Title: A General-Purpose Package for Dynamic Report Generation in R
Diff between knitr versions 1.9 dated 2015-01-20 and 1.10 dated 2015-04-23
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Ashley Manton [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb],
Yihui Xie [aut, cre]
Maintainer: Yihui Xie
DESCRIPTION | 61 ++++--------
MD5 | 171 +++++++++++++++++-----------------
NAMESPACE | 9 -
R/block.R | 59 ++++++-----
R/cache.R | 7 -
R/citation.R | 64 +++++-------
R/defaults.R | 12 +-
R/engine.R | 83 +++++++++++-----
R/header.R | 31 ++----
R/highlight.R | 18 +--
R/hooks-asciidoc.R | 2
R/hooks-extra.R | 10 +
R/hooks-html.R | 26 ++---
R/hooks-latex.R | 12 +-
R/hooks-md.R | 24 +++-
R/hooks-textile.R | 2
R/output.R | 108 +++++++++++++--------
R/package.R | 8 -
R/pandoc.R | 2
R/params.R |only
R/parser.R | 106 ++++++++++++++++-----
R/pattern.R | 3
R/plot.R | 46 +++------
R/rocco.R | 2
R/spin.R | 8 -
R/table.R | 40 +++++--
R/template.R | 9 -
R/themes-eclipse.R | 4
R/themes.R | 8 -
R/utils-base64.R | 18 +--
R/utils-conversion.R | 3
R/utils-rd2html.R | 10 -
R/utils-sweave.R | 2
R/utils-vignettes.R | 45 +++++++-
R/utils.R | 67 ++++++++++---
build/knitr.pdf |binary
build/vignette.rds |binary
inst/doc/knit_expand.html | 4
inst/doc/knit_print.html | 9 -
inst/doc/knitr-html.html | 12 +-
inst/doc/knitr-intro.Rmd | 4
inst/doc/knitr-intro.html | 18 +--
inst/doc/knitr-markdown.Rmd | 4
inst/doc/knitr-markdown.html | 8 +
inst/doc/knitr-refcard.pdf |binary
inst/examples/knitr-beamer.Rnw | 6 -
inst/examples/knitr-graphics.Rnw | 27 +----
inst/examples/knitr-listings.Rnw | 2
inst/examples/knitr-manual.Rnw | 46 +++------
inst/examples/knitr-minimal.Rnw | 2
inst/examples/knitr-packages.bib | 33 +++---
inst/examples/knitr-spin.R | 6 -
inst/examples/knitr-spin.Rmd | 4
inst/examples/knitr-subfloats.Rnw | 2
inst/examples/knitr-themes.Rnw | 22 +---
inst/examples/knitr-twocolumn.Rnw | 2
inst/misc/knitr.css | 12 +-
inst/misc/stitch-test.R | 4
inst/misc/tweak_bib.csv |only
inst/misc/vignette.css | 17 +--
man/all_labels.Rd | 29 +++++
man/all_patterns.Rd | 4
man/current_input.Rd | 6 -
man/eclipse_theme.Rd | 4
man/knit.Rd | 44 ++++----
man/knit_child.Rd | 4
man/knit_params.Rd |only
man/knit_print.Rd | 4
man/knit_rd.Rd | 2
man/knit_theme.Rd | 6 -
man/knitr-package.Rd | 4
man/rand_seed.Rd | 2
man/read_rforge.Rd | 1
man/set_alias.Rd | 2
man/stitch.Rd | 5
man/vignette_engines.Rd | 21 +++-
man/write_bib.Rd | 6 -
tests/testit/test-cache.R | 6 -
tests/testit/test-citation.R |only
tests/testit/test-closure.R | 12 +-
tests/testit/test-hooks.R | 2
tests/testit/test-params.R |only
tests/testit/test-parser.R | 32 ++++--
tests/testit/test-plot.R | 34 ++++--
tests/testit/test-table.R | 20 ++-
tests/testit/test-utils.R | 11 +-
vignettes/assets/template-refcard.tex | 2
vignettes/knitr-intro.Rmd | 4
vignettes/knitr-markdown.Rmd | 4
89 files changed, 928 insertions(+), 667 deletions(-)
Title: Acoustic Template Detection in R
Diff between monitoR versions 1.0.2 dated 2014-05-14 and 1.0.3 dated 2015-04-23
Description: Acoustic template detection and monitoring database interface. Create, modify, save, and use templates for detection of animal vocalizations. View, verify, and extract results. Upload a MySQL schema to a existing instance, manage survey metadata, write and read templates and detections locally or to the database.
