Title: Tools for Interacting with the Brazilian Flora Checklist
Diff between flora versions 0.2.3 dated 2014-07-17 and 0.2.4 dated 2015-03-20
Description: Tools to quickly compile taxonomic and distribution data from
the Brazilian Flora Checklist.
Author: Gustavo Carvalho
Maintainer: Gustavo Carvalho
DESCRIPTION | 14 ++++++------
MD5 | 54 +++++++++++++++++++++++------------------------
NAMESPACE | 2 -
NEWS | 7 ++++++
R/get.taxa.R | 17 ++++++--------
R/lower.taxa.R | 2 +
R/occurrence.R | 18 ++++++++++-----
R/remove.authors.R | 2 +
R/standardize.names.R | 2 +
R/suggest.names.R | 2 +
R/sysdata.rda |binary
R/trim.R | 2 +
R/vernacular.R | 2 +
data/plants.rda |binary
inst/plantminer/server.R | 17 ++++++++++----
inst/plantminer/ui.R | 4 +--
man/fixCase.Rd | 3 +-
man/flora.Rd | 3 +-
man/get.taxa.Rd | 9 ++++---
man/lower.taxa.Rd | 5 +++-
man/occurrence.Rd | 5 +++-
man/plants.Rd | 3 +-
man/remove.authors.Rd | 5 +++-
man/standardize.names.Rd | 5 +++-
man/suggest.names.Rd | 5 +++-
man/trim.Rd | 5 +++-
man/vernacular.Rd | 5 +++-
man/web.flora.Rd | 3 +-
28 files changed, 129 insertions(+), 72 deletions(-)
Title: Generalization of the Convex Hull of a Sample of Points in the
Plane
Diff between alphahull versions 1.0 dated 2013-11-28 and 2.0 dated 2015-03-20
Description: Computation of the alpha-shape and alpha-convex
hull of a given sample of points in the plane. The concepts of
alpha-shape and alpha-convex hull generalize the definition of
the convex hull of a finite set of points. The programming is
based on the duality between the Voronoi diagram and Delaunay
triangulation. The package also includes a function that
returns the Delaunay mesh of a given sample of points and its
dual Voronoi diagram in one single object.
Author: Beatriz Pateiro-Lopez, Alberto Rodriguez-Casal.
Maintainer: Beatriz Pateiro-Lopez
DESCRIPTION | 16 +--
MD5 | 28 ++++--
NAMESPACE | 10 +-
R/ahull_track.R |only
R/dw.R |only
R/dw_track.R |only
build/vignette.rds |binary
inst/doc/alphahull.R | 192 ++++++++---------------------------------------
inst/doc/alphahull.pdf |binary
inst/doc/alphahull.rnw | 190 ++++------------------------------------------
man/ahull.Rd | 2
man/ahull_track.Rd |only
man/alphahull-package.Rd | 8 -
man/complement.Rd | 2
man/dw.Rd |only
man/dw_track.Rd |only
vignettes/alphahull.rnw | 190 ++++------------------------------------------
vignettes/biblioJSS.bib | 174 +++++++++++++++++++++---------------------
18 files changed, 202 insertions(+), 610 deletions(-)
Title: Bayesian Emulation, Calibration and Validation of Computer
Models
Diff between SAVE versions 0.9.3.9.2 dated 2014-05-28 and 1.0 dated 2015-03-20
Description: Implements Bayesian statistical methodology for the
analysis of complex computer models.
It allows for the emulation, calibration, and validation of computer models,
following methodology described in Bayarri et al 2007, Technometrics.
Author: Jesus Palomo [aut, cre],
Gonzalo Garcia-Donato [aut],
Rui Paulo [aut],
James Berger [ctb],
Maria Jesus Bayarri [ctb],
Jerome Sacks [ctb]
Maintainer: Jesus Palomo
SAVE-0.9.3.9.2/SAVE/build |only
SAVE-0.9.3.9.2/SAVE/inst/doc |only
SAVE-0.9.3.9.2/SAVE/vignettes |only
SAVE-1.0/SAVE/DESCRIPTION | 12 -
SAVE-1.0/SAVE/MD5 | 48 ++-----
SAVE-1.0/SAVE/NAMESPACE | 7 -
SAVE-1.0/SAVE/data/synthfield.rda |binary
SAVE-1.0/SAVE/data/synthmodel.rda |binary
SAVE-1.0/SAVE/inst/CITATION | 30 ++--
SAVE-1.0/SAVE/inst/extdata/SpotweldExample.r | 93 ++++++++-------
SAVE-1.0/SAVE/inst/extdata/SyntheticExample.r | 160 ++++++++++----------------
SAVE-1.0/SAVE/man/SAVE-package.Rd | 2
SAVE-1.0/SAVE/man/SAVE.Rd | 2
SAVE-1.0/SAVE/man/Spotweld.Rd | 2
SAVE-1.0/SAVE/man/bayesfit.SAVE.Rd | 2
SAVE-1.0/SAVE/man/validate.SAVE.Rd | 2
SAVE-1.0/SAVE/src/Makevars | 2
17 files changed, 166 insertions(+), 196 deletions(-)
Title: Population (and Individual) Optimal Experimental Design
Diff between PopED versions 0.1.2 dated 2014-11-19 and 0.2.0 dated 2015-03-20
Description: Optimal experimental designs for both population and individual
studies based on nonlinear mixed-effect models. Often this is based on a
computation of the Fisher Information Matrix (FIM). This package was developed
for pharmacometric problems, and examples and predefined models are available
for these types of systems.
