Title: The Iterative Signature Algorithm
Diff between isa2 versions 0.3.1 dated 2011-10-20 and 0.3.1-1 dated 2012-06-11
Description: The ISA is a biclustering algorithm that finds modules in
an input matrix. A module or bicluster is a block of the
reordered input matrix.
Author: Gabor Csardi
Maintainer: Gabor Csardi
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/isa3.R | 2 +-
R/ppa.R | 2 +-
inst/doc/ISA_parallel.pdf |binary
inst/doc/ISA_tutorial.pdf |binary
man/isa.sweep.Rd | 8 ++++----
7 files changed, 17 insertions(+), 17 deletions(-)
Title: Estimation of caribou abundance based on large scale
aggregations monitored by radio telemetry
Diff between caribou versions 1.0 dated 2012-01-25 and 1.1 dated 2012-06-11
Description: This is a package for estimating the population size of
migratory caribou herds based on large scale aggregations
monitored by radio telemetry. It implements the methodology
found in the article by Rivest et al. (1998) about caribou
abundance estimation. It also includes a function based on the
Lincoln-Petersen Index as applied to radio telemetry data by
White and Garrott (1990).
Author: Helene Crepeau
Maintainer: Sophie Baillargeon
caribou-1.0/caribou/data/WAH09.rda |only
caribou-1.0/caribou/man/WAH09.Rd |only
caribou-1.1/caribou/DESCRIPTION | 8 ++++----
caribou-1.1/caribou/MD5 | 10 +++++-----
caribou-1.1/caribou/data/WAH11.rda |only
caribou-1.1/caribou/inst/NEWS.Rd | 7 ++++++-
caribou-1.1/caribou/man/WAH11.Rd |only
caribou-1.1/caribou/man/caribou.package.Rd | 4 ++--
8 files changed, 17 insertions(+), 12 deletions(-)
Title: Clustering high throughput sequencing (HTS) data
Diff between HTSCluster versions 1.0 dated 2011-11-07 and 1.1 dated 2012-06-11
Description: This package implements two parameterizations of a Poisson
mixture model to cluster observations (e.g., genes) in high
throughput sequencing data. Parameter estimation is performed
using either the EM or CEM algorithm, and the BIC or ICL
criteria are used for model selection (i.e., to choose the
number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy
Maugis-Rabusseau
Maintainer: Andrea Rau
DESCRIPTION | 22 ++++++++++++++--------
MD5 | 25 ++++++++++++++++---------
NAMESPACE |only
NEWS |only
R/PoisMixClus.R | 30 ++++++++++++++++++++++--------
R/kmeanInit.R | 2 +-
R/logLikePoisMix.R | 3 +--
R/plot.HTSCluster.R |only
R/summary.HTSCluster.R |only
inst |only
man/HTSCluster-package.Rd | 17 ++++++++---------
man/Init.Rd | 10 ----------
man/PoisMixClus.Rd | 21 ++++++++++++++-------
man/logLikePoisMix.Rd | 12 +++++++-----
man/plot.HTSCluster.Rd |only
man/probaPost.Rd | 9 +--------
man/summary.HTSCluster.Rd |only
17 files changed, 84 insertions(+), 67 deletions(-)
Title: Analysis of fMRI experiments
Diff between fmri versions 1.4-6 dated 2011-10-24 and 1.4-8 dated 2012-06-11
Description: The package contains R-functions to perform an fmri
analysis as described in K. Tabelow, J. Polzehl, H.U. Voss, and
V. Spokoiny, Analysing fMRI experiments with structure adaptive
smoothing procedures, NeuroImage, 33:55-62 (2006) and J.
Polzehl, H.U. Voss, K. Tabelow, Structural adaptive
segmentation for statistical parametric mapping, NeuroImage,
52:515-523 (2010).
