Title: Spatially-Explicit Power Analysis for Conservation and Ecology
Diff between rSPACE versions 1.0 dated 2014-12-16 and 1.0.4 dated 2015-01-06
Description: Conducts a spatially-explicit, simulation-based power analysis for detecting trends in population abundance through occupancy-based modeling. Applicable for evaluating monitoring designs in conservation and ecological settings.
Author: Martha Ellis, Jake Ivan, Jody Tucker, Mike Schwartz
Maintainer: Martha Ellis
DESCRIPTION | 8 +++++---
MD5 | 12 ++++++------
R/AddDropIndividuals.R | 2 +-
R/Create_Landscapes.r | 7 +------
R/Encounter_history.R | 3 ++-
R/Test_Samples.r | 2 +-
R/checkParameters.R | 27 ++++++++++++++++++++++-----
7 files changed, 38 insertions(+), 23 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.13 dated 2014-11-13 and 2.14 dated 2015-01-06
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth
lsmeans-2.13/lsmeans/R/old-lsmeans.R |only
lsmeans-2.13/lsmeans/inst/doc/lsmeans-changes.R |only
lsmeans-2.13/lsmeans/inst/doc/lsmeans-changes.pdf |only
lsmeans-2.13/lsmeans/inst/doc/lsmeans-changes.rnw |only
lsmeans-2.13/lsmeans/vignettes/lsmeans-changes.rnw |only
lsmeans-2.14/lsmeans/DESCRIPTION | 12
lsmeans-2.14/lsmeans/MD5 | 66 +--
lsmeans-2.14/lsmeans/NAMESPACE | 20 -
lsmeans-2.14/lsmeans/R/cld.lsm.R | 15
lsmeans-2.14/lsmeans/R/glht-support.R | 2
lsmeans-2.14/lsmeans/R/helpers.R | 11
lsmeans-2.14/lsmeans/R/lsm-contr.R | 21 -
lsmeans-2.14/lsmeans/R/lsmeans.R | 83 +++-
lsmeans-2.14/lsmeans/R/lsmip.R | 4
lsmeans-2.14/lsmeans/R/ordinal-support.R | 59 ++-
lsmeans-2.14/lsmeans/R/plot.lsm.R | 2
lsmeans-2.14/lsmeans/R/ref.grid.R | 413 ---------------------
lsmeans-2.14/lsmeans/R/summary.R |only
lsmeans-2.14/lsmeans/build/vignette.rds |binary
lsmeans-2.14/lsmeans/inst/NEWS | 28 +
lsmeans-2.14/lsmeans/inst/doc/extending.pdf |binary
lsmeans-2.14/lsmeans/inst/doc/using-lsmeans.R | 154 ++++---
lsmeans-2.14/lsmeans/inst/doc/using-lsmeans.pdf |binary
lsmeans-2.14/lsmeans/inst/doc/using-lsmeans.rnw | 60 +--
lsmeans-2.14/lsmeans/man/contrast.Rd | 5
lsmeans-2.14/lsmeans/man/glht.Rd | 2
lsmeans-2.14/lsmeans/man/lsmeans-package.Rd | 16
lsmeans-2.14/lsmeans/man/lsmeans.Rd | 22 -
lsmeans-2.14/lsmeans/man/models.Rd | 9
lsmeans-2.14/lsmeans/man/pairwise.lsmc.Rd | 11
lsmeans-2.14/lsmeans/man/ref.grid.Rd | 3
lsmeans-2.14/lsmeans/man/ref.grid.class.Rd | 2
lsmeans-2.14/lsmeans/man/summary.Rd | 26 -
lsmeans-2.14/lsmeans/man/update.Rd | 12
lsmeans-2.14/lsmeans/tests/tests1.Rout.save | 28 -
lsmeans-2.14/lsmeans/vignettes/lsmeans.bib | 34 +
lsmeans-2.14/lsmeans/vignettes/using-lsmeans.rnw | 60 +--
37 files changed, 512 insertions(+), 668 deletions(-)
Title: R Interface to C API of GLPK
Diff between glpkAPI versions 1.2.11 dated 2014-11-16 and 1.3.0 dated 2015-01-06
Description: R Interface to C API of GLPK, needs GLPK Version >= 4.42
Author: Claus Jonathan Fritzemeier [cre],
Gabriel Gelius-Dietrich [aut],
Louis Luangkesorn [ctb]
Maintainer: Claus Jonathan Fritzemeier
DESCRIPTION | 16 +-
MD5 | 328 ++++++++++++++++++++---------------------
README.md |only
build/vignette.rds |binary
inst/NEWS.Rd | 10 +
inst/doc/glpk-gmpl-intro.R |only
inst/doc/glpk-gmpl-intro.Rnw |only
inst/doc/glpk-gmpl-intro.pdf |only
inst/doc/glpkAPI.pdf |binary
inst/extdata |only
man/addColsGLPK.Rd | 5
man/addRowsGLPK.Rd | 5
man/advBasisGLPK.Rd | 5
man/bfExistsGLPK.Rd | 5
man/bfUpdatedGLPK.Rd | 5
man/checkDupGLPK.Rd | 5
man/copyProbGLPK.Rd | 5
man/cpxBasisGLPK.Rd | 5
man/createIndexGLPK.Rd | 5
man/delColsGLPK.Rd | 5
man/delProbGLPK.Rd | 5
man/delRowsGLPK.Rd | 5
man/deleteIndexGLPK.Rd | 5
man/eraseProbGLPK.Rd | 5
man/factorizeGLPK.Rd | 5
man/findColGLPK.Rd | 5
man/findRowGLPK.Rd | 5
man/getBfcpGLPK.Rd | 5
man/getBheadGLPK.Rd | 5
man/getCbindGLPK.Rd | 5
man/getColDualGLPK.Rd | 5
man/getColDualIptGLPK.Rd | 5
man/getColKindGLPK.Rd | 5
man/getColLowBndGLPK.Rd | 5
man/getColNameGLPK.Rd | 5
man/getColPrimGLPK.Rd | 5
man/getColPrimIptGLPK.Rd | 5
man/getColStatGLPK.Rd | 5
man/getColTypeGLPK.Rd | 5
man/getColUppBndGLPK.Rd | 5
man/getColsDualGLPK.Rd | 5
man/getColsDualIptGLPK.Rd | 5
man/getColsKindGLPK.Rd | 5
man/getColsLowBndsGLPK.Rd | 5
man/getColsPrimGLPK.Rd | 5
man/getColsPrimIptGLPK.Rd | 5
man/getColsStatGLPK.Rd | 5
man/getColsUppBndsGLPK.Rd | 5
man/getDualStatGLPK.Rd | 5
man/getInteriorParmGLPK.Rd | 5
man/getMIPParmGLPK.Rd | 5
man/getMatColGLPK.Rd | 5
man/getMatRowGLPK.Rd | 5
man/getNumBinGLPK.Rd | 5
man/getNumColsGLPK.Rd | 5
man/getNumIntGLPK.Rd | 5
man/getNumNnzGLPK.Rd | 5
man/getNumRowsGLPK.Rd | 5
man/getObjCoefGLPK.Rd | 5
man/getObjCoefsGLPK.Rd | 5
man/getObjDirGLPK.Rd | 5
man/getObjNameGLPK.Rd | 5
man/getObjValGLPK.Rd | 5
man/getObjValIptGLPK.Rd | 5
man/getPrimStatGLPK.Rd | 5
man/getProbNameGLPK.Rd | 5
man/getRbindGLPK.Rd | 5
man/getRiiGLPK.Rd | 5
man/getRowDualGLPK.Rd | 5
man/getRowDualIptGLPK.Rd | 5
man/getRowLowBndGLPK.Rd | 5
man/getRowNameGLPK.Rd | 5
man/getRowPrimGLPK.Rd | 5
man/getRowPrimIptGLPK.Rd | 5
man/getRowStatGLPK.Rd | 5
man/getRowTypeGLPK.Rd | 5
man/getRowUppBndGLPK.Rd | 5
man/getRowsDualGLPK.Rd | 5
man/getRowsDualIptGLPK.Rd | 5
man/getRowsLowBndsGLPK.Rd | 5
man/getRowsPrimGLPK.Rd | 5
man/getRowsPrimIptGLPK.Rd | 5
man/getRowsStatGLPK.Rd | 5
man/getRowsTypesGLPK.Rd | 5
man/getRowsUppBndsGLPK.Rd | 5
man/getSimplexParmGLPK.Rd | 5
man/getSjjGLPK.Rd | 5
man/getSolStatGLPK.Rd | 5
man/getSolStatIptGLPK.Rd | 5
man/getUnbndRayGLPK.Rd | 5
man/glpkAPI-package.Rd | 5
man/glpkConstants.Rd | 5
man/glpkPtr-class.Rd | 5
man/initProbGLPK.Rd | 5
man/loadMatrixGLPK.Rd | 5
man/mipColValGLPK.Rd | 5
man/mipColsValGLPK.Rd | 5
man/mipObjValGLPK.Rd | 5
man/mipRowValGLPK.Rd | 5
man/mipRowsValGLPK.Rd | 5
man/mipStatusGLPK.Rd | 5
man/mplAllocWkspGLPK.Rd | 5
man/mplBuildProbGLPK.Rd | 5
man/mplFreeWkspGLPK.Rd | 5
man/mplGenerateGLPK.Rd | 5
man/mplPostsolveGLPK.Rd | 5
man/mplReadDataGLPK.Rd | 5
man/mplReadModelGLPK.Rd | 5
man/printIptGLPK.Rd | 5
man/printMIPGLPK.Rd | 5
man/printRangesGLPK.Rd | 5
man/printSolGLPK.Rd | 5
man/readIptGLPK.Rd | 5
man/readLPGLPK.Rd | 5
man/readMIPGLPK.Rd | 5
man/readMPSGLPK.Rd | 5
man/readProbGLPK.Rd | 5
man/readSolGLPK.Rd | 5
man/return_codeGLPK.Rd | 5
man/scaleProbGLPK.Rd | 5
man/setBfcpGLPK.Rd | 5
man/setColBndGLPK.Rd | 5
man/setColKindGLPK.Rd | 5
man/setColNameGLPK.Rd | 5
man/setColStatGLPK.Rd | 5
man/setColsBndsGLPK.Rd | 5
man/setColsBndsObjCoefsGLPK.Rd | 5
man/setColsKindGLPK.Rd | 5
man/setColsNamesGLPK.Rd | 5
man/setDefaultIptParmGLPK.Rd | 5
man/setDefaultMIPParmGLPK.Rd | 5
man/setDefaultSmpParmGLPK.Rd | 5
man/setInteriorParmGLPK.Rd | 5
man/setMIPParmGLPK.Rd | 5
man/setMatColGLPK.Rd | 5
man/setMatRowGLPK.Rd | 5
man/setObjCoefGLPK.Rd | 5
man/setObjCoefsGLPK.Rd | 5
man/setObjDirGLPK.Rd | 5
man/setObjNameGLPK.Rd | 5
man/setProbNameGLPK.Rd | 5
man/setRhsZeroGLPK.Rd | 5
man/setRiiGLPK.Rd | 5
man/setRowBndGLPK.Rd | 5
man/setRowNameGLPK.Rd | 5
man/setRowStatGLPK.Rd | 5
man/setRowsBndsGLPK.Rd | 5
man/setRowsNamesGLPK.Rd | 5
man/setSimplexParmGLPK.Rd | 5
man/setSjjGLPK.Rd | 5
man/solveInteriorGLPK.Rd | 5
man/solveMIPGLPK.Rd | 5
man/solveSimplexExactGLPK.Rd | 5
man/solveSimplexGLPK.Rd | 5
man/sortMatrixGLPK.Rd | 5
man/status_codeGLPK.Rd | 5
man/stdBasisGLPK.Rd | 5
man/termOutGLPK.Rd | 5
man/unscaleProbGLPK.Rd | 5
man/versionGLPK.Rd | 5
man/warmUpGLPK.Rd | 5
man/writeIptGLPK.Rd | 5
man/writeLPGLPK.Rd | 5
man/writeMIPGLPK.Rd | 5
man/writeMPSGLPK.Rd | 5
man/writeProbGLPK.Rd | 5
man/writeSolGLPK.Rd | 5
vignettes/glpk-gmpl-intro.Rnw |only
168 files changed, 657 insertions(+), 482 deletions(-)
Title: R Unit Test Framework
Diff between RUnit versions 0.4.27 dated 2014-09-19 and 0.4.28 dated 2015-01-06
Description: R functions implementing a standard Unit Testing
framework, with additional code inspection and report
generation tools
Author: Matthias Burger
Maintainer: ORPHANED
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
R/exportHTML.r | 6 +++---
build/RUnit.pdf |binary
inst/unitTests/Makefile | 13 +++++++------
5 files changed, 18 insertions(+), 17 deletions(-)
Title: Power and Sample Size Based on Two One-sided t-Tests (TOST) for
(Bio)Equivalence Studies
Diff between PowerTOST versions 1.2-04 dated 2014-12-19 and 1.2-05 dated 2015-01-06
Description: Contains functions to calculate power and sample size for
various study designs used for bioequivalence studies.
See function known.designs() for study designs covered.
Moreover the package contains functions for power and sample size
based on 'expected' power in case of uncertain (estimated) variability.
-----
Added are functions for the power and sample size for the ratio of
two means with normally distributed data on the original scale
(based on Fieller's confidence ('fiducial') interval).
-----
Contains further functions for power and sample size calculations based on
non-inferiority t-test. This is not a TOST procedure but eventually useful
if the question of 'non-superiority' must be evaluated.
The power and sample size calculations based on non-inferiority test may
also performed via 'expected' power in case of uncertain (estimated)
variability.
-----
Contains functions power.scABEL() and sampleN.scABEL() to calculate power
and sample size for the BE decision via scaled (widened) BE acceptance
limits based on simulations.
Contains further functions power.RSABE() and sampleN.RSABE() to calculate
power and sample size for the BE decision via reference scaled ABE criterion
according to the FDA procedure based on simulations.
Contains further functions power.NTIDFDA() and sampleN.NTIDFDA() to calculate
power and sample size for the BE decision via the FDA procedure for NTID's
based on simulations.
-----
Contains functions for power analysis of a sample size plan for ABE
(pa.ABE()), scaled ABE (pa.scABE()) and scaled ABE for NTID's (pa.NTIDFDA())
analysing power if deviating from assumptions of the plan.
-----
Contains further functions for power calculations / samplesize estimation
for dose proportionality studies using the Power model.
Author: Detlew Labes [aut, cre],
Helmut Schuetz [aut],
Benjamin Lang [ctb]
Maintainer: Detlew Labes
PowerTOST-1.2-04/PowerTOST/R/CVfromCI.R |only
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PowerTOST-1.2-05/PowerTOST/NEWS | 8 +++
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PowerTOST-1.2-05/PowerTOST/R/pvalue.TOST_Benjamin.R | 3 -
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PowerTOST-1.2-05/PowerTOST/man/pvalue.TOST.Rd | 6 +-
13 files changed, 48 insertions(+), 29 deletions(-)
Title: Compares the Distribution of Sister Clades Through a Phylogeny
Diff between nodiv versions 1.0.0 dated 2014-12-01 and 1.0.1 dated 2015-01-06
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard
DESCRIPTION | 8 ++--