Author: Andrew C. Hooker [aut, cre, trl, cph],
Sebastian Ueckert [aut] (MATLAB version),
Marco Foracchia [aut] (O-Matrix version),
Joakim Nyberg [aut] (MATLAB version),
Eric Stroemberg [ctb] (MATLAB version)
Maintainer: Andrew C. Hooker
PopED-0.1.2/PopED/inst/examples/PopED_output_summary_D_cont_opt_1.txt |only
PopED-0.1.2/PopED/inst/examples/test.csv |only
PopED-0.2.0/PopED/DESCRIPTION | 46
PopED-0.2.0/PopED/MD5 | 414 +++---
PopED-0.2.0/PopED/NEWS | 14
PopED-0.2.0/PopED/R/Doptim.R | 237 +--
PopED-0.2.0/PopED/R/Dtrace.R | 58
PopED-0.2.0/PopED/R/LEDoptim.R | 46
PopED-0.2.0/PopED/R/LinMatrixH.R | 34
PopED-0.2.0/PopED/R/LinMatrixL.R | 2
PopED-0.2.0/PopED/R/LinMatrixLH.R | 30
PopED-0.2.0/PopED/R/LinMatrixL_occ.R | 2
PopED-0.2.0/PopED/R/RS_opt.R | 134 +-
PopED-0.2.0/PopED/R/RS_opt_gen.R | 117 -
PopED-0.2.0/PopED/R/a_line_search.R | 258 ++--
PopED-0.2.0/PopED/R/blockexp.R | 72 -
PopED-0.2.0/PopED/R/blockfinal.R | 44
PopED-0.2.0/PopED/R/blockheader.R | 24
PopED-0.2.0/PopED/R/blockopt.R | 24
PopED-0.2.0/PopED/R/blockother.R | 114 -
PopED-0.2.0/PopED/R/calc_ofv_and_fim.R | 50
PopED-0.2.0/PopED/R/convert_variables.R | 179 +-
PopED-0.2.0/PopED/R/create.poped.database.R | 616 ++++------
PopED-0.2.0/PopED/R/create_design.R | 2
PopED-0.2.0/PopED/R/d2fimdalpha2.R | 10
PopED-0.2.0/PopED/R/dfimdalpha.R | 8
PopED-0.2.0/PopED/R/downsizing_general_design.R | 55
PopED-0.2.0/PopED/R/ed_laplace_ofv.R | 80 -
PopED-0.2.0/PopED/R/ed_mftot.R | 24
PopED-0.2.0/PopED/R/evaluate.e.ofv.fim.R | 34
PopED-0.2.0/PopED/R/evaluate.fim.R | 26
PopED-0.2.0/PopED/R/get_all_params.R | 18
PopED-0.2.0/PopED/R/get_cv.R | 20
PopED-0.2.0/PopED/R/get_fim_size.R | 16
PopED-0.2.0/PopED/R/get_unfixed_params.R | 52
PopED-0.2.0/PopED/R/graddetmfa.R | 32
PopED-0.2.0/PopED/R/graddetmfa_ext.R | 34
PopED-0.2.0/PopED/R/graddetmfxt.R | 30
PopED-0.2.0/PopED/R/graddetmfxt_ext.R | 34
PopED-0.2.0/PopED/R/gradff.R | 48
PopED-0.2.0/PopED/R/gradfg.R | 28
PopED-0.2.0/PopED/R/gradfg_occ.R | 26
PopED-0.2.0/PopED/R/gradlndetmfa.R | 32
PopED-0.2.0/PopED/R/gradlndetmfa_ext.R | 34
PopED-0.2.0/PopED/R/gradlndetmfxt.R | 30
PopED-0.2.0/PopED/R/gradlndetmfxt_ext.R | 34
PopED-0.2.0/PopED/R/gradofv_a.R | 98 -
PopED-0.2.0/PopED/R/gradofv_xt.R | 84 -
PopED-0.2.0/PopED/R/gradtrmfa.R | 30
PopED-0.2.0/PopED/R/gradtrmfxt.R | 28
PopED-0.2.0/PopED/R/hessian_eta_complex.R | 24
PopED-0.2.0/PopED/R/hesskalpha2.R | 8
PopED-0.2.0/PopED/R/ind_estimates.R | 14
PopED-0.2.0/PopED/R/ind_likelihood.R | 46
PopED-0.2.0/PopED/R/m1.R | 154 +-
PopED-0.2.0/PopED/R/m2.R | 54
PopED-0.2.0/PopED/R/m3.R | 224 +--
PopED-0.2.0/PopED/R/mf.R | 112 -
PopED-0.2.0/PopED/R/mf3.R | 37
PopED-0.2.0/PopED/R/mf5.R | 22
PopED-0.2.0/PopED/R/mf6.R | 38
PopED-0.2.0/PopED/R/mf7.R | 22
PopED-0.2.0/PopED/R/mf8.R | 22
PopED-0.2.0/PopED/R/mf_all.R | 20
PopED-0.2.0/PopED/R/mfea.R | 179 +-
PopED-0.2.0/PopED/R/mftot.R | 2
PopED-0.2.0/PopED/R/model_prediction.R | 26
PopED-0.2.0/PopED/R/models.R | 6
PopED-0.2.0/PopED/R/ofv_criterion.R | 4
PopED-0.2.0/PopED/R/ofv_fim.R | 10
PopED-0.2.0/PopED/R/pargen.R | 12
PopED-0.2.0/PopED/R/plot_efficiency_of_windows.R | 58
PopED-0.2.0/PopED/R/plot_model_prediction.R | 15
PopED-0.2.0/PopED/R/poped_optimize.R | 58
PopED-0.2.0/PopED/R/v.R | 40
PopED-0.2.0/PopED/R/write_iterationfile.R | 12
PopED-0.2.0/PopED/inst/examples/HCV_ode.c |only
PopED-0.2.0/PopED/inst/examples/ex.1.a.PK.1.comp.oral.md.intro.R | 2
PopED-0.2.0/PopED/inst/examples/ex.1.c.PK.1.comp.oral.md.ODE.R | 2
PopED-0.2.0/PopED/inst/examples/ex.10.PKPD.HCV.compiled.R |only
PopED-0.2.0/PopED/inst/examples/ex.2.a.warfarin.evaluate.R | 2
PopED-0.2.0/PopED/inst/examples/ex.2.b.warfarin.optimize.R | 2
PopED-0.2.0/PopED/inst/examples/ex.4.PKPD.1.comp.emax.R | 2
PopED-0.2.0/PopED/inst/examples/ex.7.PK.1.comp.maturation.R | 2
PopED-0.2.0/PopED/inst/examples/ex.8.a.tmdd_qss_one_target.R | 2
PopED-0.2.0/PopED/inst/examples/ex.8.b.tmdd_qss_one_target_compiled.R | 2
PopED-0.2.0/PopED/inst/examples/ex.9.PK.2.comp.oral.md.ode.compiled.R | 1
PopED-0.2.0/PopED/inst/shinyapp/server.R | 2
PopED-0.2.0/PopED/man/Doptim.Rd | 30
PopED-0.2.0/PopED/man/Dtrace.Rd | 82 -
PopED-0.2.0/PopED/man/LEDoptim.Rd | 9
PopED-0.2.0/PopED/man/LinMatrixH.Rd | 17
