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Title: Functions for Generating Restricted Permutations of Data
Description: A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.
Author: Gavin L. Simpson [aut, cph, cre],
R Core Team [cph],
Douglas M. Bates [ctb],
Jari Oksanen [ctb]
Maintainer: Gavin L. Simpson <ucfagls@gmail.com>
Diff between permute versions 0.8-4 dated 2015-05-19 and 0.9-0 dated 2016-01-24
permute-0.8-4/permute/R/permCheck.R |only permute-0.8-4/permute/R/permuplot.R |only permute-0.8-4/permute/R/permute-deprecated.R |only permute-0.8-4/permute/R/shuffle2.R |only permute-0.8-4/permute/R/shuffleSet2.R |only permute-0.8-4/permute/inst/NEWS.Rd |only permute-0.8-4/permute/man/permCheck-deprecated.Rd |only permute-0.8-4/permute/man/permControl-deprecated.Rd |only permute-0.8-4/permute/man/permute-deprecated.Rd |only permute-0.8-4/permute/tests/test-all.R |only permute-0.9-0/permute/DESCRIPTION | 9 permute-0.9-0/permute/MD5 | 84 ++-- permute-0.9-0/permute/NAMESPACE | 37 -- permute-0.9-0/permute/R/allPerms.R | 14 permute-0.9-0/permute/R/allStrata.R | 10 permute-0.9-0/permute/R/as.matrix.allPerms.R |only permute-0.9-0/permute/R/blocks.R | 13 permute-0.9-0/permute/R/check.R | 27 + permute-0.9-0/permute/R/fixupCall.R | 10 permute-0.9-0/permute/R/getFoo-methods.R | 129 ------- permute-0.9-0/permute/R/how.R | 6 permute-0.9-0/permute/R/nobs-methods.R | 3 permute-0.9-0/permute/R/numPerms.R | 20 - permute-0.9-0/permute/R/permute.R | 15 permute-0.9-0/permute/R/print.how.R | 2 permute-0.9-0/permute/R/print.permutationMatrix.R | 5 permute-0.9-0/permute/R/setFoo-methods.R | 82 ---- permute-0.9-0/permute/R/shuffle-utils.R | 5 permute-0.9-0/permute/R/shuffle.R | 146 +++++-- permute-0.9-0/permute/R/shuffleSet.R | 216 ++++++++--- permute-0.9-0/permute/README.md | 2 permute-0.9-0/permute/build/vignette.rds |binary permute-0.9-0/permute/inst/ChangeLog | 41 ++ permute-0.9-0/permute/inst/NEWS |only permute-0.9-0/permute/inst/doc/permutations.pdf |binary permute-0.9-0/permute/man/allPerms.Rd | 10 permute-0.9-0/permute/man/check.Rd | 10 permute-0.9-0/permute/man/how.Rd | 10 permute-0.9-0/permute/man/shuffleSet.Rd | 20 + permute-0.9-0/permute/tests/Examples/permute-Ex.Rout.save | 258 +++++--------- permute-0.9-0/permute/tests/testthat.R |only permute-0.9-0/permute/tests/testthat/test-allPerms.R | 162 ++++++++ permute-0.9-0/permute/tests/testthat/test-as-methods.R |only permute-0.9-0/permute/tests/testthat/test-blocks.R |only permute-0.9-0/permute/tests/testthat/test-check.R | 11 permute-0.9-0/permute/tests/testthat/test-get-methods.R |only permute-0.9-0/permute/tests/testthat/test-how.R |only permute-0.9-0/permute/tests/testthat/test-nobs.R |only permute-0.9-0/permute/tests/testthat/test-numPerms.R |only permute-0.9-0/permute/tests/testthat/test-permute-fun.R |only permute-0.9-0/permute/tests/testthat/test-set-methods.R |only permute-0.9-0/permute/tests/testthat/test-shuffle-utils.R |only permute-0.9-0/permute/tests/testthat/test-shuffle.R | 10 permute-0.9-0/permute/tests/testthat/test-shuffleSet.R | 43 ++ 54 files changed, 837 insertions(+), 573 deletions(-)
More information about DiffusionRjgqd at CRAN
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Title: Codon Usage Bias Fits
Description: Estimating mutation and selection coefficients on synonymous
codon bias usage based on models of ribosome overhead cost (ROC).
Multinomial logistic regression and Markov Chain Monte Carlo are used to
estimate and predict protein production rates with/without the presence
of expressions and measurement errors. Work flows with examples for
simulation, estimation and prediction processes are also provided
with parallelization speedup. The whole framework is tested with
yeast genome and gene expression data of Yassour (2009).
Author: Wei-Chen Chen [aut, cre],
Russell Zaretzki [aut],
William Howell [aut],
Cedric Landerer [aut],
Drew Schmidt [aut],
Michael A. Gilchrist [aut],
Preston Hewgley [ctb],
Students REU13 [ctb]
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between cubfits versions 0.1-0 dated 2014-05-19 and 0.1-2 dated 2016-01-24
cubfits-0.1-0/cubfits/R/my.pPropType.lognormal_MH.r |only cubfits-0.1-0/cubfits/R/my.pPropTypeNoObs.lognormal_MH.r |only cubfits-0.1-0/cubfits/R/my.pPropTypeNoObs_MH.r |only cubfits-0.1-0/cubfits/R/my.proposeBeta.r |only cubfits-0.1-0/cubfits/data/bInit.rda |only cubfits-0.1-0/cubfits/demo/nsef.appr.r |only cubfits-0.1-0/cubfits/demo/nsef.pred.r |only cubfits-0.1-0/cubfits/demo/nsef.simu.r |only cubfits-0.1-0/cubfits/demo/nsef.train.r |only cubfits-0.1-0/cubfits/demo/rocnsef.appr.r |only cubfits-0.1-0/cubfits/demo/rocnsef.pred.r |only cubfits-0.1-0/cubfits/demo/rocnsef.train.r |only cubfits-0.1-0/cubfits/inst/workflow/nsef |only cubfits-0.1-0/cubfits/inst/workflow/roc/02_plots.txt |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wophi_pm-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wophi_scuo-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wphi_pm-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wphi_scuo-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wphi_wophi_pm-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/04-ad_wphi_wophi_scuo-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/05-subset_tsv.