------
R/skatOMeta.R |only
R/sparseBlockInv.R | 24 ++--
data/SNPInfo.rda |binary
data/skatExample.rda |binary
inst |only
man/SNPInfo.Rd | 3
man/burdenMeta.Rd | 13 +-
man/singlesnpMeta.Rd | 21 ++--
man/skatCohort.Rd | 20 ++-
man/skatCohortAdj.Rd |only
man/skatExample.Rd | 7 -
man/skatMeta.Rd | 22 ++--
man/skatOMeta.Rd |only
vignettes |only
25 files changed, 794 insertions(+), 732 deletions(-)
Title: R/GNU Linear Programming Kit Interface
Diff between Rglpk versions 0.3-10 dated 2012-09-12 and 0.4-1 dated 2013-06-04
Description: R interface to the GNU Linear Programming Kit (GLPK
version 4.50 is shipped with the source package). GLPK is open
source software for solving large-scale linear programming
(LP), mixed integer linear programming (MILP) and other related
problems.
Author: Stefan Theussl [aut, cre], Kurt Hornik [aut], Christian Buchta
[ctb]
Maintainer: Stefan Theussl
Rglpk-0.3-10/Rglpk/src/GLPK/glpfhv.c |only
Rglpk-0.3-10/Rglpk/src/GLPK/glpfhv.h |only
Rglpk-0.4-1/Rglpk/DESCRIPTION | 20
Rglpk-0.4-1/Rglpk/MD5 | 279 ++--
Rglpk-0.4-1/Rglpk/inst/CHANGELOG | 5
Rglpk-0.4-1/Rglpk/man/Rglpk_solve.Rd | 2
Rglpk-0.4-1/Rglpk/src/GLPK/Makefile | 211 +--
Rglpk-0.4-1/Rglpk/src/GLPK/Makefile.am | 15
Rglpk-0.4-1/Rglpk/src/GLPK/Makefile.in | 1493 ++++++++++++++++++++------
Rglpk-0.4-1/Rglpk/src/GLPK/Makefile.win | 211 +--
Rglpk-0.4-1/Rglpk/src/GLPK/amd/amd_internal.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/bflib |only
Rglpk-0.4-1/Rglpk/src/GLPK/colamd/colamd.c | 24
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi.h | 16
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi05.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi07.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi08.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi09.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi10.c | 30
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi11.c | 27
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi12.c | 24
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi13.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi14.c | 11
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi15.c | 7
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi16.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi17.c | 224 +++
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi18.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi19.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi20.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpapi21.c | 33
Rglpk-0.4-1/Rglpk/src/GLPK/glpavl.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpavl.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpbfd.c | 92 +
Rglpk-0.4-1/Rglpk/src/GLPK/glpbfd.h | 10
Rglpk-0.4-1/Rglpk/src/GLPK/glpbfx.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpbfx.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpcpx.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpdmp.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpdmp.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpdmx.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv.h | 53
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv01.c | 12
