Title: Liquid Association for Network Dynamics Detection
Description: Using Liquid Association for Network Dynamics Detection.
Author: Shangzhao Qiu, Yan Yan, Tianwei Yu
Maintainer: Shangzhao Qiu <qsz1328@gmail.com>
Diff between LANDD versions 1.0.0 dated 2015-10-06 and 1.1.0 dated 2016-09-30
DESCRIPTION | 12 +++++++----- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 7 ++++++- R/getgobp.R | 11 ++++++----- R/kernel.density.R | 17 +++++++++-------- R/lascouting.R | 8 ++++---- R/simulation.R |only R/visualize.R | 37 ++++++++++++++++++++++++++++++------- man/get.W.Rd | 10 +++++----- man/getgobp.Rd | 10 +++++----- man/graph.kd.Rd | 28 ++++++++++++++++++++++------ man/lascouting.Rd | 6 +++--- man/normalizeInputMatrix.Rd | 2 +- man/simulateLANDD.Rd |only man/visualize.Rd | 2 +- man/visualize.community.Rd | 6 +++--- man/xw.distance.Rd | 2 +- 17 files changed, 119 insertions(+), 69 deletions(-)
Title: R Client Implementing the W3C WebDriver Specification
Description: The W3C WebDriver specification defines a way for out-of-process
programs to remotely instruct the behaviour of web browsers. It is detailed
at <https://w3c.github.io/webdriver/webdriver-spec.html>. This package provides
an R client implementing the W3C specification.
Author: John Harrison [aut, cre]
Maintainer: John Harrison <johndharrison0@gmail.com>
Diff between seleniumPipes versions 0.3.0 dated 2016-08-24 and 0.3.7 dated 2016-09-30
seleniumPipes-0.3.0/seleniumPipes/inst/tests |only seleniumPipes-0.3.7/seleniumPipes/DESCRIPTION | 9 +- seleniumPipes-0.3.7/seleniumPipes/MD5 | 37 ++++++---- seleniumPipes-0.3.7/seleniumPipes/NEWS | 27 +++++++ seleniumPipes-0.3.7/seleniumPipes/R/commandContexts.R | 34 ++++----- seleniumPipes-0.3.7/seleniumPipes/README.md | 24 ++++-- seleniumPipes-0.3.7/seleniumPipes/build/vignette.rds |binary seleniumPipes-0.3.7/seleniumPipes/inst/Saucetests |only seleniumPipes-0.3.7/seleniumPipes/inst/doc/basicOperation.Rmd | 8 +- seleniumPipes-0.3.7/seleniumPipes/inst/doc/basicOperation.html | 10 +- seleniumPipes-0.3.7/seleniumPipes/inst/examples/createFunctions.R | 9 +- seleniumPipes-0.3.7/seleniumPipes/tests |only seleniumPipes-0.3.7/seleniumPipes/vignettes/basicOperation.Rmd | 8 +- 13 files changed, 108 insertions(+), 58 deletions(-)
Title: Penalized Likelihood Estimation and Dynamic Prediction under the
Joint Frailty-Copula Models Between Tumour Progression and
Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction under the joint frailty-copula model between tumour progression and death for meta-analysis.
The method is applicable for meta-analytic data combining several studies. The data should have information on both terminal event time (time-to-death) and non-terminal event time (time-to-tumour progression).
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.7 dated 2016-09-21 and 2.8 dated 2016-09-30
DESCRIPTION | 9 +++++---- MD5 | 12 +++++++----- NAMESPACE | 1 + R/F.KM.R |only R/jointCox.indep.reg.R | 6 ++++-- R/jointCox.reg.R | 8 +++++--- man/F.KM.Rd |only man/joint.Cox-package.Rd | 4 ++-- 8 files changed, 24 insertions(+), 16 deletions(-)
Title: Downscaling Species Occupancy
Description: A set of functions that downscales species occupancy at
coarse grain sizes to predict species occupancy at fine grain sizes.
