Title: Regression Models for Interval Censored Data
Description: Regression models for interval censored data. Currently supports Cox-PH and proportional odds models. Allows for both semi and fully parametric models. Includes functions for easy visual diagnostics of model fits. Includes functions for fitting both the univariate and bivariate NPMLE.
Author: Clifford Anderson-Bergman; the Eigen team for Eigen library included; uses Maarloes Maathius's HeightMap algorithm (MLEcens::reduc)
Maintainer: Clifford Anderson-Bergman <pistacliffcho@gmail.com>
Diff between icenReg versions 1.2.7 dated 2015-07-20 and 1.2.8 dated 2015-10-27
icenReg-1.2.7/icenReg/src/icenReg_files/pavaAlgorithm.cpp |only icenReg-1.2.8/icenReg/DESCRIPTION | 17 icenReg-1.2.8/icenReg/MD5 | 45 icenReg-1.2.8/icenReg/NAMESPACE | 10 icenReg-1.2.8/icenReg/NEWS | 11 icenReg-1.2.8/icenReg/R/Utilities.R | 126 - icenReg-1.2.8/icenReg/R/optCliq.R |only icenReg-1.2.8/icenReg/R/referenceClasses.R |only icenReg-1.2.8/icenReg/R/user_functions.R | 85 - icenReg-1.2.8/icenReg/man/ICNPMLE.Rd |only icenReg-1.2.8/icenReg/man/diag_baseline.Rd | 7 icenReg-1.2.8/icenReg/man/diag_covar.Rd | 4 icenReg-1.2.8/icenReg/man/essIncData.Rd | 18 icenReg-1.2.8/icenReg/man/ic_par.Rd | 6 icenReg-1.2.8/icenReg/man/ic_sp.Rd | 29 icenReg-1.2.8/icenReg/man/optCliq.Rd |only icenReg-1.2.8/icenReg/man/simBVCen.Rd |only icenReg-1.2.8/icenReg/man/simIC_weib.Rd | 4 icenReg-1.2.8/icenReg/src/icenReg.cpp | 4 icenReg-1.2.8/icenReg/src/icenReg_files/basicUtilities.cpp | 269 +++ icenReg-1.2.8/icenReg/src/icenReg_files/bivariateNPMLE.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/bivariateNPMLE.h |only icenReg-1.2.8/icenReg/src/icenReg_files/experimentalCode.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/ic_par.cpp | 174 ++ icenReg-1.2.8/icenReg/src/icenReg_files/ic_par.h | 52 icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_ch.cpp | 702 +++------- icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_ch.h | 145 +- icenReg-1.2.8/icenReg/src/icenReg_files/ic_sp_gradDescent.cpp |only icenReg-1.2.8/icenReg/src/icenReg_files/myPAVAalgorithm.cpp |only 29 files changed, 1008 insertions(+), 700 deletions(-)
Title: CLUster Evaluation (CLUE)
Description: CLUE is an R package for identifying optimal number of clusters in a given time-course dataset clustered by cmeans or kmeans algorithms.
Author: Pengyi Yang & Raja Jothi
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between ClueR versions 1.0 dated 2015-02-04 and 1.1 dated 2015-10-27
DESCRIPTION | 8 +-- MD5 | 22 ++++----- NAMESPACE | 7 ++- R/runClue.R | 12 +++-- README.md | 113 ++++++++++++++++++++++++++++++++++++++++++++++++- man/ClueR-package.Rd | 8 ++- man/clustEnrichment.Rd | 2 man/clustOptimal.Rd | 2 man/enrichmentTest.Rd | 2 man/fuzzPlot.Rd | 2 man/runClue.Rd | 6 +- man/temporalSimu.Rd | 2 12 files changed, 152 insertions(+), 34 deletions(-)
Title: Bayesian Model Averaging using Bayesian Adaptive Sampling
Description: Package for Bayesian Model Averaging in linear models and
generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
Liang et al hyper-g priors (JASA 2008) or mixtures of
g-priors in GLMS of Li and Clyde 2015. Other model
selection criteria include AIC and BIC. Sampling
probabilities may be updated based on the sampled models
using Sampling w/out Replacement or an MCMC algorithm
samples models using the BAS tree structure as an efficient
hash table. Allows uniform or beta-binomial prior distributions on
models, and may force variables to always be included.
Author: Merlise Clyde [aut, cre, cph],
Michael Littman [ctb],
Quanli Wang [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb]
Maintainer: Merlise Clyde <clyde@stat.duke.edu>
Diff between BAS versions 1.0.5 dated 2015-09-10 and 1.0.6 dated 2015-10-27
BAS-1.0.5/BAS/R/coefpriors.R |only BAS-1.0.6/BAS/CHANGELOG | 11 + BAS-1.0.6/BAS/DESCRIPTION | 8 - BAS-1.0.6/BAS/INDEX |only BAS-1.0.6/BAS/MD5 | 70 ++++++---- BAS-1.0.6/BAS/NAMESPACE | 5 BAS-1.0.6/BAS/R/bas.R | 17 +- BAS-1.0.6/BAS/R/bas.gglm.R | 64 ++++----- BAS-1.0.6/BAS/R/betapriors.R |only BAS-1.0.6/BAS/R/coefficients.R | 4 BAS-1.0.6/BAS/R/predict.bma.R | 58 ++++++-- BAS-1.0.6/BAS/R/summary.bma.R | 5 BAS-1.0.6/BAS/man/EB.Rd |only BAS-1.0.6/BAS/man/TG-priors.Rd |only BAS-1.0.6/BAS/man/bas.Rd | 12 - BAS-1.0.6/BAS/man/bas.glm.Rd | 73 +++++++---- BAS-1.0.6/BAS/man/beta.prime.Rd |only BAS-1.0.6/BAS/man/cchpriors.Rd |only BAS-1.0.6/BAS/man/coefpriors.Rd | 2 BAS-1.0.6/BAS/man/hyper-g.Rd |only BAS-1.0.6/BAS/man/predict.basglm.Rd |only BAS-1.0.6/BAS/man/predict.bma.Rd | 28 ++-- BAS-1.0.6/BAS/man/robust.Rd |only BAS-1.0.6/BAS/man/summary.bma.Rd | 16 +- BAS-1.0.6/BAS/src/amcmc.c | 4 BAS-1.0.6/BAS/src/bas-glm.h | 4 BAS-1.0.6/BAS/src/bayesreg.c | 6 BAS-1.0.6/BAS/src/betapriorfamily.c |only BAS-1.0.6/BAS/src/betapriorfamily.h |only BAS-1.0.6/BAS/src/deterministic.c | 4 BAS-1.0.6/BAS/src/glm_deterministic.c | 21 +-- BAS-1.0.6/BAS/src/glm_lpy.c | 224 ++++++++++++++++++---------------- BAS-1.0.6/BAS/src/glm_mcmc.c | 71 ++-------- BAS-1.0.6/BAS/src/glm_mcmcbas.c | 30 ++-- BAS-1.0.6/BAS/src/glm_sampleworep.c | 44 ++++-- BAS-1.0.6/BAS/src/hypergeometric1F1.c | 69 ++++++---- BAS-1.0.6/BAS/src/mcmc.c | 4 BAS-1.0.6/BAS/src/mcmc_new.c | 4 BAS-1.0.6/BAS/src/mcmcbas.c | 4 BAS-1.0.6/BAS/src/posisearch.c | 4 BAS-1.0.6/BAS/src/sampleworep.c | 8 - BAS-1.0.6/BAS/src/sampleworep_new.c | 8 - 42 files changed, 490 insertions(+), 392 deletions(-)
Title: Helper Functions for Structural Equation Modelling in OpenMx
Description: Helper functions for making, running, and reporting SEM
and twin models in OpenMx.
