Title: Analysis of Count Time Series
Description: Likelihood-based methods for model fitting and assessment, prediction and intervention analysis of count time series following generalized linear models are provided. Models with the identity and with the logarithmic link function are allowed. The conditional distribution can be Poisson or Negative Binomial.
Author: Tobias Liboschik [aut, cre],
Roland Fried [aut],
Konstantinos Fokianos [aut],
Philipp Probst [aut],
Jonathan Rathjens [ctb]
Maintainer: Tobias Liboschik <liboschik@statistik.tu-dortmund.de>
Diff between tscount versions 1.4.0 dated 2017-09-30 and 1.4.1 dated 2017-11-24
DESCRIPTION | 8 - MD5 | 22 ++-- inst/CITATION | 27 +++-- inst/doc/tsglm.Rnw | 4 inst/doc/tsglm.pdf |binary man/predict.tsglm.Rd | 228 ++++++++++++++++++++++----------------------- man/se.tsglm.Rd | 182 +++++++++++++++++------------------ man/tscount-package.Rd | 86 ++++++++-------- man/tsglm.Rd | 2 man/tsglm.sim.Rd | 188 ++++++++++++++++++------------------- vignettes/bibliography.bib | 12 +- vignettes/tsglm.Rnw | 4 12 files changed, 389 insertions(+), 374 deletions(-)
Title: Trajectories Data Mining
Description: Contains a set of methods for trajectory data preparation, such as filtering, compressing and clustering, and for trajectory pattern discovery.
Author: Diego Monteiro [aut, cre],
Karine Reis [ctb],
Carlos Alberto [ctb],
Felipe Carvalho [ctb]
Maintainer: Diego Monteiro <dvm1607@gmail.com>
Diff between TrajDataMining versions 0.1.3 dated 2017-11-23 and 0.1.4 dated 2017-11-24
DESCRIPTION | 6 +++--- MD5 | 36 ++++++++++++++++++------------------ NAMESPACE | 1 + R/A1.R | 14 +++++++------- R/A2.R | 12 ++++++------ R/DouglasPeucker.R | 10 +++++----- R/IndexToTrack.R | 8 +++++--- R/MyCompareMethod.R | 8 ++++---- R/SendGoAlong.R | 6 +----- R/tracksCollection.R | 18 +++++++++--------- inst/doc/TrajDataMining.html | 4 ++-- man/A1.Rd | 14 +++++++------- man/A2.Rd | 12 ++++++------ man/IndexToTrack.Rd | 11 +++++++---- man/douglasPeucker.Rd | 2 +- man/douglasPeuckerRP.Rd | 8 ++++---- man/sendPartnerPairsToDB.Rd | 6 +----- man/singledifftrack-class.Rd | 9 +++------ man/tracksCollection.Rd | 18 +++++++++--------- 19 files changed, 99 insertions(+), 104 deletions(-)
More information about TrajDataMining at CRAN
Permanent link
Title: Threshold Estimation
Description: Point and interval estimations of optimum thresholds for continuous diagnostic tests (two- and three- state settings).
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.5 dated 2017-08-01 and 2.6 dated 2017-11-24
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- R/ThresholdROC-2states.R | 1 + inst |only man/ThresholdROC-package.Rd | 8 ++++---- man/diagnostic.Rd | 4 ++-- man/lines-thres2.Rd | 2 +- man/lines-thres3.Rd | 2 +- man/plot-thres2.Rd | 2 +- man/plot-thres3.Rd | 2 +- 10 files changed, 24 insertions(+), 22 deletions(-)
Title: Compute and Plot Tracheidograms
Description: Functions to compute and plot tracheidograms, as in De Soto et al. (2011) <doi:10.1139/x11-045>.
Author: Marcelino de la Cruz and Lucia DeSoto
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Diff between tgram versions 0.2-2 dated 2013-07-24 and 0.2-3 dated 2017-11-24
DESCRIPTION | 14 +++++++------- MD5 | 12 ++++++------ R/tgram.R | 2 +- man/juniperus.Rd | 4 ++-- man/standz.all.Rd | 12 ++++++------ man/tgram.Rd | 10 +++++----- man/traq.profile.Rd | 2 +- 7 files changed, 28 insertions(+), 28 deletions(-)
Title: Similarity Network Fusion
Description: Similarity Network Fusion takes multiple views of a network and fuses them together to construct an overall status matrix. The input to our algorithm can be feature vectors, pairwise distances, or pairwise similarities. The learned status matrix can then be used for retrieval, clustering, and classification.
Author: Bo Wang, Aziz Mezlini, Feyyaz Demir, Marc Fiume, Zhuowen Tu, Michael Brudno, Benjamin Haibe-Kains, Anna Goldenberg
Maintainer: Daniel Cole <goldenberglab@gmail.com>
Diff between SNFtool versions 2.2 dated 2014-09-08 and 2.2.1 dated 2017-11-24
DESCRIPTION | 9 +++++---- MD5 | 10 +++++----- NAMESPACE | 3 +++ R/SNF.R | 21 +++++++++++++++------ R/displayClustersWithHeatmap.R | 2 +- R/estimateNumberOfClustersGivenGraph.R | 2 +- 6 files changed, 30 insertions(+), 17 deletions(-)
Title: Matrix Population Models
Description: Imitating the 'Ramas' (c) software, analyzes and predicts from matrix population models, (Caswell 2006) <doi:10.1002/9781118445112.stat07481>.
Author: Marcelino de la Cruz
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Diff between Rramas versions 0.1-4 dated 2014-01-28 and 0.1-5 dated 2017-11-24
DESCRIPTION | 14 +++++++------- MD5 | 21 +++++++++++---------- NAMESPACE | 1 + R/decline.R | 2 +- R/explosion.R | 2 +- R/plot.rmas.R | 4 ++-- R/summary.rmas.R | 4 ++-- inst |only man/as.tmatrix.Rd | 10 +++++----- man/coryphanthaA.Rd | 2 +- man/decline.Rd | 9 +++++---- man/projectn.Rd | 11 ++++++----- 12 files changed, 42 insertions(+), 38 deletions(-)
Title: The MCFS-ID Algorithm for Feature Selection and Interdependency
Discovery
Description: MCFS-ID (Monte Carlo Feature Selection and Interdependency Discovery) is a Monte Carlo method-based tool for feature selection. It also allows for the discovery of interdependencies between the relevant features. MCFS-ID is particularly suitable for the analysis of high-dimensional, 'small n large p' transactional and biological data. M.Draminski, A.Rada-Iglesias, S.Enroth, C.Wadelius, J. Koronacki, J.Komorowski (2008) <doi:10.1093/bioinformatics/btm486>.
Author: Michal Draminski [aut, cre],
Jacek Koronacki [aut],
Julian Zubek [ctb]
Maintainer: Michal Draminski <michal.draminski@ipipan.waw.pl>
Diff between rmcfs versions 1.2.6 dated 2017-07-03 and 1.2.7 dated 2017-11-24
rmcfs-1.2.6/rmcfs/NEWS |only rmcfs-1.2.6/rmcfs/data |only rmcfs-1.2.6/rmcfs/java/README |only rmcfs-1.2.6/rmcfs/man/alizadeh.Rd |only rmcfs-1.2.6/rmcfs/man/refine.data.Rd |only rmcfs-1.2.7/rmcfs/DESCRIPTION | 14 +-- rmcfs-1.2.7/rmcfs/LICENSE.note | 8 - rmcfs-1.2.7/rmcfs/MD5 | 61 ++++++++------ rmcfs-1.2.7/rmcfs/NAMESPACE | 2 rmcfs-1.2.7/rmcfs/NEWS.md |only rmcfs-1.2.7/rmcfs/R/rmcfs.R | 7 + rmcfs-1.2.7/rmcfs/R/rmcfs.plot.R | 2 rmcfs-1.2.7/rmcfs/build |only rmcfs-1.2.7/rmcfs/inst/doc |only rmcfs-1.2.7/rmcfs/inst/java/weka12.jar |binary rmcfs-1.2.7/rmcfs/java/README.md |only rmcfs-1.2.7/rmcfs/man/fix.data.Rd | 7 - rmcfs-1.2.7/rmcfs/man/mcfs.Rd | 8 + rmcfs-1.2.7/rmcfs/man/prune.data.Rd |only rmcfs-1.2.7/rmcfs/man/read.adh.Rd | 11 +- rmcfs-1.2.7/rmcfs/man/read.adx.Rd | 9 -- rmcfs-1.2.7/rmcfs/man/showme.Rd | 6 - rmcfs-1.2.7/rmcfs/man/write.adh.Rd | 9 -- rmcfs-1.2.7/rmcfs/man/write.adx.Rd | 9 -- rmcfs-1.2.7/rmcfs/man/write.arff.Rd | 9 -- rmcfs-1.2.7/rmcfs/tests/testthat/test-man.build.idgraph.R | 3 rmcfs-1.2.7/rmcfs/tests/testthat/test-man.mcfs.R | 3 rmcfs-1.2.7/rmcfs/tests/testthat/test-man.plot.idgraph.R | 3 rmcfs-1.2.7/rmcfs/tests/testthat/test-mcfs.M5.R |only rmcfs-1.2.7/rmcfs/tests/testthat/test-mcfs.R | 6 + rmcfs-1.2.7/rmcfs/vignettes |only 31 files changed, 103 insertions(+), 74 deletions(-)
Title: Dimension Reduction and Estimation Methods
Description: We provide a rich collection of linear and nonlinear
dimension reduction techniques implemented using 'RcppArmadillo'.