Author: Charles Marsh [aut, cre]
Maintainer: Charles Marsh <charliem2003@gmail.com>
Diff between downscale versions 1.2-2 dated 2016-08-19 and 1.2-3 dated 2016-09-30
DESCRIPTION | 13 +++++-------- MD5 | 18 ++++++++++-------- NEWS | 13 +++++++++---- R/hui.downscale.R | 10 +++++++--- build/vignette.rds |binary inst/doc/Downscaling.R | 22 +++++++++++----------- inst/doc/Downscaling.pdf |binary inst/doc/Upgraining.R | 22 +++++++++++----------- inst/doc/Upgraining.pdf |binary vignettes/Downscaling-concordance.tex |only vignettes/Downscaling.tex |only 11 files changed, 53 insertions(+), 45 deletions(-)
Title: Biological Structure Analysis
Description: Utilities to process, organize and explore protein structure,
sequence and dynamics data. Features include the ability to read and write
structure, sequence and dynamic trajectory data, perform sequence and structure
database searches, data summaries, atom selection, alignment, superposition,
rigid core identification, clustering, torsion analysis, distance matrix
analysis, structure and sequence conservation analysis, normal mode analysis,
principal component analysis of heterogeneous structure data, and correlation
network analysis from normal mode and molecular dynamics data. In addition,
various utility functions are provided to enable the statistical and graphical
power of the R environment to work with biological sequence and structural data.
Please refer to the URLs below for more information.
Author: Barry Grant [aut, cre],
Xin-Qiu Yao [aut],
Lars Skjaerven [aut],
Julien Ide [aut]
Maintainer: Barry Grant <bjgrant@umich.edu>
Diff between bio3d versions 2.2-4 dated 2015-12-12 and 2.3-0 dated 2016-09-30
bio3d-2.2-4/bio3d/R/view.cna.R |only bio3d-2.2-4/bio3d/R/view.cnapath.R |only bio3d-2.2-4/bio3d/R/view.dccm.R |only bio3d-2.2-4/bio3d/R/view.modes.R |only bio3d-2.2-4/bio3d/R/vmd.colors.R |only bio3d-2.2-4/bio3d/man/view.cna.Rd |only bio3d-2.2-4/bio3d/man/view.dccm.Rd |only bio3d-2.2-4/bio3d/man/view.modes.Rd |only bio3d-2.2-4/bio3d/man/vmd.colors.Rd |only bio3d-2.3-0/bio3d/DESCRIPTION | 34 + bio3d-2.3-0/bio3d/MD5 | 394 +++++++++-------- bio3d-2.3-0/bio3d/NAMESPACE | 21 bio3d-2.3-0/bio3d/NEWS | 47 ++ bio3d-2.3-0/bio3d/R/RcppExports.R |only bio3d-2.3-0/bio3d/R/aanma.R |only bio3d-2.3-0/bio3d/R/aanma.pdb.R |only bio3d-2.3-0/bio3d/R/aanma.pdbs.R |only bio3d-2.3-0/bio3d/R/as.pdb.mol2.R | 70 +-- bio3d-2.3-0/bio3d/R/atom.select.mol2.R |only bio3d-2.3-0/bio3d/R/atom.select.pdb.R | 31 + bio3d-2.3-0/bio3d/R/basename.pdb.R | 4 bio3d-2.3-0/bio3d/R/bhattacharyya.R | 15 bio3d-2.3-0/bio3d/R/biounit.R | 2 bio3d-2.3-0/bio3d/R/blast.pdb.R | 14 bio3d-2.3-0/bio3d/R/bounds.sse.R | 4 bio3d-2.3-0/bio3d/R/build.hessian.R | 78 --- bio3d-2.3-0/bio3d/R/check.utility.R | 11 bio3d-2.3-0/bio3d/R/clean.pdb.R | 2 bio3d-2.3-0/bio3d/R/cmap.R | 73 ++- bio3d-2.3-0/bio3d/R/cna.dccm.R | 29 - bio3d-2.3-0/bio3d/R/cnapath.R | 60 ++ bio3d-2.3-0/bio3d/R/community.aln.R |only bio3d-2.3-0/bio3d/R/core.find.R | 12 bio3d-2.3-0/bio3d/R/dccm.enma.R | 14 bio3d-2.3-0/bio3d/R/dccm.gnm.R |only bio3d-2.3-0/bio3d/R/dccm.pca.R | 29 - bio3d-2.3-0/bio3d/R/dccm.xyz.R | 8 bio3d-2.3-0/bio3d/R/dist.xyz.R | 9 bio3d-2.3-0/bio3d/R/dm.R | 7 bio3d-2.3-0/bio3d/R/dm.xyz.R | 16 bio3d-2.3-0/bio3d/R/dssp.pdb.R | 32 + bio3d-2.3-0/bio3d/R/entropy.R | 12 bio3d-2.3-0/bio3d/R/filter.cmap.R | 37 + bio3d-2.3-0/bio3d/R/filter.dccm.R | 55 +- bio3d-2.3-0/bio3d/R/filter.rmsd.R | 4 bio3d-2.3-0/bio3d/R/geostas.R | 12 bio3d-2.3-0/bio3d/R/get.blast.R | 38 - bio3d-2.3-0/bio3d/R/get.pdb.R | 20 bio3d-2.3-0/bio3d/R/get.seq.R | 54 ++ bio3d-2.3-0/bio3d/R/gnm.R |only bio3d-2.3-0/bio3d/R/gnm.pdbs.R |only bio3d-2.3-0/bio3d/R/hmmer.R | 14 bio3d-2.3-0/bio3d/R/is.mol2.R |only bio3d-2.3-0/bio3d/R/load.enmff.R | 222 ++------- bio3d-2.3-0/bio3d/R/mask.dccm.R |only bio3d-2.3-0/bio3d/R/mktrj.nma.R | 60 +- bio3d-2.3-0/bio3d/R/mktrj.pca.R | 30 + bio3d-2.3-0/bio3d/R/network.amendment.R | 2 bio3d-2.3-0/bio3d/R/nma.pdb.R | 326 +------------- bio3d-2.3-0/bio3d/R/nma.pdbs.R | 130 ++--- bio3d-2.3-0/bio3d/R/nma_funs.R |only bio3d-2.3-0/bio3d/R/pca.xyz.R | 4 bio3d-2.3-0/bio3d/R/pdb.annotate.R | 3 bio3d-2.3-0/bio3d/R/pdb.pfam.R |only bio3d-2.3-0/bio3d/R/pdb2sse.R | 2 bio3d-2.3-0/bio3d/R/pdbaln.R | 143 +++--- bio3d-2.3-0/bio3d/R/pdbs2pdb.R | 59 +- bio3d-2.3-0/bio3d/R/pdbs2sse.R |only bio3d-2.3-0/bio3d/R/pdbsplit.R | 49 +- bio3d-2.3-0/bio3d/R/pfam.R | 4 bio3d-2.3-0/bio3d/R/plot.blast.R | 47 +- bio3d-2.3-0/bio3d/R/plot.cna.R | 24 - bio3d-2.3-0/bio3d/R/plot.dccm.R | 86 ++- bio3d-2.3-0/bio3d/R/plot.enma.R | 436 +++---------------- bio3d-2.3-0/bio3d/R/plot.fasta.R | 282 +++--------- bio3d-2.3-0/bio3d/R/plot.fluct.R | 76 ++- bio3d-2.3-0/bio3d/R/plot.hmmer.R | 176 ------- bio3d-2.3-0/bio3d/R/plot.matrix.loadings.R |only bio3d-2.3-0/bio3d/R/plotb3.R | 73 +-- bio3d-2.3-0/bio3d/R/pymol.dccm.R |only bio3d-2.3-0/bio3d/R/pymol.modes.R |only bio3d-2.3-0/bio3d/R/pymol.pdbs.R |only bio3d-2.3-0/bio3d/R/read.all.R | 237 +++++++--- bio3d-2.3-0/bio3d/R/read.cif.R |only bio3d-2.3-0/bio3d/R/read.crd.amber.R | 94 +--- bio3d-2.3-0/bio3d/R/read.fasta.R | 2 bio3d-2.3-0/bio3d/R/read.fasta.pdb.R | 57 +- bio3d-2.3-0/bio3d/R/read.mol2.R | 151 +++++- bio3d-2.3-0/bio3d/R/read.ncdf.R | 4 bio3d-2.3-0/bio3d/R/read.pdb.R | 414 ++++++------------ bio3d-2.3-0/bio3d/R/read.pdb2.R |only bio3d-2.3-0/bio3d/R/read.pqr.R | 27 - bio3d-2.3-0/bio3d/R/read.prmtop.R | 97 ---- bio3d-2.3-0/bio3d/R/rmsf.R | 16 bio3d-2.3-0/bio3d/R/rtb.R |only bio3d-2.3-0/bio3d/R/seqaln.R | 213 +++++++-- bio3d-2.3-0/bio3d/R/store.atom.R | 16 bio3d-2.3-0/bio3d/R/summary.cnapath.R | 29 - bio3d-2.3-0/bio3d/R/trim.mol2.R |only bio3d-2.3-0/bio3d/R/trim.pdbs.R | 18 bio3d-2.3-0/bio3d/R/vmd.R |only bio3d-2.3-0/bio3d/R/vmd.cna.R |only bio3d-2.3-0/bio3d/R/vmd.cnapath.R |only bio3d-2.3-0/bio3d/R/vmd_colors.R |only bio3d-2.3-0/bio3d/R/write.mol2.R |only bio3d-2.3-0/bio3d/R/write.pdb.R | 57 ++ bio3d-2.3-0/bio3d/R/write.pqr.R | 113 ++-- bio3d-2.3-0/bio3d/README.md | 2 bio3d-2.3-0/bio3d/build/vignette.rds |binary bio3d-2.3-0/bio3d/data/atom.index.rda |binary bio3d-2.3-0/bio3d/data/hivp.RData |binary bio3d-2.3-0/bio3d/data/kinesin.RData |binary bio3d-2.3-0/bio3d/data/transducin.RData |binary bio3d-2.3-0/bio3d/inst/doc/bio3d_vignettes.Rmd | 4 bio3d-2.3-0/bio3d/inst/doc/bio3d_vignettes.html | 16 bio3d-2.3-0/bio3d/inst/examples/aspirin.mol2 |only bio3d-2.3-0/bio3d/inst/examples/crambin.inpcrd |only bio3d-2.3-0/bio3d/inst/examples/crambin.prmtop |only bio3d-2.3-0/bio3d/inst/examples/hivp.dcd |binary bio3d-2.3-0/bio3d/inst/examples/hivp.pdb | 21 bio3d-2.3-0/bio3d/inst/staticdocs/index.r | 51 +- bio3d-2.3-0/bio3d/man/aanma.pdb.Rd |only bio3d-2.3-0/bio3d/man/aanma.pdbs.Rd |only bio3d-2.3-0/bio3d/man/as.pdb.Rd | 22 bio3d-2.3-0/bio3d/man/atom.select.Rd | 28 - 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bio3d-2.3-0/bio3d/man/rmsf.Rd | 38 + bio3d-2.3-0/bio3d/man/seqaln.Rd | 36 + bio3d-2.3-0/bio3d/man/seqidentity.Rd | 9 bio3d-2.3-0/bio3d/man/store.atom.Rd | 5 bio3d-2.3-0/bio3d/man/trim.mol2.Rd |only bio3d-2.3-0/bio3d/man/vmd.cna.Rd |only bio3d-2.3-0/bio3d/man/vmd_colors.Rd |only bio3d-2.3-0/bio3d/man/write.mol2.Rd |only bio3d-2.3-0/bio3d/man/write.pdb.Rd | 4 bio3d-2.3-0/bio3d/man/write.pqr.Rd | 31 - bio3d-2.3-0/bio3d/src |only bio3d-2.3-0/bio3d/tests/testthat/test-aanma.R |only bio3d-2.3-0/bio3d/tests/testthat/test-aanma.pdbs.R |only bio3d-2.3-0/bio3d/tests/testthat/test-clean.pdb.R | 11 bio3d-2.3-0/bio3d/tests/testthat/test-cmap.R | 1 bio3d-2.3-0/bio3d/tests/testthat/test-cna.R |only bio3d-2.3-0/bio3d/tests/testthat/test-core.find.R | 2 bio3d-2.3-0/bio3d/tests/testthat/test-dccm.R | 12 bio3d-2.3-0/bio3d/tests/testthat/test-dssp.R | 1 bio3d-2.3-0/bio3d/tests/testthat/test-fitting.R | 3 bio3d-2.3-0/bio3d/tests/testthat/test-get.pdb.R | 2 bio3d-2.3-0/bio3d/tests/testthat/test-gnm.R |only bio3d-2.3-0/bio3d/tests/testthat/test-mol2.R |only bio3d-2.3-0/bio3d/tests/testthat/test-nma.R | 18 bio3d-2.3-0/bio3d/tests/testthat/test-nma.pdbs.R | 2 bio3d-2.3-0/bio3d/tests/testthat/test-pdb.annotate.R | 6 bio3d-2.3-0/bio3d/tests/testthat/test-pdbsplit.R | 1 bio3d-2.3-0/bio3d/tests/testthat/test-read.all.R |only bio3d-2.3-0/bio3d/tests/testthat/test-read.ncdf.R | 11 bio3d-2.3-0/bio3d/tests/testthat/test-read.pdb.R | 106 ++++ bio3d-2.3-0/bio3d/tests/testthat/test-seqaln.R |only bio3d-2.3-0/bio3d/vignettes/bio3d_vignettes.Rmd | 4 224 files changed, 3433 insertions(+), 3172 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-07 0.1.0
Title: Mendelian Randomization Package
Description: Encodes several methods for performing Mendelian randomization analyses with summarized data. Summarized data on genetic associations with the exposure and with the outcome can be obtained from large consortia. These data can be used for obtaining causal estimates using instrumental variable methods.
