Title: Spatially Explicit Capture-Recapture for Linear Habitats
Diff between secrlinear versions 1.0.4 dated 2014-12-08 and 1.0.5 dated 2015-01-11
Description: Tools for spatially explicit capture-recapture analysis of animal populations in linear habitats, extending package 'secr'
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 8 ++++----
MD5 | 28 ++++++++++++++--------------
NEWS | 5 +++++
R/clipmask.R | 4 ++--
R/networkdistance.R | 3 ++-
inst/CITATION | 5 ++---
inst/doc/secrlinear-manual.pdf |binary
inst/doc/secrlinear-vignette.Rmd | 19 +++++--------------
inst/doc/secrlinear-vignette.pdf |binary
man/clipmask.Rd | 2 +-
man/linearmask.object.Rd | 12 ++++++------
man/read.linearmask.Rd | 3 +--
man/secrlinear-package.Rd | 4 ++--
man/utility.Rd | 12 +++++++-----
vignettes/secrlinear-vignette.Rmd | 19 +++++--------------
15 files changed, 56 insertions(+), 68 deletions(-)
Title: R Interface to FOAAS
Diff between rfoaas versions 0.0.5 dated 2014-12-28 and 0.1.1 dated 2015-01-11
Description: R access to the FOAAS (F... Off As A Service) web service
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel
ChangeLog | 24 ++++++++++++++++++++++++
DESCRIPTION | 9 +++++----
MD5 | 11 ++++++-----
NAMESPACE | 1 +
R/foaas.R | 24 +++++++++++++++++-------
README.md | 4 ++--
tests |only
7 files changed, 55 insertions(+), 18 deletions(-)
Title: R port of the Scilab neldermead module
Diff between neldermead versions 1.0-9 dated 2014-03-02 and 1.0-10 dated 2015-01-11
Description: Provides several direct search optimization algorithms based on the
simplex method. The provided algorithms are direct search algorithms, i.e.
algorithms which do not use the derivative of the cost function. They are
based on the update of a simplex. The following algorithms are available: the
fixed shape simplex method of Spendley, Hext and Himsworth (unconstrained
optimization with a fixed shape simplex), the variable shape simplex method of
Nelder and Mead (unconstrained optimization with a variable shape simplex
made), and Box's complex method (constrained optimization with a variable
shape simplex).
Author: Sebastien Bihorel, Michael Baudin (author of the original
module)
Maintainer: Sebastien Bihorel
Changelog | 5 +
DESCRIPTION | 8 +--
MD5 | 98 +++++++++++++++++++--------------------
R/boxlinesearch.R | 2
R/costf.transposex.R | 2
R/fmin.gridsearch.R | 2
R/fminbnd.R | 4 -
R/fminbnd.function.R | 2
R/fminbnd.outputfun.R | 2
R/fminsearch.R | 2
R/fminsearch.function.R | 2
R/fminsearch.outputfun.R | 2
R/is.R | 2
R/neldermead.R | 2
R/neldermead.algo.R | 2
R/neldermead.autorestart.R | 2
R/neldermead.box.R | 2
R/neldermead.costf.R | 2
R/neldermead.destroy.R | 2
R/neldermead.fixed.R | 2
R/neldermead.function.R | 2
R/neldermead.get.R | 2
R/neldermead.interpolate.R | 2
R/neldermead.isrkelley.R | 2
R/neldermead.isroneill.R | 8 +--
R/neldermead.istorestart.R | 2
R/neldermead.log.R | 2
R/neldermead.outputcmd.R | 2
R/neldermead.restart.R | 2
R/neldermead.scaletocenter.R | 2
R/neldermead.scaletox0.R | 2
R/neldermead.search.R | 2
R/neldermead.set.R | 2
R/neldermead.startup.R | 2
R/neldermead.storehistory.R | 4 -
R/neldermead.termination.R | 2
R/neldermead.termstartup.R | 2
R/neldermead.updatesimp.R | 6 +-
R/neldermead.variable.R | 2
R/optimget.R | 2
R/optimset.R | 2
R/optimset.method.R | 2
R/print.neldermead.R | 2
R/scaleinconstraints.R | 2
R/summary.neldermead.R | 2
inst/doc/neldermead_manual.Rnw | 2
inst/doc/neldermead_manual.pdf |binary
man/neldermead-package.Rd | 4 -
vignettes/neldermead-package.tex | 4 -
vignettes/neldermead_manual.Rnw | 2
50 files changed, 113 insertions(+), 108 deletions(-)
Title: A Utility to Send Emails from R
Diff between mailR versions 0.3 dated 2014-05-17 and 0.4 dated 2015-01-11
Description: Interface to Apache Commons Email to send emails
from R.
