Title: Quantile Regression Coefficients Modeling
Description: Parametric modeling of quantile regression coefficient functions.
Can be used with censored and truncated data.
Author: Paolo Frumento <paolo.frumento@ki.se>
Maintainer: Paolo Frumento <paolo.frumento@ki.se>
Diff between qrcm versions 2.0 dated 2017-02-03 and 2.1 dated 2017-03-27
DESCRIPTION | 10 +++---- MD5 | 16 +++++------ NEWS.md | 15 ++-------- R/qrcm.R | 72 +++++++++++++++++++++++++++++++++------------------- man/iqr.Rd | 26 ++++++++++++------ man/plot.iqr.Rd | 2 - man/qrcm-package.Rd | 8 ++--- man/summary.iqr.Rd | 2 - man/test.fit.Rd | 13 ++++----- 9 files changed, 91 insertions(+), 73 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: Can be used to visualize data as networks as well as provides an interface for visualizing weighted graphical models.
Author: Sacha Epskamp, Giulio Costantini, Jonas Haslbeck, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.4.2 dated 2017-01-21 and 1.4.3 dated 2017-03-27
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS | 9 +++++++++ R/cor_auto.R | 10 +++++----- R/ggmFit.R | 40 ++++++++++++++++++++++++---------------- R/glasso_methods.R | 6 +++++- R/qgraph.R | 49 +++++++++++++++++++++++++++++++++++++++++++++---- man/centrality.Rd | 4 +--- man/ggmFit.Rd | 15 +++++++++++---- man/qgraph.Rd | 2 +- src/registration.c |only 11 files changed, 114 insertions(+), 46 deletions(-)
Title: Multivariate Response Generalized Linear Models
Description: Provides functions that (1) fit multivariate discrete distributions, (2) generate random numbers from multivariate discrete distributions, and (3) run regression and penalized regression on the multivariate categorical response data. Implemented models include: multinomial logit model, Dirichlet multinomial model, generalized Dirichlet multinomial model, and negative multinomial model. Making the best of the minorization-maximization (MM) algorithm and Newton-Raphson method, we derive and implement stable and efficient algorithms to find the maximum likelihood estimates. On a multi-core machine, multi-threading is supported.
Author: Yiwen Zhang <zhangyiwen1015@gmail.com> and Hua Zhou <huazhou@ucla.edu>
Maintainer: Yiwen Zhang <zhangyiwen1015@gmail.com>
Diff between MGLM versions 0.0.7 dated 2016-02-17 and 0.0.8 dated 2017-03-27
DESCRIPTION | 12 - MD5 | 58 +++---- NAMESPACE | 58 +++---- R/MGLMfit.R | 46 +++-- R/MGLMgen.R | 8 R/MGLMreg.R | 28 +-- R/MGLMsparsereg.R | 4 R/MGLMtune.R | 2 build |only inst/CITATION |only inst/doc/Vignette.R |only inst/doc/Vignette.Rnw |only inst/doc/Vignette.pdf |binary man/MGLM-package.Rd | 48 ++--- man/MGLMfit-class.Rd | 2 man/MGLMfit.Rd | 172 ++++++++++----------- man/MGLMreg-class.Rd | 2 man/MGLMreg.Rd | 60 +++---- man/MGLMsparsereg.Rd | 400 ++++++++++++++++++++++++------------------------- man/MGLMtune-class.Rd | 4 man/MGLMtune.Rd | 36 ++-- man/ddirm.Rd | 118 +++++++------- man/dgdirm.Rd | 144 ++++++++--------- man/dist.Rd | 194 +++++++++++------------ man/dmn.Rd | 128 +++++++-------- man/dnegmn.Rd | 142 ++++++++--------- man/kr.Rd | 82 +++++----- man/pkg-internal.Rd | 2 man/rdirm.Rd | 124 +++++++-------- man/rgdirm.Rd | 146 ++++++++--------- man/rnegmn.Rd | 138 ++++++++-------- vignettes/Vignette.Rnw | 202 ++++++------------------ 32 files changed, 1138 insertions(+), 1222 deletions(-)
Title: Efficient Leave-One-Out Cross-Validation and WAIC for Bayesian
Models
Description: Efficient approximate leave-one-out cross-validation (LOO)
using Pareto smoothed importance sampling (PSIS), a new procedure for
regularizing importance weights. As a byproduct of the calculations, we also
obtain approximate standard errors for estimated predictive errors and for
the comparison of predictive errors between models. We also compute the
widely applicable information criterion (WAIC).
