Title: International Assessment Data Manager
Diff between intsvy versions 1.5 dated 2014-12-02 and 1.6 dated 2014-12-08
Description: Provides tools for importing, merging, and analysing data from international assessment studies (TIMSS, PIRLS, PISA and PIAAC)
Author: Daniel Caro
Maintainer: Daniel Caro
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NAMESPACE | 2 +-
R/pirls.var.label.R | 2 +-
R/pisa.select.merge.R | 6 +++---
R/pisa.var.label.R | 4 ++--
R/timssg4.var.label.R | 2 +-
R/timssg8.var.label.R | 2 +-
man/intsvy-package.Rd | 4 ++--
man/piaac.ben.pv.Rd | 10 ++++++----
10 files changed, 30 insertions(+), 28 deletions(-)
Title: Easy access to Berlin related data
Diff between BerlinData versions 1.0.0 dated 2014-05-11 and 1.0.1 dated 2014-12-08
Description: This package provides easy access to http://daten.berlin.de
It allows you to search through the data catalogue and to download
the data directly from within R.
Author: Kate McCurdy, Dirk Schumacher
Maintainer: Dirk Schumacher
BerlinData-1.0.0/BerlinData/man/datasets_feed_tree.Rd |only
BerlinData-1.0.1/BerlinData/DESCRIPTION | 14 +--
BerlinData-1.0.1/BerlinData/MD5 | 37 ++++------
BerlinData-1.0.1/BerlinData/NAMESPACE | 3
BerlinData-1.0.1/BerlinData/R/berlin-data.R | 2
BerlinData-1.0.1/BerlinData/R/other-methods.R | 1
BerlinData-1.0.1/BerlinData/man/cached_datasets_feed.Rd | 2
BerlinData-1.0.1/BerlinData/man/download.CSV.Rd | 6 -
BerlinData-1.0.1/BerlinData/man/download.JSON.Rd | 6 -
BerlinData-1.0.1/BerlinData/man/download.Rd | 2
BerlinData-1.0.1/BerlinData/man/download.TXT.Rd | 6 -
BerlinData-1.0.1/BerlinData/man/download.XML.Rd | 6 -
BerlinData-1.0.1/BerlinData/man/download.berlin_data_resource.Rd | 2
BerlinData-1.0.1/BerlinData/man/download.default.Rd | 6 -
BerlinData-1.0.1/BerlinData/man/getDatasetMetaData.Rd | 2
BerlinData-1.0.1/BerlinData/man/parseMetaData.Rd | 2
BerlinData-1.0.1/BerlinData/man/resources.Rd | 2
BerlinData-1.0.1/BerlinData/man/resources.berlin_data_dataset.Rd | 2
BerlinData-1.0.1/BerlinData/man/searchBerlinDatasets.Rd | 2
BerlinData-1.0.1/BerlinData/man/updateCachedFeed.Rd | 2
20 files changed, 52 insertions(+), 53 deletions(-)
Title: Seasonal/Sequential (Instants/Durations, Even or not) Time
Series
Diff between timetools versions 1.6.1 dated 2014-10-11 and 1.6.5 dated 2014-12-08
Description: Objects to manipulate sequential and seasonal time series. Sequential time series based on time instants and time durations are handled. Both can be regularly or unevenly spaced (overlapping durations are allowed). Only POSIX* format are used for dates and times. The following classes are provided : POSIXcti, POSIXctp, TimeIntervalDataFrame, TimeInstantDataFrame, SubtimeDataFrame ; methods to switch from a class to another and to modify the time support of series (hourly time series to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base).
Author: Vladislav Navel
Maintainer: Vladislav Navel
DESCRIPTION | 14 +++++++-------
MD5 | 14 +++++++-------
R/02posixctp.R | 20 +++++++++++++++-----
R/SubtimeDataFrame.R | 31 +++----------------------------
R/TimeInstantDataFrame.R | 29 +++--------------------------
R/TimeIntervalDataFrame.R | 31 +++----------------------------
README | 24 ++++++++++++++++++++++++
man/timetools-package.Rd | 34 +++++++++++++++-------------------
8 files changed, 77 insertions(+), 120 deletions(-)
Title: Semiparametric Maximum Likelihood for Mother-Child Designs.
Diff between SPmlficmcm versions 1.1 dated 2013-12-10 and 1.3 dated 2014-12-08
Description: Implements the method of general semiparametric maximum likelihood estimation for logistic models in case-mother control-mother designs.