Author: Karsten Tabelow
Maintainer: Karsten Tabelow
DESCRIPTION | 8 +++---
HISTORY | 5 +++
MD5 | 26 ++++++++++---------
R/aws.r | 8 +-----
R/fmri.R | 9 ++++++
R/io.R | 10 +++++--
R/lm.R | 14 +++++-----
R/misc.r | 1
R/segm.r | 3 --
R/sysdata.rda |binary
R/utilities.r | 77 +++++++++++++++++++++++++++++++++++++++++++++-------------
data |only
demo/fmri.r | 2 -
man/hvred.Rd |only
src/Makevars | 2 +
15 files changed, 112 insertions(+), 53 deletions(-)
Title: Generation, reconstruction, simulation and analysis of
synchronous, asynchronous, and probabilistic Boolean networks
Diff between BoolNet versions 1.50 dated 2012-04-10 and 1.51 dated 2012-06-11
Description: Provides methods to reconstruct and generate synchronous,
asynchronous, and probabilistic Boolean networks, and to
analyze and visualize attractors in Boolean networks
Author: Christoph Müssel, Martin Hopfensitz, Dao Zhou, Hans Kestler
Maintainer: Hans Kestler
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/loadNetwork.R | 2 ++
R/plotNetworkWiring.R | 7 ++++++-
R/plotStateGraph.R | 15 ++++++++++-----
inst/NEWS.Rd | 13 +++++++++++++
inst/doc/BoolNet_package_vignette.Snw | 5 +++++
inst/doc/BoolNet_package_vignette.pdf |binary
inst/doc/cellcycle.txt | 22 +++++++++++-----------
man/BoolNet-package.Rd | 4 ++--
man/loadNetwork.Rd | 16 ++++++++++++----
11 files changed, 75 insertions(+), 37 deletions(-)
Title: Bayesian chronologies via compound Poisson-Gamma processes.
Diff between Bchron versions 3.1.4 dated 2010-11-03 and 3.1.5 dated 2012-06-11
Description: This package takes dating information to produce joint
chronological reconstructions for age-depth data. The package
allows for: radiocarbon and non-radiocarbon depths, thickness
errors, outlying dates, multiple calibration curves, and event
prediction. It also produces some pretty pictures, and writes
all output to files to allow for further analysis (eg
palaeoclimate reconstruction). There is a menu system for
users, as well as a command line interface for advanced and/or
batch processing. This version contains an update to produce
better plots of proxy data via the function Bchronproxyplot.
***IMPORTANT NOTE*** This version fixes a serious bug which was
present in versions 3.1.1 and 3.1.2. You should have noticed
this bug anyway when you ran the Bchronconvergecheck function.
Author: Andrew Parnell
Maintainer: Andrew Parnell
Bchron-3.1.4/Bchron/inst/Output |only
Bchron-3.1.5/Bchron/DESCRIPTION | 8 +-
Bchron-3.1.5/Bchron/MD5 |only
Bchron-3.1.5/Bchron/R/Bchron-internal.R | 3
Bchron-3.1.5/Bchron/R/Bchronmenu.R | 6 -
Bchron-3.1.5/Bchron/man/Bchronconvergecheck.Rd | 86 ++++++++++++-------------
Bchron-3.1.5/Bchron/src/use.c | 8 +-
7 files changed, 54 insertions(+), 57 deletions(-)
Title: Spatial Point Pattern analysis, model-fitting, simulation, tests
Diff between spatstat versions 1.27-0 dated 2012-05-16 and 1.28-0 dated 2012-06-11
Description: A package for analysing spatial data, mainly Spatial Point
Patterns, including multitype/marked points and spatial
covariates, in any two-dimensional spatial region. Also
supports three-dimensional point patterns, and space-time point
patterns in any number of dimensions. Contains over 1000
functions for plotting spatial data, exploratory data analysis,
model-fitting, simulation, spatial sampling, model diagnostics,
and formal inference. Data types include point patterns, line
segment patterns, spatial windows, pixel images and
tessellations. Exploratory methods include K-functions,
nearest neighbour distance and empty space statistics, Fry
plots, pair correlation function, kernel smoothed intensity,
relative risk estimation with cross-validated bandwidth
selection, mark correlation functions, segregation indices,
mark dependence diagnostics etc. Point process models can be
fitted to point pattern data using functions ppm, kppm, slrm
similar to glm. Models may include dependence on covariates,
interpoint interaction, cluster formation and dependence on
marks. Fitted models can be simulated automatically. Also
provides facilities for formal inference (such as chi-squared
tests) and model diagnostics (including simulation envelopes,
residuals, residual plots and Q-Q plots).