Author: Aki Vehtari [aut],
Andrew Gelman [aut],
Jonah Gabry [cre, aut],
Juho Piironen [ctb],
Ben Goodrich [ctb]
Maintainer: Jonah Gabry <jsg2201@columbia.edu>
Diff between loo versions 1.0.0 dated 2016-12-16 and 1.1.0 dated 2017-03-27
DESCRIPTION | 12 +-- MD5 | 53 +++++++++------- NAMESPACE | 3 NEWS.md | 3 R/compare.R | 22 ++---- R/extract_log_lik.R | 4 - R/loo.R | 29 +++----- R/loo_expectation.R |only R/loo_package.R | 11 ++- R/pareto_k.R | 33 ---------- R/psislw.R | 18 +++-- build/vignette.rds |binary inst/CITATION | 41 +++++------- man/E_loo.Rd |only man/compare.Rd | 29 +++----- man/extract_log_lik.Rd | 3 man/gpdfit.Rd | 1 man/loo-package.Rd | 20 ++++-- man/loo.Rd | 45 ++++++------- man/nlist.Rd | 7 -- man/pareto-k-diagnostic.Rd | 53 ++++++++-------- man/print.loo.Rd | 1 man/psislw.Rd | 78 ++++++++++++++++++------ man/waic.Rd | 8 +- tests/testthat/E_loo_default_mean.rds |only tests/testthat/E_loo_default_quantile_10_90.rds |only tests/testthat/E_loo_default_quantile_50.rds |only tests/testthat/E_loo_default_var.rds |only tests/testthat/E_loo_matrix_mean.rds |only tests/testthat/E_loo_matrix_quantile_10_90.rds |only tests/testthat/E_loo_matrix_quantile_50.rds |only tests/testthat/E_loo_matrix_var.rds |only tests/testthat/test_E_loo.R |only 33 files changed, 242 insertions(+), 232 deletions(-)
Title: Graph Kernels
Description: A fast C++ implementation for computing various graph kernels including (1) simple kernels between vertex and/or edge label histograms, (2) random walk kernels (popular baselines), and (3) the Weisfeiler-Lehman graph kernel (state-of-the-art).
Author: Mahito Sugiyama
Maintainer: Mahito Sugiyama <mahito@ar.sanken.osaka-u.ac.jp>
Diff between graphkernels versions 1.0 dated 2017-03-16 and 1.1 dated 2017-03-27
DESCRIPTION | 10 +++--- MD5 | 32 ++++++++++---------- man/CalculateEdgeHistGaussKernel.Rd | 6 ++- man/CalculateEdgeHistKernel.Rd | 6 ++- man/CalculateExponentialRandomWalkKernel.Rd | 6 ++- man/CalculateGeometricRandomWalkKernel.Rd | 11 +++++-- man/CalculateKStepRandomWalkKernel.Rd | 11 +++++-- man/CalculateKernelCpp.Rd | 6 ++- man/CalculateVertexEdgeHistGaussKernel.Rd | 6 ++- man/CalculateVertexEdgeHistKernel.Rd | 6 ++- man/CalculateVertexHistGaussKernel.Rd | 6 ++- man/CalculateVertexHistKernel.Rd | 6 ++- man/CalculateVertexVertexEdgeHistKernel.Rd | 6 ++- man/CalculateWLKernel.Rd | 6 ++- man/GetGraphInfo.Rd | 4 -- man/graphkernels-package.Rd | 44 +++++++++++++++++++++++----- man/mutag.Rd | 8 +++-- 17 files changed, 122 insertions(+), 58 deletions(-)
Title: Default Color Maps from 'matplotlib'
Description: Port of the new 'matplotlib' color maps ('viridis' - the default
-, 'magma', 'plasma' and 'inferno') to 'R'. 'matplotlib' <http://matplotlib.org/
> is a popular plotting library for 'python'. These color maps are designed
in such a way that they will analytically be perfectly perceptually-uniform,
both in regular form and also when converted to black-and-white. They are
also designed to be perceived by readers with the most common form of color
blindness.
Author: Simon Garnier [aut, cre],
Noam Ross [ctb, cph],
Bob Rudis [ctb, cph]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between viridis versions 0.3.4 dated 2016-03-12 and 0.4.0 dated 2017-03-27
viridis-0.3.4/viridis/R/viridis.R |only viridis-0.3.4/viridis/data |only viridis-0.3.4/viridis/man/viridis.Rd |only viridis-0.4.0/viridis/DESCRIPTION | 24 ++++---- viridis-0.4.0/viridis/MD5 | 29 ++++++---- viridis-0.4.0/viridis/NAMESPACE | 6 ++ viridis-0.4.0/viridis/R/compatibility.R |only viridis-0.4.0/viridis/R/scales.R | 78 ++++++++++++++++------------- viridis-0.4.0/viridis/README.md | 12 ++-- viridis-0.4.0/viridis/build/vignette.rds |binary viridis-0.4.0/viridis/man/reexports.Rd |only viridis-0.4.0/viridis/man/scale_viridis.Rd | 23 ++++---- viridis-0.4.0/viridis/man/viridis.map.Rd | 5 - viridis-0.4.0/viridis/man/viridis_pal.Rd | 11 ++-- viridis-0.4.0/viridis/tests |only 15 files changed, 111 insertions(+), 77 deletions(-)
Title: Two Stage Hazard Rate Comparison
Description: Two-stage procedure compares hazard rate functions,
which may or may not cross each other.
Author: Jun Sheng, Peihua Qiu <qiu@stat.umn.edu>, and Charles J. Geyer
<charlie@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between TSHRC versions 0.1-4 dated 2016-11-28 and 0.1-5 dated 2017-03-27
DESCRIPTION | 10 +++++----- MD5 | 9 ++++++--- NAMESPACE | 2 +- R/twostage.R | 5 ++--- src/Makevars |only src/init.c |only src/tshrc.h |only 7 files changed, 14 insertions(+), 12 deletions(-)
Title: Data Analysis in Ecology
Description: Miscellaneous functions for data analysis in ecology, with special emphasis on spatial data.
Author: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Maintainer: Patrick Giraudoux <patrick.giraudoux@univ-fcomte.fr>
Diff between pgirmess versions 1.6.6 dated 2017-03-26 and 1.6.7 dated 2017-03-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/distSeg.r | 2 +- man/distSeg.rd | 1 + 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Read Data from Delimited 'MTConnect' Data Files and Perform some
Analysis
Description: Read data in the 'MTConnect'<http://www.mtconnect.org/> standard.
