Title: Read, Manipulate and Explore Chess PGN Files
Description: Provides functions for reading *.PGN files with more than one game, including large files without copying it into RAM (using 'ff' package). Handle chess data and chess aggregated data, count figure moves statistics, create player profile, plot winning chances, browse openings.
Author: Wojciech Rosa
Maintainer: Wojciech Rosa <w.rosa@pollub.pl>
Diff between bigchess versions 1.1.0 dated 2018-09-25 and 1.2.0 dated 2018-11-04
DESCRIPTION | 6 +++--- MD5 | 11 +++++++++-- NAMESPACE | 3 +++ R/browse_eco_opening.R |only R/plot_tree_eco.R |only R/tree_eco.R |only README.md |only man/browse_eco_opening.Rd |only man/plot_tree_eco.Rd |only man/tree_eco.Rd |only 10 files changed, 15 insertions(+), 5 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
R. Arellano;
J. Astrom;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
K. Colyvas;
H. Commenges;
R. Constantine;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
T. Davies;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
M. Hesselbarth;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
L. Kozmian-Ledward;
M. Kuhn;
J. Laake;
R.A. Lamb;
F. Lavancier;
T. Lawrence;
T. Lazauskas;
J. Lee;
G.P. Leser;
A. Li;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
I. Moncada;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
L. Torres;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.56-1 dated 2018-08-01 and 1.57-1 dated 2018-11-04
spatstat-1.56-1/spatstat/R/copyExampleFiles.R |only spatstat-1.56-1/spatstat/R/datasetup.R |only spatstat-1.56-1/spatstat/src/massdisthack.c |only spatstat-1.56-1/spatstat/tests/testsAtoF.R |only spatstat-1.57-1/spatstat/DESCRIPTION | 22 - spatstat-1.57-1/spatstat/MD5 | 253 ++++++------ spatstat-1.57-1/spatstat/NAMESPACE | 8 spatstat-1.57-1/spatstat/NEWS | 199 +++++++++ spatstat-1.57-1/spatstat/R/Gcom.R | 4 spatstat-1.57-1/spatstat/R/Kcom.R | 7 spatstat-1.57-1/spatstat/R/Kinhom.R | 32 + spatstat-1.57-1/spatstat/R/Kmeasure.R | 22 - spatstat-1.57-1/spatstat/R/Kmulti.R | 16 spatstat-1.57-1/spatstat/R/anova.ppm.R | 165 ++++--- spatstat-1.57-1/spatstat/R/areadiff.R | 6 spatstat-1.57-1/spatstat/R/as.im.R | 10 spatstat-1.57-1/spatstat/R/blur.R | 3 spatstat-1.57-1/spatstat/R/bw.CvL.R |only spatstat-1.57-1/spatstat/R/bw.diggle.R | 2 spatstat-1.57-1/spatstat/R/cdf.test.mppm.R | 4 spatstat-1.57-1/spatstat/R/colourtables.R | 18 spatstat-1.57-1/spatstat/R/connected.R | 2 spatstat-1.57-1/spatstat/R/daogenton.R | 8 spatstat-1.57-1/spatstat/R/deldir.R | 6 spatstat-1.57-1/spatstat/R/density.lpp.R | 25 - spatstat-1.57-1/spatstat/R/density.ppp.R | 442 +++++++++++++-------- spatstat-1.57-1/spatstat/R/density.psp.R | 8 spatstat-1.57-1/spatstat/R/densityfun.R | 17 spatstat-1.57-1/spatstat/R/derivfv.R | 4 spatstat-1.57-1/spatstat/R/distances.R | 9 spatstat-1.57-1/spatstat/R/dummy.R | 4 spatstat-1.57-1/spatstat/R/edges2triangles.R | 8 spatstat-1.57-1/spatstat/R/envelopelpp.R | 4 spatstat-1.57-1/spatstat/R/eval.fv.R | 5 spatstat-1.57-1/spatstat/R/eval.im.R | 8 spatstat-1.57-1/spatstat/R/evalcovar.R | 6 spatstat-1.57-1/spatstat/R/ewcdf.R | 4 spatstat-1.57-1/spatstat/R/images.R | 6 spatstat-1.57-1/spatstat/R/indices.R | 8 spatstat-1.57-1/spatstat/R/interp.im.R | 40 + spatstat-1.57-1/spatstat/R/kernel2d.R | 69 ++- spatstat-1.57-1/spatstat/R/leverage.R | 2 spatstat-1.57-1/spatstat/R/linearK.R | 7 spatstat-1.57-1/spatstat/R/linim.R | 6 spatstat-1.57-1/spatstat/R/linnetsurgery.R | 2 spatstat-1.57-1/spatstat/R/lintess.R | 2 spatstat-1.57-1/spatstat/R/measures.R | 12 spatstat-1.57-1/spatstat/R/mincontrast.R | 34 - spatstat-1.57-1/spatstat/R/mpl.R | 6 spatstat-1.57-1/spatstat/R/nncross.R | 4 spatstat-1.57-1/spatstat/R/nndist.R | 4 spatstat-1.57-1/spatstat/R/nnorient.R | 30 - spatstat-1.57-1/spatstat/R/pixellate.R | 5 spatstat-1.57-1/spatstat/R/plot.im.R | 17 spatstat-1.57-1/spatstat/R/plot.ppp.R | 2 spatstat-1.57-1/spatstat/R/pppmatch.R | 234 +++++------ spatstat-1.57-1/spatstat/R/predict.ppm.R | 4 spatstat-1.57-1/spatstat/R/psp.R | 63 +- spatstat-1.57-1/spatstat/R/psstG.R | 4 spatstat-1.57-1/spatstat/R/random.R | 9 spatstat-1.57-1/spatstat/R/relrisk.R | 79 ++- spatstat-1.57-1/spatstat/R/rescue.rectangle.R | 18 spatstat-1.57-1/spatstat/R/rhohat.R | 68 ++- spatstat-1.57-1/spatstat/R/rmhsnoop.R | 10 spatstat-1.57-1/spatstat/R/rmhtemper.R | 24 - spatstat-1.57-1/spatstat/R/setcov.R | 3 spatstat-1.57-1/spatstat/R/simplepanel.R | 2 spatstat-1.57-1/spatstat/R/smooth.ppp.R | 351 +++++++++++++--- spatstat-1.57-1/spatstat/R/smoothfun.R | 17 spatstat-1.57-1/spatstat/R/split.ppx.R | 5 spatstat-1.57-1/spatstat/R/ssf.R | 1 spatstat-1.57-1/spatstat/R/subset.R | 39 + spatstat-1.57-1/spatstat/R/superimpose.R | 38 - spatstat-1.57-1/spatstat/R/transect.R | 4 spatstat-1.57-1/spatstat/R/unique.ppp.R | 12 spatstat-1.57-1/spatstat/R/window.R | 10 spatstat-1.57-1/spatstat/R/wingeom.R | 35 - spatstat-1.57-1/spatstat/inst/doc/Nickname.txt | 2 spatstat-1.57-1/spatstat/inst/doc/bugfixes.Rnw | 43 +- spatstat-1.57-1/spatstat/inst/doc/bugfixes.pdf |binary spatstat-1.57-1/spatstat/inst/doc/datasets.pdf |binary spatstat-1.57-1/spatstat/inst/doc/getstart.pdf |binary spatstat-1.57-1/spatstat/inst/doc/packagesizes.txt | 2 spatstat-1.57-1/spatstat/inst/doc/replicated.pdf |binary spatstat-1.57-1/spatstat/inst/doc/shapefiles.R | 24 - spatstat-1.57-1/spatstat/inst/doc/shapefiles.Rnw | 17 spatstat-1.57-1/spatstat/inst/doc/shapefiles.pdf |binary