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv01.c.orig | 12
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv05.c | 206 ++-
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv07.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpenv08.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpgmp.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpgmp.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glphbm.c | 63 -
Rglpk-0.4-1/Rglpk/src/GLPK/glphbm.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpini01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpini02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios.h | 9
Rglpk-0.4-1/Rglpk/src/GLPK/glpios01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios03.c | 15
Rglpk-0.4-1/Rglpk/src/GLPK/glpios04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios05.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios07.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios08.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios09.c | 8
Rglpk-0.4-1/Rglpk/src/GLPK/glpios10.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios11.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpios12.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpipm.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpipm.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpk.h | 772 -------------
Rglpk-0.4-1/Rglpk/src/GLPK/glplib.h | 9
Rglpk-0.4-1/Rglpk/src/GLPK/glplib01.c | 48
Rglpk-0.4-1/Rglpk/src/GLPK/glplib02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplib03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplpf.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplpf.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplpx.h |only
Rglpk-0.4-1/Rglpk/src/GLPK/glplpx01.c | 18
Rglpk-0.4-1/Rglpk/src/GLPK/glplpx02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplpx03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpluf.c | 40
Rglpk-0.4-1/Rglpk/src/GLPK/glpluf.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplux.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glplux.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmat.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmat.h | 70 -
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl.h | 14
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl05.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmpl06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpmps.c | 9
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet03.c | 243 ++++
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet07.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnet09.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp03.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp04.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp05.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpnpp06.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpqmd.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glprgr.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glprgr.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glprlx.c |only
Rglpk-0.4-1/Rglpk/src/GLPK/glprlx.h |only
