Title: Spatially explicit capture-recapture
Diff between secr versions 2.8.2 dated 2014-04-30 and 2.9.0 dated 2014-09-22
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
secr-2.8.2/secr/R/ARL.R |only
secr-2.8.2/secr/R/MMDM.R |only
secr-2.8.2/secr/R/RPSV.R |only
secr-2.8.2/secr/R/dbar.R |only
secr-2.9.0/secr/DESCRIPTION | 12
secr-2.9.0/secr/MD5 | 212 +++++----
secr-2.9.0/secr/NAMESPACE | 29 +
secr-2.9.0/secr/NEWS | 50 ++
secr-2.9.0/secr/R/D.designdata.R | 1
secr-2.9.0/secr/R/DENSITY.R | 22 -
secr-2.9.0/secr/R/Dsurface.R | 14
secr-2.9.0/secr/R/PG.R | 3
secr-2.9.0/secr/R/addCovariates.R | 25 +
secr-2.9.0/secr/R/autoini.R | 11
secr-2.9.0/secr/R/confint.secr.R | 14
secr-2.9.0/secr/R/derivedMS.R | 3
secr-2.9.0/secr/R/esa.R | 89 ++--
secr-2.9.0/secr/R/fxi.R | 408 +++++++++---------
secr-2.9.0/secr/R/homerange.R |only
secr-2.9.0/secr/R/make.mask.R | 12
secr-2.9.0/secr/R/mask.check.R | 14
secr-2.9.0/secr/R/methods.R | 345 ++-------------
secr-2.9.0/secr/R/model.average.R | 16
secr-2.9.0/secr/R/pdot.R | 17
secr-2.9.0/secr/R/plot.mask.r |only
secr-2.9.0/secr/R/plot.secr.R | 12
secr-2.9.0/secr/R/predict.secr.R |only
secr-2.9.0/secr/R/randomHabitat.R | 9
secr-2.9.0/secr/R/rbind.capthist.R | 2
secr-2.9.0/secr/R/read.traps.R | 6
secr-2.9.0/secr/R/reduce.R | 2
secr-2.9.0/secr/R/regionN.R | 149 ++++--
secr-2.9.0/secr/R/score.test.R | 11
secr-2.9.0/secr/R/secr.design.MS.R | 38 +
secr-2.9.0/secr/R/secr.fit.R | 213 ++++-----
secr-2.9.0/secr/R/secr.test.R |only
secr-2.9.0/secr/R/secrloglik.R | 160 +++----
secr-2.9.0/secr/R/sim.capthist.R | 37 +
secr-2.9.0/secr/R/sim.popn.R | 79 +--
secr-2.9.0/secr/R/sim.secr.R | 262 +++++++++---
secr-2.9.0/secr/R/split.capthist.R | 53 ++
secr-2.9.0/secr/R/suggest.buffer.R | 18
secr-2.9.0/secr/R/utility.R | 362 ++++++++++++++++
secr-2.9.0/secr/R/verify.R | 15
secr-2.9.0/secr/data/OVpossum.RData |only
secr-2.9.0/secr/data/deermouse.RData |binary
secr-2.9.0/secr/data/hornedlizard.RData |binary
secr-2.9.0/secr/data/housemouse.RData |binary
secr-2.9.0/secr/data/ovenbird.RData |binary
secr-2.9.0/secr/data/ovensong.RData |binary
secr-2.9.0/secr/data/possum.RData |binary
secr-2.9.0/secr/data/secrdemo.RData |binary
secr-2.9.0/secr/data/skink.RData |binary
secr-2.9.0/secr/data/stoatDNA.RData |binary
secr-2.9.0/secr/inst/doc/secr-datainput.pdf |binary
secr-2.9.0/secr/inst/doc/secr-densitysurfaces.pdf |binary
secr-2.9.0/secr/inst/doc/secr-finitemixtures.pdf |binary
secr-2.9.0/secr/inst/doc/secr-manual.pdf |binary
secr-2.9.0/secr/inst/doc/secr-overview.pdf |binary
secr-2.9.0/secr/inst/doc/secr-parameterisations.pdf |binary
secr-2.9.0/secr/inst/doc/secr-polygondetectors.pdf |binary
secr-2.9.0/secr/inst/doc/secr-sound.pdf |binary
secr-2.9.0/secr/inst/doc/secr-varyingeffort.pdf |binary
secr-2.9.0/secr/inst/extdata/OVforest.dbf |only
secr-2.9.0/secr/inst/extdata/OVforest.shp |only
secr-2.9.0/secr/inst/extdata/OVforest.shx |only
secr-2.9.0/secr/inst/extdata/capt.txt | 2
secr-2.9.0/secr/inst/extdata/leftbank.txt |only
secr-2.9.0/secr/man/CV.Rd | 11
secr-2.9.0/secr/man/Dsurface.Rd | 7
secr-2.9.0/secr/man/OVpossum.Rd |only
secr-2.9.0/secr/man/PG.Rd | 2
secr-2.9.0/secr/man/addCovariates.Rd | 7
secr-2.9.0/secr/man/autoini.Rd | 7
secr-2.9.0/secr/man/coulombe.Rd | 2
secr-2.9.0/secr/man/deermouse.Rd | 2
secr-2.9.0/secr/man/derivedMS.Rd | 8
secr-2.9.0/secr/man/details.Rd | 22 -
secr-2.9.0/secr/man/distancetotrap.Rd | 4
secr-2.9.0/secr/man/fx.total.Rd |only
secr-2.9.0/secr/man/fxi.Rd | 71 ++-
secr-2.9.0/secr/man/hcov.Rd | 6
secr-2.9.0/secr/man/homerange.Rd | 26 -
secr-2.9.0/secr/man/hornedlizard.Rd | 2
secr-2.9.0/secr/man/make.mask.Rd | 2
secr-2.9.0/secr/man/model.average.Rd | 2