The question on what we should use as the target dimension is
addressed by intrinsic dimension estimation methods introduced as well.
For more details on dimensionality techniques, see the paper by
Ma and Zhu (2013) <doi:10.1111/j.1751-5823.2012.00182.x> if you are interested in
statistical approach, or Engel, Huttenberger, and Hamann (2012)
<doi:10.4230/OASIcs.VLUDS.2011.135> for a broader cross-disciplinary overview.
Author: Kisung You [aut, cre],
Donggun Kim [ctb],
Yoon Mo Jung [ctb]
Maintainer: Kisung You <kyou@nd.edu>
Diff between Rdimtools versions 0.1.2 dated 2017-11-13 and 0.1.3 dated 2017-11-24
DESCRIPTION | 8 - MD5 | 43 ++++-- NAMESPACE | 6 R/RcppExports.R | 15 ++ R/auxiliary.R | 30 ++++ R/init.R | 4 R/linear_CCA.R |only R/linear_LPP.R | 6 R/linear_OLPP.R |only R/linear_OPLS.R |only R/linear_PLS.R |only R/package-Rdimtools.R | 8 + build/partial.rdb |binary inst/REFERENCES.bib | 277 +++++++++++++++++++++++++++++++++++--------- man/Rdimtools.Rd | 7 - man/aux_pkgstat.Rd |only man/linear_CCA.Rd |only man/linear_LPP.Rd | 6 man/linear_OLPP.Rd |only man/linear_OPLS.Rd |only man/linear_PLS.Rd |only src/RcppExports.cpp | 40 ++++++ src/Rdimtools_auxiliary.cpp | 39 +++++- src/methods_estimation.cpp | 18 ++ src/methods_estimation.h | 2 src/methods_linear.cpp | 58 +++++++++ src/methods_linear.h | 2 27 files changed, 483 insertions(+), 86 deletions(-)
Title: Methods for Causal Inference with Interference
Description: Provides methods for estimating causal effects in the presence of interference described in B. Saul and M. Hugdens (2017) <doi:10.18637/jss.v082.i02>. Currently it implements the inverse-probability weighted (IPW) estimators proposed by E.J. Tchetgen Tchetgen and T.J. Vanderweele (2012) <doi:10.1177/0962280210386779>.
Author: Bradley Saul
Maintainer: Bradley Saul <bradleysaul@gmail.com>
Diff between inferference versions 0.5.4 dated 2017-09-25 and 1.0.0 dated 2017-11-24
DESCRIPTION | 14 -- MD5 | 19 +-- R/inferference.R | 6 - R/interference.R | 6 - build/vignette.rds |binary inst/CITATION | 30 ++--- inst/doc/inferference_intro.html | 226 +++++++++++++++++++-------------------- inst/doc/inferference_plots.html | 52 ++++---- man/inferference.Rd | 7 + man/interference.Rd | 4 tests/testthat/test_glmer_args.R |only 11 files changed, 191 insertions(+), 173 deletions(-)
Title: Functions for Spatial Point Pattern Analysis
Description: Some wrappers, functions and data sets for for spatial point pattern analysis (mainly based on 'spatstat'), used in the book "Introduccion al Analisis Espacial de Datos en Ecologia y Ciencias Ambientales: Metodos y Aplicaciones" and in the papers by De la Cruz et al. (2008) <doi:10.1111/j.0906-7590.2008.05299.x> and Olano et al. (2009) <doi:10.1051/forest:2008074>.
Author: Marcelino de la Cruz Rot, with contributions of Philip M. Dixon and Jose M. Blanco-Moreno
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>
Diff between ecespa versions 1.1-8 dated 2015-07-04 and 1.1-9 dated 2017-11-24
ecespa-1.1-8/ecespa/src/syrjala.f |only ecespa-1.1-9/ecespa/DESCRIPTION | 14 ++++----- ecespa-1.1-9/ecespa/MD5 | 49 ++++++++++++++++---------------- ecespa-1.1-9/ecespa/NAMESPACE | 4 +- ecespa-1.1-9/ecespa/R/syrjala.R | 2 - ecespa-1.1-9/ecespa/man/00ecespa.Rd | 6 +-- ecespa-1.1-9/ecespa/man/K012.Rd | 21 +++++++++---- ecespa-1.1-9/ecespa/man/K1K2.rd | 15 +++++---- ecespa-1.1-9/ecespa/man/Kci.Rd | 19 +++++++----- ecespa-1.1-9/ecespa/man/Kinhom.log.rd | 17 +++++------ ecespa-1.1-9/ecespa/man/Kmm.Rd | 15 +++++---- ecespa-1.1-9/ecespa/man/Kmulti.ls.Rd | 6 +-- ecespa-1.1-9/ecespa/man/LF.gof.Rd | 2 - ecespa-1.1-9/ecespa/man/dixon2002.Rd | 13 ++++---- ecespa-1.1-9/ecespa/man/getis.rd | 11 ++++--- ecespa-1.1-9/ecespa/man/haz.ppp.Rd | 7 +++- ecespa-1.1-9/ecespa/man/internal.Rd | 4 +- ecespa-1.1-9/ecespa/man/ipc.estK.Rd | 29 +++++++++++------- ecespa-1.1-9/ecespa/man/marksum.rd | 6 +-- ecespa-1.1-9/ecespa/man/p2colasr.Rd | 2 - ecespa-1.1-9/ecespa/man/pc.estK.rd | 14 +++++---- ecespa-1.1-9/ecespa/man/rIPCP.Rd | 6 +-- ecespa-1.1-9/ecespa/man/sim.poissonc.rd | 15 +++++---- ecespa-1.1-9/ecespa/man/swamp.Rd | 5 --- ecespa-1.1-9/ecespa/man/syrjala.Rd | 17 ++++++----- ecespa-1.1-9/ecespa/src/init.c |only ecespa-1.1-9/ecespa/src/syrjalala.f |only 27 files changed, 169 insertions(+), 130 deletions(-)
Title: Nearest Neighbour Contingency Table Analysis
Description: Function to test spatial segregation and association based in contingency table analysis of nearest neighbour counts following Dixon (2002) <doi:10.1080/11956860.2002.11682700>. Some 'Fortran' code has been included to the original dixon2002() function of the 'ecespa' package to improve speed.
Author: Marcelino de la Cruz Rot and Philip M. Dixon
Maintainer: Marcelino de la Cruz Rot <marcelino.delacruz@urjc.es>
Diff between dixon versions 0.0-5 dated 2013-03-13 and 0.0-6 dated 2017-11-24
DESCRIPTION | 16 ++++++---------- MD5 | 13 +++++++------ NAMESPACE | 4 +++- man/dixon.Rd | 5 ++--- man/internal.Rd | 3 +-- man/p2colasr.Rd | 2 +- man/swamp.Rd | 5 +---- src/init.c |only 8 files changed, 21 insertions(+), 27 deletions(-)
Title: Draw Venn Diagrams
Description: Draws and displays Venn diagrams up to 7 sets, and any Boolean union of set intersections.