Rglpk-0.4-1/Rglpk/src/GLPK/glprng.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glprng02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpscf.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpscf.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpscl.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpsdf.c | 12
Rglpk-0.4-1/Rglpk/src/GLPK/glpsdf.h |only
Rglpk-0.4-1/Rglpk/src/GLPK/glpspm.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpspm.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpspx.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpspx01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpspx02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpsql.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpsql.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpssx.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpssx01.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpssx02.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glpstd.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glptsp.c | 6
Rglpk-0.4-1/Rglpk/src/GLPK/glptsp.h | 6
Rglpk-0.4-1/Rglpk/src/GLPK/zlib/gzwrite.c | 2
139 files changed, 2873 insertions(+), 2040 deletions(-)
Title: HIBAG -- HLA Genotype Imputation with Attribute Bagging
Diff between HIBAG versions 1.0.0 dated 2013-03-26 and 1.1.0 dated 2013-06-04
Description: To impute HLA types from unphased SNP data using an
attribute bagging method.
Author: Xiuwen Zheng, Bruce S. Weir
Maintainer: Xiuwen Zheng
HIBAG-1.0.0/HIBAG/data/hla.snp.geno.rdata |only
HIBAG-1.0.0/HIBAG/data/hla.type.table.rdata |only
HIBAG-1.0.0/HIBAG/inst/extdata/hapmap.ceu.bed |only
HIBAG-1.0.0/HIBAG/inst/extdata/hapmap.ceu.bim |only
HIBAG-1.0.0/HIBAG/inst/extdata/hapmap.ceu.fam |only
HIBAG-1.0.0/HIBAG/man/hla.snp.geno.Rd |only
HIBAG-1.0.0/HIBAG/man/hla.type.table.Rd |only
HIBAG-1.0.0/HIBAG/man/hlaAnonymize.Rd |only
HIBAG-1.0.0/HIBAG/man/hlaModelfromObj.Rd |only
HIBAG-1.1.0/HIBAG/DESCRIPTION | 12
HIBAG-1.1.0/HIBAG/MD5 | 140 +--
HIBAG-1.1.0/HIBAG/NEWS | 25
HIBAG-1.1.0/HIBAG/R/HIBAG.r | 805 ++++++++++++++++------
HIBAG-1.1.0/HIBAG/data/HLA_Type_Table.rdata |only
HIBAG-1.1.0/HIBAG/data/HapMap_CEU_Geno.rdata |only
HIBAG-1.1.0/HIBAG/inst/CITATION | 7
HIBAG-1.1.0/HIBAG/inst/doc/HIBAG_Tutorial.R |only
HIBAG-1.1.0/HIBAG/inst/doc/HIBAG_Tutorial.Rnw | 32
HIBAG-1.1.0/HIBAG/inst/doc/HIBAG_Tutorial.pdf |binary
HIBAG-1.1.0/HIBAG/inst/extdata/HapMap_CEU.bed |only
HIBAG-1.1.0/HIBAG/inst/extdata/HapMap_CEU.bim |only
HIBAG-1.1.0/HIBAG/inst/extdata/HapMap_CEU.fam |only
HIBAG-1.1.0/HIBAG/man/HIBAG-package.Rd | 78 --
HIBAG-1.1.0/HIBAG/man/HLA_Type_Table.Rd |only
HIBAG-1.1.0/HIBAG/man/HapMap_CEU_Geno.Rd |only
HIBAG-1.1.0/HIBAG/man/hlaAllele.Rd | 16
HIBAG-1.1.0/HIBAG/man/hlaAlleleClass.Rd | 3
HIBAG-1.1.0/HIBAG/man/hlaAlleleDigit.Rd | 12
HIBAG-1.1.0/HIBAG/man/hlaAlleleSubset.Rd | 12
HIBAG-1.1.0/HIBAG/man/hlaAttrBagClass.Rd | 9
HIBAG-1.1.0/HIBAG/man/hlaAttrBagObj.Rd | 11
HIBAG-1.1.0/HIBAG/man/hlaAttrBagging.Rd | 37 -
HIBAG-1.1.0/HIBAG/man/hlaBED2Geno.Rd | 22
HIBAG-1.1.0/HIBAG/man/hlaCheckSNPs.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaClose.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaCombineAllele.Rd | 12
HIBAG-1.1.0/HIBAG/man/hlaCombineModelObj.Rd | 17