MD5 | 26 ++++++++-------
NAMESPACE | 6 +--
R/General_figure_functions.R | 8 +++-
R/Methods_for_data_objects.R | 69 ++++++++++++++++++++++++++++++++++-------
R/Methods_for_result_objects.R | 7 ++++
R/Node_based_analysis.R | 19 +++++++----
R/Prepare_data.R | 26 ++++++++++++++-
man/Node_size.Rd | 2 -
man/Nspecies.Rd | 10 +++--
man/nodiv-package.Rd | 2 -
man/plotSOS.Rd | 6 ++-
man/plot_points.Rd | 5 ++
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Title: Project MOSAIC (mosaic-web.org) statistics and mathematics
teaching utilities
Diff between mosaic versions 0.9.1-3 dated 2014-08-23 and 0.9.2-2 dated 2015-01-06
Description: Data sets and utilities from Project MOSAIC (mosaic-web.org) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim
Maintainer: Randall Pruim
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tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/compareProportion.R | 13
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tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/mPlots.R | 101 +-
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/makeFun.R | 15
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/maps2.R | 7
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/mplot.R | 9
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tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/plotDist.R | 225 ++----
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/plotFun.R | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/prop.test.R | 5
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/read.file.R | 11
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tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/themes.R | 125 ++-
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tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/R/xqqmath.R | 1
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/demo/00Index | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/demo/funplots.R | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/demo/histogram.R | 2
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tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/inst/doc/V2StartTeaching.pdf |binary
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tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/aggregating.Rd | 20
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/aggregatingAux.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/aggregatingFunction1.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/aggregatingFunction2.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/as-xtabs.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/bargraph.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/binom.test.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/cdist.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/chisq.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/clustering.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/coef.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/columns.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/compareMean.Rd | 11
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/compareProportion.Rd | 14
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/confint.Rd | 52 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/cross.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/deg2rad.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/deltaMethod.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/derivedFactor.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/dfapply.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/diffmean.Rd | 13
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/do.Rd | 15
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/docFile.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/dotPlot.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/ediff.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/evalFormula.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/evalSubFormula.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/expandFun.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/factorize.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fav_stats.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fetchData.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fetchGapminder.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fetchGoogle.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/findZeros.Rd | 18
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/findZerosMult.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fitModel.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fitSpline.Rd | 14
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fitdistr.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fortify.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/fractions.Rd | 10
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/freqpolygon.Rd | 22
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/getVarFormula.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/googleMap.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/inferArgs.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/integrateODE.Rd | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/interval.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/is.wholenumber.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/joinFrames.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/ladd.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/latlon2xyz.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/linear.algebra.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/logical2factor.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/logit.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mPlotting.Rd | 15
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mUSMap.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mWorldMap.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/makeColorscheme.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/makeFun.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/makeMap.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mid.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mm.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/modelVars.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mosaic-internal.Rd | 28
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mosaic-package.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mosaic.options.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mosaicformula.Rd | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/mplot.Rd | 68 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/msummary.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/named.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/nicenames.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/ntiles.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/numD.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/oddsRatio.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/panel.levelcontourplot.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/panel.lmbands.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/panel.plotFun.Rd | 24
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/panel.plotFun1.Rd | 24
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/parseFormula.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/pdist.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/perctable.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/plotCumfreq.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/plotDist.Rd | 19
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/plotFun.Rd | 40 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/plotPoints.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/pqrdata.Rd | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/pqrdata2.Rd | 26
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/project-methods.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/prop.Rd | 17
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/prop.test.Rd | 16
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/qdist.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/r.squared.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rand.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/read.file.Rd | 8
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/repeater-class.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/resample.Rd | 22
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rescale.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rflip.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rfun.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rgeo-internals.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rgeo.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rkintegrate.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rspin.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rsquared.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/rstudio.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/simplify.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/sp2df.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/standardName.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/statTally.Rd | 14
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/surround.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/swap.Rd |only
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/symbolicD.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/symbolicInt.Rd | 6
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/tally.Rd | 46 -
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/theme_map.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/themes.Rd | 9
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/ttest.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/xchisq.test.Rd | 7
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/xhistogram.Rd | 24
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/xpnorm.Rd | 12
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/xqqmath.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/man/zscore.Rd | 2
tmp/cranberry5dfb3a3c204e/mosaic-0.9.2-2/mosaic/vignettes/mosaicresources.Rnw | 2
188 files changed, 1602 insertions(+), 1104 deletions(-)
Title: Toolkit Implementation of gWidgets2 for tcltk
Diff between gWidgets2tcltk versions 1.0-3 dated 2014-12-06 and 1.0-4 dated 2015-01-06
More information about gWidgets2tcltk at CRAN
Description: Port of the gWidgets2 API for the tcltk
package.