secr-2.9.0/secr/man/ovenbird.Rd | 2
secr-2.9.0/secr/man/ovensong.Rd | 2
secr-2.9.0/secr/man/pdot.Rd | 9
secr-2.9.0/secr/man/plot.mask.Rd | 34 -
secr-2.9.0/secr/man/pointsInPolygon.Rd | 6
secr-2.9.0/secr/man/popn.Rd | 2
secr-2.9.0/secr/man/possum.Rd | 21
secr-2.9.0/secr/man/predict.secr.Rd | 2
secr-2.9.0/secr/man/predictDsurface.Rd | 7
secr-2.9.0/secr/man/randomHabitat.Rd | 2
secr-2.9.0/secr/man/reduce.capthist.Rd | 3
secr-2.9.0/secr/man/secr-package.Rd | 8
secr-2.9.0/secr/man/secr.design.MS.Rd | 4
secr-2.9.0/secr/man/secr.fit.Rd | 47 +-
secr-2.9.0/secr/man/secr.test.Rd |only
secr-2.9.0/secr/man/secrtest.Rd |only
secr-2.9.0/secr/man/sim.capthist.Rd | 14
secr-2.9.0/secr/man/sim.popn.Rd | 20
secr-2.9.0/secr/man/sim.secr.Rd | 32 +
secr-2.9.0/secr/man/smooths.Rd |only
secr-2.9.0/secr/man/stoatDNA.Rd | 2
secr-2.9.0/secr/man/strip.legend.Rd |only
secr-2.9.0/secr/man/subset.capthist.Rd | 8
secr-2.9.0/secr/man/utility.Rd |only
secr-2.9.0/secr/src/detectfn.c | 434 +++++++++++++++++++-
secr-2.9.0/secr/src/secr.c | 429 ++++++++++---------
secr-2.9.0/secr/src/secr.h | 159 ++++++-
secr-2.9.0/secr/src/simsecr.c | 58 ++
secr-2.9.0/secr/src/trapping.c | 113 ++++-
secr-2.9.0/secr/src/unmarked.c | 1
secr-2.9.0/secr/src/utils.c | 72 +--
117 files changed, 2871 insertions(+), 1528 deletions(-)
Title: Testthat code. Tools to make testing fun :)
Diff between testthat versions 0.8.1 dated 2014-02-21 and 0.9 dated 2014-09-22
Description: A testing package specifically tailored for R
that's fun, flexible and easy to set up.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham
testthat-0.8.1/testthat/man/is_false.Rd |only
testthat-0.9/testthat/DESCRIPTION | 44 ++--
testthat-0.9/testthat/LICENSE | 4
testthat-0.9/testthat/MD5 | 154 +++++++-------
testthat-0.9/testthat/NAMESPACE | 11 -
testthat-0.9/testthat/R/auto-test.r | 50 +++-
testthat-0.9/testthat/R/colour-text.r | 8
testthat-0.9/testthat/R/compare.r | 2
testthat-0.9/testthat/R/describe.r |only
testthat-0.9/testthat/R/expect-that.r | 1
testthat-0.9/testthat/R/expectation.r | 48 ++++
testthat-0.9/testthat/R/expectations.r | 141 +++++++-----
testthat-0.9/testthat/R/library.r | 3
testthat-0.9/testthat/R/mock.r |only
testthat-0.9/testthat/R/reporter-minimal.r | 4
testthat-0.9/testthat/R/reporter-stop.r | 1
testthat-0.9/testthat/R/reporter-summary.r | 6
testthat-0.9/testthat/R/reporter-tap.r | 2
testthat-0.9/testthat/R/reporter-teamcity.r | 78 ++++---
testthat-0.9/testthat/R/test-package.r | 2
testthat-0.9/testthat/R/test-that.r | 81 +++++--
testthat-0.9/testthat/R/traceback.r | 18 -
testthat-0.9/testthat/R/utils.r | 37 +++
testthat-0.9/testthat/R/watcher.r | 18 -
testthat-0.9/testthat/README.md | 14 -
testthat-0.9/testthat/man/ListReporter-class.Rd | 3
testthat-0.9/testthat/man/MinimalReporter-class.Rd | 3
testthat-0.9/testthat/man/MultiReporter-class.Rd | 3
testthat-0.9/testthat/man/Reporter-class.Rd | 3
testthat-0.9/testthat/man/SilentReporter-class.Rd | 3
testthat-0.9/testthat/man/StopReporter-class.Rd | 3
testthat-0.9/testthat/man/SummaryReporter-class.Rd | 3
testthat-0.9/testthat/man/TapReporter-class.Rd | 3
testthat-0.9/testthat/man/TeamcityReporter-class.Rd | 3
testthat-0.9/testthat/man/auto_test.Rd | 9
testthat-0.9/testthat/man/auto_test_package.Rd | 7
testthat-0.9/testthat/man/colourise.Rd | 10
testthat-0.9/testthat/man/compare_state.Rd | 5
testthat-0.9/testthat/man/context.Rd | 4
testthat-0.9/testthat/man/describe.Rd |only
testthat-0.9/testthat/man/dir_state.Rd | 10
testthat-0.9/testthat/man/equals.Rd | 40 +--
testthat-0.9/testthat/man/equals_reference.Rd |only
testthat-0.9/testthat/man/evaluate_promise.Rd | 11 -