You can use the package to read data from historical 'MTConnect logs' along
with the 'devices.xml' describing
the device. The data is organised into a 'MTConnectDevice' S4 data structure
and some convenience methods are also provided for basic read/view operations.
The package also includes some functions for analysis of 'MTConnect' data. This includes
functions to simulate data (primarily position data, feed rate and velocities)
based on the G code and visualisation functions to compare the actual and simulated data.
Author: Alex Joseph [aut],
Sainath Adapa [aut],
Nitin Madasu [aut],
Subramanyam Ravishankar [aut, cre]
Maintainer: Subramanyam Ravishankar <subramanyam@systeminsights.com>
Diff between mtconnectR versions 1.0.1 dated 2016-08-02 and 1.1.0 dated 2017-03-27
DESCRIPTION | 6 +++--- MD5 | 26 +++++++++++++------------- NAMESPACE | 2 ++ R/common.R | 29 +++++++++++++---------------- build/vignette.rds |binary data/example_mapped_plot.rda |binary inst/doc/create_mtc_device.html | 6 +++--- inst/doc/simulate_map_gcode.html | 20 ++++++++++---------- man/convert_interval_to_ts.Rd | 7 ++++++- man/convert_ts_to_interval.Rd | 2 +- tests/testthat/test-MTCDevice.R | 2 +- tests/testthat/test-common.R | 15 ++++++++++++--- tests/testthat/test-map_gcode_mtc.R | 15 ++++++++------- tests/testthat/test-mtconnectR_staging.R | 2 +- 14 files changed, 73 insertions(+), 59 deletions(-)
Title: Land Use Change Modelling in R
Description: Classes and methods for spatially explicit land use change
modelling in R.
Author: Simon Moulds <sim.moulds@gmail.com>
Maintainer: Simon Moulds <sim.moulds@gmail.com>
Diff between lulcc versions 1.0.1 dated 2015-08-19 and 1.0.2 dated 2017-03-27
DESCRIPTION | 17 +++-- MD5 | 105 ++++++++++++++++++------------------- NAMESPACE | 2 man/AgreementBudget-class.Rd | 4 - man/AgreementBudget.Rd | 8 +- man/CategoryLabel-class.Rd | 2 man/CluesModel-class.Rd | 2 man/CluesModel.Rd | 8 +- man/ExpVarRasterList-class.Rd | 2 man/ExpVarRasterList.Rd | 21 +++---- man/FigureOfMerit-class.Rd | 2 man/FigureOfMerit.Rd | 6 +- man/Model-class.Rd | 2 man/Model-fitting.Rd | 6 +- man/NeighbRasterStack-class.Rd | 4 - man/NeighbRasterStack.Rd | 11 ++- man/ObsLulcRasterStack-class.Rd | 2 man/ObsLulcRasterStack.Rd | 17 +++-- man/OrderedModel-class.Rd | 2 man/OrderedModel.Rd | 8 +- man/PerformanceList-class.Rd | 2 man/PerformanceList.Rd | 4 - man/PredictionList-class.Rd | 2 man/PredictionList.Rd | 4 - man/PredictiveModelList-class.Rd | 2 man/ThreeMapComparison-class.Rd | 4 - man/ThreeMapComparison.Rd | 8 +- man/allocate.Rd | 8 +- man/allow.Rd | 7 +- man/allowNeighb.Rd | 5 + man/approxExtrapDemand.Rd | 5 + man/as.data.frame.Rd | 14 ++-- man/c.PredictiveModelList.Rd | 10 +-- man/compareAUC.Rd | 8 +- man/crossTabulate.Rd | 13 ++-- man/extractIndex.Rd | 7 +- man/getPredictiveModelInputData.Rd | 4 - man/lulcc-package.Rd | 25 ++++---- man/partition.Rd | 4 - man/performance.rocr.Rd | 7 +- man/pie.Rd | 4 - man/plot.AgreementBudget.Rd | 8 +- man/plot.FigureOfMerit.Rd | 12 ++-- man/plot.PerformanceList.Rd | 6 +- man/plot.Rd | 18 +++--- man/predict.Rd | 6 +- man/resample.Rd | 4 - man/roundSum.Rd | 5 + man/show-methods.Rd | 9 +-- man/sibuyan.Rd | 4 - man/subset-methods.Rd | 7 +- man/summary-methods.Rd | 7 +- man/total.Rd | 7 +- src/lulcc_init.c |only 54 files changed, 241 insertions(+), 230 deletions(-)
Title: Joint Modelling of Multivariate Longitudinal Data and
Time-to-Event Outcomes
Description: Fits the joint model proposed by Henderson and colleagues (2000)
<doi:10.1093/biostatistics/1.4.465>, but extended to the case of multiple
continuous longitudinal measures. The time-to-event data is modelled using a
Cox proportional hazards regression model with time-varying covariates. The
multiple longitudinal outcomes are modelled using a multivariate version of the
Laird and Ware linear mixed model. The association is captured by a multivariate
latent Gaussian process. The model is estimated using a Monte Carlo Expectation
Maximization algorithm. This project is funded by the Medical Research Council
(Grant number MR/M013227/1).