Author: Moliere Nguile-Makao
Maintainer: Moliere Nguile Makao
DESCRIPTION | 15 ++----
MD5 | 42 ++++++++++-------
NAMESPACE | 3 -
R/Est.Inpar.R | 32 ++++++++++---
R/FtSmlrmCMCM.R | 8 ++-
R/Nlsysteq.R | 4 -
R/S0.R |only
R/S1.R |only
R/Spmlficmcm.R | 92 ++++++++++++++++++++++++++++++-------
R/dPrgcm_HW1.theta.R |only
R/dPrgm_HW1.theta.R |only
R/dlogPrgcm_HW1.theta.R |only
R/fct_invCap.R | 4 -
R/fctcd.R | 24 ++++++---
R/fgp_mf1.R | 1
R/fpol1.R | 26 +++++-----
R/fpolm.R |only
R/ft_gradientCas1.R |only
R/ft_gradientCasM.R |only
R/ft_likhoodCas1.R | 16 +-----
R/ft_likhoodCasM.R | 103 ++++++++++++++++++++++++++---------------
man/Est.Inpar.Rd | 10 ++--
man/FtSmlrmCMCM.Rd | 113 ++++++++++++++++++++++------------------------
man/SPmlficmcm-package.Rd | 12 ++--
man/SeltcEch.Rd | 109 +++++++++++++++++++++-----------------------
man/Spmlficmcm.Rd | 48 +++++++++++++------
26 files changed, 395 insertions(+), 267 deletions(-)
Title: Web Application Framework for R
Diff between shiny versions 0.10.2.1 dated 2014-10-01 and 0.10.2.2 dated 2014-12-08
Description: Shiny makes it incredibly easy to build interactive web
applications with R. Automatic "reactive" binding between inputs and
outputs and extensive pre-built widgets make it possible to build
beautiful, responsive, and powerful applications with minimal effort.
Author: RStudio, Inc.
Maintainer: Winston Chang
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
NEWS | 5 +++++
R/app.R | 3 +--
man/shinyApp.Rd | 3 +--
5 files changed, 14 insertions(+), 11 deletions(-)
Title: Rcpp Bindings for Annoy, a Library for Approximate Nearest
Neighbors
Diff between RcppAnnoy versions 0.0.3 dated 2014-11-18 and 0.0.4 dated 2014-12-08
Description: Annoy is a small C++ library for Approximate Nearest Neighbors
written for efficient memory usage as well an ability to load from / save to
disk. This package provides an R interface by relying on the Rcpp and BH
packages, exposing the same interface as the original Python wrapper to
Annoy. See https://github.com/spotify/annoy for more on Annoy. Annoy is
released under Version 2.0 of the Apache License. Also included is a small
Windows port of mmap which is release under the MIT license.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 7 +++++++
DESCRIPTION | 9 +++++----
MD5 | 4 ++--
3 files changed, 14 insertions(+), 6 deletions(-)
Title: Power and Sample-size Distribution of 2-stage Bioequivalence
Studies
Diff between Power2Stage versions 0.1-5 dated 2014-10-10 and 0.2-2 dated 2014-12-08
Description: - Contains a function to calculate power and sample-size distribution
of 2-stage bioequivalence (BE) studies with a 2x2 crossover design
according to Potvin et al. / Montague et al. modified to include a
futility Nmax and modified to do the sample size estimation step
with PE and mse of stage 1.
- Contains further a function with the modifications according to
Karalis & Macheras which use PE and mse from stage 1 also for the
power monitoring steps.
- The third function power.2stage.fC() calculates power and sample
size distribution of 2-stage BE studies with a futility criterion
for the point estimator or CI of T/R from stage 1.
- The fourth function power.2stage.GS() calculates power of non-adaptive
group sequential (2-stage) BE studies.
- The fifth function power.2stage.p() calculates power and sample size
distribution of 2-stage BE studies with 2 parallel groups.
- Another function power.2stage.ssr() allows the power calculation
for 2-stage studies with (blinded) interim sample size re-estimation.
All the functions use simulations to obtain their results.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes
Power2Stage-0.1-5/Power2Stage/R/power_2stage_Bf.R |only
Power2Stage-0.1-5/Power2Stage/man/power.2stage.Bf.Rd |only
Power2Stage-0.2-2/Power2Stage/DESCRIPTION | 36 ++++----
Power2Stage-0.2-2/Power2Stage/MD5 | 32 +++----
Power2Stage-0.2-2/Power2Stage/NAMESPACE | 2
Power2Stage-0.2-2/Power2Stage/NEWS | 42 ++++++---
Power2Stage-0.2-2/Power2Stage/R/power_2stage.R | 71 ++++++++++------
Power2Stage-0.2-2/Power2Stage/R/power_2stage_GS.R | 16 +--
Power2Stage-0.2-2/Power2Stage/R/power_2stage_KM.R | 25 +++--
Power2Stage-0.2-2/Power2Stage/R/power_2stage_SSR.R |only
Power2Stage-0.2-2/Power2Stage/R/power_2stage_fC.R | 52 ++++++-----
Power2Stage-0.2-2/Power2Stage/R/power_2stage_parallel.R | 38 ++++----
Power2Stage-0.2-2/Power2Stage/R/sampsiz.R | 38 ++++++++
Power2Stage-0.2-2/Power2Stage/man/power.2stage.GS.Rd | 22 ++--
Power2Stage-0.2-2/Power2Stage/man/power.2stage.KM.Rd | 2
Power2Stage-0.2-2/Power2Stage/man/power.2stage.Rd | 12 +-
Power2Stage-0.2-2/Power2Stage/man/power.2stage.fC.Rd | 9 +-
Power2Stage-0.2-2/Power2Stage/man/power.2stage.p.Rd | 2
Power2Stage-0.2-2/Power2Stage/man/power.2stage.ssr.Rd |only
19 files changed, 250 insertions(+), 149 deletions(-)
Title: Miscellaneous functions for (primarily) finance / credit risk
analysts
Diff between optiRum versions 0.33 dated 2014-04-25 and 0.35 dated 2014-12-08
Description: This fills the gaps credit analysts and loan modellers at
Optimum Credit identify in the existing R code body.