HIBAG-1.1.0/HIBAG/man/hlaCompareAllele.Rd | 5
HIBAG-1.1.0/HIBAG/man/hlaErrMsg.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaFlankingSNP.Rd | 21
HIBAG-1.1.0/HIBAG/man/hlaGeno2PED.Rd | 16
HIBAG-1.1.0/HIBAG/man/hlaGenoAFreq.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoCombine.Rd | 18
HIBAG-1.1.0/HIBAG/man/hlaGenoLD.Rd |only
HIBAG-1.1.0/HIBAG/man/hlaGenoMFreq.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoMRate.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoMRate_Samp.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoSubset.Rd | 8
HIBAG-1.1.0/HIBAG/man/hlaGenoSwitchStrand.Rd | 16
HIBAG-1.1.0/HIBAG/man/hlaHaplo2Geno.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaHaploSubset.Rd | 2
HIBAG-1.1.0/HIBAG/man/hlaLociInfo.Rd | 13
HIBAG-1.1.0/HIBAG/man/hlaMakeSNPGeno.Rd | 19
HIBAG-1.1.0/HIBAG/man/hlaMakeSNPHaplo.Rd | 7
HIBAG-1.1.0/HIBAG/man/hlaModelFiles.Rd | 24
HIBAG-1.1.0/HIBAG/man/hlaModelFromObj.Rd |only
HIBAG-1.1.0/HIBAG/man/hlaModelToObj.Rd | 4
HIBAG-1.1.0/HIBAG/man/hlaParallelAttrBagging.Rd | 62 -
HIBAG-1.1.0/HIBAG/man/hlaPublish.Rd |only
HIBAG-1.1.0/HIBAG/man/hlaSNPGenoClass.Rd | 3
HIBAG-1.1.0/HIBAG/man/hlaSNPHaploClass.Rd | 3
HIBAG-1.1.0/HIBAG/man/hlaSNPID.Rd | 9
HIBAG-1.1.0/HIBAG/man/hlaSampleAllele.Rd | 6
HIBAG-1.1.0/HIBAG/man/hlaSplitAllele.Rd | 10
HIBAG-1.1.0/HIBAG/man/hlaSubModelObj.Rd | 19
HIBAG-1.1.0/HIBAG/man/hlaUniqueAllele.Rd | 8
HIBAG-1.1.0/HIBAG/man/plot.hlaAttrBagClass.Rd | 28
HIBAG-1.1.0/HIBAG/man/plot.hlaAttrBagObj.Rd | 33
HIBAG-1.1.0/HIBAG/man/predict.hlaAttrBagClass.Rd | 8
HIBAG-1.1.0/HIBAG/man/print.hlaAttrBagClass.Rd | 2
HIBAG-1.1.0/HIBAG/man/print.hlaAttrBagObj.Rd | 2
HIBAG-1.1.0/HIBAG/man/summary.hlaAlleleClass.Rd | 8
HIBAG-1.1.0/HIBAG/man/summary.hlaAttrBagClass.Rd | 2
HIBAG-1.1.0/HIBAG/man/summary.hlaAttrBagObj.Rd | 2
HIBAG-1.1.0/HIBAG/man/summary.hlaSNPGenoClass.Rd | 8
HIBAG-1.1.0/HIBAG/man/summary.hlaSNPHaploClass.Rd | 2
HIBAG-1.1.0/HIBAG/src/HIBAG.cpp | 90 +-
HIBAG-1.1.0/HIBAG/src/LibHLA.cpp | 56 +
HIBAG-1.1.0/HIBAG/src/LibHLA.h | 33
HIBAG-1.1.0/HIBAG/vignettes/HIBAG_Ref.bib | 7
HIBAG-1.1.0/HIBAG/vignettes/HIBAG_Tutorial.Rnw | 32
81 files changed, 1188 insertions(+), 688 deletions(-)
Title: Empirical Mode Decomposition and Hilbert Spectral Analysis
Diff between EMD versions 1.5.3 dated 2013-04-25 and 1.5.5 dated 2013-06-04
Description: This package carries out empirical mode decomposition and
Hilbert spectral analysis. For usage of EMD, see Kim and Oh,
2009 (Kim, D and Oh, H.-S. (2009) EMD: A Package for Empirical
Mode Decomposition and Hilbert Spectrum, The R Journal, 1,
40-46).
Author: Donghoh Kim and Hee-Seok Oh
Maintainer: Donghoh Kim
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
R/Hilbert.R | 2 +-
man/semd.Rd | 26 +++++++++++++-------------
4 files changed, 22 insertions(+), 22 deletions(-)
Title: R tools for making it easier to combine and clean data sets.
Diff between DataCombine versions 0.1.5 dated 2013-05-21 and 0.1.5.2 dated 2013-06-04
Description: R tools for combining and cleaning data sets, including
filling in missing observations with data from another data
frame.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 8 ++++----
MD5 | 14 +++++++-------
NAMESPACE | 1 +