Author: Adrian Baddeley
Maintainer: Adrian Baddeley
DESCRIPTION | 28 +++---
MD5 | 122 ++++++++++++++--------------
NEWS | 141 ++++++++++++++++++++++++++++++++
R/GJfox.R | 4
R/as.im.R | 12 ++
R/distances.psp.R | 30 +++++-
R/envelope.R | 77 +++++++++++------
R/envelope3.R | 20 ++--
R/eval.fasp.R | 9 +-
R/eval.fv.R | 203 +++++++++++++++++++++++++----------------------
R/exactMPLEstrauss.R |only
R/fgk3.R | 71 ++++++++++++----
R/hyperframe.R | 62 ++++++++++++--
R/images.R | 58 +++++++------
R/kppm.R | 22 ++++-
R/lpp.R | 81 ++++++++++++++++--
R/lppm.R | 37 ++++++++
R/marks.R | 60 +++++++------
R/mincontrast.R | 30 ++++--
R/options.R | 15 +++
R/pairdistlpp.R | 23 ++---
R/plot.fv.R | 4
R/plot.im.R | 2
R/ppmclass.R | 33 +++++--
R/ppx.R | 112 +++++++++++++++----------
R/randomlpp.R | 10 +-
R/randomonlines.R | 56 +++++++++---
R/rmh.default.R | 96 ++++++++++++++--------
R/rmhmodel.R | 7 +
R/rmhstart.R | 4
R/split.ppx.R |only
R/util.R | 6 -
data/chicago.rda |binary
inst/doc/getstart.pdf |binary
inst/doc/shapefiles.pdf |binary
man/Extract.ppx.Rd | 2
man/F3est.Rd | 47 +++++++++-
man/G3est.Rd | 3
man/as.hyperframe.Rd | 19 +++-
man/as.hyperframe.ppx.Rd | 2
man/as.im.Rd | 7 +
man/as.owin.Rd | 26 +++++-
man/coords.Rd | 16 +--
man/eval.fasp.Rd | 6 -
man/eval.fv.Rd | 25 +++++
man/exactMPLEstrauss.Rd |only
man/fv.Rd | 3
man/lgcp.estK.Rd | 8 +
man/lpp.Rd | 31 ++++++-
man/methods.lppm.Rd | 4
man/model.frame.ppm.Rd | 21 +++-
man/model.images.Rd | 32 ++++++-
man/model.matrix.ppm.Rd | 33 +++++--
man/plot.fv.Rd | 16 ++-
man/plot.im.Rd | 8 +
man/ppx.Rd | 45 ++++++----
man/quad.ppm.Rd | 5 -
man/rmh.default.Rd | 21 +++-
man/rmhstart.Rd | 9 +-
man/spatstat-internal.Rd | 30 ++++++
man/spatstat-package.Rd | 2
man/spatstat.options.Rd | 16 +++
man/split.ppx.Rd |only
src/g3.c | 18 ++--
64 files changed, 1337 insertions(+), 553 deletions(-)
Title: Log-Gaussian Cox Process
Diff between lgcp versions 0.9-4-2 dated 2012-05-30 and 0.9-5 dated 2012-06-11
Description: Spatial and spatio-temporal modelling of point patterns
using the log-Gaussian Cox process
Author: B. M. Taylor, T. M. Davies, B. S. Rowlingson, P. J. Diggle
Maintainer: Benjamin M. Taylor
DESCRIPTION | 6 -
MD5 | 48 +++++++-------
NAMESPACE | 2
R/fftgrid.R | 27 ++++----
R/lgcpForecast.R | 2
R/lgcpMethods.R | 31 ++++++---
R/lgcpPredictSpatial.R | 4 -
R/lgcpPredictSpatioTemporal.R | 6 -
R/lgcpSimSpatioTemporal.R | 2
R/parameterEstimation.R | 106 ++++++++++++++++++++++++++++++++-
R/spatialOnly.R | 2
inst/doc/lgcp.pdf |binary
inst/doc/pdf/hvals.pdf |binary
inst/doc/pdf/mut1.pdf |binary
inst/doc/pdf/mut2.pdf |binary
inst/doc/pdf/notrot.pdf |binary
man/fftgrid.Rd | 7 --
man/fftinterpolate-dot-fromFunction.Rd | 3
man/fftinterpolate-dot-fromSPDF.Rd | 3
man/fftinterpolate-dot-fromXYZ.Rd | 3
man/lambdaEst-dot-ppp.Rd |only
man/lambdaEst-dot-stppp.Rd |only
man/lambdaEst.Rd | 31 +--------
man/plot-dot-lgcpPredict.Rd | 2
man/plotExceed-dot-array.Rd | 4 -
man/plotExceed-dot-lgcpPredict.Rd | 4 -
26 files changed, 198 insertions(+), 95 deletions(-)
Title: Centrality-based pathway enrichment
Diff between CePa versions 0.1 dated 2012-04-28 and 0.2 dated 2012-06-11
Description: Use pathway topology information to assign weight to
pathway nodes.
