Title: Semantic Annotation and Discoverability System for R-Based
Artifacts
Description: Automatically annotates R-based artifacts
with relevant descriptive and provenance-related
and provides a backend-agnostic storage and
discoverability system for organizing, retrieving, and
interrogating such artifacts.
Author: Gabriel Becker [aut, cre],
Sara Moore [aut]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between trackr versions 0.7.4 dated 2018-02-20 and 0.7.5 dated 2018-03-01
DESCRIPTION | 12 ++++++------ MD5 | 15 ++++++++------- NAMESPACE | 2 ++ R/knitr.R | 23 ++++++++++++++++++++--- inst/doc/Extending-trackr.pdf |binary inst/doc/index.html | 10 +++++----- man/checkPandoc.Rd |only man/knit_and_record.Rd | 2 +- tests/trackr-tests.R | 14 ++++++++++---- 9 files changed, 52 insertions(+), 26 deletions(-)
Title: Global Charcoal Database
Description: Contains the Global Charcoal database data. Data include charcoal
series (age, depth, charcoal quantity, associated units and methods) and
information on sedimentary sites (localisation, depositional environment, biome,
etc.) as well as publications informations. Since 4.0.0 the GCD mirrors the online SQL database at <http://paleofire.org>.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between GCD versions 3.0.5 dated 2015-04-22 and 4.0.0 dated 2018-03-01
DESCRIPTION | 14 ++- MD5 | 31 ++++--- NAMESPACE | 2 NEWS | 12 +++ R/GCD-package.R | 183 +++++++++++++++++++++++++--------------------- data/charcoal_methods.rda |only data/charcoal_units.rda |only data/datalist | 2 data/paleofiredata.rda |binary data/paleofiresites.rda |binary data/pub.rda |binary data/pub_key.rda |binary man/GCD-internal.Rd | 5 - man/GCD-package.Rd | 11 +- man/charcoal_methods.Rd |only man/charcoal_units.Rd |only man/paleofiredata.Rd | 6 + man/paleofiresites.Rd | 97 ++++++------------------ man/pub.Rd |only 19 files changed, 181 insertions(+), 182 deletions(-)
Title: Creation of Arrays by Mixed Integer Programming
Description: 'CRAN' package 'DoE.base' and non-'CRAN' packages 'gurobi' and 'Rmosek' are enhanced with functionality for the creation of optimized arrays for experimentation, where optimization is in terms of generalized minimum aberration. It is also possible to optimally extend existing arrays to larger run size. Optimization requires the availability of at least one of the commercial products 'Gurobi' or 'Mosek' (free academic licenses available for both). For installing 'Gurobi' and its R package 'gurobi', follow instructions at <http://www.gurobi.com/downloads/gurobi-optimizer> and <http://www.gurobi.com/documentation/7.5/refman/r_api_overview.html>. For installing 'Mosek' and its R package 'Rmosek', follow instructions at <https://www.mosek.com/downloads/> and <http://docs.mosek.com/8.1/rmosek/install-interface.html>.
Author: Ulrike Groemping
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.MIParray versions 0.10 dated 2017-09-28 and 0.11 dated 2018-03-01
DoE.MIParray-0.10/DoE.MIParray/R/lowerbound_AR.R |only DoE.MIParray-0.10/DoE.MIParray/man/lowerbound_AR.Rd |only DoE.MIParray-0.11/DoE.MIParray/DESCRIPTION | 10 +- DoE.MIParray-0.11/DoE.MIParray/MD5 | 25 ++--- DoE.MIParray-0.11/DoE.MIParray/NAMESPACE | 3 DoE.MIParray-0.11/DoE.MIParray/R/gurobi_MIParray.R | 11 +- DoE.MIParray-0.11/DoE.MIParray/R/gurobi_MIPcontinue.R | 10 +- DoE.MIParray-0.11/DoE.MIParray/R/mosek_MIParray.R | 17 ++- DoE.MIParray-0.11/DoE.MIParray/R/mosek_MIPcontinue.R | 16 ++- DoE.MIParray-0.11/DoE.MIParray/inst/NEWS | 10 +- DoE.MIParray-0.11/DoE.MIParray/inst/testsWithGurobiAndMosek/testcombis.Rout.save | 50 +++++++++- DoE.MIParray-0.11/DoE.MIParray/inst/testsWithGurobiAndMosek/teststartforced.Rout.save | 14 ++ DoE.MIParray-0.11/DoE.MIParray/man/DoE.MIParray-package.Rd | 10 ++ DoE.MIParray-0.11/DoE.MIParray/man/functionsFromDoEbase.Rd |only DoE.MIParray-0.11/DoE.MIParray/man/mosek_MIParray.Rd | 30 ++---- 15 files changed, 152 insertions(+), 54 deletions(-)
Title: Methods for Adaptive Shrinkage, using Empirical Bayes
Description: The R package 'ashr' implements an Empirical Bayes
approach for large-scale hypothesis testing and false discovery
rate (FDR) estimation based on the methods proposed in
M. Stephens, 2016, "False discovery rates: a new deal",
<DOI:10.1093/biostatistics/kxw041>. These methods can be applied
whenever two sets of summary statistics---estimated effects and
standard errors---are available, just as 'qvalue' can be applied
to previously computed p-values. Two main interfaces are
provided: ash(), which is more user-friendly; and ash.workhorse(),
which has more options and is geared toward advanced users. The
ash() and ash.workhorse() also provides a flexible modeling
interface that can accomodate a variety of likelihoods (e.g.,
normal, Poisson) and mixture priors (e.g., uniform, normal).
Author: Matthew Stephens [aut],
Peter Carbonetto [aut, cre],
Chaoxing Dai [ctb],
David Gerard [aut],
Mengyin Lu [aut],
Lei Sun [aut],
Jason Willwerscheid [aut],
Nan Xiao [aut],
Mazon Zeng [ctb]
Maintainer: Peter Carbonetto <pcarbo@uchicago.edu>
Diff between ashr versions 2.0.5 dated 2016-12-21 and 2.2-7 dated 2018-03-01