NEWS | 12 ++++++++++--
R/FillIn.R | 35 +++++++++++++++++++++++------------
R/slide.R | 5 +++--
README.md | 2 +-
man/FillIn.Rd | 18 ++++++++++++++----
8 files changed, 63 insertions(+), 32 deletions(-)
Title: Agricultural datasets
Diff between agridat versions 1.5 dated 2013-04-26 and 1.6 dated 2013-06-04
Description: Datasets from books and papers related to agriculture.
Example analyses included.
Author: Kevin Wright
Maintainer: Kevin Wright
agridat-1.5/agridat/data/batchelor.apple.txt.gz |only
agridat-1.5/agridat/data/batchelor.lemon.txt.gz |only
agridat-1.5/agridat/data/batchelor.navel1.txt.gz |only
agridat-1.5/agridat/data/batchelor.navel2.txt.gz |only
agridat-1.5/agridat/data/batchelor.valencia.txt.gz |only
agridat-1.5/agridat/data/batchelor.walnut.txt.gz |only
agridat-1.5/agridat/data/gomez.uniformity.txt.gz |only
agridat-1.5/agridat/data/goulden.barley.txt.gz |only
agridat-1.5/agridat/data/immer.sugarbeet.txt.gz |only
agridat-1.5/agridat/data/kempton.uniformity.txt.gz |only
agridat-1.5/agridat/data/lyon.potato.txt.gz |only
agridat-1.5/agridat/data/mercer.wheat.txt.gz |only
agridat-1.5/agridat/data/smith.uniformity3.txt.gz |only
agridat-1.5/agridat/data/wiebe.wheat.txt.gz |only
agridat-1.5/agridat/data/williams.barley.txt.gz |only
agridat-1.5/agridat/data/williams.cotton.txt.gz |only
agridat-1.5/agridat/man/batchelor.Rd |only
agridat-1.5/agridat/man/gomez.uniformity.Rd |only
agridat-1.5/agridat/man/goulden.barley.Rd |only
agridat-1.5/agridat/man/immer.sugarbeet.Rd |only
agridat-1.5/agridat/man/kempton.uniformity.Rd |only
agridat-1.5/agridat/man/lyon.potato.Rd |only
agridat-1.5/agridat/man/mercer.wheat.Rd |only
agridat-1.5/agridat/man/smith.uniformity3.Rd |only
agridat-1.5/agridat/man/wiebe.wheat.Rd |only
agridat-1.5/agridat/man/williams.barley.Rd |only
agridat-1.5/agridat/man/williams.cotton.Rd |only
agridat-1.6/agridat/DESCRIPTION | 14
agridat-1.6/agridat/MD5 | 289 +++++-----
agridat-1.6/agridat/NEWS | 39 -
agridat-1.6/agridat/data/batchelor.apple.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.lemon.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.navel1.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.navel2.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.valencia.uniformity.txt.gz |only
agridat-1.6/agridat/data/batchelor.walnut.uniformity.txt.gz |only
agridat-1.6/agridat/data/crossa.wheat.txt.gz |only
agridat-1.6/agridat/data/datalist | 41 -
agridat-1.6/agridat/data/garber.multi.uniformity.txt.gz |only
agridat-1.6/agridat/data/gomez.nitrogen.txt.gz |only
agridat-1.6/agridat/data/gomez.rice.uniformity.txt.gz |only
agridat-1.6/agridat/data/goulden.barley.uniformity.txt.gz |only
agridat-1.6/agridat/data/harris.multi.uniformity.txt.gz |only
agridat-1.6/agridat/data/immer.sugarbeet.uniformity.txt.gz |only
agridat-1.6/agridat/data/kempton.barley.uniformity.txt.gz |only
agridat-1.6/agridat/data/li.millet.uniformity.txt.gz |only
agridat-1.6/agridat/data/lyon.potato.uniformity.txt.gz |only
agridat-1.6/agridat/data/mercer.wheat.uniformity.txt.gz |only
agridat-1.6/agridat/data/odland.soybean.uniformity.txt.gz |only
agridat-1.6/agridat/data/odland.soyhay.uniformity.txt.gz |only
agridat-1.6/agridat/data/ratkowsky.onions.txt.gz |only