Author: Olena Yavorska <yavorsko@tcd.ie>
Maintainer: Stephen Burgess <sb452@medschl.cam.ac.uk>
Diff between MendelianRandomization versions 0.1.0 dated 2016-08-31 and 0.2.0 dated 2016-09-30
DESCRIPTION | 8 MD5 | 58 +- NAMESPACE | 9 NEWS |only R/1Data.R | 31 + R/AllClasses.R | 44 + R/AllData.R | 13 R/AllGenerics.R | 79 +++ R/getter-methods.R | 5 R/mr_allmethods-methods.R | 23 R/mr_ivw-methods.R | 95 +++ R/mr_maxlik-methods.R |only R/mr_plot-methods.R | 287 ++++++------ R/show-methods.R | 38 + R/values-methods.R | 15 build/vignette.rds |binary inst/doc/Vignette_MR.R | 300 ++++++------ inst/doc/Vignette_MR.Rmd | 65 ++ inst/doc/Vignette_MR.pdf |binary man/MaxLik-class.Rd |only man/calcium.Rd | 2 man/coursedata.Rd |only man/getter.Rd | 3 man/loglikelihood.Rd |only man/loglikelihoodcorrel.Rd |only man/loglikelihoodrhocorrel.Rd |only man/mr_ivw.Rd | 15 man/mr_maxlik.Rd |only man/mr_plot.Rd | 15 man/penalised.weights.delta.Rd |only man/r.weights.Rd | 2 man/r.weights.delta.Rd |only man/values.Rd | 3 vignettes/Vignette_MR.Rmd | 65 ++ vignettes/Vignette_MR.html | 975 ++++++++++++++++++++++------------------- 35 files changed, 1358 insertions(+), 792 deletions(-)
More information about MendelianRandomization at CRAN
Permanent link
Title: Family Age-at-Onset Data Simulation and Penetrance Estimation
Description: Simulates age-at-onset traits associated with a segregating major gene in family data
obtained from population-based, clinic-based, or multi-stage designs. Appropriate ascertainment
correction is utilized to estimate age-dependent penetrance functions either parametrically from
the fitted model or nonparametrically from the data. The Expectation and Maximization algorithm
can infer missing genotypes and carrier probabilities estimated from family's genotype and
phenotype information or from a fitted model. Plot functions include pedigrees of simulated
families and predicted penetrance curves based on specified parameter values.
Author: Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais
Maintainer: Yun-Hee Choi <yun-hee.choi@schulich.uwo.ca>
Diff between FamEvent versions 1.1 dated 2016-03-09 and 1.2 dated 2016-09-30
FamEvent-1.1/FamEvent/man/carrierprobgeno.Rd |only FamEvent-1.1/FamEvent/man/carrierprobpheno.Rd |only FamEvent-1.2/FamEvent/DESCRIPTION | 19 +- FamEvent-1.2/FamEvent/MD5 | 76 ++++++----- FamEvent-1.2/FamEvent/NAMESPACE | 2 FamEvent-1.2/FamEvent/R/carrierprob.R |only FamEvent-1.2/FamEvent/R/carrierprobgeno.R | 172 ++++++++++++-------------- FamEvent-1.2/FamEvent/R/carrierprobpheno.R | 86 ++++++++----- FamEvent-1.2/FamEvent/R/cprob.R | 5 FamEvent-1.2/FamEvent/R/cprob.frailty.R |only FamEvent-1.2/FamEvent/R/dlaplace.R |only FamEvent-1.2/FamEvent/R/familyStructure.R | 102 +++++++-------- FamEvent-1.2/FamEvent/R/fgene.R | 6 FamEvent-1.2/FamEvent/R/floglik.R |only FamEvent-1.2/FamEvent/R/floglik.vec.R |only FamEvent-1.2/FamEvent/R/floglikem.R |only FamEvent-1.2/FamEvent/R/inv.surv.R | 9 - FamEvent-1.2/FamEvent/R/inv.survp.R |only FamEvent-1.2/FamEvent/R/laplace.R | 4 FamEvent-1.2/FamEvent/R/loglik.R | 9 - FamEvent-1.2/FamEvent/R/loglik.vec.R | 16 +- FamEvent-1.2/FamEvent/R/loglikem.R | 60 +++++---- FamEvent-1.2/FamEvent/R/parents.g.R | 3 FamEvent-1.2/FamEvent/R/pen.ci.R | 18 +- FamEvent-1.2/FamEvent/R/penf.R | 6 FamEvent-1.2/FamEvent/R/penfrailtymodel.R |only FamEvent-1.2/FamEvent/R/penmodel.R | 24 +-- FamEvent-1.2/FamEvent/R/penmodelEM.R | 19 +- FamEvent-1.2/FamEvent/R/penplot.R | 10 + FamEvent-1.2/FamEvent/R/plot.penmodel.R | 4 FamEvent-1.2/FamEvent/R/plot.simfam.R | 2 FamEvent-1.2/FamEvent/R/simfam.R | 4 FamEvent-1.2/FamEvent/R/summary.penmodel.R | 10 - FamEvent-1.2/FamEvent/R/summary.simfam.R | 2 FamEvent-1.2/FamEvent/R/surv.dist.R | 2 FamEvent-1.2/FamEvent/R/survp.dist.R |only FamEvent-1.2/FamEvent/man/FamEvent-package.Rd | 48 +++++-- FamEvent-1.2/FamEvent/man/carrierprob.Rd |only FamEvent-1.2/FamEvent/man/penmodel.Rd | 9 - FamEvent-1.2/FamEvent/man/penmodelEM.Rd | 14 +- FamEvent-1.2/FamEvent/man/penplot.Rd | 8 - FamEvent-1.2/FamEvent/man/plot.penmodel.Rd | 5 FamEvent-1.2/FamEvent/man/plot.simfam.Rd | 13 - FamEvent-1.2/FamEvent/man/simfam.Rd | 2 FamEvent-1.2/FamEvent/man/summary.penmodel.Rd | 2 45 files changed, 422 insertions(+), 349 deletions(-)
Title: Bootstrapped Robustness Assessment for Qualitative Comparative
Analysis
Description: Test the robustness of a user's Qualitative Comparative Analysis
solutions to randomness, using the bootstrapped assessment: baQCA(). This
package also includes a function that provides recommendations for improving
solutions to reach typical significance levels: brQCA().
Author: C. Ben Gibson [aut, cre],
Burrel Vann Jr [aut]
Maintainer: C. Ben Gibson <cbgibson@uci.edu>
Diff between braQCA versions 0.9.9.1 dated 2016-05-17 and 0.9.9.3 dated 2016-09-30
DESCRIPTION | 16 ++++++++++------ MD5 | 14 +++++++------- NAMESPACE | 3 +-- R/baQCA.R | 4 ++-- man/baQCA.Rd | 4 ++-- man/brQCA.Rd | 2 +- man/conf.table.Rd | 4 ++-- man/sim.brQCA.Rd | 2 +- 8 files changed, 26 insertions(+), 23 deletions(-)
Title: Fractional Factorial Designs with 2-Level Factors
Description: Regular and non-regular Fractional Factorial 2-level designs
can be created. Furthermore, analysis tools for Fractional
Factorial designs with 2-level factors are offered (main
effects and interaction plots for all factors simultaneously,
cube plot for looking at the simultaneous effects of three
factors, full or half normal plot, alias structure in a more
readable format than with the built-in function alias).
Author: Ulrike Groemping
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between FrF2 versions 1.7-1 dated 2014-07-31 and 1.7-2 dated 2016-09-30
DESCRIPTION | 22 MD5 | 20 NAMESPACE | 11 R/FrF2.R | 2 inst/NEWS | 9 tests/FrF2test.Rout.save | 12 tests/addcentertest.Rout.save | 3136 ++++++++++++++--------------- tests/foldtest.Rout.save | 12 tests/generators.from.designtest.Rout.save | 28 tests/generators.summary.test.Rout.save | 12 tests/pbtest.Rout.save | 12 11 files changed, 1659 insertions(+), 1617 deletions(-)
Title: Dynamic Modeling and Parameter Estimation in ODE Models
Description: The framework provides functions to generate ODEs of reaction
networks, parameter transformations, observation functions, residual functions,