Author: Adrian Dusa [aut, cre, cph]
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between venn versions 1.2 dated 2016-05-10 and 1.5 dated 2017-11-24
venn-1.2/venn/inst/web |only venn-1.5/venn/DESCRIPTION | 10 +-- venn-1.5/venn/MD5 | 59 ++----------------- venn-1.5/venn/R/getZones.R | 101 +++++++++++++++++++++++++++++--- venn-1.5/venn/R/plotRules.R | 12 ++- venn-1.5/venn/R/venn.R | 117 ++++++++++++++++++++++++++------------ venn-1.5/venn/inst/ChangeLog | 21 +++++- venn-1.5/venn/man/getCentroid.Rd | 13 +--- venn-1.5/venn/man/getZones.Rd | 43 +++++++------ venn-1.5/venn/man/venn.Rd | 57 ++++++++++++------ venn-1.5/venn/man/venn.package.Rd | 80 ++++++++++++------------- 11 files changed, 321 insertions(+), 192 deletions(-)
Title: Two-Way ANOVA-Like Method to Analyze Replicated Point Patterns
Description: Test for effects of both individual factors and their interaction on replicated spatial patterns in a two factorial design, as explained in Ramon et al. (2016) <doi:10.1111/ecog.01848>.
Author: Marcelino de la Cruz Rot
Maintainer: Marcelino de la Cruz <marcelino.delacruz@urjc.es>
Diff between replicatedpp2w versions 0.1-1 dated 2015-04-29 and 0.1-2 dated 2017-11-24
DESCRIPTION | 13 +++++++------ MD5 | 7 ++++--- NAMESPACE | 1 + inst |only man/K2w.Rd | 6 ++---- 5 files changed, 14 insertions(+), 13 deletions(-)
More information about replicatedpp2w at CRAN
Permanent link
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.4 dated 2017-09-01 and 1.4.5 dated 2017-11-24
unitizer-1.4.4/unitizer/R/testfuns.R |only unitizer-1.4.4/unitizer/inst/doc/unitizer.Rmd |only unitizer-1.4.4/unitizer/inst/doc/unitizer.html |only unitizer-1.4.4/unitizer/inst/doc/unitizer_index.Rmd |only unitizer-1.4.4/unitizer/inst/doc/unitizer_index.html |only unitizer-1.4.4/unitizer/inst/doc/unitizer_interactive_env.Rmd |only unitizer-1.4.4/unitizer/inst/doc/unitizer_interactive_env.html |only unitizer-1.4.4/unitizer/inst/doc/unitizer_miscellaneous.Rmd |only unitizer-1.4.4/unitizer/inst/doc/unitizer_miscellaneous.html |only unitizer-1.4.4/unitizer/inst/doc/unitizer_reproducible_tests.Rmd |only unitizer-1.4.4/unitizer/inst/doc/unitizer_reproducible_tests.html |only unitizer-1.4.4/unitizer/inst/doc/unitizer_tests.Rmd |only unitizer-1.4.4/unitizer/inst/doc/unitizer_tests.html |only unitizer-1.4.4/unitizer/vignettes/unitizer.Rmd |only unitizer-1.4.4/unitizer/vignettes/unitizer_index.Rmd |only unitizer-1.4.4/unitizer/vignettes/unitizer_interactive_env.Rmd |only unitizer-1.4.4/unitizer/vignettes/unitizer_miscellaneous.Rmd |only unitizer-1.4.4/unitizer/vignettes/unitizer_reproducible_tests.Rmd |only unitizer-1.4.4/unitizer/vignettes/unitizer_tests.Rmd |only unitizer-1.4.5/unitizer/DESCRIPTION | 11 unitizer-1.4.5/unitizer/MD5 | 115 ++++--- unitizer-1.4.5/unitizer/NAMESPACE | 1 unitizer-1.4.5/unitizer/NEWS.md | 24 + unitizer-1.4.5/unitizer/R/browse.R | 17 - unitizer-1.4.5/unitizer/R/browse.struct.R | 37 +- unitizer-1.4.5/unitizer/R/faux_prompt.R | 11 unitizer-1.4.5/unitizer/R/get.R | 11 unitizer-1.4.5/unitizer/R/item.sub.R | 152 +++++----- unitizer-1.4.5/unitizer/R/list.R | 7 unitizer-1.4.5/unitizer/R/misc.R | 2 unitizer-1.4.5/unitizer/R/options.R | 23 + unitizer-1.4.5/unitizer/R/prompt.R | 13 unitizer-1.4.5/unitizer/R/section.R | 13 unitizer-1.4.5/unitizer/R/shims.R | 18 - unitizer-1.4.5/unitizer/R/size.R | 4 unitizer-1.4.5/unitizer/R/unitize.R | 15 unitizer-1.4.5/unitizer/R/unitize.core.R | 19 - unitizer-1.4.5/unitizer/build/vignette.rds |binary unitizer-1.4.5/unitizer/inst/doc/u0_unitizer_index.Rmd |only unitizer-1.4.5/unitizer/inst/doc/u0_unitizer_index.html |only unitizer-1.4.5/unitizer/inst/doc/u1_intro.R |only unitizer-1.4.5/unitizer/inst/doc/u1_intro.Rmd |only unitizer-1.4.5/unitizer/inst/doc/u1_intro.html |only unitizer-1.4.5/unitizer/inst/doc/u2_tests.Rmd |only unitizer-1.4.5/unitizer/inst/doc/u2_tests.html |only unitizer-1.4.5/unitizer/inst/doc/u3_interactive-env.Rmd |only unitizer-1.4.5/unitizer/inst/doc/u3_interactive-env.html |only unitizer-1.4.5/unitizer/inst/doc/u4_reproducible-tests.Rmd |only unitizer-1.4.5/unitizer/inst/doc/u4_reproducible-tests.html |only unitizer-1.4.5/unitizer/inst/doc/u5_miscellanous.Rmd |only unitizer-1.4.5/unitizer/inst/doc/u5_miscellanous.html |only unitizer-1.4.5/unitizer/man/unitize.Rd | 7 unitizer-1.4.5/unitizer/man/unitizer.opts.Rd | 2 unitizer-1.4.5/unitizer/tests/testthat/helper/refobjs/browse_aschar3.rds |only unitizer-1.4.5/unitizer/tests/testthat/helper/refobjs/browse_ascharnarrow.rds |only unitizer-1.4.5/unitizer/tests/testthat/helper/refobjs/unitize_faildiff.rds |only unitizer-1.4.5/unitizer/tests/testthat/helper/refobjs/unitize_invalid_unrev.rds |only unitizer-1.4.5/unitizer/tests/testthat/helper/refobjs/unitize_multinput.rds |only unitizer-1.4.5/unitizer/tests/testthat/helper/refobjs/unitize_showdiff.rds |only unitizer-1.4.5/unitizer/tests/testthat/helper/refobjs/unitize_txtdir_quitall.rds |only unitizer-1.4.5/unitizer/tests/testthat/helper/refobjs/unitize_usediff_no.rds |only unitizer-1.4.5/unitizer/tests/testthat/helper/runtt.R | 81 ++--- unitizer-1.4.5/unitizer/tests/testthat/testthat.browse.R | 73 ++++ unitizer-1.4.5/unitizer/tests/testthat/testthat.capture.R | 54 +++ unitizer-1.4.5/unitizer/tests/testthat/testthat.demo.R | 79 +++++ unitizer-1.4.5/unitizer/tests/testthat/testthat.error.R | 4 unitizer-1.4.5/unitizer/tests/testthat/testthat.get.R | 37 ++ unitizer-1.4.5/unitizer/tests/testthat/testthat.list.R | 20 + unitizer-1.4.5/unitizer/tests/testthat/testthat.misc.R | 13 unitizer-1.4.5/unitizer/tests/testthat/testthat.prompt.R | 12 unitizer-1.4.5/unitizer/tests/testthat/testthat.random.R |only unitizer-1.4.5/unitizer/tests/testthat/testthat.search.R | 1 unitizer-1.4.5/unitizer/tests/testthat/testthat.section.R | 3 unitizer-1.4.5/unitizer/tests/testthat/testthat.shim.R | 49 +++ unitizer-1.4.5/unitizer/tests/testthat/testthat.utz1.R | 51 ++- unitizer-1.4.5/unitizer/tests/testthat/testthat.utz2.R | 2 unitizer-1.4.5/unitizer/vignettes/u0_unitizer_index.Rmd |only unitizer-1.4.5/unitizer/vignettes/u1_intro.Rmd |only unitizer-1.4.5/unitizer/vignettes/u2_tests.Rmd |only unitizer-1.4.5/unitizer/vignettes/u3_interactive-env.Rmd |only unitizer-1.4.5/unitizer/vignettes/u4_reproducible-tests.Rmd |only unitizer-1.4.5/unitizer/vignettes/u5_miscellanous.Rmd |only 82 files changed, 732 insertions(+), 249 deletions(-)
Title: Thematic Map Tools
Description: Set of tools for reading and processing spatial data. The aim is to supply the workflow to create thematic maps. This package also facilitates 'tmap', the package for visualizing thematic maps.
