Title: Polynomial spline routines
Diff between polspline versions 1.1.8 dated 2013-04-24 and 1.1.9 dated 2013-11-20
Description: Routines for the polynomial spline fitting routines
hazard regression, hazard estimation with flexible tails, logspline,
lspec, polyclass, and polymars, by C. Kooperberg and co-authors
Author: Charles Kooperberg
Maintainer: Charles Kooperberg
polspline-1.1.8/polspline/INDEX |only
polspline-1.1.9/polspline/DESCRIPTION | 14 +++++++-------
polspline-1.1.9/polspline/MD5 | 7 +++----
polspline-1.1.9/polspline/R/polspline.R | 2 +-
polspline-1.1.9/polspline/src/polymars.c | 3 ++-
5 files changed, 13 insertions(+), 13 deletions(-)
Title: Visualizes the scoring and binning of microsatellite fragment
sizes
Diff between MsatAllele versions 1.04 dated 2013-08-02 and 1.05 dated 2013-11-20
Description: The package contains functions to: 1) load ah files from Strand software and build a R data
base; 2) plot different graphical displays of the fragment sizes obtained for each locus and their bins; 3)
interact with graphs to sort the data base for a given locus and range, allowing to easily trace back a
particular group of samples to its original Strand file; bin fragment size data into population genetics files.
4) From version 1.04 on, the user can set manually bin limits and write files combining the manual and
automatic methods to bin alleles.
Author: Filipe Alberto
Maintainer: Filipe Alberto
DESCRIPTION | 8 ++--
MD5 | 8 ++--
R/read.frag.sizes.R | 85 ++++++++++++++++++++++++++--------------------
man/MsatAllele-package.Rd | 4 +-
man/read.frag.sizes.Rd | 3 +
5 files changed, 61 insertions(+), 47 deletions(-)
Title: Interpolation of data with variable spatial support
Diff between rtop versions 0.3-42 dated 2013-08-21 and 0.3-43 dated 2013-11-20
Description: Package for geostatistical interpolation of data with irregular spatial support such as runoff related data or data from administrative units.
Author: Jon Olav Skoien
Maintainer: Jon Olav Skoien
DESCRIPTION | 10 ++--
MD5 | 16 +++----
R/findOverlap.R | 113 +++++++++++++++++++++++++++++++++++--------------------
R/fitVariogram.R | 8 +++
R/gDist.r | 8 +--
R/rtop.R | 29 ++++----------
R/sceua.R | 35 ++++++++++-------
R/varMat.R | 16 ++++---
demo/rtopCandG.r | 2
9 files changed, 137 insertions(+), 100 deletions(-)
Title: General Frailty models: shared, joint and nested frailty models
with prediction
Diff between frailtypack versions 2.4.1 dated 2013-04-26 and 2.5 dated 2013-11-20
Description: Frailtypack now fits several classes of frailty models
using a penalized likelihood estimation on the hazard function
but also a parametric estimation. 1) A shared frailty
model (with gamma or log-normal frailty distribution) and
Cox proportional hazard model. Clustered and
recurrent survival times can be studied. 2) Additive frailty
models for proportional hazard models with two
correlated random effects (intercept random effect with random
slope). 3) Nested frailty models for hierarchically clustered
data (with 2 levels of clustering) by including two iid gamma
random effects. 4) Joint frailty models in the context of joint
modelling for recurrent events with terminal event for clustered
data or not. Prediction values are available. Left truncated (not for Joint model),
right-censored data, interval-censored data (only for Cox proportional
hazard and shared frailty model) and strata (max=2) are allowed. In each model,
the random effects have a gamma distribution, but you can switch to a log-normal
in shared and joint models. Now, you can also consider time-varying
covariates effects in Cox, shared and joint models. The package includes concordance
measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Amadou Diakite and Alexandre Laurent
Maintainer: Virginie Rondeau
frailtypack-2.4.1/frailtypack/R/CbootstrapFP.R |only
frailtypack-2.4.1/frailtypack/R/event2.R |only
frailtypack-2.4.1/frailtypack/R/multivePenal.R |only
frailtypack-2.4.1/frailtypack/R/plot.multivePenal.R |only
frailtypack-2.4.1/frailtypack/R/print.multivePenal.R |only
frailtypack-2.4.1/frailtypack/R/summary.multivePenal.R |only
frailtypack-2.4.1/frailtypack/R/transfo.table.R |only
frailtypack-2.4.1/frailtypack/data/dataMultiv.rda |only
frailtypack-2.4.1/frailtypack/man/dataMultiv.Rd |only
frailtypack-2.4.1/frailtypack/man/event2.Rd |only
frailtypack-2.4.1/frailtypack/man/multivePenal.Rd |only
frailtypack-2.4.1/frailtypack/man/plot.multivePenal.Rd |only
frailtypack-2.4.1/frailtypack/man/print.multivePenal.Rd |only
frailtypack-2.4.1/frailtypack/man/summary.multivePenal.Rd |only
frailtypack-2.4.1/frailtypack/src/AparamMultive.f90 |only