Author: Sasha D. Hafner
Maintainer: Sasha D. Hafner
ChangeLog | 159 +++++++++++++++++++++++++++++++++++
DESCRIPTION | 12 +-
MD5 | 132 ++++++++++++++---------------
NAMESPACE | 2
R/binMatch.R | 54 ++++++------
R/bindEvents.R | 6 -
R/corMatch.R | 55 +++++-------
R/dbDownloadCardRecorderID.R | 47 +++++++---
R/dbDownloadResult.R | 18 +---
R/dbDownloadSurvey.R | 81 ++++++++++++------
R/dbDownloadTemplate.R | 76 +++++++++-------
R/dbSchema.R | 19 ++--
R/dbUploadAnno.R | 13 +-
R/dbUploadResult.R | 17 +--
R/dbUploadSurvey.R | 15 +--
R/dbUploadTemplate.R | 17 +--
R/eventEval.R | 10 --
R/fileCopyRename.R | 5 -
R/findPeaks.R | 5 -
R/getClip.R | 19 ++--
R/makeBinTemplate.R | 75 ++++++----------
R/makeCorTemplate.R | 42 +++++----
R/readBinTemplates.R | 5 -
R/readCorTemplates.R | 5 -
R/showPeaks.R | 52 +++++++++--
R/stft.R | 13 +-
R/templatePath.R |only
R/viewSpec.R | 29 ++++--
R/writeBinTemplates.R | 5 -
R/writeCorTemplates.R | 5 -
build/vignette.rds |binary
data/btnw.rda |binary
data/oven.rda |binary
data/survey.rda |binary
data/survey_anno.rda |binary
inst/doc/monitoR_QuickStart.R | 175 ++++++++++++++-------------------------
inst/doc/monitoR_QuickStart.Rnw | 39 +++++---
inst/doc/monitoR_QuickStart.pdf |binary
man/changeSampRate.Rd | 2
man/collapseClips.Rd | 10 --
man/combineTemplates.Rd | 46 ++++++----
man/compareTemplates.Rd | 32 ++++---
man/dbDownload.Rd | 10 +-
man/dbDownloadTemplate.Rd | 22 ++--
man/dbUploadResult.Rd | 24 ++++-
man/dbUploadTemplate.Rd | 6 -
man/eventEval.Rd | 31 ++++--
man/fileCopyRename.Rd | 13 +-
man/findPeaks.Rd | 43 ++++++---
man/getDetections.Rd | 37 +++++---
man/makeTemplate.Rd | 71 +++++++++------
man/monitoR-package.Rd | 32 ++++---
man/mp3Subsamp.Rd | 2
man/plot-methods.Rd | 50 ++++++-----
man/readTemplates.Rd | 31 ++++--
man/show-methods.Rd | 26 ++++-
man/showPeaks.Rd | 51 ++++++++---
man/specCols.Rd | 20 ++--
man/survey_anno.Rd | 8 +
man/templateComment.Rd | 54 ++++++------
man/templateCutoff.Rd | 32 ++++---
man/templateMatching.Rd | 12 +-
man/templateNames.Rd | 31 ++++--
man/templatePath.Rd |only
man/timeAlign.Rd | 17 ++-
man/viewSpec.Rd | 25 +++--
man/writeTemplates.Rd | 29 ++++--
vignettes/monitoR_QuickStart.Rnw | 39 +++++---
68 files changed, 1209 insertions(+), 804 deletions(-)
Title: Analysis of Geostatistical Data
Diff between geoR versions 1.7-4.1 dated 2014-09-14 and 1.7-5.1 dated 2015-04-23
Description: Geostatistical analysis including traditional, likelihood-based and Bayesian methods.