It allows for the production of documentation with less coding,
replicates a number of Microsoft Excel functions useful for
modelling loans (without rounding), and other helpful functions
for producing charts and tables. It also has some additional scales for
use, including a GBP scale.
Author: Stephanie Locke [aut, cre]
Maintainer: Stephanie Locke
DESCRIPTION | 20 -
MD5 | 138 +++++-----
NAMESPACE | 11
NEWS | 19 +
R/APR.R | 10
R/CJ.dt.R | 13
R/PMT.R | 6
R/PV.R | 13
R/RATE.R | 41 +--
R/convertToXML.R | 53 +--
R/generatePDF.R | 56 +---
R/giniChart.R | 44 +--
R/giniCoef.R | 18 -
R/logit.odd.R | 6
R/logit.prob.R | 6
R/multiplot.R | 59 ++--
R/odd.logit.R | 6
R/odd.prob.R | 6
R/optiRum-package.r | 4
R/pounds.R | 25 -
R/prob.logit.R | 6
R/prob.odd.R | 6
R/sanitise.R | 41 +--
R/scaledScore.R | 6
R/theme_optimum.R | 25 -
R/thousands.R | 15 -
R/wordwrap.R |only
README.md | 8
man/APR.Rd | 25 -
man/CJ.dt.Rd | 13
man/PMT.Rd | 25 -
man/PV.Rd | 28 +-
man/RATE.Rd | 26 -
man/convertToXML.Rd | 16 -
man/generatePDF.Rd | 49 +--
man/giniChart.Rd | 20 -
man/giniCoef.Rd | 18 -
man/logit.odd.Rd | 11
man/logit.prob.Rd | 13
man/multiplot.Rd | 23 -
man/odd.logit.Rd | 16 -
man/odd.prob.Rd | 13
man/optiRum.Rd | 12
man/pounds_format.Rd | 19 -
man/prob.logit.Rd | 16 -
man/prob.odd.Rd | 13
man/sanitise.Rd | 11
man/scaledScore.Rd | 19 -
man/theme_optimum.Rd | 17 -
man/thousands_format.Rd | 10
man/wordwrap.Rd |only
tests/testthat/datatabletest.pdf |binary
tests/testthat/test-APR.R | 40 +-
tests/testthat/test-CJ.dt.R | 26 -
tests/testthat/test-PMT.R | 31 +-
tests/testthat/test-PV.R | 41 +--
tests/testthat/test-RATE.R | 41 +--
tests/testthat/test-convertToXML.R | 26 -
tests/testthat/test-formatters.R | 63 +---
tests/testthat/test-generatePDF.R | 484 +++++++++++++++---------------------
tests/testthat/test-giniChart.R | 46 +--
tests/testthat/test-giniCoef.R | 46 +--
tests/testthat/test-logit.odd.R | 16 -
tests/testthat/test-logit.prob.R | 10
tests/testthat/test-odd.logit.R | 14 -
tests/testthat/test-odd.prob.R | 8
tests/testthat/test-prob.logit.R | 8
tests/testthat/test-prob.odd.R | 12
tests/testthat/test-sanitise.R | 12
tests/testthat/test-scaledScore.R | 48 +--
tests/testthat/test-theme_optimum.R | 8
71 files changed, 992 insertions(+), 1062 deletions(-)
Title: A copy number and expression-based classifier for breast tumours
Diff between iC10 versions 1.1.1 dated 2014-09-26 and 1.1.2 dated 2014-12-08
Description: iC10 implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group.
Author: Oscar M Rueda
Maintainer: Oscar M. Rueda
DESCRIPTION | 11 +++++------
MD5 | 6 +++---
NEWS | 2 ++
R/compare.R | 8 ++++++--
4 files changed, 16 insertions(+), 11 deletions(-)
Title: Social Relations Analyses With Roles ("Family SRM")
Diff between fSRM versions 0.6 dated 2014-09-29 and 0.6.1 dated 2014-12-08
Description: Social Relations Analysis with roles ("Family
SRM") are computed, using a structural equation modeling approach. Groups ranging from
three members up to an unlimited number of members are supported and the
mean structure can be computed. Means and variances can be compared between
different groups of families and between roles.
Author: Felix Schönbrodt, Lara Stas, Tom Loeys
Maintainer: Felix Schönbrodt
DESCRIPTION | 14 +++++++-------
MD5 | 38 +++++++++++++++++++-------------------
NAMESPACE | 2 +-
R/fSRM.R | 2 +-
R/generics.R | 8 ++++++--
R/plots.R | 5 +++--
inst/NEWS.Rd | 9 +++++++++
man/buildSRMSyntax.Rd | 24 ++++++++++++------------
man/clinical.Rd | 2 +-
man/equalMeans.Rd | 2 +-
man/fSRM.Rd | 22 +++++++++++-----------
man/four.person.Rd | 2 +-
man/import.Rd | 2 +-
man/mod.Rd | 2 +-
man/plot.fSRM.Rd | 10 +++++++---
man/predict.fSRM.Rd | 2 +-
man/three.person.Rd | 2 +-
man/two.groups.Rd | 2 +-
man/two.indicators.Rd | 2 +-
man/update.fSRM.Rd | 2 +-
20 files changed, 86 insertions(+), 68 deletions(-)
Title: Modelization for Functional AutoRegressive processes
Diff between far versions 0.6-3 dated 2010-03-09 and 0.6-4 dated 2014-12-08
Description: Modelizations and previsions functions for
Functional AutoRegressive processes using
nonparametric methods: functional kernel,
estimation of the covariance operator in
a subspace, ...
