Title: Dose-finding in drug combination Phase I trials using the
partial order continual reassessment method (PO-CRM).
Diff between pocrm versions 0.7 dated 2014-03-11 and 0.8 dated 2014-07-24
Description: This package provides functions to implement and simulate the partial order continual reassessment method (PO-CRM) for use in Phase I trials of combinations of agents. It also provides a function for generating a set of initial guesses (skeleton) for the toxicity probabilities at each combination that correspond to the set of possible orderings of the toxicity probabilities specified by the user.
Author: Nolan A. Wages
Maintainer: "Varhegyi, Nikole (nev4g)"
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/pocrm.imp.R | 6 ++----
man/pocrm.imp.Rd | 3 +++
4 files changed, 12 insertions(+), 11 deletions(-)
Title: Interface to Bold Systems API
Diff between bold versions 0.1.0 dated 2014-05-28 and 0.1.2 dated 2014-07-24
Description: A programmatic interface to the Web Service methods provided by
Bold Systems for genetic barcode data. Functions include methods for
searching by sequences by taxonomic names, ids, collectors, and
institutions; as well as a function for searching for specimens, and
downloading trace files.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
DESCRIPTION | 8
MD5 | 28 +--
NEWS | 13 +
R/bold_seq.R | 10 -
R/bold_seqspec.R | 1
R/bold_specimens.R | 1
R/zzz.R | 13 +
README.md | 4
build/vignette.rds |binary
inst/doc/bold_vignette.Rmd | 310 ++++++++++++++++++++++++++++++-----
inst/doc/bold_vignette.html | 270 +++++++++++++++++++++++++-----
tests/testthat/test-bold_seq.R | 6
tests/testthat/test-bold_seqspec.R | 6
tests/testthat/test-bold_specimens.R | 6
vignettes/bold_vignette.Rmd | 310 ++++++++++++++++++++++++++++++-----
15 files changed, 837 insertions(+), 149 deletions(-)
Title: Simultaneous Inference in General Parametric Models
Diff between multcomp versions 1.3-4 dated 2014-07-09 and 1.3-5 dated 2014-07-24
Description: Simultaneous tests and confidence intervals
for general linear hypotheses in parametric models, including
linear, generalized linear, linear mixed effects, and survival models.
The package includes demos reproducing analyzes presented
in the book "Multiple Comparisons Using R" (Bretz, Hothorn,
Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre],
Frank Bretz [aut],
Peter Westfall [aut],
Richard M. Heiberger [ctb],
Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 20 ++++++++++----------
R/helpers.R | 12 +++++++++++-
build/vignette.rds |binary
data/cholesterol.rda |binary
data/litter.rda |binary
inst/NEWS | 5 +++++
inst/doc/chfls1.pdf |binary
inst/doc/generalsiminf.pdf |binary
inst/doc/multcomp-examples.pdf |binary
man/modelparm.Rd | 4 ++--
11 files changed, 32 insertions(+), 17 deletions(-)
Title: Tools for simulating and plotting quantities of interest
estimated from Cox Proportional Hazards models
Diff between simPH versions 1.2.1 dated 2014-05-16 and 1.2.2 dated 2014-07-24
Description: The package simulates and plots quantities of interest (relative
hazards, first differences, and hazard ratios) for linear coefficients,
multiplicative interactions, polynomials, penalised splines, and
non-proportional hazards, as well as stratified survival curves from Cox
Proportional Hazard models. It also simulates and plots marginal effects
for multiplicative interactions.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 8
MD5 | 61 ++--
NAMESPACE | 5
NEWS | 15 +
R/MinMaxLines.R | 173 +++++++----
R/SurvExpand.R | 234 ++++++++--------
R/coxsimInteract.R | 420 ++++++++++++++---------------
R/coxsimLinear.R | 158 +++++-----
R/coxsimPoly.R | 164 +++++------
R/simGG.siminteract.R | 680 +++++++++++++++++++++++------------------------
R/simGG.simlinear.R | 380 +++++++++++++-------------
README.md | 136 +++++----
build/vignette.rds |binary
man/CarpenterFdaData.Rd | 2
man/GolubEUPData.Rd | 2
man/MinMaxLines.Rd |only
man/SurvExpand.Rd | 8
man/coxsimInteract.Rd | 2
man/coxsimLinear.Rd | 2
man/coxsimPoly.Rd | 2
man/coxsimSpline.Rd | 2
man/coxsimtvc.Rd | 2
man/ggfitStrata.Rd | 2
man/setXl.Rd | 2
man/simGG.Rd | 2
man/simGG.siminteract.Rd | 2
man/simGG.simlinear.Rd | 4
man/simGG.simpoly.Rd | 2
man/simGG.simspline.Rd | 2
man/simGG.simtvc.Rd | 2
man/simPH.Rd | 2
man/tvc.Rd | 2
32 files changed, 1281 insertions(+), 1197 deletions(-)
Title: Randomization inference tools
Diff between RItools versions 0.1-11 dated 2011-03-05 and 0.1-12 dated 2014-07-24
Description: Tools for randomization inference.