Author: John Verzani
Maintainer: John Verzani
DESCRIPTION | 6 +++---
MD5 | 4 ++--
R/gtable.R | 43 ++++++++++++++++++++++++-------------------
3 files changed, 29 insertions(+), 24 deletions(-)
Permanent link
Title: Test Analysis Modules
Diff between TAM versions 1.2 dated 2014-11-22 and 1.3 dated 2015-01-06
Description:
The package includes marginal and joint maximum likelihood
estimation of uni- and multidimensional item response models
(Rasch, 2PL, 3PL, Generalized Partial Credit, Multi Facets,
Nominal Item Response, Structured Latent Class Analysis,
Mixture Distribution IRT Models, Located Latent Class Models,
Cognitive Diagnostic Models). Latent regression models and
plausible value imputation are also supported.
Author: Thomas Kiefer [aut], Alexander Robitzsch [aut, cre], Margaret Wu [aut]
Maintainer: Alexander Robitzsch
TAM-1.2/TAM/R/TAM-internal_intermediate.R |only
TAM-1.2/TAM/R/TAM-internal_mstep.R |only
TAM-1.2/TAM/R/TAM-internal_postproc.R |only
TAM-1.2/TAM/R/tam.mml.3pl.postproc.R |only
TAM-1.3/TAM/DESCRIPTION | 25
TAM-1.3/TAM/MD5 | 163 +++--
TAM-1.3/TAM/NAMESPACE | 76 ++
TAM-1.3/TAM/R/IRT.factor.scores.tam.R | 18
TAM-1.3/TAM/R/IRT.irfprob.tam.R | 15
TAM-1.3/TAM/R/IRT.likelihood.TAM.R | 28
TAM-1.3/TAM/R/Mstep_slope.v2.R |only
TAM-1.3/TAM/R/TAM.ic.R |only
TAM-1.3/TAM/R/TAM.itempartable.R |only
TAM-1.3/TAM/R/add.colnames.resp.R |only
TAM-1.3/TAM/R/anova.tam.R | 7
TAM-1.3/TAM/R/calc_exp_TK.R |only
TAM-1.3/TAM/R/calc_posterior.v2.R |only
TAM-1.3/TAM/R/calc_prob.v5.R |only
TAM-1.3/TAM/R/change.grep.lavpartable.R |only
TAM-1.3/TAM/R/create.deltaDesign.R |only
TAM-1.3/TAM/R/designMatrices.R | 38 +
TAM-1.3/TAM/R/designMatrices.mfr2.R | 6
TAM-1.3/TAM/R/designMatrices_aux.R | 33 +
TAM-1.3/TAM/R/doparse.R |only
TAM-1.3/TAM/R/extend.label.group.R |only
TAM-1.3/TAM/R/latreg.mstep.regression.R |only
TAM-1.3/TAM/R/latreg_TAM.ic.R |only
TAM-1.3/TAM/R/lavaanify.IRT.R | 324 +----------
TAM-1.3/TAM/R/lavaanify.grep.nonlinear.R |only
TAM-1.3/TAM/R/lavaanify.sirt.v1.R |only
TAM-1.3/TAM/R/lavpartable.grep.underbrace.R |only
TAM-1.3/TAM/R/lavpartable2lavsyntax.R |only
TAM-1.3/TAM/R/logLik_tam.R | 3
TAM-1.3/TAM/R/mml.3pl.TAM.ic.R |only
TAM-1.3/TAM/R/mml.3pl.TAM.itempartable.R |only
TAM-1.3/TAM/R/mml.3pl.calc_prob.v5.R |only
TAM-1.3/TAM/R/mml.3pl.distrubutionmoments.R |only
TAM-1.3/TAM/R/mstep.regression.R |only
TAM-1.3/TAM/R/plot.tam.R | 210 +++++--
TAM-1.3/TAM/R/plotDevianceTAM.R | 2
TAM-1.3/TAM/R/rbind.twomatrices.R |only
TAM-1.3/TAM/R/remove.duplicated.variances.lavsyn.R |only
TAM-1.3/TAM/R/split.syn.string.R |only
TAM-1.3/TAM/R/stud_prior.R |only
TAM-1.3/TAM/R/summary.tam.R | 133 ++--
TAM-1.3/TAM/R/summary.tam.mml.3pl.R | 7
TAM-1.3/TAM/R/summary.tamaan.3pl.intro.R |only
TAM-1.3/TAM/R/summary.tamaan.R |only
TAM-1.3/TAM/R/summary.tamaan.aux.R |only
TAM-1.3/TAM/R/taamanify.proc.lavaanmodel.R |only
TAM-1.3/TAM/R/tam.calc.counts.R |only
TAM-1.3/TAM/R/tam.jml.R | 4
TAM-1.3/TAM/R/tam.jml2.R | 3
TAM-1.3/TAM/R/tam.latreg.R |only
TAM-1.3/TAM/R/tam.mml.2pl.R | 11
TAM-1.3/TAM/R/tam.mml.3pl.R | 150 +++--
TAM-1.3/TAM/R/tam.mml.3pl.algorithm.R | 84 --
TAM-1.3/TAM/R/tam.mml.3pl.est.intercepts.R | 18
TAM-1.3/TAM/R/tam.mml.3pl.est.slopes.R | 57 +
TAM-1.3/TAM/R/tam.mml.R | 27
TAM-1.3/TAM/R/tam.mml.mfr.R | 2
TAM-1.3/TAM/R/tam.modelfit.R | 12
TAM-1.3/TAM/R/tam.pv.R | 233 +++++--
TAM-1.3/TAM/R/tamaan.3pl.lca.R |only
TAM-1.3/TAM/R/tamaan.3pl.loclca.R |only
TAM-1.3/TAM/R/tamaan.3pl.mixture.R |only
TAM-1.3/TAM/R/tamaan.3pl.olca.R |only
TAM-1.3/TAM/R/tamaan.3pl.trait.R |only
TAM-1.3/TAM/R/tamaan.R |only
TAM-1.3/TAM/R/tamaanify.R |only
TAM-1.3/TAM/R/tamaanify.create.A.R |only
TAM-1.3/TAM/R/tamaanify.create.Q.R |only
TAM-1.3/TAM/R/tamaanify.define.method.R |only
TAM-1.3/TAM/R/tamaanify.grep.linequations.R |only
TAM-1.3/TAM/R/tamaanify.modelconstraint.loadings.R |only
TAM-1.3/TAM/R/tamaanify.modelprior.R |only
TAM-1.3/TAM/R/tamaanify.proc.analysis.R |only
TAM-1.3/TAM/R/tamaanify.proc.items.R |only
TAM-1.3/TAM/R/tamaanify.proc.itemtype.R |only
TAM-1.3/TAM/R/tamaanify.proc.loadings.B.fixed.R |only
TAM-1.3/TAM/R/tamaanify.proc.modelconstraint.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.deltadesign.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.LCA.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.LOCLCA.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.MIXTURE.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.OLCA.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pl.designMatrices.TRAIT.R |only
TAM-1.3/TAM/R/tamaanify.tam.mml.3pldesignMatrices.R |only
TAM-1.3/TAM/R/tamaanify.variance.fixed.R |only
TAM-1.3/TAM/R/tampv2datalist.R |only
TAM-1.3/TAM/data/data.geiser.rda |only
TAM-1.3/TAM/data/data.janssen.rda |only
TAM-1.3/TAM/data/data.janssen2.rda |only
TAM-1.3/TAM/inst/NEWS | 73 ++
TAM-1.3/TAM/man/IRT.factor.scores.tam.Rd | 10
TAM-1.3/TAM/man/IRT.irfprob.tam.Rd | 10
TAM-1.3/TAM/man/IRT.likelihood.tam.Rd | 17
TAM-1.3/TAM/man/TAM-internal.Rd | 2
TAM-1.3/TAM/man/TAM-package.Rd | 16
TAM-1.3/TAM/man/anova.tam.Rd | 39 -
TAM-1.3/TAM/man/data.examples.Rd | 1
TAM-1.3/TAM/man/data.geiser.Rd |only
TAM-1.3/TAM/man/data.janssen.Rd |only
TAM-1.3/TAM/man/designMatrices.Rd | 4
TAM-1.3/TAM/man/doparse.Rd |only
TAM-1.3/TAM/man/lavaanify.IRT.Rd | 116 +++
TAM-1.3/TAM/man/plot.tam.Rd | 34 +
TAM-1.3/TAM/man/tam.fit.Rd | 4
TAM-1.3/TAM/man/tam.latreg.Rd |only
TAM-1.3/TAM/man/tam.mml.3pl.Rd | 188 +++++-
TAM-1.3/TAM/man/tam.mml.Rd | 316 +++++++++-
TAM-1.3/TAM/man/tam.modelfit.Rd | 15
TAM-1.3/TAM/man/tam.pv.Rd | 134 ++++
TAM-1.3/TAM/man/tam.threshold.Rd | 41 +
TAM-1.3/TAM/man/tam.wle.Rd | 94 +++
TAM-1.3/TAM/man/tamaan.Rd |only
TAM-1.3/TAM/man/tamaanify.Rd |only
TAM-1.3/TAM/man/tampv2datalist.Rd |only
TAM-1.3/TAM/src/tam_caux.c | 50 +
119 files changed, 2014 insertions(+), 839 deletions(-)
Title: Inverse Estimation/Calibration Functions
Diff between investr versions 1.2.0 dated 2014-12-23 and 1.2.1 dated 2015-01-06
Description: Functions to facilitate inverse estimation/calibration in linear,
nonlinear, and (linear) mixed models. A generic function is also provided
for plotting fitted regression models with or without confidence/prediction
bands that may be of use to the general user.