frailtypack-2.4.1/frailtypack/src/aGhermite.f90 |only
frailtypack-2.4.1/frailtypack/src/funcpaMultivCpm.f90 |only
frailtypack-2.4.1/frailtypack/src/funcpaMultivSplines.f90 |only
frailtypack-2.4.1/frailtypack/src/funcpaMultivWeib.f90 |only
frailtypack-2.4.1/frailtypack/src/multiveJoint.f90 |only
frailtypack-2.5/frailtypack/DESCRIPTION | 48
frailtypack-2.5/frailtypack/MD5 | 229
frailtypack-2.5/frailtypack/NAMESPACE | 14
frailtypack-2.5/frailtypack/NEWS | 13
frailtypack-2.5/frailtypack/R/Cmeasures.R | 178
frailtypack-2.5/frailtypack/R/additivePenal.R | 18
frailtypack-2.5/frailtypack/R/cindexes.B.R | 33
frailtypack-2.5/frailtypack/R/cindexes.R | 30
frailtypack-2.5/frailtypack/R/cindexes.W.R | 22
frailtypack-2.5/frailtypack/R/cindexes.frailty.R | 106
frailtypack-2.5/frailtypack/R/frailtyPenal.R | 56
frailtypack-2.5/frailtypack/R/hazard.R | 4
frailtypack-2.5/frailtypack/R/plot.jointPenal.R | 3
frailtypack-2.5/frailtypack/R/plot.predFrailty.R |only
frailtypack-2.5/frailtypack/R/plot.predJoint.R |only
frailtypack-2.5/frailtypack/R/prediction.R |only
frailtypack-2.5/frailtypack/R/print.Cmeasures.R | 179
frailtypack-2.5/frailtypack/R/print.additivePenal.R | 13
frailtypack-2.5/frailtypack/R/print.frailtyPenal.R | 19
frailtypack-2.5/frailtypack/R/print.jointPenal.R | 25
frailtypack-2.5/frailtypack/R/print.nestedPenal.R | 15
frailtypack-2.5/frailtypack/R/print.predFrailty.R |only
frailtypack-2.5/frailtypack/R/print.predJoint.R |only
frailtypack-2.5/frailtypack/R/statFP.R | 62
frailtypack-2.5/frailtypack/R/summary.frailtyPenal.R | 5
frailtypack-2.5/frailtypack/R/survival.R | 30
frailtypack-2.5/frailtypack/demo/frailtypack_additivePenal.R | 2
frailtypack-2.5/frailtypack/demo/frailtypack_frailtyPenal.R | 2
frailtypack-2.5/frailtypack/demo/frailtypack_jointPenal.R | 4
frailtypack-2.5/frailtypack/demo/frailtypack_nestedPenal.R | 2
frailtypack-2.5/frailtypack/man/Cmeasures.Rd | 67
frailtypack-2.5/frailtypack/man/SurvIC.Rd | 6
frailtypack-2.5/frailtypack/man/additivePenal.Rd | 23
frailtypack-2.5/frailtypack/man/frailtyPenal.Rd | 63
frailtypack-2.5/frailtypack/man/frailtypack-package.Rd | 16
frailtypack-2.5/frailtypack/man/hazard.Rd | 4
frailtypack-2.5/frailtypack/man/num.id.Rd | 6
frailtypack-2.5/frailtypack/man/plot.prediction.Rd |only
frailtypack-2.5/frailtypack/man/plotAdditive.Rd | 2
frailtypack-2.5/frailtypack/man/plotFrailtyPenal.Rd | 8
frailtypack-2.5/frailtypack/man/plotJointPenal.Rd | 15
frailtypack-2.5/frailtypack/man/plotNestedPenal.Rd | 4
frailtypack-2.5/frailtypack/man/prediction.Rd |only
frailtypack-2.5/frailtypack/man/print.Cmeasures.Rd | 54
frailtypack-2.5/frailtypack/man/print.prediction.Rd |only
frailtypack-2.5/frailtypack/man/printAdditive.Rd | 31
frailtypack-2.5/frailtypack/man/printFrailtyPenal.Rd | 44
frailtypack-2.5/frailtypack/man/printJointPenal.Rd | 40
frailtypack-2.5/frailtypack/man/printNestedPenal.Rd | 20
frailtypack-2.5/frailtypack/man/readmission.Rd | 2
frailtypack-2.5/frailtypack/man/slope.Rd | 7
frailtypack-2.5/frailtypack/man/summaryAdditive.Rd | 2
frailtypack-2.5/frailtypack/man/summaryFrailtyPenal.Rd | 8
frailtypack-2.5/frailtypack/man/summaryJointPenal.Rd | 10
frailtypack-2.5/frailtypack/man/summaryNestedPenal.Rd | 2
frailtypack-2.5/frailtypack/man/survival.Rd | 4
frailtypack-2.5/frailtypack/man/timedep.Rd | 12
frailtypack-2.5/frailtypack/src/Adonnees.f90 | 152
frailtypack-2.5/frailtypack/src/Aparameters.f90 | 250
frailtypack-2.5/frailtypack/src/aaOptim.f90 | 1428 +--
frailtypack-2.5/frailtypack/src/aaOptimres.f90 | 224
frailtypack-2.5/frailtypack/src/aaUseFunction.f90 | 1031 +-
frailtypack-2.5/frailtypack/src/aaUseFunctionG.f90 | 438 -
frailtypack-2.5/frailtypack/src/aamarq98o.f90 | 828 -
frailtypack-2.5/frailtypack/src/additive.f90 | 4419 +++++-----
frailtypack-2.5/frailtypack/src/afuncpasres.f90 | 597 -
frailtypack-2.5/frailtypack/src/aresidusMartingale.f90 | 659 -
frailtypack-2.5/frailtypack/src/atestWald.f90 | 88
frailtypack-2.5/frailtypack/src/distance.f90 | 3407 ++-----
frailtypack-2.5/frailtypack/src/frailtypack.f90 | 4596 +++++-----
frailtypack-2.5/frailtypack/src/funcpaG_tps.f90 | 504 -
frailtypack-2.5/frailtypack/src/funcpaGcpm.f90 | 802 -
frailtypack-2.5/frailtypack/src/funcpaGcpm_intcens.f90 | 910 +-
frailtypack-2.5/frailtypack/src/funcpaGcpm_log.f90 | 780 -
frailtypack-2.5/frailtypack/src/funcpaGsplines.f90 | 678 -
frailtypack-2.5/frailtypack/src/funcpaGsplines_intcens.f90 | 735 -
frailtypack-2.5/frailtypack/src/funcpaGsplines_log.f90 | 686 -
frailtypack-2.5/frailtypack/src/funcpaGweib.f90 | 544 -
frailtypack-2.5/frailtypack/src/funcpaGweib_intcens.f90 | 552 -
frailtypack-2.5/frailtypack/src/funcpaGweib_log.f90 | 514 -