spatstat-1.57-1/spatstat/inst/doc/updates.R | 13 spatstat-1.57-1/spatstat/inst/doc/updates.Rnw | 125 ++++- spatstat-1.57-1/spatstat/inst/doc/updates.pdf |binary spatstat-1.57-1/spatstat/man/BadGey.Rd | 5 spatstat-1.57-1/spatstat/man/Smooth.ppp.Rd | 35 + spatstat-1.57-1/spatstat/man/as.owin.Rd | 15 spatstat-1.57-1/spatstat/man/bw.CvL.Rd |only spatstat-1.57-1/spatstat/man/bw.diggle.Rd | 11 spatstat-1.57-1/spatstat/man/bw.frac.Rd | 15 spatstat-1.57-1/spatstat/man/bw.pcf.Rd | 11 spatstat-1.57-1/spatstat/man/bw.ppl.Rd | 13 spatstat-1.57-1/spatstat/man/bw.scott.Rd | 8 spatstat-1.57-1/spatstat/man/bw.smoothppp.Rd | 8 spatstat-1.57-1/spatstat/man/density.ppp.Rd | 60 ++ spatstat-1.57-1/spatstat/man/eval.im.Rd | 11 spatstat-1.57-1/spatstat/man/eval.linim.Rd | 11 spatstat-1.57-1/spatstat/man/idw.Rd | 6 spatstat-1.57-1/spatstat/man/interp.im.Rd | 19 spatstat-1.57-1/spatstat/man/lohboot.Rd | 4 spatstat-1.57-1/spatstat/man/methods.ssf.Rd | 2 spatstat-1.57-1/spatstat/man/pairdist.default.Rd | 17 spatstat-1.57-1/spatstat/man/parameters.Rd | 1 spatstat-1.57-1/spatstat/man/pixellate.ppp.Rd | 12 spatstat-1.57-1/spatstat/man/plot.colourmap.Rd | 16 spatstat-1.57-1/spatstat/man/ppm.Rd | 3 spatstat-1.57-1/spatstat/man/relrisk.ppm.Rd | 9 spatstat-1.57-1/spatstat/man/relrisk.ppp.Rd | 30 + spatstat-1.57-1/spatstat/man/rhohat.Rd | 32 + spatstat-1.57-1/spatstat/man/rmh.default.Rd | 4 spatstat-1.57-1/spatstat/man/rtemper.Rd | 22 - spatstat-1.57-1/spatstat/man/spatstat-internal.Rd | 28 - spatstat-1.57-1/spatstat/man/spatstat-package.Rd | 10 spatstat-1.57-1/spatstat/man/split.ppx.Rd | 2 spatstat-1.57-1/spatstat/man/subset.psp.Rd |only spatstat-1.57-1/spatstat/man/tess.Rd | 7 spatstat-1.57-1/spatstat/tests/testsAtoD.R |only spatstat-1.57-1/spatstat/tests/testsEtoF.R |only spatstat-1.57-1/spatstat/tests/testsGtoK.R | 75 +++ spatstat-1.57-1/spatstat/tests/testsLtoM.R | 3 spatstat-1.57-1/spatstat/tests/testsNtoP.R | 53 ++ spatstat-1.57-1/spatstat/tests/testsQtoR.R | 57 ++ spatstat-1.57-1/spatstat/tests/testsStoZ.R | 148 ++++++- spatstat-1.57-1/spatstat/vignettes/bugfixes.Rnw | 43 +- spatstat-1.57-1/spatstat/vignettes/shapefiles.Rnw | 17 spatstat-1.57-1/spatstat/vignettes/updates.Rnw | 125 ++++- 132 files changed, 2697 insertions(+), 1094 deletions(-)
Title: An Interface for Microclimate Time Series Analysis
Description: An R graphical user interface for microclimate time series, with an emphasis on underground environments. 'KarsTS' provides linear and nonlinear methods, including recurrence analysis (Marwan et al. (2007) <10.1016/j.physrep.2006.11.001>) and filling methods (Moffat et al. (2007) <doi:10.1016/j.agrformet.2007.08.011>), as well as tools to manipulate easily time series and gap sets.