Author: Martijn Tennekes [aut, cre]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmaptools versions 1.2-1 dated 2017-05-11 and 1.2-2 dated 2017-11-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 3 +++ R/smooth_map.R | 34 ++++++++++++++++++++++------------ R/xxx_raster.R | 4 +--- R/xxx_scales.R | 39 +++++++++++++++++++++++++++++++++++---- 6 files changed, 70 insertions(+), 28 deletions(-)
Title: R Interface to Python
Description: R interface to Python modules, classes, and functions. When calling
into Python R data types are automatically converted to their equivalent Python
types. When values are returned from Python to R they are converted back to R
types. Compatible with all versions of Python >= 2.7.
Author: JJ Allaire [aut, cre],
Kevin Ushey [ctb],
RStudio [cph, fnd],
Yuan Tang [aut, cph],
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Marcus Geelnard [aut, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between reticulate versions 1.3 dated 2017-11-16 and 1.3.1 dated 2017-11-24
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 8 +++++++- R/knitr-engine.R | 2 +- tests/testthat/resources/example.Rmd | 10 ++++++++++ tests/testthat/test-python-knitr-engine.R | 2 ++ 6 files changed, 28 insertions(+), 10 deletions(-)
Title: R-Friendly Threading in C++
Description: Provides a C++11-style thread class and thread pool that can safely
be interrupted from R.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <mail@tnagler.com>
Diff between RcppThread versions 0.1.1 dated 2017-11-07 and 0.1.2 dated 2017-11-24
DESCRIPTION | 8 MD5 | 10 NEWS.md | 11 + README.md | 1 inst/doc/RcppThread.html | 472 ++++++++++++++++++++++++++++++++--------------- src/test.cpp | 7 6 files changed, 348 insertions(+), 161 deletions(-)
Title: Some Latent Variable Models
Description: Contains some procedures for latent variable modelling with a
particular focus on multilevel data.
The LAM package contains mean and covariance structure modelling
for multivariate normally distributed data ('mlnormal'),
a general Metropolis-Hastings algorithm ('amh') and penalized
maximum likelihood estimation ('pmle').
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between LAM versions 0.0-17 dated 2017-05-11 and 0.1-22 dated 2017-11-24
LAM-0.0-17/LAM/R/mlnormalCheckMatrixListDifference.R |only LAM-0.0-17/LAM/R/mlnormalMatrix2List.R |only LAM-0.0-17/LAM/src/init.c |only LAM-0.1-22/LAM/DESCRIPTION | 9 LAM-0.1-22/LAM/MD5 | 197 ++--- LAM-0.1-22/LAM/NAMESPACE | 1 LAM-0.1-22/LAM/R/RcppExports.R | 10 LAM-0.1-22/LAM/R/amh.R | 11 LAM-0.1-22/LAM/R/amh_compare_estimators.R | 2 LAM-0.1-22/LAM/R/amh_eval_prior.R | 2 LAM-0.1-22/LAM/R/amh_ic.R | 2 LAM-0.1-22/LAM/R/amh_loglike.R | 2 LAM-0.1-22/LAM/R/amh_posterior.R | 2 LAM-0.1-22/LAM/R/amh_proposal_refresh.R | 2 LAM-0.1-22/LAM/R/amh_sampling.R | 2 LAM-0.1-22/LAM/R/coef.amh.R | 2 LAM-0.1-22/LAM/R/coef.mlnormal.R | 2 LAM-0.1-22/LAM/R/coef.pmle.R | 7 LAM-0.1-22/LAM/R/confint.amh.R | 2 LAM-0.1-22/LAM/R/confint.mlnormal.R | 2 LAM-0.1-22/LAM/R/confint.pmle.R | 2 LAM-0.1-22/LAM/R/logLik.amh.R | 2 LAM-0.1-22/LAM/R/logLik.mlnormal.R | 2 LAM-0.1-22/LAM/R/logLik.pmle.R | 2 LAM-0.1-22/LAM/R/loglike_mvnorm.R | 2 LAM-0.1-22/LAM/R/mlnormal.R | 2 LAM-0.1-22/LAM/R/mlnormal_abs_approx.R | 2 LAM-0.1-22/LAM/R/mlnormal_adjust_numdiff_parameter.R | 2 LAM-0.1-22/LAM/R/mlnormal_as_vector_names.R | 2 LAM-0.1-22/LAM/R/mlnormal_check_matrix_list_difference.R |only LAM-0.1-22/LAM/R/mlnormal_covmat_add_ridge.R | 2 LAM-0.1-22/LAM/R/mlnormal_create_disp.R | 2 LAM-0.1-22/LAM/R/mlnormal_equal_list_matrices.R | 2 LAM-0.1-22/LAM/R/mlnormal_equal_matrix.R | 2 LAM-0.1-22/LAM/R/mlnormal_eval_penalty.R | 2 LAM-0.1-22/LAM/R/mlnormal_eval_penalty_update_theta.R | 2 LAM-0.1-22/LAM/R/mlnormal_eval_priors.R | 2 LAM-0.1-22/LAM/R/mlnormal_eval_priors_derivative.R | 2 LAM-0.1-22/LAM/R/mlnormal_eval_priors_derivative2.R | 2 LAM-0.1-22/LAM/R/mlnormal_fill_matrix_from_list.R | 2 LAM-0.1-22/LAM/R/mlnormal_fit_function_ml.R | 2 LAM-0.1-22/LAM/R/mlnormal_ic.R | 2 LAM-0.1-22/LAM/R/mlnormal_information_matrix_reml.R | 2 LAM-0.1-22/LAM/R/mlnormal_linear_regression_bayes.R | 2 LAM-0.1-22/LAM/R/mlnormal_log_2pi.R | 2 LAM-0.1-22/LAM/R/mlnormal_log_det.R | 2 LAM-0.1-22/LAM/R/mlnormal_matrix2list.R |only LAM-0.1-22/LAM/R/mlnormal_parameter_change.R | 2 LAM-0.1-22/LAM/R/mlnormal_postproc_eval_posterior.R | 2 LAM-0.1-22/LAM/R/mlnormal_postproc_parameters.R | 2 LAM-0.1-22/LAM/R/mlnormal_proc.R | 2 LAM-0.1-22/LAM/R/mlnormal_proc_control.R | 2 LAM-0.1-22/LAM/R/mlnormal_proc_variance_shortcut.R | 2 LAM-0.1-22/LAM/R/mlnormal_proc_variance_shortcut_XY_R.R | 2 LAM-0.1-22/LAM/R/mlnormal_proc_variance_shortcut_XY_Rcpp.R | 2 LAM-0.1-22/LAM/R/mlnormal_proc_variance_shortcut_Z_R.R | 2 LAM-0.1-22/LAM/R/mlnormal_proc_variance_shortcut_Z_Rcpp.R | 2 LAM-0.1-22/LAM/R/mlnormal_process_prior.R | 2 LAM-0.1-22/LAM/R/mlnormal_soft_thresholding.R | 2 LAM-0.1-22/LAM/R/mlnormal_sqrt_diag.R | 2 LAM-0.1-22/LAM/R/mlnormal_summary_round_helper.R | 23 LAM-0.1-22/LAM/R/mlnormal_update_V_R.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_V_Rcpp.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_beta.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_beta_GLS.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_beta_XVX_R.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_beta_XVX_Rcpp.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_beta_iterations_penalty.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_beta_iterations_priors.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_control_list.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_ml_derivative_V.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_theta_ml.R | 2 LAM-0.1-22/LAM/R/mlnormal_update_theta_newton_step.R | 5 LAM-0.1-22/LAM/R/mlnormal_verbose_f0.R | 2 LAM-0.1-22/LAM/R/mlnormal_verbose_f1.R | 2 LAM-0.1-22/LAM/R/mlnormal_verbose_f2.R | 2 LAM-0.1-22/LAM/R/plot.amh.R | 7 LAM-0.1-22/LAM/R/pmle.R | 4 LAM-0.1-22/LAM/R/pmle_data_proc.R | 2 LAM-0.1-22/LAM/R/pmle_eval_posterior.R | 2 LAM-0.1-22/LAM/R/pmle_ic.R | 2 LAM-0.1-22/LAM/R/pmle_prior_extract_density.R | 2 LAM-0.1-22/LAM/R/pmle_process_prior.R | 2 LAM-0.1-22/LAM/R/print.mlnormal.R | 8 LAM-0.1-22/LAM/R/summary.amh.R | 11 LAM-0.1-22/LAM/R/summary.mlnormal.R | 10 LAM-0.1-22/LAM/R/summary.pmle.R | 6 LAM-0.1-22/LAM/R/vcov.amh.R | 2 LAM-0.1-22/LAM/R/vcov.mlnormal.R | 2 LAM-0.1-22/LAM/R/vcov.pmle.R | 2 LAM-0.1-22/LAM/R/zzz.R | 2 LAM-0.1-22/LAM/README.md |only LAM-0.1-22/LAM/data/data.HT12.rda |binary LAM-0.1-22/LAM/data/datalist |only LAM-0.1-22/LAM/inst/CITATION | 32 LAM-0.1-22/LAM/inst/NEWS | 8 LAM-0.1-22/LAM/man/LAM-package.Rd | 3 LAM-0.1-22/LAM/man/amh.Rd | 190 +++++ LAM-0.1-22/LAM/man/data.HT.Rd | 4 LAM-0.1-22/LAM/man/loglike_mvnorm.Rd | 3 LAM-0.1-22/LAM/man/mlnormal.Rd | 3 LAM-0.1-22/LAM/src/RcppExports.cpp | 23 LAM-0.1-22/LAM/src/mlnormal_helper_functions.cpp | 453 ++++++------- 103 files changed, 791 insertions(+), 381 deletions(-)
Title: Covariance Matrix Tests
Description: Testing functions for Covariance Matrices. These tests include high-dimension homogeneity of covariance
matrix testing described by Schott (2007) <doi:10.1016/j.csda.2007.03.004> and high-dimensional one-sample tests of
covariance matrix structure described by Fisher, et al. (2010) <doi:10.1016/j.jmva.2010.07.004>. Covariance matrix
tests use C++ to speed performance and allow larger data sets.