PopED-0.2.0/PopED/man/LinMatrixL.Rd | 15
PopED-0.2.0/PopED/man/LinMatrixLH.Rd | 19
PopED-0.2.0/PopED/man/LinMatrixL_occ.Rd | 15
PopED-0.2.0/PopED/man/PopED-package.Rd | 5
PopED-0.2.0/PopED/man/RS_opt.Rd | 15
PopED-0.2.0/PopED/man/RS_opt_gen.Rd | 22
PopED-0.2.0/PopED/man/a_line_search.Rd | 12
PopED-0.2.0/PopED/man/bfgsb_min.Rd | 26
PopED-0.2.0/PopED/man/blockexp.Rd | 10
PopED-0.2.0/PopED/man/blockfinal.Rd | 46
PopED-0.2.0/PopED/man/blockheader.Rd | 37
PopED-0.2.0/PopED/man/blockopt.Rd | 3
PopED-0.2.0/PopED/man/calc_autofocus.Rd | 5
PopED-0.2.0/PopED/man/calc_ofv_and_fim.Rd | 22
PopED-0.2.0/PopED/man/calc_ofv_and_grad.Rd | 29
PopED-0.2.0/PopED/man/cell.Rd | 3
PopED-0.2.0/PopED/man/convert_variables.Rd | 3
PopED-0.2.0/PopED/man/create.poped.database.Rd | 9
PopED-0.2.0/PopED/man/create_design.Rd | 3
PopED-0.2.0/PopED/man/create_design_space.Rd | 3
PopED-0.2.0/PopED/man/diag_matlab.Rd | 3
PopED-0.2.0/PopED/man/downsizing_general_design.Rd | 13
PopED-0.2.0/PopED/man/ed_laplace_ofv.Rd | 6
PopED-0.2.0/PopED/man/ed_mftot.Rd | 27
PopED-0.2.0/PopED/man/evaluate.e.ofv.fim.Rd | 21
PopED-0.2.0/PopED/man/evaluate.fim.Rd | 3
PopED-0.2.0/PopED/man/feps.add.Rd | 3
PopED-0.2.0/PopED/man/feps.add.prop.Rd | 3
PopED-0.2.0/PopED/man/feps.prop.Rd | 3
PopED-0.2.0/PopED/man/feval.Rd | 3
PopED-0.2.0/PopED/man/ff.PK.1.comp.oral.md.CL.Rd | 3
PopED-0.2.0/PopED/man/ff.PK.1.comp.oral.md.KE.Rd | 3
PopED-0.2.0/PopED/man/ff.PK.1.comp.oral.sd.CL.Rd | 3
PopED-0.2.0/PopED/man/ff.PK.1.comp.oral.sd.KE.Rd | 3
PopED-0.2.0/PopED/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd | 5
PopED-0.2.0/PopED/man/ff.PKPD.1.comp.sd.CL.emax.Rd | 5
PopED-0.2.0/PopED/man/fileparts.Rd | 3
PopED-0.2.0/PopED/man/getTruncatedNormal.Rd | 3
PopED-0.2.0/PopED/man/get_all_params.Rd | 3
PopED-0.2.0/PopED/man/get_rse.Rd | 11
PopED-0.2.0/PopED/man/getfulld.Rd | 3
PopED-0.2.0/PopED/man/gradf_eps.Rd | 17
PopED-0.2.0/PopED/man/isempty.Rd | 3
PopED-0.2.0/PopED/man/isfield.Rd | 3
PopED-0.2.0/PopED/man/log_prior_pdf.Rd | 9
PopED-0.2.0/PopED/man/mf.Rd | 17
PopED-0.2.0/PopED/man/mf3.Rd | 17
PopED-0.2.0/PopED/man/mf5.Rd | 17
PopED-0.2.0/PopED/man/mf6.Rd | 17
PopED-0.2.0/PopED/man/mf7.Rd | 17
PopED-0.2.0/PopED/man/mf8.Rd | 17
PopED-0.2.0/PopED/man/mfea.Rd | 10
PopED-0.2.0/PopED/man/mftot.Rd | 23
PopED-0.2.0/PopED/man/mftot0.Rd | 23
PopED-0.2.0/PopED/man/mftot1.Rd | 23
PopED-0.2.0/PopED/man/mftot2.Rd | 3
PopED-0.2.0/PopED/man/mftot3.Rd | 3
PopED-0.2.0/PopED/man/mftot4.Rd | 23
PopED-0.2.0/PopED/man/mftot5.Rd | 23
PopED-0.2.0/PopED/man/mftot6.Rd | 23
PopED-0.2.0/PopED/man/mftot7.Rd | 23
PopED-0.2.0/PopED/man/model_prediction.Rd | 27
PopED-0.2.0/PopED/man/ofv_criterion.Rd | 5
PopED-0.2.0/PopED/man/ofv_fim.Rd | 7
PopED-0.2.0/PopED/man/ones.Rd | 3
PopED-0.2.0/PopED/man/pargen.Rd | 8
PopED-0.2.0/PopED/man/plot_efficiency_of_windows.Rd | 11
PopED-0.2.0/PopED/man/plot_model_prediction.Rd | 3
PopED-0.2.0/PopED/man/poped.choose.Rd | 3
PopED-0.2.0/PopED/man/poped_optimize.Rd | 28
PopED-0.2.0/PopED/man/rand.Rd | 3
PopED-0.2.0/PopED/man/randn.Rd | 3
PopED-0.2.0/PopED/man/randperm.Rd | 3
PopED-0.2.0/PopED/man/size.Rd | 3
PopED-0.2.0/PopED/man/test_for_max.Rd | 3
PopED-0.2.0/PopED/man/test_for_min.Rd | 3
PopED-0.2.0/PopED/man/test_for_zeros.Rd | 3
PopED-0.2.0/PopED/man/test_mat_size.Rd | 3
PopED-0.2.0/PopED/man/tic.Rd | 3
PopED-0.2.0/PopED/man/toc.Rd | 3
PopED-0.2.0/PopED/man/zeros.Rd | 3
PopED-0.2.0/PopED/tests/testthat/PopED_output_summary_D_cont_opt_1.txt | 266 ++--
PopED-0.2.0/PopED/tests/testthat/PopED_output_summary_ED_Laplace_opt.txt | 87 -
PopED-0.2.0/PopED/tests/testthat/PopED_output_summary_RS_1.txt | 69 -
PopED-0.2.0/PopED/tests/testthat/PopED_output_summary_mfea_opt_1.txt | 10
PopED-0.2.0/PopED/tests/testthat/Rplots.pdf |binary
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_Doptim.R | 2
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_Dtrace.R | 70 -
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixH.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixL.R | 12
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixLH.R | 16
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_LinMatrixL_occ.R | 12