Author: Marina Saez [aut, cre],
David Benavente [ths],
Soledad Cuezva [ths],
Concepcion Pla [ctb]
Maintainer: Marina Saez <marinasaez_andreu@hotmail.com>
Diff between KarsTS versions 2.1 dated 2018-04-05 and 2.2 dated 2018-11-04
DESCRIPTION | 14 MD5 | 328 +++---- NAMESPACE | 2 R/E1dAndE2d.R | 148 +-- R/KarsTS.R | 60 - R/RPKTS.R | 296 +++--- R/aboutKTS.R | 14 R/aggregateKTS.R | 312 +++--- R/anaSamPer.R | 174 +-- R/applyGap2TSer.R | 116 +- R/applyTheiler.R | 20 R/are2TsTimeCompatible.R | 16 R/areTsGapTimeCompatible.R | 22 R/areTsRmTimeCompatible.R | 14 R/arimaKalman.R | 530 +++++------ R/arimaXKalman.R | 640 ++++++------- R/assignMultiple.R | 22 R/buttons1.R | 106 +- R/buttons2.R | 94 +- R/buttons3.R | 118 +- R/buttons4.R | 110 +- R/buttons5.R | 88 - R/checkIfAny.R | 24 R/checkIfAnyGapOrTs.R | 26 R/checkIfAnyGapTs.R | 40 R/checkIfAnyRm.R | 22 R/checkIfAnyRmTs.R | 40 R/checkIfAnyTs.R | 22 R/cleanEnvir.R | 224 ++-- R/compareVecVec.R | 28 R/composeKTS.R | 890 +++++++++---------- R/createChb.R | 16 R/createChbChb.R | 32 R/createChbEntry.R | 34 R/createCrossRM.R | 382 ++++---- R/createCrossRMPlot.R | 1270 +++++++++++++-------------- R/createDistMatrix.R | 1120 ++++++++++++------------ R/createEachRb.R | 18 R/createEntry.R | 26 R/createGapChb.R | 32 R/createGapRb.R | 40 R/createJointRM.R | 380 ++++---- R/createNote.R | 16 R/createOK.R | 14 R/createRandGaps.R | 172 +-- R/createRandName.R | 8 R/createRb.R | 12 R/createRmChb.R | 32 R/createRmRb.R | 40 R/createSimpleRM.R | 238 ++--- R/createSimpleRMPlot.R | 1270 +++++++++++++-------------- R/createSpecGaps.R | 240 ++--- R/createSubPanR4C1.R | 40 R/createTitle.R | 16 R/createTsChb.R | 32 R/createTsRb.R | 42 R/createtitle_1.R | 18 R/cumuKTS.R | 130 +- R/destroyMainScreen.R | 8 R/destroyWelcome.R | 8 R/determinismKTS.R | 570 ++++++------ R/diffKTS.R | 162 +-- R/embedData.R | 22 R/endingLines.R | 24 R/exportall.R | 474 +++++----- R/fillWithTwins.R | 566 ++++++------ R/findDateFormat.R | 72 - R/findTwins.R | 148 +-- R/fnnKTS.R | 200 ++-- R/functToExport.R | 14 R/gamKTS.R | 698 +++++++-------- R/gapCheckedTF.R | 24 R/gapDetect.R | 60 - R/gapForSelMethod.R | 50 - R/genGapExample.R | 42 R/genRmExample.R | 128 +- R/genTSExample.R | 68 - R/getCRP.R | 70 - R/getClassEnvir.R | 24 R/getCoordsKTS.R | 276 ++--- R/getDelayCharTimes.R | 24 R/getGapsAfterFill.R | 26 R/getMaxNegSlope.R | 20 R/getMaxPosSlope.R | 20 R/getNAsGaps.R | 28 R/getNewGapsInd.R | 48 - R/getOtherErrEstim.R | 18 R/getProTaos.R | 68 - R/getRecurrencePoints.R | 100 +- R/getRollStatistics.R | 208 ++-- R/getSamPerTable.1Freq.R | 48 - R/getSamPerTable.R | 258 ++--- R/getScreenSize.R | 82 - R/getStatistics.R | 30 R/getUniqueSampPer.R | 32 R/goodnessFilling.R | 318 +++--- R/groupDates.R | 18 R/groupIndices.R | 24 R/histKTS.R | 148 +-- R/invariantsKTS.R | 420 ++++----- R/isTimeAlright.R | 62 - R/laminarityKTS.R | 374 ++++---- R/linCorrKTS.R | 238 ++--- R/linearityKTS.R | 326 +++---- R/littleTest.R | 238 ++--- R/loadAllTypes.R | 1370 ++++++++++++++--------------- R/loadKarsTSFonts.R | 54 - R/loessKTS.R | 282 +++--- R/mainScreen.R | 354 +++---- R/meanValue.R | 492 +++++----- R/mergeTsOrGap.R | 290 +++--- R/missForestKTS.R | 878 +++++++++--------- R/modeKTS.R | 12 R/mutInf.R | 734 +++++++-------- R/mutualKTS.R | 226 ++-- R/myApplyVector.R | 42 R/myLinModel.R | 230 ++-- R/myScale.R | 64 - R/naApproxKTS.R | 214 ++-- R/naSplinesKTS.R | 221 ++-- R/normalityKTS.R | 314 +++--- R/packagesToImport.R | 78 - R/pcaKTS.R | 224 ++-- R/plotTimeSeries.R | 1810 +++++++++++++++++++-------------------- R/readMultEntryvalues.R | 44 R/refreshDataSetsList.R | 228 ++-- R/removeAllTypes.R | 118 +- R/removeIfExists.R | 18 R/removePoints.R | 318 +++--- R/renameAllTypes.R | 180 +-- R/rmCheckedTF.R | 24 R/rmDetect.R | 64 - R/rmSlopeOutliers.R | 162 +-- R/rollStatisticsKTS.R | 176 +-- R/roundKTS.R | 164 +-- R/saveAllTypes.R | 180 +-- R/saveReport.R | 32 R/scaleKTS.R | 96 +- R/scattTimeSeries.R | 896 +++++++++---------- R/selectionGaps.R | 642 ++++++------- R/selectionTS.R | 248 ++--- R/separateEntry.R | 36 R/setCorrectDate.R | 82 - R/setwdKTS.R | 14 R/showHelp.R | 14 R/slopeOutliersBut.R | 340 +++---- R/stationarityKTS.R | 120 +- R/statisticsKTS.R | 94 +- R/stinemannKTS.R | 541 ++++++----- R/stlplusKTS.R | 492 +++++----- R/theilerKTS.R | 120 +- R/tsCheckedTF.R | 24 R/tsDetect.R | 66 - R/verifyCharEntry.R | 24 R/verifyDateEntry.R | 58 - R/verifyIntEntry.R | 24 R/verifyRealEntry.R | 26 R/welcomeScreen.R | 122 +- R/windRoseKTS.R | 280 +++--- R/writeMethodSummary.R | 56 - R/writeMethodTitle.R | 12 build/partial.rdb |binary inst/extdata/KarsTS-manual.pdf |binary inst/extdata/KarsTSUserGuide.pdf |binary man/KarsTS-package.Rd | 2 165 files changed, 15644 insertions(+), 15496 deletions(-)
Title: Analysis of Convergent Evolution
Description: Quantifies and assesses the significance of convergent evolution using two different methods (and 5 different measures) as described in Stayton (2015) <DOI: 10.1111/evo.12729>. Also displays results in a phylomorphospace framework.
Author: C. Tristan Stayton [aut, cre]
Maintainer: C. Tristan Stayton <tstayton@bucknell.edu>
Diff between convevol versions 1.2 dated 2018-08-20 and 1.3 dated 2018-11-04
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- R/convrat.R | 8 ++++---- 3 files changed, 11 insertions(+), 12 deletions(-)
More information about TwoSampleTest.HD at CRAN
Permanent link
Title: Landscape and Range Expansion Simulation
Description: Tools to generate random landscape graphs, evaluate species
occurrence in dynamic landscapes, simulate future landscape occupation and
evaluate range expansion when new empty patches are available (e.g. as a
result of climate change).
Author: Frederico Mestre, Fernando Canovas, Benjamin Risk, Ricardo Pita,
Antonio Mira, Pedro Beja.
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between MetaLandSim versions 1.0.4 dated 2018-06-17 and 1.0.5 dated 2018-11-04
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/matrix.graph.R | 6 +++--- inst/doc/landscape_simulation-knitr.pdf |binary inst/doc/parameter_estimation-knitr.pdf |binary inst/doc/range_expansion-knitr.pdf |binary man/MetaLandSim-package.Rd | 4 ++-- 7 files changed, 15 insertions(+), 15 deletions(-)
Title: Trellis Graphics for R
Description: A powerful and elegant high-level data visualization
system inspired by Trellis graphics, with an emphasis on
multivariate data. Lattice is sufficient for typical graphics needs,
and is also flexible enough to handle most nonstandard requirements.
See ?Lattice for an introduction.
Author: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Maintainer: Deepayan Sarkar <deepayan.sarkar@r-project.org>
Diff between lattice versions 0.20-35 dated 2017-03-25 and 0.20-38 dated 2018-11-04
DESCRIPTION | 8 +- MD5 | 51 ++++++++--------- R/miscellaneous.R | 1 R/panels.R | 8 +- R/print.trellis.R | 10 ++- R/qqmath.R | 84 ---------------------------- R/xyplot.R | 10 +++ README.md | 7 ++ data/USMortality.rda |binary data/USRegionalMortality.rda |binary data/barley.rda |binary data/environmental.rda |binary data/ethanol.rda |binary data/melanoma.rda |binary data/singer.rda |binary inst/po/de/LC_MESSAGES/R-lattice.mo |binary inst/po/en@quot/LC_MESSAGES/R-lattice.mo |binary inst/po/fr/LC_MESSAGES/R-lattice.mo |binary inst/po/ko/LC_MESSAGES/R-lattice.mo |binary inst/po/pl/LC_MESSAGES/R-lattice.mo |binary po/R-de.po | 92 +++++++++---------------------- po/R-en@quot.po | 14 ++-- po/R-fr.po | 14 ++-- po/R-ko.po | 14 ++-- po/R-lattice.pot | 10 --- po/R-pl.po | 22 +++---- tests/summary.R |only 27 files changed, 119 insertions(+), 226 deletions(-)
Title: Bayesian Framework for Computational Modeling
Description: Derived from the work of Kruschke (2015, <ISBN:9780124058880>),
the present package aims to provide a framework for conducting Bayesian
analysis using Markov chain Monte Carlo (MCMC) sampling utilizing the
Just Another Gibbs Sampler ('JAGS', Plummer, 2003, <http://mcmc-jags.sourceforge.net/>).