Author: Jake Bowers
Maintainer: Jake Bowers
RItools-0.1-11/RItools/inst/doc/RItools.pdf |only
RItools-0.1-12/RItools/.Rinstignore |only
RItools-0.1-12/RItools/DESCRIPTION | 25
RItools-0.1-12/RItools/MD5 |only
RItools-0.1-12/RItools/NAMESPACE | 6
RItools-0.1-12/RItools/NEWS | 35 +
RItools-0.1-12/RItools/R/flatten.xbalresult.R | 206 +++----
RItools-0.1-12/RItools/R/harmonic.R | 5
RItools-0.1-12/RItools/R/naImpute.R | 46 -
RItools-0.1-12/RItools/R/plot.xbal.R | 485 +++++++++++++++---
RItools-0.1-12/RItools/R/print.xbal.R | 157 +++--
RItools-0.1-12/RItools/R/utils.R | 81 ++-
RItools-0.1-12/RItools/R/xBalance.R | 206 ++++---
RItools-0.1-12/RItools/R/xBalance.find.goodstrats.R | 25
RItools-0.1-12/RItools/R/xBalance.make.stratwts.R | 106 ++-
RItools-0.1-12/RItools/R/xBalance.makeMM.R | 33 -
RItools-0.1-12/RItools/R/xBalance.makepooledsd.R | 21
RItools-0.1-12/RItools/R/xBalanceEngine.R | 132 ++--
RItools-0.1-12/RItools/R/xtable.xbal.R | 58 +-
RItools-0.1-12/RItools/inst/examples |only
RItools-0.1-12/RItools/inst/tests |only
RItools-0.1-12/RItools/man/balanceplot.Rd |only
RItools-0.1-12/RItools/man/plot.xbal.Rd | 166 +++---
RItools-0.1-12/RItools/man/print.xbal.Rd | 47 +
RItools-0.1-12/RItools/man/subset.xbal.Rd |only
RItools-0.1-12/RItools/man/xBalance.Rd | 34 -
RItools-0.1-12/RItools/man/xtable.xbal.Rd | 19
RItools-0.1-12/RItools/tests/naImputeTests.R | 20
RItools-0.1-12/RItools/tests/naImputeTests.Rout.save | 34 -
RItools-0.1-12/RItools/tests/xBalanceTests.R | 42 +
RItools-0.1-12/RItools/tests/xBalanceTests.Rout.save | 93 +--
RItools-0.1-12/RItools/tests/xBalanceTests2.R | 1
RItools-0.1-12/RItools/tests/xBalanceTests2.Rout.save | 54 +-
RItools-0.1-12/RItools/tests/zzz.R |only
34 files changed, 1336 insertions(+), 801 deletions(-)
Title: Distributed Lag Non-linear Models
Diff between dlnm versions 2.1.0 dated 2014-05-21 and 2.1.2 dated 2014-07-24
Description: The package dlnm contains functions to specify and run distributed lag linear and non-linear models.