Author: Ben Barnard [aut, cre],
Dean Young [aut]
Maintainer: Ben Barnard <ben_barnard@outlook.com>
Diff between covTestR versions 0.1.0 dated 2017-11-22 and 0.1.1 dated 2017-11-24
covTestR-0.1.0/covTestR/build |only covTestR-0.1.0/covTestR/inst |only covTestR-0.1.1/covTestR/DESCRIPTION | 9 covTestR-0.1.1/covTestR/MD5 | 111 +++--- covTestR-0.1.1/covTestR/NAMESPACE | 104 ++--- covTestR-0.1.1/covTestR/R/Ahmad2015.R | 226 ++++++------ covTestR-0.1.1/covTestR/R/Ahmad2017.R | 115 +++--- covTestR-0.1.1/covTestR/R/BoxesM.R | 104 ++--- covTestR-0.1.1/covTestR/R/Chaipitak2013.R | 119 +++--- covTestR-0.1.1/covTestR/R/Chen2010.R | 219 ++++++------ covTestR-0.1.1/covTestR/R/Fisher2012.R | 262 +++++++-------- covTestR-0.1.1/covTestR/R/Ishii2016.R | 120 +++--- covTestR-0.1.1/covTestR/R/LedoitWolf2002.R | 218 ++++++------ covTestR-0.1.1/covTestR/R/Nagao1973.R | 232 ++++++------- covTestR-0.1.1/covTestR/R/RcppExports.R | 118 +++--- covTestR-0.1.1/covTestR/R/Schott2001.R | 120 +++--- covTestR-0.1.1/covTestR/R/Schott2007.R | 121 +++--- covTestR-0.1.1/covTestR/R/Srivastava2005.R | 237 ++++++------- covTestR-0.1.1/covTestR/R/Srivastava2007.R | 120 +++--- covTestR-0.1.1/covTestR/R/Srivastava2011.R | 240 ++++++------- covTestR-0.1.1/covTestR/R/Srivastava2014.R | 115 +++--- covTestR-0.1.1/covTestR/R/SrivastavaYanagihara2010.R | 117 +++--- covTestR-0.1.1/covTestR/R/covTestR-package.R | 24 - covTestR-0.1.1/covTestR/R/helpers.R | 44 +- covTestR-0.1.1/covTestR/R/homogeneityCovariances.R | 215 ++++++------ covTestR-0.1.1/covTestR/R/structureCovariances.R | 193 +++++------ covTestR-0.1.1/covTestR/man/Ahmad2015.Rd | 105 +++--- covTestR-0.1.1/covTestR/man/Ahmad2017.Rd | 113 +++--- covTestR-0.1.1/covTestR/man/BoxesM.Rd | 104 ++--- covTestR-0.1.1/covTestR/man/Chaipitak2013.Rd | 115 +++--- covTestR-0.1.1/covTestR/man/Chen2010.Rd | 102 ++--- covTestR-0.1.1/covTestR/man/Fisher2012.Rd | 103 +++-- covTestR-0.1.1/covTestR/man/Ishii2016.Rd | 116 +++--- covTestR-0.1.1/covTestR/man/LedoitWolf2002.Rd | 103 +++-- covTestR-0.1.1/covTestR/man/Nagao1973.Rd | 101 ++--- covTestR-0.1.1/covTestR/man/Schott2001.Rd | 114 +++--- covTestR-0.1.1/covTestR/man/Schott2007.Rd | 77 ++-- covTestR-0.1.1/covTestR/man/Srivastava2005.Rd | 102 ++--- covTestR-0.1.1/covTestR/man/Srivastava2007.Rd | 114 +++--- covTestR-0.1.1/covTestR/man/Srivastava2011.Rd | 103 +++-- covTestR-0.1.1/covTestR/man/Srivastava2014.Rd | 113 +++--- covTestR-0.1.1/covTestR/man/SrivastavaYanagihara2010.Rd | 113 +++--- covTestR-0.1.1/covTestR/man/covTestR-package.Rd | 28 - covTestR-0.1.1/covTestR/man/homogeneityCovariances.Rd | 94 ++--- covTestR-0.1.1/covTestR/man/past.Rd | 24 - covTestR-0.1.1/covTestR/man/structureCovariances.Rd | 90 ++--- covTestR-0.1.1/covTestR/man/tr.Rd | 24 - covTestR-0.1.1/covTestR/src/Ahmad2015.cpp | 4 covTestR-0.1.1/covTestR/src/Ahmad2017.cpp | 22 - covTestR-0.1.1/covTestR/src/BoxesM.cpp | 6 covTestR-0.1.1/covTestR/src/Chaipitak2013.cpp | 108 +++--- covTestR-0.1.1/covTestR/src/Chen2010.cpp | 16 covTestR-0.1.1/covTestR/src/Ishii2016.cpp | 16 covTestR-0.1.1/covTestR/src/Schott2001.cpp | 10 covTestR-0.1.1/covTestR/src/Schott2007.cpp | 48 +- covTestR-0.1.1/covTestR/src/Srivastava2014.cpp | 34 - covTestR-0.1.1/covTestR/src/SrivastavaYanagihara2010.cpp | 74 ++-- 57 files changed, 2911 insertions(+), 2888 deletions(-)
Title: Tools for the Continuous Convolution Trick in Nonparametric
Estimation
Description: Implements the uniform scaled beta distribution and
the continuous convolution kernel density estimator.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between cctools versions 0.1.0 dated 2017-04-26 and 0.1.1 dated 2017-11-24
cctools-0.1.0/cctools/src/init.c |only cctools-0.1.1/cctools/DESCRIPTION | 6 ++-- cctools-0.1.1/cctools/MD5 | 20 ++++++------- cctools-0.1.1/cctools/NAMESPACE | 1 cctools-0.1.1/cctools/NEWS.md | 7 ++++ cctools-0.1.1/cctools/R/RcppExports.R | 4 +- cctools-0.1.1/cctools/R/expansions.R | 33 ++++++++++++++++++++-- cctools-0.1.1/cctools/README.md | 9 +++++- cctools-0.1.1/cctools/man/expand_names.Rd |only cctools-0.1.1/cctools/man/expand_vec.Rd | 2 - cctools-0.1.1/cctools/src/RcppExports.cpp | 15 ++++++++-- cctools-0.1.1/cctools/tests/testthat/test-cckde.R | 2 - 12 files changed, 77 insertions(+), 22 deletions(-)
Title: Functions for the STARTS Model
Description: Contains functions for estimating the STARTS model of
Kenny and Zautra (1995, 2001) <DOI:10.1037/0022-006X.63.1.52>,
<DOI:10.1037/10409-008>.