testthat-0.9/testthat/man/expect-compare.Rd | 37 +--
testthat-0.9/testthat/man/expect_that.Rd | 16 -
testthat-0.9/testthat/man/expectation.Rd | 12 -
testthat-0.9/testthat/man/fail.Rd | 3
testthat-0.9/testthat/man/find_reporter.Rd | 3
testthat-0.9/testthat/man/gives_warning.Rd | 39 +--
testthat-0.9/testthat/man/has_names.Rd | 41 +--
testthat-0.9/testthat/man/is_a.Rd | 32 +-
testthat-0.9/testthat/man/is_equivalent_to.Rd | 34 +--
testthat-0.9/testthat/man/is_identical_to.Rd | 35 +--
testthat-0.9/testthat/man/is_null.Rd | 23 +-
testthat-0.9/testthat/man/is_true.Rd | 38 ++-
testthat-0.9/testthat/man/library_if_available.Rd | 5
testthat-0.9/testthat/man/make_expectation.Rd | 8
testthat-0.9/testthat/man/matches.Rd | 38 +--
testthat-0.9/testthat/man/not.Rd | 3
testthat-0.9/testthat/man/prints_text.Rd | 30 +-
testthat-0.9/testthat/man/reporter-accessors.Rd | 5
testthat-0.9/testthat/man/safe_digest.Rd | 3
testthat-0.9/testthat/man/shows_message.Rd | 39 +--
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testthat-0.9/testthat/man/takes_less_than.Rd | 15 -
testthat-0.9/testthat/man/test_dir.Rd | 14 -
testthat-0.9/testthat/man/test_env.Rd | 1
testthat-0.9/testthat/man/test_file.Rd | 7
testthat-0.9/testthat/man/test_package.Rd | 26 +-
testthat-0.9/testthat/man/test_that.Rd | 7
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testthat-0.9/testthat/man/throws_error.Rd | 32 +-
testthat-0.9/testthat/man/watch.Rd | 20 -
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testthat-0.9/testthat/src |only
testthat-0.9/testthat/tests/testthat/one.rds |only
testthat-0.9/testthat/tests/testthat/test-compare.r | 13 +
testthat-0.9/testthat/tests/testthat/test-context.r | 65 +++--
testthat-0.9/testthat/tests/testthat/test-describe.r |only
testthat-0.9/testthat/tests/testthat/test-expectations.r | 5
testthat-0.9/testthat/tests/testthat/test-mock.r |only
testthat-0.9/testthat/tests/testthat/test-watcher.r | 163 +++++++--------
84 files changed, 956 insertions(+), 715 deletions(-)
Title: Lasso method for RCON(V,E) models
Diff between sglasso versions 1.0-1 dated 2014-06-17 and 1.1-0 dated 2014-09-22
Description: RCON(V, E) models (Højsgaard, et al.,2008) are a kind of restriction of the Gaussian Graphical Models defined by a set of equality constraints on the entries of the concentration matrix. sglasso package implements the structured graphical lasso (sglasso) estimator proposed in Abbruzzo et al. (2014) for the weighted l1-penalized RCON(V, E) model. Two cyclic coordinate algorithms are implemented to compute the sglasso estimator, i.e., a cyclic coordinate minimization (CCM) algorithm and a cyclic coordinate descent (CCD) algorithm.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro
ChangeLog | 12 ++++++++++--
DESCRIPTION | 11 ++++++-----
MD5 | 32 +++++++++++++++++++-------------
R/fglasso.R |only
R/fglasso_model2mask.R |only
R/klcv.R |only
R/loglik.R | 5 ++---
R/mask2Te.R | 4 ++--
R/sglasso.R | 26 ++++++++++++++++++--------
man/Kh.Rd | 5 ++---
man/dglars-internal.Rd | 3 ++-
man/fglasso.Rd |only
man/klcv.Rd |only
man/loglik.Rd | 5 ++---
man/plot.sglasso.Rd | 5 ++---
man/sglasso-package.Rd | 11 ++++++-----
man/sglasso.Rd | 19 ++++++++++---------
man/summary.sglasso.Rd | 5 ++---
src/Makevars | 2 +-
src/gdf_fun.f90 |only
20 files changed, 84 insertions(+), 61 deletions(-)
Title: Distance and Similarity Measures
Diff between proxy versions 0.4-12 dated 2014-01-15 and 0.4-13 dated 2014-09-22
Description: Provides an extensible framework for the efficient calculation of auto- and cross-proximities, along with implementations of the most popular ones.