Author: Antonio Gasparrini and Ben Armstrong
Maintainer: Antonio Gasparrini
DESCRIPTION | 8 ++++----
MD5 | 25 +++++++++++++------------
R/exphist.R | 1 +
R/mklag.R | 32 ++++++++++++++++----------------
R/plot.crosspred.R | 4 ++--
build/vignette.rds |binary
inst/ChangeLog | 11 +++++++++++
inst/doc/biblioVignette.bib |only
inst/doc/dlnmExtended.pdf |binary
inst/doc/dlnmOverview.pdf |binary
inst/doc/dlnmTS.pdf |binary
man/crossbasis.Rd | 2 +-
man/dlnm-internal.Rd | 1 +
man/exphist.Rd | 2 +-
14 files changed, 50 insertions(+), 36 deletions(-)
Title: Formula-driven table generation
Diff between tables versions 0.7.64 dated 2013-11-12 and 0.7.79 dated 2014-07-24
Description: Computes and displays complex tables of summary statistics
Author: Duncan Murdoch
Maintainer: Duncan Murdoch
DESCRIPTION | 11
MD5 | 40 +-
NAMESPACE | 10
R/RowFactor.R | 21 -
R/asTabular.R |only
R/html.tabular.R | 3
R/options.R | 1
R/pseudo.R | 5
R/subset.R | 140 ++++---
R/tabular.R | 197 ++++++++--
build/vignette.rds |binary
inst/NEWS | 24 +
inst/doc/tables.R | 821 +++++++++++++++++++++++----------------------
inst/doc/tables.Rnw | 155 +++++++-
inst/doc/tables.pdf |binary
man/Arguments.Rd |only
man/Heading.Rd | 15
man/Percent.Rd | 28 +
man/as.tabular.Rd |only
man/labelSubset.Rd |only
man/table_options.Rd | 14
vignettes/tables.Rnw | 155 +++++++-
vignettes/tables.Rout.save | 81 +++-
23 files changed, 1130 insertions(+), 591 deletions(-)
Title: The Rebmix Package
Diff between rebmix versions 2.6.0 dated 2014-06-25 and 2.6.1 dated 2014-07-24
Description: R functions for random univariate and multivariate finite mixture generation, number of components, component weights and component parameters estimation, printing and plotting of finite mixtures, bootstrapping and class membership prediction. Variables can be either continuous or discrete, may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families and should be independent within components.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode
DESCRIPTION | 10
MD5 | 90 ++---
R/IC.R | 28 +
R/REBMIX.R | 2
R/RNGMIX.R | 2
R/defaults.R | 2
R/predict.list.R | 2
build/vignette.rds |binary
data/adult.rda |binary
data/galaxy.rda |binary
data/weibull.rda |binary
data/wine.rda |binary
inst/NEWS.Rd | 8
inst/doc/rebmix.R | 322 ++++--------------
inst/doc/rebmix.Rnw | 702 ++++++++++++---------------------------
inst/doc/rebmix.pdf |binary
man/AIC.Rd | 14
man/AWE.Rd | 4
man/BIC.Rd | 2
man/CLC.Rd | 4
man/HQC.Rd | 4
man/ICL.Rd | 4
man/ICLBIC.Rd | 4
man/MDL.Rd | 5
man/PC.Rd |only
man/PRD.Rd | 8
man/REBMIX.Rd | 31 -
man/RNGMIX.Rd | 4
man/SSE.Rd | 2
man/adult.Rd | 4
man/boot.Rd | 12
man/demix.Rd | 8
man/dfmix.Rd | 8
man/galaxy.Rd | 16
man/logL.Rd | 2
man/pemix.Rd | 4
man/pfmix.Rd | 8
man/plot.REBMIX.Rd | 2
man/predict.list.Rd | 3
man/weibull.Rd | 2
man/wine.Rd | 6
src/rebmixf.c | 10
src/rebmixf.h | 1
src/rngmixf.c | 2
vignettes/algorithm.pdf |only
vignettes/rebmix.Rnw | 702 ++++++++++++---------------------------
vignettes/rebmix.bib | 843 +++++++++++++++++++++++++++++-------------------
47 files changed, 1198 insertions(+), 1689 deletions(-)
Title: toolbox for pseudo and quasi random number generation and RNG
tests.
Diff between randtoolbox versions 1.14 dated 2013-06-11 and 1.15 dated 2014-07-24
Description: The package provides (1) pseudo random generators - general linear congruential generators (Park Miller) and multiple recursive generators (Knuth TAOCP), generalized feedback shift register (SF-Mersenne Twister algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the Sobol sequence, the Halton sequence (thus include Van der Corput sequence) and (3) some additional tests such as the gap test, the serial test, the poker test... The package depends on rngWELL package but it can be provided without this dependency on demand to the maintainer. For true random number generation, use the 'random' package, for Latin Hypercube Sampling (a hybrid QMC method), use the 'lhs' package, a number of RNGs and tests for RNGs are provided by 'RDieHarder', all available on CRAN. There is also a small stand-alone package 'rngwell19937' for the WELL19937a RNG.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz (underlying C codes of (i) the SFMT algorithm from M. Matsumoto and M. Saito, (ii) the Knuth-TAOCP RNG from D. Knuth).