Author: Brandon M. Greenwell
Maintainer: Brandon M. Greenwell
DESCRIPTION | 6 +++---
MD5 | 23 ++++++++++++-----------
NEWS | 9 +++++++--
R/calibrate.R | 13 +++++++++++--
R/invest.R | 16 +++++++++-------
R/plotFit.R | 22 ++++++----------------
R/utilities.R | 15 +++++++++++++++
man/AnyNA.Rd |only
man/calibrate.Rd | 13 +++++++++++--
man/invest.Rd | 12 +++++++-----
man/investr-package.Rd | 10 ++++++----
man/plotFit.Rd | 4 ++--
tests/testthat/test-invest.R | 4 ++++
13 files changed, 93 insertions(+), 54 deletions(-)
Title: "Hit and Run" and "Shake and Bake" for Sampling Uniformly From
Convex Shapes
Diff between hitandrun versions 0.4-2 dated 2014-08-04 and 0.5 dated 2015-01-06
Description: The "Hit and Run" Markov Chain Monte Carlo method for sampling uniformly from convex shapes defined by linear constraints, and the "Shake and Bake" method for sampling from the boundary of such shapes. Includes specialized functions for sampling normalized weights with arbitrary linear constraints.
Author: Gert van Valkenhoef, Tommi Tervonen
Maintainer: Gert van Valkenhoef
DESCRIPTION | 13 +++++-----
MD5 | 31 ++++++++++++++----------
NAMESPACE | 8 +++---
NEWS | 9 +++++++
R/sample.R | 60 +++++++++++++++++++++++++++++++++++++++++++----
R/shakeandbake.R |only
R/transformSimplex.R | 4 ++-
man/findFace.Rd |only
man/har-constraint.Rd | 2 -
man/hitandrun-package.Rd | 5 ++-
man/sab.Rd |only
man/shakeandbake.Rd |only
src/Makevars | 3 +-
src/bbReject.c | 2 -
src/har.c | 2 -
src/har.h | 21 +++++++++++++++-
src/hit.c | 4 +--
src/intersect.c |only
src/rsabDir.c |only
src/sab.c |only
20 files changed, 128 insertions(+), 36 deletions(-)
Title: Forecasting functions for time series and linear models
Diff between forecast versions 5.7 dated 2014-12-17 and 5.8 dated 2015-01-06
Description: Methods and tools for displaying and analysing
univariate time series forecasts including exponential smoothing
via state space models and automatic ARIMA modelling.
Author: Rob J Hyndman
Maintainer: Rob J Hyndman
ChangeLog | 4 ++++
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
R/guerrero.R | 11 ++++++-----
R/season.R | 7 +++++++
README.md | 2 +-
6 files changed, 27 insertions(+), 15 deletions(-)
Title: Dave Armstrong's Miscellaneous Functions
Diff between DAMisc versions 1.2 dated 2013-04-09 and 1.3 dated 2015-01-06
Description: This package contains a miscellaneous set of functions I use in my teaching either at UWM or the ICPSR Summer Program. Broadly, the functions help with presentation and interpretation of GLMs.
Author: Dave Armstrong (UW-Milwaukee, Department of Political Science)
Maintainer: Dave Armstrong
DAMisc-1.2/DAMisc/man/multiChange.Rd |only
DAMisc-1.3/DAMisc/DESCRIPTION | 17
DAMisc-1.3/DAMisc/MD5 | 36
DAMisc-1.3/DAMisc/NAMESPACE | 74 +-
DAMisc-1.3/DAMisc/R/DAMisc_functions.R | 1118 ++++++++++++++++++++++++++++---
DAMisc-1.3/DAMisc/README.md |only
DAMisc-1.3/DAMisc/man/DAMisc-package.Rd | 10
DAMisc-1.3/DAMisc/man/aveEffPlot.Rd |only
DAMisc-1.3/DAMisc/man/combTest.Rd |only
DAMisc-1.3/DAMisc/man/crSpanTest.Rd | 3
DAMisc-1.3/DAMisc/man/glmChange.Rd | 6
DAMisc-1.3/DAMisc/man/glmChange2.Rd |only
DAMisc-1.3/DAMisc/man/intQualQuant.Rd | 32
DAMisc-1.3/DAMisc/man/mnlAveEffPlot.Rd |only
DAMisc-1.3/DAMisc/man/mnlChange.Rd |only
DAMisc-1.3/DAMisc/man/mnlChange2.Rd |only
DAMisc-1.3/DAMisc/man/mnlfit.Rd |only
DAMisc-1.3/DAMisc/man/ordAveEffPlot.Rd |only
DAMisc-1.3/DAMisc/man/ordChange.Rd | 8
DAMisc-1.3/DAMisc/man/ordChange2.Rd |only
DAMisc-1.3/DAMisc/man/ordFit.Rd |only
DAMisc-1.3/DAMisc/man/panel.ci.Rd | 2
DAMisc-1.3/DAMisc/man/panel.doublerug.Rd |only
DAMisc-1.3/DAMisc/man/panel.transci.Rd |only
DAMisc-1.3/DAMisc/man/prepanel.ci.Rd | 2
DAMisc-1.3/DAMisc/man/ziChange.Rd | 3
26 files changed, 1149 insertions(+), 162 deletions(-)
Title: Process Control And Internal Validation Of Forensic STR Kits
Diff between strvalidator versions 1.3.1 dated 2014-10-15 and 1.4.0 dated 2015-01-06
Description: strvalidator is an open source platform for validation and process
control. It provide tools to analyse data from internal validation of
forensic short tandem repeat (STR) kits. The tools are developed to provide
the necessary data to conform with the ENFSI guidelines for internal
validation. More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson
DESCRIPTION | 13
MD5 | 310 +++----
NAMESPACE | 9
NEWS | 37
R/addColor.r | 32
R/addData.r | 85 +-
R/addData_gui.r | 8
R/addMarker.r | 15
R/addMarker_gui.r | 2
R/addSize_gui.r | 11
R/calculateBalance.r | 45 -
R/calculateBalance_gui.r | 23
R/calculateCapillary.r | 51 -
R/calculateCapillary_gui.r | 4
R/calculateDropout.r | 9
R/calculateDropout_gui.r | 22
R/calculatePullup.r |only
R/calculatePullup_gui.r |only
R/calculateResultType.r | 107 +-
R/calculateResultType_gui.r | 10
R/calculateStutter.r | 15
R/calculateStutter_gui.r | 26
R/checkDataset.r | 2
R/combineBinsAndPanels.r | 2
R/combine_gui.r | 2
R/compact.r |only
R/detectKit.r | 2
R/editData_gui.r | 4
R/export.r | 17
R/export_gui.r | 2
R/filterProfile.r | 53 -
R/filterProfile_gui.r | 6
R/generateEPG.r |only
R/generateEPG_gui.r |only
R/getDb.r | 13
R/getKit.r | 20
R/heightToPeak.r |only
R/import.r | 49 -
R/import_gui.r | 4
R/makeKit_gui.r | 373 ++++-----
R/modelDropout_gui.r | 87 +-
R/plotBalance_gui.r | 37
R/plotDropout_gui.r | 2
R/plotPrecision_gui.r | 2
R/plotPullup_gui.r |only
R/plotStutter_gui.r | 61 -
R/readBinsFile.r | 9
R/readPanelsFile.r | 9
R/sortMarker.r | 11
R/strvalidator.r | 230 ++++-
R/tablePrecision_gui.r | 4
R/trim.r | 53 -
R/trim_gui.r | 4
README.md | 45 -
inst/extdata/kit.txt | 1363 ++++++++++++++++++++++-----------
man/addColor.Rd | 6
man/addData.Rd | 22
man/addData_gui.Rd | 2
man/addDye_gui.Rd | 2
man/addMarker.Rd | 6
man/addMarker_gui.Rd | 2
man/addSize.Rd | 2
man/addSize_gui.Rd | 2
man/calculateBalance.Rd | 10
man/calculateBalance_gui.Rd | 2
man/calculateCapillary.Rd | 10
man/calculateCapillary_gui.Rd | 2
man/calculateConcordance.Rd | 2
man/calculateConcordance_gui.Rd | 2
man/calculateDropout.Rd | 8
man/calculateDropout_gui.Rd | 2
man/calculateHeight.Rd | 8
man/calculateHeight_gui.Rd | 2
man/calculateHeterozygous.Rd | 2
man/calculateHeterozygous_gui.Rd | 2
man/calculateMixture.Rd | 2
man/calculateMixture_gui.Rd | 2
man/calculateOL.Rd | 2
man/calculateOL_gui.Rd | 2
man/calculateOverlap.Rd | 2
man/calculateOverlap_gui.Rd | 2
man/calculatePeaks.Rd | 6
man/calculatePeaks_gui.Rd | 2
man/calculatePullup.Rd |only
man/calculatePullup_gui.Rd |only
man/calculateResultType.Rd | 26
man/calculateResultType_gui.Rd | 2
man/calculateStutter.Rd | 8
man/calculateStutter_gui.Rd | 2
man/checkDataset.Rd | 2
man/checkSubset.Rd | 2
man/checkSubset_gui.Rd | 2
man/colNames.Rd | 2
man/combineBinsAndPanels.Rd | 4
man/combine_gui.Rd | 2
man/compact.Rd |only
man/cropData_gui.Rd | 2
man/detectKit.Rd | 2
man/editData_gui.Rd | 2
man/export.Rd | 6
man/export_gui.Rd | 2
man/filterProfile.Rd | 18
man/filterProfile_gui.Rd | 2
man/generateEPG.Rd |only
man/generateEPG_gui.Rd |only
man/getDb.Rd | 6
man/getKit.Rd | 4
man/ggsave_gui.Rd | 2
man/guessProfile.Rd | 2
man/guessProfile_gui.Rd | 2
man/heightToPeak.Rd |only
man/import.Rd | 12
man/import_gui.Rd | 2
man/listObjects.Rd | 2
man/loadPackage.Rd | 2
man/makeKit_gui.Rd | 2
man/modelDropout_gui.Rd | 2
man/plotBalance_gui.Rd | 4
man/plotCapillary_gui.Rd | 2
man/plotDistribution_gui.Rd | 2
man/plotDropout_gui.Rd | 2
man/plotKit_gui.Rd | 2
man/plotPeaks_gui.Rd | 2
man/plotPrecision_gui.Rd | 2
man/plotPullup_gui.Rd |only
man/plotResultType_gui.Rd | 2
man/plotStutter_gui.Rd | 2
man/readBinsFile.Rd | 6
man/readPanelsFile.Rd | 6
man/ref1.Rd | 2
man/ref11.Rd | 2
man/ref2.Rd | 2
man/ref3.Rd | 2
man/ref4.Rd | 2
man/ref51.Rd | 2
man/ref52.Rd | 2
man/saveObject.Rd | 2
man/set1.Rd | 2
man/set2.Rd | 2
man/set3.Rd | 2
man/set4.Rd | 2
man/set5.Rd | 2
man/slim.Rd | 2
man/slim_gui.Rd | 2
man/sortMarker.Rd | 6
man/strValidator-package.Rd | 2
man/strvalidator.Rd | 2
man/tableBalance.Rd | 2
man/tableBalance_gui.Rd | 2
man/tableCapillary.Rd | 2
man/tableCapillary_gui.Rd | 2
man/tablePrecision.Rd | 2
man/tablePrecision_gui.Rd | 2
man/tableStutter.Rd | 2
man/tableStutter_gui.Rd | 2
man/trim.Rd | 16
man/trim_gui.Rd | 2
tests/testthat/test-calculateBalance.r | 52 -
tests/testthat/test-calculateDropout.r | 16
tests/testthat/test-calculateStutter.r | 40
tests/testthat/test-filterProfile.r | 60 -
tests/testthat/test-tableBalance.r | 8
tests/testthat/test-trim.r | 44 -
163 files changed, 2370 insertions(+), 1496 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Diff between spdep versions 0.5-77 dated 2014-09-19 and 0.5-81 dated 2015-01-06
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
ChangeLog | 174 ++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 22 ++---
MD5 | 134 ++++++++++++++++----------------
NAMESPACE | 4
R/ME.R | 5 -
R/SpatialFiltering.R | 1
R/aple.R | 3
R/aple.mc.R | 9 +-
R/edit.nb.R | 1
R/eigenw.R | 3
R/error.spsarlm.R | 5 -
R/globalG.R | 8 +
R/impacts.R | 16 ++-
R/jacobian.R | 22 ++---
R/jacobian_setup.R | 12 ++
R/kpgm_new.R | 6 -
R/lag.spsarlm.R | 1