agridat-1.6/agridat/data/smith.corn.uniformity.txt.gz |only
agridat-1.6/agridat/data/stephens.sorghum.uniformity.txt.gz |only
agridat-1.6/agridat/data/wiebe.wheat.uniformity.txt.gz |only
agridat-1.6/agridat/data/williams.barley.uniformity.txt.gz |only
agridat-1.6/agridat/data/williams.cotton.uniformity.txt.gz |only
agridat-1.6/agridat/man/aastveit.barley.Rd | 6
agridat-1.6/agridat/man/adugna.sorghum.Rd | 7
agridat-1.6/agridat/man/agridat.Rd | 68 +-
agridat-1.6/agridat/man/allcroft.lodging.Rd | 5
agridat-1.6/agridat/man/archbold.apple.Rd | 25
agridat-1.6/agridat/man/ars.earlywhitecorn96.Rd | 11
agridat-1.6/agridat/man/australia.soybean.Rd | 2
agridat-1.6/agridat/man/batchelor.uniformity.Rd |only
agridat-1.6/agridat/man/besag.bayesian.Rd | 2
agridat-1.6/agridat/man/besag.elbatan.Rd | 4
agridat-1.6/agridat/man/besag.met.Rd | 4
agridat-1.6/agridat/man/blackman.wheat.Rd | 8
agridat-1.6/agridat/man/bond.diallel.Rd | 2
agridat-1.6/agridat/man/box.cork.Rd | 2
agridat-1.6/agridat/man/bridges.cucmber.Rd | 5
agridat-1.6/agridat/man/broadbalk.wheat.Rd | 2
agridat-1.6/agridat/man/byers.apple.Rd | 2
agridat-1.6/agridat/man/caribbean.maize.Rd | 2
agridat-1.6/agridat/man/carmer.density.Rd | 3
agridat-1.6/agridat/man/cate.potassium.Rd | 5
agridat-1.6/agridat/man/cleveland.soil.Rd | 3
agridat-1.6/agridat/man/cochran.bib.Rd | 2
agridat-1.6/agridat/man/cochran.crd.Rd | 4
agridat-1.6/agridat/man/cochran.eelworms.Rd | 4
agridat-1.6/agridat/man/cochran.latin.Rd | 4
agridat-1.6/agridat/man/cochran.wireworms.Rd | 2
agridat-1.6/agridat/man/corsten.interaction.Rd | 2
agridat-1.6/agridat/man/cox.stripsplit.Rd | 2
agridat-1.6/agridat/man/crossa.wheat.Rd |only
agridat-1.6/agridat/man/crowder.seeds.Rd | 2
agridat-1.6/agridat/man/darwin.maize.Rd | 2
agridat-1.6/agridat/man/denis.missing.Rd | 2
agridat-1.6/agridat/man/denis.ryegrass.Rd | 2
agridat-1.6/agridat/man/desplot.Rd | 28
agridat-1.6/agridat/man/digby.jointregression.Rd | 2
agridat-1.6/agridat/man/diggle.cow.Rd | 10
agridat-1.6/agridat/man/durban.competition.Rd | 5
agridat-1.6/agridat/man/durban.rowcol.Rd | 4
agridat-1.6/agridat/man/durban.splitplot.Rd | 5
agridat-1.6/agridat/man/eden.potato.Rd | 2
agridat-1.6/agridat/man/engelstad.nitro.Rd | 2
agridat-1.6/agridat/man/fan.stability.Rd | 4
agridat-1.6/agridat/man/federer.diagcheck.Rd | 3
agridat-1.6/agridat/man/federer.tobacco.Rd | 2
agridat-1.6/agridat/man/garber.mulit.uniformity.Rd |only
agridat-1.6/agridat/man/gathmann.bt.Rd | 4
agridat-1.6/agridat/man/gauch.soy.Rd | 4
agridat-1.6/agridat/man/gilmour.serpentine.Rd | 5
agridat-1.6/agridat/man/gilmour.slatehall.Rd | 4
agridat-1.6/agridat/man/gomez.fractionalfactorial.Rd | 5
agridat-1.6/agridat/man/gomez.groupsplit.Rd | 2
agridat-1.6/agridat/man/gomez.multilocsplitplot.Rd | 2
agridat-1.6/agridat/man/gomez.nitrogen.Rd |only
agridat-1.6/agridat/man/gomez.rice.uniformity.Rd |only
agridat-1.6/agridat/man/gomez.seedrate.Rd | 3
agridat-1.6/agridat/man/gomez.splitsplit.Rd | 5
agridat-1.6/agridat/man/gomez.stripplot.Rd | 2
agridat-1.6/agridat/man/gomez.stripsplitplot.Rd | 2
agridat-1.6/agridat/man/gotway.hessianfly.Rd | 5
agridat-1.6/agridat/man/goulden.barley.uniformity.Rd |only
agridat-1.6/agridat/man/graybill.heteroskedastic.Rd | 2