The initial version includes several modules for conducting Bayesian
equivalents of chi-squared tests, analysis of variance (ANOVA),
multiple (hierarchical) regression, softmax regression, and for fitting data
(e.g., structural equation modeling).
Author: Øystein Olav Skaar [aut, cre]
Maintainer: Øystein Olav Skaar <bayesianfw@gmail.com>
Diff between bfw versions 0.2.0 dated 2018-09-11 and 0.3.0 dated 2018-11-04
bfw-0.2.0/bfw/R/plotdata.R |only bfw-0.2.0/bfw/inst/doc/plot_data.R |only bfw-0.2.0/bfw/inst/doc/plot_data.Rmd |only bfw-0.2.0/bfw/inst/doc/plot_data.html |only bfw-0.2.0/bfw/inst/doc/plot_data.md |only bfw-0.2.0/bfw/vignettes/plot_data.Rmd |only bfw-0.3.0/bfw/DESCRIPTION | 20 bfw-0.3.0/bfw/MD5 | 124 - bfw-0.3.0/bfw/NAMESPACE | 13 bfw-0.3.0/bfw/NEWS.md | 103 + bfw-0.3.0/bfw/R/basic_functions.R | 518 ----- bfw-0.3.0/bfw/R/mcmc.R | 267 +- bfw-0.3.0/bfw/R/mcmc_misc.R | 41 bfw-0.3.0/bfw/R/mcmc_summary.R | 19 bfw-0.3.0/bfw/R/plot.R |only bfw-0.3.0/bfw/R/plot_circlize.R |only bfw-0.3.0/bfw/R/plot_mean.R |only bfw-0.3.0/bfw/R/plot_nominal.R |only bfw-0.3.0/bfw/R/plot_param.R |only bfw-0.3.0/bfw/R/plot_parse.R |only bfw-0.3.0/bfw/R/settings.R | 134 - bfw-0.3.0/bfw/R/stats_bernoulli.R | 8 bfw-0.3.0/bfw/R/stats_covariate.R | 45 bfw-0.3.0/bfw/R/stats_fit.R | 36 bfw-0.3.0/bfw/R/stats_kappa.R | 15 bfw-0.3.0/bfw/R/stats_mean.R | 12 bfw-0.3.0/bfw/R/stats_metric.R | 28 bfw-0.3.0/bfw/R/stats_nominal.R | 46 bfw-0.3.0/bfw/R/stats_regression.R | 42 bfw-0.3.0/bfw/R/stats_softmax.R | 16 bfw-0.3.0/bfw/README.md | 434 ++-- bfw-0.3.0/bfw/build/vignette.rds |binary bfw-0.3.0/bfw/inst/doc/fit_latent_data.html | 582 ++++-- bfw-0.3.0/bfw/inst/doc/fit_latent_data.md | 318 +-- bfw-0.3.0/bfw/inst/doc/fit_observed_data.html | 940 ++++++---- bfw-0.3.0/bfw/inst/doc/fit_observed_data.md | 678 +++---- bfw-0.3.0/bfw/inst/doc/metric.html | 492 +++-- bfw-0.3.0/bfw/inst/doc/metric.md | 258 +- bfw-0.3.0/bfw/inst/doc/plot_mean.R |only bfw-0.3.0/bfw/inst/doc/plot_mean.Rmd |only bfw-0.3.0/bfw/inst/doc/plot_mean.html |only bfw-0.3.0/bfw/inst/doc/plot_mean.md |only bfw-0.3.0/bfw/inst/doc/regression.html | 482 +++-- bfw-0.3.0/bfw/inst/doc/regression.md | 221 +- bfw-0.3.0/bfw/inst/extdata/models/stats_fit_cfa.txt | 10 bfw-0.3.0/bfw/inst/extdata/models/stats_regression.txt | 8 bfw-0.3.0/bfw/inst/extdata/models/stats_regression_robust.txt | 8 bfw-0.3.0/bfw/inst/extdata/templates/apa.pptx |only bfw-0.3.0/bfw/man/FileName.Rd | 2 bfw-0.3.0/bfw/man/MatrixCombn.Rd | 11 bfw-0.3.0/bfw/man/MergeMCMC.Rd | 2 bfw-0.3.0/bfw/man/MultiGrep.Rd |only bfw-0.3.0/bfw/man/ParsePlot.Rd | 32 bfw-0.3.0/bfw/man/PlotCirclize.Rd |only bfw-0.3.0/bfw/man/PlotData.Rd | 93 bfw-0.3.0/bfw/man/PlotMean.Rd |only bfw-0.3.0/bfw/man/PlotNominal.Rd |only bfw-0.3.0/bfw/man/PlotParam.Rd |only