Author: Graeme L. Hickey [cre, aut],
Pete Philipson [aut],
Andrea Jorgensen [aut],
Ruwanthi Kolamunnage-Dona [aut],
Paula Williamson [ctb],
Dimitris Rizopoulos [ctb, dtc] (data/renal.rda, R/hessian.R, R/vcov.R)
Maintainer: Graeme L. Hickey <graeme.hickey@liverpool.ac.uk>
Diff between joineRML versions 0.1.1 dated 2016-12-30 and 0.2.0 dated 2017-03-27
joineRML-0.1.1/joineRML/R/approxSE.R |only joineRML-0.1.1/joineRML/R/fast_nearPD.R |only joineRML-0.1.1/joineRML/man/EexpWArma.Rd |only joineRML-0.1.1/joineRML/man/approxSE.Rd |only joineRML-0.1.1/joineRML/man/bSim.Rd |only joineRML-0.1.1/joineRML/man/convMonitor.Rd |only joineRML-0.1.1/joineRML/man/expWArma.Rd |only joineRML-0.1.1/joineRML/man/fast_nearPD.Rd |only joineRML-0.1.1/joineRML/man/gammaUpdate.Rd |only joineRML-0.1.1/joineRML/man/gammaUpdate_approx.Rd |only joineRML-0.1.1/joineRML/man/hazHat.Rd |only joineRML-0.1.1/joineRML/man/initsLong.Rd |only joineRML-0.1.1/joineRML/man/initsSurv_balanced.Rd |only joineRML-0.1.1/joineRML/man/lambdaUpdate.Rd |only joineRML-0.1.1/joineRML/man/mvlme.Rd |only joineRML-0.1.1/joineRML/man/mvrnormArma.Rd |only joineRML-0.1.1/joineRML/man/print.bootSE.Rd |only joineRML-0.1.1/joineRML/man/print.mjoint.Rd |only joineRML-0.1.1/joineRML/man/print.summary.mjoint.Rd |only joineRML-0.1.1/joineRML/man/stepEM.Rd |only joineRML-0.1.1/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_32f249ce86980d00e58a7f3ac608bcfd.RData |only joineRML-0.1.1/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_32f249ce86980d00e58a7f3ac608bcfd.rdb |only joineRML-0.1.1/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_32f249ce86980d00e58a7f3ac608bcfd.rdx |only joineRML-0.1.1/joineRML/vignettes/joineRML_cache/html/joineRML_e6df4d36d4bc503a72e7155fcbd02a4c.RData |only joineRML-0.1.1/joineRML/vignettes/joineRML_cache/html/joineRML_e6df4d36d4bc503a72e7155fcbd02a4c.rdb |only joineRML-0.1.1/joineRML/vignettes/joineRML_cache/html/joineRML_e6df4d36d4bc503a72e7155fcbd02a4c.rdx |only joineRML-0.2.0/joineRML/DESCRIPTION | 28 joineRML-0.2.0/joineRML/LICENSE | 898 +++++++--- joineRML-0.2.0/joineRML/MD5 | 188 +- joineRML-0.2.0/joineRML/NAMESPACE | 21 joineRML-0.2.0/joineRML/NEWS.md | 74 joineRML-0.2.0/joineRML/R/RcppExports.R | 27 joineRML-0.2.0/joineRML/R/bootSE.R | 41 joineRML-0.2.0/joineRML/R/confint.mjoint.R | 18 joineRML-0.2.0/joineRML/R/convMonitor.R | 2 joineRML-0.2.0/joineRML/R/epileptic.qol.R | 31 joineRML-0.2.0/joineRML/R/fitted.mjoint.R |only joineRML-0.2.0/joineRML/R/fixef.mjoint.R | 9 joineRML-0.2.0/joineRML/R/formula.mjoint.R | 10 joineRML-0.2.0/joineRML/R/getVarCov.mjoint.R | 18 joineRML-0.2.0/joineRML/R/heart.valve.R | 48 joineRML-0.2.0/joineRML/R/hessian.R |only joineRML-0.2.0/joineRML/R/initsLong.R | 25 joineRML-0.2.0/joineRML/R/initsSurv.R | 7 joineRML-0.2.0/joineRML/R/joineRML.R | 33 joineRML-0.2.0/joineRML/R/logLik.mjoint.R | 2 joineRML-0.2.0/joineRML/R/mjoint.R | 214 +- joineRML-0.2.0/joineRML/R/mjoint.object.R | 55 joineRML-0.2.0/joineRML/R/mvlme.R | 24 joineRML-0.2.0/joineRML/R/pbc2.R | 18 joineRML-0.2.0/joineRML/R/plot.mjoint.R | 7 joineRML-0.2.0/joineRML/R/plot.ranef.mjoint.R |only joineRML-0.2.0/joineRML/R/plotConvergence.R | 83 joineRML-0.2.0/joineRML/R/print.bootSE.R | 2 joineRML-0.2.0/joineRML/R/print.mjoint.R | 4 joineRML-0.2.0/joineRML/R/print.summary.mjoint.R | 2 joineRML-0.2.0/joineRML/R/ranef.mjoint.R | 17 joineRML-0.2.0/joineRML/R/renal.R | 23 joineRML-0.2.0/joineRML/R/residuals.mjoint.R |only joineRML-0.2.0/joineRML/R/sampleData.R | 39 joineRML-0.2.0/joineRML/R/sigma.mjoint.R | 11 joineRML-0.2.0/joineRML/R/simData.R | 90 - joineRML-0.2.0/joineRML/R/stepEM.R | 79 joineRML-0.2.0/joineRML/R/summary.mjoint.R | 12 joineRML-0.2.0/joineRML/R/vcov.mjoint.R | 25 joineRML-0.2.0/joineRML/README.md | 4 joineRML-0.2.0/joineRML/build/vignette.rds |binary joineRML-0.2.0/joineRML/inst/doc/joineRML.Rmd | 4 joineRML-0.2.0/joineRML/inst/doc/joineRML.html | 232 +- joineRML-0.2.0/joineRML/inst/doc/technical.ltx | 2 joineRML-0.2.0/joineRML/inst/doc/technical.pdf |binary joineRML-0.2.0/joineRML/man/bootSE.Rd | 71 joineRML-0.2.0/joineRML/man/confint.mjoint.Rd | 21 joineRML-0.2.0/joineRML/man/epileptic.qol.Rd | 32 joineRML-0.2.0/joineRML/man/fitted.mjoint.Rd |only joineRML-0.2.0/joineRML/man/fixef.mjoint.Rd | 13 joineRML-0.2.0/joineRML/man/formula.mjoint.Rd | 13 joineRML-0.2.0/joineRML/man/getVarCov.mjoint.Rd | 17 joineRML-0.2.0/joineRML/man/heart.valve.Rd | 49 joineRML-0.2.0/joineRML/man/initsSurv.Rd | 1 joineRML-0.2.0/joineRML/man/initsSurv_unbalanced.Rd | 1 joineRML-0.2.0/joineRML/man/joineRML.Rd |only joineRML-0.2.0/joineRML/man/logLik.mjoint.Rd | 7 joineRML-0.2.0/joineRML/man/mjoint.Rd | 113 - joineRML-0.2.0/joineRML/man/mjoint.object.Rd | 62 joineRML-0.2.0/joineRML/man/pbc2.Rd | 19 joineRML-0.2.0/joineRML/man/plot.mjoint.Rd | 12 joineRML-0.2.0/joineRML/man/plot.ranef.mjoint.Rd |only joineRML-0.2.0/joineRML/man/plotConvergence.Rd | 29 joineRML-0.2.0/joineRML/man/ranef.mjoint.Rd | 17 joineRML-0.2.0/joineRML/man/renal.Rd | 24 joineRML-0.2.0/joineRML/man/residuals.mjoint.Rd |only joineRML-0.2.0/joineRML/man/sampleData.Rd | 19 joineRML-0.2.0/joineRML/man/sigma.mjoint.Rd | 10 joineRML-0.2.0/joineRML/man/simData.Rd | 92 - joineRML-0.2.0/joineRML/man/summary.mjoint.Rd | 9 joineRML-0.2.0/joineRML/man/vcov.mjoint.Rd | 15 joineRML-0.2.0/joineRML/src/RcppExports.cpp | 117 - joineRML-0.2.0/joineRML/src/expW.cpp | 23 joineRML-0.2.0/joineRML/src/gammaUpdate.cpp | 42 joineRML-0.2.0/joineRML/src/gammaUpdate_approx.cpp | 24 joineRML-0.2.0/joineRML/src/joineRML_init.c |only joineRML-0.2.0/joineRML/src/lambdaUpdate.cpp | 23 joineRML-0.2.0/joineRML/src/mvnorm.cpp | 19 joineRML-0.2.0/joineRML/tests |only joineRML-0.2.0/joineRML/vignettes/joineRML.Rmd | 4 joineRML-0.2.0/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_f450182d26c4fe8447b1a85588ff46ea.RData |only joineRML-0.2.0/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_f450182d26c4fe8447b1a85588ff46ea.rdb |only joineRML-0.2.0/joineRML/vignettes/joineRML_cache/html/hvd_model_boot_f450182d26c4fe8447b1a85588ff46ea.rdx |only joineRML-0.2.0/joineRML/vignettes/joineRML_cache/html/joineRML_c93014128247f4f1d85a458110b8bff3.RData |only joineRML-0.2.0/joineRML/vignettes/joineRML_cache/html/joineRML_c93014128247f4f1d85a458110b8bff3.rdb |only joineRML-0.2.0/joineRML/vignettes/joineRML_cache/html/joineRML_c93014128247f4f1d85a458110b8bff3.rdx |only joineRML-0.2.0/joineRML/vignettes/joineRML_files/figure-html/re_comp_plot-1.png |binary joineRML-0.2.0/joineRML/vignettes/technical.ltx | 2 114 files changed, 2002 insertions(+), 1325 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: 'jamovi' is a framework for creating rich interactive statistical
analyses (see <https://www.jamovi.org> for more information). This package
represents the core libraries which jamovi analyses written in R depend
upon.
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 0.5.0 dated 2017-03-25 and 0.5.1 dated 2017-03-27
DESCRIPTION | 8 ++++---- MD5 | 6 ++++-- R/table.R | 4 ++-- tests/testthat/test-profiletable.R |only tests/testthat/test-table.R |only 5 files changed, 10 insertions(+), 8 deletions(-)
Title: Graphical VAR for Experience Sampling Data
Description: Estimates within and between time point interactions in experience sampling data, using the Graphical VAR model in combination with LASSO and EBIC.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between graphicalVAR versions 0.1.4 dated 2016-07-03 and 0.2 dated 2017-03-27
DESCRIPTION | 8 ++-- MD5 | 28 +++++++++------ NAMESPACE | 13 ++++++- NEWS | 10 +++++ R/RcppExports.R | 2 - R/Rothmana.R | 15 ++++++-- R/dataPrep.R |only R/gVARsimulator.R | 4 +- R/graphicalVAR.R | 91 +++++++++++++++++++++++++++++++++++--------------- R/lambdas.R | 72 ++++++++++++++++++++++++++++++++++++++- R/methods.R | 2 - R/mlGraphicalVAR.R |only R/simMLgvar.R |only man/graphicalVAR.Rd | 22 +++++++++++- man/mlGraphicalVAR.Rd |only man/simMLgvar.Rd |only src/RcppExports.cpp | 34 +++++++++--------- src/registration.c |only 18 files changed, 231 insertions(+), 70 deletions(-)
Title: Flexible Parametric Survival and Multi-State Models
Description: Flexible parametric models for time-to-event data,
including the Royston-Parmar spline model, generalized gamma and
generalized F distributions. Any user-defined parametric
distribution can be fitted, given at least an R function defining
the probability density or hazard. There are also tools for
fitting and predicting from fully parametric multi-state models.