Author: Zuguang Gu
Maintainer: Zuguang Gu
CHANGE |only
DESCRIPTION | 8 ++++----
MD5 | 7 ++++---
R/generate.pathway.R | 6 +++++-
inst/doc/CePa.pdf |binary
5 files changed, 13 insertions(+), 8 deletions(-)
Title: Less Code, More Results
Diff between lessR versions 2.2 dated 2012-03-28 and 2.3 dated 2012-06-11
Description: Each function accomplishes the work of several or more
standard R functions. For example, two function calls, Read()
and CountAll(), read the data and generate descriptive
statistics for all variables in the data frame, plus histograms
and bar charts as appropriate. Other functions provide for
descriptive statistics, a comprehensive regression analysis,
anova and t-test, color plotting, color bar chart, color
histogram, color box plot, color density curves, a calibrated
power curve, and the reading and display of csv and other
formatted data. The function Help provides a help system that
suggests specific analyses and functions. Variable labels, and
color themes with the set function, are also available.
Author: David W. Gerbing, School of Business Administration, Portland
State University
Maintainer: David W. Gerbing
lessR-2.2/lessR/R/bc.brief.R |only
lessR-2.2/lessR/R/color.plot.R |only
lessR-2.2/lessR/R/color.show.R |only
lessR-2.2/lessR/R/dens.R |only
lessR-2.2/lessR/R/dots.R |only
lessR-2.2/lessR/R/full.R |only
lessR-2.2/lessR/R/help.me.R |only
lessR-2.2/lessR/R/out.R |only
lessR-2.2/lessR/R/powercurve.ttest.R |only
lessR-2.2/lessR/R/prob.t.R |only
lessR-2.2/lessR/R/ptt.R |only
lessR-2.2/lessR/R/ss.character.R |only
lessR-2.2/lessR/R/ss.data.frame.R |only
lessR-2.2/lessR/R/ss.default.R |only
lessR-2.2/lessR/R/ss.factor.R |only
lessR-2.2/lessR/R/ss.numeric.R |only
lessR-2.2/lessR/R/tt.default.R |only
lessR-2.2/lessR/R/tt.formula.R |only
lessR-2.2/lessR/man/bc.Rd |only
lessR-2.2/lessR/man/bx.Rd |only
lessR-2.2/lessR/man/color.show.Rd |only
lessR-2.2/lessR/man/dens.Rd |only
lessR-2.2/lessR/man/dots.Rd |only
lessR-2.2/lessR/man/full.Rd |only
lessR-2.2/lessR/man/help.me.Rd |only
lessR-2.2/lessR/man/hst.Rd |only
lessR-2.2/lessR/man/out.Rd |only
lessR-2.2/lessR/man/pc.Rd |only
lessR-2.2/lessR/man/plt.Rd |only
lessR-2.2/lessR/man/prob.t.Rd |only
lessR-2.2/lessR/man/ptt.Rd |only
lessR-2.2/lessR/man/rad.Rd |only
lessR-2.2/lessR/man/reg.Rd |only
lessR-2.2/lessR/man/ss.Rd |only
lessR-2.2/lessR/man/tt.Rd |only
lessR-2.3/lessR/DESCRIPTION | 35 -
lessR-2.3/lessR/MD5 | 195 ++++---
lessR-2.3/lessR/NAMESPACE | 52 +-
lessR-2.3/lessR/NEWS |only
lessR-2.3/lessR/R/ANOVA.R |only
lessR-2.3/lessR/R/BarChart.R |only
lessR-2.3/lessR/R/BoxPlot.R |only
lessR-2.3/lessR/R/Correlation.R |only
lessR-2.3/lessR/R/CountAll.R |only
lessR-2.3/lessR/R/Density.R |only
lessR-2.3/lessR/R/Help.R |only
lessR-2.3/lessR/R/Histogram.R |only
lessR-2.3/lessR/R/Model.R |only
lessR-2.3/lessR/R/PieChart.R |only
lessR-2.3/lessR/R/Plot.R |only
lessR-2.3/lessR/R/Read.R |only
lessR-2.3/lessR/R/Regression.R |only
lessR-2.3/lessR/R/RunChart.R |only