bfw-0.3.0/bfw/man/RemoveGarbage.Rd |only bfw-0.3.0/bfw/man/RunMCMC.Rd | 33 bfw-0.3.0/bfw/man/StatsBernoulli.Rd | 3 bfw-0.3.0/bfw/man/StatsCovariate.Rd | 5 bfw-0.3.0/bfw/man/StatsFit.Rd | 10 bfw-0.3.0/bfw/man/StatsKappa.Rd | 3 bfw-0.3.0/bfw/man/StatsMean.Rd | 3 bfw-0.3.0/bfw/man/StatsMetric.Rd | 11 bfw-0.3.0/bfw/man/StatsNominal.Rd | 5 bfw-0.3.0/bfw/man/StatsRegression.Rd | 5 bfw-0.3.0/bfw/man/StatsSoftmax.Rd | 5 bfw-0.3.0/bfw/man/SumMCMC.Rd | 2 bfw-0.3.0/bfw/man/TidyCode.Rd | 2 bfw-0.3.0/bfw/man/TrimSplit.Rd | 2 bfw-0.3.0/bfw/man/bfw.Rd | 97 - bfw-0.3.0/bfw/man/figures |only bfw-0.3.0/bfw/vignettes/plot_mean.Rmd |only 75 files changed, 3359 insertions(+), 2885 deletions(-)
Title: Joint Mean-Covariance Models using 'Armadillo' and S4
Description: Fit joint mean-covariance models for longitudinal data. The models
and their components are represented using S4 classes and methods. The core
computational algorithms are implemented using the 'Armadillo' C++ library
for numerical linear algebra and 'RcppArmadillo' glue.
Author: Jianxin Pan [aut, cre],
Yi Pan [aut]
Maintainer: Jianxin Pan <Jianxin.Pan@manchester.ac.uk>
Diff between jmcm versions 0.1.8.0 dated 2017-11-25 and 0.2.0 dated 2018-11-04
jmcm-0.1.8.0/jmcm/src/acd.cpp |only jmcm-0.1.8.0/jmcm/src/bfgs-impl.h |only jmcm-0.1.8.0/jmcm/src/hpc.cpp |only jmcm-0.1.8.0/jmcm/src/linesearch-impl.h |only jmcm-0.1.8.0/jmcm/src/mcd.cpp |only jmcm-0.2.0/jmcm/DESCRIPTION | 11 jmcm-0.2.0/jmcm/MD5 | 58 - jmcm-0.2.0/jmcm/R/AllClass.R | 86 -- jmcm-0.2.0/jmcm/R/RcppExports.R | 18 jmcm-0.2.0/jmcm/R/jmcm.R | 21 jmcm-0.2.0/jmcm/R/utilities.R | 63 -- jmcm-0.2.0/jmcm/inst/NEWS.Rd |only jmcm-0.2.0/jmcm/man/acd_estimation.Rd | 5 jmcm-0.2.0/jmcm/man/getJMCM.Rd | 7 jmcm-0.2.0/jmcm/man/hpc_estimation.Rd | 5 jmcm-0.2.0/jmcm/man/jmcm.Rd | 5 jmcm-0.2.0/jmcm/man/mcd_estimation.Rd | 5 jmcm-0.2.0/jmcm/man/modular.Rd | 9 jmcm-0.2.0/jmcm/src/Makevars | 4 jmcm-0.2.0/jmcm/src/Makevars.win | 4 jmcm-0.2.0/jmcm/src/RcppExports.cpp | 21 jmcm-0.2.0/jmcm/src/acd.h | 831 ++++++++++++++++---------- jmcm-0.2.0/jmcm/src/arma_util.cpp | 21 jmcm-0.2.0/jmcm/src/arma_util.h | 27 jmcm-0.2.0/jmcm/src/bfgs.h | 4 jmcm-0.2.0/jmcm/src/bfgs_impl.h |only jmcm-0.2.0/jmcm/src/external.cpp | 792 ++----------------------- jmcm-0.2.0/jmcm/src/hpc.h | 991 +++++++++++++++++++------------- jmcm-0.2.0/jmcm/src/init.c | 102 --- jmcm-0.2.0/jmcm/src/jmcm_base.h |only jmcm-0.2.0/jmcm/src/jmcm_fit.h |only jmcm-0.2.0/jmcm/src/linesearch.h | 2 jmcm-0.2.0/jmcm/src/linesearch_impl.h |only jmcm-0.2.0/jmcm/src/mcd.h | 774 ++++++++++++++---------- jmcm-0.2.0/jmcm/tests |only 35 files changed, 1866 insertions(+), 2000 deletions(-)
Title: A Framework for Creating, Managing and Training Multiple Caret
Models
Description: A minimalistic but flexible framework that facilitates the creation,