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/s4-ad_wophi_true-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code/s4-ad_wphi_true-tp.r |only cubfits-0.1-0/cubfits/inst/workflow/roc/code_plot_nps |only cubfits-0.1-0/cubfits/inst/workflow/roc/script/simu_run_2_nps.sh |only cubfits-0.1-0/cubfits/inst/workflow/roc/script/wophi_run_2_nps.sh |only cubfits-0.1-0/cubfits/inst/workflow/roc/script/wphi_run_2_nps.sh |only cubfits-0.1-0/cubfits/inst/workflow/roc/script/wphi_wophi_run_2_nps.sh |only cubfits-0.1-0/cubfits/vignettes/cubfits-include/06-misc.tex |only cubfits-0.1-0/cubfits/vignettes/cubfits-include/jss.bst |only cubfits-0.1-0/cubfits/vignettes/cubfits-include/jss.cls |only cubfits-0.1-2/cubfits/ChangeLog | 25 cubfits-0.1-2/cubfits/DESCRIPTION | 23 cubfits-0.1-2/cubfits/INSTALL | 4 cubfits-0.1-2/cubfits/MD5 | 468 ++++------ cubfits-0.1-2/cubfits/NAMESPACE | 20 cubfits-0.1-2/cubfits/R/000_globalVariables.r |only cubfits-0.1-2/cubfits/R/cedric.convergence.r |only cubfits-0.1-2/cubfits/R/cedric.io.r |only cubfits-0.1-2/cubfits/R/cedric.mapBMatNames.r |only cubfits-0.1-2/cubfits/R/cedric.plotting.r |only cubfits-0.1-2/cubfits/R/data.codon.convert.r | 5 cubfits-0.1-2/cubfits/R/data.convert.r | 14 cubfits-0.1-2/cubfits/R/data.io.r | 2 cubfits-0.1-2/cubfits/R/logan.plotting.r |only cubfits-0.1-2/cubfits/R/my.acceptance.r | 61 - cubfits-0.1-2/cubfits/R/my.adaptive.DrawScale.r | 105 +- cubfits-0.1-2/cubfits/R/my.adaptive.r | 46 cubfits-0.1-2/cubfits/R/my.check.data.r |only cubfits-0.1-2/cubfits/R/my.check.rearrange.r | 14 cubfits-0.1-2/cubfits/R/my.coef.r | 19 cubfits-0.1-2/cubfits/R/my.cubappr.r | 189 ++-- cubfits-0.1-2/cubfits/R/my.cubfits.r | 197 ++-- cubfits-0.1-2/cubfits/R/my.cubpred.r | 236 ++--- cubfits-0.1-2/cubfits/R/my.drawBConditionalAll.r | 18 cubfits-0.1-2/cubfits/R/my.drawBConditionalFit.r | 47 - cubfits-0.1-2/cubfits/R/my.drawPhiConditionalAll.r | 15 cubfits-0.1-2/cubfits/R/my.drawPhiConditionalAllPred.r | 17 cubfits-0.1-2/cubfits/R/my.drawRestrictHP.r |only cubfits-0.1-2/cubfits/R/my.drawbiasPhi.r |only cubfits-0.1-2/cubfits/R/my.fitMultinomOne.r | 6 cubfits-0.1-2/cubfits/R/my.init.r | 8 cubfits-0.1-2/cubfits/R/my.init_param.r | 14 cubfits-0.1-2/cubfits/R/my.logPosteriorAll.r | 45 cubfits-0.1-2/cubfits/R/my.logdmultinomCodOne.r | 18 cubfits-0.1-2/cubfits/R/my.pPropType.logmixture.r | 17 cubfits-0.1-2/cubfits/R/my.pPropType.lognormal_RW.r | 46 cubfits-0.1-2/cubfits/R/my.pPropType.lognormal_bias.r |only cubfits-0.1-2/cubfits/R/my.pPropType.r | 13 cubfits-0.1-2/cubfits/R/my.pPropTypeNoObs.logmixture.r | 2 cubfits-0.1-2/cubfits/R/my.pPropTypeNoObs.lognormal_RW.r | 12 cubfits-0.1-2/cubfits/R/my.pPropTypeNoObs.lognormal_bias.r |only cubfits-0.1-2/cubfits/R/my.pPropTypeNoObs.r | 2 cubfits-0.1-2/cubfits/R/my.proposeB.r |only cubfits-0.1-2/cubfits/R/my.proposePhiAll.r | 46 cubfits-0.1-2/cubfits/R/my.proposePhiAllPred.r | 43 cubfits-0.1-2/cubfits/R/my.proposebiasPhi.r |only cubfits-0.1-2/cubfits/R/my.proposesigmaPhi.r |only cubfits-0.1-2/cubfits/R/plotbin.r | 34 cubfits-0.1-2/cubfits/R/plotmodel.r | 24 cubfits-0.1-2/cubfits/R/prop.bin.roc.r | 66 + cubfits-0.1-2/cubfits/R/prop.model.nse.r |only cubfits-0.1-2/cubfits/R/prop.model.roc.r | 23 cubfits-0.1-2/cubfits/R/simu.orf.r | 44 cubfits-0.1-2/cubfits/R/simu.phi.Obs.r | 7 cubfits-0.1-2/cubfits/R/workflow.create.r | 12 cubfits-0.1-2/cubfits/configure | 4 cubfits-0.1-2/cubfits/configure.ac | 4 cubfits-0.1-2/cubfits/data/b.Init.rda |only cubfits-0.1-2/cubfits/data/control.r | 49 - cubfits-0.1-2/cubfits/data/global.r | 11 cubfits-0.1-2/cubfits/data/plot.r | 11 cubfits-0.1-2/cubfits/demo/00Index | 7 cubfits-0.1-2/cubfits/demo/mSCU.r | 2 cubfits-0.1-2/cubfits/demo/plotbin.r | 4 cubfits-0.1-2/cubfits/demo/roc.appr.r | 4 cubfits-0.1-2/cubfits/demo/roc.pred.r | 18 cubfits-0.1-2/cubfits/demo/roc.simu.r | 11 cubfits-0.1-2/cubfits/demo/roc.train.r | 8 cubfits-0.1-2/cubfits/inst/CITATION | 10 cubfits-0.1-2/cubfits/inst/doc/cubfits-guide.Rnw | 14 cubfits-0.1-2/cubfits/inst/doc/cubfits-guide.pdf |binary cubfits-0.1-2/cubfits/inst/workflow/00_readme.txt | 6 cubfits-0.1-2/cubfits/inst/workflow/param/small_bInit.rda |binary cubfits-0.1-2/cubfits/inst/workflow/roc/00_readme.txt | 4 cubfits-0.1-2/cubfits/inst/workflow/roc/01_code.txt | 13 cubfits-0.1-2/cubfits/inst/workflow/roc/code/00-set_env_simu.r | 48 - cubfits-0.1-2/cubfits/inst/workflow/roc/code/00-set_env_wophi.r | 42 cubfits-0.1-2/cubfits/inst/workflow/roc/code/00-set_env_wphi.r | 49 - cubfits-0.1-2/cubfits/inst/workflow/roc/code/00-set_env_wphi_wophi.r | 48 - cubfits-0.1-2/cubfits/inst/workflow/roc/code/02-get_data.r | 15 cubfits-0.1-2/cubfits/inst/workflow/roc/code/03-get_init-tp.r | 21 cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wophi_pm-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wophi_scuo-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wphi_pm-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wphi_scuo-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wphi_wophi_pm-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/04-wphi_wophi_scuo-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/05-subset-tp.r | 52 - cubfits-0.1-2/cubfits/inst/workflow/roc/code/s1-generate_data.r | 10 cubfits-0.1-2/cubfits/inst/workflow/roc/code/s4-wophi_true-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code/s4-wphi_true-tp.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/03-plotdiag_bin_est.r | 45 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/03-plotdiag_init.r | 5 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/05-subset_tsv.