ashr-2.0.5/ashr/R/ashr-package.r |only ashr-2.0.5/ashr/README.md |only ashr-2.0.5/ashr/man/ash.workhorse.Rd |only ashr-2.0.5/ashr/man/get_lfsr.Rd |only ashr-2.0.5/ashr/man/logF_lik.Rd |only ashr-2.0.5/ashr/man/normal_lik.Rd |only ashr-2.0.5/ashr/man/t_lik.Rd |only ashr-2.2-7/ashr/DESCRIPTION | 62 +- ashr-2.2-7/ashr/MD5 | 252 ++++---- ashr-2.2-7/ashr/NAMESPACE | 33 - ashr-2.2-7/ashr/R/RcppExports.R | 9 ashr-2.2-7/ashr/R/ash.R | 607 ++++++++++++-------- ashr-2.2-7/ashr/R/ashCI.R | 6 ashr-2.2-7/ashr/R/ashn.R | 5 ashr-2.2-7/ashr/R/ashr-package.R |only ashr-2.2-7/ashr/R/ashutility.R | 141 ++++ ashr-2.2-7/ashr/R/get_functions.R | 42 - ashr-2.2-7/ashr/R/igmix.R | 2 ashr-2.2-7/ashr/R/lik.R | 142 ++++ ashr-2.2-7/ashr/R/mix.R | 62 ++ ashr-2.2-7/ashr/R/mix_opt.R | 124 +++- ashr-2.2-7/ashr/R/normalmix.R | 46 + ashr-2.2-7/ashr/R/output.R | 21 ashr-2.2-7/ashr/R/process_args.R | 35 - ashr-2.2-7/ashr/R/set_data.R | 6 ashr-2.2-7/ashr/R/tnormalmix.R |only ashr-2.2-7/ashr/R/truncbeta.R |only ashr-2.2-7/ashr/R/truncgamma.R |only ashr-2.2-7/ashr/R/truncnorm.R | 65 +- ashr-2.2-7/ashr/R/unimix.R | 44 + ashr-2.2-7/ashr/build |only ashr-2.2-7/ashr/inst/doc |only ashr-2.2-7/ashr/inst/rmosek-linux.md | 2 ashr-2.2-7/ashr/inst/rmosek-mac.md | 6 ashr-2.2-7/ashr/man/ash.Rd | 244 ++++++-- ashr-2.2-7/ashr/man/ashci.Rd | 3 ashr-2.2-7/ashr/man/ashr.Rd | 3 ashr-2.2-7/ashr/man/calc_logLR.Rd | 1 ashr-2.2-7/ashr/man/calc_loglik.Rd | 1 ashr-2.2-7/ashr/man/calc_mixmean.Rd | 1 ashr-2.2-7/ashr/man/calc_mixsd.Rd | 1 ashr-2.2-7/ashr/man/calc_null_loglik.Rd | 1 ashr-2.2-7/ashr/man/calc_null_vloglik.Rd | 1 ashr-2.2-7/ashr/man/calc_vlogLR.Rd | 1 ashr-2.2-7/ashr/man/calc_vloglik.Rd | 1 ashr-2.2-7/ashr/man/cdf.ash.Rd | 1 ashr-2.2-7/ashr/man/cdf_conv.Rd |only ashr-2.2-7/ashr/man/cdf_post.Rd | 1 ashr-2.2-7/ashr/man/comp_cdf.Rd | 1 ashr-2.2-7/ashr/man/comp_cdf_conv.Rd |only ashr-2.2-7/ashr/man/comp_cdf_conv.normalmix.Rd |only ashr-2.2-7/ashr/man/comp_cdf_conv.unimix.Rd |only ashr-2.2-7/ashr/man/comp_cdf_post.Rd | 1 ashr-2.2-7/ashr/man/comp_dens.Rd | 1 ashr-2.2-7/ashr/man/comp_dens_conv.Rd | 1 ashr-2.2-7/ashr/man/comp_dens_conv.normalmix.Rd | 1 ashr-2.2-7/ashr/man/comp_dens_conv.unimix.Rd | 1 ashr-2.2-7/ashr/man/comp_mean.Rd | 1 ashr-2.2-7/ashr/man/comp_mean.normalmix.Rd | 1 ashr-2.2-7/ashr/man/comp_mean2.Rd | 1 ashr-2.2-7/ashr/man/comp_postmean.Rd | 1 ashr-2.2-7/ashr/man/comp_postmean2.Rd | 1 ashr-2.2-7/ashr/man/comp_postprob.Rd | 1 ashr-2.2-7/ashr/man/comp_postsd.Rd | 1 ashr-2.2-7/ashr/man/comp_sd.Rd | 1 ashr-2.2-7/ashr/man/comp_sd.normalmix.Rd | 1 ashr-2.2-7/ashr/man/compute_lfsr.Rd | 1 ashr-2.2-7/ashr/man/cxxMixSquarem.Rd |only ashr-2.2-7/ashr/man/dens.Rd | 1 ashr-2.2-7/ashr/man/dens_conv.Rd | 1 ashr-2.2-7/ashr/man/dlogf.Rd | 1 ashr-2.2-7/ashr/man/estimate_mixprop.Rd | 5 ashr-2.2-7/ashr/man/gen_etruncFUN.Rd | 1 ashr-2.2-7/ashr/man/get_density.Rd | 1 ashr-2.2-7/ashr/man/get_lfdr.Rd |only ashr-2.2-7/ashr/man/get_post_sample.Rd |only ashr-2.2-7/ashr/man/igmix.Rd | 1 ashr-2.2-7/ashr/man/lik_binom.Rd |only ashr-2.2-7/ashr/man/lik_logF.Rd |only ashr-2.2-7/ashr/man/lik_normal.Rd |only ashr-2.2-7/ashr/man/lik_normalmix.Rd |only ashr-2.2-7/ashr/man/lik_pois.Rd |only ashr-2.2-7/ashr/man/lik_t.Rd |only ashr-2.2-7/ashr/man/log_comp_dens_conv.Rd | 1 ashr-2.2-7/ashr/man/log_comp_dens_conv.normalmix.Rd | 1 ashr-2.2-7/ashr/man/log_comp_dens_conv.unimix.Rd | 1 ashr-2.2-7/ashr/man/loglik_conv.Rd | 1 ashr-2.2-7/ashr/man/loglik_conv.default.Rd | 1 ashr-2.2-7/ashr/man/mixEM.Rd | 1 ashr-2.2-7/ashr/man/mixIP.Rd | 18 ashr-2.2-7/ashr/man/mixVBEM.Rd | 1 ashr-2.2-7/ashr/man/mixcdf.Rd | 1 ashr-2.2-7/ashr/man/mixcdf.default.Rd | 1 ashr-2.2-7/ashr/man/mixmean2.Rd | 1 ashr-2.2-7/ashr/man/mixprop.Rd | 1 ashr-2.2-7/ashr/man/my_e2truncbeta.Rd |only ashr-2.2-7/ashr/man/my_e2truncgamma.Rd |only ashr-2.2-7/ashr/man/my_e2truncnorm.Rd | 1 ashr-2.2-7/ashr/man/my_e2trunct.Rd | 1 ashr-2.2-7/ashr/man/my_etruncbeta.Rd |only ashr-2.2-7/ashr/man/my_etruncgamma.Rd |only ashr-2.2-7/ashr/man/my_etrunclogf.Rd | 1 ashr-2.2-7/ashr/man/my_etruncnorm.Rd | 1 ashr-2.2-7/ashr/man/my_etrunct.Rd | 1 ashr-2.2-7/ashr/man/my_vtruncnorm.Rd | 1 ashr-2.2-7/ashr/man/ncomp.Rd | 1 ashr-2.2-7/ashr/man/ncomp.default.Rd | 1 ashr-2.2-7/ashr/man/normalmix.Rd | 1 ashr-2.2-7/ashr/man/pcdf_post.Rd | 1 ashr-2.2-7/ashr/man/plogf.Rd | 1 ashr-2.2-7/ashr/man/plot.ash.Rd | 1 ashr-2.2-7/ashr/man/plot_diagnostic.Rd |only ashr-2.2-7/ashr/man/pm_on_zero.Rd | 1 ashr-2.2-7/ashr/man/post_sample.Rd |only ashr-2.2-7/ashr/man/post_sample.normalmix.Rd |only ashr-2.2-7/ashr/man/posterior_dist.Rd | 1 ashr-2.2-7/ashr/man/postmean.Rd | 1 ashr-2.2-7/ashr/man/postmean2.Rd | 1 ashr-2.2-7/ashr/man/postsd.Rd | 1 ashr-2.2-7/ashr/man/print.ash.Rd | 1 ashr-2.2-7/ashr/man/prune.Rd |only ashr-2.2-7/ashr/man/qval.from.lfdr.Rd | 1 ashr-2.2-7/ashr/man/set_data.Rd | 3 ashr-2.2-7/ashr/man/summary.ash.Rd | 1 ashr-2.2-7/ashr/man/unimix.Rd | 1 ashr-2.2-7/ashr/man/vcdf_post.Rd | 1 ashr-2.2-7/ashr/man/w_mixEM.Rd |only ashr-2.2-7/ashr/src/MixSquarem.cpp | 14 ashr-2.2-7/ashr/src/RcppExports.cpp | 12 ashr-2.2-7/ashr/tests/testthat/test_binom.R |only ashr-2.2-7/ashr/tests/testthat/test_flashdata.R | 7 ashr-2.2-7/ashr/tests/testthat/test_lik.R | 12 ashr-2.2-7/ashr/tests/testthat/test_logF.R | 2 ashr-2.2-7/ashr/tests/testthat/test_log_comp_dens.R | 6 ashr-2.2-7/ashr/tests/testthat/test_loglik.R | 10 ashr-2.2-7/ashr/tests/testthat/test_moments.R | 2 ashr-2.2-7/ashr/tests/testthat/test_myetruncnorm.R | 19 ashr-2.2-7/ashr/tests/testthat/test_optmethod.R | 27 ashr-2.2-7/ashr/tests/testthat/test_output.R | 8 ashr-2.2-7/ashr/tests/testthat/test_pois.R |only ashr-2.2-7/ashr/tests/testthat/test_postsample.R |only ashr-2.2-7/ashr/tests/testthat/test_prune.R |only ashr-2.2-7/ashr/tests/testthat/test_tnormal.R |only ashr-2.2-7/ashr/tests/testthat/test_truncgen.R | 2 ashr-2.2-7/ashr/tests/testthat/test_trunct.R | 8 ashr-2.2-7/ashr/tests/testthat/test_w_mixEM.R |only ashr-2.2-7/ashr/vignettes |only 147 files changed, 1580 insertions(+), 602 deletions(-)
Title: Analysis of Charcoal Records from the Global Charcoal Database
Description: Tools to extract and analyse charcoal sedimentary data stored in
the Global Charcoal Database. Main functionalities includes data extraction
and sites selection, transformation and interpolation of the charcoal
records as well as compositing.