R/lee.test.R | 2
R/listw2Matrix.R | 11 ++
R/listw2sn.R | 9 +-
R/mcmcsamp.R | 6 -
R/mess.R | 3
R/nb2blocknb.R | 3
R/nb2listw.R | 4
R/nb2mat.R | 2
R/nbcosts.R | 18 +++-
R/prunecost.R | 16 ++-
R/read.gal.R | 4
R/s2sls.R | 1
R/sacsarlm.R | 1
R/sarlm.R | 4
R/spautolm.R | 3
R/utils.R | 2
build/vignette.rds |binary
inst/ChangeLog | 174 ++++++++++++++++++++++++++++++++++++++++++
inst/doc/CO69.pdf |binary
inst/doc/SpatialFiltering.pdf |binary
inst/doc/nb.pdf |binary
inst/doc/nb_igraph.R |only
inst/doc/nb_igraph.Rmd |only
inst/doc/nb_igraph.html |only
inst/doc/sids.R | 43 +++++-----
inst/doc/sids.Rnw | 1
inst/doc/sids.pdf |binary
man/aple.mc.Rd | 2
man/as_dgRMatrix_listw.Rd | 22 ++---
man/boston.Rd | 68 ++++++++--------
man/compon.Rd | 14 +++
man/edit.nb.Rd | 3
man/eigenw.Rd | 19 ++++
man/errorsarlm.Rd | 3
man/globalG.test.Rd | 16 ++-
man/gstsls.Rd | 2
man/house.Rd | 48 +++++------
man/impacts.sarlm.Rd | 18 +---
man/invIrM.Rd | 4
man/lagsarlm.Rd | 4
man/mat2listw.Rd | 2
man/nblag.Rd | 14 +++
man/sacsarlm.Rd | 2
man/set.mcOption.Rd | 4
man/skater.Rd | 2
man/spautolm.Rd | 24 +----
man/trW.Rd | 6 -
src/card.c | 13 ++-
src/dnn.c | 4
src/insiders.c | 4
src/nbdists.c | 10 +-
vignettes/nb_igraph.Rmd |only
vignettes/sids.Rnw | 1
70 files changed, 758 insertions(+), 284 deletions(-)
Title: R Client for Adobe Analytics API v1.4
Diff between RSiteCatalyst versions 1.4.2 dated 2014-12-03 and 1.4.3 dated 2015-01-06
Description: Functions for interacting with the Adobe Analytics API v1.4
(https://api.omniture.com/admin/1.4/rest/)
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch
RSiteCatalyst-1.4.2/RSiteCatalyst/README.md |only
RSiteCatalyst-1.4.3/RSiteCatalyst/DESCRIPTION | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/MD5 | 251 ++++++----
RSiteCatalyst-1.4.3/RSiteCatalyst/NAMESPACE | 9
RSiteCatalyst-1.4.3/RSiteCatalyst/NEWS | 13
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ApiRequest.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/BuildInnerBreakdownsRecursively.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetCalculatedMetrics.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetFeed.R |only
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetFeeds.R |only
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetPermanentTraffic.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetScheduledSpike.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetTimeZone.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/GetUniqueVisitorVariable.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/JsonQueueRealTimeReport.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParseFallout.R | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParseOvertime.R | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParsePathing.R | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParseRanked.R | 11
RSiteCatalyst-1.4.3/RSiteCatalyst/R/ParseTrended.R | 11
RSiteCatalyst-1.4.3/RSiteCatalyst/R/QueueOvertime.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/R/RSiteCatalyst.R | 4
RSiteCatalyst-1.4.3/RSiteCatalyst/R/SCAuth.R | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/R/buildHeader.R | 2
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ApiRequest.Rd | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildClassificationValueSegment.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildHeader.Rd | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildInnerBreakdownsRecursively.Rd | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildLineItemSegment.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/BuildRealTimeReportStructure.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/CancelReport.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetActivation.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetAxleStartDate.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetBaseCurrency.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetBaseURL.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetBookmarks.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetCalculatedMetrics.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetClassifications.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetCustomCalendar.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetDashboards.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetDataWarehouseDisplay.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetDefaultPage.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetDiscoverEnabled.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetEcommerce.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetElements.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetEndpoint.Rd | 9
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetEvars.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetFeed.Rd |only
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetFeeds.Rd |only
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetGeoSegmentation.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetGroups.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetIPAddressExclusions.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetIPObfuscation.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetInternalURLFilters.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetKeyVisitors.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetListVariables.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetLocalization.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetLogin.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetLogins.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMarketingChannelExpiration.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMarketingChannelRules.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMarketingChannels.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMetrics.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetMobileAppReporting.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetPaidSearchDetection.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetPermanentTraffic.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetProps.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetQueue.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetRealTimeReport.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetRealTimeSettings.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetReportDescription.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetReportSuites.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetScheduledSpike.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetSegments.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetSiteTitle.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetSuccessEvents.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetTimeZone.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetTrackingServer.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetTransactionEnabled.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetUniqueVisitorVariable.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetUsageLog.Rd | 9
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetVersionAccess.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/GetVideoSettings.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/JsonQueueRealTimeReport.Rd | 12
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParseFallout.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParseOvertime.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParsePathing.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParseRanked.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ParseTrended.Rd | 14
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueueFallout.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueueOvertime.Rd | 5
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueuePathing.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueueRanked.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/QueueTrended.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/RSiteCatalyst.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/SCAuth.Rd | 7
RSiteCatalyst-1.4.3/RSiteCatalyst/man/SaveRealTimeSettings.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/SubmitJsonQueueReport.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/man/ValidateReport.Rd | 3
RSiteCatalyst-1.4.3/RSiteCatalyst/tests |only
100 files changed, 444 insertions(+), 291 deletions(-)
Title: Multi-state Markov and Hidden Markov Models in Continuous Time
Diff between msm versions 1.4 dated 2014-07-08 and 1.5 dated 2015-01-06
Description: Continuous-time Markov and hidden Markov multi-state
models for longitudinal data. Designed for processes observed at
arbitrary times in continuous time (panel data) but some other
observation schemes are supported. Both Markov transition rates and
the hidden Markov output process can be modelled in terms of
covariates, which may be constant or piecewise-constant in time.