Author: Damon Julien
Maintainer: Damon Julien
DESCRIPTION | 22 ++++++++++++----------
MD5 |only
R/zzz.R | 12 ++++++------
man/coef.far.Rd | 2 +-
man/is.na.fdata.Rd | 2 +-
man/multplot.Rd | 2 +-
man/plot.fdata.Rd | 2 +-
man/predict.far.Rd | 2 +-
man/predict.kerfon.Rd | 2 +-
9 files changed, 24 insertions(+), 22 deletions(-)
Title: Tools for using fonts
Diff between extrafont versions 0.16 dated 2014-03-19 and 0.17 dated 2014-12-08
Description: Tools to using fonts other than the standard PostScript fonts.
This package makes it easy to use system TrueType fonts and with PDF or
PostScript output files, and with bitmap output files in Windows. extrafont
can also be used with fonts packaged specifically to be used with, such as
the fontcm package, which has Computer Modern PostScript fonts with math
symbols. See https://github.com/wch/extrafont for instructions and
examples.
Author: Winston Chang
Maintainer: Winston Chang
DESCRIPTION | 8 ++++----
MD5 | 36 ++++++++++++++++++------------------
NAMESPACE | 2 ++
NEWS | 10 ++++++++++
R/afm.r | 4 +++-
R/font.r | 4 ++--
R/load.r | 2 +-
R/truetype.r | 5 +++--
R/utils.r | 30 ++++++++++++++++++++++++++++++
man/choose_font.Rd | 21 ++++++++++-----------
man/embed_fonts.Rd | 13 ++++++-------
man/extrafont.Rd | 8 ++++----
man/font_addpackage.Rd | 7 +++----
man/font_import.Rd | 12 +++++-------
man/font_install.Rd | 15 +++++++--------
man/fonts.Rd | 5 +++--
man/fonttable.Rd | 1 +
man/loadfonts.Rd | 9 +++++----
man/ttf_import.Rd | 13 +++++--------
19 files changed, 122 insertions(+), 83 deletions(-)
Title: R tools for making it easier to combine and clean data sets.
Diff between DataCombine versions 0.2.7 dated 2014-11-19 and 0.2.7.1 dated 2014-12-08
Description: R tools for combining and cleaning data sets, including filling in
missing observations with data from another data frame and creating
lag/lead variables.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
NEWS | 6 ++++++
R/FillIn.R | 4 ++--
man/FillIn.Rd | 2 +-
5 files changed, 18 insertions(+), 12 deletions(-)
Title: Circular Visualization in R
Diff between circlize versions 0.1.3 dated 2014-11-06 and 0.2.0 dated 2014-12-08
Description: This package implements circular visualization
(http://circos.ca/) in R. Due to the natural born feature of R to draw statistical
graphics, this package can provide a more general and flexible way to
visualize huge information in a circular style.
Author: Zuguang Gu
Maintainer: Zuguang Gu
circlize-0.1.3/circlize/inst/doc/circular_view_of_tables.R |only
circlize-0.1.3/circlize/inst/doc/circular_view_of_tables.Rnw |only
circlize-0.1.3/circlize/inst/doc/circular_view_of_tables.pdf |only
circlize-0.1.3/circlize/inst/extdata/gencode_TP_gene.RData |only
circlize-0.1.3/circlize/vignettes/circular_view_of_tables.Rnw |only
circlize-0.1.3/circlize/vignettes/figures/phylogenetic-tree.pdf |only
circlize-0.1.3/circlize/vignettes/src/chordDiagram-01-basic.R |only
circlize-0.1.3/circlize/vignettes/src/chordDiagram-02-color.R |only
circlize-0.1.3/circlize/vignettes/src/chordDiagram-03-advanced.R |only
circlize-0.1.3/circlize/vignettes/src/chordDiagram-04-other.R |only
circlize-0.1.3/circlize/vignettes/src/chordDiagram-05-compare.R |only
circlize-0.1.3/circlize/vignettes/src/chordDiagram-06-misc.R |only
circlize-0.1.3/circlize/vignettes/src/genomic-01-circos.initializeWithIdeogram.R |only
circlize-0.1.3/circlize/vignettes/src/genomic-02-customize_ideogram.R |only
circlize-0.1.3/circlize/vignettes/src/genomic-03-TPgenemodel.R |only
circlize-0.1.3/circlize/vignettes/src/genomic-04-genomicTrackPlotRegion.R |only
circlize-0.1.3/circlize/vignettes/src/genomic-05-genomicLink.R |only
circlize-0.1.3/circlize/vignettes/src/genomic-06-highlight.chromosome.R |only
circlize-0.1.3/circlize/vignettes/src/genomic-07-posTransformLines.R |only
circlize-0.1.3/circlize/vignettes/src/genomic-08-rainfallplot.R |only
circlize-0.1.3/circlize/vignettes/src/ideogram-01-simple.R |only
circlize-0.1.3/circlize/vignettes/src/intro-01-glance.R |only
circlize-0.1.3/circlize/vignettes/src/intro-16-combine.R |only
circlize-0.1.3/circlize/vignettes/src/intro-16-highlight.R |only
circlize-0.1.3/circlize/vignettes/src/phylogenetic_tree.R |only
circlize-0.1.3/circlize/vignettes/src/relation-02-table.R |only
circlize-0.2.0/circlize/DESCRIPTION | 14
circlize-0.2.0/circlize/MD5 | 151