Author: Rahul Premraj
Maintainer: Rahul Premraj
mailR-0.3/mailR/NEWS |only
mailR-0.3/mailR/inst/java/commons-email-1.3.2.jar |only
mailR-0.3/mailR/inst/java/javax.mail-1.5.1.jar |only
mailR-0.4/mailR/DESCRIPTION | 14
mailR-0.4/mailR/MD5 | 587 +++++++++++++++++++++-
mailR-0.4/mailR/NAMESPACE | 3
mailR-0.4/mailR/R/mailR.R | 39 -
mailR-0.4/mailR/README.md | 131 +++-
mailR-0.4/mailR/inst/java/commons-email-1.3.3.jar |only
mailR-0.4/mailR/inst/java/javax.mail.jar |only
mailR-0.4/mailR/java |only
mailR-0.4/mailR/man/send.mail.Rd | 78 --
12 files changed, 721 insertions(+), 131 deletions(-)
Title: Robust multivariate classification using highly optimised SVM
ensembles
Diff between classyfire versions 0.1-1 dated 2014-11-22 and 0.1-2 dated 2015-01-11
Description: A collection of functions for the creation and application of highly optimised, robustly evaluated ensembles of support vector machines (SVMs). The package takes care of training individual SVM classifiers using a fast parallel heuristic algorithm, and combines individual classifiers into ensembles. Robust metrics of classification performance are offered by bootstrap resampling and permutation testing.
Author: Eleni Chatzimichali
Maintainer: Eleni Chatzimichali
classyfire-0.1-1/classyfire/R/init.R |only
classyfire-0.1-2/classyfire/DESCRIPTION | 11 +++--
classyfire-0.1-2/classyfire/MD5 | 37 +++++++++++-------
classyfire-0.1-2/classyfire/NAMESPACE | 1
classyfire-0.1-2/classyfire/NEWS |only
classyfire-0.1-2/classyfire/R/attach.R |only
classyfire-0.1-2/classyfire/R/cfBuild.R | 35 +++++++++--------
classyfire-0.1-2/classyfire/R/cfPermute.R | 35 ++++++++---------
classyfire-0.1-2/classyfire/R/checks.R |only
classyfire-0.1-2/classyfire/R/complex.R | 13 +++---
classyfire-0.1-2/classyfire/R/parallel.R | 15 +++----
classyfire-0.1-2/classyfire/R/plots.R | 36 +++++++++++++++--
classyfire-0.1-2/classyfire/R/stats.R | 12 +++++
classyfire-0.1-2/classyfire/build |only
classyfire-0.1-2/classyfire/inst |only
classyfire-0.1-2/classyfire/man/cfBuild.Rd | 16 ++-----
classyfire-0.1-2/classyfire/man/cfPermute.Rd | 3 -
classyfire-0.1-2/classyfire/man/cfPredict.Rd | 14 ++++++
classyfire-0.1-2/classyfire/man/classyfire-package.Rd | 4 -
classyfire-0.1-2/classyfire/man/ggEnsHist.Rd | 2
classyfire-0.1-2/classyfire/man/ggFusedHist.Rd |only
classyfire-0.1-2/classyfire/tests |only
classyfire-0.1-2/classyfire/vignettes |only
23 files changed, 147 insertions(+), 87 deletions(-)
Title: Analysis of Growth Data
Diff between AGD versions 0.31 dated 2014-12-21 and 0.32 dated 2015-01-11
Description: Tools for NIHES course EP18 'Analysis of Growth Data', May 22-23
2012, Rotterdam.