Author: Christopher Jackson
Maintainer: Christopher Jackson
ChangeLog | 107 +++
DESCRIPTION | 31 -
MD5 | 79 +-
NAMESPACE | 8
R/boot.R | 64 +-
R/draic.R | 50 +
R/hmm.R | 18
R/msm.R | 146 +++--
R/optim.R | 32 -
R/outputs.R | 1096 +++++++++++++++++++-------------------
R/phase.R |only
R/utils.R | 8
TODO | 61 --
data/bos3.rda |only
data/bos4.rda |only
data/msmdata.rda |binary
inst/NEWS | 54 +
inst/NEWS.mine |only
inst/NEWS.r57 |only
inst/NEWS.r64 |only
inst/doc/msm-manual.R | 26
man/2phase.Rd |only
man/bos.Rd | 6
man/cav.Rd | 16
man/draic.msm.Rd | 6
man/efpt.msm.Rd | 4
man/logLik.msm.Rd | 5
man/lrtest.msm.Rd | 4
man/msm.Rd | 107 +++
man/msm2Surv.Rd | 13
man/paramdata.object.Rd | 3
man/phasemeans.msm.Rd |only
man/plot.survfit.msm.Rd | 13
man/pmatrix.msm.Rd | 9
man/pmatrix.piecewise.msm.Rd | 10
man/ppass.msm.Rd | 2
man/statetable.msm.Rd | 12
man/viterbi.msm.Rd | 14
src/analyticp.c | 2
src/doc/figures/fev_viterbi.pdf |only
src/doc/msm-manual.Rnw | 25
src/lik.c | 124 +++-
src/pijt.c | 5
tests/testthat/test_models.r | 30 -
tests/testthat/test_models_misc.r | 1
45 files changed, 1342 insertions(+), 849 deletions(-)
Title: Procedures to Generate Patterns under Computerized Adaptive
Testing
Diff between catR versions 3.3 dated 2014-11-26 and 3.4 dated 2015-01-06
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis
DESCRIPTION | 10 -
MD5 | 20 +-
NEWS | 47 +++++
R/genPattern.R | 29 +--
R/genPolyMatrix.R | 36 ++--
R/randomCAT.R | 63 ++++---
R/simulateRespondents.R | 396 +++++++++++++++++++++++----------------------
man/genPattern.Rd | 7
man/genPolyMatrix.Rd | 12 -
man/randomCAT.Rd | 28 +--
man/simulateRespondents.Rd | 24 +-
11 files changed, 381 insertions(+), 291 deletions(-)
Title: Supplementary Item Response Theory Models
Diff between sirt versions 1.2 dated 2014-12-12 and 1.3 dated 2015-01-06
Description:
Supplementary item response theory models to complement existing
functions in R, including multidimensional compensatory and
noncompensatory IRT models, MCMC for hierarchical IRT models and
testlet models, NOHARM, faceted and hierarchical rater models,
ordinal IRT model (ISOP), discrete grade of membership model,
latent regression models, DETECT statistic.
Author: Alexander Robitzsch [aut,cre]
Maintainer: Alexander Robitzsch
DESCRIPTION | 29 +++--
MD5 | 87 +++++++++-------
NAMESPACE | 144 ++++++++++++++++++++-------
R/ARb_utils.R | 11 +-
R/IRT.factor.scores.sirt.R |only
R/IRT.irfprob.sirt.R |only
R/IRT.likelihood_sirt.R |only
R/IRT.mle.R |only
R/IRT.modelfit.sirt.R |only
R/IRT.posterior_sirt.R |only
R/anova_sirt.R |only
R/gom.em.R | 5
R/logLik_sirt.R |only
R/mirt.IRT.functions.R | 3
R/mle.reliability.R |only
R/modelfit.cor.R | 17 +++
R/modelfit.cor.poly.R |only
R/rasch.conquest.R | 75 ++++++++++----
R/rasch.copula2.R | 3
R/rasch.copula3.R | 3
R/rasch.copula3.covariance.R | 2
R/rasch.mirtlc.R | 17 +++
R/rasch.mml2.R | 18 ++-
R/rm.facets.IC.R |only
R/rm.facets.R | 92 +++++++++++------
R/rm.facets_IC.R |only
R/rm.facets_PP.R |only
R/rm.facets_alg.R | 78 +++++++++++---
R/rm.sdt.R | 22 +++-
R/rm.smooth.distribution.R |only
R/rm_proc.R | 2
R/smirt.R | 2
R/summary.rm.facets.R | 10 +
inst/NEWS | 35 ++++++
man/IRT.mle.Rd |only
man/R2conquest.Rd | 6 -
man/data.eid.Rd | 9 -
man/data.g308.Rd | 23 ++--
man/f1d.irt.Rd | 7 -
man/gom.em.Rd | 30 +++++
man/mirt.wrapper.Rd | 19 +--
man/modelfit.sirt.Rd | 20 +++
man/pcm.fit.Rd | 24 +++-
man/person.parameter.rasch.copula.Rd | 3
man/personfit.stat.Rd | 2
man/rasch.copula.Rd | 30 +++++
man/rasch.mirtlc.Rd | 56 ++++++++--
man/rasch.mml.Rd | 39 +++++++
man/rm.facets.Rd | 117 +++++++++++++++++++---
man/rm.sdt.Rd | 35 ++++++
man/sirt-package.Rd | 186 +++++++++++++++++++----------------
man/smirt.Rd | 22 ++++
52 files changed, 959 insertions(+), 324 deletions(-)
Title: COBS -- COnstrained B-Splines (Sparse matrix based)
Diff between cobs versions 1.2-2 dated 2011-04-26 and 1.3-0 dated 2015-01-06
Description: Qualitatively Constrained (Regression) Smoothing Splines via
Linear Programming and Sparse Matrices.