If you are just starting, try typing ?umx.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 0.50 dated 2015-08-27 and 1.0.0 dated 2015-10-27
umx-0.50/umx/man/coef.MxModel.Rd |only umx-1.0.0/umx/DESCRIPTION | 13 umx-1.0.0/umx/INSTALL | 16 umx-1.0.0/umx/MD5 | 257 +++--- umx-1.0.0/umx/NAMESPACE | 28 umx-1.0.0/umx/NEWS | 15 umx-1.0.0/umx/R/build_run_modify.r | 956 +++++++++++++++++++---- umx-1.0.0/umx/R/deprecated.r | 44 - umx-1.0.0/umx/R/fit_and_reporting.r | 778 +++++++++++++++++- umx-1.0.0/umx/R/misc_and_utility.r | 223 ++++- umx-1.0.0/umx/R/xmu.r | 58 - umx-1.0.0/umx/README.md | 15 umx-1.0.0/umx/man/RMSEA.MxModel.Rd | 3 umx-1.0.0/umx/man/RMSEA.Rd | 1 umx-1.0.0/umx/man/RMSEA.summary.mxmodel.Rd | 3 umx-1.0.0/umx/man/confint.MxModel.Rd | 1 umx-1.0.0/umx/man/extractAIC.MxModel.Rd | 1 umx-1.0.0/umx/man/logLik.Rd | 1 umx-1.0.0/umx/man/plot.MxModel.Rd | 14 umx-1.0.0/umx/man/qm.Rd | 9 umx-1.0.0/umx/man/residuals.MxModel.Rd | 1 umx-1.0.0/umx/man/umx-deprecated.Rd | 30 umx-1.0.0/umx/man/umx.Rd | 58 - umx-1.0.0/umx/man/umxACE.Rd | 6 umx-1.0.0/umx/man/umxAdd1.Rd | 3 umx-1.0.0/umx/man/umxCI.Rd | 1 umx-1.0.0/umx/man/umxCI_boot.Rd | 1 umx-1.0.0/umx/man/umxCP.Rd |only umx-1.0.0/umx/man/umxCompare.Rd | 1 umx-1.0.0/umx/man/umxCovData.Rd | 13 umx-1.0.0/umx/man/umxDiagnose.Rd | 12 umx-1.0.0/umx/man/umxDrop1.Rd | 3 umx-1.0.0/umx/man/umxEFA.Rd | 3 umx-1.0.0/umx/man/umxEquate.Rd | 3 umx-1.0.0/umx/man/umxEval.Rd | 14 umx-1.0.0/umx/man/umxExpCov.Rd | 1 umx-1.0.0/umx/man/umxExpMeans.Rd | 1 umx-1.0.0/umx/man/umxFitIndices.Rd | 1 umx-1.0.0/umx/man/umxFixAll.Rd | 3 umx-1.0.0/umx/man/umxGetParameters.Rd | 3 umx-1.0.0/umx/man/umxGxE.Rd |only umx-1.0.0/umx/man/umxHetCor.Rd | 3 umx-1.0.0/umx/man/umxIP.Rd |only umx-1.0.0/umx/man/umxJiggle.Rd | 14 umx-1.0.0/umx/man/umxLabel.Rd | 4 umx-1.0.0/umx/man/umxLatent.Rd | 4 umx-1.0.0/umx/man/umxMI.Rd | 3 umx-1.0.0/umx/man/umxPadAndPruneForDefVars.Rd | 4 umx-1.0.0/umx/man/umxPath.Rd | 91 +- umx-1.0.0/umx/man/umxPlotACE.Rd | 1 umx-1.0.0/umx/man/umxPlotCP.Rd |only umx-1.0.0/umx/man/umxPlotGxE.Rd |only umx-1.0.0/umx/man/umxPlotIP.Rd |only umx-1.0.0/umx/man/umxRAM.Rd | 30 umx-1.0.0/umx/man/umxReRun.Rd | 4 umx-1.0.0/umx/man/umxReduce.Rd | 5 umx-1.0.0/umx/man/umxRun.Rd | 4 umx-1.0.0/umx/man/umxSetParameters.Rd | 3 umx-1.0.0/umx/man/umxStandardizeACE.Rd | 3 umx-1.0.0/umx/man/umxStandardizeModel.Rd | 1 umx-1.0.0/umx/man/umxSummary.MxModel.Rd | 1 umx-1.0.0/umx/man/umxSummary.Rd | 14 umx-1.0.0/umx/man/umxSummaryCP.Rd |only umx-1.0.0/umx/man/umxSummaryGxE.Rd |only umx-1.0.0/umx/man/umxSummaryIP.Rd |only umx-1.0.0/umx/man/umxThresholdMatrix.Rd | 4 umx-1.0.0/umx/man/umxUnexplainedCausalNexus.Rd | 3 umx-1.0.0/umx/man/umxValues.Rd | 4 umx-1.0.0/umx/man/umx_APA_CI.Rd | 9 umx-1.0.0/umx/man/umx_APA_pval.Rd | 25 umx-1.0.0/umx/man/umx_RAM_ordinal_objective.Rd | 4 umx-1.0.0/umx/man/umx_add_variances.Rd | 16 umx-1.0.0/umx/man/umx_aggregate.Rd | 9 umx-1.0.0/umx/man/umx_apply.Rd | 14 umx-1.0.0/umx/man/umx_as_numeric.Rd | 3 umx-1.0.0/umx/man/umx_check.Rd | 14 umx-1.0.0/umx/man/umx_check_OS.Rd | 32 umx-1.0.0/umx/man/umx_check_model.Rd | 14 umx-1.0.0/umx/man/umx_check_multi_core.Rd | 14 