Author: Global Paleofire Working Group <paleofire@univ-fcomte.fr>
Maintainer: Olivier Blarquez <blarquez@gmail.com>
Diff between paleofire versions 1.2.0 dated 2017-09-28 and 1.2.1 dated 2018-03-01
DESCRIPTION | 10 +-- MD5 | 113 +++++++++++++++++++++---------------------- NEWS | 10 +++ R/pfCircular.R | 4 - R/pfComposite.R | 8 +-- R/pfCompositeLF.R | 6 +- R/pfDiagnostic.R | 2 R/pfDotMap.r | 2 R/pfExtract.R | 2 R/pfGridding.R | 8 +-- R/pfKruskal.R | 4 - R/pfMinMax.R | 4 - R/pfSimpleGrid.r | 2 R/pfSiteSel.R | 34 ++++++------ R/pfTransform.R | 33 ++++++------ R/potveg.R | 23 ++++---- build/vignette.rds |binary inst/doc/paleofire-paper.pdf |binary man/checkGCDversion.Rd | 1 man/contiguous.Rd | 7 +- man/contrib.pfCompositeLF.Rd | 3 - man/kdffreq.Rd | 7 +- man/paleofire-internal.Rd | 13 ++-- man/paleofire-package.Rd | 4 - man/pfAddData.Rd | 7 +- man/pfBoxCox.Rd | 7 +- man/pfCircular.Rd | 9 +-- man/pfComposite.Rd | 11 +--- man/pfCompositeLF.Rd | 9 +-- man/pfDiagnostic.Rd | 3 - man/pfDotMap.Rd | 9 +-- man/pfExtract.Rd | 3 - man/pfGridding.Rd | 13 ++-- man/pfInteractive.Rd | 7 +- man/pfKruskal.Rd | 9 +-- man/pfMinMax.Rd | 11 +--- man/pfPublication.Rd | 1 man/pfResolution.Rd | 1 man/pfSimpleGrid.Rd | 9 +-- man/pfSiteSel.Rd | 30 ++++------- man/pfToKml.Rd | 1 man/pfTransform.Rd | 1 man/plot.CHAR.Rd | 1 man/plot.contiguous.Rd | 7 +- man/plot.kdffreq.Rd | 1 man/plot.pfCircular.Rd | 1 man/plot.pfComposite.Rd | 5 - man/plot.pfCompositeLF.Rd | 3 - man/plot.pfGridding.Rd | 9 +-- man/plot.pfKruskal.Rd | 9 +-- man/plot.pfSiteSel.Rd | 7 +- man/plot.potveg.Rd | 28 ++++------ man/potveg.Rd | 7 +- man/pretreatment.Rd | 1 man/rbind.pfAddData.Rd | 7 +- man/summary.pfSiteSel.Rd | 3 - man/triCube.Rd | 1 vignettes/elsarticle.cls |only 58 files changed, 250 insertions(+), 281 deletions(-)
Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories,
consisting in four stages, pre-processing activity data, preparing
emissions factors, estimating the emissions and post-processing of emissions
in maps and databases.
Author: Sergio Ibarra-Espinosa [aut, cre]
(<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between vein versions 0.2.3 dated 2018-01-24 and 0.3.9 dated 2018-03-01
DESCRIPTION | 14 +- MD5 | 167 +++++++++++++++++--------------- NAMESPACE | 26 +++-- NEWS.md | 221 +++++++++++++++++++++++++++++++++---------- R/EmissionFactors.R | 2 R/EmissionFactorsList.R | 2 R/Emissions.R | 6 - R/EmissionsArray.R | 4 R/EmissionsList.R | 4 R/Evaporative.R | 11 -- R/GriddedEmissionsArray.R |only R/Speed.R | 2 R/Vehicles.R | 2 R/adt.R | 8 - R/age_hdv.R | 3 R/age_ldv.R | 3 R/age_moto.R | 7 - R/ef_evap.R | 2 R/ef_hdv_scaled.R | 2 R/ef_hdv_speed.R | 7 - R/ef_ldv_cold.R | 6 - R/ef_ldv_cold_list.R | 2 R/ef_ldv_scaled.R | 2 R/ef_ldv_speed.R | 28 ++--- R/ef_nitro.R | 10 + R/ef_wear.R | 10 - R/emis.R | 53 ++++++---- R/emis_cold.R | 61 +++++++---- R/emis_evap.R | 3 R/emis_grid.R | 111 ++++++++++++--------- R/emis_merge.R |only R/emis_paved.R | 4 R/emis_post.R | 13 +- R/emis_wrf.R | 3 R/hot_soak.R | 2 R/inventory.R | 146 +++++++++++++++++----------- R/make_grid.R | 64 ++++-------- R/my_age.R | 3 R/netspeed.R | 16 +-- R/profiles.R |only R/running_losses.R | 3 R/speciate.R | 4 R/temp_fact.R | 2 R/vkm.R | 4 data/profiles.rda |only demo/VEIN.R | 63 +++--------- inst/README.Rmd | 85 ++++++++-------- inst/README.html | 92 +++++++++++------ man/EmissionFactors.Rd | 2 man/EmissionFactorsList.Rd | 2 man/Emissions.Rd | 6 - man/EmissionsArray.Rd | 4 man/EmissionsList.Rd | 4 man/Evaporative.Rd | 9 - man/GriddedEmissionsArray.Rd |only man/Speed.Rd | 2 man/Vehicles.Rd | 2 man/adt.Rd | 5 man/age_hdv.Rd | 3 man/age_ldv.Rd | 3 man/age_moto.Rd | 7 - man/ef_evap.Rd | 2 man/ef_hdv_scaled.Rd | 2 man/ef_hdv_speed.Rd | 7 - man/ef_ldv_cold.Rd | 6 - man/ef_ldv_cold_list.Rd | 2 man/ef_ldv_scaled.Rd | 2 man/ef_ldv_speed.Rd | 28 ++--- man/ef_nitro.Rd | 10 + man/ef_wear.Rd | 10 - man/emis.Rd | 9 - man/emis_cold.Rd | 16 +-- man/emis_evap.Rd | 3 man/emis_grid.Rd | 39 +++---- man/emis_merge.Rd |only man/emis_paved.Rd | 4 man/emis_post.Rd | 3 man/hot_soak.Rd | 2 man/inventory.Rd | 34 +++--- man/make_grid.Rd | 26 ++--- man/my_age.Rd | 3 man/netspeed.Rd | 9 - man/profiles.Rd |only man/running_losses.Rd | 3 man/speciate.Rd | 4 man/temp_fact.Rd | 2 man/vkm.Rd | 4 tests |only 88 files changed, 877 insertions(+), 685 deletions(-)
Title: Continuous Biomarker Assessment by Exhaustive Survival Analysis
Description: In routine practice, biomarker performance is calculated by
splitting a patient cohort at some arbitrary level, often by median gene
expression. The logic behind this is to divide patients into “high” or “low”
expression groups that in turn correlate with either good or poor prognosis.
However, this median-split approach assumes that the data set composition
adheres to a strict 1:1 proportion of high vs. low expression, that for
every one “low” there is an equivalent “high”. In reality, data sets are
often heterogeneous in their composition (Perou, CM et al., 2000
<doi:10.1038/35021093>)- i.e. this 1:1 relationship is unlikely to exist and
the true relationship unknown. Given this limitation, it remains difficult
to determine where the most significant separation should be made. For
example, estrogen receptor (ER) status determined by immunohistochemistry is
standard practice in predicting hormone therapy response, where ER is found
in an ~1:3 ratio (-:+) in the population (Selli, C et al., 2016
<doi:10.1186/s13058-016-0779-0>). We would expect therefore, upon dividing
patients by ER expression, 25% to be classified “low” and 75% “high”, and
an otherwise 50-50 split to incorrectly classify 25% of our patient cohort,
rendering our survival estimate under powered. 'survivALL' is a data-driven
approach to calculate the relative survival estimates for all possible
points of separation - i.e. at all possible ratios of “high” vs. “low” -
allowing a measure’s relationship with survival to be more reliably
determined and quantified. We see this as a solution to a flaw in common
research practice, namely the failure of a true biomarker as part of a
meta-analysis.
Author: Dominic Pearce [aut, cre]
Maintainer: Dominic Pearce <dominic.pearce@ed.ac.uk>
Diff between survivALL versions 0.9.1 dated 2017-10-09 and 0.9.2 dated 2018-03-01
DESCRIPTION | 15 MD5 | 40 + NAMESPACE | 1 R/allHR.R | 5 R/allPvals.R | 10 R/checkContSig.R |only R/hrSignificance.R |only R/plotALL.R | 250 ++++------- R/survivALL.R | 145 +++--- inst/doc/basic-usage.R | 37 - inst/doc/basic-usage.Rmd | 52 -- inst/doc/basic-usage.html | 556 ++++++++------------------ inst/doc/bootstrapping-and-hr-thresholds.Rmd | 10 inst/doc/bootstrapping-and-hr-thresholds.html | 426 ++++++------------- inst/doc/rationale.Rmd | 2 inst/doc/rationale.html | 481 ++++++---------------- man/checkContSig.Rd |only man/hrSignificance.Rd |only man/plotALL.Rd |binary man/survivALL.Rd | 2 vignettes/basic-usage.Rmd | 52 -- vignettes/bootstrapping-and-hr-thresholds.Rmd | 10 vignettes/rationale.Rmd | 2 23 files changed, 747 insertions(+), 1349 deletions(-)
Title: Graph/Network Visualization
Description: Build graph/network structures using functions for stepwise addition and
deletion of nodes and edges. Work with data available in tables for bulk
addition of nodes, edges, and associated metadata. Use graph selections
and traversals to apply changes to specific nodes or edges. A wide
selection of graph algorithms allow for the analysis of graphs. Visualize
the graphs and take advantage of any aesthetic properties assigned to
nodes and edges.