Maintainer: Christophe Dutang
randtoolbox-1.14/randtoolbox/ax_ext.m4 |only
randtoolbox-1.14/randtoolbox/inst/DocCopying.pdf |only
randtoolbox-1.15/randtoolbox/DESCRIPTION | 29 +----
randtoolbox-1.15/randtoolbox/LICENSE | 40 ------
randtoolbox-1.15/randtoolbox/MD5 | 36 +++---
randtoolbox-1.15/randtoolbox/build |only
randtoolbox-1.15/randtoolbox/inst/CITATION | 20 +--
randtoolbox-1.15/randtoolbox/inst/NEWS | 12 ++
randtoolbox-1.15/randtoolbox/inst/doc/fullpres.Rnw | 4
randtoolbox-1.15/randtoolbox/inst/doc/fullpres.pdf |binary
randtoolbox-1.15/randtoolbox/inst/doc/shortintro.Rnw | 4
randtoolbox-1.15/randtoolbox/inst/doc/shortintro.pdf |binary
randtoolbox-1.15/randtoolbox/man/colltest.Rd | 4
randtoolbox-1.15/randtoolbox/man/runifInterface.Rd | 4
randtoolbox-1.15/randtoolbox/src/SFMT.c | 104 +++++++++---------
randtoolbox-1.15/randtoolbox/src/congruRand.c | 45 ++++---
randtoolbox-1.15/randtoolbox/src/congruRand.h | 38 +++++-
randtoolbox-1.15/randtoolbox/src/version.c | 2
randtoolbox-1.15/randtoolbox/tools |only
randtoolbox-1.15/randtoolbox/vignettes/fullpres.Rnw | 4
randtoolbox-1.15/randtoolbox/vignettes/shortintro.Rnw | 4
21 files changed, 171 insertions(+), 179 deletions(-)
Title: Power and Sample size distribution of 2-stage BE studies via
simulations
Diff between Power2Stage versions 0.1-3 dated 2014-07-02 and 0.1-4 dated 2014-07-24
Description: Contains functions to calculate power and sample size distribution
of 2-stage 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 as well as the power calculation steps according to
Karalis & Macheras.
The third function calculates power and sample size distribution
of 2-stage BE studies with a futility criterion for the point
estimator of T/R from stage 1.
The fourth function calculates power of non-adaptive group
sequential (2-stage) BE studies.
The fifth function calculates power and sample size distribution
of 2-stage BE studies in 2 parallel groups.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [ctb]
Maintainer: Detlew Labes
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 6 +++++-
R/power_2stage_GS.R | 12 +++++++-----
R/power_2stage_KM.R | 2 +-
man/power.2stage.GS.Rd | 7 ++++---
6 files changed, 26 insertions(+), 19 deletions(-)
Title: Routines for fitting kinetic models with one or more state
variables to chemical degradation data
Diff between mkin versions 0.9-31 dated 2014-07-14 and 0.9-32 dated 2014-07-24
Description: Calculation routines based on the FOCUS Kinetics Report (2006).
Includes a function for conveniently defining differential equation models,
model solution based on eigenvalues if possible or using numerical solvers
and a choice of the optimisation methods made available by the FME package
(default is a Levenberg-Marquardt variant). Please note that no warranty is
implied for correctness of results or fitness for a particular purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke
DESCRIPTION | 8
MD5 | 32 +--
NEWS | 176 +++++++++++++++------
R/mkinerrmin.R | 7
R/mkinfit.R | 149 +++++++++++++-----
R/mkinresplot.R | 3
R/transform_odeparms.R | 22 +-
README.md | 28 ++-
TODO | 2
inst/doc/FOCUS_L.R | 28 +--
inst/doc/FOCUS_L.Rmd | 83 ++++------
inst/doc/FOCUS_L.html | 380 +++++++++++++++++++++++-----------------------
inst/doc/FOCUS_Z.pdf |binary
inst/doc/mkin.pdf |binary
man/mkinfit.Rd | 40 +++-
man/transform_odeparms.Rd | 2
vignettes/FOCUS_L.Rmd | 83 ++++------
17 files changed, 614 insertions(+), 429 deletions(-)
Title: Multiple testing procedures of Cox (2011) and Wang and Cox
(2007).