Author: Christopher Jackson [aut, cre],
Paul Metcalfe [ctb],
Jordan Amdahl [ctb]
Maintainer: Christopher Jackson <chris.jackson@mrc-bsu.cam.ac.uk>
Diff between flexsurv versions 1.0.0 dated 2016-05-11 and 1.1 dated 2017-03-27
flexsurv-1.0.0/flexsurv/data/bc.txt.gz |only flexsurv-1.1/flexsurv/DESCRIPTION | 40 flexsurv-1.1/flexsurv/MD5 | 139 - flexsurv-1.1/flexsurv/NAMESPACE | 237 +- flexsurv-1.1/flexsurv/R/Exp.R |only flexsurv-1.1/flexsurv/R/Gamma.R |only flexsurv-1.1/flexsurv/R/GenF.R | 508 +++- flexsurv-1.1/flexsurv/R/GenGamma.R | 474 +++- flexsurv-1.1/flexsurv/R/Gompertz.R | 230 +- flexsurv-1.1/flexsurv/R/Llogis.R | 95 flexsurv-1.1/flexsurv/R/Lnorm.R |only flexsurv-1.1/flexsurv/R/RcppExports.R |only flexsurv-1.1/flexsurv/R/Weibull.R |only flexsurv-1.1/flexsurv/R/WeibullPH.R |only flexsurv-1.1/flexsurv/R/custom.R | 317 +- flexsurv-1.1/flexsurv/R/distributions.R |only flexsurv-1.1/flexsurv/R/flexsurv-package.R |only flexsurv-1.1/flexsurv/R/flexsurvreg.R | 1296 +++++++++--- flexsurv-1.1/flexsurv/R/mstate.R | 1487 +++++++++----- flexsurv-1.1/flexsurv/R/spline.R | 1217 +++++++---- flexsurv-1.1/flexsurv/R/unroll.function.R |only flexsurv-1.1/flexsurv/R/utils.R | 527 ++-- flexsurv-1.1/flexsurv/build/vignette.rds |binary flexsurv-1.1/flexsurv/data/bc.txt |only flexsurv-1.1/flexsurv/inst/NEWS | 780 +++---- flexsurv-1.1/flexsurv/inst/doc/flexsurv-examples.R | 17 flexsurv-1.1/flexsurv/inst/doc/flexsurv-examples.pdf |binary flexsurv-1.1/flexsurv/inst/doc/flexsurv.R | 6 flexsurv-1.1/flexsurv/inst/doc/flexsurv.pdf |binary flexsurv-1.1/flexsurv/man/GenF.Rd | 240 +- flexsurv-1.1/flexsurv/man/GenF.orig.Rd | 189 - flexsurv-1.1/flexsurv/man/GenGamma.Rd | 237 +- flexsurv-1.1/flexsurv/man/GenGamma.orig.Rd | 209 + flexsurv-1.1/flexsurv/man/Gompertz.Rd | 184 - flexsurv-1.1/flexsurv/man/Llogis.Rd | 166 - flexsurv-1.1/flexsurv/man/Survspline.Rd | 211 + flexsurv-1.1/flexsurv/man/WeibullPH.Rd | 147 - flexsurv-1.1/flexsurv/man/basis.Rd | 97 flexsurv-1.1/flexsurv/man/bc.Rd | 83 flexsurv-1.1/flexsurv/man/bos.Rd | 113 - flexsurv-1.1/flexsurv/man/coef.flexsurvreg.Rd |only flexsurv-1.1/flexsurv/man/flexsurv-package.Rd | 200 - flexsurv-1.1/flexsurv/man/flexsurvreg.Rd | 870 ++++---- flexsurv-1.1/flexsurv/man/flexsurvspline.Rd | 493 ++-- flexsurv-1.1/flexsurv/man/hazard.Rd | 121 - flexsurv-1.1/flexsurv/man/lines.flexsurvreg.Rd | 123 - flexsurv-1.1/flexsurv/man/means.Rd |only flexsurv-1.1/flexsurv/man/model.frame.flexsurvreg.Rd | 89 flexsurv-1.1/flexsurv/man/msfit.flexsurvreg.Rd | 333 +-- flexsurv-1.1/flexsurv/man/normboot.flexsurvreg.Rd | 140 - flexsurv-1.1/flexsurv/man/pars.fmsm.Rd | 53 flexsurv-1.1/flexsurv/man/plot.flexsurvreg.Rd | 240 +- flexsurv-1.1/flexsurv/man/pmatrix.fs.Rd | 231 +- flexsurv-1.1/flexsurv/man/pmatrix.simfs.Rd | 213 +- flexsurv-1.1/flexsurv/man/qgeneric.Rd | 126 - flexsurv-1.1/flexsurv/man/rmst_generic.Rd |only flexsurv-1.1/flexsurv/man/sim.fmsm.Rd | 178 - flexsurv-1.1/flexsurv/man/summary.flexsurvreg.Rd | 293 +- flexsurv-1.1/flexsurv/man/totlos.fs.Rd | 264 +- flexsurv-1.1/flexsurv/man/totlos.simfs.Rd | 205 + flexsurv-1.1/flexsurv/man/unroll.function.Rd | 169 - flexsurv-1.1/flexsurv/src |only flexsurv-1.1/flexsurv/tests/testthat/test_flexsurvreg.R | 913 ++++---- flexsurv-1.1/flexsurv/tests/testthat/test_genf.R |only flexsurv-1.1/flexsurv/tests/testthat/test_genf_orig.R |only flexsurv-1.1/flexsurv/tests/testthat/test_gengamma.R |only flexsurv-1.1/flexsurv/tests/testthat/test_gengamma_orig.R |only flexsurv-1.1/flexsurv/tests/testthat/test_gompertz.R |only flexsurv-1.1/flexsurv/tests/testthat/test_llogis.R |only flexsurv-1.1/flexsurv/tests/testthat/test_outputs.R | 175 - flexsurv-1.1/flexsurv/tests/testthat/test_spline.R | 12 flexsurv-1.1/flexsurv/tests/testthat/test_splinedist.R |only flexsurv-1.1/flexsurv/tests/testthat/test_utils.R | 530 ---- flexsurv-1.1/flexsurv/vignettes/flexsurv-examples.Rnw | 428 ++-- flexsurv-1.1/flexsurv/vignettes/flexsurv.Rnw | 26 75 files changed, 8833 insertions(+), 6838 deletions(-)