Author: David Meyer [aut, cre],
Christian Buchta [aut]
Maintainer: David Meyer
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/dissimilarities.R | 8 ++++++--
R/dist.R | 15 ++++++++++++---
build/vignette.rds |binary
inst/doc/overview.pdf |binary
tests/apply.Rout.save | 26 ++++++++++++++------------
7 files changed, 42 insertions(+), 27 deletions(-)
Title: Calculate Predicted Means for Linear Models
Diff between predictmeans versions 0.98 dated 2014-09-03 and 0.99 dated 2014-09-22
Description: This package provides functions to diagnose
and make inferences from various linear models, such as those obtained from 'aov',
'lm', 'glm', 'gls', 'lme', and 'lmer'. Inferences include predicted
means and standard errors, contrasts, multiple comparisons, permutation tests and graphs.
Author: Dongwen Luo, Siva Ganesh and John Koolaard
Maintainer: Dongwen Luo
DESCRIPTION | 8 +-
MD5 | 12 +--
NAMESPACE | 4 -
R/Kmatrix.R | 4 -
R/covariatemeans.R | 161 ++++++++++++++++++++++++--------------------
inst/NEWS | 5 +
man/predictmeans-package.Rd | 2
7 files changed, 110 insertions(+), 86 deletions(-)
Title: Flexible parametric survival and multi-state models
Diff between flexsurv versions 0.3 dated 2014-01-20 and 0.5 dated 2014-09-22
Description: Flexible parametric models for time-to-event data, including the Royston-Parmar spline model, generalized gamma and generalized F distributions. Any user-defined parametric distribution can be fitted, given at least an R function defining the probability density or hazard. There are also tools for fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson
Maintainer: Christopher Jackson
flexsurv-0.3/flexsurv/tests/flexsurv.R |only
flexsurv-0.3/flexsurv/tests/spline.R |only
flexsurv-0.3/flexsurv/tests/utils.R |only
flexsurv-0.5/flexsurv/DESCRIPTION | 22
flexsurv-0.5/flexsurv/MD5 | 86 -
flexsurv-0.5/flexsurv/NAMESPACE | 135 +
flexsurv-0.5/flexsurv/R/GenF.R | 420 ++---
flexsurv-0.5/flexsurv/R/GenGamma.R | 356 +---
flexsurv-0.5/flexsurv/R/Gompertz.R | 196 +-
flexsurv-0.5/flexsurv/R/custom.R |only
flexsurv-0.5/flexsurv/R/deriv.R | 181 +-
flexsurv-0.5/flexsurv/R/flexsurvreg.R | 1466 +++++++++++--------
flexsurv-0.5/flexsurv/R/fracpoly.R |only
flexsurv-0.5/flexsurv/R/mstate.R |only
flexsurv-0.5/flexsurv/R/spline.R | 580 ++++---
flexsurv-0.5/flexsurv/R/utils.R | 291 +++
flexsurv-0.5/flexsurv/build |only
flexsurv-0.5/flexsurv/data/bc.rda |only
flexsurv-0.5/flexsurv/data/bosms3.rda |only
flexsurv-0.5/flexsurv/data/bosms4.rda |only
flexsurv-0.5/flexsurv/inst/NEWS | 132 +
flexsurv-0.5/flexsurv/inst/doc |only
flexsurv-0.5/flexsurv/man/GenF.Rd | 218 +-
flexsurv-0.5/flexsurv/man/GenF.orig.Rd | 172 +-
flexsurv-0.5/flexsurv/man/GenGamma.Rd | 220 +-
flexsurv-0.5/flexsurv/man/GenGamma.orig.Rd | 188 +-
flexsurv-0.5/flexsurv/man/Gompertz.Rd | 174 +-
flexsurv-0.5/flexsurv/man/Survspline.Rd | 164 +-
flexsurv-0.5/flexsurv/man/basis.Rd |only
flexsurv-0.5/flexsurv/man/bc.Rd | 86 -
flexsurv-0.5/flexsurv/man/bos.Rd |only
flexsurv-0.5/flexsurv/man/flexsurv-package.Rd | 208 +-
flexsurv-0.5/flexsurv/man/flexsurvreg.Rd | 663 +++++---
flexsurv-0.5/flexsurv/man/flexsurvspline.Rd | 440 ++---
flexsurv-0.5/flexsurv/man/hazard.Rd |only
flexsurv-0.5/flexsurv/man/lines.flexsurvreg.Rd | 104 -
flexsurv-0.5/flexsurv/man/model.frame.flexsurvreg.Rd |only
flexsurv-0.5/flexsurv/man/msfit.flexsurvreg.Rd |only
flexsurv-0.5/flexsurv/man/normboot.flexsurvreg.Rd |only
flexsurv-0.5/flexsurv/man/plot.flexsurvreg.Rd | 227 +-
flexsurv-0.5/flexsurv/man/pmatrix.fs.Rd |only
flexsurv-0.5/flexsurv/man/pmatrix.simfs.Rd |only
flexsurv-0.5/flexsurv/man/qgeneric.Rd | 120 -