Author: Stef van Buuren
Maintainer: Stef van Buuren
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
inst/CITATION | 32 ++++++++++++++++----------------
inst/NEWS | 3 +++
4 files changed, 26 insertions(+), 23 deletions(-)
Title: Target Inhibition Interaction using Maximization and
Minimization Averaging
Diff between timma versions 1.1.0 dated 2015-01-05 and 1.2.0 dated 2015-01-11
Description: Target Inhibition Interaction using Maximization/Minimization
Averaging
Author: Liye He
Maintainer: Liye He
DESCRIPTION | 8 +++++---
MD5 | 10 +++++++---
R/drugRank.R | 9 +++++++--
R/timma.R | 2 +-
build |only
inst |only
vignettes |only
7 files changed, 20 insertions(+), 9 deletions(-)
Title: Sampling Design for Spatially Explicit Capture-Recapture
Diff between secrdesign versions 2.2.1 dated 2014-11-26 and 2.2.2 dated 2015-01-11
Description: Tools for designing spatially explicit capture--recapture studies of animal populations (primarily a simulation manager for package secr)
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 8 ++++----
MD5 | 18 +++++++++---------
NEWS | 5 +++++
R/methods.R | 1 +
inst/CITATION | 5 ++---
inst/doc/secrdesign-manual.pdf |binary
inst/doc/secrdesign-vignette.pdf |binary
man/secrdesign-package.Rd | 4 ++--
vignettes/runsims1.RData |binary
vignettes/runsims2.RData |binary
10 files changed, 23 insertions(+), 18 deletions(-)
Title: Spatially Explicit Capture-Recapture
Diff between secr versions 2.9.2 dated 2014-11-26 and 2.9.3 dated 2015-01-11
Description: Functions to estimate the density and size of a spatially distributed animal population sampled with an array of passive detectors, such as traps, or by searching polygons or transects. Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.
Author: Murray Efford
Maintainer: Murray Efford
DESCRIPTION | 10 ++--
MD5 | 60 ++++++++++++++---------------
NAMESPACE | 1
NEWS | 28 +++++++++++++
R/addCovariates.R | 8 ++-
R/autoini.R | 2
R/clone.R | 59 ++++++++++++++++++++++++++++
R/empirical.R | 2
R/homerange.R | 4 +
R/make.capthist.R | 4 -
R/make.grid.R | 2
R/methods.R | 26 +++++++-----
R/plot.mask.r | 1
R/rbind.capthist.R | 18 ++++++--
R/secr.fit.R | 75 ++++++++++++++++++------------------
R/secrloglik.R | 16 ++++---
R/sim.popn.R | 93 ++++++++++++++++++++++++++++++++++++++-------
R/telemetry.R | 4 -
R/trap.builder.R | 22 +++++++---
R/utility.R | 17 +++++---
R/verify.R | 7 ++-
R/writeGPS.R | 2
inst/CITATION | 5 --
inst/doc/index.html | 33 ++++++++++++---
inst/doc/secr-manual.pdf |binary
inst/doc/secr-overview.pdf |binary
man/clone.Rd | 23 ++++++++---
man/secr-package.Rd | 14 +++++-
man/signalmatrix.Rd | 4 -
man/sim.popn.Rd | 17 +++-----
man/subset.capthist.Rd | 3 -
31 files changed, 399 insertions(+), 161 deletions(-)
Title: Bivariate Linear Errors-In-Variables Estimation
Diff between leiv versions 2.0-6 dated 2014-03-04 and 2.0-7 dated 2015-01-11
Description: Estimate the slope and intercept of a bivariate
linear relationship by calculating a posterior density
that is invariant to interchange and scaling of the
coordinates.
Author: David Leonard [aut, cre]
Maintainer: David Leonard
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
build/vignette.rds |binary
inst/CITATION | 5 ++---
inst/NEWS | 10 ++++++++++
5 files changed, 21 insertions(+), 12 deletions(-)
Title: Automated caret feature selection
Diff between fscaret versions 0.8.6.3 dated 2014-10-06 and 0.9 dated 2015-01-11
Description: Automated feature selection using variety of models
provided by caret package
Author: Jakub Szlek
Maintainer: Jakub Szlek
DESCRIPTION | 10 -
MD5 | 30 ++---
NAMESPACE | 2
R/classVarImp.R | 188 +++++++++++++++++++++++----------
R/fscaret.R | 61 +++++++++-
R/impCalc.R | 283 ++++++++++++++++++++++++++++++++++++++++++++------
R/regVarImp.R | 41 +++++--
build/vignette.rds |binary
inst/NEWS.Rd | 11 +
inst/doc/fscaret.R | 93 ++++++++++++++--
inst/doc/fscaret.Rnw | 90 +++++++++++++--
inst/doc/fscaret.pdf |binary
man/classVarImp.Rd | 14 --
man/fscaret.Rd | 2
man/impCalc.Rd | 15 +-
vignettes/fscaret.Rnw | 90 +++++++++++++--
16 files changed, 750 insertions(+), 180 deletions(-)
Title: Soil Physical Analysis
Diff between soilphysics versions 1.2 dated 2014-10-14 and 2.0 dated 2015-01-11
Description: Basic and model-based soil physical analyses.