Author: Alexander Robitzsch [aut,cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between STARTS versions 0.1-51 dated 2017-08-27 and 0.2-10 dated 2017-11-24
DESCRIPTION | 10 MD5 | 62 ++-- NAMESPACE | 12 R/coef.starts_uni.R |only R/logLik.starts_uni.R |only R/plot.starts_uni.R |only R/starts_cov.R | 1 R/starts_deprecated.R | 1 R/starts_estimate_description.R | 14 - R/starts_estimate_model_fit.R | 1 R/starts_estimate_model_fit_rmsea.R | 1 R/starts_estimate_model_fit_srmr.R | 1 R/starts_sim1dim.R | 1 R/starts_summary_print_computation_time.R |only R/starts_summary_print_ic.R |only R/starts_uni_cov.R | 1 R/starts_uni_cov_pars.R | 1 R/starts_uni_estimate.R | 52 ++- R/starts_uni_estimate_prepare_fitting.R | 12 R/starts_uni_estimate_prepare_fitting_prior_model.R | 1 R/starts_uni_estimate_prepare_fitting_prior_variance.R | 1 R/starts_uni_estimate_proc.R | 5 R/starts_uni_sim.R | 1 R/starts_vector_with_names.R | 1 R/summary.starts_uni.R | 89 +++--- R/vcov.starts_uni.R |only R/zzz.R | 1 README.md | 6 data/data.starts01a.rda |binary data/data.starts01b.rda |binary inst/CITATION | 9 inst/NEWS | 20 + man/STARTS-package.Rd | 1 man/data.starts.Rd | 1 man/starts_uni.Rd | 235 +++-------------- 35 files changed, 217 insertions(+), 324 deletions(-)
Title: Dynamic Model Averaging and Dynamic Model Selection for
Continuous Outcomes
Description: Allows to estimate dynamic model averaging, dynamic model selection and median probability model. The original methods are implemented, as well as, selected further modifications of these methods. In particular the user might choose between recursive moment estimation and exponentially moving average for variance updating. Inclusion probabilities might be modified in a way using 'Google Trends'. The code is written in a way which minimises the computational burden (which is quite an obstacle for dynamic model averaging if many variables are used). For example, this package allows for parallel computations and Occam's window approach. The package is designed in a way that is hoped to be especially useful in economics and finance. Main reference: Raftery, A.E., Karny, M., Ettler, P. (2010) <doi:10.1198/TECH.2009.08104>.
Author: Krzysztof Drachal [aut, cre] (Faculty of Economic Sciences, University of Warsaw, Poland)
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between fDMA versions 2.2 dated 2017-11-15 and 2.2.1 dated 2017-11-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 3 ++- NEWS | 8 ++++++++ 4 files changed, 17 insertions(+), 8 deletions(-)
Title: A-Optimal Block Designs for Comparing Test Treatments with
Controls
Description: A collection of functions to construct A-optimal block designs for comparing test treatments with one or more control(s). Mainly A-optimal balanced treatment incomplete block designs, weighted A-optimal balanced treatment incomplete block designs, A-optimal group divisible treatment designs and A-optimal balanced bipartite block designs can be constructed using the package. The designs are constructed using algorithms based on linear integer programming. To the best of our knowledge, these facilities to construct A-optimal block designs for comparing test treatments with one or more controls are not available in the existing R packages. For more details on designs for tests versus control(s) comparisons, please see Hedayat, A. S. and Majumdar, D. (1984) <doi:10.1080/00401706.1984.10487989> A-Optimal Incomplete Block Designs for Control-Test Treatment Comparisons, Technometrics, 26, 363-370 and Mandal, B. N. , Gupta, V. K., Parsad, Rajender. (2017) <doi:10.1080/03610926.2015.1071394> Balanced treatment incomplete block designs through integer programming. Communications in Statistics - Theory and Methods 46(8), 3728-3737.
Author: Baidya Nath Mandal [aut, cre], Sukanta Dash [aut], Rajender Parsad [aut]
Maintainer: Baidya Nath Mandal <mandal.stat@gmail.com>
Diff between Aoptbdtvc versions 0.0.1 dated 2017-11-22 and 0.0.2 dated 2017-11-24
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/Aoptbdtvc.R | 54 ++++++++++++------------------------------------------ man/aoptbbpb.Rd | 6 ++---- man/aoptgdtd.Rd | 6 ++---- man/bbpbwq.Rd | 3 +-- man/btibts.Rd | 3 +-- man/wtaoptbtib.Rd | 5 ++--- 9 files changed, 32 insertions(+), 69 deletions(-)
Title: Visual Data Mining Tools
Description: This provides web-based visual data-mining tools by adding
interactive functions to 'ggplot2' graphics. Brushing and linking between the
multiple plots is one of the main feature of this package. Currently scatter
plots, histograms, parallel coordinate plots and choropleth maps are supported.
Author: Tomokazu Fujino
Maintainer: Tomokazu Fujino <fujino@fwu.ac.jp>
Diff between vdmR versions 0.2.4 dated 2017-06-23 and 0.2.5 dated 2017-11-24
vdmR-0.2.4/vdmR/inst/tests |only vdmR-0.2.4/vdmR/tests/run-all.R |only vdmR-0.2.5/vdmR/DESCRIPTION | 13 +- vdmR-0.2.5/vdmR/MD5 | 49 +++++----- vdmR-0.2.5/vdmR/NAMESPACE | 22 ++-- vdmR-0.2.5/vdmR/R/misc.R | 8 + vdmR-0.2.5/vdmR/R/vcmap.R | 10 +- vdmR-0.2.5/vdmR/R/vdmR-package.R | 5 - vdmR-0.2.5/vdmR/R/vhist.R | 13 +- vdmR-0.2.5/vdmR/R/vlaunch.R | 24 ++-- vdmR-0.2.5/vdmR/R/vpcp.R | 99 ++++++++++---------- vdmR-0.2.5/vdmR/R/vscat.R | 137 ++++++++++++++-------------- vdmR-0.2.5/vdmR/build/partial.rdb |only vdmR-0.2.5/vdmR/build/vignette.rds |binary vdmR-0.2.5/vdmR/inst/CITATION |only vdmR-0.2.5/vdmR/inst/REFERENCES.bib |only vdmR-0.2.5/vdmR/inst/doc/vdmR-vignette.R | 2 vdmR-0.2.5/vdmR/inst/doc/vdmR-vignette.Rnw | 2 vdmR-0.2.5/vdmR/inst/doc/vdmR-vignette.pdf |binary vdmR-0.2.5/vdmR/man/kw2011.Rd | 98 ++++++++++---------- vdmR-0.2.5/vdmR/man/vcmap.Rd | 77 ++++++++------- vdmR-0.2.5/vdmR/man/vdmR-package.Rd | 45 ++++----- vdmR-0.2.5/vdmR/man/vhist.Rd | 60 ++++++------ vdmR-0.2.5/vdmR/man/vlaunch.Rd | 62 ++++++------ vdmR-0.2.5/vdmR/man/vpcp.Rd | 74 +++++++-------- vdmR-0.2.5/vdmR/man/vscat.Rd | 60 ++++++------ vdmR-0.2.5/vdmR/man/vsfuk2012.Rd | 80 ++++++++-------- vdmR-0.2.5/vdmR/vignettes/vdmR-vignette.Rnw | 2 28 files changed, 489 insertions(+), 453 deletions(-)
Title: Thematic Maps
Description: Thematic maps are geographical maps in which spatial data distributions are visualized. This package offers a flexible, layer-based, and easy to use approach to create thematic maps, such as choropleths and bubble maps.