frailtypack-2.5/frailtypack/src/funcpaacpm.f90 | 1210 +-
frailtypack-2.5/frailtypack/src/funcpaasplines.f90 | 1198 +-
frailtypack-2.5/frailtypack/src/funcpaaweib.f90 | 964 +-
frailtypack-2.5/frailtypack/src/funcpaj_tps.f90 | 708 -
frailtypack-2.5/frailtypack/src/funcpajcpm.f90 | 392
frailtypack-2.5/frailtypack/src/funcpajcpm_log.f90 | 472 -
frailtypack-2.5/frailtypack/src/funcpajsplines.f90 | 560 -
frailtypack-2.5/frailtypack/src/funcpajsplines_intcens.f90 | 544 -
frailtypack-2.5/frailtypack/src/funcpajsplines_log.f90 | 530 -
frailtypack-2.5/frailtypack/src/funcpajweib.f90 | 352
frailtypack-2.5/frailtypack/src/funcpajweib_intcens.f90 | 376
frailtypack-2.5/frailtypack/src/funcpajweib_log.f90 | 372
frailtypack-2.5/frailtypack/src/funcpancpm.f90 | 1044 +-
frailtypack-2.5/frailtypack/src/funcpansplines.f90 | 1100 +-
frailtypack-2.5/frailtypack/src/funcpanweib.f90 | 676 -
frailtypack-2.5/frailtypack/src/funcpas_tps.f90 | 656 -
frailtypack-2.5/frailtypack/src/funcpascpm.f90 | 718 -
frailtypack-2.5/frailtypack/src/funcpascpm_intcens.f90 | 544 -
frailtypack-2.5/frailtypack/src/funcpascpm_log.f90 | 693 -
frailtypack-2.5/frailtypack/src/funcpassplines.f90 | 590 -
frailtypack-2.5/frailtypack/src/funcpassplines_intcens.f90 | 612 -
frailtypack-2.5/frailtypack/src/funcpassplines_log.f90 | 576 -
frailtypack-2.5/frailtypack/src/funcpasweib.f90 | 420
frailtypack-2.5/frailtypack/src/funcpasweib_intcens.f90 | 458 -
frailtypack-2.5/frailtypack/src/funcpasweib_log.f90 | 448 -
frailtypack-2.5/frailtypack/src/joint.f90 | 4332 ++++-----
frailtypack-2.5/frailtypack/src/nested.f90 | 4787 +++++------
frailtypack-2.5/frailtypack/src/prediction.f90 |only
frailtypack-2.5/frailtypack/src/risque.f90 | 116
frailtypack-2.5/frailtypack/src/survival.f90 | 486 -
130 files changed, 25522 insertions(+), 26796 deletions(-)
Title: This package fits eyewitness data using Clark's (2003) WITNESS
model
Diff between witness versions 1.1 dated 2013-09-20 and 1.2 dated 2013-11-20
Description: WITNESS is a computational model intended to understand the
psychological processes underlying eyewitness identification. This package
contains the WITNESS computational model as well as two methods of fitting
the model to data.
Author: Dustin Fife
Maintainer: Dustin Fife
ChangeLog | 7 ++++++-
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/witness.est.r | 3 +--
R/witness.genetic.R | 12 +++++++-----
R/witness.optim.R | 3 +--
R/witness.starting.params.R | 3 +--
7 files changed, 26 insertions(+), 22 deletions(-)
Title: Nonparametric Multiple Change Point Analysis of Multivariate
Data
Diff between ecp versions 1.5.4 dated 2013-06-08 and 1.5.5 dated 2013-11-20
Description: This package performs hierarchical change point analysis
through the use of U-statistics. Both agglomerative
and divisive procedures return the set of change points estimates,
and other summary information.
Author: Nicholas A. James and David S. Matteson
Maintainer: Nicholas A. James
DESCRIPTION | 16 ++++++++--------
MD5 | 14 +++++++-------
NEWS | 8 ++++++++
data/ACGH.RData |binary
data/DJIA.RData |binary
man/DJIA.RData.Rd | 4 +++-
man/e.agglo.Rd | 2 ++
man/e.divisive.Rd | 4 +---
8 files changed, 29 insertions(+), 19 deletions(-)
Title: Tools to make developing R code easier
Diff between devtools versions 1.3 dated 2013-07-04 and 1.4 dated 2013-11-20
Description: Collection of package development tools
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Hadley Wickham
devtools-1.3/devtools/NEWS |only
devtools-1.3/devtools/tests/testthat/testInvalidDescription |only
devtools-1.3/devtools/tests/testthat/testVignettes/inst |only
devtools-1.4/devtools/DESCRIPTION | 42 -
devtools-1.4/devtools/MD5 | 224 +++++-----
devtools-1.4/devtools/NAMESPACE | 2
devtools-1.4/devtools/R/build-github-devtools.r |only
devtools-1.4/devtools/R/build.r | 3
devtools-1.4/devtools/R/check-cran.r | 7
devtools-1.4/devtools/R/check-devtools.r | 2
devtools-1.4/devtools/R/check-doc.r | 8
devtools-1.4/devtools/R/check.r | 5
devtools-1.4/devtools/R/decompress.r | 18
devtools-1.4/devtools/R/dev-help.r | 7
devtools-1.4/devtools/R/document.r | 25 -
devtools-1.4/devtools/R/has-devel.r | 1
devtools-1.4/devtools/R/install-bitbucket.r | 1
devtools-1.4/devtools/R/install-github.r | 86 +++
devtools-1.4/devtools/R/install-local.r | 18
devtools-1.4/devtools/R/install-url.r | 12
devtools-1.4/devtools/R/install-version.r | 12
devtools-1.4/devtools/R/install.r | 64 ++
devtools-1.4/devtools/R/load.r | 57 +-
devtools-1.4/devtools/R/namespace-env.r | 159 +++++++
devtools-1.4/devtools/R/package-deps.r | 1
devtools-1.4/devtools/R/release.r | 56 +-
devtools-1.4/devtools/R/reverse-dependencies.r | 20