Title: An Easy Way to Descriptive Analysis
Description:
Descriptive analysis is essential for publishing medical articles.
This package provides an easy way to conduct the descriptive analysis.
1. Both numeric and factor variables can be handled. For numeric variables, normality test will be applied to choose the parametric and nonparametric test.
2. Both two or more groups can be handled. For groups more than two, the post hoc test will be applied, 'Tukey' for the numeric variables and 'FDR' for the factor variables.
3. T test, ANOVA or Fisher test can be forced to apply.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>
Diff between easyDes versions 1.0 dated 2017-01-03 and 2.0 dated 2017-03-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/eastDes.R | 39 +++++++++++++++++++++++++++++++++------ man/easyDes.Rd | 8 ++++++-- 4 files changed, 46 insertions(+), 15 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for MTA
Description: Phase I/II adaptive dose-finding design for single-agent
Molecularly Targeted Agent (MTA), according to the paper "Phase
I/II Dose-Finding Design for Molecularly Targeted Agent: Plateau
Determination using Adaptive Randomization" (in review).
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfmta versions 1.3-4 dated 2016-06-21 and 1.4 dated 2017-03-27
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/dfmta.cpp | 6 ++++-- 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Phase I/II Adaptive Dose-Finding Design for Combination Studies
Description: Phase I/II adaptive dose-finding design for combination
studies. Several methods are proposed depending on the type of
combinations: (1) the combination of two cytotoxic agents, and (2)
combination of a molecularly targeted agent with a cytotoxic agent.
Author: Marie-Karelle Riviere and Jacques-Henri Jourdan
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between dfcomb versions 2.1-6 dated 2016-06-21 and 2.2 dated 2017-03-27
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/dfcomb.c | 6 ++++-- 3 files changed, 10 insertions(+), 8 deletions(-)
Title: Business Process Analytics in R
Description: Functionalities for process analysis in R. This packages implements an S3-class for event log objects, and related handler functions. Imports related packages for subsetting event data, computation of descriptive statistics, handling of Petri Net objects and visualization of process maps.
Author: Gert Janssenswillen
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between bupaR versions 0.1.0 dated 2017-03-26 and 0.1.1 dated 2017-03-27
DESCRIPTION | 10 ++++----- MD5 | 48 ++++++++++++++++++++++---------------------- R/activities.R | 4 --- R/activity_id.R | 3 -- R/activity_instance_id.R | 4 --- R/bupar.R | 2 - R/case_id.r | 3 -- R/cases.r | 6 ----- R/durations.R | 4 --- R/eventlog.R | 13 +++++++++++ R/resource_id.R | 4 --- R/timestamp.R | 6 ----- R/traces.R | 4 --- R/utils.R | 3 -- man/activities.Rd | 6 ----- man/activity_id.Rd | 4 --- man/activity_instance_id.Rd | 4 --- man/bupaR.Rd | 2 - man/case_id.Rd | 7 ------ man/cases.Rd | 7 ------ man/durations.Rd | 7 ------ man/eventlog.Rd | 15 +++++++++++++ man/resource_id.Rd | 4 --- man/timestamp.Rd | 8 ------- man/traces.Rd | 6 ----- 25 files changed, 65 insertions(+), 119 deletions(-)
Title: Post-Processing of the Markov Chain Simulated by 'ChronoModel',
'Oxcal' or 'BCal'
Description: Provides a list of functions for the statistical analysis of archaeological dates and groups of dates. It is based on the post-processing of the Markov Chains whose stationary distribution is the posterior distribution of a series of dates. Such output can be simulated by different applications as for instance 'ChronoModel' (see <http://www.chronomodel.fr>), 'Oxcal' (see <https://c14.arch.ox.ac.uk/oxcal.html>) or 'BCal' (see http://bcal.shef.ac.uk/). The only requirement is to have a csv file containing a sample from the posterior distribution.