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_bfgsb_min.R | 23
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_blockfinal.R | 34
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_blockheader.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_calc_ofv_and_grad.R | 26
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_downsizing_general_design.R | 10
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_ed_mftot.R | 24
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_ff.PKPD.1.comp.oral.md.CL.imax.R | 2
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_ff.PKPD.1.comp.sd.CL.emax.R | 2
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_gradf_eps.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_log_prior_pdf.R | 6
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf3.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf5.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf6.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf7.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mf8.R | 14
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot0.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot1.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot4.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot5.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot6.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_mftot7.R | 20
PopED-0.2.0/PopED/tests/testthat/examples_fcn_doc/examples_poped-package.R | 2
PopED-0.2.0/PopED/tests/testthat/test_distributions.R | 6
PopED-0.2.0/PopED/tests/testthat/test_examples.R | 8
210 files changed, 3403 insertions(+), 3265 deletions(-)
Title: Normalize NanoString miRNA and mRNA Data
Diff between NanoStringNorm versions 1.1.17 dated 2014-01-17 and 1.1.19 dated 2015-03-20
More information about NanoStringNorm at CRAN
Description: A set of tools for normalizing, diagnostics and visualization of NanoString nCounter data.
Author: Daryl M. Waggott
Maintainer: Paul Boutros
DESCRIPTION | 14 ++++++-------
MD5 | 24 +++++++++++-----------
R/Plot.NanoStringNorm.gvis.R | 8 +++----
R/norm.comp.R | 8 +++----
R/other.normalization.rank.normal.R | 33 +++++++++++++++++--------------
R/other.normalization.vsn.R | 6 ++---
R/read.markup.RCC.R | 22 +++++++++++++++++---
R/unit.testing.NanoStringNorm.R | 8 +++----
build/vignette.rds |binary
inst/doc/NanoStringNorm_Introduction.pdf |binary
man/Plot.NanoStringNorm.gvis.Rd | 16 +++++++++++++--
man/norm.comp.Rd | 2 -
man/read.markup.RCC.Rd | 4 ++-
13 files changed, 90 insertions(+), 55 deletions(-)
Permanent link
Title: Generalized Hermite Distribution
Diff between hermite versions 1.0.1 dated 2014-12-18 and 1.0.2 dated 2015-03-20
Description: Probability functions and other utilities for the generalized Hermite distribution.
Author: David Moriña, Manuel Higueras, Pedro Puig and María Oliveira
Maintainer: David Moriña Soler
hermite-1.0.1/hermite/R/mle.hermite.R |only
hermite-1.0.1/hermite/man/mle.hermite.Rd |only
hermite-1.0.2/hermite/DESCRIPTION | 14 +++---
hermite-1.0.2/hermite/MD5 | 28 ++++++------
hermite-1.0.2/hermite/NAMESPACE | 5 ++
hermite-1.0.2/hermite/R/dhermite.R | 54 +++++++++++-------------
hermite-1.0.2/hermite/R/glm.hermite.R |only
hermite-1.0.2/hermite/R/int.hermite.R | 58 +++++++++++++-------------
hermite-1.0.2/hermite/R/rhermite.R | 4 +
hermite-1.0.2/hermite/data |only
hermite-1.0.2/hermite/man/dhermite.Rd | 44 +++++++++++++------
hermite-1.0.2/hermite/man/glm.hermite.Rd |only
hermite-1.0.2/hermite/man/hermite-internal.Rd | 3 -
hermite-1.0.2/hermite/man/hermite-package.Rd | 56 ++++++++++++++++++-------
hermite-1.0.2/hermite/man/hi_let.Rd |only
hermite-1.0.2/hermite/man/phermite.Rd | 46 ++++++++++++++------
hermite-1.0.2/hermite/man/qhermite.Rd | 49 +++++++++++++++------
hermite-1.0.2/hermite/man/rhermite.Rd | 41 ++++++++++++------
18 files changed, 255 insertions(+), 147 deletions(-)
Title: Genealogical Data Analysis
Diff between GENLIB versions 1.0.2 dated 2014-12-04 and 1.0.3 dated 2015-03-20
Description: Genealogical data analysis including descriptive statistics (e.g., kinship and inbreeding coefficients) and gene-dropping simulations.