flexsurv-0.5/flexsurv/man/sim.fmsm.Rd |only
flexsurv-0.5/flexsurv/man/summary.flexsurvreg.Rd | 241 +--
flexsurv-0.5/flexsurv/man/totlos.fs.Rd |only
flexsurv-0.5/flexsurv/man/totlos.simfs.Rd |only
flexsurv-0.5/flexsurv/man/unroll.function.Rd |only
flexsurv-0.5/flexsurv/tests/test_base.R |only
flexsurv-0.5/flexsurv/tests/testthat |only
flexsurv-0.5/flexsurv/vignettes |only
51 files changed, 4021 insertions(+), 3069 deletions(-)
Title: Extending R's dendrogram functionality
Diff between dendextend versions 0.17.1 dated 2014-08-19 and 0.17.5 dated 2014-09-22
Description: The dendextend package offers a set of functions for extending
dendrogram objects in R, letting you visualize and compare trees of
hierarchical clusterings. You can (1) Adjust a trees graphical parameters
- the color, size, type, etc of its branches, nodes and labels. (2)
Visually and statistically compare different dendrograms to one another.
Author: Tal Galili [aut, cre, cph] (http://www.r-statistics.com),
Gavin Simpson [ctb],
Gregory Jefferis [ctb] (imported code from his dendroextras package),
Marco Gallotta [ctb] (a.k.a: marcog),
Johan Renaudie [ctb] (https://github.com/plannapus),
The R Core Team [ctb] (Thanks for the Infastructure, and code in the
examples),
Kurt Hornik [ctb],
Uwe Ligges [ctb],
Andrej-Nikolai Spiess [ctb],
Steve Horvath [ctb],
Peter Langfelder [ctb],
skullkey [ctb],
Mark Van Der Loo [ctb] (https://github.com/markvanderloo d3dendrogram),
Yoav Benjamini [ths]
Maintainer: Tal Galili
dendextend-0.17.1/dendextend/man/plot.dendlist.Rd |only
dendextend-0.17.1/dendextend/tests/test-all.R |only
dendextend-0.17.5/dendextend/DESCRIPTION | 14
dendextend-0.17.5/dendextend/MD5 | 54 -
dendextend-0.17.5/dendextend/NAMESPACE | 3
dendextend-0.17.5/dendextend/NEWS | 61 +
dendextend-0.17.5/dendextend/R/attr_access.R | 92 +
dendextend-0.17.5/dendextend/R/color_branches.R | 8
dendextend-0.17.5/dendextend/R/cor_bakers_gamma.R | 513 +++++-----
dendextend-0.17.5/dendextend/R/dendlist.R | 64 -
dendextend-0.17.5/dendextend/R/labels.R | 4
dendextend-0.17.5/dendextend/R/set.dendrogram.R | 11
dendextend-0.17.5/dendextend/R/zzz.R | 30
dendextend-0.17.5/dendextend/README.md | 6
dendextend-0.17.5/dendextend/TODO | 75 +
dendextend-0.17.5/dendextend/build/vignette.rds |binary
dendextend-0.17.5/dendextend/inst/doc/introduction.R | 5
dendextend-0.17.5/dendextend/inst/doc/introduction.Rmd | 80 +
dendextend-0.17.5/dendextend/inst/doc/introduction.html | 153 ++
dendextend-0.17.5/dendextend/inst/tests/test-cutree.dendrogram.R | 86 -
dendextend-0.17.5/dendextend/inst/tests/test-labels-assign.R | 397 +++----
dendextend-0.17.5/dendextend/inst/tests/test-labels_colors.R | 35
dendextend-0.17.5/dendextend/man/assign_values_to_leaves_edgePar.Rd |only
dendextend-0.17.5/dendextend/man/color_labels.Rd | 3
dendextend-0.17.5/dendextend/man/cor_bakers_gamma.Rd | 15
dendextend-0.17.5/dendextend/man/dendlist.Rd | 14
dendextend-0.17.5/dendextend/man/order.dendrogram-assign.Rd | 4
dendextend-0.17.5/dendextend/man/set.Rd | 3
dendextend-0.17.5/dendextend/tests/test-all.r |only
dendextend-0.17.5/dendextend/vignettes/introduction.Rmd | 80 +
30 files changed, 1156 insertions(+), 654 deletions(-)
Title: Response Probability Functions
Diff between rpf versions 0.38 dated 2014-09-04 and 0.39 dated 2014-09-22
Description: The purpose of this package is to factor out logic and math common
to Item Factor Analysis fitting, diagnostics, and analysis. It is
envisioned as core support code suitable for more specialized IRT packages
to build upon. Complete access to optimized C functions are made available
with R_RegisterCCallable.