Author: Richard Iannone [aut, cre]
Maintainer: Richard Iannone <riannone@me.com>
Diff between DiagrammeR versions 0.9.2 dated 2017-09-06 and 1.0.0 dated 2018-03-01
DiagrammeR-0.9.2/DiagrammeR/R/add_to_series.R |only DiagrammeR-0.9.2/DiagrammeR/R/cache_edge_attrs.R |only DiagrammeR-0.9.2/DiagrammeR/R/cache_edge_attrs_ws.R |only DiagrammeR-0.9.2/DiagrammeR/R/cache_edge_count_ws.R |only DiagrammeR-0.9.2/DiagrammeR/R/cache_node_attrs.R |only DiagrammeR-0.9.2/DiagrammeR/R/cache_node_attrs_ws.R |only DiagrammeR-0.9.2/DiagrammeR/R/cache_node_count_ws.R |only DiagrammeR-0.9.2/DiagrammeR/R/clear_global_graph_attrs.R |only DiagrammeR-0.9.2/DiagrammeR/R/create_complement_graph.R |only DiagrammeR-0.9.2/DiagrammeR/R/create_random_graph.R |only DiagrammeR-0.9.2/DiagrammeR/R/create_series.R |only DiagrammeR-0.9.2/DiagrammeR/R/create_subgraph_ws.R |only DiagrammeR-0.9.2/DiagrammeR/R/edge_count.R |only DiagrammeR-0.9.2/DiagrammeR/R/edge_info.R |only DiagrammeR-0.9.2/DiagrammeR/R/edge_present.R |only DiagrammeR-0.9.2/DiagrammeR/R/edge_rel.R |only DiagrammeR-0.9.2/DiagrammeR/R/get_global_graph_attrs.R |only DiagrammeR-0.9.2/DiagrammeR/R/get_graph_from_series.R |only DiagrammeR-0.9.2/DiagrammeR/R/get_min_spanning_tree.R |only DiagrammeR-0.9.2/DiagrammeR/R/graph_count.R |only DiagrammeR-0.9.2/DiagrammeR/R/graph_info.R |only DiagrammeR-0.9.2/DiagrammeR/R/image_icon.R |only DiagrammeR-0.9.2/DiagrammeR/R/node_count.R |only DiagrammeR-0.9.2/DiagrammeR/R/node_info.R |only DiagrammeR-0.9.2/DiagrammeR/R/node_present.R |only DiagrammeR-0.9.2/DiagrammeR/R/node_type.R |only DiagrammeR-0.9.2/DiagrammeR/R/remove_from_series.R |only DiagrammeR-0.9.2/DiagrammeR/R/render_graph_from_series.R |only DiagrammeR-0.9.2/DiagrammeR/R/series_info.R |only DiagrammeR-0.9.2/DiagrammeR/R/set_global_graph_attrs.R |only DiagrammeR-0.9.2/DiagrammeR/R/subset_series.R |only DiagrammeR-0.9.2/DiagrammeR/README.md |only DiagrammeR-0.9.2/DiagrammeR/inst/img |only DiagrammeR-0.9.2/DiagrammeR/man/add_to_series.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/cache_edge_attrs.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/cache_edge_attrs_ws.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/cache_edge_count_ws.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/cache_node_attrs.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/cache_node_attrs_ws.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/cache_node_count_ws.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/clear_global_graph_attrs.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/create_complement_graph.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/create_random_graph.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/create_series.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/create_subgraph_ws.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/edge_count.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/edge_info.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/edge_present.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/edge_rel.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/get_global_graph_attrs.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/get_graph_from_series.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/get_min_spanning_tree.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/graph_count.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/graph_info.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/image_icon.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/node_count.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/node_info.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/node_present.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/node_type.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/remove_from_series.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/render_graph_from_series.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/series_info.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/set_global_graph_attrs.Rd |only DiagrammeR-0.9.2/DiagrammeR/man/subset_series.Rd |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test-create_random_graph.R |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test-edge_present.R |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test-edge_relationship.R |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test-image_icon.R |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test-node_edge_count.R |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test-node_present.R |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test-node_type.R |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test-set_node_attr_to_display.R |only DiagrammeR-0.9.2/DiagrammeR/tests/testthat/test_htmlwidgets.R |only DiagrammeR-1.0.0/DiagrammeR/DESCRIPTION | 73 DiagrammeR-1.0.0/DiagrammeR/LICENSE | 2 DiagrammeR-1.0.0/DiagrammeR/MD5 | 1023 +++++----- DiagrammeR-1.0.0/DiagrammeR/NAMESPACE | 95 DiagrammeR-1.0.0/DiagrammeR/NEWS.md | 20 DiagrammeR-1.0.0/DiagrammeR/R/DiagrammeR.R | 17 DiagrammeR-1.0.0/DiagrammeR/R/add_balanced_tree.R | 318 ++- DiagrammeR-1.0.0/DiagrammeR/R/add_cycle.R | 385 ++- DiagrammeR-1.0.0/DiagrammeR/R/add_edge.R | 231 +- DiagrammeR-1.0.0/DiagrammeR/R/add_edge_clone.R | 68 DiagrammeR-1.0.0/DiagrammeR/R/add_edge_df.R | 91 DiagrammeR-1.0.0/DiagrammeR/R/add_edges_from_table.R | 339 +-- DiagrammeR-1.0.0/DiagrammeR/R/add_edges_w_string.R | 121 - DiagrammeR-1.0.0/DiagrammeR/R/add_forward_edges_ws.R | 41 DiagrammeR-1.0.0/DiagrammeR/R/add_full_graph.R | 356 ++- DiagrammeR-1.0.0/DiagrammeR/R/add_global_graph_attrs.R | 57 DiagrammeR-1.0.0/DiagrammeR/R/add_gnm_graph.R |only DiagrammeR-1.0.0/DiagrammeR/R/add_gnp_graph.R | 350 ++- DiagrammeR-1.0.0/DiagrammeR/R/add_graph_action.R | 25 DiagrammeR-1.0.0/DiagrammeR/R/add_graph_to_graph_series.R |only DiagrammeR-1.0.0/DiagrammeR/R/add_grid_2d.R | 362 ++- DiagrammeR-1.0.0/DiagrammeR/R/add_grid_3d.R | 399 ++- DiagrammeR-1.0.0/DiagrammeR/R/add_growing_graph.R |only DiagrammeR-1.0.0/DiagrammeR/R/add_islands_graph.R |only DiagrammeR-1.0.0/DiagrammeR/R/add_n_node_clones.R | 87 DiagrammeR-1.0.0/DiagrammeR/R/add_n_nodes.R | 97 DiagrammeR-1.0.0/DiagrammeR/R/add_n_nodes_ws.R | 302 ++ DiagrammeR-1.0.0/DiagrammeR/R/add_node.R | 481 ++++ DiagrammeR-1.0.0/DiagrammeR/R/add_node_clones_ws.R |only DiagrammeR-1.0.0/DiagrammeR/R/add_node_df.R | 86 DiagrammeR-1.0.0/DiagrammeR/R/add_nodes_from_df_cols.R | 77 DiagrammeR-1.0.0/DiagrammeR/R/add_nodes_from_table.R | 260 +- DiagrammeR-1.0.0/DiagrammeR/R/add_pa_graph.R | 419 +++- DiagrammeR-1.0.0/DiagrammeR/R/add_path.R | 344 ++- DiagrammeR-1.0.0/DiagrammeR/R/add_prism.R | 355 ++- DiagrammeR-1.0.0/DiagrammeR/R/add_reverse_edges_ws.R | 125 + DiagrammeR-1.0.0/DiagrammeR/R/add_smallworld_graph.R |only DiagrammeR-1.0.0/DiagrammeR/R/add_star.R | 388 ++- DiagrammeR-1.0.0/DiagrammeR/R/clear_selection.R | 89 DiagrammeR-1.0.0/DiagrammeR/R/colorize_edge_attrs.R | 39 DiagrammeR-1.0.0/DiagrammeR/R/colorize_node_attrs.R | 78 DiagrammeR-1.0.0/DiagrammeR/R/combine_edfs.R | 9 DiagrammeR-1.0.0/DiagrammeR/R/combine_graphs.R | 101 DiagrammeR-1.0.0/DiagrammeR/R/combine_ndfs.R | 29 DiagrammeR-1.0.0/DiagrammeR/R/copy_edge_attrs.R | 89 DiagrammeR-1.0.0/DiagrammeR/R/copy_node_attrs.R | 89 DiagrammeR-1.0.0/DiagrammeR/R/count_asymmetric_node_pairs.R | 23 DiagrammeR-1.0.0/DiagrammeR/R/count_automorphisms.R | 32 DiagrammeR-1.0.0/DiagrammeR/R/count_edges.R |only DiagrammeR-1.0.0/DiagrammeR/R/count_graphs_in_graph_series.R |only DiagrammeR-1.0.0/DiagrammeR/R/count_loop_edges.R |only DiagrammeR-1.0.0/DiagrammeR/R/count_mutual_node_pairs.R | 30 DiagrammeR-1.0.0/DiagrammeR/R/count_nodes.R |only DiagrammeR-1.0.0/DiagrammeR/R/count_s_connected_cmpts.R |only DiagrammeR-1.0.0/DiagrammeR/R/count_unconnected_node_pairs.R | 17 DiagrammeR-1.0.0/DiagrammeR/R/count_unconnected_nodes.R |only DiagrammeR-1.0.0/DiagrammeR/R/count_w_connected_cmpts.R |only DiagrammeR-1.0.0/DiagrammeR/R/create_edge_df.R | 23 DiagrammeR-1.0.0/DiagrammeR/R/create_graph.R | 300 +- DiagrammeR-1.0.0/DiagrammeR/R/create_graph_series.R |only DiagrammeR-1.0.0/DiagrammeR/R/create_node_df.R | 36 DiagrammeR-1.0.0/DiagrammeR/R/data.R |only DiagrammeR-1.0.0/DiagrammeR/R/delete_cache.R |only DiagrammeR-1.0.0/DiagrammeR/R/delete_edge.R | 93 DiagrammeR-1.0.0/DiagrammeR/R/delete_edges_ws.R | 47 DiagrammeR-1.0.0/DiagrammeR/R/delete_global_graph_attrs.R | 150 + DiagrammeR-1.0.0/DiagrammeR/R/delete_graph_actions.R | 57 DiagrammeR-1.0.0/DiagrammeR/R/delete_loop_edges_ws.R |only DiagrammeR-1.0.0/DiagrammeR/R/delete_node.R | 57 DiagrammeR-1.0.0/DiagrammeR/R/delete_nodes_ws.R | 48 DiagrammeR-1.0.0/DiagrammeR/R/deselect_edges.R |only DiagrammeR-1.0.0/DiagrammeR/R/deselect_nodes.R |only DiagrammeR-1.0.0/DiagrammeR/R/display_metagraph.R | 94 DiagrammeR-1.0.0/DiagrammeR/R/do_bfs.R | 79 DiagrammeR-1.0.0/DiagrammeR/R/do_dfs.R | 77 DiagrammeR-1.0.0/DiagrammeR/R/drop_edge_attrs.R | 83 DiagrammeR-1.0.0/DiagrammeR/R/drop_node_attrs.R | 79 DiagrammeR-1.0.0/DiagrammeR/R/edge_aes.R |only DiagrammeR-1.0.0/DiagrammeR/R/edge_data.R |only DiagrammeR-1.0.0/DiagrammeR/R/export_csv.R | 29 DiagrammeR-1.0.0/DiagrammeR/R/export_graph.R | 87 DiagrammeR-1.0.0/DiagrammeR/R/filter_graph_series.R |only DiagrammeR-1.0.0/DiagrammeR/R/from_adj_matrix.R | 16 DiagrammeR-1.0.0/DiagrammeR/R/from_igraph.R | 41 DiagrammeR-1.0.0/DiagrammeR/R/fully_connect_nodes_ws.R |only DiagrammeR-1.0.0/DiagrammeR/R/fully_disconnect_nodes_ws.R |only DiagrammeR-1.0.0/DiagrammeR/R/generate_dot.R | 215 +- DiagrammeR-1.0.0/DiagrammeR/R/get_adhesion.R | 13 DiagrammeR-1.0.0/DiagrammeR/R/get_agg_degree_in.R | 116 - DiagrammeR-1.0.0/DiagrammeR/R/get_agg_degree_out.R | 95 DiagrammeR-1.0.0/DiagrammeR/R/get_agg_degree_total.R | 114 - DiagrammeR-1.0.0/DiagrammeR/R/get_all_connected_nodes.R | 69 DiagrammeR-1.0.0/DiagrammeR/R/get_alpha_centrality.R | 93 DiagrammeR-1.0.0/DiagrammeR/R/get_articulation_points.R | 39 DiagrammeR-1.0.0/DiagrammeR/R/get_attr_dfs.R | 51 DiagrammeR-1.0.0/DiagrammeR/R/get_authority_centrality.R | 73 DiagrammeR-1.0.0/DiagrammeR/R/get_betweenness.R | 58 DiagrammeR-1.0.0/DiagrammeR/R/get_bridging.R | 49 DiagrammeR-1.0.0/DiagrammeR/R/get_cache.R | 36 DiagrammeR-1.0.0/DiagrammeR/R/get_closeness.R | 54 DiagrammeR-1.0.0/DiagrammeR/R/get_closeness_vitality.R | 74 DiagrammeR-1.0.0/DiagrammeR/R/get_cmty_edge_btwns.R | 62 DiagrammeR-1.0.0/DiagrammeR/R/get_cmty_fast_greedy.R | 70 DiagrammeR-1.0.0/DiagrammeR/R/get_cmty_l_eigenvec.R | 61 DiagrammeR-1.0.0/DiagrammeR/R/get_cmty_louvain.R | 61 DiagrammeR-1.0.0/DiagrammeR/R/get_cmty_walktrap.R | 79 DiagrammeR-1.0.0/DiagrammeR/R/get_common_nbrs.R | 16 DiagrammeR-1.0.0/DiagrammeR/R/get_constraint.R | 67 DiagrammeR-1.0.0/DiagrammeR/R/get_coreness.R | 60 DiagrammeR-1.0.0/DiagrammeR/R/get_degree_distribution.R | 37 DiagrammeR-1.0.0/DiagrammeR/R/get_degree_histogram.R | 43 DiagrammeR-1.0.0/DiagrammeR/R/get_degree_in.R | 58 DiagrammeR-1.0.0/DiagrammeR/R/get_degree_out.R | 58 DiagrammeR-1.0.0/DiagrammeR/R/get_degree_total.R | 58 DiagrammeR-1.0.0/DiagrammeR/R/get_dice_similarity.R | 36 DiagrammeR-1.0.0/DiagrammeR/R/get_eccentricity.R | 87 DiagrammeR-1.0.0/DiagrammeR/R/get_edge_attrs.R | 28 DiagrammeR-1.0.0/DiagrammeR/R/get_edge_attrs_ws.R | 26 DiagrammeR-1.0.0/DiagrammeR/R/get_edge_count_w_multiedge.R | 17 DiagrammeR-1.0.0/DiagrammeR/R/get_edge_df.R | 25 DiagrammeR-1.0.0/DiagrammeR/R/get_edge_df_ws.R |only DiagrammeR-1.0.0/DiagrammeR/R/get_edge_ids.R | 17 DiagrammeR-1.0.0/DiagrammeR/R/get_edge_info.R |only DiagrammeR-1.0.0/DiagrammeR/R/get_edges.R | 188 - DiagrammeR-1.0.0/DiagrammeR/R/get_eigen_centrality.R | 70 DiagrammeR-1.0.0/DiagrammeR/R/get_girth.R | 13 DiagrammeR-1.0.0/DiagrammeR/R/get_global_graph_attr_info.R |only DiagrammeR-1.0.0/DiagrammeR/R/get_graph_actions.R | 27 DiagrammeR-1.0.0/DiagrammeR/R/get_graph_from_graph_series.R |only DiagrammeR-1.0.0/DiagrammeR/R/get_graph_info.R |only DiagrammeR-1.0.0/DiagrammeR/R/get_graph_log.R | 34 DiagrammeR-1.0.0/DiagrammeR/R/get_graph_name.R | 23 DiagrammeR-1.0.0/DiagrammeR/R/get_graph_series_info.R |only DiagrammeR-1.0.0/DiagrammeR/R/get_graph_time.R | 18 DiagrammeR-1.0.0/DiagrammeR/R/get_jaccard_similarity.R | 41 DiagrammeR-1.0.0/DiagrammeR/R/get_last_edges_created.R | 20 DiagrammeR-1.0.0/DiagrammeR/R/get_last_nodes_created.R | 19 DiagrammeR-1.0.0/DiagrammeR/R/get_leverage_centrality.R | 60 DiagrammeR-1.0.0/DiagrammeR/R/get_max_eccentricity.R | 13 DiagrammeR-1.0.0/DiagrammeR/R/get_mean_distance.R | 13 DiagrammeR-1.0.0/DiagrammeR/R/get_min_cut_between.R | 29 DiagrammeR-1.0.0/DiagrammeR/R/get_min_eccentricity.R | 18 DiagrammeR-1.0.0/DiagrammeR/R/get_multiedge_count.R | 36 DiagrammeR-1.0.0/DiagrammeR/R/get_nbrs.R | 10 DiagrammeR-1.0.0/DiagrammeR/R/get_node_attrs.R | 39 DiagrammeR-1.0.0/DiagrammeR/R/get_node_attrs_ws.R | 42 DiagrammeR-1.0.0/DiagrammeR/R/get_node_df.R | 31 DiagrammeR-1.0.0/DiagrammeR/R/get_node_df_ws.R |only DiagrammeR-1.0.0/DiagrammeR/R/get_node_ids.R | 105 - DiagrammeR-1.0.0/DiagrammeR/R/get_node_info.R |only DiagrammeR-1.0.0/DiagrammeR/R/get_non_nbrs.R | 13 DiagrammeR-1.0.0/DiagrammeR/R/get_pagerank.R | 59 