lessR-2.3/lessR/R/SummaryStats.R |only
lessR-2.3/lessR/R/Write.R |only
lessR-2.3/lessR/R/av.R |only
lessR-2.3/lessR/R/av.brief.R |only
lessR-2.3/lessR/R/bc.R | 109 ----
lessR-2.3/lessR/R/bc.data.frame.R | 14
lessR-2.3/lessR/R/bc.default.R | 373 ---------------
lessR-2.3/lessR/R/bc.zdefault.R |only
lessR-2.3/lessR/R/bx.R | 60 --
lessR-2.3/lessR/R/bx.default.R | 98 ---
lessR-2.3/lessR/R/bx.zdefault.R |only
lessR-2.3/lessR/R/ca.R |only
lessR-2.3/lessR/R/color.density.R | 2
lessR-2.3/lessR/R/cr.R |only
lessR-2.3/lessR/R/cr.brief.R |only
lessR-2.3/lessR/R/cr.data.frame.R |only
lessR-2.3/lessR/R/cr.default.R |only
lessR-2.3/lessR/R/cr.zdefault.R |only
lessR-2.3/lessR/R/den.R |only
lessR-2.3/lessR/R/den.zmain.R |only
lessR-2.3/lessR/R/dp.zmain.R |only
lessR-2.3/lessR/R/hlp.R |only
lessR-2.3/lessR/R/hst.R | 59 --
lessR-2.3/lessR/R/hst.data.frame.R | 12
lessR-2.3/lessR/R/hst.default.R | 176 -------
lessR-2.3/lessR/R/hst.zdefault.R |only
lessR-2.3/lessR/R/label.R | 23
lessR-2.3/lessR/R/model.brief.R |only
lessR-2.3/lessR/R/model2.R |only
lessR-2.3/lessR/R/pc.R | 150 ------
lessR-2.3/lessR/R/pc.zmain.R |only
lessR-2.3/lessR/R/plt.R | 523 ---------------------
lessR-2.3/lessR/R/plt.zmain.R |only
lessR-2.3/lessR/R/powercurve.t.test.R | 2
lessR-2.3/lessR/R/prob.norm.R | 3
lessR-2.3/lessR/R/prob.znorm.R | 1
lessR-2.3/lessR/R/qnt.t.R |only
lessR-2.3/lessR/R/rad.R | 212 --------
lessR-2.3/lessR/R/rad.both.R | 2
lessR-2.3/lessR/R/rad.brief.R | 2
lessR-2.3/lessR/R/rad.labels.R | 2
lessR-2.3/lessR/R/rad2.R | 2
lessR-2.3/lessR/R/rc.R |only
lessR-2.3/lessR/R/rc.zmain.R |only
lessR-2.3/lessR/R/reg.R | 792 --------------------------------
lessR-2.3/lessR/R/reg.brief.R | 2
lessR-2.3/lessR/R/reg.explain.R | 2
lessR-2.3/lessR/R/reg.z1Basic.R |only
lessR-2.3/lessR/R/reg.z2Relations.R |only
lessR-2.3/lessR/R/reg.z3Residual.R |only
lessR-2.3/lessR/R/reg.z4PredGraph.R |only
lessR-2.3/lessR/R/set.R |only
lessR-2.3/lessR/R/showColors.R |only
lessR-2.3/lessR/R/sim.CImean.R | 13
lessR-2.3/lessR/R/sim.CLT.R | 36 -
lessR-2.3/lessR/R/sim.flips.R | 1
lessR-2.3/lessR/R/sim.means.R | 2
lessR-2.3/lessR/R/ss.R | 115 ----
lessR-2.3/lessR/R/ss.brief.R | 2
lessR-2.3/lessR/R/ss.zdata.frame.R |only
lessR-2.3/lessR/R/ss.zfactor.R |only
lessR-2.3/lessR/R/ss.znumeric.R |only
lessR-2.3/lessR/R/to.R |only
lessR-2.3/lessR/R/tt.R | 59 --
lessR-2.3/lessR/R/tt.brief.R | 2
lessR-2.3/lessR/R/tt.z1group.R |only
lessR-2.3/lessR/R/tt.z2group.R |only
lessR-2.3/lessR/R/tt.zformula.R |only
lessR-2.3/lessR/R/ttest.R | 149 +++++-
lessR-2.3/lessR/R/ttestPower.R |only
lessR-2.3/lessR/R/ttp.R |only
lessR-2.3/lessR/R/values.R | 59 --
lessR-2.3/lessR/R/wrt.R |only
lessR-2.3/lessR/R/wrt.r.R |only
lessR-2.3/lessR/R/zFirst.R |only
lessR-2.3/lessR/R/zInternal.R |only
lessR-2.3/lessR/man/ANOVA.Rd |only
lessR-2.3/lessR/man/BarChart.Rd |only
lessR-2.3/lessR/man/BoxPlot.Rd |only
lessR-2.3/lessR/man/Correlation.Rd |only
lessR-2.3/lessR/man/CountAll.Rd |only
lessR-2.3/lessR/man/Density.Rd |only