circlize-0.2.0/circlize/NAMESPACE | 2
circlize-0.2.0/circlize/NEWS | 21
circlize-0.2.0/circlize/R/chordDiagram.R | 57
circlize-0.2.0/circlize/R/genomic.R | 142
circlize-0.2.0/circlize/R/genomic_utils.R | 10
circlize-0.2.0/circlize/R/global.R | 25
circlize-0.2.0/circlize/R/link.R | 39
circlize-0.2.0/circlize/R/overview.R | 6
circlize-0.2.0/circlize/R/plot.R | 77
circlize-0.2.0/circlize/R/utils.R | 42
circlize-0.2.0/circlize/build/vignette.rds |binary
circlize-0.2.0/circlize/inst/doc/circlize.R | 1115 ++++---
circlize-0.2.0/circlize/inst/doc/circlize.Rnw | 1558 ++++-----
circlize-0.2.0/circlize/inst/doc/circlize.pdf |binary
circlize-0.2.0/circlize/inst/doc/circular_phylogenetic_tree.R | 229 -
circlize-0.2.0/circlize/inst/doc/circular_phylogenetic_tree.Rnw | 182 -
circlize-0.2.0/circlize/inst/doc/circular_phylogenetic_tree.pdf |binary
circlize-0.2.0/circlize/inst/doc/circular_visualization_of_matrix.R |only
circlize-0.2.0/circlize/inst/doc/circular_visualization_of_matrix.Rnw |only
circlize-0.2.0/circlize/inst/doc/circular_visualization_of_matrix.pdf |only
circlize-0.2.0/circlize/inst/doc/draw_ideogram.R | 238 -
circlize-0.2.0/circlize/inst/doc/draw_ideogram.Rnw | 150
circlize-0.2.0/circlize/inst/doc/draw_ideogram.pdf |binary
circlize-0.2.0/circlize/inst/doc/genomic_plot.R | 1591 ++++++----
circlize-0.2.0/circlize/inst/doc/genomic_plot.Rnw | 1147 +++++--
circlize-0.2.0/circlize/inst/doc/genomic_plot.pdf |binary
circlize-0.2.0/circlize/inst/doc/interesting_graphics.R | 225 -
circlize-0.2.0/circlize/inst/doc/interesting_graphics.Rnw | 198 -
circlize-0.2.0/circlize/inst/doc/interesting_graphics.pdf |binary
circlize-0.2.0/circlize/inst/extdata/bird.orders.RData |only
circlize-0.2.0/circlize/inst/extdata/tp_family.RData |only
circlize-0.2.0/circlize/man/chordDiagram.rd | 10
circlize-0.2.0/circlize/man/circlize-package.rd | 6
circlize-0.2.0/circlize/man/circos.axis.rd | 7
circlize-0.2.0/circlize/man/circos.genomicLines.rd | 4
circlize-0.2.0/circlize/man/circos.genomicLink.rd | 13
circlize-0.2.0/circlize/man/circos.genomicPoints.rd | 2
circlize-0.2.0/circlize/man/circos.genomicPosTransformLines.rd | 2
circlize-0.2.0/circlize/man/circos.genomicRect.rd | 6
circlize-0.2.0/circlize/man/circos.genomicText.rd | 2
circlize-0.2.0/circlize/man/circos.genomicTrackPlotRegion.rd | 4
circlize-0.2.0/circlize/man/circos.initializeWithIdeogram.rd | 4
circlize-0.2.0/circlize/man/circos.link.rd | 11
circlize-0.2.0/circlize/man/circos.polygon.rd | 2
circlize-0.2.0/circlize/man/draw.sector.rd | 89
circlize-0.2.0/circlize/man/generateRandomBed.rd | 2
circlize-0.2.0/circlize/man/highlight.chromosome.rd | 10
circlize-0.2.0/circlize/man/posTransform.default.rd | 2
circlize-0.2.0/circlize/man/posTransform.text.rd | 127
circlize-0.2.0/circlize/man/rand_color.rd |only
circlize-0.2.0/circlize/man/read.cytoband.rd | 4
circlize-0.2.0/circlize/vignettes/circlize.Rnw | 1558 ++++-----
circlize-0.2.0/circlize/vignettes/circular_phylogenetic_tree.Rnw | 182 -
circlize-0.2.0/circlize/vignettes/circular_visualization_of_matrix.Rnw |only
circlize-0.2.0/circlize/vignettes/draw_ideogram.Rnw | 150
circlize-0.2.0/circlize/vignettes/genomic_plot.Rnw | 1147 +++++--
circlize-0.2.0/circlize/vignettes/interesting_graphics.Rnw | 198 -
circlize-0.2.0/circlize/vignettes/src/intro-03-transformation.R | 18
circlize-0.2.0/circlize/vignettes/src/intro-05-factor.R | 2
circlize-0.2.0/circlize/vignettes/src/intro-05-sectorwidth.R | 2
circlize-0.2.0/circlize/vignettes/src/intro-06-region.R | 8
circlize-0.2.0/circlize/vignettes/src/intro-07-direction.R | 2
circlize-0.2.0/circlize/vignettes/src/intro-08-lines.R | 2
circlize-0.2.0/circlize/vignettes/src/intro-12-link.R | 8
circlize-0.2.0/circlize/vignettes/src/intro-22-outside.R | 1
93 files changed, 6229 insertions(+), 4575 deletions(-)
Title: Combined Cluster and Discriminant Analysis
Diff between ccda versions 1.0 dated 2014-01-13 and 1.1 dated 2014-12-08
Description: This package implements the combined cluster and discriminant analysis method for finding homogeneous groups of data with known origin as described in Kovacs et. al (2014): Classification into homogeneous groups using combined cluster and discriminant analysis (CCDA). Environmental Modelling & Software. DOI: http://dx.doi.org/10.1016/j.envsoft.2014.01.010
Author: Solt Kovacs, Jozsef Kovacs, Peter Tanos