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/06-plotsingle_model.r | 120 +- cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/06-plotsingle_prxy.r | 23 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/06-plotsingle_prxy_wci.r | 21 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_EPhi_hist.r | 17 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_accept_hist.r | 2 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_acceptvsEPhi.r | 19 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_bin.r | 111 +- cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_medPhi_EPhi.r | 1 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_scuo_cai.r | 8 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plotdiag_sigmaW_hist.r | 1 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plottrace_logL-tp.r | 32 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plottrace_param_meanEPhi.r | 26 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plottrace_prior.r | 8 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/07-plottrace_quantile_Phi.r | 21 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/08-plotmulti_wophi_wphi.r | 44 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m6-plot_b_corr.r | 26 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m6-plot_b_corr_negsel.r | 22 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m6-plot_prxy.r | 18 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m6-plot_prxy_wci.r | 18 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/m7-plot_bin.r | 92 + cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s1-plotdiag_simu_phi.r | 1 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s2-plotdiag_bin_true.r | 90 + cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s3-plotdiag_bin_est.r | 46 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_b_corr_true.r | 28 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_model_true.r | 55 - cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_mscu.r | 27 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_prxy_true.r | 27 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_prxy_true_wci.r | 31 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s6-plotsingle_scu_mscu.r | 26 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s7-plotaa_deltat_true.r | 25 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/s8-plotmulti_true.r | 67 + cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u0-get_case_main.r | 27 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u2-plot_b_corr.r | 94 +- cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u3-plot_trace.r | 11 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u4-plot_aa_allinone.r | 4 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u5-new_page.r | 5 cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot/u6-adjust_focal_codon.r |only cubfits-0.1-2/cubfits/inst/workflow/roc/code_plot_ps |only cubfits-0.1-2/cubfits/inst/workflow/roc/script/simu_run_0.sh | 16 cubfits-0.1-2/cubfits/inst/workflow/roc/script/simu_run_1.sh | 41 cubfits-0.1-2/cubfits/inst/workflow/roc/script/simu_run_2.sh | 36 cubfits-0.1-2/cubfits/inst/workflow/roc/script/simu_run_2_ps.sh |only cubfits-0.1-2/cubfits/inst/workflow/roc/script/wophi_run_0.sh | 14 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wophi_run_1.sh | 21 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wophi_run_2.sh | 26 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wophi_run_2_ps.sh |only cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_run_0.sh | 15 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_run_1.sh | 33 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_run_2.sh | 30 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_run_2_ps.sh |only cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_wophi_run_0.sh | 15 cubfits-0.1-2/cubfits/inst/workflow/roc/script/wphi_wophi_run_1.sh | 48 - 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Title: Programming with Big Data -- Demonstrations and Examples Using
'pbdR' Packages
Description: A set of demos of 'pbdR' packages, together with a useful,
unifying vignette.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut]
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdDEMO versions 0.2-0 dated 2014-02-18 and 0.3-0 dated 2016-01-24
pbdDEMO-0.2-0/pbdDEMO/R/read_sql_csv.R |only pbdDEMO-0.2-0/pbdDEMO/README |only pbdDEMO-0.2-0/pbdDEMO/data/control.rda |only pbdDEMO-0.2-0/pbdDEMO/demo/read_sql.r |only pbdDEMO-0.2-0/pbdDEMO/inst/extra/data/data |only pbdDEMO-0.2-0/pbdDEMO/man/00_pbdDEMO-package.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/01_control.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/05_timer.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/10_mpi.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/20_gbd_dmat.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/21_balance.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/ca_dmat_readsql.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/cb_dmat_readcsv.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/cc_plot.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/da_verify.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/ea_examples.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/eb_nc4.Rd |only pbdDEMO-0.2-0/pbdDEMO/man/zz_demo.internal.Rd |only pbdDEMO-0.2-0/pbdDEMO/vignettes/pbdDEMO-include/applications/a5-ts.tex |only pbdDEMO-0.2-0/pbdDEMO/vignettes/pbdDEMO-include/applications/a6-tbd.tex |only pbdDEMO-0.2-0/pbdDEMO/vignettes/pbdDEMO-include/jss.bst |only pbdDEMO-0.2-0/pbdDEMO/vignettes/pbdDEMO-include/jss.cls |only pbdDEMO-0.3-0/pbdDEMO/COPYING | 711 +++++----- pbdDEMO-0.3-0/pbdDEMO/ChangeLog | 58 pbdDEMO-0.3-0/pbdDEMO/DESCRIPTION | 40 pbdDEMO-0.3-0/pbdDEMO/MD5 | 154 +- pbdDEMO-0.3-0/pbdDEMO/NAMESPACE | 63 pbdDEMO-0.3-0/pbdDEMO/R/gbd_dmat.r | 87 - pbdDEMO-0.3-0/pbdDEMO/R/load_balance.r | 141 + pbdDEMO-0.3-0/pbdDEMO/R/mpi_example.r | 59 pbdDEMO-0.3-0/pbdDEMO/R/ncvar_2d.r | 222 ++- pbdDEMO-0.3-0/pbdDEMO/R/pbdDEMO-package.r |only pbdDEMO-0.3-0/pbdDEMO/R/plot_dmat.r | 25 