lessR-2.3/lessR/man/Help.Rd |only
lessR-2.3/lessR/man/Histogram.Rd |only
lessR-2.3/lessR/man/Model.Rd |only
lessR-2.3/lessR/man/PieChart.Rd |only
lessR-2.3/lessR/man/Plot.Rd |only
lessR-2.3/lessR/man/Read.Rd |only
lessR-2.3/lessR/man/Regression.Rd |only
lessR-2.3/lessR/man/RunChart.Rd |only
lessR-2.3/lessR/man/SummaryStats.Rd |only
lessR-2.3/lessR/man/Write.Rd |only
lessR-2.3/lessR/man/dat.employee.csv.Rd | 2
lessR-2.3/lessR/man/dat.twogroup.csv.Rd | 2
lessR-2.3/lessR/man/label.Rd | 33 -
lessR-2.3/lessR/man/prob.znorm.Rd | 4
lessR-2.3/lessR/man/qnt.t.Rd |only
lessR-2.3/lessR/man/set.Rd |only
lessR-2.3/lessR/man/showColors.Rd |only
lessR-2.3/lessR/man/sim.flips.Rd | 4
lessR-2.3/lessR/man/to.Rd |only
lessR-2.3/lessR/man/ttest.Rd |only
lessR-2.3/lessR/man/ttestPower.Rd |only
156 files changed, 493 insertions(+), 2893 deletions(-)
Title: A general-purpose package for dynamic report generation in R
Diff between knitr versions 0.5 dated 2012-04-29 and 0.6 dated 2012-06-11
Description: This package provides a general-purpose tool for dynamic
report generation in R, which can be used to deal with any type
of (plain text) files, including Sweave, HTML, Markdown and
reStructuredText. The patterns of code chunks and inline R
expressions can be customized. R code is evaluated as if it
were copied and pasted in an R terminal thanks to the evaluate
package (e.g. we do not need to explicitly print() plots from
ggplot2 or lattice). R code can be reformatted by the formatR
package so that long lines are automatically wrapped, with
indent and spaces being added, and comments being preserved. A
simple caching mechanism is provided to cache results from
computations for the first time and the computations will be
skipped the next time. Almost all common graphics devices,
including those in base R and add-on packages like Cairo,
cairoDevice and tikzDevice, are built-in with this package and
it is straightforward to switch between devices without writing
any special functions. The width and height as well as
alignment of plots in the output document can be specified in
chunk options (the size of plots for graphics devices is still
supported as usual). Multiple plots can be recorded in a single
code chunk, and it is also allowed to rearrange plots to the
end of a chunk or just keep the last plot. Warnings, messages
and errors are written in the output document by default (can
be turned off). Currently LaTeX, HTML, Markdown and reST are
supported, and other output formats can be supported by hook
functions. The large collection of hooks in this package makes
it possible for the user to control almost everything in the R
code input and output. Hooks can be used either to format the
output or to run a specified R code fragment before or after a
code chunk. The language in code chunks is not restricted to R
only (there is simple support to Python and Awk, etc). Many
features are borrowed or inspired by Sweave, cacheSweave,
pgfSweave, brew and decumar.