Author: Louis Houde [aut],
Jean-Francois Lefebvre [aut],
Valery Roy-Lagace [aut],
Sebastien Lemieux [aut],
Michael J. Fromberger [ctb],
Marie-Helene Roy-Gagnon [cre]
Maintainer: Marie-Helene Roy-Gagnon
GENLIB-1.0.2/GENLIB/man/gen.entropy.Rd |only
GENLIB-1.0.2/GENLIB/man/gen.entropyVar.Rd |only
GENLIB-1.0.2/GENLIB/man/gen.grimperPAR.Rd |only
GENLIB-1.0.3/GENLIB/DESCRIPTION | 9
GENLIB-1.0.3/GENLIB/MD5 | 142 +++++++-------
GENLIB-1.0.3/GENLIB/NAMESPACE | 2
GENLIB-1.0.3/GENLIB/R/classes_methodes.R | 6
GENLIB-1.0.3/GENLIB/R/fonctionsBase.R | 246 +++++++++++--------------
GENLIB-1.0.3/GENLIB/R/fonctionsGraph.R | 4
GENLIB-1.0.3/GENLIB/R/fonctionsPAR.R | 10 -
GENLIB-1.0.3/GENLIB/R/fonctionsPriv.R | 19 +
GENLIB-1.0.3/GENLIB/R/fonctionsSimul.R | 10 -
GENLIB-1.0.3/GENLIB/R/fonctionsStat.R | 14 -
GENLIB-1.0.3/GENLIB/man/gen.branching.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.children.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.climbPAR.Rd |only
GENLIB-1.0.3/GENLIB/man/gen.completeness.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.completenessVar.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.depth.Rd | 2
GENLIB-1.0.3/GENLIB/man/gen.f.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.fCI.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.founder.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.gc.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.genealogy.Rd | 8
GENLIB-1.0.3/GENLIB/man/gen.genout.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.getAncestorsPAR.Rd | 2
GENLIB-1.0.3/GENLIB/man/gen.half.founder.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.implex.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.implexVar.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.lineages.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.max.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.mean.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.meangendepth.Rd |only
GENLIB-1.0.3/GENLIB/man/gen.meangendepthVar.Rd |only
GENLIB-1.0.3/GENLIB/man/gen.min.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.nochildren.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.noind.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.nomen.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.nowomen.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.occ.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.parent.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.phi.Rd | 4
GENLIB-1.0.3/GENLIB/man/gen.phiCI.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.phiMean.Rd | 3
GENLIB-1.0.3/GENLIB/man/gen.pro.Rd | 9
GENLIB-1.0.3/GENLIB/man/gen.rec.Rd | 7
GENLIB-1.0.3/GENLIB/man/gen.sibship.Rd | 5
GENLIB-1.0.3/GENLIB/man/gen.simuProb.Rd | 4
GENLIB-1.0.3/GENLIB/man/gen.simuSample.Rd | 8
GENLIB-1.0.3/GENLIB/man/gen.simuSet.Rd | 12 -
GENLIB-1.0.3/GENLIB/src/Makevars | 2
GENLIB-1.0.3/GENLIB/src/apparentement.cpp | 3
GENLIB-1.0.3/GENLIB/src/apparentement.h | 1
GENLIB-1.0.3/GENLIB/src/base.h | 18 +
GENLIB-1.0.3/GENLIB/src/cbignum.h | 1
GENLIB-1.0.3/GENLIB/src/congen.cpp | 1
GENLIB-1.0.3/GENLIB/src/congen.h | 1
GENLIB-1.0.3/GENLIB/src/consanguinite.cpp | 1
GENLIB-1.0.3/GENLIB/src/consanguinite.h | 1
GENLIB-1.0.3/GENLIB/src/fondateur.cpp | 178 ++++++++++++++----
GENLIB-1.0.3/GENLIB/src/fondateur.h | 1
GENLIB-1.0.3/GENLIB/src/genphi.cpp | 2
GENLIB-1.0.3/GENLIB/src/hal.cpp | 3
GENLIB-1.0.3/GENLIB/src/hal.h | 5
GENLIB-1.0.3/GENLIB/src/hashtable.h | 1
GENLIB-1.0.3/GENLIB/src/interface.cpp | 1
GENLIB-1.0.3/GENLIB/src/mpi-types.h | 2
GENLIB-1.0.3/GENLIB/src/mpi.c | 6
GENLIB-1.0.3/GENLIB/src/outils.cpp | 15 +
GENLIB-1.0.3/GENLIB/src/outils.h | 1
GENLIB-1.0.3/GENLIB/src/outilsalloc.h | 1
GENLIB-1.0.3/GENLIB/src/probsimul.cpp | 1
GENLIB-1.0.3/GENLIB/src/probsimul.h | 1
GENLIB-1.0.3/GENLIB/src/userInterface.cpp | 1
GENLIB-1.0.3/GENLIB/src/userInterface.h | 1
75 files changed, 493 insertions(+), 385 deletions(-)
Title: Database Preferences and Skyline Computation
Diff between rPref versions 0.4 dated 2015-01-15 and 0.5 dated 2015-03-20
Description: Routines to select and visualize the maxima for a given strict
partial order. This especially includes the computation of the Pareto
frontier, also known as (Top-k) Skyline operator, and some
generalizations (database preferences).
Author: Patrick Roocks
Maintainer: Patrick Roocks
DESCRIPTION | 13 +-
MD5 | 61 +++++------
NAMESPACE | 10 +
NEWS | 14 +-
R/base-pref.r | 46 +++++++-
R/complex-pref.r | 59 ++++------
R/pred-succ.r | 42 +++++--
R/pref-classes.r | 256 ++++++++++++++++++++++++++++++++---------------
R/pref-eval.r | 29 ++---
R/rPref.r | 5
R/show-pref.r | 79 +++++++++++---
R/visualize.r | 5
inst/test/test-hasse.R | 48 ++++++++
inst/test/test-pref.r |only
inst/test/test-strings.R | 29 ++++-
man/base_pref.Rd | 42 ++++++-
man/base_pref_macros.Rd | 5
man/complex_pref.Rd | 24 +++-
man/get_btg.Rd | 5
man/get_hasse_diag.Rd | 7 -
man/plot_front.Rd | 8 -
man/pred_succ.Rd | 39 ++++---
man/psel.Rd | 34 +++---
man/rPref.Rd | 9 -
man/show.pref.Rd | 49 +++++++-
man/show.query.Rd | 20 ++-
src/Makevars |only
src/Makevars.win |only
src/RcppExports.cpp | 120 +++++++++-------------
src/psel-par-top.cpp | 48 +++++---
src/psel-par.cpp | 21 ++-
src/scalagon.cpp | 37 ++++--
src/scalagon.h | 19 ++-
33 files changed, 792 insertions(+), 391 deletions(-)
Title: Connect MonetDB to R
Diff between MonetDB.R versions 0.9.5 dated 2014-10-06 and 0.9.6 dated 2015-03-20
Description: Allows to pull data from MonetDB into R. Includes a DBI implementation and a dplyr backend.