pbdDEMO-0.3-0/pbdDEMO/R/read_csv.r |only pbdDEMO-0.3-0/pbdDEMO/R/timer.R | 17 pbdDEMO-0.3-0/pbdDEMO/R/treft.r |only pbdDEMO-0.3-0/pbdDEMO/R/verify.R | 137 + pbdDEMO-0.3-0/pbdDEMO/R/zzz.R |only pbdDEMO-0.3-0/pbdDEMO/README.md |only pbdDEMO-0.3-0/pbdDEMO/build/vignette.rds |binary pbdDEMO-0.3-0/pbdDEMO/data/TREFHT.rda |binary pbdDEMO-0.3-0/pbdDEMO/demo/00Index | 8 pbdDEMO-0.3-0/pbdDEMO/demo/dist_iris.r |only pbdDEMO-0.3-0/pbdDEMO/demo/dist_pony.r |only pbdDEMO-0.3-0/pbdDEMO/demo/gbd_dmat.r | 2 pbdDEMO-0.3-0/pbdDEMO/demo/iris_dmat.r | 7 pbdDEMO-0.3-0/pbdDEMO/demo/iris_gbd.r | 8 pbdDEMO-0.3-0/pbdDEMO/demo/nc4_dmat.r | 11 pbdDEMO-0.3-0/pbdDEMO/demo/nc4_gbdc.r | 8 pbdDEMO-0.3-0/pbdDEMO/demo/nc4_par_read_1d.r |only pbdDEMO-0.3-0/pbdDEMO/demo/nc4_par_read_2d.r |only pbdDEMO-0.3-0/pbdDEMO/demo/nc4_par_write_1d.r |only pbdDEMO-0.3-0/pbdDEMO/demo/nc4_par_write_2d.r |only pbdDEMO-0.3-0/pbdDEMO/demo/nc4_parallel.r | 4 pbdDEMO-0.3-0/pbdDEMO/demo/ols_dmat.r | 4 pbdDEMO-0.3-0/pbdDEMO/demo/read_csv.r | 20 pbdDEMO-0.3-0/pbdDEMO/demo/read_ncdf.r | 2 pbdDEMO-0.3-0/pbdDEMO/demo/reblock.r | 2 pbdDEMO-0.3-0/pbdDEMO/demo/sample_stat_dmat.r | 12 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_cov.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_lmfit.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/balance_pca.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/cov.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/lmfit.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/Benchmarks/pca.r | 2 pbdDEMO-0.3-0/pbdDEMO/inst/CITATION | 4 pbdDEMO-0.3-0/pbdDEMO/inst/doc/pbdDEMO-guide.Rnw | 15 pbdDEMO-0.3-0/pbdDEMO/inst/doc/pbdDEMO-guide.pdf |binary pbdDEMO-0.3-0/pbdDEMO/man/Temperature-at-Reference-Height.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/gbd_dmat.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/load_balance.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/mpi_example.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/ncvar.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/pbdDEMO-package.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/plot_dmat.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/read.csv.ddmatrix.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/timer.Rd |only pbdDEMO-0.3-0/pbdDEMO/man/verify.Rd |only pbdDEMO-0.3-0/pbdDEMO/src |only pbdDEMO-0.3-0/pbdDEMO/vignettes/build_pdf.sh | 5 pbdDEMO-0.3-0/pbdDEMO/vignettes/cover/build_cover.sh | 4 pbdDEMO-0.3-0/pbdDEMO/vignettes/cover/cover.pdf |binary pbdDEMO-0.3-0/pbdDEMO/vignettes/cover/cover.tex | 27 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-guide.Rnw | 15 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/01-introduction.tex | 15 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/03-mpi.tex | 68 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/07-dmat_basic.tex | 4 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/09-reading.tex | 26 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/10-pbdNCDF4.tex | 44 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/applications/a4-Bayes.tex | 13 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/applications/a5-pairwise.tex |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/applications/b1-ts.tex |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/applications/c1-tbd.tex |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/frontmatter/00-acknowledgement.tex | 9 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/frontmatter/00-copyright.tex | 10 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/frontmatter/00-covernote.tex |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/frontmatter/00-warn.tex | 5 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/pbdDEMO.bib | 102 + pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/pics/dist_iris.pdf |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/pics/dist_pony.pdf |only pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/preamble.tex | 91 - pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/style.tex | 7 pbdDEMO-0.3-0/pbdDEMO/vignettes/pbdDEMO-include/titlepage.tex | 3 103 files changed, 1441 insertions(+), 840 deletions(-)
Title: Safely Access the RStudio API
Description: Access the RStudio API (if available) and provide informative error
messages when it's not.
Author: Hadley Wickham [aut],
JJ Allaire [aut, cre],
Kevin Ushey [ctb],
RStudio [cph]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between rstudioapi versions 0.4.0 dated 2015-12-09 and 0.5 dated 2016-01-24
rstudioapi-0.4.0/rstudioapi/NEWS |only rstudioapi-0.5/rstudioapi/DESCRIPTION | 7 ++- rstudioapi-0.5/rstudioapi/MD5 | 26 +++++++------- rstudioapi-0.5/rstudioapi/NAMESPACE | 4 +- rstudioapi-0.5/rstudioapi/R/stubs.R | 10 +++++ rstudioapi-0.5/rstudioapi/inst |only rstudioapi-0.5/rstudioapi/man/askForPassword.Rd |only rstudioapi-0.5/rstudioapi/man/callFun.Rd | 6 +-- rstudioapi-0.5/rstudioapi/man/document-mutation.Rd | 20 +++++----- rstudioapi-0.5/rstudioapi/man/document_position.Rd | 2 - rstudioapi-0.5/rstudioapi/man/document_range.Rd | 2 - rstudioapi-0.5/rstudioapi/man/getActiveDocumentContext.Rd | 2 - rstudioapi-0.5/rstudioapi/man/getActiveProject.Rd |only rstudioapi-0.5/rstudioapi/man/getVersion.Rd | 2 - rstudioapi-0.5/rstudioapi/man/hasFun.Rd | 12 +++--- rstudioapi-0.5/rstudioapi/man/isAvailable.Rd | 4 +- 16 files changed, 56 insertions(+), 41 deletions(-)
Title: Examples using 'Rcpp' to Interface R and C++
Description: Examples for Seamless R and C++ integration
The 'Rcpp' package contains a C++ library that facilitates the integration of
R and C++ in various ways. This package provides some usage examples.