etc. The framework follows the paradigm that derivative information should be
used for optimization whenever possible. Therefore, all major functions produce
and can handle expressions for symbolic derivatives.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@physik.uni-freiburg.de>
Diff between dMod versions 0.3.1 dated 2016-05-18 and 0.3.2 dated 2016-09-30
dMod-0.3.1/dMod/vignettes/trial-1-12-05-2016-161829 |only dMod-0.3.2/dMod/DESCRIPTION | 6 dMod-0.3.2/dMod/MD5 | 94 +-- dMod-0.3.2/dMod/NAMESPACE | 6 dMod-0.3.2/dMod/R/classes.R | 21 dMod-0.3.2/dMod/R/dMod.R | 3 dMod-0.3.2/dMod/R/dataClass.R | 13 dMod-0.3.2/dMod/R/eqnClass.R | 32 - dMod-0.3.2/dMod/R/objClass.R | 20 dMod-0.3.2/dMod/R/parClass.R | 7 dMod-0.3.2/dMod/R/parameters.R | 15 dMod-0.3.2/dMod/R/plots.R | 37 - dMod-0.3.2/dMod/R/prdClass.R | 35 + dMod-0.3.2/dMod/R/prediction.R | 21 dMod-0.3.2/dMod/R/remoteComputing.R | 51 + dMod-0.3.2/dMod/R/sparseMatrix.R |only dMod-0.3.2/dMod/R/statistics.R | 613 ++++++++++---------- dMod-0.3.2/dMod/R/toolsMarcus.R | 74 ++ dMod-0.3.2/dMod/R/toolsWolfgang.R | 2 dMod-0.3.2/dMod/inst/code/quasiSteadyStates.py |only dMod-0.3.2/dMod/inst/doc/dMod.R | 26 dMod-0.3.2/dMod/inst/doc/dMod.Rmd | 28 dMod-0.3.2/dMod/inst/doc/dMod.html | 132 +--- dMod-0.3.2/dMod/inst/examples/eqnlist.R | 1 dMod-0.3.2/dMod/inst/examples/equations.R | 71 +- dMod-0.3.2/dMod/inst/examples/objective.R | 56 - dMod-0.3.2/dMod/inst/examples/profiles.R | 10 dMod-0.3.2/dMod/inst/examples/sumdatalist.R | 62 +- dMod-0.3.2/dMod/inst/examples/test_blocks.R | 4 dMod-0.3.2/dMod/man/Pimpl.Rd | 5 dMod-0.3.2/dMod/man/Xs.Rd | 4 dMod-0.3.2/dMod/man/Y.Rd | 6 dMod-0.3.2/dMod/man/addReaction.Rd | 71 +- dMod-0.3.2/dMod/man/conservedQuantities.Rd | 71 +- dMod-0.3.2/dMod/man/dot.Rd | 71 +- dMod-0.3.2/dMod/man/eqnlist.Rd | 1 dMod-0.3.2/dMod/man/getFluxes.Rd | 76 +- dMod-0.3.2/dMod/man/getReactions.Rd | 71 +- dMod-0.3.2/dMod/man/mstrust.Rd | 4 dMod-0.3.2/dMod/man/normL2.Rd | 6 dMod-0.3.2/dMod/man/plotPars.Rd | 6 dMod-0.3.2/dMod/man/plotValues.Rd | 4 dMod-0.3.2/dMod/man/plus-.datalist.Rd | 62 +- dMod-0.3.2/dMod/man/plus-.objfn.Rd | 56 - dMod-0.3.2/dMod/man/profile.Rd | 18 dMod-0.3.2/dMod/man/quasiSteadyStates.Rd |only dMod-0.3.2/dMod/man/runbg.install.Rd |only dMod-0.3.2/dMod/vignettes/dMod.Rmd | 28 dMod-0.3.2/dMod/vignettes/framework.Rmd |only dMod-0.3.2/dMod/vignettes/topology.csv | 16 dMod-0.3.2/dMod/vignettes/topology_linchain.csv |only 51 files changed, 1174 insertions(+), 842 deletions(-)
Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, this approach lacks statistical validity
when applied to relative data, including those biological count data produced by
microarray assays or high-throughput RNA-sequencing. Two metrics of proportionality,
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and rho [Erb and
Notredame (2016) <DOI:10.1007/s12064-015-0220-8>], both derived from compositional
data analysis, a branch of math dealing specifically with relative data,
represent novel alternatives to correlation. This package introduces a programmatic
framework for the calculation of feature dependence through proportionality, as
discussed in the cited publications.