Author: Pin T. Ng
Maintainer: Martin Maechler
cobs-1.2-2/cobs/Notes-MM |only
cobs-1.2-2/cobs/Pin-notes_2009-02.txt |only
cobs-1.2-2/cobs/R_README |only
cobs-1.2-2/cobs/data/DublinWind.tab.gz |only
cobs-1.2-2/cobs/data/USArmyRoofs.tab.gz |only
cobs-1.2-2/cobs/data/exHe.tab.gz |only
cobs-1.2-2/cobs/data/globtemp.rda |only
cobs-1.2-2/cobs/no-NAMESPACE.R |only
cobs-1.2-2/cobs/scobs_02_09.txt |only
cobs-1.2-2/cobs/tests/ex1.Rout.save |only
cobs-1.2-2/cobs/tests/ex2-long.Rout.save |only
cobs-1.2-2/cobs/tests/pt-ex.R |only
cobs-1.2-2/cobs/tests/wind.Rout.save |only
cobs-1.3-0/cobs/ChangeLog | 10 ++++++
cobs-1.3-0/cobs/DESCRIPTION | 22 ++++++++------
cobs-1.3-0/cobs/MD5 |only
cobs-1.3-0/cobs/NAMESPACE | 5 ++-
cobs-1.3-0/cobs/R/concaveRegr.R | 2 -
cobs-1.3-0/cobs/R/scobs.R | 12 +++----
cobs-1.3-0/cobs/README | 42 +++++++++++++++++++++++++++
cobs-1.3-0/cobs/TODO | 22 +++++++++++---
cobs-1.3-0/cobs/data/DublinWind.tab |only
cobs-1.3-0/cobs/data/USArmyRoofs.tab |only
cobs-1.3-0/cobs/data/exHe.tab |only
cobs-1.3-0/cobs/data/globtemp.R |only
cobs-1.3-0/cobs/inst/CITATION |only
cobs-1.3-0/cobs/man/plot.cobs.Rd | 2 -
cobs-1.3-0/cobs/src/Makevars | 5 ---
cobs-1.3-0/cobs/tests/0_pt-ex.R |only
cobs-1.3-0/cobs/tests/README | 11 +++++--
cobs-1.3-0/cobs/tests/ex1.Rout-N-save |only
cobs-1.3-0/cobs/tests/ex1Old.Rout-N-save |only
cobs-1.3-0/cobs/tests/ex2-long.Rout-N-save |only
cobs-1.3-0/cobs/tests/multi-constr.Rout.save | 12 +++++--
cobs-1.3-0/cobs/tests/roof.Rout-N-save |only
cobs-1.3-0/cobs/tests/temp.Rout-N-save |only
cobs-1.3-0/cobs/tests/wind.Rout-N-save |only
37 files changed, 111 insertions(+), 34 deletions(-)
Title: Choose univariate class intervals
Diff between classInt versions 0.1-21 dated 2013-09-01 and 0.1-22 dated 2015-01-06
Description: A package for choosing univariate class intervals for mapping or other graphics purposes
Author: Roger Bivand [aut, cre],
Hisaji Ono [ctb],
Richard Dunlap [ctb],
Matthieu Stigler [ctb]
Maintainer: Roger Bivand
ChangeLog | 17 +++++++++++++++++
DESCRIPTION | 15 +++++++++------
MD5 | 8 ++++----
inst/ChangeLog | 17 +++++++++++++++++
man/classIntervals.Rd | 8 +++++---
5 files changed, 52 insertions(+), 13 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Diff between surveillance versions 1.8-2 dated 2014-12-20 and 1.8-3 dated 2015-01-06
Description: A package implementing statistical methods for the modeling and
change-point detection in time series of counts, proportions and
categorical data, as well as for the modeling of continuous-time
epidemic phenomena, e.g. discrete-space setups such as the spatially
enriched Susceptible-Exposed-Infectious-Recovered (SEIR) models for
surveillance data, or continuous-space point process data such as the
occurrence of disease or earthquakes. Main focus is on outbreak
detection in count data time series originating from public health
surveillance of infectious diseases, but applications could just as well
originate from environmetrics, reliability engineering, econometrics or
social sciences.
Currently the package contains implementations of typical
outbreak detection procedures such as Farrington et al (1996),
Noufaily et al (2012) or the negative binomial LR-CUSUM method
described in Hoehle and Paul (2008). Furthermore, inference
methods for the retrospective infectious disease model in Held
et al (2005), Held et al (2006), Paul et al (2008) and Paul
and Held (2011) are provided. A novel CUSUM approach combining
logistic and multinomial logistic modelling is also included.
Continuous self-exciting spatio-temporal point processes are
modeled through additive-multiplicative conditional
intensities as described in Höhle (2009) ("twinSIR", discrete
space) and Meyer et al (2012) ("twinstim", continuous space).
The package contains several real-world data sets, the ability
to simulate outbreak data, visualize the results of the
monitoring in temporal, spatial or spatio-temporal fashion.
Note: Using the 'boda' algorithm requires the the INLA
package, which should be installed automatically through the
specified Additional_repositories, if uninstalled dependencies
are also requested. As this might not work under Mac OS X it
might be necessary to manually install the INLA package as
specified at http://www.r-inla.org/download.
Author: Michael Höhle [aut, cre, ths], Sebastian Meyer [aut],
Michaela Paul [aut], Leonhard Held [ctb, ths],
Thais Correa [ctb], Mathias Hofmann [ctb], Christian Lang [ctb],
Juliane Manitz [ctb], Andrea Riebler [ctb], Daniel Sabanés Bové [ctb],
Maëlle Salmon [ctb], Dirk Schumacher [ctb], Stefan Steiner [ctb],
Mikko Virtanen [ctb], Valentin Wimmer [ctb], R Core Team [ctb]
(A few code segments are modified versions of code from base R)
Maintainer: Michael Höhle
DESCRIPTION | 19 ++++---
MD5 | 38 +++++++--------
R/boda.R | 2
R/isoWeekYear.R | 72 +++++++++++++++-------------
R/linelist2sts.R | 35 +++++++-------
R/spatial_tools.R | 16 ++++--
R/sts_animate.R | 28 ++++++++---
build/partial.rdb |binary
inst/NEWS.Rd | 6 ++
inst/doc/glrnb.pdf |binary
inst/doc/hhh4.pdf |binary
inst/doc/surveillance.pdf |binary
man/algo.twins.Rd | 11 ++++
man/hepatitisA.Rd | 2
man/isoWeekYear.Rd | 5 +-
man/linelist2sts.Rd | 97 +++++++++++++++++++++++----------------
man/nowcast.Rd | 31 ++++++++----
man/sim.pointSource.Rd | 8 +--
man/sts_animate.Rd | 14 ++++-
tests/testthat/test-formatDate.R | 7 ++
20 files changed, 244 insertions(+), 147 deletions(-)
Title: Miscellaneous Functions for Survival Data
Diff between survMisc versions 0.4.2 dated 2014-05-13 and 0.4.4 dated 2015-01-06
Description: A collection of functions for analysis of survival data. These
extend the methods available in the survival package.
Author: Chris Dardis
Maintainer: Chris Dardis
survMisc-0.4.2/survMisc/R/autoplot.R |only
survMisc-0.4.2/survMisc/R/calcSurv.R |only
survMisc-0.4.2/survMisc/R/dxPlot.R |only
survMisc-0.4.2/survMisc/R/multiPlot.R |only
survMisc-0.4.2/survMisc/R/survEst.R |only
survMisc-0.4.2/survMisc/man/autoplot.rpart.Rd |only
survMisc-0.4.2/survMisc/man/autoplot.survfit.Rd |only
survMisc-0.4.2/survMisc/man/autoplot.tableAndPlot.Rd |only
survMisc-0.4.2/survMisc/man/calcSurv.Rd |only
survMisc-0.4.2/survMisc/man/dxPlot.Rd |only
survMisc-0.4.2/survMisc/man/mean.Surv.Rd |only
survMisc-0.4.2/survMisc/man/survEst.Rd |only
survMisc-0.4.4/survMisc/DESCRIPTION | 38
survMisc-0.4.4/survMisc/MD5 | 160 +-
survMisc-0.4.4/survMisc/NAMESPACE | 134 +-
survMisc-0.4.4/survMisc/R/air.R | 47
survMisc-0.4.4/survMisc/R/asSurv.R |only
survMisc-0.4.4/survMisc/R/autoplotRpart.R | 807 +++++++-------
survMisc-0.4.4/survMisc/R/autoplotSurvfit.R |only
survMisc-0.4.4/survMisc/R/autoplotTAP.R | 47
survMisc-0.4.4/survMisc/R/btumors.R | 53
survMisc-0.4.4/survMisc/R/ci.R |only
survMisc-0.4.4/survMisc/R/comp.R | 1068 +++++++++----------
survMisc-0.4.4/survMisc/R/covMatSurv.R | 143 +-
survMisc-0.4.4/survMisc/R/cutp.R | 120 +-
survMisc-0.4.4/survMisc/R/d1.R |only
survMisc-0.4.4/survMisc/R/dx.R |only
survMisc-0.4.4/survMisc/R/gamTerms.R | 104 +
survMisc-0.4.4/survMisc/R/gastric.R | 52
survMisc-0.4.4/survMisc/R/genSurv.R | 23
survMisc-0.4.4/survMisc/R/gof.R |only
survMisc-0.4.4/survMisc/R/ic.R | 186 +--
survMisc-0.4.4/survMisc/R/local.R | 788 +++++++-------