Diff between ManyTests versions 1.0 dated 2014-03-31 and 1.1 dated 2014-07-24
Description: Performs the multiple testing procedures of Cox (2011) and Wang and Cox (2007).
Author: Christiana Kartsonaki
Maintainer: Christiana Kartsonaki
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/plot_pvalues.R | 2 +-
man/ManyTests-package.Rd | 4 ++--
4 files changed, 10 insertions(+), 10 deletions(-)
Title: Tests for random and fixed effects for linear mixed effect
models (lmer objects of lme4 package).
Diff between lmerTest versions 2.0-6 dated 2014-02-24 and 2.0-11 dated 2014-07-24
Description: The package provides different kinds of tests on lmer
objects (of lme4 package). The tests comprise type 3 and type 1 F tests for
fixed effects, LRT tests for random effects, calculation of
population means for fixed factors with confidence intervals
and corresponding plots. Package also provides backward
elimination of non-significant effects
Author: Alexandra Kuznetsova [aut, cre],
Per Bruun Brockhoff [aut, ths],
Rune Haubo Bojesen Christensen [aut]
Maintainer: Alexandra Kuznetsova
DESCRIPTION | 6
MD5 | 29 +--
NAMESPACE | 6
R/classes.R | 2
R/lmerTestFunctions.R | 310 ++++++++++++++++++++++-------------
R/randelim.R | 43 +++-
R/utils.R | 164 ++++++++++++------
inst |only
man/TVbo.Rd | 1
man/anova-methods.Rd | 14 +
man/carrots.Rd | 4
man/lmer.Rd | 5
man/lmerTest-package.Rd | 4
man/merModLmerTest-class.Rd | 4
man/step.Rd | 10 +
tests/Examples/lmerTest-Ex.Rout.save | 189 ++++++++-------------
16 files changed, 467 insertions(+), 324 deletions(-)
Title: Imgur API Client Package for R
Diff between imguR versions 0.1.5 dated 2012-10-15 and 1.0.0 dated 2014-07-24
Description: A package to share plots using the image hosting service Imgur.com
Author: Thomas J. Leeper [aut, cre],
Aaron Statham [ctb],
Yihui Xie [ctb]
Maintainer: Thomas J. Leeper
imguR-0.1.5/imguR/R/dev.off.R |only
imguR-0.1.5/imguR/R/imguRupload.R |only
imguR-0.1.5/imguR/man/dev.off.Rd |only
imguR-0.1.5/imguR/man/imguRupload.Rd |only
imguR-0.1.5/imguR/man/to.imguR.Rd |only
imguR-1.0.0/imguR/DESCRIPTION | 29 +++---
imguR-1.0.0/imguR/MD5 | 122 ++++++++++++++++++++++++--
imguR-1.0.0/imguR/NAMESPACE | 16 +--
imguR-1.0.0/imguR/NEWS |only
imguR-1.0.0/imguR/R/account.r |only
imguR-1.0.0/imguR/R/account_album_count.r |only
imguR-1.0.0/imguR/R/account_albums.r |only
imguR-1.0.0/imguR/R/account_comment_count.r |only
imguR-1.0.0/imguR/R/account_comments.r |only
imguR-1.0.0/imguR/R/account_favorites.r |only
imguR-1.0.0/imguR/R/account_gallery.r |only
imguR-1.0.0/imguR/R/account_image_count.r |only
imguR-1.0.0/imguR/R/account_images.r |only
imguR-1.0.0/imguR/R/account_settings.r |only
imguR-1.0.0/imguR/R/account_verified.r |only
imguR-1.0.0/imguR/R/add_album_images.r |only
imguR-1.0.0/imguR/R/add_gallery_images.r |only
imguR-1.0.0/imguR/R/block_sender.r |only
imguR-1.0.0/imguR/R/create_album.r |only
imguR-1.0.0/imguR/R/create_comment.r |only
imguR-1.0.0/imguR/R/create_message.r |only
imguR-1.0.0/imguR/R/default_memes.r |only
imguR-1.0.0/imguR/R/delete_album.r |only
imguR-1.0.0/imguR/R/delete_comment.r |only
imguR-1.0.0/imguR/R/delete_conversation.r |only
imguR-1.0.0/imguR/R/delete_image.r |only
imguR-1.0.0/imguR/R/favorite_album.r |only
imguR-1.0.0/imguR/R/favorite_image.r |only
imguR-1.0.0/imguR/R/get_album.r |only
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imguR-1.0.0/imguR/R/get_comment.r |only