Maintainer: Solt Kovacs
DESCRIPTION | 10 +-
MD5 | 12 +-
R/ccda-internal.R | 250 +++++++++++++++++++++++++--------------------------
R/ccda.main.R | 149 ++++++++++++++++++------------
R/percentage.R | 25 ++---
R/plotccda.q95.R | 45 +++++----
R/plotccda.results.R | 35 ++++---
7 files changed, 289 insertions(+), 237 deletions(-)
Title: SICM pipette tip geometry estimation
Diff between breakage versions 1.0-1 dated 2012-10-18 and 1.1-1 dated 2014-12-08
Description: Estimates geometry of SICM pipette tips by fitting a physical model to recorded breakage-current data.
Author: Matthew Caldwell
Maintainer: Matthew Caldwell
DESCRIPTION | 12 ++++++------
MD5 | 14 +++++++-------
R/breakage.R | 10 ++++++++--
man/break.clust.Rd | 4 ++--
man/breakage-package.Rd | 8 ++++----
man/breakage.plot.Rd | 2 +-
man/fit.breakage.Rd | 5 ++++-
man/resist.breakage.Rd | 2 +-
8 files changed, 33 insertions(+), 24 deletions(-)
Title: Vector Generalized Linear and Additive Models
Diff between VGAM versions 0.9-5 dated 2014-11-05 and 0.9-6 dated 2014-12-08
Description: An implementation of about 6 major classes of
statistical regression models. At the heart of it are the
vector generalized linear and additive model (VGLM/VGAM)
classes. Many (150+) models and distributions are estimated
by maximum likelihood estimation (MLE) or penalized MLE, using
Fisher scoring. VGLMs can be loosely thought of as multivariate
GLMs. VGAMs are data-driven VGLMs (i.e., with smoothing). The
other classes are RR-VGLMs (reduced-rank VGLMs), quadratic
RR-VGLMs, reduced-rank VGAMs, RCIMs (row-column interaction
models)---these classes perform constrained and unconstrained
quadratic ordination (CQO/UQO) models in ecology, as well
as constrained additive ordination (CAO). Note that these
functions are subject to change, especially before version
1.0.0 is released; see the NEWS file for latest changes.
Author: Thomas W. Yee
Maintainer: Thomas Yee
DESCRIPTION | 35 ++++++------
MD5 | 124 +++++++++++++++++++++----------------------
NEWS | 15 +++++
R/aamethods.q | 4 -
R/cqo.fit.q | 6 +-
R/family.aunivariate.R | 11 ++-
R/family.binomial.R | 40 ++++++++-----
R/family.categorical.R | 1
R/family.censored.R | 5 -
R/family.circular.R | 15 +++--
R/family.functions.R | 2
R/family.math.R | 6 --
R/family.normal.R | 18 +++---
R/family.rrr.R | 70 ++++++++++++------------
R/family.univariate.R | 27 ++++++---
R/family.zeroinf.R | 1
R/predict.vlm.q | 2
R/print.vlm.q | 12 ++--
R/rrvglm.R | 2
R/rrvglm.fit.q | 2
R/s.vam.q | 2
R/summary.vlm.q | 10 +--
R/vgam.R | 2
R/vglm.R | 2
R/vglm.control.q | 2
R/vglm.fit.q | 2
R/vlm.R | 6 +-
R/vlm.wfit.q | 18 +++---
inst/doc/categoricalVGAM.pdf |binary
man/ParetoUC.Rd | 6 +-
man/SURff.Rd | 8 ++
man/bifgmcopUC.Rd | 6 +-
man/bifrankcopUC.Rd | 5 +
man/binom2.orUC.Rd | 5 +
man/binom2.rhoUC.Rd | 7 +-
man/biplackettcopUC.Rd | 5 +
man/cardUC.Rd | 6 +-
man/frechet.Rd | 8 ++
man/gengammaUC.Rd | 6 +-
man/gompertzUC.Rd | 6 +-
man/gumbelIIUC.Rd | 6 +-
man/lgammaUC.Rd | 6 +-
man/lindUC.Rd | 1
man/linoUC.Rd | 5 +
man/logUC.Rd | 6 +-
man/makehamUC.Rd | 6 +-
man/nakagamiUC.Rd | 8 ++
man/paretoIVUC.Rd | 6 +-
man/perksUC.Rd | 5 +
man/riceUC.Rd | 2
man/rrvglm-class.Rd | 2
man/s.Rd | 15 +++--
man/slashUC.Rd | 2
man/tikuvUC.Rd | 5 +
man/vgam-class.Rd | 8 ++
man/vglm-class.Rd | 2
man/vglm.Rd | 2
man/yulesimonUC.Rd | 2
man/zibinomUC.Rd | 2
man/zigeomUC.Rd | 2
man/zinegbinUC.Rd | 2
src/vdigami.f | 15 ++++-
src/vgam3.c | 5 +
63 files changed, 381 insertions(+), 244 deletions(-)
Title: Bayesian treed Gaussian process models
Diff between tgp versions 2.4-9 dated 2013-04-04 and 2.4-11 dated 2014-12-08
Description: Bayesian nonstationary, semiparametric nonlinear regression
and design by treed Gaussian processes (GPs) with jumps to the limiting
linear model (LLM). Special cases also implemented include Bayesian
linear models, CART, treed linear models, stationary separable and
isotropic GPs, and GP single-index models. Provides 1-d and 2-d plotting functions
(with projection and slice capabilities) and tree drawing, designed for
visualization of tgp-class output. Sensitivity analysis and
multi-resolution models are supported. Sequential experimental
design and adaptive sampling functions are also provided, including ALM,
ALC, and expected improvement. The latter supports derivative-free
optimization of noisy black-box functions.