Author: Paulo J. Ribeiro Jr
Maintainer: Paulo J. Ribeiro Jr
geoR-1.7-4.1/geoR/R/likOLD.R |only
geoR-1.7-4.1/geoR/inst/CITATION |only
geoR-1.7-5.1/geoR/DESCRIPTION | 25 +++----
geoR-1.7-5.1/geoR/MD5 | 79 ++++++++++++-------------
geoR-1.7-5.1/geoR/NAMESPACE | 28 ++++++--
geoR-1.7-5.1/geoR/R/Cwrappers.R | 1
geoR-1.7-5.1/geoR/R/auxiliar.R | 11 +--
geoR-1.7-5.1/geoR/R/corcov.R | 2
geoR-1.7-5.1/geoR/R/eyefit.R | 2
geoR-1.7-5.1/geoR/R/geobayes.R | 6 -
geoR-1.7-5.1/geoR/R/geodata.R | 4 -
geoR-1.7-5.1/geoR/R/profiles.R | 69 +++++++++++++++++++++
geoR-1.7-5.1/geoR/R/simul.R | 3
geoR-1.7-5.1/geoR/data/Ksat.rda |binary
geoR-1.7-5.1/geoR/data/SIC.rda |binary
geoR-1.7-5.1/geoR/data/ca20.rda |binary
geoR-1.7-5.1/geoR/data/camg.rda |binary
geoR-1.7-5.1/geoR/data/elevation.rda |binary
geoR-1.7-5.1/geoR/data/gambia.rda |binary
geoR-1.7-5.1/geoR/data/head.rda |binary
geoR-1.7-5.1/geoR/data/hoef.rda |binary
geoR-1.7-5.1/geoR/data/isaaks.rda |binary
geoR-1.7-5.1/geoR/data/kattegat.rda |binary
geoR-1.7-5.1/geoR/data/landim1.rda |binary
geoR-1.7-5.1/geoR/data/parana.rda |binary
geoR-1.7-5.1/geoR/data/s100.rda |binary
geoR-1.7-5.1/geoR/data/s121.rda |binary
geoR-1.7-5.1/geoR/data/s256i.rda |binary
geoR-1.7-5.1/geoR/data/soil250.rda |binary
geoR-1.7-5.1/geoR/data/soja98.rda |binary
geoR-1.7-5.1/geoR/data/tce.rda |binary
geoR-1.7-5.1/geoR/data/wo.rda |binary
geoR-1.7-5.1/geoR/data/wolfcamp.rda |binary
geoR-1.7-5.1/geoR/data/wrc.rda |binary
geoR-1.7-5.1/geoR/inst/CHANGES | 13 +++-
geoR-1.7-5.1/geoR/inst/doc/CHANGES |only
geoR-1.7-5.1/geoR/man/SIC.Rd | 2
geoR-1.7-5.1/geoR/man/coords2coords.Rd | 6 +
geoR-1.7-5.1/geoR/man/grf.Rd | 3
geoR-1.7-5.1/geoR/man/sample.prior.Rd | 5 +
geoR-1.7-5.1/geoR/man/statistics.predictive.Rd | 2
geoR-1.7-5.1/geoR/man/subarea.Rd | 8 +-
42 files changed, 184 insertions(+), 85 deletions(-)
Title: Doubly Robust Generalized Estimating Equations
Diff between drgee versions 1.0.1 dated 2014-01-27 and 1.1.0 dated 2015-04-23
Description: Fit restricted mean models for the conditional association
between an exposure and an outcome, given covariates. Three methods
are implemented: O-estimation, where a nuisance model for the
association between the covariates and the outcome is used;
E-estimation where a nuisance model for the association
between the covariates and the exposure is used, and doubly robust (DR)
estimation where both nuisance models are used. In DR-estimation,
the estimates will be consistent when at least one of the nuisance
models is correctly specified, not necessarily both.