umx-1.0.0/umx/man/umx_cont_2_ordinal.Rd | 3 umx-1.0.0/umx/man/umx_cov2raw.Rd | 3 umx-1.0.0/umx/man/umx_cov_diag.Rd | 4 umx-1.0.0/umx/man/umx_default_option.Rd | 15 umx-1.0.0/umx/man/umx_drop_ok.Rd | 1 umx-1.0.0/umx/man/umx_explode.Rd | 39 umx-1.0.0/umx/man/umx_find_object.Rd | 9 umx-1.0.0/umx/man/umx_fix_first_loadings.Rd | 4 umx-1.0.0/umx/man/umx_fix_latents.Rd | 4 umx-1.0.0/umx/man/umx_get_CI_as_APA_string.Rd | 14 umx-1.0.0/umx/man/umx_get_bracket_addresses.Rd | 14 umx-1.0.0/umx/man/umx_get_checkpoint.Rd | 18 umx-1.0.0/umx/man/umx_get_cores.Rd | 14 umx-1.0.0/umx/man/umx_get_optimizer.Rd | 14 umx-1.0.0/umx/man/umx_grep.Rd | 7 umx-1.0.0/umx/man/umx_has_CIs.Rd | 14 umx-1.0.0/umx/man/umx_has_been_run.Rd | 14 umx-1.0.0/umx/man/umx_has_means.Rd | 14 umx-1.0.0/umx/man/umx_has_square_brackets.Rd | 14 umx-1.0.0/umx/man/umx_is_MxMatrix.Rd | 14 umx-1.0.0/umx/man/umx_is_MxModel.Rd | 14 umx-1.0.0/umx/man/umx_is_RAM.Rd | 14 umx-1.0.0/umx/man/umx_is_cov.Rd | 14 umx-1.0.0/umx/man/umx_is_endogenous.Rd | 14 umx-1.0.0/umx/man/umx_is_exogenous.Rd | 14 umx-1.0.0/umx/man/umx_is_ordered.Rd | 14 umx-1.0.0/umx/man/umx_lower2full.Rd | 26 umx-1.0.0/umx/man/umx_make_bin_cont_pair_data.Rd | 3 umx-1.0.0/umx/man/umx_merge_CIs.Rd | 3 umx-1.0.0/umx/man/umx_msg.Rd | 40 umx-1.0.0/umx/man/umx_names.Rd | 40 umx-1.0.0/umx/man/umx_object_as_str.Rd | 11 umx-1.0.0/umx/man/umx_paste_names.Rd | 38 umx-1.0.0/umx/man/umx_pb_note.Rd | 7 umx-1.0.0/umx/man/umx_print.Rd | 49 - umx-1.0.0/umx/man/umx_read_lower.Rd | 3 umx-1.0.0/umx/man/umx_rename.Rd | 44 - umx-1.0.0/umx/man/umx_reorder.Rd | 12 umx-1.0.0/umx/man/umx_residualize.Rd | 3 umx-1.0.0/umx/man/umx_rot.Rd | 44 - umx-1.0.0/umx/man/umx_round.Rd | 3 umx-1.0.0/umx/man/umx_scale.Rd | 3 umx-1.0.0/umx/man/umx_scale_wide_twin_data.Rd | 3 umx-1.0.0/umx/man/umx_set_checkpoint.Rd | 14 umx-1.0.0/umx/man/umx_set_cores.Rd | 15 umx-1.0.0/umx/man/umx_set_optimizer.Rd | 14 umx-1.0.0/umx/man/umx_show.Rd | 13 umx-1.0.0/umx/man/umx_standardize_IP.Rd |only umx-1.0.0/umx/man/umx_string_to_algebra.Rd | 15 umx-1.0.0/umx/man/umx_swap_a_block.Rd | 3 umx-1.0.0/umx/man/umx_time.Rd | 9 umx-1.0.0/umx/man/umx_trim.Rd | 39 umx-1.0.0/umx/man/xmuLabel_Matrix.Rd | 4 umx-1.0.0/umx/man/xmu_dot_make_paths.Rd | 2 umx-1.0.0/umx/man/xmu_dot_make_residuals.Rd | 13 umx-1.0.0/umx/tests/testthat |only umx-1.0.0/umx/tests/testthat.R |only 136 files changed, 2508 insertions(+), 1230 deletions(-)
Title: Computations over Distributed Data without Aggregation
Description: Implementing algorithms and fitting models when sites (possibly remote) share
computation summaries rather than actual data over HTTP with a master R process (using
'opencpu', for example). A stratified Cox model and a singular value decomposition are
provided. The former makes direct use of code from the R 'survival' package. (That is,
the underlying Cox model code is derived from that in the R 'survival' package.)
Sites may provide data via several means: CSV files, Redcap API, etc. An extensible
design allows for new methods to be added in the future. Web applications are provided
(via 'shiny') for the implemented methods to help in designing and deploying the
computations.