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy
tgp-2.4-11/tgp/ChangeLog | 17 +++++++
tgp-2.4-11/tgp/DESCRIPTION | 39 ++++++++---------
tgp-2.4-11/tgp/MD5 | 69 +++++++++++++------------------
tgp-2.4-11/tgp/NAMESPACE | 4 -
tgp-2.4-11/tgp/R/mrtgp.R | 6 +-
tgp-2.4-11/tgp/R/plot.tgp.R | 8 +--
tgp-2.4-11/tgp/R/tgp.plot.proj.R | 10 ++--
tgp-2.4-11/tgp/R/tgp.plot.slice.R | 43 ++++++-------------
tgp-2.4-11/tgp/R/tgp.trees.R | 4 -
tgp-2.4-11/tgp/build |only
tgp-2.4-11/tgp/data/exp2d.rda |binary
tgp-2.4-11/tgp/inst/doc/tgp.R |only
tgp-2.4-11/tgp/inst/doc/tgp.pdf |binary
tgp-2.4-11/tgp/inst/doc/tgp2.R |only
tgp-2.4-11/tgp/inst/doc/tgp2.pdf |binary
tgp-2.4-11/tgp/man/dopt.gp.Rd | 2
tgp-2.4-11/tgp/man/plot.tgp.Rd | 38 ++---------------
tgp-2.4-11/tgp/man/predict.tgp.Rd | 19 +++++++-
tgp-2.4-11/tgp/man/tgp.default.params.Rd | 16 +++----
tgp-2.4-11/tgp/src/all_draws.c | 20 ++++----
tgp-2.4-11/tgp/src/gen_covar.c | 8 +--
tgp-2.4-11/tgp/src/matrix.c | 14 +++---
tgp-2.4-11/tgp/src/model.cc | 46 ++++++++++++++++----
tgp-2.4-11/tgp/src/predict.c | 10 ++--
tgp-2.4-11/tgp/src/predict_linear.c | 4 -
tgp-2.4-11/tgp/src/rand_draws.c | 4 -
tgp-2.4-11/tgp/src/rand_pdf.c | 4 -
tgp-2.4-11/tgp/src/sim.cc | 4 -
tgp-2.4-11/tgp/src/tree.cc | 63 ++++++++++++++++++++++++++--
tgp-2.4-11/tgp/src/tree.h | 4 +
tgp-2.4-11/tgp/vignettes/as.iRnw | 3 -
tgp-2.4-9/tgp/inst/doc/as.iRnw |only
tgp-2.4-9/tgp/inst/doc/cat.iRnw |only
tgp-2.4-9/tgp/inst/doc/exp.iRnw |only
tgp-2.4-9/tgp/inst/doc/fried.iRnw |only
tgp-2.4-9/tgp/inst/doc/it.iRnw |only
tgp-2.4-9/tgp/inst/doc/linear.iRnw |only
tgp-2.4-9/tgp/inst/doc/moto.iRnw |only
tgp-2.4-9/tgp/inst/doc/optim.iRnw |only
tgp-2.4-9/tgp/inst/doc/pred.iRnw |only
tgp-2.4-9/tgp/inst/doc/sens.iRnw |only
tgp-2.4-9/tgp/inst/doc/sin.iRnw |only
tgp-2.4-9/tgp/inst/doc/traces.iRnw |only
43 files changed, 256 insertions(+), 203 deletions(-)
Title: Spatially Explicit Capture-Recapture for Linear Habitats
Diff between secrlinear versions 1.0.3 dated 2014-12-02 and 1.0.4 dated 2014-12-08
Description: Tools for spatially explicit capture-recapture analysis of animal populations in linear habitats, extending package 'secr'
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 12 ++++++------
MD5 | 26 +++++++++++++-------------
NAMESPACE | 6 +++---
NEWS | 29 ++++++++++-------------------
R/clipmask.R | 10 ++++++----
R/networkdistance.R | 4 +++-
inst/doc/secrlinear-manual.pdf |binary
inst/doc/secrlinear-vignette.R | 2 +-
inst/doc/secrlinear-vignette.Rmd | 6 +++---
inst/doc/secrlinear-vignette.pdf |binary
man/clipmask.Rd | 8 +++++---
man/glymemask.Rd | 15 +++++++--------
man/secrlinear-package.Rd | 4 ++--
vignettes/secrlinear-vignette.Rmd | 6 +++---
14 files changed, 62 insertions(+), 66 deletions(-)
Title: Perform Rosenbaum bounds sensitivity tests for matched and
unmatched data.