devtools-1.4/devtools/R/run-source.r | 109 +++-
devtools-1.4/devtools/R/show-news.r | 2
devtools-1.4/devtools/R/source.r | 5
devtools-1.4/devtools/R/utils.r | 21
devtools-1.4/devtools/R/vignettes.r | 4
devtools-1.4/devtools/R/zzz.r | 2
devtools-1.4/devtools/README.md | 2
devtools-1.4/devtools/man/as.envlist.Rd | 2
devtools-1.4/devtools/man/as.package.Rd | 2
devtools-1.4/devtools/man/bash.Rd | 2
devtools-1.4/devtools/man/build.Rd | 4
devtools-1.4/devtools/man/build_github_devtools.Rd |only
devtools-1.4/devtools/man/build_vignettes.Rd | 7
devtools-1.4/devtools/man/build_win.Rd | 3
devtools-1.4/devtools/man/check.Rd | 12
devtools-1.4/devtools/man/check_cran.Rd | 10
devtools-1.4/devtools/man/check_dep_version.Rd | 3
devtools-1.4/devtools/man/check_doc.Rd | 2
devtools-1.4/devtools/man/clean_dll.Rd | 2
devtools-1.4/devtools/man/clean_source.Rd | 2
devtools-1.4/devtools/man/clean_vignettes.Rd | 2
devtools-1.4/devtools/man/compile_dll.Rd | 2
devtools-1.4/devtools/man/compiler_flags.Rd | 2
devtools-1.4/devtools/man/cran_env_vars.Rd | 2
devtools-1.4/devtools/man/create.Rd | 3
devtools-1.4/devtools/man/create_description.Rd | 5
devtools-1.4/devtools/man/dev_example.Rd | 2
devtools-1.4/devtools/man/dev_help.Rd | 3
devtools-1.4/devtools/man/dev_meta.Rd | 2
devtools-1.4/devtools/man/dev_mode.Rd | 2
devtools-1.4/devtools/man/dev_packages.Rd | 2
devtools-1.4/devtools/man/devtest.Rd | 2
devtools-1.4/devtools/man/document.Rd | 5
devtools-1.4/devtools/man/eval_clean.Rd | 4
devtools-1.4/devtools/man/find_rtools.Rd | 2
devtools-1.4/devtools/man/git_path.Rd | 2
devtools-1.4/devtools/man/has_devel.Rd | 3
devtools-1.4/devtools/man/has_tests.Rd | 2
devtools-1.4/devtools/man/imports_env.Rd | 2
devtools-1.4/devtools/man/inst.Rd | 2
devtools-1.4/devtools/man/install.Rd | 32 -
devtools-1.4/devtools/man/install_bitbucket.Rd | 8
devtools-1.4/devtools/man/install_deps.Rd |only
devtools-1.4/devtools/man/install_git.Rd | 5
devtools-1.4/devtools/man/install_git_single.Rd | 5
devtools-1.4/devtools/man/install_github.Rd | 18
devtools-1.4/devtools/man/install_gitorious.Rd | 4
devtools-1.4/devtools/man/install_local.Rd | 2
devtools-1.4/devtools/man/install_url.Rd | 11
devtools-1.4/devtools/man/install_version.Rd | 5
devtools-1.4/devtools/man/is.package.Rd | 2
devtools-1.4/devtools/man/load_all.Rd | 4
devtools-1.4/devtools/man/load_code.Rd | 2
devtools-1.4/devtools/man/load_data.Rd | 2
devtools-1.4/devtools/man/load_dll.Rd | 2
devtools-1.4/devtools/man/load_imports.Rd | 2
devtools-1.4/devtools/man/loaded_packages.Rd | 2
devtools-1.4/devtools/man/missing_s3.Rd | 2
devtools-1.4/devtools/man/ns_env.Rd | 2
devtools-1.4/devtools/man/on_path.Rd | 2
devtools-1.4/devtools/man/parenvs.Rd | 2
devtools-1.4/devtools/man/parse_deps.Rd | 2
devtools-1.4/devtools/man/parse_ns_file.Rd | 2
devtools-1.4/devtools/man/path.Rd | 6
devtools-1.4/devtools/man/pkg_env.Rd | 2
devtools-1.4/devtools/man/print.envlist.Rd | 3
devtools-1.4/devtools/man/r_env_vars.Rd | 2
devtools-1.4/devtools/man/release.Rd | 2
devtools-1.4/devtools/man/reload.Rd | 2
devtools-1.4/devtools/man/revdep.Rd | 21
devtools-1.4/devtools/man/run_examples.Rd | 4
devtools-1.4/devtools/man/run_pkg_hook.Rd | 4
devtools-1.4/devtools/man/show_news.Rd | 2
devtools-1.4/devtools/man/source_gist.Rd | 48 +-
devtools-1.4/devtools/man/source_url.Rd | 21
devtools-1.4/devtools/man/test.Rd | 2
devtools-1.4/devtools/man/unload.Rd | 2
devtools-1.4/devtools/man/wd.Rd | 2
devtools-1.4/devtools/man/with_debug.Rd | 6
devtools-1.4/devtools/man/with_something.Rd | 20
devtools-1.4/devtools/tests/testthat/test-description.r | 10
devtools-1.4/devtools/tests/testthat/test-s4-export.r |only
devtools-1.4/devtools/tests/testthat/test-vignettes.r | 17
devtools-1.4/devtools/tests/testthat/testDllRcpp/src/RcppExports.cpp | 11
devtools-1.4/devtools/tests/testthat/testS4export |only
devtools-1.4/devtools/tests/testthat/testS4import |only
devtools-1.4/devtools/tests/testthat/testVignettesBuilt |only
114 files changed, 914 insertions(+), 468 deletions(-)
Title: Analysis of Ecological Data : Exploratory and Euclidean methods
in Environmental sciences
Diff between ade4 versions 1.5-2 dated 2013-04-11 and 1.6-2 dated 2013-11-20
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray
Maintainer: Simon Penel
ade4-1.5-2/ade4/man/randtest-internal.Rd |only
ade4-1.6-2/ade4/ChangeLog | 173 +
ade4-1.6-2/ade4/DESCRIPTION | 20
ade4-1.6-2/ade4/MD5 | 440 ++--
ade4-1.6-2/ade4/NAMESPACE | 262 ++
ade4-1.6-2/ade4/R/PI2newick.R | 14
ade4-1.6-2/ade4/R/ade4toR.R | 2
ade4-1.6-2/ade4/R/area.plot.R | 18
ade4-1.6-2/ade4/R/betweencoinertia.R | 46
ade4-1.6-2/ade4/R/coinertia.R | 37
ade4-1.6-2/ade4/R/combine.4thcorner.R | 127 -