Note that the documentation in this package currently does not cover all the
features in the package. It is not even close. On the other hand, the site
<http://gallery.rcpp.org> is regrouping a large number of examples for 'Rcpp'.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppExamples versions 0.1.6 dated 2013-01-16 and 0.1.7 dated 2016-01-24
RcppExamples-0.1.6/RcppExamples/R/RcppParamsExample.R |only RcppExamples-0.1.6/RcppExamples/man/RcppDate.Rd |only RcppExamples-0.1.6/RcppExamples/man/RcppParams.Rd |only RcppExamples-0.1.6/RcppExamples/man/RcppRNGs.Rd |only RcppExamples-0.1.6/RcppExamples/man/RcppResultSet.Rd |only RcppExamples-0.1.6/RcppExamples/man/RcppVector.Rd |only RcppExamples-0.1.6/RcppExamples/src/RcppDataFrame.cpp |only RcppExamples-0.1.6/RcppExamples/src/RcppRNGs.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppDateExample.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppMatrixExample.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppParamsExample.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppStringVectorExample.cpp |only RcppExamples-0.1.6/RcppExamples/src/newRcppVectorExample.cpp |only RcppExamples-0.1.7/RcppExamples/ChangeLog | 26 ++++ RcppExamples-0.1.7/RcppExamples/DESCRIPTION | 31 ++--- RcppExamples-0.1.7/RcppExamples/MD5 | 58 +++++----- RcppExamples-0.1.7/RcppExamples/NAMESPACE | 11 - RcppExamples-0.1.7/RcppExamples/R/RcppDataFrame.R | 17 +- RcppExamples-0.1.7/RcppExamples/R/RcppDateExample.R | 14 +- RcppExamples-0.1.7/RcppExamples/R/RcppExports.R |only RcppExamples-0.1.7/RcppExamples/R/RcppListExample.R |only RcppExamples-0.1.7/RcppExamples/R/RcppMatrixExample.R | 16 +- RcppExamples-0.1.7/RcppExamples/R/RcppRNGs.R | 17 +- RcppExamples-0.1.7/RcppExamples/R/RcppStringVectorExample.R | 14 +- RcppExamples-0.1.7/RcppExamples/R/RcppVectorExample.R | 18 +-- RcppExamples-0.1.7/RcppExamples/README.md |only RcppExamples-0.1.7/RcppExamples/inst/NEWS.Rd | 13 ++ RcppExamples-0.1.7/RcppExamples/man/RcppDataFrame.Rd | 8 - RcppExamples-0.1.7/RcppExamples/man/RcppDateExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppExamples-package.Rd | 11 - RcppExamples-0.1.7/RcppExamples/man/RcppListExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppMatrixExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppNumericVectorExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppRNGsExample.Rd |only RcppExamples-0.1.7/RcppExamples/man/RcppStringVectorExample.Rd |only RcppExamples-0.1.7/RcppExamples/src/DataFrameExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/DateExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/ListExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/Makevars | 7 - RcppExamples-0.1.7/RcppExamples/src/Makevars.win | 13 +- RcppExamples-0.1.7/RcppExamples/src/MatrixExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/NumericVectorExample.cpp |only RcppExamples-0.1.7/RcppExamples/src/RNGs.cpp |only RcppExamples-0.1.7/RcppExamples/src/RcppExports.cpp |only RcppExamples-0.1.7/RcppExamples/src/StringVectorExample.cpp |only 45 files changed, 153 insertions(+), 121 deletions(-)
Title: Analytical Tools for Radiation Oncology
Description: Designed for the import, analysis, and visualization of dosimetric and volumetric data in Radiation Oncology, the tools herein enable import of dose-volume histogram information from multiple treatment planning system platforms and 3D structural representations and dosimetric information from 'DICOM-RT' files. These tools also enable subsequent visualization and statistical analysis of these data.
Author: Reid F. Thompson <reid.thompson@gmail.com>
Maintainer: Reid F. Thompson <reid.thompson@gmail.com>
Diff between RadOnc versions 1.1.0 dated 2015-04-22 and 1.1.1 dated 2016-01-24
DESCRIPTION | 10 +-- MD5 | 18 +++--- R/CLASSES.R | 5 - R/DVH.R | 32 ++++++------ R/plot.DVH.R | 6 +- R/read.DVH.R | 133 +++++++++++++++++++++++++++++++++++++++++++++++++-- inst/NEWS.Rd | 36 +++++++++++++ man/plot-methods.Rd | 9 +++ man/read.DVH.Rd | 4 - vignettes/RadOnc.Rnw | 8 +-- 10 files changed, 215 insertions(+), 46 deletions(-)
Title: Programming with Big Data -- Distributed Matrix Methods
Description: A set of classes for managing distributed matrices, and
a collection of methods for computing linear algebra and
statistics. Computation is handled mostly by routines from the
'pbdBASE' package, which itself relies on the 'ScaLAPACK' and
'PBLAS' numerical libraries for distributed computing.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
ZhaoKang Wang [ctb],
Michael Lawrence [ctb],
R Core team [ctb] (some wrappers taken from the base and stats
packages)
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdDMAT versions 0.2-3 dated 2013-12-16 and 0.4-0 dated 2016-01-24
pbdDMAT-0.2-3/pbdDMAT/R/00-ddmatrix_class.R |only pbdDMAT-0.2-3/pbdDMAT/R/02-utility.R |only pbdDMAT-0.2-3/pbdDMAT/R/03-redistributions.R |only pbdDMAT-0.2-3/pbdDMAT/R/a_ddmatrix_utility.R |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_algebra.R |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_condition.R |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_create.R |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_matexp.r |only pbdDMAT-0.2-3/pbdDMAT/R/ddmatrix_r_math.R |only pbdDMAT-0.2-3/pbdDMAT/README |only pbdDMAT-0.2-3/pbdDMAT/data |only pbdDMAT-0.2-3/pbdDMAT/man/00_pbdDMAT-package.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/00_zz_dmatclass.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/00_zzz_control.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/aa_dimensions.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ba_randmat.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/bb_hilb.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/bd_companion.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/bz_diag.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ca_asddm.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ca_asmat.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/cb_distrib.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/cc_redist.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/da_print.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/db_summary.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/dz_extract.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/dz_insert.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ea_comparators.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/eb_type.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ec_nas.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/fa_apply.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/fb_bind.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ia_reductions.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ib_arith.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ib_matmult.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ka_miscmath.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/kb_rounding.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/la_linalg.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/lb_qr.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/lc_chol2inv.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ld_kappa.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/le_norm.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ls_eigen2.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/lz_expm.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/ra_scale.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/rb_sweep.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/sa_cov.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/sa_pca.