Author: Anderson Rodrigo da Silva, Renato Paiva de Lima
Maintainer: Anderson Rodrigo da Silva
DESCRIPTION | 8 -
MD5 | 49 ++++++---
NAMESPACE | 13 ++
NEWS | 14 ++
R/fitsoilwater.R | 127 ++++++++++++------------
R/fitsoilwater2.R |only
R/fitsoilwater3.R |only
R/fitsoilwater4.R |only
R/fitsoilwater5.R |only
R/hemc.R |only
R/hydraulicCutOff.R |only
R/iwc.R |only
R/llwr.R | 231 ++++++++++++++++++++++++++++----------------
R/sigmaP.r | 2
R/soilwater2.R |only
R/soilwater3.R |only
R/soilwater4.R |only
R/soilwater5.R |only
man/figures/Thumbs.db |binary
man/figures/sigmaPfluxo.jpg |only
man/fitsoilwater.Rd | 3
man/fitsoilwater2.Rd |only
man/fitsoilwater3.Rd |only
man/fitsoilwater4.Rd |only
man/fitsoilwater5.Rd |only
man/hemc.Rd |only
man/hydraulicCutOff.Rd |only
man/iwc.Rd |only
man/llwr.Rd | 55 ++++++----
man/sigmaP.Rd | 11 +-
man/soilphysics-package.Rd | 38 +++++--
man/soilwater.Rd | 2
man/soilwater2.Rd |only
man/soilwater3.Rd |only
man/soilwater4.Rd |only
man/soilwater5.Rd |only
man/voidratio.Rd | 4
37 files changed, 360 insertions(+), 197 deletions(-)
Title: Readable Regular Expressions
Diff between regexr versions 0.0.2 dated 2014-12-22 and 1.0.2 dated 2015-01-11
Description: An R framework for constructing and managing human readable regular
expressions. It aims to provide tools that enable the user to write
regular expressions in a way that is similar to the ways R code is written.
The tools allow the user to (1) write in smaller, modular, named,
sub-expressions, (2) write top to bottom, rather than a single string (3)
comment individual chunks, (4) indent expressions to clearly present regular
expression groups, (5) add vertical line spaces and R comments (i.e., #),
and (6) test the validity of the concatenated expression and the modular
sub-expressions.
Author: Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker
regexr-0.0.2/regexr/R/regex.R |only
regexr-0.0.2/regexr/man/print.regex.Rd |only
regexr-0.0.2/regexr/man/regex-set-.regexr.Rd |only
regexr-0.0.2/regexr/man/regex.Rd |only
regexr-0.0.2/regexr/man/regex.regexr.Rd |only
regexr-0.0.2/regexr/tests/testthat/test-regex.R |only
regexr-1.0.2/regexr/DESCRIPTION | 21
regexr-1.0.2/regexr/MD5 | 86 +-
regexr-1.0.2/regexr/NAMESPACE | 19
regexr-1.0.2/regexr/NEWS | 64 +
regexr-1.0.2/regexr/R/add_comments.R | 4
regexr-1.0.2/regexr/R/as.regexr.R |only
regexr-1.0.2/regexr/R/comments.R | 19
regexr-1.0.2/regexr/R/construct.R | 125 +--
regexr-1.0.2/regexr/R/regex-class.R | 10
regexr-1.0.2/regexr/R/regexr-class.R | 81 +-
regexr-1.0.2/regexr/R/regexr-package.R | 20
regexr-1.0.2/regexr/R/set_names.R |only
regexr-1.0.2/regexr/R/subs.R |only
regexr-1.0.2/regexr/R/test.R | 8
regexr-1.0.2/regexr/R/unglue.R | 4
regexr-1.0.2/regexr/README.md | 351 +++++++---
regexr-1.0.2/regexr/inst/CITATION | 5
regexr-1.0.2/regexr/inst/functions_table/functions.R | 13
regexr-1.0.2/regexr/man/add_comments.Rd | 2
regexr-1.0.2/regexr/man/as.regexr.Rd |only
regexr-1.0.2/regexr/man/as.regexr.character.Rd |only
regexr-1.0.2/regexr/man/as.regexr.default.Rd |only
regexr-1.0.2/regexr/man/comments.Rd | 15
regexr-1.0.2/regexr/man/construct.Rd | 123 +--
regexr-1.0.2/regexr/man/get_construct.Rd |only
regexr-1.0.2/regexr/man/get_construct.reverse_construct.Rd |only