Author: Yihui Xie
Maintainer: Yihui Xie
DESCRIPTION | 10 +-
FAQ.md | 4 -
MD5 | 117 +++++++++++++++++++-------------
NAMESPACE | 1
NEWS | 123 ++++++++++++++++++++++++++++++++++
R/block.R | 32 ++++++---
R/cache.R | 27 ++++---
R/concordance.R | 65 ++++++++++--------
R/defaults.R | 54 ---------------
R/eclipse.R | 5 -
R/header.R | 25 +++++--
R/hooks-extra.R | 3
R/hooks-html.R | 22 +++---
R/hooks-latex.R | 4 -
R/hooks-md.R | 7 +
R/hooks-rst.R | 6 -
R/hooks.R | 6 +
R/output.R | 135 ++++++++++++++++++++++++++------------
R/parser.R | 14 +++
R/pattern.R | 55 +++++++++++++++
R/plot.R | 5 -
R/spin.R |only
R/themes.R | 4 -
R/utils.R | 96 ++++++++++++++++-----------
README.md | 2
inst/doc/knitr-intro.Rnw | 6 +
inst/doc/knitr-intro.lyx | 33 +++++++++
inst/doc/knitr-intro.pdf |binary
inst/examples/child |only
inst/examples/knit-all.R | 21 +++++
inst/examples/knitr-beamer.Rnw | 5 -
inst/examples/knitr-beamer.lyx | 5 -
inst/examples/knitr-lang.md | 4 -
inst/examples/knitr-manual.Rnw | 5 +
inst/examples/knitr-manual.lyx | 17 ++++
inst/examples/knitr-minimal.Rhtml | 3
inst/examples/knitr-minimal.Rmd | 19 ++---
inst/examples/knitr-minimal.brew |only
inst/examples/knitr-minimal.rst | 11 +--
inst/examples/knitr-packages.bib | 6 -
inst/examples/knitr-slides.Rmd |only
inst/examples/knitr-slides.md |only
inst/examples/knitr-spin.R |only
inst/examples/knitr-spin.Rmd |only
inst/examples/knitr-upload.md | 4 -
inst/misc/knitr-template.Rhtml | 2
inst/misc/knitr-template.Rmd |only
inst/misc/knitr-template.Rnw | 2
inst/opencpu |only
inst/tests/knit-envir.Rmd |only
inst/tests/test-envir.R |only
inst/tests/test-utils.R | 25 +++++--
inst/themes/.knitr.css | 20 ++++-
inst/themes/eclipse.brew | 30 ++++----
man/all_patterns.Rd | 4 -
man/eclipse_theme.Rd | 1
man/knit.Rd | 6 +
man/knit2html.Rd | 6 +
man/knit2pdf.Rd | 6 +
man/knit_child.Rd | 24 +++---
man/knit_theme.Rd | 3
man/spin.Rd |only
man/stitch.Rd | 12 ++-
63 files changed, 755 insertions(+), 347 deletions(-)