imguR-1.0.0/imguR/R/get_conversations.r |only
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imguR-1.0.0/imguR/R/get_gallery_images.r |only
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imguR-1.0.0/imguR/R/get_meme.r |only
imguR-1.0.0/imguR/R/get_memes_gallery.r |only
imguR-1.0.0/imguR/R/get_notifications.r |only
imguR-1.0.0/imguR/R/get_random_images.r |only
imguR-1.0.0/imguR/R/get_reddit_gallery.r |only
imguR-1.0.0/imguR/R/get_reddit_image.r |only
imguR-1.0.0/imguR/R/get_replies.r |only
imguR-1.0.0/imguR/R/http.r |only
imguR-1.0.0/imguR/R/imguR.R | 58 +++++++++---
imguR-1.0.0/imguR/R/imgur_login.r |only
imguR-1.0.0/imguR/R/mark_notification.r |only
imguR-1.0.0/imguR/R/onLoad.r |only
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imguR-1.0.0/imguR/R/update_album.r |only
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imguR-1.0.0/imguR/man/create_message.Rd |only
imguR-1.0.0/imguR/man/delete_album.Rd |only
imguR-1.0.0/imguR/man/delete_comment.Rd |only
imguR-1.0.0/imguR/man/delete_conversation.Rd |only
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imguR-1.0.0/imguR/man/favorite_image.Rd |only
imguR-1.0.0/imguR/man/get_album.Rd |only
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imguR-1.0.0/imguR/man/imguR.Rd | 89 +++++++++---------
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119 files changed, 224 insertions(+), 90 deletions(-)
Title: Functions and Datasets for "Introduction to Scientific
Programming and Simulation Using R".
Diff between spuRs versions 1.0.5 dated 2012-08-03 and 2.0.0 dated 2014-07-24
Description: This package provides functions and datasets from the book "Introduction to Scientific Programming and Simulation Using R".
Author: Owen Jones, Robert Maillardet, Andrew Robinson, Olga Borovkova, and Steven Carnie
Maintainer: Andrew Robinson
spuRs-1.0.5/spuRs/inst/resources/scripts/binom.sim.fig.r |only
spuRs-1.0.5/spuRs/inst/resources/scripts/bp_tree.r |only
spuRs-1.0.5/spuRs/inst/resources/scripts/mult_table.r |only
spuRs-1.0.5/spuRs/inst/resources/scripts/square_cube.r |only
spuRs-2.0.0/spuRs/DESCRIPTION | 16 -
spuRs-2.0.0/spuRs/MD5 | 85 ++++++----
spuRs-2.0.0/spuRs/NAMESPACE | 14 -
spuRs-2.0.0/spuRs/R/CMCSimulation.R |only
spuRs-2.0.0/spuRs/R/MCEstimation.R |only
spuRs-2.0.0/spuRs/R/MCSimulation.R |only
spuRs-2.0.0/spuRs/R/RK4adapt.R |only
spuRs-2.0.0/spuRs/R/booking_clerkMC.R |only
spuRs-2.0.0/spuRs/R/fitDistances.R | 1
spuRs-2.0.0/spuRs/data/kew.rda |binary
spuRs-2.0.0/spuRs/data/treeg.rda |binary
spuRs-2.0.0/spuRs/data/trees.rda |binary
spuRs-2.0.0/spuRs/data/ufc.plots.rda |binary
spuRs-2.0.0/spuRs/data/ufc.rda |binary
spuRs-2.0.0/spuRs/inst/resources/data/Melbourne_rainfall_mm.csv |only
spuRs-2.0.0/spuRs/inst/resources/data/Melbourne_rainfall_mm.txt |only
spuRs-2.0.0/spuRs/inst/resources/data/cars.txt |only
spuRs-2.0.0/spuRs/inst/resources/data/teeth.txt | 2
spuRs-2.0.0/spuRs/inst/resources/errata.pdf |binary
spuRs-2.0.0/spuRs/inst/resources/scripts/CMCSimulation.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/LotkaVolterra.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/MCEstimation.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/MCSimulation.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/ODEtest.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/RK4.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/RK4_fig.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/RK4adapt.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/Ti_lander.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/a_lander.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/add_event.r | 6