survMisc-0.4.4/survMisc/R/lrSS.R | 208 ++-
survMisc-0.4.4/survMisc/R/meanSurv.R | 198 +--
survMisc-0.4.4/survMisc/R/mpip.R |only
survMisc-0.4.4/survMisc/R/multiCoxph.R | 882 +++++++--------
survMisc-0.4.4/survMisc/R/plotMultiCoxph.R | 148 +-
survMisc-0.4.4/survMisc/R/plotSurv.R | 236 ++--
survMisc-0.4.4/survMisc/R/plotTerm.R |only
survMisc-0.4.4/survMisc/R/profLik.R | 238 ++--
survMisc-0.4.4/survMisc/R/quantile.R | 477 ++++----
survMisc-0.4.4/survMisc/R/rsq.R |only
survMisc-0.4.4/survMisc/R/sf.R |only
survMisc-0.4.4/survMisc/R/sig.R | 112 -
survMisc-0.4.4/survMisc/R/survMisc_package.R | 74 -
survMisc-0.4.4/survMisc/R/tableRhs.R | 85 +
survMisc-0.4.4/survMisc/R/tne.R | 707 ++++++------
survMisc-0.4.4/survMisc/R/tneBMT.R | 70 -
survMisc-0.4.4/survMisc/R/tneKidney.R | 38
survMisc-0.4.4/survMisc/R/whas100.R | 69 -
survMisc-0.4.4/survMisc/R/whas500.R |only
survMisc-0.4.4/survMisc/data/air.rda |binary
survMisc-0.4.4/survMisc/data/btumors.rda |binary
survMisc-0.4.4/survMisc/data/gastric.rda |binary
survMisc-0.4.4/survMisc/data/mpip.rda |only
survMisc-0.4.4/survMisc/data/tneBMT.rda |binary
survMisc-0.4.4/survMisc/data/tneKidney.rda |binary
survMisc-0.4.4/survMisc/data/whas100.rda |binary
survMisc-0.4.4/survMisc/data/whas500.rda |only
survMisc-0.4.4/survMisc/inst |only
survMisc-0.4.4/survMisc/man/air.Rd | 63 -
survMisc-0.4.4/survMisc/man/asSurv.Rd |only
survMisc-0.4.4/survMisc/man/autoplotRpart.Rd |only
survMisc-0.4.4/survMisc/man/autoplotSurvfit.Rd |only
survMisc-0.4.4/survMisc/man/autoplotTableAndPlot.Rd |only
survMisc-0.4.4/survMisc/man/btumors.Rd | 68 -
survMisc-0.4.4/survMisc/man/ci.Rd |only
survMisc-0.4.4/survMisc/man/comp.Rd | 432 +++----
survMisc-0.4.4/survMisc/man/covMatSurv.Rd | 114 +-
survMisc-0.4.4/survMisc/man/cutp.Rd | 172 +--
survMisc-0.4.4/survMisc/man/d1.Rd |only
survMisc-0.4.4/survMisc/man/dx.Rd |only
survMisc-0.4.4/survMisc/man/gamTerms.Rd | 138 +-
survMisc-0.4.4/survMisc/man/gastric.Rd | 82 -
survMisc-0.4.4/survMisc/man/genSurv.Rd | 186 +--
survMisc-0.4.4/survMisc/man/gof.Rd |only
survMisc-0.4.4/survMisc/man/ic.Rd | 138 +-
survMisc-0.4.4/survMisc/man/local.Rd | 249 ++--
survMisc-0.4.4/survMisc/man/lrSS.Rd | 190 +--
survMisc-0.4.4/survMisc/man/meanSurv.Rd |only
survMisc-0.4.4/survMisc/man/mpip.Rd |only
survMisc-0.4.4/survMisc/man/multi.Rd | 335 ++---
survMisc-0.4.4/survMisc/man/plot.Surv.Rd | 85 -
survMisc-0.4.4/survMisc/man/plotMultiCoxph.Rd | 99 -
survMisc-0.4.4/survMisc/man/plotTerm.Rd |only
survMisc-0.4.4/survMisc/man/profLik.Rd | 117 --
survMisc-0.4.4/survMisc/man/quantile.Rd | 266 ++--
survMisc-0.4.4/survMisc/man/rsq.Rd |only
survMisc-0.4.4/survMisc/man/sf.Rd |only
survMisc-0.4.4/survMisc/man/sig.Rd | 90 -
survMisc-0.4.4/survMisc/man/survMisc-package.Rd | 68 -
survMisc-0.4.4/survMisc/man/tableRhs.Rd | 161 +-
survMisc-0.4.4/survMisc/man/tne.Rd | 246 ++--
survMisc-0.4.4/survMisc/man/tneBMT.Rd | 93 -
survMisc-0.4.4/survMisc/man/tneKidney.Rd | 44
survMisc-0.4.4/survMisc/man/whas100.Rd | 86 -
survMisc-0.4.4/survMisc/man/whas500.Rd |only
survMisc-0.4.4/survMisc/src |only
99 files changed, 5666 insertions(+), 5168 deletions(-)
Title: R Interface to DSDP Semidefinite Programming Library
Diff between Rdsdp versions 1.0.1 dated 2015-01-01 and 1.0.2 dated 2015-01-06
Description: R interface to DSDP semidefinite programming library. Installs version 5.8 of DSDP from DSDP website. An existing installation of DSDP may be used by passing the proper configure arguments to the installation command.
Author: Zhisu Zhu, Yinyu Ye (DSDP by Steve Benson, Yinyu Ye and Xiong Zhang)
Maintainer: Zhisu Zhu
DESCRIPTION | 8 ++---
MD5 | 12 ++++----
man/dsdp.Rd | 1
src/Rdsdp.c | 19 +++++--------
src/Rreadsdpa.c | 60 ++++++++++++++++++++-----------------------
src/dsdp/src/vecmat/dufull.c | 20 +++++++-------
tests/test2.R | 2 -
7 files changed, 56 insertions(+), 66 deletions(-)
Title: Read-Write Support for NumPy Files via Rcpp
Diff between RcppCNPy versions 0.2.3 dated 2014-04-10 and 0.2.4 dated 2015-01-06
Description: The cnpy library written by Carl Rogers provides read and write
facilities for files created with (or for) the NumPy extension for Python.
Vectors and matrices of numeric types can be read or written to and from
files as well as compressed files. Support for integer files is available if
the package has been built with -std=c++11 which is the default starting
with release 0.2.3 following the release of R 3.1.0.
Author: Dirk Eddelbuettel and Wush Wu
Maintainer: Dirk Eddelbuettel
ChangeLog | 78 +++++++++++++++++++++++++++++++++++++++++++
DESCRIPTION | 24 ++++++-------
MD5 | 30 ++++++++--------
build/vignette.rds |binary
inst/NEWS.Rd | 14 +++++++
inst/doc/RcppCNPy-intro.R | 17 ++-------
inst/doc/RcppCNPy-intro.Rnw | 9 +---
inst/doc/RcppCNPy-intro.pdf |binary
src/cnpy.cpp | 8 ----
src/cnpy.h | 24 +++++++++++--
src/cnpyMod.cpp | 78 ++++++++++++++++++++++++++++++-------------
tests/loadFiles.R | 23 +++++-------
tests/loadFiles.Rout.save | 36 +++++++++----------
tests/saveAndLoad.R | 40 +++++++++++++++++++++-
tests/saveAndLoad.Rout.save | 54 +++++++++++++++++++++++++++--
vignettes/RcppCNPy-intro.Rnw | 9 +---
16 files changed, 322 insertions(+), 122 deletions(-)
Title: Random Uniform Forests for Classification, Regression and
Unsupervised Learning
Diff between randomUniformForest versions 1.1.1 dated 2014-12-03 and 1.1.2 dated 2015-01-06
More information about randomUniformForest at CRAN
Description: Ensemble model, for classification, regression
and unsupervised learning, based on a forest of unpruned
and randomized binary decision trees. Each tree is grown
by sampling, with replacement, a set of variables at each node.
Each cut-point is generated randomly, according to the continuous
Uniform distribution. For each tree, data are either bootstrapped
or subsampled. The unsupervised mode introduces clustering, dimension reduction
and variable importance, using a three-layer engine. Random Uniform Forests are mainly
aimed to lower correlation between trees (or trees residuals), to provide a deep analysis
of variable importance and to allow native distributed and incremental learning.
Author: Saip Ciss
Maintainer: Saip Ciss
DESCRIPTION | 8
MD5 | 45
NAMESPACE | 6
NEWS | 62 -
R/DecisionTreesCPP.R | 252 +++-
R/OnliningRandomUniformForests.R | 107 +
R/RandomUniformForestsCPP.R | 712 +++++++++---
R/genericFunctions.R | 158 +-
build/vignette.rds |binary
inst/doc/VariableImportanceInRandomUniformForests.pdf |only
inst/doc/VariableImportanceInRandomUniformForests.pdf.asis |only
inst/doc/randomUniformForestsOverview.pdf |binary
man/clusteringObservations.Rd | 30
man/combine.unsupervised.Rd |only
man/generic.cv.Rd | 49
man/internalFunctions.Rd | 4
man/model.stats.Rd | 68 +
man/partialDependenceBetweenPredictors.Rd | 6
man/partialDependenceOverResponses.Rd | 6
man/predict.randomUniformForest.Rd | 6
man/rUniformForest.big.Rd | 8
man/randomUniformForest-package.Rd | 16
man/randomUniformForest.Rd | 82 -
man/unsupervised.randomUniformForest.Rd | 42
man/update.unsupervised.Rd |only
vignettes/VariableImportanceInRandomUniformForests.pdf.asis |only
26 files changed, 1229 insertions(+), 438 deletions(-)
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