DiagrammeR-1.0.0/DiagrammeR/R/get_paths.R | 54 DiagrammeR-1.0.0/DiagrammeR/R/get_periphery.R | 22 DiagrammeR-1.0.0/DiagrammeR/R/get_predecessors.R | 40 DiagrammeR-1.0.0/DiagrammeR/R/get_radiality.R | 59 DiagrammeR-1.0.0/DiagrammeR/R/get_reciprocity.R | 16 DiagrammeR-1.0.0/DiagrammeR/R/get_s_connected_cmpts.R | 53 DiagrammeR-1.0.0/DiagrammeR/R/get_selection.R | 95 DiagrammeR-1.0.0/DiagrammeR/R/get_similar_nbrs.R | 93 DiagrammeR-1.0.0/DiagrammeR/R/get_successors.R | 40 DiagrammeR-1.0.0/DiagrammeR/R/get_w_connected_cmpts.R | 47 DiagrammeR-1.0.0/DiagrammeR/R/import_graph.R | 44 DiagrammeR-1.0.0/DiagrammeR/R/invert_selection.R | 73 DiagrammeR-1.0.0/DiagrammeR/R/is_edge_loop.R | 38 DiagrammeR-1.0.0/DiagrammeR/R/is_edge_multiple.R | 36 DiagrammeR-1.0.0/DiagrammeR/R/is_edge_mutual.R | 36 DiagrammeR-1.0.0/DiagrammeR/R/is_edge_present.R |only DiagrammeR-1.0.0/DiagrammeR/R/is_graph_connected.R | 55 DiagrammeR-1.0.0/DiagrammeR/R/is_graph_dag.R | 20 DiagrammeR-1.0.0/DiagrammeR/R/is_graph_directed.R | 32 DiagrammeR-1.0.0/DiagrammeR/R/is_graph_empty.R | 16 DiagrammeR-1.0.0/DiagrammeR/R/is_graph_simple.R | 12 DiagrammeR-1.0.0/DiagrammeR/R/is_graph_undirected.R |only DiagrammeR-1.0.0/DiagrammeR/R/is_graph_weighted.R | 16 DiagrammeR-1.0.0/DiagrammeR/R/is_node_present.R |only DiagrammeR-1.0.0/DiagrammeR/R/is_property_graph.R | 37 DiagrammeR-1.0.0/DiagrammeR/R/join_edge_attrs.R | 40 DiagrammeR-1.0.0/DiagrammeR/R/join_node_attrs.R | 40 DiagrammeR-1.0.0/DiagrammeR/R/layout_nodes_w_string.R | 37 DiagrammeR-1.0.0/DiagrammeR/R/mutate_edge_attrs.R | 48 DiagrammeR-1.0.0/DiagrammeR/R/mutate_edge_attrs_ws.R | 64 DiagrammeR-1.0.0/DiagrammeR/R/mutate_node_attrs.R | 48 DiagrammeR-1.0.0/DiagrammeR/R/mutate_node_attrs_ws.R | 64 DiagrammeR-1.0.0/DiagrammeR/R/node_aes.R |only DiagrammeR-1.0.0/DiagrammeR/R/node_data.R |only DiagrammeR-1.0.0/DiagrammeR/R/nudge_node_positions_ws.R | 85 DiagrammeR-1.0.0/DiagrammeR/R/open_graph.R | 13 DiagrammeR-1.0.0/DiagrammeR/R/print.R | 99 DiagrammeR-1.0.0/DiagrammeR/R/recode_edge_attrs.R | 102 DiagrammeR-1.0.0/DiagrammeR/R/recode_node_attrs.R | 137 - DiagrammeR-1.0.0/DiagrammeR/R/remove_graph_from_graph_series.R |only DiagrammeR-1.0.0/DiagrammeR/R/rename_edge_attrs.R | 84 DiagrammeR-1.0.0/DiagrammeR/R/rename_node_attrs.R | 84 DiagrammeR-1.0.0/DiagrammeR/R/render_graph.R | 66 DiagrammeR-1.0.0/DiagrammeR/R/render_graph_from_graph_series.R |only DiagrammeR-1.0.0/DiagrammeR/R/reorder_graph_actions.R | 45 DiagrammeR-1.0.0/DiagrammeR/R/rescale_edge_attrs.R | 98 DiagrammeR-1.0.0/DiagrammeR/R/rescale_node_attrs.R | 93 DiagrammeR-1.0.0/DiagrammeR/R/rev_edge_dir.R | 35 DiagrammeR-1.0.0/DiagrammeR/R/rev_edge_dir_ws.R | 51 DiagrammeR-1.0.0/DiagrammeR/R/save_graph.R | 13 DiagrammeR-1.0.0/DiagrammeR/R/select_edges.R | 110 - DiagrammeR-1.0.0/DiagrammeR/R/select_edges_by_edge_id.R | 81 DiagrammeR-1.0.0/DiagrammeR/R/select_edges_by_node_id.R | 86 DiagrammeR-1.0.0/DiagrammeR/R/select_last_edges_created.R | 42 DiagrammeR-1.0.0/DiagrammeR/R/select_last_nodes_created.R | 36 DiagrammeR-1.0.0/DiagrammeR/R/select_nodes.R | 93 DiagrammeR-1.0.0/DiagrammeR/R/select_nodes_by_degree.R | 172 + DiagrammeR-1.0.0/DiagrammeR/R/select_nodes_by_id.R | 78 DiagrammeR-1.0.0/DiagrammeR/R/select_nodes_in_neighborhood.R | 121 - DiagrammeR-1.0.0/DiagrammeR/R/set_cache.R | 90 DiagrammeR-1.0.0/DiagrammeR/R/set_df_as_edge_attr.R | 34 DiagrammeR-1.0.0/DiagrammeR/R/set_df_as_node_attr.R | 36 DiagrammeR-1.0.0/DiagrammeR/R/set_edge_attr_to_display.R |only DiagrammeR-1.0.0/DiagrammeR/R/set_edge_attrs.R | 198 - DiagrammeR-1.0.0/DiagrammeR/R/set_edge_attrs_ws.R | 37 DiagrammeR-1.0.0/DiagrammeR/R/set_graph_directed.R |only DiagrammeR-1.0.0/DiagrammeR/R/set_graph_name.R | 13 DiagrammeR-1.0.0/DiagrammeR/R/set_graph_time.R | 21 DiagrammeR-1.0.0/DiagrammeR/R/set_graph_undirected.R | 33 DiagrammeR-1.0.0/DiagrammeR/R/set_node_attr_to_display.R | 103 - DiagrammeR-1.0.0/DiagrammeR/R/set_node_attr_w_fcn.R | 84 DiagrammeR-1.0.0/DiagrammeR/R/set_node_attrs.R | 183 - DiagrammeR-1.0.0/DiagrammeR/R/set_node_attrs_ws.R | 39 DiagrammeR-1.0.0/DiagrammeR/R/set_node_position.R | 49 DiagrammeR-1.0.0/DiagrammeR/R/to_igraph.R | 37 DiagrammeR-1.0.0/DiagrammeR/R/transform_to_complement_graph.R |only DiagrammeR-1.0.0/DiagrammeR/R/transform_to_min_spanning_tree.R |only DiagrammeR-1.0.0/DiagrammeR/R/transform_to_subgraph_ws.R |only DiagrammeR-1.0.0/DiagrammeR/R/trav_both.R | 207 +- DiagrammeR-1.0.0/DiagrammeR/R/trav_both_edge.R | 159 + DiagrammeR-1.0.0/DiagrammeR/R/trav_in.R | 202 + DiagrammeR-1.0.0/DiagrammeR/R/trav_in_edge.R | 140 - DiagrammeR-1.0.0/DiagrammeR/R/trav_in_node.R | 134 - DiagrammeR-1.0.0/DiagrammeR/R/trav_in_until.R |only DiagrammeR-1.0.0/DiagrammeR/R/trav_out.R | 202 + DiagrammeR-1.0.0/DiagrammeR/R/trav_out_edge.R | 144 - DiagrammeR-1.0.0/DiagrammeR/R/trav_out_node.R | 134 - DiagrammeR-1.0.0/DiagrammeR/R/trav_out_until.R |only DiagrammeR-1.0.0/DiagrammeR/R/trav_reverse_edge.R | 37 DiagrammeR-1.0.0/DiagrammeR/R/trigger_graph_actions.R | 39 DiagrammeR-1.0.0/DiagrammeR/R/utils.R | 340 ++- DiagrammeR-1.0.0/DiagrammeR/data |only DiagrammeR-1.0.0/DiagrammeR/inst/extdata/example_graphs_dgr/repository.dgr |binary DiagrammeR-1.0.0/DiagrammeR/inst/htmlwidgets/lib/mermaid/dist/mermaid.slim.min.js | 2 DiagrammeR-1.0.0/DiagrammeR/man/DiagrammeR.Rd | 2 DiagrammeR-1.0.0/DiagrammeR/man/add_balanced_tree.Rd | 90 DiagrammeR-1.0.0/DiagrammeR/man/add_cycle.Rd | 162 - DiagrammeR-1.0.0/DiagrammeR/man/add_edge.Rd | 78 DiagrammeR-1.0.0/DiagrammeR/man/add_edge_clone.Rd | 35 DiagrammeR-1.0.0/DiagrammeR/man/add_edge_df.Rd | 60 DiagrammeR-1.0.0/DiagrammeR/man/add_edges_from_table.Rd | 159 - DiagrammeR-1.0.0/DiagrammeR/man/add_edges_w_string.Rd | 96 DiagrammeR-1.0.0/DiagrammeR/man/add_forward_edges_ws.Rd | 8 DiagrammeR-1.0.0/DiagrammeR/man/add_full_graph.Rd | 164 - DiagrammeR-1.0.0/DiagrammeR/man/add_global_graph_attrs.Rd | 42 DiagrammeR-1.0.0/DiagrammeR/man/add_gnm_graph.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/add_gnp_graph.Rd | 96 DiagrammeR-1.0.0/DiagrammeR/man/add_graph_action.Rd | 15 DiagrammeR-1.0.0/DiagrammeR/man/add_graph_to_graph_series.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/add_grid_2d.Rd | 99 DiagrammeR-1.0.0/DiagrammeR/man/add_grid_3d.Rd | 129 - DiagrammeR-1.0.0/DiagrammeR/man/add_growing_graph.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/add_islands_graph.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/add_n_node_clones.Rd | 14 DiagrammeR-1.0.0/DiagrammeR/man/add_n_nodes.Rd | 27 DiagrammeR-1.0.0/DiagrammeR/man/add_n_nodes_ws.Rd | 40 DiagrammeR-1.0.0/DiagrammeR/man/add_node.Rd | 68 DiagrammeR-1.0.0/DiagrammeR/man/add_node_clones_ws.