Author: Martijn Tennekes [aut, cre],
Joel Gombin [ctb],
Sebastian Jeworutzki [ctb],
Kent Russell [ctb],
Richard Zijdeman [ctb],
John Clouse [ctb]
Maintainer: Martijn Tennekes <mtennekes@gmail.com>
Diff between tmap versions 1.10 dated 2017-05-11 and 1.11 dated 2017-11-24
DESCRIPTION | 14 +++-- MD5 | 104 ++++++++++++++++++++++---------------------- NEWS | 11 ++++ R/cat2pal.R | 39 +++++++++++----- R/cat2shape.R | 56 +++++++++++++++++------ R/legend_prepare.R | 22 ++++++--- R/meta_plot.R | 5 +- R/meta_plot_items.R | 64 ++++++++++++++++++++++++--- R/num2pal.R | 51 +++++++++++++++++++-- R/num2shape.R | 17 +++++-- R/plot_map.R | 6 +- R/plot_misc_functions.R | 35 +++++++++++--- R/preprocess_gt.R | 6 +- R/preprocess_shapes.R | 15 ++++-- R/print_tmap.R | 9 ++- R/process_color_aes.R | 23 +++++++-- R/process_fill.R | 44 ++++++++++-------- R/process_gps.R | 4 - R/process_lines.R | 15 ++++-- R/process_meta.R | 7 ++ R/process_other_aes.R | 36 +++++++++++---- R/process_raster.R | 22 +++++---- R/process_shapes.R | 18 ++++++- R/process_symbols.R | 49 +++++++++++++++----- R/process_text.R | 16 ++++-- R/process_tm.R | 13 +++++ R/save_tmap.R | 5 +- R/split_tm.R | 4 + R/text_functions.R | 45 +++++++++++++++++-- R/tm_add_legend.R | 6 ++ R/tm_layers.R | 54 ++++++++++++++++++---- R/tm_layout.R | 15 ++++-- R/tm_misc_elements.R | 15 +++++- R/tm_shape.R | 4 + R/tmap_icons.R | 24 ++++++++-- R/view_tmap.R | 30 ++++++++---- R/xxx_scales.R | 39 ++++++++++++++-- build/vignette.rds |binary inst/doc/tmap-nutshell.R | 6 +- inst/doc/tmap-nutshell.Rmd | 8 +-- inst/doc/tmap-nutshell.html | 20 ++++---- man/save_tmap.Rd | 2 man/tm_add_legend.Rd | 9 ++- man/tm_facets.Rd | 18 ++----- man/tm_grid.Rd | 12 +++++ man/tm_layout.Rd | 11 +++- man/tm_lines.Rd | 17 +++++-- man/tm_polygons.Rd | 14 +++-- man/tm_raster.Rd | 12 +++-- man/tm_shape.Rd | 6 +- man/tm_symbols.Rd | 49 +++++++++++++------- man/tm_text.Rd | 18 +++++-- vignettes/tmap-nutshell.Rmd | 8 +-- 53 files changed, 835 insertions(+), 317 deletions(-)
Title: Simulation-Based Quasi-Likelihood Estimation
Description: A simulation-based quasi-likelihood method (Baaske, M., Ballani, F., v.d. Boogaart, K.G. (2014) <doi:10.5566/ias.v33.p107-119>) for parameter estimation of parametric statistical models for which closed-form representations of distributional characteristics are unavailable and can only be obtained by computationally intensive simulations of the model.
Author: Markus Baaske [aut, cre, cph], K. Gerald van den Boogaart [ths]
Maintainer: Markus Baaske <markus.baaske@uni-jena.de>
Diff between qle versions 0.16-5 dated 2017-11-16 and 0.16-6 dated 2017-11-24
qle-0.16-5/qle/src/qloptr.h |only qle-0.16-6/qle/DESCRIPTION | 12 +- qle-0.16-6/qle/MD5 | 41 +++---- qle-0.16-6/qle/R/qle-package.R | 2 qle-0.16-6/qle/data/matclust.rda |binary qle-0.16-6/qle/inst/doc/qle_with_R.R | 88 ++++++++-------- qle-0.16-6/qle/inst/doc/qle_with_R.Rnw | 3 qle-0.16-6/qle/inst/doc/qle_with_R.pdf |binary qle-0.16-6/qle/man/qle-package.Rd | 2 qle-0.16-6/qle/src/auxil.cc | 24 ---- qle-0.16-6/qle/src/auxil.h | 7 - qle-0.16-6/qle/src/basics.h | 41 ------- qle-0.16-6/qle/src/covariance.cc | 16 ++ qle-0.16-6/qle/src/covariance.h | 5 qle-0.16-6/qle/src/error.h | 104 +++++++------------ qle-0.16-6/qle/src/initError.cc | 171 ++------------------------------ qle-0.16-6/qle/src/kriging.cc | 52 ++++----- qle-0.16-6/qle/src/kriging.h | 14 +- qle-0.16-6/qle/src/qloptr.cc | 11 +- qle-0.16-6/qle/src/qsoptim.cc | 7 - qle-0.16-6/qle/src/qsoptim.h | 13 -- qle-0.16-6/qle/vignettes/qle_with_R.Rnw | 3 22 files changed, 196 insertions(+), 420 deletions(-)
Title: Lattice Options and Add-Ins
Description: Various plots and functions that make use of the lattice/trellis plotting framework.
The plots, which include loaPlot(), GoogleMap() and trianglePlot(), use panelPal(), a function that
extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel
and panel-to-key synchronization/management.
Author: Karl Ropkins
Maintainer: Karl Ropkins <k.ropkins@its.leeds.ac.uk>
Diff between loa versions 0.2.38 dated 2016-03-01 and 0.2.43.1 dated 2017-11-24
DESCRIPTION | 18 +- MD5 | 54 +++--- NAMESPACE | 16 + NEWS | 66 +++++++ R/0pts.R |only R/googleMap.R | 27 +++ R/key.handlers.R | 127 +++++++++++--- R/loaBarPlot.R |only R/loaShapes.R | 43 ++++ R/plot.argument.handlers.R | 242 ++++++++++++++++++++++++++ R/specialist.panels.01.R | 230 ++++++++++++++++++++----- R/specialist.panels.03.zcase.glyphs.R | 45 ++++- R/trianglePlot.R | 305 +++++++++++++++++++++++++++++++++- R/working.R |only data/lat.lon.meuse.RData |binary data/roadmap.meuse.RData |binary man/1.1.loaPlot.Rd | 16 - man/1.2.googleMap.Rd | 22 +- man/1.3.trianglePlot.Rd | 85 +++++---- man/1.4.stackPlot.Rd | 11 - man/1.5.loaBarPlot.Rd |only man/2.1.specialist.panels.Rd | 60 +----- man/2.3.specialist.panels.Rd | 20 +- man/3.1.example.data.Rd | 7 man/4.1.panel.pal.Rd | 6 man/4.5.plot.argument.handlers.Rd | 42 +++- man/4.6.key.handlers.Rd | 9 - man/4.8.list.handlers.Rd | 35 ++- man/4.9.loa.shapes.Rd | 11 + man/loa-package.Rd | 6 30 files changed, 1221 insertions(+), 282 deletions(-)
Title: Artificial Neural Networks for Anomaly Detection
Description: Training of general classification and regression neural networks using
gradient descent. Special features include a function for training replicator
neural networks and a function for training autoencoders. Multiple activation and
cost functions (including Huber and pseudo-Huber) are supported, as well as L1
and L2 regularization, momentum, early stopping and the possibility to specify
a learning rate schedule. The package contains a vectorized gradient descent
implementation which facilitates faster training through batch learning.
Author: Bart Lammers
Maintainer: Bart Lammers <bart.f.lammers@gmail.com>
Diff between ANN2 versions 1.3 dated 2017-11-16 and 1.4 dated 2017-11-24
DESCRIPTION | 8 +- MD5 | 30 +++++----- NAMESPACE | 2 R/RcppExports.R | 4 + R/callable.R | 143 ++++++++++++++++++++++++++++++++++-------------- R/required-functions.R | 21 ++++++- man/autoencoder.Rd | 2 man/decode.Rd |only man/encode.Rd |only man/neuralnetwork.Rd | 2 man/plot.ANN.Rd | 2 man/plotStepFunction.Rd | 17 +++-- man/predict.ANN.Rd | 2 man/reconstruct.Rd | 4 - man/replicator.Rd | 2 src/RcppExports.cpp | 17 +++++ src/rcpp-nn.cpp | 39 +++++++++++++ 17 files changed, 223 insertions(+), 72 deletions(-)
Title: Local Interpretable Model-Agnostic Explanations
Description: When building complex models, it is often difficult to explain why
the model should be trusted. While global measures such as accuracy are
useful, they cannot be used for explaining why a model made a specific
prediction. 'lime' (a port of the 'lime' 'Python' package) is a method for
explaining the outcome of black box models by fitting a local model around
the point in question an perturbations of this point. The approach is
described in more detail in the article by Ribeiro et al. (2016)
<arXiv:1602.04938>.
Author: Thomas Lin Pedersen [cre, aut],
Michaël Benesty [aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between lime versions 0.3.0 dated 2017-09-15 and 0.3.1 dated 2017-11-24
DESCRIPTION | 10 - MD5 | 37 ++-- NAMESPACE | 2 NEWS.md |only R/character.R | 8 - R/dataframe.R | 27 ++- R/lime.R | 11 + R/models.R | 44 ++++- R/permute_cases.R | 9 + R/plot.R | 58 +++++++ R/plot_text.R | 1 README.md | 50 +++--- build/vignette.rds |binary inst/doc/Understanding_lime.html | 240 +++++++++++++++---------------- man/explain.Rd | 4 man/figures/README-unnamed-chunk-2-1.png |binary man/lime.Rd | 4 man/plot_explanations.Rd |only man/plot_features.Rd | 8 - man/text_explanations.Rd | 4 tests/testthat/test-h2o.R |only 21 files changed, 327 insertions(+), 190 deletions(-)
Title: Genetic Algorithms and C-Steps Based LTS (Least Trimmed Squares)
Estimation
Description: Includes the ga.lts() function that estimates
LTS (Least Trimmed Squares) parameters using genetic algorithms
and C-steps. ga.lts() constructs a genetic algorithm to form a
basic subset and iterates C-steps as defined in Rousseeuw and
van-Driessen (2006) to calculate the cost value of the LTS
criterion. OLS (Ordinary Least Squares) regression is known to
be sensitive to outliers. A single outlying observation can
change the values of estimated parameters. LTS is a resistant
estimator even the number of outliers is up to half of the
data. This package is for estimating the LTS parameters with
lower bias and variance in a reasonable time. Version >=1.3
includes the function medmad for fast outlier detection in
linear regression.