Author: Balasubramanian Narasimhan [aut, cre],
Marina Bendersky [aut],
Sam Gross [aut],
Terry M. Therneau [ctb],
Thomas Lumley [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.Stanford.EDU>
Diff between distcomp versions 0.25.3 dated 2015-08-01 and 0.25.4 dated 2015-10-27
distcomp-0.25.3/distcomp/inst/ex/STCoxDefn.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxDefn.rds |only distcomp-0.25.3/distcomp/inst/ex/STCoxMasterSetup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxSite1Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxSite2Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/STCoxTest.R |only distcomp-0.25.3/distcomp/inst/ex/STCoxTest.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDDefn.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDDefn.rds |only distcomp-0.25.3/distcomp/inst/ex/SVDMasterSetup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite1Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite2Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDSite3Setup.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.R |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.Rout |only distcomp-0.25.3/distcomp/inst/ex/SVDTest.rds |only distcomp-0.25.3/distcomp/inst/ex/svd-example-full-new.Rout |only distcomp-0.25.3/distcomp/inst/ex/svd-example-full.Rout |only distcomp-0.25.3/distcomp/inst/webApps/setupSlaveApp |only distcomp-0.25.3/distcomp/man/coxMaster.Rd |only distcomp-0.25.3/distcomp/man/coxSlave.Rd |only distcomp-0.25.3/distcomp/man/makeSlave.Rd |only distcomp-0.25.3/distcomp/man/setupSlave.Rd |only distcomp-0.25.3/distcomp/man/svdMaster.Rd |only distcomp-0.25.3/distcomp/man/svdSlave.Rd |only distcomp-0.25.4/distcomp/DESCRIPTION | 6 distcomp-0.25.4/distcomp/MD5 | 97 distcomp-0.25.4/distcomp/NAMESPACE | 8 distcomp-0.25.4/distcomp/R/coxstuff.R | 16 distcomp-0.25.4/distcomp/R/distcomp.R | 72 distcomp-0.25.4/distcomp/R/svdstuff.R | 25 distcomp-0.25.4/distcomp/README.md | 15 distcomp-0.25.4/distcomp/inst/doc/examples.html | 60 distcomp-0.25.4/distcomp/inst/doc/examples.pdf |binary distcomp-0.25.4/distcomp/inst/doc_src/examples.Rmd | 10 distcomp-0.25.4/distcomp/inst/doc_src/examples.md | 64 distcomp-0.25.4/distcomp/inst/ex/README.Rmd | 70 distcomp-0.25.4/distcomp/inst/ex/README.html | 82 distcomp-0.25.4/distcomp/inst/ex/README.md | 70 distcomp-0.25.4/distcomp/inst/ex/Rprofile |only distcomp-0.25.4/distcomp/inst/ex/STCoxMaster.R |only distcomp-0.25.4/distcomp/inst/ex/STCoxMaster.Rout |only distcomp-0.25.4/distcomp/inst/ex/STCoxSetup.Rout |only distcomp-0.25.4/distcomp/inst/ex/STCoxTest.rds |only distcomp-0.25.4/distcomp/inst/ex/SVDMaster.R |only distcomp-0.25.4/distcomp/inst/ex/SVDMaster.Rout |only distcomp-0.25.4/distcomp/inst/ex/SVDSetup.Rout |only distcomp-0.25.4/distcomp/inst/ex/SVDTestDefn.rds |only distcomp-0.25.4/distcomp/inst/ex/svd-example.R | 3 distcomp-0.25.4/distcomp/inst/ex/svd-example.Rout | 5051 +++++++++- distcomp-0.25.4/distcomp/inst/ex/uis-example.R | 2 distcomp-0.25.4/distcomp/inst/ex/uis-example.Rout | 38 distcomp-0.25.4/distcomp/inst/webApps/definitionApp/defineNewCoxModel/server.R | 4 distcomp-0.25.4/distcomp/inst/webApps/setupWorkerApp |only distcomp-0.25.4/distcomp/man/CoxMaster.Rd |only distcomp-0.25.4/distcomp/man/CoxWorker.Rd |only distcomp-0.25.4/distcomp/man/SVDMaster.Rd |only distcomp-0.25.4/distcomp/man/SVDWorker.Rd |only distcomp-0.25.4/distcomp/man/availableComputations.Rd | 8 distcomp-0.25.4/distcomp/man/distcomp-internal.Rd | 12 distcomp-0.25.4/distcomp/man/makeWorker.Rd |only distcomp-0.25.4/distcomp/man/runDistcompApp.Rd | 8 distcomp-0.25.4/distcomp/man/saveNewComputation.Rd | 2 distcomp-0.25.4/distcomp/man/setupWorker.Rd |only distcomp-0.25.4/distcomp/man/writeCode.Rd | 2 65 files changed, 5380 insertions(+), 345 deletions(-)
Title: Continuous Time Autoregressive Models
Description: Functions to Fit Continuous Time Autoregressive Models with the Kalman Filter.
Author: Fortran original by G. Tunnicliffe-Wilson and Zhu Wang, R port by Zhu Wang with contribution from John Nash, Netlib and NAG authors
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between cts versions 1.0-19 dated 2014-02-26 and 1.0-20 dated 2015-10-27
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 7 ++++++- build/vignette.rds |binary inst/doc/kf.pdf |binary 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Buckley-James Regression for Survival Data with High-Dimensional
Covariates
Description: Buckley-James regression for right-censoring survival data with high-dimensional covariates. Including L_2 boosting with componentwise linear least squares, componentwise smoothing splines, P-splines, regression trees and boosted MARS. Other high-dimensional tools include elastic net and MARS.
Author: Zhu Wang and others (see COPYRIGHTS)
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between bujar versions 0.1-4 dated 2014-06-24 and 0.1-5 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- NAMESPACE | 7 +++++++ NEWS | 5 +++++ 4 files changed, 20 insertions(+), 8 deletions(-)
Title: Copy-Number Analysis of Large Microarray Data Sets
Description: Methods for analyzing DNA copy-number data. Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies. It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.
Author: Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between aroma.cn versions 1.6.0 dated 2015-02-24 and 1.6.1 dated 2015-10-27
aroma.cn-1.6.0/aroma.cn/R/makeSmoothSplinePredict.DEPRECATED.R |only aroma.cn-1.6.1/aroma.cn/DESCRIPTION | 21 +- aroma.cn-1.6.1/aroma.cn/MD5 | 16 - aroma.cn-1.6.1/aroma.cn/NAMESPACE | 14 + aroma.cn-1.6.1/aroma.cn/NEWS | 11 + aroma.cn-1.6.1/aroma.cn/R/021.dynamic_imports.R | 100 +++++----- aroma.cn-1.6.1/aroma.cn/R/999.DEPRECATED.R |only aroma.cn-1.6.1/aroma.cn/R/CartesianSnpData.R | 4 aroma.cn-1.6.1/aroma.cn/R/PeaksAndValleys.EXTS.R | 12 - aroma.cn-1.6.1/aroma.cn/man/MultiSourceCopyNumberNormalization.Rd | 6 10 files changed, 96 insertions(+), 88 deletions(-)
Title: Utility Functions for Web Applications
Description: Utility functions for developing web applications. Includes parsers
for application/x-www-form-urlencoded as well as multipart/form-data
and examples of using the parser with either httpuv or rhttpd.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between webutils versions 0.3 dated 2015-01-24 and 0.4 dated 2015-10-27
DESCRIPTION | 9 ++++----- MD5 | 16 ++++++++-------- NAMESPACE | 8 +++++++- R/demo_httpuv.R | 2 ++ man/demo_httpuv.Rd | 3 ++- man/demo_rhttpd.Rd | 3 ++- man/parse_http.Rd | 3 ++- man/parse_multipart.Rd | 3 ++- man/parse_query.Rd | 3 ++- 9 files changed, 31 insertions(+), 19 deletions(-)
Title: Split-Population Duration (Cure) Regression
Description: Functions for estimating split-duration regression models and various associated generic function methods.