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/add_node_df.Rd | 63 DiagrammeR-1.0.0/DiagrammeR/man/add_nodes_from_df_cols.Rd | 35 DiagrammeR-1.0.0/DiagrammeR/man/add_nodes_from_table.Rd | 101 DiagrammeR-1.0.0/DiagrammeR/man/add_pa_graph.Rd | 170 + DiagrammeR-1.0.0/DiagrammeR/man/add_path.Rd | 114 - DiagrammeR-1.0.0/DiagrammeR/man/add_prism.Rd | 124 - DiagrammeR-1.0.0/DiagrammeR/man/add_reverse_edges_ws.Rd | 24 DiagrammeR-1.0.0/DiagrammeR/man/add_smallworld_graph.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/add_star.Rd | 171 + DiagrammeR-1.0.0/DiagrammeR/man/clear_selection.Rd | 58 DiagrammeR-1.0.0/DiagrammeR/man/colorize_edge_attrs.Rd | 8 DiagrammeR-1.0.0/DiagrammeR/man/colorize_node_attrs.Rd | 47 DiagrammeR-1.0.0/DiagrammeR/man/combine_edfs.Rd | 9 DiagrammeR-1.0.0/DiagrammeR/man/combine_graphs.Rd | 57 DiagrammeR-1.0.0/DiagrammeR/man/combine_ndfs.Rd | 29 DiagrammeR-1.0.0/DiagrammeR/man/copy_edge_attrs.Rd | 50 DiagrammeR-1.0.0/DiagrammeR/man/copy_node_attrs.Rd | 50 DiagrammeR-1.0.0/DiagrammeR/man/count_asymmetric_node_pairs.Rd | 15 DiagrammeR-1.0.0/DiagrammeR/man/count_automorphisms.Rd | 22 DiagrammeR-1.0.0/DiagrammeR/man/count_edges.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/count_graphs_in_graph_series.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/count_loop_edges.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/count_mutual_node_pairs.Rd | 22 DiagrammeR-1.0.0/DiagrammeR/man/count_nodes.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/count_s_connected_cmpts.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/count_unconnected_node_pairs.Rd | 9 DiagrammeR-1.0.0/DiagrammeR/man/count_unconnected_nodes.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/count_w_connected_cmpts.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/create_edge_df.Rd | 23 DiagrammeR-1.0.0/DiagrammeR/man/create_graph.Rd | 183 - DiagrammeR-1.0.0/DiagrammeR/man/create_graph_series.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/create_node_df.Rd | 23 DiagrammeR-1.0.0/DiagrammeR/man/currencies.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/delete_cache.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/delete_edge.Rd | 24 DiagrammeR-1.0.0/DiagrammeR/man/delete_edges_ws.Rd | 9 DiagrammeR-1.0.0/DiagrammeR/man/delete_global_graph_attrs.Rd | 26 DiagrammeR-1.0.0/DiagrammeR/man/delete_graph_actions.Rd | 32 DiagrammeR-1.0.0/DiagrammeR/man/delete_loop_edges_ws.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/delete_node.Rd | 8 DiagrammeR-1.0.0/DiagrammeR/man/delete_nodes_ws.Rd | 4 DiagrammeR-1.0.0/DiagrammeR/man/deselect_edges.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/deselect_nodes.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/display_metagraph.Rd | 29 DiagrammeR-1.0.0/DiagrammeR/man/do_bfs.Rd | 55 DiagrammeR-1.0.0/DiagrammeR/man/do_dfs.Rd | 53 DiagrammeR-1.0.0/DiagrammeR/man/drop_edge_attrs.Rd | 52 DiagrammeR-1.0.0/DiagrammeR/man/drop_node_attrs.Rd | 47 DiagrammeR-1.0.0/DiagrammeR/man/edge_aes.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/edge_data.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/edge_list_1.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/edge_list_2.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/export_graph.Rd | 40 DiagrammeR-1.0.0/DiagrammeR/man/filter_graph_series.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/from_adj_matrix.Rd | 3 DiagrammeR-1.0.0/DiagrammeR/man/from_igraph.Rd | 30 DiagrammeR-1.0.0/DiagrammeR/man/fully_connect_nodes_ws.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/fully_disconnect_nodes_ws.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/get_adhesion.Rd | 5 DiagrammeR-1.0.0/DiagrammeR/man/get_agg_degree_in.Rd | 92 DiagrammeR-1.0.0/DiagrammeR/man/get_agg_degree_out.Rd | 71 DiagrammeR-1.0.0/DiagrammeR/man/get_agg_degree_total.Rd | 88 DiagrammeR-1.0.0/DiagrammeR/man/get_all_connected_nodes.Rd | 56 DiagrammeR-1.0.0/DiagrammeR/man/get_alpha_centrality.Rd | 89 DiagrammeR-1.0.0/DiagrammeR/man/get_articulation_points.Rd | 31 DiagrammeR-1.0.0/DiagrammeR/man/get_attr_dfs.Rd | 26 DiagrammeR-1.0.0/DiagrammeR/man/get_authority_centrality.Rd | 55 DiagrammeR-1.0.0/DiagrammeR/man/get_betweenness.Rd | 46 DiagrammeR-1.0.0/DiagrammeR/man/get_bridging.Rd | 41 DiagrammeR-1.0.0/DiagrammeR/man/get_cache.Rd | 28 DiagrammeR-1.0.0/DiagrammeR/man/get_closeness.Rd | 41 DiagrammeR-1.0.0/DiagrammeR/man/get_closeness_vitality.Rd | 66 DiagrammeR-1.0.0/DiagrammeR/man/get_cmty_edge_btwns.Rd | 54 DiagrammeR-1.0.0/DiagrammeR/man/get_cmty_fast_greedy.Rd | 62 DiagrammeR-1.0.0/DiagrammeR/man/get_cmty_l_eigenvec.Rd | 53 DiagrammeR-1.0.0/DiagrammeR/man/get_cmty_louvain.Rd | 53 DiagrammeR-1.0.0/DiagrammeR/man/get_cmty_walktrap.Rd | 71 DiagrammeR-1.0.0/DiagrammeR/man/get_common_nbrs.Rd | 8 DiagrammeR-1.0.0/DiagrammeR/man/get_constraint.Rd | 54 DiagrammeR-1.0.0/DiagrammeR/man/get_coreness.Rd | 47 DiagrammeR-1.0.0/DiagrammeR/man/get_degree_distribution.Rd | 24 DiagrammeR-1.0.0/DiagrammeR/man/get_degree_histogram.Rd | 24 DiagrammeR-1.0.0/DiagrammeR/man/get_degree_in.Rd | 50 DiagrammeR-1.0.0/DiagrammeR/man/get_degree_out.Rd | 50 DiagrammeR-1.0.0/DiagrammeR/man/get_degree_total.Rd | 50 DiagrammeR-1.0.0/DiagrammeR/man/get_dice_similarity.Rd | 23 DiagrammeR-1.0.0/DiagrammeR/man/get_eccentricity.Rd | 44 DiagrammeR-1.0.0/DiagrammeR/man/get_edge_attrs.Rd | 4 DiagrammeR-1.0.0/DiagrammeR/man/get_edge_attrs_ws.Rd | 2 DiagrammeR-1.0.0/DiagrammeR/man/get_edge_count_w_multiedge.Rd | 4 DiagrammeR-1.0.0/DiagrammeR/man/get_edge_df.Rd | 17 DiagrammeR-1.0.0/DiagrammeR/man/get_edge_df_ws.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/get_edge_ids.Rd | 7 DiagrammeR-1.0.0/DiagrammeR/man/get_edge_info.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/get_edges.Rd | 153 - 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DiagrammeR-1.0.0/DiagrammeR/man/select_nodes_by_id.Rd | 8 DiagrammeR-1.0.0/DiagrammeR/man/select_nodes_in_neighborhood.Rd | 58 DiagrammeR-1.0.0/DiagrammeR/man/set_cache.Rd | 75 DiagrammeR-1.0.0/DiagrammeR/man/set_df_as_edge_attr.Rd | 2 DiagrammeR-1.0.0/DiagrammeR/man/set_df_as_node_attr.Rd | 4 DiagrammeR-1.0.0/DiagrammeR/man/set_edge_attr_to_display.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/set_edge_attrs.Rd | 69 DiagrammeR-1.0.0/DiagrammeR/man/set_edge_attrs_ws.Rd | 9 DiagrammeR-1.0.0/DiagrammeR/man/set_graph_directed.