Author: Hannes Muehleisen [aut, cre], Thomas Lumley [ctb], Anthony Damico [ctb]
Maintainer: Hannes Muehleisen
MonetDB.R-0.9.5/MonetDB.R/src/Makevars.win |only
MonetDB.R-0.9.5/MonetDB.R/src/mapi.c |only
MonetDB.R-0.9.6/MonetDB.R/DESCRIPTION | 6
MonetDB.R-0.9.6/MonetDB.R/MD5 | 30 +--
MonetDB.R-0.9.6/MonetDB.R/NAMESPACE | 6
MonetDB.R-0.9.6/MonetDB.R/NEWS | 7
MonetDB.R-0.9.6/MonetDB.R/R/control.R | 16 +
MonetDB.R-0.9.6/MonetDB.R/R/dbi.R | 174 ++++++++++---------
MonetDB.R-0.9.6/MonetDB.R/R/dplyr.R | 25 ++
MonetDB.R-0.9.6/MonetDB.R/R/mapi.R | 124 +++++--------
MonetDB.R-0.9.6/MonetDB.R/man/control.Rd | 3
MonetDB.R-0.9.6/MonetDB.R/man/mc.Rd | 2
MonetDB.R-0.9.6/MonetDB.R/man/monetdb.read.csv.Rd | 3
MonetDB.R-0.9.6/MonetDB.R/man/monetdbRtype.Rd | 2
MonetDB.R-0.9.6/MonetDB.R/man/src_monetdb.Rd | 2
MonetDB.R-0.9.6/MonetDB.R/src/mapisplit-r.c |only
MonetDB.R-0.9.6/MonetDB.R/src/mapisplit.c | 195 ++++++----------------
MonetDB.R-0.9.6/MonetDB.R/src/mapisplit.h |only
18 files changed, 267 insertions(+), 328 deletions(-)
Title: Latent Markov Models with and without Covariates
Diff between LMest versions 2.0 dated 2014-11-18 and 2.1 dated 2015-03-20
Description: Fit certain versions of the Latent Markov model for longitudinal categorical data.
Author: Francesco Bartolucci, Silvia Pandolfi - University of Perugia (IT)
Maintainer: Francesco Bartolucci
LMest-2.0/LMest/R/deconding.R |only
LMest-2.0/LMest/data/data_SRHS.rda |only
LMest-2.0/LMest/man/data_SRHS.Rd |only
LMest-2.0/LMest/man/deconding.Rd |only
LMest-2.1/LMest/DESCRIPTION | 12 +--
LMest-2.1/LMest/MD5 | 86 ++++++++++++-------------
LMest-2.1/LMest/NAMESPACE | 15 ++++
LMest-2.1/LMest/R/bootstrap_lm_cov_latent.R | 34 ++++++++-
LMest-2.1/LMest/R/decoding.R |only
LMest-2.1/LMest/R/draw_lm_cov_latent.R | 9 +-
LMest-2.1/LMest/R/draw_lm_mixed.R | 2
LMest-2.1/LMest/R/est_lm_basic.R | 2
LMest-2.1/LMest/R/est_lm_cov_latent.R | 50 ++++++++------
LMest-2.1/LMest/R/est_lm_cov_manifest.R | 69 +++++++++++---------
LMest-2.1/LMest/R/est_lm_mixed.R | 6 -
LMest-2.1/LMest/R/lk_comp_latent.R | 19 +----
LMest-2.1/LMest/R/lk_obs_mixed.R | 2
LMest-2.1/LMest/R/long2matrices.R |only
LMest-2.1/LMest/R/sq.R | 15 +---
LMest-2.1/LMest/R/summary.LMbasic.R | 5 -
LMest-2.1/LMest/data/data_SRHS_long.rda |only
LMest-2.1/LMest/man/LMest-package.Rd | 10 +-
LMest-2.1/LMest/man/bootstrap_lm_basic.Rd | 6 -
LMest-2.1/LMest/man/bootstrap_lm_cov_latent.Rd | 36 ++++------
LMest-2.1/LMest/man/complk.Rd | 10 +-
LMest-2.1/LMest/man/data_SRHS_long.Rd |only
LMest-2.1/LMest/man/decoding.Rd |only
LMest-2.1/LMest/man/draw_lm_basic.Rd | 6 -
LMest-2.1/LMest/man/draw_lm_cov_latent.Rd | 12 +--
LMest-2.1/LMest/man/draw_lm_mixed.Rd | 2
LMest-2.1/LMest/man/est_lm_basic.Rd | 6 -
LMest-2.1/LMest/man/est_lm_cov_latent.Rd | 44 ++++++------
LMest-2.1/LMest/man/est_lm_cov_manifest.Rd | 47 +++++--------
LMest-2.1/LMest/man/est_lm_mixed.Rd | 2
LMest-2.1/LMest/man/est_multilogit.Rd | 2
LMest-2.1/LMest/man/invglob.Rd | 2
LMest-2.1/LMest/man/lk_comp_latent.Rd | 10 +-
LMest-2.1/LMest/man/lk_obs.Rd | 6 -
LMest-2.1/LMest/man/lk_obs_manifest.Rd | 2
LMest-2.1/LMest/man/lk_sta.Rd | 2
LMest-2.1/LMest/man/long2matrices.Rd |only
LMest-2.1/LMest/man/long2wide.Rd | 4 -
LMest-2.1/LMest/man/marg_param.Rd | 2
LMest-2.1/LMest/man/prob_multilogit.Rd | 4 -
LMest-2.1/LMest/man/prob_post_cov.Rd | 6 -
LMest-2.1/LMest/man/prod_array.Rd | 4 -
LMest-2.1/LMest/man/rec1.Rd | 2
LMest-2.1/LMest/man/recursions.Rd | 6 -
LMest-2.1/LMest/man/sq.Rd | 2
49 files changed, 298 insertions(+), 263 deletions(-)
Title: Circular Visualization in R
Diff between circlize versions 0.2.3 dated 2015-02-22 and 0.2.4 dated 2015-03-20
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here the circlize package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of this package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
circlize gives users more convenience and freedom to design figures for
better understanding complex patterns behind multi-dimensional data.