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/sc_lmfit.Rd |only pbdDMAT-0.2-3/pbdDMAT/man/zz_dmat.internal.Rd |only pbdDMAT-0.2-3/pbdDMAT/vignettes/pbdDMAT-include |only pbdDMAT-0.4-0/pbdDMAT/ChangeLog | 93 +--- pbdDMAT-0.4-0/pbdDMAT/DESCRIPTION | 45 +- pbdDMAT-0.4-0/pbdDMAT/MD5 | 263 +++++++---- pbdDMAT-0.4-0/pbdDMAT/NAMESPACE | 323 +++++++------- pbdDMAT-0.4-0/pbdDMAT/R/00-classes.r |only pbdDMAT-0.4-0/pbdDMAT/R/000_globalVariables.r |only pbdDMAT-0.4-0/pbdDMAT/R/01-generics.R | 228 ---------- pbdDMAT-0.4-0/pbdDMAT/R/04-misc.R | 131 ----- pbdDMAT-0.4-0/pbdDMAT/R/accessors.r |only pbdDMAT-0.4-0/pbdDMAT/R/as.ddmatrix.r |only pbdDMAT-0.4-0/pbdDMAT/R/as.matrix.r |only pbdDMAT-0.4-0/pbdDMAT/R/as.vector.r |only pbdDMAT-0.4-0/pbdDMAT/R/constructors.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_[.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_apply.R | 235 ++++++++-- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_arithmetic.R | 98 +++- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_bind.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_chol.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_chol2inv.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_cond.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_cov.R | 102 ++-- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_diag.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_eigen.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_eigen2.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_expm.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_head.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_isdot.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_lm.R | 121 ++++- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_logic.r | 213 ++++----- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_lu.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_math.R |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_matmult.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_misc.R | 445 +------------------- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_na.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_norm.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_prcomp.R | 85 +++ pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_print.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_qr.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_redistribute.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_reductions.R | 286 +++++------- pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_round.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_scale.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_sd.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_solve.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_special.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_summary.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_sumstats.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_svd.r |only pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_sweep.R | 297 +------------ pbdDMAT-0.4-0/pbdDMAT/R/ddmatrix_transpose.r |only pbdDMAT-0.4-0/pbdDMAT/R/dsmatrix |only pbdDMAT-0.4-0/pbdDMAT/R/error_stuff.r |only pbdDMAT-0.4-0/pbdDMAT/R/getLocal.r |only pbdDMAT-0.4-0/pbdDMAT/R/isSymmetric.r |only pbdDMAT-0.4-0/pbdDMAT/R/ownany.r |only pbdDMAT-0.4-0/pbdDMAT/R/pbdDMAT-package.R |only pbdDMAT-0.4-0/pbdDMAT/R/sparsity.r |only pbdDMAT-0.4-0/pbdDMAT/R/test_utils.r |only pbdDMAT-0.4-0/pbdDMAT/R/utils.r |only pbdDMAT-0.4-0/pbdDMAT/R/wrappers.r |only pbdDMAT-0.4-0/pbdDMAT/R/zzz.R | 18 pbdDMAT-0.4-0/pbdDMAT/README.md |only pbdDMAT-0.4-0/pbdDMAT/TODO | 11 pbdDMAT-0.4-0/pbdDMAT/build/vignette.rds |binary pbdDMAT-0.4-0/pbdDMAT/cleanup | 10 pbdDMAT-0.4-0/pbdDMAT/demo/cholesky.r | 2 pbdDMAT-0.4-0/pbdDMAT/demo/matprod.r | 2 pbdDMAT-0.4-0/pbdDMAT/demo/reductions.r | 2 pbdDMAT-0.4-0/pbdDMAT/demo/solve.r | 10 pbdDMAT-0.4-0/pbdDMAT/demo/svd.r | 12 pbdDMAT-0.4-0/pbdDMAT/inst/RNACI |only pbdDMAT-0.4-0/pbdDMAT/inst/doc/pbdDMAT-guide.Rnw | 181 +------- pbdDMAT-0.4-0/pbdDMAT/inst/doc/pbdDMAT-guide.pdf |binary pbdDMAT-0.4-0/pbdDMAT/inst/tests |only pbdDMAT-0.4-0/pbdDMAT/man/Comparators.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/Hilbert.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/accessors.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/arithmetic.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/as.ddmatrix.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/as.matrix.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/as.rowcyclic.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/as.vector.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/binds.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/chol2inv.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/companion.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/condnums.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/control.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/covariance.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-apply.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-chol.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-class.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-constructors.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-eigen.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-lu.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-norm.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-prcomp.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-print.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-scale.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-solve.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-summary.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-sumstats.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/ddmatrix-svd.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/diag-constructors.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/eigen2.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/expm.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/extract.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/getLocal.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/headsortails.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/insert.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/isSymmetric.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/isdot.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/lm.fit.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/math.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/matmult.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/na.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/pbdDMAT-package.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/qr.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/redistribute.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/reductions.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/rounding.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/sd.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/sparsity.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/sweep.Rd |only pbdDMAT-0.4-0/pbdDMAT/man/transpose.Rd |only pbdDMAT-0.4-0/pbdDMAT/src |only pbdDMAT-0.4-0/pbdDMAT/tests |only pbdDMAT-0.4-0/pbdDMAT/vignettes/build_pdf.sh | 6 pbdDMAT-0.4-0/pbdDMAT/vignettes/include |only pbdDMAT-0.4-0/pbdDMAT/vignettes/pbdDMAT-guide.Rnw | 181 +------- pbdDMAT-0.4-0/pbdDMAT/vignettes/workingwith-include |only 181 files changed, 1337 insertions(+), 2063 deletions(-)
Title: Programming with Big Data -- Base Wrappers for Distributed
Matrices
Description: An interface to and extensions for the 'PBLAS' and
'ScaLAPACK' numerical libraries. This enables R to utilize
distributed linear algebra for codes written in the 'SPMD' fashion.