Author: Andreas Beger [aut, cre],
Daina Chiba [aut],
Daniel Hill [aut],
Nils Metternich [aut],
Shahryar Minhas [aut],
Michael Ward [cph]
Maintainer: Andreas Beger <adbeger@gmail.com>
Diff between spduration versions 0.13.1 dated 2015-07-09 and 0.14.0 dated 2015-10-27
spduration-0.13.1/spduration/R/attemptDate.R |only spduration-0.13.1/spduration/R/forecast.default.R |only spduration-0.13.1/spduration/R/forecast.spdur.R |only spduration-0.13.1/spduration/R/model.coups.R |only spduration-0.13.1/spduration/R/plot_hazard.r |only spduration-0.13.1/spduration/man/attemptDate.Rd |only spduration-0.13.1/spduration/man/loglog_hazard.Rd |only spduration-0.13.1/spduration/man/weibull_hazard.Rd |only spduration-0.14.0/spduration/DESCRIPTION | 11 spduration-0.14.0/spduration/MD5 | 93 +++--- spduration-0.14.0/spduration/NAMESPACE | 4 spduration-0.14.0/spduration/R/RcppExports.R | 8 spduration-0.14.0/spduration/R/add_duration.R | 89 ------ spduration-0.14.0/spduration/R/attempt_date.R |only spduration-0.14.0/spduration/R/data-docs.R |only spduration-0.14.0/spduration/R/forecast.R | 193 +++++++++++++ spduration-0.14.0/spduration/R/panel_lag.R | 25 - spduration-0.14.0/spduration/R/plot.spdur.R | 264 +++++++++++++------ spduration-0.14.0/spduration/R/predict.spdur.R | 28 -- spduration-0.14.0/spduration/R/spdur.R | 7 spduration-0.14.0/spduration/R/spduration-package.R | 38 -- spduration-0.14.0/spduration/R/sploglog.R | 4 spduration-0.14.0/spduration/R/spweibull.R | 4 spduration-0.14.0/spduration/R/summary.spdur.R | 9 spduration-0.14.0/spduration/README.md | 41 -- spduration-0.14.0/spduration/data/bscoup.rda |only spduration-0.14.0/spduration/man/add_duration.Rd | 3 spduration-0.14.0/spduration/man/attempt_date.Rd |only spduration-0.14.0/spduration/man/bscoup.Rd |only spduration-0.14.0/spduration/man/coups.Rd | 2 spduration-0.14.0/spduration/man/forecast.Rd | 2 spduration-0.14.0/spduration/man/forecast.default.Rd | 2 spduration-0.14.0/spduration/man/forecast.spdur.Rd | 2 spduration-0.14.0/spduration/man/hazard.Rd | 7 spduration-0.14.0/spduration/man/loglog.Rd | 1 spduration-0.14.0/spduration/man/loglog_lnl.Rd | 1 spduration-0.14.0/spduration/man/model.coups.Rd | 2 spduration-0.14.0/spduration/man/plot.spdur.Rd | 21 - spduration-0.14.0/spduration/man/plot_hazard.Rd |only spduration-0.14.0/spduration/man/plot_hazard1.Rd | 16 - spduration-0.14.0/spduration/man/plot_hazard2.Rd | 20 - spduration-0.14.0/spduration/man/spdur.Rd | 2 spduration-0.14.0/spduration/man/sploglog.Rd | 1 spduration-0.14.0/spduration/man/sploglog_lnl.Rd | 1 spduration-0.14.0/spduration/man/spweib_lnl.Rd | 1 spduration-0.14.0/spduration/man/spweibull.Rd | 1 spduration-0.14.0/spduration/man/weib_lnl.Rd | 1 spduration-0.14.0/spduration/man/weibull.Rd | 1 spduration-0.14.0/spduration/src/loglog_lnl.cpp | 3 spduration-0.14.0/spduration/src/sploglog_lnl.cpp | 2 spduration-0.14.0/spduration/src/spweib_lnl.cpp | 2 spduration-0.14.0/spduration/src/weib_lnl.cpp | 2 spduration-0.14.0/spduration/tests |only 53 files changed, 540 insertions(+), 374 deletions(-)
Title: Database Interface and 'MySQL' Driver for R
Description: Implements 'DBI' Interface to 'MySQL' and 'MariaDB' Databases.
Author: Jeroen Ooms [aut, cre],
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
RStudio [cph]
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between RMySQL versions 0.10.6 dated 2015-09-05 and 0.10.7 dated 2015-10-27
DESCRIPTION | 12 ++++++------ MD5 | 4 ++-- configure | 17 +++++++++-------- 3 files changed, 17 insertions(+), 16 deletions(-)
Title: Regularization Paths for SCAD and MCP Penalized Regression
Models
Description: Efficient algorithms for fitting regularization paths for linear or logistic regression models penalized by MCP or SCAD, with optional additional L2 penalty.
Author: Patrick Breheny [aut,cre], Sangin Lee [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between ncvreg versions 3.4-0 dated 2015-05-04 and 3.5-0 dated 2015-10-27
ncvreg-3.4-0/ncvreg/inst/tests/test.R |only ncvreg-3.5-0/ncvreg/DESCRIPTION | 8 +- ncvreg-3.5-0/ncvreg/MD5 | 43 +++++------ ncvreg-3.5-0/ncvreg/NAMESPACE | 10 +- ncvreg-3.5-0/ncvreg/NEWS | 19 ++++ ncvreg-3.5-0/ncvreg/R/auc.R |only ncvreg-3.5-0/ncvreg/R/convexMin.R | 23 ++--- ncvreg-3.5-0/ncvreg/R/cv.ncvreg.R | 34 ++++---- ncvreg-3.5-0/ncvreg/R/cv.ncvsurv.R | 116 ++++++++++++++++++------------ ncvreg-3.5-0/ncvreg/R/loss.R | 4 - ncvreg-3.5-0/ncvreg/R/ncvreg.R | 31 ++++---- ncvreg-3.5-0/ncvreg/R/ncvsurv.R | 22 ++--- ncvreg-3.5-0/ncvreg/R/plot.cv.ncvreg.R | 2 ncvreg-3.5-0/ncvreg/R/setupLambda.R | 6 - ncvreg-3.5-0/ncvreg/R/setupLambdaCox.R | 10 +- ncvreg-3.5-0/ncvreg/inst/tests/auc.R |only ncvreg-3.5-0/ncvreg/inst/tests/ncvreg.R |only ncvreg-3.5-0/ncvreg/inst/tests/parallel.R | 34 ++++++++ ncvreg-3.5-0/ncvreg/inst/tests/surv.R | 13 +++ ncvreg-3.5-0/ncvreg/man/auc.Rd |only ncvreg-3.5-0/ncvreg/man/cv.ncvreg.Rd | 14 +++ ncvreg-3.5-0/ncvreg/man/cv.ncvsurv.Rd | 43 ++++++++--- ncvreg-3.5-0/ncvreg/man/ncvreg-package.Rd | 4 - ncvreg-3.5-0/ncvreg/man/ncvreg.Rd | 2 ncvreg-3.5-0/ncvreg/src/cox-dh.c | 41 +++++++--- 25 files changed, 310 insertions(+), 169 deletions(-)
Title: Group Iterative Multiple Model Estimation
Description: Automated identification and estimation of group- and
individual-level relations in time series data from within a structural
equation modeling framework.