ade4-1.6-2/ade4/R/dist.binary.R | 2
ade4-1.6-2/ade4/R/dist.genet.R | 2
ade4-1.6-2/ade4/R/dotchart.phylog.R | 18
ade4-1.6-2/ade4/R/dpcoa.R | 1
ade4-1.6-2/ade4/R/dudi.acm.R | 17
ade4-1.6-2/ade4/R/dudi.hillsmith.R | 10
ade4-1.6-2/ade4/R/dudi.mix.R | 11
ade4-1.6-2/ade4/R/foucart.R | 10
ade4-1.6-2/ade4/R/fourthcorner.R | 595 ++---
ade4-1.6-2/ade4/R/fourthcorner.rlq.R |only
ade4-1.6-2/ade4/R/fourthcorner2.R | 451 ++--
ade4-1.6-2/ade4/R/fuzzygenet.R | 40
ade4-1.6-2/ade4/R/gearymoran.R | 8
ade4-1.6-2/ade4/R/genet.R | 84
ade4-1.6-2/ade4/R/gridrowcol.R | 10
ade4-1.6-2/ade4/R/kdist.R | 10
ade4-1.6-2/ade4/R/kdist2ktab.R | 2
ade4-1.6-2/ade4/R/krandtest.R | 147 -
ade4-1.6-2/ade4/R/ktab.R | 22
ade4-1.6-2/ade4/R/ktab.match2ktabs.R | 2
ade4-1.6-2/ade4/R/ktab.within.R | 9
ade4-1.6-2/ade4/R/mcoa.R | 2
ade4-1.6-2/ade4/R/mld.R | 28
ade4-1.6-2/ade4/R/neig.R | 12
ade4-1.6-2/ade4/R/newick2phylog.R | 116 -
ade4-1.6-2/ade4/R/orthobasis.R | 52
ade4-1.6-2/ade4/R/orthogram.R | 14
ade4-1.6-2/ade4/R/p.adjust.4thcorner.R |only
ade4-1.6-2/ade4/R/phylog.R | 18
ade4-1.6-2/ade4/R/plot.4thcorner.R | 309 ++-
ade4-1.6-2/ade4/R/plot.phylog.R | 10
ade4-1.6-2/ade4/R/print.4thcorner.R | 254 --
ade4-1.6-2/ade4/R/pta.R | 6
ade4-1.6-2/ade4/R/randtest-internal.R | 236 +-
ade4-1.6-2/ade4/R/randtest.coinertia.R | 126 -
ade4-1.6-2/ade4/R/randtest.rlq.R |only
ade4-1.6-2/ade4/R/rlq.R | 503 +---
ade4-1.6-2/ade4/R/rtest.between.R | 2
ade4-1.6-2/ade4/R/s.class.R | 13
ade4-1.6-2/ade4/R/s.hist.R | 6
ade4-1.6-2/ade4/R/s.match.class.R | 11
ade4-1.6-2/ade4/R/s.multinom.R | 2
ade4-1.6-2/ade4/R/s.value.R | 4
ade4-1.6-2/ade4/R/scalewt.R | 176 +
ade4-1.6-2/ade4/R/scatter.acm.R | 4
ade4-1.6-2/ade4/R/scatter.fca.R | 2
ade4-1.6-2/ade4/R/scatterutil.R | 6
ade4-1.6-2/ade4/R/statis.R | 6
ade4-1.6-2/ade4/R/summary.4thcorner.R | 61
ade4-1.6-2/ade4/R/supcol.R | 4
ade4-1.6-2/ade4/R/suprow.R | 6
ade4-1.6-2/ade4/R/table.phylog.R | 4
ade4-1.6-2/ade4/R/table.value.R | 384 +--
ade4-1.6-2/ade4/R/triangle.class.R | 15
ade4-1.6-2/ade4/R/triangle.plot.R | 4
ade4-1.6-2/ade4/R/utilities.R |only
ade4-1.6-2/ade4/R/witwit.R | 2
ade4-1.6-2/ade4/data/abouheif.eg.rda |binary
ade4-1.6-2/ade4/data/acacia.rda |binary
ade4-1.6-2/ade4/data/aminoacyl.rda |binary
ade4-1.6-2/ade4/data/apis108.rda |binary
ade4-1.6-2/ade4/data/aravo.rda |only
ade4-1.6-2/ade4/data/ardeche.rda |binary
ade4-1.6-2/ade4/data/arrival.rda |binary
ade4-1.6-2/ade4/data/atlas.rda |binary
ade4-1.6-2/ade4/data/atya.rda |binary
ade4-1.6-2/ade4/data/avijons.rda |binary
ade4-1.6-2/ade4/data/avimedi.rda |binary
ade4-1.6-2/ade4/data/aviurba.rda |binary
ade4-1.6-2/ade4/data/bacteria.rda |binary
ade4-1.6-2/ade4/data/banque.rda |binary
ade4-1.6-2/ade4/data/baran95.rda |binary
ade4-1.6-2/ade4/data/bf88.rda |binary
ade4-1.6-2/ade4/data/bordeaux.rda |binary
ade4-1.6-2/ade4/data/bsetal97.rda |binary
ade4-1.6-2/ade4/data/buech.rda |binary
ade4-1.6-2/ade4/data/butterfly.rda |binary
ade4-1.6-2/ade4/data/capitales.rda |binary
ade4-1.6-2/ade4/data/carni19.rda |binary
ade4-1.6-2/ade4/data/carni70.rda |binary
ade4-1.6-2/ade4/data/carniherbi49.rda |binary
ade4-1.6-2/ade4/data/casitas.rda |binary
ade4-1.6-2/ade4/data/chatcat.rda |binary
ade4-1.6-2/ade4/data/chats.rda |binary
ade4-1.6-2/ade4/data/chazeb.rda |binary
ade4-1.6-2/ade4/data/chevaine.rda |binary
ade4-1.6-2/ade4/data/clementines.rda |binary
ade4-1.6-2/ade4/data/cnc2003.rda |binary
ade4-1.6-2/ade4/data/coleo.rda |binary
ade4-1.6-2/ade4/data/corvus.rda |binary
ade4-1.6-2/ade4/data/datalist |only
ade4-1.6-2/ade4/data/deug.rda |binary
ade4-1.6-2/ade4/data/doubs.rda |binary
ade4-1.6-2/ade4/data/dunedata.rda |binary
ade4-1.6-2/ade4/data/ecg.rda |binary
ade4-1.6-2/ade4/data/ecomor.rda |binary
ade4-1.6-2/ade4/data/elec88.rda |binary
ade4-1.6-2/ade4/data/escopage.rda |binary
ade4-1.6-2/ade4/data/euro123.rda |binary
ade4-1.6-2/ade4/data/fission.rda |binary
ade4-1.6-2/ade4/data/friday87.rda |binary
ade4-1.6-2/ade4/data/fruits.rda |binary
ade4-1.6-2/ade4/data/ggtortoises.rda |binary
ade4-1.6-2/ade4/data/granulo.rda |binary
ade4-1.6-2/ade4/data/hdpg.rda |binary
ade4-1.6-2/ade4/data/housetasks.rda |binary
ade4-1.6-2/ade4/data/humDNAm.rda |binary
ade4-1.6-2/ade4/data/ichtyo.rda |binary
ade4-1.6-2/ade4/data/irishdata.rda |binary
ade4-1.6-2/ade4/data/julliot.rda |binary
ade4-1.6-2/ade4/data/jv73.rda |binary
ade4-1.6-2/ade4/data/kcponds.rda |binary
ade4-1.6-2/ade4/data/lascaux.rda |binary
ade4-1.6-2/ade4/data/lizards.rda |binary
ade4-1.6-2/ade4/data/macaca.rda |binary
ade4-1.6-2/ade4/data/macon.rda |binary
ade4-1.6-2/ade4/data/macroloire.rda |binary
ade4-1.6-2/ade4/data/mafragh.rda |binary
ade4-1.6-2/ade4/data/maples.rda |binary
ade4-1.6-2/ade4/data/mariages.rda |binary