Author: Zuguang Gu
Maintainer: Zuguang Gu
DESCRIPTION | 26
MD5 | 189 -
NAMESPACE | 110
NEWS | 13
R/chordDiagram.R | 211 +
R/link.R | 199 +
R/plot.R | 3128 +++++++++++------------
R/utils.R | 704 ++---
R/zzz.R | 6
build/vignette.rds |binary
inst/CITATION | 38
inst/doc/circlize.R | 1532 +++++------
inst/doc/circlize.Rnw | 2835 ++++++++++----------
inst/doc/circlize.pdf |binary
inst/doc/circular_phylogenetic_tree.R | 242 -
inst/doc/circular_phylogenetic_tree.Rnw | 348 +-
inst/doc/circular_phylogenetic_tree.pdf |binary
inst/doc/circular_visualization_of_matrix.R | 1244 ++++-----
inst/doc/circular_visualization_of_matrix.Rnw | 1727 ++++++------
inst/doc/circular_visualization_of_matrix.pdf |binary
inst/doc/draw_ideogram.R | 302 +-
inst/doc/draw_ideogram.Rnw | 508 +--
inst/doc/draw_ideogram.pdf |binary
inst/doc/genomic_plot.R | 2424 ++++++++---------
inst/doc/genomic_plot.Rnw | 3016 +++++++++++-----------
inst/doc/genomic_plot.pdf |binary
inst/doc/interesting_graphics.R | 200 -
inst/doc/interesting_graphics.Rnw | 356 +-
inst/doc/interesting_graphics.pdf |binary
inst/extdata/chromInfo.txt | 186 -
inst/extdata/cytoBand.txt | 1724 ++++++------
man/adjacencyList2Matrix.rd | 58
man/chordDiagram.rd | 132
man/circlize-package.rd | 132
man/circlize.rd | 68
man/circos.axis.rd | 110
man/circos.clear.rd | 50
man/circos.dendrogram.rd |only
man/circos.genomicDensity.rd | 90
man/circos.genomicInitialize.rd | 86
man/circos.genomicLines.rd | 108
man/circos.genomicLink.rd | 88
man/circos.genomicPoints.rd | 86
man/circos.genomicPosTransformLines.rd | 86
man/circos.genomicRainfall.rd | 82
man/circos.genomicRect.rd | 96
man/circos.genomicText.rd | 104
man/circos.genomicTrackPlotRegion.rd | 96
man/circos.info.rd | 70
man/circos.initialize.rd | 84
man/circos.initializeWithIdeogram.rd | 94
man/circos.lines.rd | 104
man/circos.link.rd | 117
man/circos.par.rd | 94
man/circos.points.rd | 84
man/circos.polygon.rd | 80
man/circos.rect.rd | 84
man/circos.text.rd | 94
man/circos.trackHist.rd | 102
man/circos.trackLines.rd | 96
man/circos.trackPlotRegion.rd | 122
man/circos.trackPoints.rd | 78
man/circos.trackText.rd | 88
man/circos.updatePlotRegion.rd | 74
man/colorRamp2.rd | 76
man/cytoband.col.rd | 62
man/draw.sector.rd | 84
man/generateRandomBed.rd | 70
man/genomicDensity.rd | 76
man/get.all.sector.index.rd | 52
man/get.all.track.index.rd | 46
man/get.cell.meta.data.rd | 116
man/get.current.chromosome.rd | 52
man/getI.rd | 64
man/highlight.chromosome.rd | 62
man/highlight.sector.rd | 86
man/posTransform.default.rd | 68
man/posTransform.text.rd | 76
man/rainfallTransform.rd | 64
man/rand_color.rd | 52
man/read.chromInfo.rd | 84
man/read.cytoband.rd | 96
man/reverse.circlize.rd | 74
man/show.index.rd | 46
vignettes/circlize.Rnw | 2835 ++++++++++----------
vignettes/circular_phylogenetic_tree.Rnw | 348 +-
vignettes/circular_visualization_of_matrix.Rnw | 1727 ++++++------
vignettes/draw_ideogram.Rnw | 508 +--
vignettes/genomic_plot.Rnw | 3016 +++++++++++-----------
vignettes/interesting_graphics.Rnw | 356 +-
vignettes/src/genomic-07-posTransformLinesText.R | 198 -
vignettes/src/intro-00-correspondence.R | 48
vignettes/src/intro-08-linescurve.R | 40
vignettes/src/intro-09-text-niceFacing.R | 338 +-
vignettes/src/intro-12-link.R | 19
vignettes/src/intro-15-heatmap.R | 43
96 files changed, 17723 insertions(+), 17364 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-12 0.13.0
2015-02-24 0.9.0
2015-02-23 0.7.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-10 4.0.4
2014-10-05 4.0
2014-08-25 3.72
2014-06-22 3.69
2014-04-07 3.63
2014-03-15 3.62
2014-02-26 3.58
2014-02-25 3.57
2013-11-21 3.55
2013-10-23 3.54
2013-07-11 3.51
2013-07-10 3.50
2013-06-23 3.49
2013-06-03 3.47
2013-01-29 3.44
2013-01-03 3.43
2012-11-26 3.41
2012-10-07 3.40
2012-05-15 3.31
2012-04-11 3.29
2012-04-08 3.28
2012-04-06 3.25
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-13 0.5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-10-06 5.1
2014-08-15 5.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-11-25 1.6
2014-04-29 1.5
2014-03-26 1.4
2013-04-11 1.3
2013-02-22 1.2
2013-02-11 1.1
2012-02-07 1.0
Title: Easy to Use Tools for Common Forms of Random Assignment
Diff between randomizr versions 0.2.0 dated 2015-01-30 and 0.2.2 dated 2015-03-20
Description: Generates random assignments for common experimental
designs: simple, complete, blocked, and clustered.
Author: Alexander Coppock [aut, cre]
Maintainer: Alexander Coppock
DESCRIPTION | 10 ++++++----
MD5 | 13 +++++++++----
R/randomizr.r | 52 +++++++++++++++++++++++++++++++++++++++++++---------
README.md | 29 ++++++++++++++++++++++++++++-
build |only
inst |only
man/complete_ra.Rd | 4 +++-
vignettes |only
8 files changed, 89 insertions(+), 19 deletions(-)
Title: Methods for Patient-Centered Network Meta-Analysis
Diff between pcnetmeta versions 1.3 dated 2015-03-13 and 2.0 dated 2015-03-20
Description: Provides functions to conduct network meta-analysis using arm-based methods for different data types, which include binary and continuous outcomes.