Author: Stephanie Lane [aut, cre, trl],
Kathleen Gates [aut],
Peter Molenaar [aut],
Michael Hallquist [ctb],
Hallie Pike [ctb]
Maintainer: Stephanie Lane <slane@unc.edu>
Diff between gimme versions 0.1-5 dated 2015-10-20 and 0.1-6 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/gimme.R | 18 ++++++++++-------- 3 files changed, 17 insertions(+), 15 deletions(-)
Title: Create a Simple Web API for your R Functions
Description: A set of convenience functions to build simple APIs.
Author: Bart Smeets
Maintainer: Bart Smeets <bartsmeets86@gmail.com>
Diff between jug versions 0.1.0 dated 2015-10-27 and 0.1.1 dated 2015-10-27
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- R/middleware_core.R | 6 +++--- R/middleware_error.R | 1 + R/response.R | 4 ++++ build/vignette.rds |binary inst/doc/jug.Rmd | 4 ++-- inst/doc/jug.html | 2 +- man/Error.Rd | 2 +- man/Middleware.Rd | 2 +- man/MiddlewareHandler.Rd | 2 +- man/RawTestRequest.Rd | 2 +- man/Request.Rd | 2 +- man/Response.Rd | 2 +- vignettes/jug.Rmd | 4 ++-- 15 files changed, 36 insertions(+), 31 deletions(-)
Title: Graph Edge Computations for Spatial Point Patterns
Description: Graphs (or networks) and graph component
calculations for spatial locations in *D.
Author: Tuomas Rajala
Maintainer: Tuomas Rajala <tuomas.rajala@iki.fi>
Diff between spatgraphs versions 2.62 dated 2012-09-26 and 3.0 dated 2015-10-27
spatgraphs-2.62/spatgraphs/R/First.R |only spatgraphs-2.62/spatgraphs/R/adjacency.R |only spatgraphs-2.62/spatgraphs/R/class.R |only spatgraphs-2.62/spatgraphs/R/clip.R |only spatgraphs-2.62/spatgraphs/R/clustering.R |only spatgraphs-2.62/spatgraphs/R/edgelengths.R |only spatgraphs-2.62/spatgraphs/R/mstoperations.R |only spatgraphs-2.62/spatgraphs/R/others.R |only spatgraphs-2.62/spatgraphs/R/plot.R |only spatgraphs-2.62/spatgraphs/R/runif3d.R |only spatgraphs-2.62/spatgraphs/R/spectral.R |only spatgraphs-2.62/spatgraphs/R/summary.R |only spatgraphs-2.62/spatgraphs/R/weights.R |only spatgraphs-2.62/spatgraphs/ToAdd.TXT0 |only spatgraphs-2.62/spatgraphs/change.log |only spatgraphs-2.62/spatgraphs/man/spatgraphs-clip.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-cut.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-legacy.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-mailer.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-other.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-package.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-plot.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-print.sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-runif3d.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg2dxf.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sg2igraph.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-sgc.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-shake.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-shortestPath.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spatcluster.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spatgraph.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-spectral.Rd |only spatgraphs-2.62/spatgraphs/man/spatgraphs-weight.Rd |only spatgraphs-2.62/spatgraphs/src/Point.cpp |only spatgraphs-2.62/spatgraphs/src/Point.h |only spatgraphs-2.62/spatgraphs/src/Rextras.cpp |only spatgraphs-2.62/spatgraphs/src/Rextras.h |only spatgraphs-2.62/spatgraphs/src/clustering.cpp |only spatgraphs-2.62/spatgraphs/src/cutprune.cpp |only spatgraphs-2.62/spatgraphs/src/dists.cpp |only spatgraphs-2.62/spatgraphs/src/dists.h |only spatgraphs-2.62/spatgraphs/src/rgraph.cpp |only spatgraphs-3.0/spatgraphs/DESCRIPTION | 22 spatgraphs-3.0/spatgraphs/MD5 | 119 - spatgraphs-3.0/spatgraphs/NAMESPACE | 57 spatgraphs-3.0/spatgraphs/NEWS |only spatgraphs-3.0/spatgraphs/R/RcppExports.R |only spatgraphs-3.0/spatgraphs/R/adjacency_matrix.R |only spatgraphs-3.0/spatgraphs/R/class_sg.R |only spatgraphs-3.0/spatgraphs/R/class_sgc.R |only spatgraphs-3.0/spatgraphs/R/constants.R |only spatgraphs-3.0/spatgraphs/R/cut_sg.R |only spatgraphs-3.0/spatgraphs/R/edgeLengths.R |only spatgraphs-3.0/spatgraphs/R/parse_input_coordinates.R |only spatgraphs-3.0/spatgraphs/R/plot_sg.R |only spatgraphs-3.0/spatgraphs/R/plot_sgc.R |only spatgraphs-3.0/spatgraphs/R/prune_sg.R |only spatgraphs-3.0/spatgraphs/R/set_weights.R |only spatgraphs-3.0/spatgraphs/R/sg2dxf.R | 100 - spatgraphs-3.0/spatgraphs/R/sg2igraph.R | 96 - spatgraphs-3.0/spatgraphs/R/shortestPath.R | 157 +- spatgraphs-3.0/spatgraphs/R/spatcluster.R |only spatgraphs-3.0/spatgraphs/R/spatgraph.R | 245 --- spatgraphs-3.0/spatgraphs/R/spectral_sg.R |only spatgraphs-3.0/spatgraphs/R/verify_parameters.R |only spatgraphs-3.0/spatgraphs/man/SG_GRAPH_PARAMETERS.Rd |only spatgraphs-3.0/spatgraphs/man/adj2sg.Rd |only spatgraphs-3.0/spatgraphs/man/as.sg.Rd |only spatgraphs-3.0/spatgraphs/man/as.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/as.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/cut.sg.Rd |only spatgraphs-3.0/spatgraphs/man/edgeLengths.Rd |only spatgraphs-3.0/spatgraphs/man/is_sg.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sg.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/plot.sgspectral.Rd |only spatgraphs-3.0/spatgraphs/man/plot3.sg.Rd |only spatgraphs-3.0/spatgraphs/man/print.sg.Rd |only spatgraphs-3.0/spatgraphs/man/print.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/print.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/prune.sg.Rd |only spatgraphs-3.0/spatgraphs/man/sg2adj.Rd |only spatgraphs-3.0/spatgraphs/man/sg2dxf.Rd |only spatgraphs-3.0/spatgraphs/man/sg2igraph.Rd |only spatgraphs-3.0/spatgraphs/man/sg2sparse.Rd |only spatgraphs-3.0/spatgraphs/man/sg2sym.Rd |only spatgraphs-3.0/spatgraphs/man/sg2wadj.Rd |only spatgraphs-3.0/spatgraphs/man/sg_parse_coordinates.Rd |only spatgraphs-3.0/spatgraphs/man/sg_verify_parameters.Rd |only spatgraphs-3.0/spatgraphs/man/shortestPath.Rd |only spatgraphs-3.0/spatgraphs/man/sparse2sg.Rd |only spatgraphs-3.0/spatgraphs/man/spatcluster.Rd |only spatgraphs-3.0/spatgraphs/man/spatgraph.Rd |only spatgraphs-3.0/spatgraphs/man/spectral.sg.Rd |only spatgraphs-3.0/spatgraphs/man/summary.sg.Rd |only spatgraphs-3.0/spatgraphs/man/summary.sgc.Rd |only spatgraphs-3.0/spatgraphs/man/t.sg.Rd |only spatgraphs-3.0/spatgraphs/man/t.sgadj.Rd |only spatgraphs-3.0/spatgraphs/man/weight.sg.Rd |only spatgraphs-3.0/spatgraphs/src/Graph.cpp | 1096 ++++---------- spatgraphs-3.0/spatgraphs/src/Graph.h | 97 - spatgraphs-3.0/spatgraphs/src/Pp.cpp | 298 --- spatgraphs-3.0/spatgraphs/src/Pp.h | 107 - spatgraphs-3.0/spatgraphs/src/RcppExports.cpp |only spatgraphs-3.0/spatgraphs/src/cut.cpp |only spatgraphs-3.0/spatgraphs/src/prune.cpp |only spatgraphs-3.0/spatgraphs/src/spatcluster.cpp |only spatgraphs-3.0/spatgraphs/src/spatgraph.cpp |only 110 files changed, 842 insertions(+), 1552 deletions(-)
Title: Statistical Modeling
Description: A collection of algorithms and functions to aid statistical modeling. Includes growth curve comparisons, limiting dilution analysis (aka ELDA), mixed linear models, heteroscedastic regression, inverse-Gaussian probability calculations, Gauss quadrature and a secure convergence algorithm for nonlinear models. Includes advanced generalized linear model functions that implement secure convergence, dispersion modeling and Tweedie power-law families.