Author: Thomas Quinn [aut, cre],
David Lovell [aut]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 2.0.0 dated 2016-08-27 and 2.0.1 dated 2016-09-30
propr-2.0.0/propr/R/backend.R |only propr-2.0.1/propr/DESCRIPTION | 16 ++-- propr-2.0.1/propr/MD5 | 45 +++++++------ propr-2.0.1/propr/NAMESPACE | 1 propr-2.0.1/propr/NEWS.md | 8 ++ propr-2.0.1/propr/R/RcppExports.R | 2 propr-2.0.1/propr/R/deprecated.R |only propr-2.0.1/propr/R/perb.R | 7 ++ propr-2.0.1/propr/R/phit.R | 21 ++++-- propr-2.0.1/propr/R/simplify.R |only propr-2.0.1/propr/inst/doc/propr-vignette.R | 4 - propr-2.0.1/propr/inst/doc/propr-vignette.Rmd | 16 ++-- propr-2.0.1/propr/inst/doc/propr-vignette.html | 34 ++++------ propr-2.0.1/propr/man/proprALR.Rd | 2 propr-2.0.1/propr/man/proprCLR.Rd | 2 propr-2.0.1/propr/man/proprPairs.Rd | 2 propr-2.0.1/propr/man/proprPerb.Rd | 2 propr-2.0.1/propr/man/proprPhit.Rd | 2 propr-2.0.1/propr/man/proprSym.Rd | 2 propr-2.0.1/propr/man/proprTri.Rd | 2 propr-2.0.1/propr/man/proprVLR.Rd | 2 propr-2.0.1/propr/man/simplify.Rd |only propr-2.0.1/propr/src/RcppExports.cpp | 74 +++++++++++------------ propr-2.0.1/propr/src/backend.cpp | 1 propr-2.0.1/propr/tests/testthat/test-simplify.R |only propr-2.0.1/propr/vignettes/propr-vignette.Rmd | 16 ++-- 26 files changed, 141 insertions(+), 120 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut]
Maintainer: Woo-Young Ahn <ahn.280@osu.edu>
Diff between hBayesDM versions 0.2.3 dated 2016-07-17 and 0.2.3.1 dated 2016-09-30
hBayesDM-0.2.3.1/hBayesDM/DESCRIPTION | 8 ++--- hBayesDM-0.2.3.1/hBayesDM/MD5 | 16 +++++----- hBayesDM-0.2.3.1/hBayesDM/NAMESPACE | 2 + hBayesDM-0.2.3.1/hBayesDM/R/plotInd.R |only hBayesDM-0.2.3.1/hBayesDM/inst/NEWS | 8 +++-- hBayesDM-0.2.3.1/hBayesDM/inst/extdata/probWeightAversive_exampleData.txt |only hBayesDM-0.2.3.1/hBayesDM/inst/plotting/plot_functions.R | 5 +-- hBayesDM-0.2.3.1/hBayesDM/inst/stan/prl_ewa.stan | 2 - hBayesDM-0.2.3.1/hBayesDM/inst/stan/prl_rp.stan | 2 - hBayesDM-0.2.3.1/hBayesDM/man/plotInd.Rd |only hBayesDM-0.2.3/hBayesDM/inst/stan/gng_m4_reg.rda |only 11 files changed, 26 insertions(+), 17 deletions(-)
Title: Streamlined Plot Theme and Plot Annotations for 'ggplot2'
Description: Some helpful extensions and modifications to the 'ggplot2'
package. In particular, this package makes it easy to combine multiple
'ggplot2' plots into one and label them with letters, e.g. A, B, C, etc.,
as is often required for scientific publications. The package also provides
a streamlined and clean theme that is used in the Wilke lab, hence the
package name, which stands for Claus O. Wilke's plot package.
Author: Claus O. Wilke [aut, cre],
Hadley Wickham [cph]
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between cowplot versions 0.6.2 dated 2016-04-20 and 0.6.3 dated 2016-09-30
DESCRIPTION | 15 ++-- MD5 | 81 +++++++++++----------- NAMESPACE | 4 - NEWS | 8 ++ R/draw.R | 16 +++- R/get_legend.R |only R/plot_grid.R | 146 ++++++++++++++++++++++++----------------- R/switch_axis.R | 5 - R/themes.R | 2 README.md | 5 - build/vignette.rds |binary inst/doc/axis_position.html | 11 +-- inst/doc/introduction.html | 26 +++---- inst/doc/plot_annotations.html | 6 - inst/doc/plot_grid.html | 30 ++++---- inst/doc/shared_legends.R | 6 - inst/doc/shared_legends.Rmd | 6 - inst/doc/shared_legends.html | 18 ++--- man/add_sub.Rd | 2 man/align_plots.Rd |only man/background_grid.Rd | 2 man/cowplot.Rd | 2 man/draw_figure_label.Rd | 4 - man/draw_grob.Rd | 2 man/draw_label.Rd | 2 man/draw_line.Rd | 2 man/draw_plot.Rd | 2 man/draw_plot_label.Rd | 2 man/draw_text.Rd | 2 man/get_legend.Rd |only man/ggdraw.Rd | 8 +- man/ggsave.Rd | 2 man/gtable_remove_grobs.Rd | 2 man/gtable_squash_cols.Rd | 2 man/gtable_squash_rows.Rd | 2 man/panel_border.Rd | 2 man/plot_grid.Rd | 2 man/plot_theme.Rd | 2 man/save_plot.Rd | 2 man/switch_axis_position.Rd | 6 - man/theme_cowplot.Rd | 2 man/theme_nothing.Rd | 2 vignettes/shared_legends.Rmd | 6 - 43 files changed, 245 insertions(+), 202 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-06-04 1.4.3
2013-04-01 1.3.1
2013-03-27 1.3