Author: Anne Philippe [aut, cre],
Marie-Anne Vibet [aut],
Thomas S. Dye [ctb]
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between ArchaeoPhases versions 1.0 dated 2017-02-07 and 1.1 dated 2017-03-27
DESCRIPTION | 28 + MD5 | 80 ++-- NAMESPACE | 5 NEWS | 20 + R/prog.R | 753 ++++++++++++++++++++++++++++++------------- build |only data/Fishpond.RData |only data/datalist | 1 inst/doc |only inst/shiny/server.R | 364 +++++++++++++++++--- inst/shiny/ui.R | 184 ++++++++-- man/ArchaeoPhases.Rd |only man/CredibleInterval.Rd | 4 man/DatesHiatus.Rd | 6 man/Events.Rd | 2 man/Fishpond.Rd |only man/ImportCSV.Rd | 22 - man/KADatesChronoModel.Rd | 2 man/KADatesOxcal.Rd | 2 man/KAPhasesChronoModel.Rd | 2 man/MarginalPlot.Rd | 28 - man/MarginalProba.Rd | 6 man/MarginalStatistics.Rd | 5 man/MultiCredibleInterval.Rd | 4 man/MultiDatesPlot.Rd | 14 man/MultiHPD.Rd | 4 man/MultiPhasePlot.Rd | 27 - man/MultiPhaseTimeRange.Rd | 12 man/MultiPhasesGap.Rd | 14 man/MultiPhasesTransition.Rd | 14 man/MultiSuccessionPlot.Rd | 27 - man/PhaseDurationPlot.Rd | 15 man/PhasePlot.Rd | 19 - man/PhaseStatistics.Rd | 7 man/PhaseTimeRange.Rd | 2 man/Phases.Rd | 2 man/PhasesGap.Rd | 6 man/PhasesTransition.Rd | 2 man/SuccessionPlot.Rd | 32 - man/TempoActivityPlot.Rd | 4 man/TempoPlot.Rd | 23 + man/coda.mcmc.Rd | 13 vignettes |only 43 files changed, 1265 insertions(+), 490 deletions(-)
Title: Path Diagrams and Visual Analysis of Various SEM Packages'
Output
Description: Path diagrams and visual analysis of various SEM packages' output.
Author: Sacha Epskamp, with contributions from Simon Stuber
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between semPlot versions 1.0.1 dated 2014-08-15 and 1.1 dated 2017-03-27
DESCRIPTION | 17 ++-- MD5 | 28 +++---- NAMESPACE | 9 ++ NEWS | 7 + R/00classes.R | 6 - R/OpenMx.R | 161 +++++++++++++++++++++++++---------------- R/Pars2Matrix.R | 19 ++-- R/lavaan.R | 18 +++- R/mplus.R | 50 ++++++++++-- R/semPaths.R | 5 - README | 9 -- inst/COPYRIGHTS | 20 ++--- man/semPaths.Rd | 21 +---- man/semPlotModel.Rd | 5 + man/semPlotModel.S4-methods.Rd | 8 +- 15 files changed, 233 insertions(+), 150 deletions(-)
Title: The Phylogenetic Ornstein-Uhlenbeck Mixed Model
Description: The Phylogenetic Ornstein-Uhlenbeck Mixed Model (POUMM) allows to
estimate the phylogenetic heritability of continuous traits, to test
hypotheses of neutral evolution versus stabilizing selection, to quantify
the strength of stabilizing selection, to estimate measurement error and to
make predictions about the evolution of a phenotype and phenotypic variation
in a population. The package implements combined maximum likelihood and
Bayesian inference of the univariate Phylogenetic Ornstein-Uhlenbeck Mixed
Model, fast POUMM likelihood calculation, maximum likelihood inference of
the genotypic values at the tips, functions for summarizing and plotting
traces and posterior samples, functions for simulation of a univariate
continuous trait evolution along a phylogenetic tree. A quick example on
using the POUMM package can be found in the README. More elaborate
examples and use-cases are provided in the vignette
"A User Guide to The POUMM R-package".
Author: Venelin Mitov [aut, cre, cph]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between POUMM versions 1.2.1 dated 2017-03-12 and 1.2.2 dated 2017-03-27
DESCRIPTION | 32 +++-- MD5 | 23 ++- NAMESPACE | 6 + R/summaryPOUMM.R | 269 +++++++++++++++++++++++++++++++++++++++++---- README.md | 12 ++ inst/REFERENCES.bib | 7 + inst/doc/UserGuide.R | 17 +- inst/doc/UserGuide.Rmd | 17 +- inst/doc/UserGuide.html | 32 +++-- man/plot.summary.POUMM.Rd | 58 +++++++-- src/Integrator.cpp | 3 vignettes/REFERENCES-R.bib |only vignettes/UserGuide.Rmd | 17 +- 13 files changed, 399 insertions(+), 94 deletions(-)
Title: Nanosecond-Resolution Time for R
Description: Full 64-bit resolution date and time support with resolution up
to nanosecond granularity is provided, with easy transition to and from the
standard 'POSIXct' type.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.1.1 dated 2017-02-04 and 0.1.2 dated 2017-03-27
ChangeLog | 12 ++++++++++++ DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 3 ++- R/nanotime.R | 17 ++++++++++++++--- build/partial.rdb |binary inst/NEWS.Rd | 6 ++++++ man/nanotime.Rd | 12 +++++++++--- 8 files changed, 55 insertions(+), 19 deletions(-)