Author: Gordon Smyth [cre, aut], Yifang Hu [ctb], Peter Dunn [ctb], Belinda Phipson [ctb], Yunshun Chen [ctb]
Maintainer: Gordon Smyth <smyth@wehi.edu.au>
Diff between statmod versions 1.4.21 dated 2015-03-30 and 1.4.22 dated 2015-10-27
DESCRIPTION | 9 +++++---- MD5 | 8 ++++---- NAMESPACE | 10 ++++++++++ R/elda.R | 4 ++-- inst/NEWS | 5 +++++ 5 files changed, 26 insertions(+), 10 deletions(-)
Title: Software Option Settings Manager for R
Description: Provides option settings management that goes
beyond R's default 'options' function. With this package, users can define
their own option settings manager holding option names, default values and
(if so desired) ranges or sets of allowed option values that will be
automatically checked. Settings can then be retrieved, altered and reset
to defaults with ease. For R programmers and package developers it offers
cloning and merging functionality which allows for conveniently defining
global and local options, possibly in a multilevel options hierarchy. See
the package vignette for some examples concerning functions, S4 classes,
and reference classes. There are convenience functions to reset par()
and options() to their 'factory defaults'.
Author: Mark van der Loo
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between settings versions 0.2.2 dated 2015-06-01 and 0.2.4 dated 2015-10-27
DESCRIPTION | 26 ++++++------ MD5 | 23 +++++----- NAMESPACE | 2 NEWS | 4 + R/options.R | 91 +++++++++++++++++++++++++++++++++++++++++-- inst/doc/settings.R | 14 ++++++ inst/doc/settings.Rmd | 31 ++++++++++++++ inst/doc/settings.html | 32 ++++++++++++++- man/clone_and_merge.Rd | 15 +++++++ man/inlist.Rd |only man/options_manager.Rd | 16 +++++++ tests/testthat/testOptions.R | 20 +++++++++ vignettes/settings.Rmd | 31 ++++++++++++++ 13 files changed, 276 insertions(+), 29 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.1-5 dated 2015-05-11 and 1.2-0 dated 2015-10-27
DESCRIPTION | 10 +- MD5 | 30 ++++-- NAMESPACE | 9 + R/g.analyse.R | 1 R/g.create.sp.mat.R |only R/g.getbout.R |only R/g.loadlog.R |only R/g.part3.R |only R/g.part4.R |only R/g.plot5.R |only R/g.report.part2.R | 6 - R/g.report.part4.R |only R/g.shell.GGIR.R | 95 ++++++++++++++++++-- R/g.sib.det.R |only R/g.sib.plot.R |only R/g.sib.sum.R |only data/datalist | 6 - inst/NEWS.Rd | 192 +++++++++++++++++++++-------------------- man/GGIR-package.Rd | 238 ++++++++++++++++++++++++++-------------------------- man/g.part3.Rd |only man/g.part4.Rd |only man/g.shell.GGIR.Rd | 124 ++++++++++++++++++++++----- 22 files changed, 450 insertions(+), 261 deletions(-)
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Diff between geomorph versions 2.1.7 dated 2015-09-21 and 2.1.7-1 dated 2015-10-27
DESCRIPTION | 8 ++-- MD5 | 39 ++++++++++++----------- NEWS | 9 ++++- R/advanced.procD.lm.r | 36 +++++++++++----------- R/bilat.symmetry.r | 23 ++++---------- R/geomorph.support.code.r | 75 ++++++++++++++++++++++++++++++---------------- R/gpagen.r | 2 - R/morphol.disparity.r | 7 ++-- R/plotAllometry.r | 50 ++++++++++++++---------------- R/procD.lm.r | 2 - R/procD.pgls.r | 22 +++++++++---- R/readland.nts.r | 6 ++- R/trajectory.analysis.r | 5 +-- R/two.b.pls.r | 17 +++++----- R/warpRefMesh.r | 15 ++++----- README.md |only man/gpagen.Rd | 2 - man/plotAllometry.Rd | 8 ++-- man/procD.pgls.Rd | 4 +- man/two.b.pls.Rd | 11 ++++-- src/geomorph.c | 7 +++- 21 files changed, 195 insertions(+), 153 deletions(-)
Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units
and control units in observational studies. Provisions are
made for refined covariate balance constraints, which include
fine and near-fine balance as special cases. Matches are
optimal in the sense that they are computed as solutions to
network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>
Diff between rcbalance versions 1.7.1 dated 2015-09-01 and 1.7.2 dated 2015-10-27
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/build.dist.struct.R | 3 +-- R/rcbalance-internal.R | 6 ++---- R/rcbalance.R | 6 ++++-- man/dist2net.Rd | 6 +++++- 6 files changed, 21 insertions(+), 18 deletions(-)
Title: Converting Odds Ratio to Relative Risk in Cohort Studies with
Partial Data Information
Description: Convert the Odds Ratio to the Relative Risk in Cohort Studies with Partial Data Information.