spuRs-2.0.0/spuRs/inst/resources/scripts/ascent.r | 5
spuRs-2.0.0/spuRs/inst/resources/scripts/booking_clerkMC.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/ch12ex6_f_gradf.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/ellipsis.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/euler.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/ev_web.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/hit_miss.r | 1
spuRs-2.0.0/spuRs/inst/resources/scripts/hit_miss2.r | 2
spuRs-2.0.0/spuRs/inst/resources/scripts/inventory_sim.r | 3
spuRs-2.0.0/spuRs/inst/resources/scripts/lander.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/ma.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/mc_bookingclerk.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/mc_machineshop.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/mc_tennis.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/midpoint.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/newtonraphson.r | 2
spuRs-2.0.0/spuRs/inst/resources/scripts/nfact2.r | 2
spuRs-2.0.0/spuRs/inst/resources/scripts/parachute_incomplete.r |only
spuRs-2.0.0/spuRs/inst/resources/scripts/ppoint.r | 8
spuRs-2.0.0/spuRs/inst/resources/scripts/primedensity.r | 4
spuRs-2.0.0/spuRs/inst/resources/scripts/rejecttriangle.r | 2
spuRs-2.0.0/spuRs/inst/resources/scripts/search.r | 2
spuRs-2.0.0/spuRs/inst/resources/scripts/seed-test.r | 28 +--
spuRs-2.0.0/spuRs/man/CMCSimulation.Rd |only
spuRs-2.0.0/spuRs/man/MCEstimation.Rd |only
spuRs-2.0.0/spuRs/man/MCSimulation.Rd |only
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spuRs-2.0.0/spuRs/man/fitDistances.Rd | 1
63 files changed, 104 insertions(+), 80 deletions(-)
Title: Sensitivity analysis using weighted M-statistics
Diff between sensitivitymw versions 1.0 dated 2014-05-13 and 1.1 dated 2014-07-24
Description: Sensitivity analysis analysis in matched observational studies with multiple controls using weighted M-statistics to increase design sensitivity.
Author: Paul R. Rosenbaum
Maintainer: Paul R. Rosenbaum
DESCRIPTION | 6 +++---
MD5 | 6 +++---
R/senmwCI.R | 6 ++++++
man/sensitivitymw-package.Rd | 2 +-
4 files changed, 13 insertions(+), 7 deletions(-)
Title: an R package for genetic analysis of populations with mixed
reproduction
Diff between poppr versions 1.0.6 dated 2014-03-05 and 1.1.0 dated 2014-07-24
Description: Population genetic analyses for hierarchical analysis of partially
clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar
Maintainer: Zhian N. Kamvar
poppr-1.0.6/poppr/R/bruvoclass.r |only
poppr-1.0.6/poppr/vignettes/getfile.png |only
poppr-1.0.6/poppr/vignettes/poppr_manual-117.pdf |only
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poppr-1.1.0/poppr/DESCRIPTION | 18
poppr-1.1.0/poppr/MD5 | 201
poppr-1.1.0/poppr/NAMESPACE | 52
poppr-1.1.0/poppr/NEWS | 65
poppr-1.1.0/poppr/R/Index_calculations.r | 822 +
poppr-1.1.0/poppr/R/amova.r |only
poppr-1.1.0/poppr/R/bruvo.r | 480
poppr-1.1.0/poppr/R/classes.r |only
poppr-1.1.0/poppr/R/data_subset.r | 658 -
poppr-1.1.0/poppr/R/distances.r | 512 -
poppr-1.1.0/poppr/R/file_handling.r | 418
poppr-1.1.0/poppr/R/internal.r | 1072 +-
poppr-1.1.0/poppr/R/messages.r |only