Author: Joshua Pritikin [cre, aut],
Jonathan Weeks [ctb],
Li Cai [ctb],
Carrie Houts [ctb],
Phil Chalmers [ctb]
Maintainer: Joshua Pritikin
rpf-0.38/rpf/inst/tests/test-plink.R |only
rpf-0.39/rpf/DESCRIPTION | 12 ++++----
rpf-0.39/rpf/MD5 | 5 +--
rpf-0.39/rpf/inst/doc/diagnostics.html | 46 ++++++++++++++++-----------------
4 files changed, 31 insertions(+), 32 deletions(-)
Title: Rcpp Integration for Armadillo Templated Linear Algebra Library
Diff between RcppArmadillo versions 0.4.400.0 dated 2014-08-19 and 0.4.450.1.0 dated 2014-09-22
Description: R and Armadillo integration using Rcpp
Armadillo is a templated C++ linear algebra library (by Conrad Sanderson)
that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
A delayed evaluation approach is employed (during compile time) to combine
several operations into one, and to reduce (or eliminate) the need for
temporaries. This is accomplished through recursive templates and template
meta-programming.
This library is useful if C++ has been decided as the language of choice
(due to speed and/or integration capabilities), rather than another language.
The RcppArmadillo package includes the header files from the templated
Armadillo library. Thus users do not need to install Armadillo itself in
order to use RcppArmadillo.
This Armadillo integration provides a nice illustration of the
capabilities of the Rcpp package for seamless R and C++ integration.
Armadillo is licensed under the MPL 2.0, while RcppArmadillo (the Rcpp
bindings/bridge to Armadillo) is licensed under the GNU GPL version 2
or later, as is the rest of Rcpp.
Author: Romain Francois, Dirk Eddelbuettel and Doug Bates
Maintainer: Dirk Eddelbuettel
ChangeLog | 50 ++++
DESCRIPTION | 12 -
MD5 | 62 +++--
R/RcppArmadillo.package.skeleton.R | 44 ++--
R/inline.R | 2
inst/NEWS.Rd | 27 ++
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/include/RcppArmadillo/Alt_R_RNG.h |only
inst/include/RcppArmadilloConfig.h | 8
inst/include/RcppArmadilloForward.h | 11 -
inst/include/armadillo | 11 -
inst/include/armadillo_bits/Mat_bones.hpp | 11 -
inst/include/armadillo_bits/Mat_meat.hpp | 20 +
inst/include/armadillo_bits/Proxy.hpp | 213 ++++++++++++++++----
inst/include/armadillo_bits/arma_rng.hpp | 58 ++++-
inst/include/armadillo_bits/arma_version.hpp | 6
inst/include/armadillo_bits/compiler_setup.hpp | 2
inst/include/armadillo_bits/fn_elem.hpp | 8
inst/include/armadillo_bits/fn_norm.hpp | 6
inst/include/armadillo_bits/fn_sort_index.hpp | 208 ++++++++++++-------
inst/include/armadillo_bits/fn_symmat.hpp | 38 +++
inst/include/armadillo_bits/forward_bones.hpp | 3
inst/include/armadillo_bits/gmm_diag_bones.hpp | 37 +--
inst/include/armadillo_bits/gmm_diag_meat.hpp | 117 +++++++++-
inst/include/armadillo_bits/op_symmat_bones.hpp | 15 +
inst/include/armadillo_bits/op_symmat_meat.hpp | 88 +++++---
inst/include/armadillo_bits/operator_cube_minus.hpp | 4
inst/include/armadillo_bits/operator_minus.hpp | 4
inst/include/armadillo_bits/xtrans_mat_bones.hpp |only
inst/include/armadillo_bits/xtrans_mat_meat.hpp |only
inst/skeleton/rcpparma_hello_world.Rd |only
inst/unitTests/cpp/rng.cpp |only
inst/unitTests/runit.rng.R |only
man/RcppArmadillo-package.Rd | 93 +++-----
35 files changed, 821 insertions(+), 337 deletions(-)
Title: Simulation and Analysis of Random Fields
Diff between RandomFields versions 3.0.35 dated 2014-08-12 and 3.0.42 dated 2014-09-22
Description: Simulation of Gaussian and extreme value random fields;
conditional simulation; kriging; maximum likelihood estimation
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Peter Menck [aut], Sebastian Gross [aut], Ulrike Ober [ctb], Katharina Burmeister [ctb], Juliane Manitz [ctb], Paulo Ribeiro [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather
DESCRIPTION | 10
MD5 | 252 +++++++++--------