This interface is deliberately low-level and mimics the style of
the native libraries it wraps. For a much higher level way of
managing distributed matrices, see the 'pbdDMAT' package.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Ewan Higgs [ctb]
Maintainer: Drew Schmidt <schmidt@math.utk.edu>
Diff between pbdBASE versions 0.2-3 dated 2013-12-14 and 0.4-3 dated 2016-01-24
pbdBASE-0.2-3/pbdBASE/R/lm.R |only pbdBASE-0.2-3/pbdBASE/R/utility_blacs.R |only pbdBASE-0.2-3/pbdBASE/R/utility_scalapack.R |only pbdBASE-0.2-3/pbdBASE/R/wrappers_blacs.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_matexp.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_misc.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_p_matexp.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_pblas.R |only pbdBASE-0.2-3/pbdBASE/R/wrappers_plinalg.r |only pbdBASE-0.2-3/pbdBASE/R/wrappers_putil.R |only pbdBASE-0.2-3/pbdBASE/R/wrappers_scalapack.R |only pbdBASE-0.2-3/pbdBASE/README |only pbdBASE-0.2-3/pbdBASE/data |only pbdBASE-0.2-3/pbdBASE/man/00_pbdBASE-package.Rd |only pbdBASE-0.2-3/pbdBASE/man/aa_initgrid.Rd |only pbdBASE-0.2-3/pbdBASE/man/aa_z_gridexit.Rd |only pbdBASE-0.2-3/pbdBASE/man/ab_blacs.Rd |only pbdBASE-0.2-3/pbdBASE/man/ab_d_minctxt.Rd |only pbdBASE-0.2-3/pbdBASE/man/ab_z_blacsexit.Rd |only pbdBASE-0.2-3/pbdBASE/man/ab_z_coords.Rd |only pbdBASE-0.2-3/pbdBASE/man/ac_envir.Rd |only pbdBASE-0.2-3/pbdBASE/man/ba_a_ownership.Rd |only pbdBASE-0.2-3/pbdBASE/man/zz_base.internal.Rd |only pbdBASE-0.2-3/pbdBASE/src/Rtools |only pbdBASE-0.2-3/pbdBASE/src/base/R_plm.f |only pbdBASE-0.2-3/pbdBASE/src/base/plinalg.f |only pbdBASE-0.2-3/pbdBASE/src/base/prblas.f |only pbdBASE-0.2-3/pbdBASE/src/base/util |only pbdBASE-0.2-3/pbdBASE/src/base/variance.f |only pbdBASE-0.2-3/pbdBASE/src/base_global.h |only pbdBASE-0.2-3/pbdBASE/src/base_mpi_blac.c |only pbdBASE-0.2-3/pbdBASE/vignettes/pbdBASE-include |only pbdBASE-0.4-3/pbdBASE/ChangeLog | 118 - pbdBASE-0.4-3/pbdBASE/DESCRIPTION | 40 pbdBASE-0.4-3/pbdBASE/MD5 | 263 ++- pbdBASE-0.4-3/pbdBASE/NAMESPACE | 118 + pbdBASE-0.4-3/pbdBASE/R/000_globalVariables.r |only pbdBASE-0.4-3/pbdBASE/R/base_lm.R |only pbdBASE-0.4-3/pbdBASE/R/base_matexp.r |only pbdBASE-0.4-3/pbdBASE/R/base_mpi_blacs.r |only pbdBASE-0.4-3/pbdBASE/R/base_mpi_blacs_reductions.r |only pbdBASE-0.4-3/pbdBASE/R/base_p_matexp.r |only pbdBASE-0.4-3/pbdBASE/R/base_pblas_level3.r |only pbdBASE-0.4-3/pbdBASE/R/base_plinalg.r |only pbdBASE-0.4-3/pbdBASE/R/base_prblas.r |only pbdBASE-0.4-3/pbdBASE/R/base_putil.R |only pbdBASE-0.4-3/pbdBASE/R/base_qr.r |only pbdBASE-0.4-3/pbdBASE/R/base_scalapack.r |only pbdBASE-0.4-3/pbdBASE/R/base_scalapack_utility.r |only pbdBASE-0.4-3/pbdBASE/R/base_variance.r |only pbdBASE-0.4-3/pbdBASE/R/coords.r |only pbdBASE-0.4-3/pbdBASE/R/get_conf.r | 11 pbdBASE-0.4-3/pbdBASE/R/get_lib.r | 2 pbdBASE-0.4-3/pbdBASE/R/misc.r | 38 pbdBASE-0.4-3/pbdBASE/R/pbdBASE-package.r |only pbdBASE-0.4-3/pbdBASE/R/pkg_blacs_apts.r | 4 pbdBASE-0.4-3/pbdBASE/R/utility_blacs.r |only pbdBASE-0.4-3/pbdBASE/R/zzz.r | 13 pbdBASE-0.4-3/pbdBASE/README.md |only pbdBASE-0.4-3/pbdBASE/build/vignette.rds |binary pbdBASE-0.4-3/pbdBASE/cleanup | 10 pbdBASE-0.4-3/pbdBASE/configure | 306 ++-- pbdBASE-0.4-3/pbdBASE/configure.ac | 56 pbdBASE-0.4-3/pbdBASE/inst/CITATION | 4 pbdBASE-0.4-3/pbdBASE/inst/RNACI |only pbdBASE-0.4-3/pbdBASE/inst/doc/pbdBASE-guide.Rnw | 140 - pbdBASE-0.4-3/pbdBASE/inst/doc/pbdBASE-guide.pdf |binary pbdBASE-0.4-3/pbdBASE/man/BASE-Global-Environment.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.crossprod.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.dallreduce.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.descinit.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.dhilbmk.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.dim0.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.indxg2p.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.matexp.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.maxdim.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.minctxt.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.nbd.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.numroc.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.ownany.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.p_matexp_pade_wrap.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.p_matpow_by_squaring_wrap.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdchtri.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdclvar.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdhilbmk.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdmkcpn1.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdmvsum.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.pdsweep.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.procgrid.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rcolcpy.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rcolcpy2.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rl2blas.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rl2insert.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgecon.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgels.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgemm.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgemr2d.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgeqpf.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgesv.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgesvd.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgetrf.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdgetri.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdlange.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdlaprnt.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdorgqr.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdormqr.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdpotrf.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdsyev.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdsyevx.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdtran.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rpdtrcon.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rrowcpy.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.rrowcpy2.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.tri2zero.Rd |only pbdBASE-0.4-3/pbdBASE/man/base.valid_context.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacs-max.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacs-min.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacs-p2p.