Author: Lifeng Lin, Jing Zhang, and Haitao Chu
Maintainer: Lifeng Lin
pcnetmeta-1.3/pcnetmeta/R/create.tab.R |only
pcnetmeta-1.3/pcnetmeta/data/Middleton10.rda |only
pcnetmeta-1.3/pcnetmeta/man/Middleton10.Rd |only
pcnetmeta-1.3/pcnetmeta/man/create.tab.Rd |only
pcnetmeta-2.0/pcnetmeta/DESCRIPTION | 18
pcnetmeta-2.0/pcnetmeta/MD5 | 48 +-
pcnetmeta-2.0/pcnetmeta/NAMESPACE | 5
pcnetmeta-2.0/pcnetmeta/R/ci.plot.R | 68 +-
pcnetmeta-2.0/pcnetmeta/R/model.binary.het.cor.R |only
pcnetmeta-2.0/pcnetmeta/R/model.binary.het.ind.R |only
pcnetmeta-2.0/pcnetmeta/R/model.binary.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.cont.het.cor.R |only
pcnetmeta-2.0/pcnetmeta/R/model.cont.het.ind.R |only
pcnetmeta-2.0/pcnetmeta/R/model.cont.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.followup.het.cor.R |only
pcnetmeta-2.0/pcnetmeta/R/model.followup.het.ind.R |only
pcnetmeta-2.0/pcnetmeta/R/model.followup.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/model.py.het.cor.R |only
pcnetmeta-2.0/pcnetmeta/R/model.py.het.ind.R |only
pcnetmeta-2.0/pcnetmeta/R/model.py.hom.R |only
pcnetmeta-2.0/pcnetmeta/R/nma.ab.R | 489 ++++++++++++++-------
pcnetmeta-2.0/pcnetmeta/R/nma.ab.cont.R |only
pcnetmeta-2.0/pcnetmeta/R/nma.ab.followup.R |only
pcnetmeta-2.0/pcnetmeta/R/nma.ab.py.R |only
pcnetmeta-2.0/pcnetmeta/R/nma.networkplot.R | 214 ++++-----
pcnetmeta-2.0/pcnetmeta/data/diabetes.rda |only
pcnetmeta-2.0/pcnetmeta/data/dietaryfat.rda |only
pcnetmeta-2.0/pcnetmeta/data/parkinson.rda |only
pcnetmeta-2.0/pcnetmeta/data/smoke.rda |only
pcnetmeta-2.0/pcnetmeta/man/ci.plot.Rd | 46 -
pcnetmeta-2.0/pcnetmeta/man/diabetes.Rd |only
pcnetmeta-2.0/pcnetmeta/man/dietaryfat.Rd |only
pcnetmeta-2.0/pcnetmeta/man/nma.ab.Rd | 221 +++------
pcnetmeta-2.0/pcnetmeta/man/nma.ab.cont.Rd |only
pcnetmeta-2.0/pcnetmeta/man/nma.ab.followup.Rd |only
pcnetmeta-2.0/pcnetmeta/man/nma.ab.py.Rd |only
pcnetmeta-2.0/pcnetmeta/man/nma.networkplot.Rd | 88 +--
pcnetmeta-2.0/pcnetmeta/man/parkinson.Rd |only
pcnetmeta-2.0/pcnetmeta/man/pcnetmeta-package.Rd | 29 -
pcnetmeta-2.0/pcnetmeta/man/smoke.Rd |only
40 files changed, 685 insertions(+), 541 deletions(-)
Title: Modeling Data with Functional Programming
Diff between lambda.r versions 1.1.6 dated 2014-01-23 and 1.1.7 dated 2015-03-20
Description: A language extension to efficiently write functional programs in R. Syntax extensions include multi-part function definitions, pattern matching, guard statements, built-in (optional) type safety.
Author: Brian Lee Yung Rowe
Maintainer: Brian Lee Yung Rowe
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/framework.R | 2 +-
man/lambda.r-package.Rd | 17 +++++++++++++----
4 files changed, 21 insertions(+), 12 deletions(-)
Title: Diversity-Dependent Diversification
Diff between DDD versions 2.6 dated 2014-12-18 and 2.7 dated 2015-03-20
Description:
Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, doi: 10.1086/667574.
Finally, DDD contains a function to simulate the diversity-dependent process.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne
DDD-2.6/DDD/R/dd_KI_loglikold.R |only
DDD-2.7/DDD/DESCRIPTION | 12 ++--
DDD-2.7/DDD/MD5 | 39 +++++++--------
DDD-2.7/DDD/R/bd_ML.R | 4 +
DDD-2.7/DDD/R/dd_KI_ML.R | 7 +-
DDD-2.7/DDD/R/dd_KI_loglik.R | 71 ++++++++++++++-------------
DDD-2.7/DDD/R/dd_ML.R | 6 +-
DDD-2.7/DDD/R/dd_SR_ML.R | 10 ++-
DDD-2.7/DDD/R/dd_SR_loglik.R | 26 +++++-----
DDD-2.7/DDD/R/dd_SR_loglik_choosepar.R | 2
DDD-2.7/DDD/R/dd_loglik.R | 11 +---
DDD-2.7/DDD/R/dd_loglik_rhs.R | 6 +-
DDD-2.7/DDD/R/dd_logliknorm_rhs2.R | 21 --------
DDD-2.7/DDD/R/flavec.R | 13 +++--
DDD-2.7/DDD/man/DDD-package.Rd | 84 +++++++++++++++++----------------
DDD-2.7/DDD/man/bd_ML.Rd | 5 +
DDD-2.7/DDD/man/dd_KI_ML.Rd | 21 ++++----
DDD-2.7/DDD/man/dd_KI_loglik.Rd | 3 -
DDD-2.7/DDD/man/dd_ML.Rd | 15 ++---
DDD-2.7/DDD/man/dd_SR_ML.Rd | 20 ++++---
DDD-2.7/DDD/man/dd_loglik.Rd | 2
21 files changed, 191 insertions(+), 187 deletions(-)