ade4-1.6-2/ade4/data/meau.rda |binary
ade4-1.6-2/ade4/data/meaudret.rda |binary
ade4-1.6-2/ade4/data/microsatt.rda |binary
ade4-1.6-2/ade4/data/mjrochet.rda |binary
ade4-1.6-2/ade4/data/mollusc.rda |binary
ade4-1.6-2/ade4/data/monde84.rda |binary
ade4-1.6-2/ade4/data/morphosport.rda |binary
ade4-1.6-2/ade4/data/newick.eg.rda |binary
ade4-1.6-2/ade4/data/njplot.rda |binary
ade4-1.6-2/ade4/data/olympic.rda |binary
ade4-1.6-2/ade4/data/oribatid.rda |binary
ade4-1.6-2/ade4/data/ours.rda |binary
ade4-1.6-2/ade4/data/palm.rda |binary
ade4-1.6-2/ade4/data/pap.rda |binary
ade4-1.6-2/ade4/data/perthi02.rda |binary
ade4-1.6-2/ade4/data/piosphere.rda |binary
ade4-1.6-2/ade4/data/presid2002.rda |binary
ade4-1.6-2/ade4/data/procella.rda |binary
ade4-1.6-2/ade4/data/rankrock.rda |binary
ade4-1.6-2/ade4/data/rhizobium.rda |binary
ade4-1.6-2/ade4/data/rhone.rda |binary
ade4-1.6-2/ade4/data/rpjdl.rda |binary
ade4-1.6-2/ade4/data/santacatalina.rda |binary
ade4-1.6-2/ade4/data/sarcelles.rda |binary
ade4-1.6-2/ade4/data/seconde.rda |binary
ade4-1.6-2/ade4/data/skulls.rda |binary
ade4-1.6-2/ade4/data/steppe.rda |binary
ade4-1.6-2/ade4/data/syndicats.rda |binary
ade4-1.6-2/ade4/data/t3012.rda |binary
ade4-1.6-2/ade4/data/tarentaise.rda |binary
ade4-1.6-2/ade4/data/taxo.eg.rda |binary
ade4-1.6-2/ade4/data/tintoodiel.rda |binary
ade4-1.6-2/ade4/data/tithonia.rda |binary
ade4-1.6-2/ade4/data/tortues.rda |binary
ade4-1.6-2/ade4/data/toxicity.rda |binary
ade4-1.6-2/ade4/data/trichometeo.rda |binary
ade4-1.6-2/ade4/data/ungulates.rda |binary
ade4-1.6-2/ade4/data/vegtf.rda |binary
ade4-1.6-2/ade4/data/veuvage.rda |binary
ade4-1.6-2/ade4/data/westafrica.rda |binary
ade4-1.6-2/ade4/data/woangers.rda |binary
ade4-1.6-2/ade4/data/worksurv.rda |binary
ade4-1.6-2/ade4/data/yanomama.rda |binary
ade4-1.6-2/ade4/data/zealand.rda |binary
ade4-1.6-2/ade4/man/acacia.Rd | 2
ade4-1.6-2/ade4/man/add.scatter.Rd | 10
ade4-1.6-2/ade4/man/ade4-internal.Rd |only
ade4-1.6-2/ade4/man/ade4toR.Rd | 9
ade4-1.6-2/ade4/man/aravo.Rd |only
ade4-1.6-2/ade4/man/as.taxo.Rd | 4
ade4-1.6-2/ade4/man/avimedi.Rd | 4
ade4-1.6-2/ade4/man/baran95.Rd | 2
ade4-1.6-2/ade4/man/cailliez.Rd | 2
ade4-1.6-2/ade4/man/capitales.Rd | 20
ade4-1.6-2/ade4/man/coinertia.Rd | 28
ade4-1.6-2/ade4/man/combine.4thcorner.Rd |only
ade4-1.6-2/ade4/man/costatis.Rd | 2
ade4-1.6-2/ade4/man/dist.ktab.Rd | 15
ade4-1.6-2/ade4/man/dotchart.phylog.Rd | 6
ade4-1.6-2/ade4/man/fourthcorner.Rd | 154 +
ade4-1.6-2/ade4/man/granulo.Rd | 2
ade4-1.6-2/ade4/man/kplot.pta.Rd | 2
ade4-1.6-2/ade4/man/kplot.sepan.Rd | 2
ade4-1.6-2/ade4/man/kplot.statis.Rd | 2
ade4-1.6-2/ade4/man/krandtest.Rd | 5
ade4-1.6-2/ade4/man/ktab.match2ktabs.Rd | 2
ade4-1.6-2/ade4/man/ktab.within.Rd | 2
ade4-1.6-2/ade4/man/lingoes.Rd | 2
ade4-1.6-2/ade4/man/meau.Rd | 2
ade4-1.6-2/ade4/man/meaudret.Rd | 2
ade4-1.6-2/ade4/man/nipals.Rd | 3
ade4-1.6-2/ade4/man/pcaivortho.Rd | 2
ade4-1.6-2/ade4/man/phylog.Rd | 4
ade4-1.6-2/ade4/man/plot.phylog.Rd | 10
ade4-1.6-2/ade4/man/randtest.amova.Rd | 2
ade4-1.6-2/ade4/man/reconst.Rd | 2
ade4-1.6-2/ade4/man/rhone.Rd | 2
ade4-1.6-2/ade4/man/rlq.Rd | 24
ade4-1.6-2/ade4/man/rtest.between.Rd | 2
ade4-1.6-2/ade4/man/s.logo.Rd | 2
ade4-1.6-2/ade4/man/s.match.class.Rd | 8
ade4-1.6-2/ade4/man/scalewt.Rd | 59
ade4-1.6-2/ade4/man/scatter.Rd | 3
ade4-1.6-2/ade4/man/scatterutil.Rd | 26
ade4-1.6-2/ade4/man/statico.Rd | 2
ade4-1.6-2/ade4/man/statis.Rd | 2
ade4-1.6-2/ade4/man/supcol.Rd | 8
ade4-1.6-2/ade4/man/suprow.Rd | 8
ade4-1.6-2/ade4/man/taxo.eg.Rd | 2
ade4-1.6-2/ade4/man/ungulates.Rd | 2
ade4-1.6-2/ade4/src/adesub.c | 2103 ++++++++++----------
ade4-1.6-2/ade4/src/adesub.h | 3
ade4-1.6-2/ade4/src/fourthcorner.c | 3133 +++++++++++++++++--------------
ade4-1.6-2/ade4/src/testrlq.c | 499 ++--
ade4-1.6-2/ade4/src/tests.c | 1973 +++++++++----------
226 files changed, 7006 insertions(+), 6147 deletions(-)
Title: Semi-parametric estimators of truncated regression models
Diff between truncSP versions 1.2 dated 2013-05-13 and 1.2.1 dated 2013-11-20
Description: Semi-parametric estimation of truncated linear regression models
Author: Anita Lindmark and Maria Karlsson, Department of Statistics, Umea University
Maintainer: Anita Lindmark
DESCRIPTION | 14 ++++++--------
MD5 | 4 ++--
R/qme.R | 10 ++++++----
3 files changed, 14 insertions(+), 14 deletions(-)
Title: Pearson Distribution System
Diff between PearsonDS versions 0.96 dated 2013-10-02 and 0.97 dated 2013-11-20
Description: Implementation of the Pearson distribution system, including full
support for the (d,p,q,r)-family of functions for probability distributions
and fitting via method of moments and maximum likelihood method.