Author: Johan Zetterqvist
Maintainer: Johan Zetterqvist
drgee-1.0.1/drgee/R/ebeFit.R |only
drgee-1.0.1/drgee/R/obeFit.R |only
drgee-1.0.1/drgee/man/drFit.Rd |only
drgee-1.0.1/drgee/man/ebeFit.Rd |only
drgee-1.0.1/drgee/man/geeFit.Rd |only
drgee-1.0.1/drgee/man/obeFit.Rd |only
drgee-1.1.0/drgee/DESCRIPTION | 29 -
drgee-1.1.0/drgee/MD5 | 42 +-
drgee-1.1.0/drgee/NAMESPACE | 12
drgee-1.1.0/drgee/NEWS | 27 +
drgee-1.1.0/drgee/R/clogitRes.R |only
drgee-1.1.0/drgee/R/drFit.R | 191 -----------
drgee-1.1.0/drgee/R/dreFit.R |only
drgee-1.1.0/drgee/R/dreFitCond.R |only
drgee-1.1.0/drgee/R/drgee.R | 199 +++++++-----
drgee-1.1.0/drgee/R/drgeeData.R | 538 +++++++++++++++++++++++++--------
drgee-1.1.0/drgee/R/eFit.R |only
drgee-1.1.0/drgee/R/findRoots.R | 23 -
drgee-1.1.0/drgee/R/gee.R |only
drgee-1.1.0/drgee/R/geeFit.R | 51 +--
drgee-1.1.0/drgee/R/geeFitCond.R |only
drgee-1.1.0/drgee/R/oFit.R |only
drgee-1.1.0/drgee/R/robVcov.R | 29 -
drgee-1.1.0/drgee/man/drgee-package.Rd | 38 +-
drgee-1.1.0/drgee/man/drgee.Rd | 335 +++++++++++---------
drgee-1.1.0/drgee/man/drgeeData.Rd | 112 ++++--
drgee-1.1.0/drgee/man/findRoots.Rd | 16
drgee-1.1.0/drgee/man/gee.Rd |only
drgee-1.1.0/drgee/man/robVcov.Rd | 16
29 files changed, 971 insertions(+), 687 deletions(-)
Title: Visualization of Spatial and Spatio-temporal Objects in Google
Earth
Diff between plotKML versions 0.5-0 dated 2015-01-28 and 0.5-1 dated 2015-04-23
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut],
Pierre Roudier [ctb],
Dylan Beaudette [ctb],
Edzer Pebesma [ctb],
Michael Blaschek [ctb]
Maintainer: Tomislav Hengl
DESCRIPTION | 10 ++++----
MD5 | 34 ++++++++++++++++--------------
R/AAA-md.R | 6 +++++
R/AAAA.R | 10 ++++----
R/aesthetics.R | 3 --
R/kml.tiles.R |only
R/legend.bar.R | 2 -
R/plot.SpatialPredictions.R | 25 +++++++++++++++-------
R/plotKML.GDALobj.R | 25 ++++++++++++----------
R/spMetadata.R | 14 ++++++++++++
build/vignette.rds |binary
inst/INSPIRE_ISO19139.xml | 23 +++++++++++++++++++-
inst/doc/jss1079.pdf |binary
man/baranja.Rd | 49 ++++++++++++++++++++++++++------------------
man/kml.Rd | 4 ++-
man/kml.tiles.Rd |only
man/plotKML.GDALobj.Rd | 12 ++++++----
man/plotKML.Rd | 9 ++++++++
man/plotKML.env.Rd | 12 +++++-----
19 files changed, 158 insertions(+), 80 deletions(-)
Title: Interactive Interpretation of Linear Regression Models
Diff between LinRegInteractive versions 0.3-0 dated 2014-11-12 and 0.3-1 dated 2015-04-23
More information about LinRegInteractive at CRAN
Description: Interactive visualization of effects, response functions
and marginal effects for different kinds of regression models. In this version
linear regression models, generalized linear models, generalized additive
models and linear mixed-effects models are supported.