Diff between rbounds versions 2.0 dated 2014-01-24 and 2.1 dated 2014-12-08
Description: Takes matched and unmatched data and calculates Rosenbaum bounds for the treatment effect. Calculates bounds for binary outcome data, Hodges-Lehmann point estimates, Wilcoxon signed-rank test for matched data and matched IV estimators, Wilcoxon sum rank test, and for data with multiple matched controls. Package is also designed to work with the Matching package and operate on Match() objects.
Author: Luke J. Keele
Maintainer: Luke J. Keele
DESCRIPTION | 8 +--
MD5 | 8 +--
R/hlsens.R | 139 ++++++++++++++++++++++++-----------------------------
man/SumTestSens.Rd | 18 +++---
man/hlsens.Rd | 2
5 files changed, 82 insertions(+), 93 deletions(-)
Title: Bayesian Dynamical System Model
Diff between bdynsys versions 1.2 dated 2014-01-16 and 1.3 dated 2014-12-08
Description: The package bdynsys for panel/longitudinal data combines methods to model
changes in up to four indicators over times as a function of the indicators
themselves and up to three predictors using ordinary differential equations
(ODEs) with polynomial terms that allow to model complex and nonlinear
effects. A Bayesian model selection approach is implemented. The package
provides also visualisation tools to plot phase portraits of the dynamic
system, showing the complex co-evolution of two indicators over time with the
possibility to highlight trajectories for specified entities (e.g. countries,
individuals). Furthermore the visualisation tools allow for making
predictions of the trajectories of specified entities with respect to the
indicators.
Author: Shyam Ranganathan, Viktoria Spaiser, Richard P. Mann, David J.T. Sumpter
Maintainer: Viktoria Spaiser
DESCRIPTION | 10 +++++-----
MD5 | 30 +++++++++++++++---------------
man/bayesfac.Rd | 2 +-
man/bayfacfig.Rd | 2 +-
man/bdynsys.Rd | 10 +++++-----
man/bestfitmod.Rd | 2 +-
man/dysymod.Rd | 2 +-
man/errorcorr.Rd | 6 +++---
man/findindexM.Rd | 2 +-
man/phaseportdat.Rd | 6 +++---
man/phaseportmod.Rd | 8 ++++----
man/plot_data.Rd | 4 ++--
man/polyfitbayes.Rd | 2 +-
man/polyfitreg.Rd | 2 +-
man/preprocess_data.Rd | 2 +-
man/selectterms.Rd | 2 +-
16 files changed, 46 insertions(+), 46 deletions(-)
Title: Visualizing Association Rules and Frequent Itemsets
Diff between arulesViz versions 0.1-9 dated 2014-03-10 and 1.0-0 dated 2014-12-08
Description: Various visualization techniques for association rules and itemsets. The packages also includes several interactive visualizations for rule exploration. This package extends package arules.
Author: Michael Hahsler and Sudheer Chelluboina
Maintainer: Michael Hahsler
DESCRIPTION | 12 ++--
MD5 | 22 ++++-----
R/AAA_helpers.R | 116 ++++++++++++++++++++++++------------------------
R/graph.R | 45 +++++++++---------
R/groupedmatrix.R | 15 ++++--
build/vignette.rds |binary
inst/NEWS | 6 ++
inst/doc/arulesViz.R | 11 ++--
inst/doc/arulesViz.Rnw | 7 +-
inst/doc/arulesViz.pdf |binary
man/plot.Rd | 31 +++++++-----
vignettes/arulesViz.Rnw | 7 +-
12 files changed, 141 insertions(+), 131 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Diff between arules versions 1.1-5 dated 2014-08-19 and 1.1-6 dated 2014-12-08
Description: Provides the infrastructure for representing,
manipulating and analyzing transaction data and patterns (frequent
itemsets and association rules). Also provides interfaces to
C implementations of the association mining algorithms Apriori and Eclat
by C. Borgelt.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph]
Maintainer: Michael Hahsler
DESCRIPTION | 8 -
MD5 | 42 +++---
R/apriori.R | 8 -
R/discretize.R | 2
R/dissimilarity.R | 20 +--
R/is.superset.R | 9 -
R/itemCoding.R | 5
R/itemMatrix.R | 3
R/transactions.R | 278 +++++++++++++++++++++++-----------------------
build/vignette.rds |binary
data/Adult.rda |binary
data/AdultUCI.rda |binary
data/Epub.rda |binary
data/Groceries.rda |binary
data/Income.rda |binary
data/IncomeESL.rda |binary
inst/NEWS | 9 +
inst/doc/arules.pdf |binary
man/discretize.Rd | 3
man/dissimilarity.Rd | 8 -
man/match.Rd | 10 -
man/transactions-class.Rd | 62 ++++------
22 files changed, 244 insertions(+), 223 deletions(-)