Author: Mehmet Hakan Satman
Maintainer: Mehmet Hakan Satman <mhsatman@istanbul.edu.tr>
Diff between galts versions 1.3 dated 2013-02-07 and 1.3.1 dated 2017-11-24
DESCRIPTION | 21 ++++++++------- MD5 | 16 ++++++------ NAMESPACE | 4 +++ R/galts.r | 67 ++++++++++++++++++++++++++------------------------- R/medmad.r | 56 +++++++++++++++++++++--------------------- man/ga.lts.Rd | 36 +++++++++++++++------------ man/galts-package.Rd | 32 +++++++++++++----------- man/medmad.Rd | 31 ++++++++++++----------- man/medmad.cov.Rd | 20 +++++++-------- 9 files changed, 150 insertions(+), 133 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management
procedures for data-limited fisheries
(see Carruthers et al (2014) <doi:10.1016/j.fishres.2013.12.014>).
Author: Tom Carruthers [aut, cre],
Adrian Hordyk [aut]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 5.0 dated 2017-10-24 and 5.0.1 dated 2017-11-24
DLMtool-5.0.1/DLMtool/DESCRIPTION | 8 DLMtool-5.0.1/DLMtool/MD5 | 158 +++--- DLMtool-5.0.1/DLMtool/NEWS.md | 14 DLMtool-5.0.1/DLMtool/R/DefineClasses.r | 15 DLMtool-5.0.1/DLMtool/R/MSEplotting.R | 3 DLMtool-5.0.1/DLMtool/R/MiscFuns.r | 6 DLMtool-5.0.1/DLMtool/R/OMinit_doc.R | 158 ++++-- DLMtool-5.0.1/DLMtool/R/OMinit_doc_plots.R | 4 DLMtool-5.0.1/DLMtool/R/PMobjects.R | 8 DLMtool-5.0.1/DLMtool/R/SampleCpars.R | 2 DLMtool-5.0.1/DLMtool/R/SampleStockPars.R | 11 DLMtool-5.0.1/DLMtool/R/StochasticSRA.R | 431 +++++++++++------ DLMtool-5.0.1/DLMtool/R/popdyn.R | 3 DLMtool-5.0.1/DLMtool/R/runMSE.r | 35 - DLMtool-5.0.1/DLMtool/README.md | 2 DLMtool-5.0.1/DLMtool/data/Albacore.RData |binary DLMtool-5.0.1/DLMtool/data/Atlantic_mackerel.RData |binary DLMtool-5.0.1/DLMtool/data/Blue_shark.RData |binary DLMtool-5.0.1/DLMtool/data/Bluefin_tuna.RData |binary DLMtool-5.0.1/DLMtool/data/Bluefin_tuna_WAtl.RData |binary DLMtool-5.0.1/DLMtool/data/Butterfish.RData |binary DLMtool-5.0.1/DLMtool/data/China_rockfish.RData |binary DLMtool-5.0.1/DLMtool/data/Cobia.RData |binary DLMtool-5.0.1/DLMtool/data/DataDescription.RData |binary DLMtool-5.0.1/DLMtool/data/DecE_Dom.RData |binary DLMtool-5.0.1/DLMtool/data/DecE_HDom.RData |binary DLMtool-5.0.1/DLMtool/data/DecE_NDom.RData |binary DLMtool-5.0.1/DLMtool/data/Example_datafile.RData |binary DLMtool-5.0.1/DLMtool/data/Feasibility.RData |binary DLMtool-5.0.1/DLMtool/data/Feasibility2.RData |binary DLMtool-5.0.1/DLMtool/data/FlatE_Dom.RData |binary DLMtool-5.0.1/DLMtool/data/FlatE_HDom.RData |binary DLMtool-5.0.1/DLMtool/data/FlatE_NDom.RData |binary DLMtool-5.0.1/DLMtool/data/FleetDescription.RData |binary DLMtool-5.0.1/DLMtool/data/Generic_DecE.RData |binary DLMtool-5.0.1/DLMtool/data/Generic_FlatE.RData |binary DLMtool-5.0.1/DLMtool/data/Generic_IncE.RData |binary DLMtool-5.0.1/DLMtool/data/Generic_fleet.RData |binary DLMtool-5.0.1/DLMtool/data/Generic_obs.RData |binary DLMtool-5.0.1/DLMtool/data/Gulf_blue_tilefish.RData |binary DLMtool-5.0.1/DLMtool/data/Herring.RData |binary DLMtool-5.0.1/DLMtool/data/ImpDescription.RData |binary DLMtool-5.0.1/DLMtool/data/Imprecise_Biased.RData |binary DLMtool-5.0.1/DLMtool/data/Imprecise_Unbiased.RData |binary DLMtool-5.0.1/DLMtool/data/IncE_HDom.RData |binary DLMtool-5.0.1/DLMtool/data/IncE_NDom.RData |binary DLMtool-5.0.1/DLMtool/data/Low_Effort_Non_Target.RData |binary DLMtool-5.0.1/DLMtool/data/Mackerel.RData |binary DLMtool-5.0.1/DLMtool/data/OMDescription.RData |binary DLMtool-5.0.1/DLMtool/data/ObsDescription.RData |binary DLMtool-5.0.1/DLMtool/data/Overages.RData |binary DLMtool-5.0.1/DLMtool/data/Perfect_Imp.RData |binary DLMtool-5.0.1/DLMtool/data/Perfect_Info.RData |binary DLMtool-5.0.1/DLMtool/data/Porgy.RData |binary DLMtool-5.0.1/DLMtool/data/Precise_Biased.RData |binary DLMtool-5.0.1/DLMtool/data/Precise_Unbiased.RData |binary DLMtool-5.0.1/DLMtool/data/Red_snapper.RData |binary DLMtool-5.0.1/DLMtool/data/Rockfish.RData |binary DLMtool-5.0.1/DLMtool/data/Simulation_1.RData |binary DLMtool-5.0.1/DLMtool/data/Snapper.RData |binary DLMtool-5.0.1/DLMtool/data/Sole.RData |binary DLMtool-5.0.1/DLMtool/data/StockDescription.RData |binary DLMtool-5.0.1/DLMtool/data/Target_All_Fish.RData |binary DLMtool-5.0.1/DLMtool/data/Targeting_Small_Fish.RData |binary DLMtool-5.0.1/DLMtool/data/Toothfish.RData |binary DLMtool-5.0.1/DLMtool/data/ourReefFish.RData |binary DLMtool-5.0.1/DLMtool/data/testOM.RData |binary DLMtool-5.0.1/DLMtool/inst/Example_Chile_Hake.rmd |only DLMtool-5.0.1/DLMtool/inst/Example_Chile_Hake.xlsx |binary DLMtool-5.0.1/DLMtool/man/OM-class.Rd | 10 DLMtool-5.0.1/DLMtool/man/OMDescription.Rd | 2 DLMtool-5.0.1/DLMtool/man/OMdoc.Rd | 2 DLMtool-5.0.1/DLMtool/man/OMinit.Rd | 10 DLMtool-5.0.1/DLMtool/man/SRAsim.Rd | 17 DLMtool-5.0.1/DLMtool/man/SampleStockPars.Rd | 4 DLMtool-5.0.1/DLMtool/man/StochasticSRA.Rd | 23 DLMtool-5.0.1/DLMtool/man/StochasticSRAcpp.Rd |only DLMtool-5.0.1/DLMtool/man/Stock-class.Rd | 2 DLMtool-5.0.1/DLMtool/man/StockDescription.Rd | 2 DLMtool-5.0.1/DLMtool/src/LSRA_opt_cpp.cpp | 1 DLMtool-5.0/DLMtool/inst/Example_Chile_hake_source.rmd |only DLMtool-5.0/DLMtool/man/StochasticSRA2.Rd |only 82 files changed, 597 insertions(+), 334 deletions(-)