Author: Zhu Wang
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between orsk versions 1.0-1 dated 2013-10-10 and 1.0-2 dated 2015-10-27
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- NAMESPACE | 3 ++- build/vignette.rds |binary 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Normal Mixture Modelling for Model-Based Clustering,
Classification, and Density Estimation
Description: Normal Mixture Modelling fitted via EM algorithm for Model-Based Clustering, Classification, and Density Estimation, including Bayesian regularization.
Author: Chris Fraley [aut],
Adrian E. Raftery [aut],
Luca Scrucca [aut, cre],
Thomas Brendan Murphy [ctb],
Michael Fop [ctb]
Maintainer: Luca Scrucca <luca@stat.unipg.it>
Diff between mclust versions 5.0.2 dated 2015-07-08 and 5.1 dated 2015-10-27
DESCRIPTION | 10 MD5 | 68 ++--- R/bootstrap.R | 4 R/densityMclust.R | 48 ++- R/mclust.R | 34 ++ R/mclustaddson.R | 82 +++--- R/mclustda.R | 148 +++++------ R/mclustdr.R | 12 R/util.R | 5 build/vignette.rds |binary data/Baudry_etal_2010_JCGS_examples.rda |binary data/GvHD.rda |binary data/acidity.rda |binary data/chevron.rda |binary data/cross.rda |binary data/diabetes.rda |binary data/thyroid.rda |binary data/wreath.rda |binary inst/NEWS | 6 inst/doc/mclust.Rmd | 1 inst/doc/mclust.html | 410 ++++++++++++++++---------------- man/Mclust.Rd | 2 man/MclustDA.Rd | 4 man/bic.Rd | 2 man/clustCombi.Rd | 2 man/diabetes.Rd | 2 man/emControl.Rd | 15 - man/estep.Rd | 2 man/mclustModel.Rd | 4 man/mvn.Rd | 2 man/mvnX.Rd | 2 man/plot.densityMclust.Rd | 36 +- man/summary.mclustBIC.Rd | 4 src/mclustaddson.f | 240 ++++++++++++++++-- vignettes/mclust.Rmd | 1 35 files changed, 698 insertions(+), 448 deletions(-)
Title: Methods that Apply to Rows and Columns of Matrices (and to
Vectors)
Description: Methods operating on rows and columns of matrices, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). There are also some vector-based methods, e.g. binMeans(), madDiff() and weightedMedians(). All methods have been optimized for speed and memory usage.
Author: Henrik Bengtsson [aut, cre, cph], Hector Corrada Bravo [ctb], Robert Gentleman [ctb], Ola Hossjer [ctb], Harris Jaffee [ctb], Dongcan Jiang [ctb], Peter Langfelder [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between matrixStats versions 0.14.2 dated 2015-06-24 and 0.15.0 dated 2015-10-27
DESCRIPTION | 8 ++-- MD5 | 64 +++++++++++++++++++---------------- NAMESPACE | 4 ++ NEWS | 22 ++++++++++-- R/rowMads.R | 8 ++-- R/weightedMad.R | 13 ++++--- R/weightedMean.R | 12 +++++- R/weightedMedian.R | 8 +++- R/weightedVar.R | 45 ++++++++++++++++-------- build/vignette.rds |binary inst/doc/matrixStats-methods.html | 4 +- man/matrixStats-package.Rd | 2 - man/weightedMad.Rd | 2 - man/weightedMean.Rd | 2 - man/weightedMedian.Rd | 3 - man/weightedVar.Rd | 11 +++++- src/allocMatrix2.c | 2 - src/binMeans-BINBY-template.h | 3 + src/diff2_TYPE-template.h | 2 - src/logSumExp_internal.c | 36 ++++++++++++------- src/meanOver_TYPE-template.h | 22 +++++++++--- src/productExpSumLog_TYPE-template.h | 7 +++ src/rowDiffs_TYPE-template.h | 2 - src/sumOver_TYPE-template.h | 10 ++++- src/weightedMean_TYPE-template.h | 13 ++++++- src/weightedMedian_TYPE-template.h | 8 ---- tests/reports |only tests/rowWeightedVars.R | 7 ++- tests/weightedMedian.R | 13 +++++++ tests/weightedVar.R |only tests/weightedVar_etal.R | 3 - 31 files changed, 228 insertions(+), 108 deletions(-)
Title: Nomograms for High-Dimensional Cox Models
Description: Build nomograms for high-dimensional Cox models, with support for model validation and calibration.
Author: Miaozhu Li <miaozhu.li@duke.edu>, Nan Xiao <nanx@uchicago.edu>
Maintainer: Nan Xiao <nanx@uchicago.edu>
Diff between hdnom versions 2.0 dated 2015-09-16 and 2.1 dated 2015-10-27
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- NEWS.md | 15 ++++++++++++++- R/hdnom.calibrate.R | 2 +- R/hdnom.models.R | 47 ++++++++++++++++++++++++++++++++++++++++++----- README.md | 2 +- TODO | 2 +- inst/doc/hdnom.Rmd | 4 ++-- inst/doc/hdnom.html | 12 ++++++------ man/hdcox.mcp.Rd | 10 +++++----- man/hdnom.calibrate.Rd | 2 +- vignettes/hdnom.Rmd | 4 ++-- 12 files changed, 91 insertions(+), 41 deletions(-)
Title: Improved Allele-Specific Copy Number of SNP Microarrays for
Downstream Segmentation
Description: A multi-array post-processing method of allele-specific copy-number estimates (ASCNs).
Author: Maria Ortiz [aut, ctb],
Ander Aramburu [ctb],
Henrik Bengtsson [aut, cre, cph],
Pierre Neuvial [aut, ctb],
Angel Rubio [aut, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between calmate versions 0.12.0 dated 2015-02-23 and 0.12.1 dated 2015-10-27
DESCRIPTION | 14 ++++---- MD5 | 10 +++--- NAMESPACE | 3 + NEWS | 6 +++ tests/calmateByTotalAndFracB.R | 68 ++++++++++++++++++++--------------------- tests/thetaAB2TotalAndFracB.R | 28 ++++++++-------- 6 files changed, 68 insertions(+), 61 deletions(-)
Title: Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization
Description: A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).
Author: Maria Ortiz [aut],
Henrik Bengtsson [aut, cre, cph],
Angel Rubio [aut]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between ACNE versions 0.8.0 dated 2015-02-23 and 0.8.1 dated 2015-10-27
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 6 ++++++ NEWS | 4 ++++ man/ACNE-package.Rd | 2 +- 5 files changed, 25 insertions(+), 14 deletions(-)