management and training of multiple 'caret' models. A model grid consists of
two components: (1) a set of settings that is shared by all models by
default, and (2) specifications that apply only to the individual models.
When the model grid is trained, model and training specifications are first
consolidated from the shared and the model specific settings into complete
'caret' model configurations. These models are then trained with the 'train'
function from the 'caret' package.
Author: Lars Kjeldgaard [aut, cre]
Maintainer: Lars Kjeldgaard <lars_kjeldgaard@hotmail.com>
Diff between modelgrid versions 1.1.0.0 dated 2018-07-13 and 1.1.1.0 dated 2018-11-04
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/add_model.R | 4 ---- R/edit_model.R | 5 ----- R/share_settings.R | 8 ++------ inst/doc/modelgrid.html | 18 ++++++++++-------- man/figures/mglogo.png |binary tests/testthat/test_add_model.R | 12 ------------ 8 files changed, 23 insertions(+), 46 deletions(-)
Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of
various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting
of experimental results, working around issue such as the difficulty of
extracting model summary facts (such as with 'lm'/'glm'). This package also
includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 1.0.2 dated 2018-10-05 and 1.0.3 dated 2018-11-04
DESCRIPTION | 10 +++---- MD5 | 13 +++++----- NEWS.md | 4 +++ R/DifferenceDistribution.R | 55 ++++++++++++++++++++++++++++++++++++++----- R/DifferenceDistribution2.R |only inst/doc/lmExample.html | 4 +-- inst/doc/sigrFormatting.html | 4 +-- man/Bernoulli_diff_stat.Rd | 4 ++- 8 files changed, 72 insertions(+), 22 deletions(-)
Title: Generalized Array Arithmetic for Ragged Arrays with Named
Margins
Description: Organize a so-called ragged array as generalized arrays, which
is simply an array with sub-dimensions denoting the subdivision of
dimensions (grouping of members within dimensions).
By the margins (names of dimensions and sub-dimensions) in generalized
arrays, operators and utility functions provided in this package
automatically match the margins,
doing map-reduce style parallel computation
along margins. Generalized arrays are also cooperative to R's native
functions that work on simple arrays.
Author: Qingsheng Huang
Maintainer: Qingsheng Huang <huangqqss@126.com>
Diff between garray versions 1.0.2 dated 2018-08-13 and 1.1.1 dated 2018-11-04
DESCRIPTION | 11 +-- MD5 | 19 ++--- NAMESPACE | 1 R/main.R | 173 +++++++++++++++++++++++++++----------------------- R/zzz.R |only man/amap.Rd | 3 man/areduce.Rd | 45 +++++++------ man/dim.garray.Rd | 2 man/garray-package.Rd | 3 man/garray.Rd | 16 ++-- man/sub-.garray.Rd | 35 ++++++---- 11 files changed, 177 insertions(+), 131 deletions(-)