NAMESPACE | 54 ++-
R/Class.R | 24 -
R/Crossvalidation.R | 12
R/D.H.R | 75 ++---
R/Methods-RFestimation.R | 12
R/Methods-RFmodel.R | 47 ++-
R/Methods-RFsp.R | 351 ++++--------------------
R/Methods-aux.R |only
R/RF_GLOBALS.R | 2
R/RFfit.R | 2
R/RFgui.R | 497 ++++++++++++++++------------------
R/RFsp-plots.R | 110 ++++---
R/RMConvenienceModels.R | 8
R/RMmodels.R | 148 +++++++++-
R/auxiliary.R | 92 ++++--
R/convert.R | 60 ++--
R/empvario.R | 132 ++++-----
R/fitgauss.R | 236 +++++++++-------
R/generatemodels.R | 67 +---
R/getNset.R | 23 -
R/internal_use.R | 100 +++---
R/kriging.R | 207 +++++++++-----
R/rf.R | 34 +-
build |only
cleanup |only
inst |only
man/BRspecific.Rd | 4
man/Baysian.Rd | 7
man/Changings.Rd |only
man/Circulant.Rd | 36 +-
man/Constants.Rd | 2
man/Gaussian.Rd | 16 -
man/MajorRevisions.Rd | 3
man/Maxstable.Rd | 18 -
man/Print.Rd | 12
man/RF.Rd | 45 +--
man/RFempVariog-class.Rd | 4
man/RFfit-class.Rd | 21 -
man/RFgetMethodNames.Rd | 10
man/RFgetModelInfo.Rd | 5
man/RFgetModelNames.Rd | 4
man/RFinterpolate.Rd | 3
man/RFoldstyle.Rd | 10
man/RFoptions.Rd | 386 +++++++++++++++++---------
man/RFsimulate.Rd | 7
man/RFsimulateAdvanced.Rd | 5
man/RFsp-class.Rd | 3
man/RFspatialGridDataFrame-class.Rd | 17 -
man/RFspatialPointsDataFrame-class.Rd | 16 -
man/RMS.Rd | 4
man/RMangle.Rd | 31 +-
man/RMaskey.Rd | 73 ++--
man/RMbr2.Rd | 8
man/RMbr2bg.Rd | 8
man/RMbrownresnick.Rd | 17 -
man/RMcoxisham.Rd | 8
man/RMcutoff.Rd | 9
man/RMdagum.Rd | 2
man/RMexp.Rd | 23 +
man/RMexponential.Rd | 5
man/RMgauss.Rd | 12
man/RMgencauchy.Rd | 13
man/RMgengneiting.Rd | 2
man/RMgneiting.Rd | 46 ++-
man/RMintern.Rd | 43 +-
man/RMmatern.Rd | 53 ++-
man/RMmodel-class.Rd | 14
man/RMmodel.Rd | 2
man/RMmodelExt-class.Rd | 3
man/RMmodelsAdvanced.Rd | 40 +-
man/RMmqam.Rd | 5
man/RMmult.Rd | 10
man/RMnsst.Rd | 6
man/RMpoissonpoly.Rd | 35 ++
man/RMqam.Rd | 6
man/RMrational.Rd | 2
man/RMstable.Rd | 41 +-
man/RMstp.Rd | 9
man/RMtbm.Rd | 96 +++---
man/RMuser.Rd | 9
man/RP.Rd | 5
man/RPgauss.Rd | 9
man/RPopitz.Rd |only
man/RPt.Rd |only
man/RR.Rd | 16 -
man/RandomFields.Rd | 70 +++-
man/Tbm.Rd | 255 +++++++++--------
man/obsolete.Rd | 18 -
man/papers.Rd | 6
man/papers.jss14.Rd | 6
man/plot-method.Rd | 16 -
man/sp2RF.Rd |only
src/Brown.cc | 6
src/D.H.cc | 247 ++++++++++------
src/Families.cc | 4
src/Gneiting.cc | 34 +-
src/Huetchen.cc | 5
src/InternalCov.cc | 25 -
src/KeyInfo.cc | 23 +
src/MLE.cc | 6
src/Primitive.cc | 337 ++++++++++++++++-------
src/RF.h | 204 ++++++++++---
src/RandomFields.h | 59 +---
src/auxiliary.cc | 62 ++--
src/auxiliary.h | 21 -
src/basic.h | 4
src/circulant.cc | 77 +++--
src/direct.cc | 12
src/empvario.cc | 3
src/extremes.cc | 70 +++-
src/fftVario.cc | 111 ++++---
src/gauss.cc | 87 ++++-
src/getNset.cc | 212 ++++++++------
src/initNerror.cc | 183 ++++++++----
src/metropolis.cc | 10
src/nugget.cc | 4
src/operator.cc | 54 ++-
src/plusmalS.cc | 71 ++--
src/primitive.h | 4
src/randomshape.h | 6
src/sequential.cc | 10
src/simu.cc | 35 +-
src/startGetNset.cc | 56 ++-
src/tbm.cc | 46 +--
src/trend.cc | 25 +
src/userinterfaces.cc | 423 ++++++++++++++++++----------
vignettes |only
129 files changed, 4052 insertions(+), 2709 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Diff between polysat versions 1.3-2 dated 2013-09-06 and 1.3-3 dated 2014-09-22
Description: polysat is a collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export data in
ABI GeneMapper, Structure, ATetra, Tetrasat/Tetra, GenoDive, SPAGeDi,
POPDIST, STRand, and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics are also available. polysat can assist the user in estimating the
ploidy of samples, and lastly it can estimate allele frequencies in
populations, calculate pairwise Fst values based on those frequencies, and
export allele frequencies to SPAGeDi and adegenet.