Major features are the interactive approach and the handling of the effects of categorical covariates:
if two or more factors are used as covariates every combination of the levels of each
factor is treated separately. The automatic calculation of
marginal effects and a number of possibilities to customize the graphical output
are useful features as well.
Author: Martin Meermeyer
Maintainer: Martin Meermeyer
DESCRIPTION | 10
MD5 | 24
build/vignette.rds |binary
inst/doc/LinRegInteractive.Rnw | 1647 +++++++++++++++++++--------------------
inst/doc/LinRegInteractive.pdf |binary
man/LinRegInteractive-package.Rd | 6
man/fxInteractive.Rd | 2
man/fxInteractive.glm.Rd | 2
man/fxInteractive.lm.Rd | 2
man/fxInteractive.lme.Rd | 2
man/munichrent03.Rd | 2
vignettes/LinRegInteractive.Rnw | 1647 +++++++++++++++++++--------------------
vignettes/LinRegInteractive.tex | 11
13 files changed, 1670 insertions(+), 1685 deletions(-)
Permanent link
Title: Soil Database Interface
Diff between soilDB versions 1.5-2 dated 2015-02-25 and 1.5-4 dated 2015-04-23
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: D.E. Beaudette and J.M. Skovlin
Maintainer: D.E. Beaudette
DESCRIPTION | 11 -
MD5 | 34 +--
NEWS | 20 +-
R/AAAA.R | 2
R/fetchNASIS.R | 24 +-
R/getHzErrorsNASIS.R | 2
R/get_colors_from_NASIS_db.R | 1
R/get_extended_data_from_NASIS_db.R | 16 -
R/get_hz_data_from_NASIS_db.R | 14 -
R/get_site_data_from_NASIS_db.R | 10 -
R/nasis_component_data.R | 343 ++++++++++++++++++------------------
R/utils.R | 24 ++
data/andic.subset.rda |binary
data/cisne.rda |binary
data/gSSURGO.chunk.rda |binary
data/gopheridge.rda |binary
data/loafercreek.rda |binary
man/fetchNASIS.Rd | 25 +-
18 files changed, 280 insertions(+), 246 deletions(-)
Title: Algorithms for Quantitative Pedology
Diff between aqp versions 1.8 dated 2015-02-20 and 1.8-6 dated 2015-04-23
Description: A collection of algorithms related to modeling of soil resources, soil classification, soil profile aggregation, and visualization.
Author: Dylan Beaudette
Maintainer: Dylan Beaudette
DESCRIPTION | 12 +--
MD5 | 25 ++++---
NAMESPACE | 4 +
NEWS | 13 +++
R/SoilProfileCollection-methods.R | 19 ++---
R/aggregateSoilDepth.R |only
R/evalGenHz.R | 121 ++++++++++++++++++++-----------------
R/profile_plot.R | 85 +++++++++++++++++++++----
R/setters.R | 5 -
man/SPC-plotting.Rd | 18 ++++-
man/SPC-slab-methods.Rd | 9 +-
man/SPC-unique-methods.Rd |only
man/SoilProfileCollection-class.Rd | 28 --------
man/aggregateSoilDepth.Rd |only
man/plotMultipleSPC.Rd |only
man/profileGroupLabels.Rd |only
16 files changed, 209 insertions(+), 130 deletions(-)