regexr-1.0.2/regexr/man/names-set-.regexr.Rd | 4
regexr-1.0.2/regexr/man/names.regexr.Rd | 2
regexr-1.0.2/regexr/man/print.reverse_construct.Rd |only
regexr-1.0.2/regexr/man/print.subcom.Rd |only
regexr-1.0.2/regexr/man/regexr.Rd | 20
regexr-1.0.2/regexr/man/set_names.Rd |only
regexr-1.0.2/regexr/man/subs-set-.regexr.Rd |only
regexr-1.0.2/regexr/man/subs.Rd |only
regexr-1.0.2/regexr/man/subs.regexr.Rd |only
regexr-1.0.2/regexr/man/test.Rd | 8
regexr-1.0.2/regexr/man/test.regexr.Rd | 4
regexr-1.0.2/regexr/man/unglue.Rd | 4
regexr-1.0.2/regexr/tests/testthat.R | 1
regexr-1.0.2/regexr/tests/testthat/test-as.regexr.R |only
regexr-1.0.2/regexr/tests/testthat/test-comment_binary_operator.R | 15
regexr-1.0.2/regexr/tests/testthat/test-comments.R | 29
regexr-1.0.2/regexr/tests/testthat/test-construct.R | 4
regexr-1.0.2/regexr/tests/testthat/test-get_construct.R |only
regexr-1.0.2/regexr/tests/testthat/test-names.R | 20
regexr-1.0.2/regexr/tests/testthat/test-print.subcom.R |only
regexr-1.0.2/regexr/tests/testthat/test-subs.R |only
regexr-1.0.2/regexr/tests/testthat/test-summary.R | 27
regexr-1.0.2/regexr/tests/testthat/test-test.R | 21
regexr-1.0.2/regexr/tests/testthat/test-unglue.R | 17
56 files changed, 750 insertions(+), 396 deletions(-)
Title: Quantile Regression
Diff between quantreg versions 5.08 dated 2015-01-09 and 5.11 dated 2015-01-11
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also included.
Author: Roger Koenker with contributions from Stephen Portnoy, Pin Ng, Achim Zeileis, Philip Grosjean and Brian Ripley
Maintainer: Roger Koenker
DESCRIPTION | 18 +++++++++++-------
MD5 | 8 ++++----
R/quantreg.R | 2 +-
man/qrisk.Rd | 8 +++++---
man/rq.fit.hogg.Rd | 5 +++--
5 files changed, 24 insertions(+), 17 deletions(-)
Title: Robust Meta-analysis and Meta-regression
Diff between metaplus versions 0.6-1 dated 2014-10-14 and 0.7-0 dated 2015-01-11
Description: Performs meta-analysis using standard and robust methods with confidence intervals from profile likelihood.
Author: Ken Beath
Maintainer: Ken Beath
DESCRIPTION | 12 +-
MD5 | 35 +++---
NAMESPACE | 8 -
R/aaaaa.R |only
R/confint.R |only
R/globals.R | 2
R/makestart.profilemix.metaplus.R | 6 -
R/makestart.profilenorm.metaplus.R | 24 ++--
R/mymle.R |only
R/myoptim.R |only
R/plot.metaplus.R | 72 ++++++------
R/profile.R |only
R/profilemix.metaplus.R | 56 ++++-----
R/profilemix.profile.R | 14 --
R/profilenorm.metaplus.R | 195 +++++++++++++++++-----------------
R/profilet.metaplus.R | 114 +++++++++++--------
R/profilet.profile.R | 23 +---
R/test.outliers.profilemix.metaplus.R | 83 +++++++-------
R/test.outliers.profilet.metaplus.R | 85 +++++++-------
inst/NEWS | 6 +
man/metaplus.Rd | 1
21 files changed, 381 insertions(+), 355 deletions(-)
Title: Hierarchical Exponential-Family Random Graph Models with Local
Dependence
Diff between hergm versions 2.1-0 dated 2015-01-04 and 2.1-1 dated 2015-01-11
Description: Estimate and simulate hierarchical exponential-family random graph models with local dependence.
Author: Michael Schweinberger
Maintainer: Michael Schweinberger
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/hergm.preprocess.R | 12 ++++--------
inst/CITATION | 25 +++++++++----------------
4 files changed, 20 insertions(+), 31 deletions(-)