Author: Lindsay V. Clark
Maintainer: "Lindsay V. Clark"
DESCRIPTION | 16 -
MD5 | 44 +++--
NAMESPACE | 1
NEWS | 41 ++++
R/classes_generics_methods.R | 9 -
R/dataexport.R | 3
R/dataimport.R | 27 ++-
R/individual_distance.R | 6
R/population_stats.R | 2
build |only
inst/doc/polysattutorial.R | 310 ++++---------------------------------
inst/doc/polysattutorial.Rnw | 28 +--
inst/doc/polysattutorial.pdf |binary
inst/extdata/ATetraExample.txt |only
inst/extdata/GeneMapperCBA15.txt |only
inst/extdata/GeneMapperCBA23.txt |only
inst/extdata/GeneMapperCBA28.txt |only
inst/extdata/GeneMapperExample.txt |only
inst/extdata/POPDISTexample1.txt |only
inst/extdata/POPDISTexample2.txt |only
inst/extdata/STRandExample.txt |only
inst/extdata/dominantExample.txt |only
inst/extdata/genodiveExample.txt |only
inst/extdata/spagediExample.txt |only
inst/extdata/structureExample.txt |only
inst/extdata/tetrasatExample.txt |only
man/assignClones.Rd | 8
man/read.STRand.Rd | 6
man/read.Structure.Rd | 13 +
vignettes/polysattutorial.Rnw | 28 +--
30 files changed, 209 insertions(+), 333 deletions(-)
Title: Draw Geographical Maps
Diff between maps versions 2.3-7 dated 2014-06-03 and 2.3-9 dated 2014-09-22
Description: Display of maps. Projection code and larger maps are in
separate packages (mapproj and mapdata).
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg
Maintainer: Ray Brownrigg
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/misc.r | 14 +++++++-------
data/world.cities.rda |binary
4 files changed, 14 insertions(+), 14 deletions(-)
Title: Tools for descriptive statistics
Diff between DescTools versions 0.99.8 dated 2014-09-20 and 0.99.8.1 dated 2014-09-22
Description: DescTools contains a bunch of basic statistic functions and convenience wrappers for efficiently describing data, creating specific plots, doing reports using MS Word, Excel or PowerPoint. The package's intention is to offer a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'camel style' was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell. Includes R source code and/or documentation previously published by (in alphabetical order): Nanina Anderegg, Tomas Aragon, Antti Arppe, Adrian Baddeley, Ben Bolker, Frederico Caeiro, Stephane Champely, Daniel Chessel, Leanne Chhay, Michael Dewey, Harold C. Doran, Stephane Dray, Charles Dupont, Jeff Enos, Claus Ekstrom, Martin Elff, John Fox, Tal Galili, Matthias Gamer, Joseph L. Gastwirth, Yulia R. Gel, Juergen Gross, Gabor Grothendieck, Frank E. Harrell Jr, Michael Hoehle, Christian W. Hoffmann, Markus Huerzeler, Wallace W. Hui, Rob J. Hyndman, Pablo J. Villacorta Iglesias, Matthias Kohl, Mikko Korpela, Detlew Labes, Friederich Leisch, Jim Lemon, Martin Maechler, Arni Magnusson, Daniel Malter, George Marsaglia, John Marsaglia, Alina Matei, David Meyer, Weiwen Miao, Yongyi Min, Markus Naepflin, Daniel Navarro, Klaus Nordhausen, Derek Ogle, Nick Parsons, Sandrine Pavoine, Roland Rapold, William Revelle, Tyler Rinker, Caroline Rodriguez, Venkatraman E. Seshan, Greg Snow, Michael Smithson, Werner A. Stahel, Yves Tille, Adrian Trapletti, Kevin Ushey, Jeremy VanDerWal, Bill Venables, John Verzani, Gregory R. Warnes, Stefan Wellek, Peter Wolf, Daniel Wollschlaeger, Achim Zeileis
Maintainer: Andri Signorell
DESCRIPTION | 9 -
MD5 | 12 -
R/DescTools-internal.R | 250 ++++++++++++++++++++--------------------
inst/doc/DescTools.pdf |binary
inst/doc/DescToolsCompanion.pdf |binary
man/DescTools-package.Rd | 12 -
src/pointinpolygon.c | 2
7 files changed, 143 insertions(+), 142 deletions(-)