agridat-1.6/agridat/man/hanks.sprinkler.Rd | 9
agridat-1.6/agridat/man/harris.multi.uniformity.Rd |only
agridat-1.6/agridat/man/henderson.milkfat.Rd | 3
agridat-1.6/agridat/man/hernandez.nitrogen.Rd | 5
agridat-1.6/agridat/man/hessling.argentina.Rd | 2
agridat-1.6/agridat/man/hildebrand.systems.Rd | 2
agridat-1.6/agridat/man/hughes.grapes.Rd | 2
agridat-1.6/agridat/man/ilri.sheep.Rd | 2
agridat-1.6/agridat/man/immer.sugarbeet.uniformity.Rd |only
agridat-1.6/agridat/man/ivins.herbs.Rd | 2
agridat-1.6/agridat/man/jenkyn.mildew.Rd | 3
agridat-1.6/agridat/man/john.alpha.Rd | 2
agridat-1.6/agridat/man/johnson.blight.Rd | 3
agridat-1.6/agridat/man/kempton.barley.uniformity.Rd |only
agridat-1.6/agridat/man/kempton.competition.Rd | 5
agridat-1.6/agridat/man/kempton.rowcol.Rd | 5
agridat-1.6/agridat/man/kempton.slatehall.Rd | 5
agridat-1.6/agridat/man/lambert.soiltemp.Rd | 2
agridat-1.6/agridat/man/lavoranti.eucalyptus.Rd | 3
agridat-1.6/agridat/man/li.millet.uniformity.Rd |only
agridat-1.6/agridat/man/lyon.potato.uniformity.Rd |only
agridat-1.6/agridat/man/lyons.wheat.Rd | 2
agridat-1.6/agridat/man/mcconway.turnip.Rd | 2
agridat-1.6/agridat/man/mead.cowpeamaize.Rd | 2
agridat-1.6/agridat/man/mead.germination.Rd | 3
agridat-1.6/agridat/man/mead.strawberry.Rd | 5
agridat-1.6/agridat/man/mercer.wheat.uniformity.Rd |only
agridat-1.6/agridat/man/minnesota.barley.weather.Rd | 38 +
agridat-1.6/agridat/man/minnesota.barley.yield.Rd | 25
agridat-1.6/agridat/man/nass.corn.Rd | 2
agridat-1.6/agridat/man/nebraska.farmincome.Rd | 2
agridat-1.6/agridat/man/odland.soy.uniformity.Rd |only
agridat-1.6/agridat/man/ortiz.tomato.Rd | 5
agridat-1.6/agridat/man/pacheco.soybean.Rd | 3
agridat-1.6/agridat/man/pearl.kernels.Rd | 4
agridat-1.6/agridat/man/ratkowsky.onions.Rd |only
agridat-1.6/agridat/man/rothamsted.brussels.Rd | 5
agridat-1.6/agridat/man/ryder.groundnut.Rd | 4
agridat-1.6/agridat/man/senshu.rice.Rd | 2
agridat-1.6/agridat/man/shafii.rapeseed.Rd | 2
agridat-1.6/agridat/man/smith.corn.uniformity.Rd |only
agridat-1.6/agridat/man/snedecor.asparagus.Rd | 3
agridat-1.6/agridat/man/steel.soybeanmet.Rd | 15
agridat-1.6/agridat/man/stephens.sorghum.uniformity.Rd |only
agridat-1.6/agridat/man/streibig.competition.Rd | 4
agridat-1.6/agridat/man/stroup.nin.Rd | 2
agridat-1.6/agridat/man/stroup.splitplot.Rd | 2
agridat-1.6/agridat/man/student.barley.Rd | 2
agridat-1.6/agridat/man/talbot.potato.Rd | 2
agridat-1.6/agridat/man/theobald.covariate.Rd | 2
agridat-1.6/agridat/man/thompson.cornsoy.Rd | 8
agridat-1.6/agridat/man/vargas.wheat1.Rd | 2
agridat-1.6/agridat/man/vargas.wheat2.Rd | 3
agridat-1.6/agridat/man/verbyla.lupin.Rd | 2
agridat-1.6/agridat/man/vsn.lupin3.Rd | 4
agridat-1.6/agridat/man/wedderburn.barley.Rd | 4
agridat-1.6/agridat/man/wiebe.wheat.uniformity.Rd |only
agridat-1.6/agridat/man/williams.barley.uniformity.Rd |only
agridat-1.6/agridat/man/williams.cotton.uniformity.Rd |only
agridat-1.6/agridat/man/williams.trees.Rd | 2
agridat-1.6/agridat/man/yan.winterwheat.Rd | 2
agridat-1.6/agridat/man/yates.missing.Rd | 2
agridat-1.6/agridat/man/yates.oats.Rd | 5
agridat-1.6/agridat/man/zuidhof.broiler.Rd | 2
181 files changed, 503 insertions(+), 417 deletions(-)