Author: Martin Becker and Stefan Klößner
Maintainer: Martin Becker
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/pearsonIV.r | 12 ++++++------
inst/CHANGES | 5 +++++
src/pearsonIV.c | 40 ++++++++++++++++++++++++++++++++++++++++
5 files changed, 59 insertions(+), 14 deletions(-)
Title: Simulation of genomic data in applied genetics
Diff between hypred versions 0.2 dated 2012-08-01 and 0.4 dated 2013-11-20
Description: The package is intended for simulating high density
genomic data. The meiosis is
simulated under a count-location model, the genetic
structure can include additive and dominance effects. The
low level nature of the package provides great
flexibility in creating all kinds of populations.
Author: Frank Technow
Maintainer: Frank Technow
DESCRIPTION | 21 ++++++++++-----------
MD5 | 13 ++++++++-----
build |only
inst/doc/hypred.R |only
inst/doc/hypred.Rnw | 16 +++++++++-------
inst/doc/hypred.pdf |binary
man/hypred-package.Rd | 15 ++++++---------
src/hypredRoutines.c | 31 ++++++++++++++++++++++++-------
vignettes |only
9 files changed, 57 insertions(+), 39 deletions(-)
Title: An R package for the analysis of epidemiological data
Diff between epiR versions 0.9-48 dated 2013-04-08 and 0.9-51 dated 2013-11-20
Description: An R package for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson
Maintainer: Mark Stevenson
epiR-0.9-48/epiR/doc |only
epiR-0.9-51/epiR/DESCRIPTION | 24 +---
epiR-0.9-51/epiR/MD5 | 13 +-
epiR-0.9-51/epiR/R/epi.2by2.r | 32 ++++--
epiR-0.9-51/epiR/man/epi.2by2.Rd | 187 +++++++++++++++-----------------------
epiR-0.9-51/epiR/man/epi.kappa.Rd | 3
epiR-0.9-51/epiR/man/epi.occc.Rd | 2
epiR-0.9-51/epiR/man/epi.prcc.Rd | 4
8 files changed, 120 insertions(+), 145 deletions(-)
Title: Efficiently Read Sequence Data (VCF format, BCF format and METAL
format) into R
Diff between seqminer versions 1.9.1 dated 2013-11-15 and 2.0 dated 2013-11-20
Description: Integrate sequencing data (VCF) or meta-analysis results in R
Author: Xiaowei Zhan
Maintainer: Xiaowei Zhan
seqminer-1.9.1/seqminer/src/VCFRecord_flymake.h |only
seqminer-2.0/seqminer/ChangeLog | 8 ++++++++
seqminer-2.0/seqminer/DESCRIPTION | 10 +++++-----
seqminer-2.0/seqminer/MD5 | 24 +++++++++++++-----------
seqminer-2.0/seqminer/configure.ac | 6 +++---
seqminer-2.0/seqminer/configure.win |only
seqminer-2.0/seqminer/src/GeneLoader.cpp | 3 +--
seqminer-2.0/seqminer/src/IO.h | 2 ++
seqminer-2.0/seqminer/src/Makevars.win |only
seqminer-2.0/seqminer/src/OrderedMap.h | 3 ++-
seqminer-2.0/seqminer/src/bcfutils.c | 7 +++++--
seqminer-2.0/seqminer/src/bgzf.c | 3 ++-
seqminer-2.0/seqminer/src/config.h |only
seqminer-2.0/seqminer/src/rvMetaLoader.cpp | 1 +
seqminer-2.0/seqminer/src/vcf2genoLoader.cpp | 2 +-
15 files changed, 43 insertions(+), 26 deletions(-)
Title: Interface to the Global Biodiversity Information Facility API
Diff between rgbif versions 0.3.0 dated 2013-07-19 and 0.4.0 dated 2013-11-20
Description: A programmatic interface to the
Web Service methods provided by the Global
Biodiversity Information Facility.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain
rgbif-0.3.0/rgbif/R/density_spplist.r |only
rgbif-0.3.0/rgbif/R/densitylist.r |only
rgbif-0.3.0/rgbif/R/methods.r |only
rgbif-0.3.0/rgbif/R/occurrencecount.R |only
rgbif-0.3.0/rgbif/R/occurrencedensity.r |only
rgbif-0.3.0/rgbif/R/occurrenceget.R |only
rgbif-0.3.0/rgbif/R/occurrencelist.R |only
rgbif-0.3.0/rgbif/R/occurrencelist_many.R |only
rgbif-0.3.0/rgbif/R/providers.r |only
rgbif-0.3.0/rgbif/R/resources.r |only
rgbif-0.3.0/rgbif/R/rgbif-package.R |only
rgbif-0.3.0/rgbif/R/taxoncount.R |only
rgbif-0.3.0/rgbif/R/taxonget.r |only
rgbif-0.3.0/rgbif/R/taxonsearch.R |only
rgbif-0.3.0/rgbif/R/taxrank.r |only
rgbif-0.3.0/rgbif/demo |only
rgbif-0.3.0/rgbif/inst |only
rgbif-0.3.0/rgbif/man/capwords.Rd |only
rgbif-0.3.0/rgbif/man/colClasses.Rd |only
rgbif-0.3.0/rgbif/man/density_spplist.Rd |only
rgbif-0.3.0/rgbif/man/densitylist.Rd |only
rgbif-0.3.0/rgbif/man/gbifdata.Rd |only