poppr-1.1.0/poppr/R/methods.r |only
poppr-1.1.0/poppr/R/mlg.r | 329
poppr-1.1.0/poppr/R/poppr.R |only
poppr-1.1.0/poppr/R/print_methods.r |only
poppr-1.1.0/poppr/R/sample_schemes.r | 88
poppr-1.1.0/poppr/R/sandbox.r | 592 -
poppr-1.1.0/poppr/R/visualizations.r | 776 +
poppr-1.1.0/poppr/R/zzz.r |only
poppr-1.1.0/poppr/README.md | 40
poppr-1.1.0/poppr/build/vignette.rds |binary
poppr-1.1.0/poppr/data/Aeut.rda |binary
poppr-1.1.0/poppr/data/Pinf.rda |only
poppr-1.1.0/poppr/data/monpop.rda |only
poppr-1.1.0/poppr/data/partial_clone.rda |binary
poppr-1.1.0/poppr/inst/CITATION | 2
poppr-1.1.0/poppr/inst/README |only
poppr-1.1.0/poppr/inst/doc/algo.R |only
poppr-1.1.0/poppr/inst/doc/algo.Rnw |only
poppr-1.1.0/poppr/inst/doc/algo.pdf |only
poppr-1.1.0/poppr/inst/doc/poppr_manual.R | 1739 +--
poppr-1.1.0/poppr/inst/doc/poppr_manual.Rnw | 5540 ++++++++---
poppr-1.1.0/poppr/inst/doc/poppr_manual.pdf |binary
poppr-1.1.0/poppr/man/Aeut.Rd | 23
poppr-1.1.0/poppr/man/Pinf.Rd |only
poppr-1.1.0/poppr/man/aboot.Rd |only
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poppr-1.1.0/poppr/man/bruvo.boot.Rd | 83
poppr-1.1.0/poppr/man/bruvo.dist.Rd | 92
poppr-1.1.0/poppr/man/bruvo.msn.Rd | 167
poppr-1.1.0/poppr/man/bruvomat-class.Rd | 8
poppr-1.1.0/poppr/man/bruvomat-methods.Rd | 25
poppr-1.1.0/poppr/man/clonecorrect.Rd | 82
poppr-1.1.0/poppr/man/coercion-methods.Rd |only
poppr-1.1.0/poppr/man/diss.dist.Rd | 35
poppr-1.1.0/poppr/man/genclone-class.Rd |only
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poppr-1.1.0/poppr/man/genind2genalex.Rd | 46
poppr-1.1.0/poppr/man/genotype_curve.Rd |only
poppr-1.1.0/poppr/man/getfile.Rd | 42
poppr-1.1.0/poppr/man/greycurve.Rd | 44
poppr-1.1.0/poppr/man/hierarchy-methods.Rd |only
poppr-1.1.0/poppr/man/ia.Rd | 167
poppr-1.1.0/poppr/man/info_table.Rd |only
poppr-1.1.0/poppr/man/informloci.Rd | 50
poppr-1.1.0/poppr/man/is.genclone.Rd |only
poppr-1.1.0/poppr/man/locus_table.Rd |only
poppr-1.1.0/poppr/man/missingno.Rd | 62
poppr-1.1.0/poppr/man/mlg.Rd | 160
poppr-1.1.0/poppr/man/monpop.Rd |only
poppr-1.1.0/poppr/man/partial_clone.Rd | 16
poppr-1.1.0/poppr/man/plot_poppr_msn.Rd |only
poppr-1.1.0/poppr/man/poppr-package.Rd |only
poppr-1.1.0/poppr/man/poppr.Rd | 299
poppr-1.1.0/poppr/man/poppr.all.Rd | 13
poppr-1.1.0/poppr/man/poppr.amova.Rd |only
poppr-1.1.0/poppr/man/poppr.msn.Rd | 121
poppr-1.1.0/poppr/man/popsub.Rd | 36
poppr-1.1.0/poppr/man/population-methods.Rd |only
poppr-1.1.0/poppr/man/private_alleles.Rd |only
poppr-1.1.0/poppr/man/read.genalex.Rd | 88
poppr-1.1.0/poppr/man/recode_polyploids.Rd |only
poppr-1.1.0/poppr/man/shufflepop.Rd | 54
poppr-1.1.0/poppr/man/splitcombine.Rd | 82
poppr-1.1.0/poppr/src/permut_shuffler.c | 109
poppr-1.1.0/poppr/src/poppr_distance.c | 693 +
poppr-1.1.0/poppr/tests |only
poppr-1.1.0/poppr/vignettes/algo-concordance.tex |only
poppr-1.1.0/poppr/vignettes/algo.Rnw |only
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poppr-1.1.0/poppr/vignettes/figure/bruvo_msn.pdf |binary
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poppr-1.1.0/poppr/vignettes/figure/greywidth_inverse.pdf |binary
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poppr-1.1.0/poppr/vignettes/poppr_manual-concordance.tex |only
poppr-1.1.0/poppr/vignettes/poppr_manual.Rnw | 5540 ++++++++---
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128 files changed, 15305 insertions(+), 6354 deletions(-)