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacs-sums.Rd |only pbdBASE-0.4-3/pbdBASE/man/blacsexit.Rd |only pbdBASE-0.4-3/pbdBASE/man/coords.Rd |only pbdBASE-0.4-3/pbdBASE/man/coordspair.Rd |only pbdBASE-0.4-3/pbdBASE/man/diag.Rd |only pbdBASE-0.4-3/pbdBASE/man/finalizer.Rd |only pbdBASE-0.4-3/pbdBASE/man/g2l_coord.Rd |only pbdBASE-0.4-3/pbdBASE/man/g2lcoord.Rd |only pbdBASE-0.4-3/pbdBASE/man/gridexit.Rd |only pbdBASE-0.4-3/pbdBASE/man/gridinfo.Rd |only pbdBASE-0.4-3/pbdBASE/man/gridinit.Rd |only pbdBASE-0.4-3/pbdBASE/man/init.grid.Rd |only pbdBASE-0.4-3/pbdBASE/man/l2g_coord.Rd |only pbdBASE-0.4-3/pbdBASE/man/lclgblmat.Rd |only pbdBASE-0.4-3/pbdBASE/man/numroc2.Rd |only pbdBASE-0.4-3/pbdBASE/man/pbdBASE-package.Rd |only pbdBASE-0.4-3/pbdBASE/man/pcoords.Rd |only pbdBASE-0.4-3/pbdBASE/src/Makevars.in | 179 +- pbdBASE-0.4-3/pbdBASE/src/Makevars.win | 69 pbdBASE-0.4-3/pbdBASE/src/base/bprnt.f | 11 pbdBASE-0.4-3/pbdBASE/src/base/bprnt_c.c | 8 pbdBASE-0.4-3/pbdBASE/src/base/expm/matexp.c | 297 ++-- pbdBASE-0.4-3/pbdBASE/src/base/expm/matexp.h | 18 pbdBASE-0.4-3/pbdBASE/src/base/expm/p_matexp.c | 92 - pbdBASE-0.4-3/pbdBASE/src/base/expm/pade_coefs.c | 6 pbdBASE-0.4-3/pbdBASE/src/base/linalg |only pbdBASE-0.4-3/pbdBASE/src/base/stats |only pbdBASE-0.4-3/pbdBASE/src/base/utils |only pbdBASE-0.4-3/pbdBASE/src/base_lm.c | 433 +----- pbdBASE-0.4-3/pbdBASE/src/base_matexp.c | 59 pbdBASE-0.4-3/pbdBASE/src/base_mpi_blacs.c |only pbdBASE-0.4-3/pbdBASE/src/base_mpi_blacs_reductions.c |only pbdBASE-0.4-3/pbdBASE/src/base_p_matexp.c | 48 pbdBASE-0.4-3/pbdBASE/src/base_pblas_level3.c | 78 - pbdBASE-0.4-3/pbdBASE/src/base_plinalg.c | 57 pbdBASE-0.4-3/pbdBASE/src/base_prblas.c | 14 pbdBASE-0.4-3/pbdBASE/src/base_putil.c | 21 pbdBASE-0.4-3/pbdBASE/src/base_qr.c |only pbdBASE-0.4-3/pbdBASE/src/base_scalapack.c | 842 +++++------- pbdBASE-0.4-3/pbdBASE/src/base_scalapack_utility.c | 113 - pbdBASE-0.4-3/pbdBASE/src/base_variance.c | 21 pbdBASE-0.4-3/pbdBASE/src/comm_utils.c |only pbdBASE-0.4-3/pbdBASE/src/coords.c |only pbdBASE-0.4-3/pbdBASE/src/descinit.c |only pbdBASE-0.4-3/pbdBASE/src/export_blacs/pkg_tools.c | 13 pbdBASE-0.4-3/pbdBASE/src/other.c | 68 pbdBASE-0.4-3/pbdBASE/src/pbdBASE.h |only pbdBASE-0.4-3/pbdBASE/src/scalapack.h |only pbdBASE-0.4-3/pbdBASE/src/utils |only pbdBASE-0.4-3/pbdBASE/vignettes/build_pdf.sh | 6 pbdBASE-0.4-3/pbdBASE/vignettes/include |only pbdBASE-0.4-3/pbdBASE/vignettes/pbdBASE-guide.Rnw | 140 - 170 files changed, 1847 insertions(+), 1869 deletions(-)
Title: Medical Risk and Comorbidity Tools for ICD-9-CM Data
Description: Generates risk estimates and comorbidity flags from ICD-9-CM
codes available in administrative medical datasets. The package supports
the Charlson Comorbidity Index, the Elixhauser Comorbidity
classification, the Revised Cardiac Risk Index, and the Risk Stratification
Index. Methods are table-based, fast, and use the 'plyr' package, so
parallelization is possible for large jobs. Also includes a sample of
real ICD-9 data for 100 patients from a publicly available dataset.
Author: Patrick McCormick [aut, cre],
Thomas Joseph [aut]
Maintainer: Patrick McCormick <patrick.mccormick@alum.mit.edu>
Diff between medicalrisk versions 1.1 dated 2015-01-06 and 1.2 dated 2016-01-24
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Title: Ordination and Multivariate Analysis for Ecology
Description: A variety of ordination and community analyses
useful in analysis of data sets in community ecology.
Includes many of the common ordination methods, with
graphical routines to facilitate their interpretation,
as well as several novel analyses.
Author: David W. Roberts <droberts@montana.edu>
Maintainer: David W. Roberts <droberts@montana.edu>
Diff between labdsv versions 1.7-0 dated 2015-05-04 and 1.8-0 dated 2016-01-24
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Title: Chi-Square and Exact Tests for Non-Parametric Functional
Dependencies
Description: Statistical hypothesis testing methods for non-parametric functional dependencies based on asymptotic chi-square and exact statistics. These tests were designed to reveal evidence for causality based on functional dependencies. They include asymptotic functional chi-square tests, an exact functional test, and a comparative functional chi-square test. The normalized non-constant functional chi-square test was used by the Best Performer NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network Inference Challenges. These tests offer an advantage over regression analysis when a parametric functional form cannot be assumed.
Author: Yang Zhang, Hua Zhong, and Joe Song
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.1.0 dated 2015-06-29 and 2.2.0 dated 2016-01-24
DESCRIPTION | 11 +- MD5 | 20 ++-- NAMESPACE | 1 NEWS | 45 +++++++--- R/CPChisq.R |only R/FunChisq.R | 124 ++++++++++++++++++----------- inst/CITATION | 31 ++++++- man/cp.chisq.test.Rd |only man/cp.fun.chisq.test.Rd | 5 - man/fun.chisq.test.Rd | 27 ++++-- tests/testthat.R | 8 - tests/testthat/test_FunChisq.R | 170 ++++++++++++++++++++++++++++++++++------- 12 files changed, 324 insertions(+), 118 deletions(-)
Title: Quantile Regression for Random Variables on the Unit Interval
Description: Employs a two-parameter family of
distributions for modelling random variables on the (0, 1) interval by
applying the cumulative distribution function (cdf) of one parent
distribution to the quantile function of another.
Author: Yiyun Shou [aut, cre],
Michael Smithson [aut]
Maintainer: Yiyun Shou <yiyun.shou@anu.edu.au>
Diff between cdfquantreg versions 1.0.0 dated 2015-12-27 and 1.0.1 dated 2016-01-24
DESCRIPTION | 8 - MD5 | 41 ++++----- NAMESPACE | 3 NEWS |only R/bugsModel.R | 6 - R/cdfquantreg.R | 4 R/qrBugs.R | 25 +++++ R/qrDistributions.R | 16 +-- R/qrInfluence.R | 22 ++--- R/qrMethod.R | 30 +++--- R/qrPlot.R | 42 ++++++++- inst/doc/IPCCExample.Rmd | 2 inst/doc/IPCCExample.html | 36 ++++---- inst/doc/Smithson_Verkuilen2006Example.R | 14 --- inst/doc/Smithson_Verkuilen2006Example.Rmd | 17 --- inst/doc/Smithson_Verkuilen2006Example.html | 121 ++++++++++++---------------- man/cdfquantreg-package.Rd | 6 - man/dq.Rd | 13 +-- man/influence.cdfqr.Rd | 6 - man/qrBugs.Rd | 16 +++ vignettes/IPCCExample.Rmd | 2 vignettes/Smithson_Verkuilen2006Example.Rmd | 17 --- 22 files changed, 231 insertions(+), 216 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between BiodiversityR versions 2.5-4 dated 2015-09-23 and 2.6-1 dated 2016-01-24
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