rgbif-0.3.0/rgbif/man/gbifdata.gbifdens.Rd |only
rgbif-0.3.0/rgbif/man/gbifdata.gbiflist.Rd |only
rgbif-0.3.0/rgbif/man/gbifmap_dens.Rd |only
rgbif-0.3.0/rgbif/man/gbifmap_list.Rd |only
rgbif-0.3.0/rgbif/man/is.gbifdens.Rd |only
rgbif-0.3.0/rgbif/man/is.gbiflist.Rd |only
rgbif-0.3.0/rgbif/man/occurrencecount.Rd |only
rgbif-0.3.0/rgbif/man/occurrencedensity.Rd |only
rgbif-0.3.0/rgbif/man/occurrenceget.Rd |only
rgbif-0.3.0/rgbif/man/occurrencelist.Rd |only
rgbif-0.3.0/rgbif/man/occurrencelist_many.Rd |only
rgbif-0.3.0/rgbif/man/print.gbifdens.Rd |only
rgbif-0.3.0/rgbif/man/print.gbiflist.Rd |only
rgbif-0.3.0/rgbif/man/providers.Rd |only
rgbif-0.3.0/rgbif/man/resources.Rd |only
rgbif-0.3.0/rgbif/man/taxoncount.Rd |only
rgbif-0.3.0/rgbif/man/taxonget.Rd |only
rgbif-0.3.0/rgbif/man/taxonsearch.Rd |only
rgbif-0.4.0/rgbif/DESCRIPTION | 34 -
rgbif-0.4.0/rgbif/MD5 | 165 ++++---
rgbif-0.4.0/rgbif/NAMESPACE | 34 +
rgbif-0.4.0/rgbif/NEWS | 43 +
rgbif-0.4.0/rgbif/R/dataset_metrics.r |only
rgbif-0.4.0/rgbif/R/dataset_search.r |only
rgbif-0.4.0/rgbif/R/dataset_suggest.r |only
rgbif-0.4.0/rgbif/R/datasets.r |only
rgbif-0.4.0/rgbif/R/deprecated.r |only
rgbif-0.4.0/rgbif/R/gbifmap.r | 140 +-----
rgbif-0.4.0/rgbif/R/gist.r |only
rgbif-0.4.0/rgbif/R/name_backbone.r |only
rgbif-0.4.0/rgbif/R/name_lookup.r |only
rgbif-0.4.0/rgbif/R/name_suggest.r |only
rgbif-0.4.0/rgbif/R/name_usage.r |only
rgbif-0.4.0/rgbif/R/networks.r | 98 ++--
rgbif-0.4.0/rgbif/R/nodes.r |only
rgbif-0.4.0/rgbif/R/occ_count.r |only
rgbif-0.4.0/rgbif/R/occ_get.r |only
rgbif-0.4.0/rgbif/R/occ_metadata.r |only
rgbif-0.4.0/rgbif/R/occ_search.r |only
rgbif-0.4.0/rgbif/R/organizations.r |only
rgbif-0.4.0/rgbif/R/parsenames.R |only
rgbif-0.4.0/rgbif/R/rgbif-package.r |only
rgbif-0.4.0/rgbif/R/stylegeojson.r | 5
rgbif-0.4.0/rgbif/R/togeojson.r | 30 -
rgbif-0.4.0/rgbif/R/zzz.r | 366 ++++++++++------
rgbif-0.4.0/rgbif/README.md | 150 +++++-
rgbif-0.4.0/rgbif/data/isocodes.rda |binary
rgbif-0.4.0/rgbif/man/create_gist.Rd |only
rgbif-0.4.0/rgbif/man/dataset_metrics.Rd |only
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rgbif-0.4.0/rgbif/man/gbifparser.Rd |only
rgbif-0.4.0/rgbif/man/gbifparser_verbatim.Rd |only
rgbif-0.4.0/rgbif/man/get_credentials.Rd |only
rgbif-0.4.0/rgbif/man/gist.Rd |only
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rgbif-0.4.0/rgbif/man/is.gbiflist-deprecated.Rd |only
rgbif-0.4.0/rgbif/man/is.gbiflist_na-deprecated.Rd |only
rgbif-0.4.0/rgbif/man/isocodes.Rd | 2
rgbif-0.4.0/rgbif/man/ldfast.Rd |only
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rgbif-0.4.0/rgbif/man/namelkupparser.Rd |only
rgbif-0.4.0/rgbif/man/networks.Rd | 53 +-
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rgbif-0.4.0/rgbif/man/occurrencelist-deprecated.Rd |only
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rgbif-0.4.0/rgbif/man/parsenames.Rd |only
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rgbif-0.4.0/rgbif/man/taxoncount-deprecated.Rd |only
rgbif-0.4.0/rgbif/man/taxonget-deprecated.Rd |only
rgbif-0.4.0/rgbif/man/taxonsearch-deprecated.Rd |only
rgbif-0.4.0/rgbif/man/taxrank.Rd | 2
rgbif-0.4.0/rgbif/man/togeojson.Rd | 23 -
rgbif-0.4.0/rgbif/tests |only
124 files changed, 721 insertions(+), 424 deletions(-)
Title: Rcpp integration for Armadillo templated linear algebra library
Diff between RcppArmadillo versions 0.3.920.1 dated 2013-09-29 and 0.3.920.3 dated 2013-11-20
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 (currently version 3.920.1). 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 | 13 +++++++++++++
DESCRIPTION | 8 ++++----
MD5 | 20 +++++++++++---------
README.md |only
build |only
inst/NEWS.Rd | 9 +++++++++
inst/doc/RcppArmadillo-intro.pdf |binary
inst/doc/RcppArmadillo-unitTests.pdf |binary
inst/examples/fastLm.r | 24 +++++++++++++++++++++++-
inst/examples/varSimulation.r | 4 ++--
inst/include/armadillo_bits/Mat_meat.hpp | 11 +++++++----
inst/include/armadillo_bits/arma_version.hpp | 2 +-
12 files changed, 70 insertions(+), 21 deletions(-)