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/set_graph_name.Rd | 3 DiagrammeR-1.0.0/DiagrammeR/man/set_graph_time.Rd | 6 DiagrammeR-1.0.0/DiagrammeR/man/set_graph_undirected.Rd | 20 DiagrammeR-1.0.0/DiagrammeR/man/set_node_attr_to_display.Rd | 46 DiagrammeR-1.0.0/DiagrammeR/man/set_node_attr_w_fcn.Rd | 66 DiagrammeR-1.0.0/DiagrammeR/man/set_node_attrs.Rd | 78 DiagrammeR-1.0.0/DiagrammeR/man/set_node_attrs_ws.Rd | 10 DiagrammeR-1.0.0/DiagrammeR/man/set_node_position.Rd | 24 DiagrammeR-1.0.0/DiagrammeR/man/to_igraph.Rd | 29 DiagrammeR-1.0.0/DiagrammeR/man/transform_to_complement_graph.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/transform_to_min_spanning_tree.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/transform_to_subgraph_ws.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/trav_both.Rd | 60 DiagrammeR-1.0.0/DiagrammeR/man/trav_both_edge.Rd | 44 DiagrammeR-1.0.0/DiagrammeR/man/trav_in.Rd | 57 DiagrammeR-1.0.0/DiagrammeR/man/trav_in_edge.Rd | 48 DiagrammeR-1.0.0/DiagrammeR/man/trav_in_node.Rd | 45 DiagrammeR-1.0.0/DiagrammeR/man/trav_in_until.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/trav_out.Rd | 59 DiagrammeR-1.0.0/DiagrammeR/man/trav_out_edge.Rd | 44 DiagrammeR-1.0.0/DiagrammeR/man/trav_out_node.Rd | 45 DiagrammeR-1.0.0/DiagrammeR/man/trav_out_until.Rd |only DiagrammeR-1.0.0/DiagrammeR/man/trav_reverse_edge.Rd | 10 DiagrammeR-1.0.0/DiagrammeR/man/trigger_graph_actions.Rd | 27 DiagrammeR-1.0.0/DiagrammeR/man/usd_exchange_rates.Rd |only DiagrammeR-1.0.0/DiagrammeR/tests/testthat/test-add_forward_reverse_edges.R | 18 DiagrammeR-1.0.0/DiagrammeR/tests/testthat/test-add_graphs.R | 973 ++++++++- DiagrammeR-1.0.0/DiagrammeR/tests/testthat/test-add_node_edge.R | 390 ++- DiagrammeR-1.0.0/DiagrammeR/tests/testthat/test-add_nodes_edges_from_table.R | 90 DiagrammeR-1.0.0/DiagrammeR/tests/testthat/test-cache_attrs.R | 715 +----- DiagrammeR-1.0.0/DiagrammeR/tests/testthat/test-colorize_nodes_edges.R | 118 - 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Title: Taxonomic Information from Around the Web
Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
such as getting database specific taxonomic identifiers, verifying
species names, getting taxonomic hierarchies, fetching downstream and
upstream taxonomic names, getting taxonomic synonyms, converting
scientific to common names and vice versa, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Eduard Szoecs [aut],
Zachary Foster [aut],
Zebulun Arendsee [aut],
Carl Boettiger [ctb],
Karthik Ram [ctb],
Ignasi Bartomeus [ctb],
John Baumgartner [ctb],
James O'Donnell [ctb],
Jari Oksanen [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between taxize versions 0.9.0 dated 2017-09-28 and 0.9.2 dated 2018-03-01
DESCRIPTION | 30 +- LICENSE | 2 MD5 | 252 +++++++++++------------ NAMESPACE | 3 NEWS.md | 32 ++ R/children.R | 50 ++++ R/class2tree.R | 243 ++++++++++++++++++++++ R/classification.R | 53 ++-- R/col_children.R | 7 R/col_search.R | 20 + R/comm2sci.R | 18 + R/downstream.R | 28 +- R/eol_dataobjects.R | 31 +- R/eol_pages.R | 26 +- R/eol_search.R | 24 +- R/gbif_downstream.R | 12 - R/gbif_helpers.R | 16 - R/gbif_name_usage.R | 11 - R/gbif_parse.R | 2 R/genbank2uid.R | 118 ++++++----- R/get_colid.R | 24 +- R/get_eolid.R | 33 +-- R/get_gbifid.R | 30 +- R/get_ids.R | 9 R/get_nbnid.R | 30 +- R/get_tpsid.R | 30 +- R/get_tsn.R | 24 +- R/get_uid.R | 150 ++++++++----- R/get_wormsid.R | 24 +- R/getkey.R | 101 +++++++-- R/globals.R | 3 R/gnr_resolve.R | 112 +++------- R/limited_print.R |only R/lowest_common.R | 4 R/nbn_search.R | 18 + R/ncbi_children.R | 81 +++++-- R/ncbi_downstream.R | 9 R/plantminer.R | 31 +- R/sci2comm.R | 32 +- R/synonyms.R | 3 R/tax_name.R | 71 ++++-- R/taxize-package.R | 8 R/tnrs.R | 2 R/tp_accnames.R | 20 - R/tp_dist.R | 21 - R/tp_refs.R | 22 -- R/tp_search.R | 13 - R/tp_summary.R | 24 +- R/tp_synonyms.R | 13 - R/upstream.R | 2 R/vascan_search.r | 26 +- R/zzz.R | 20 + README.md | 60 +---- build/vignette.rds |binary inst/doc/name_cleaning.Rmd | 99 ++------- inst/doc/name_cleaning.html | 99 ++------- inst/doc/taxize_vignette.Rmd | 343 ++++++++------------------------ inst/doc/taxize_vignette.html | 343 ++++++++------------------------ inst/vign/name_cleaning.md | 99 ++------- inst/vign/taxize_vignette.Rmd | 9 inst/vign/taxize_vignette.md | 343 ++++++++------------------------ man/children.Rd | 3 man/class2tree.Rd | 2 man/classification.Rd | 14 - man/col_search.Rd | 5 man/comm2sci.Rd | 5 man/downstream.Rd | 21 + man/eol_dataobjects.Rd | 19 - man/eol_pages.Rd | 6 man/eol_search.Rd | 10 man/gbif_downstream.Rd | 7 man/gbif_name_usage.Rd | 2 man/gbif_parse.Rd | 2 man/genbank2uid.Rd | 6 man/get_colid.Rd | 6 man/get_eolid.Rd | 11 - man/get_gbifid.Rd | 10 man/get_ids.Rd | 11 - man/get_nbnid.Rd | 10 man/get_tpsid.Rd | 10 man/get_tsn.Rd | 6 man/get_uid.Rd | 26 +- man/get_wormsid.Rd | 6 man/getkey.Rd | 63 +++++ man/gnr_resolve.Rd | 9 man/limited_print.Rd |only man/lowest_common.Rd | 5 man/nbn_search.Rd | 5 man/ncbi_children.Rd | 15 + man/ncbi_downstream.Rd | 8 man/plantminer.Rd | 15 - man/sci2comm.Rd | 17 - man/synonyms.Rd | 2 man/tax_name.Rd | 9 man/taxize-package.Rd | 3 man/tp_acceptednames-deprecated.Rd | 10 man/tp_accnames.Rd | 5 man/tp_dist.Rd | 6 man/tp_namedistributions-deprecated.Rd | 9 man/tp_namereferences-deprecated.Rd | 13 - man/tp_refs.Rd | 5 man/tp_search.Rd | 5 man/tp_summary.Rd | 5 man/tp_synonyms.Rd | 5 man/upstream.Rd | 2 man/vascan_search.Rd | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test-children.R | 50 ++++ tests/testthat/test-class2tree.R | 9 tests/testthat/test-col_children.R | 1 tests/testthat/test-downstream.R | 2 tests/testthat/test-eol_ping.R | 8 tests/testthat/test-gbif_downstream.R | 11 + tests/testthat/test-gbif_parse.R | 4 tests/testthat/test-genbank2uid.R | 103 +++++---- tests/testthat/test-get_eolid.R | 9 tests/testthat/test-get_gbifid.R | 40 +-- tests/testthat/test-get_ids.R | 13 - tests/testthat/test-get_tsn.R | 2 tests/testthat/test-get_uid.R | 36 +-- tests/testthat/test-gnr_resolve.R | 7 tests/testthat/test-itis_kingdomnames.R | 3 tests/testthat/test-ncbi_children.R | 5 tests/testthat/test-plantminer.R | 38 +-- tests/testthat/test-tax_name.R | 4 tests/testthat/test-tax_rank.R | 2 vignettes/name_cleaning.Rmd | 99 ++------- vignettes/taxize_vignette.Rmd | 343 ++++++++------------------------ 128 files changed, 2208 insertions(+), 2363 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Jeff Allen [ctb],
Roy Storey [ctb],
Rob Hyndman [ctb],
Ruben Arslan [ctb],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 1.8 dated 2017-11-17 and 1.9 dated 2018-03-01
DESCRIPTION | 13 ++++--- MD5 | 39 ++++++++++++----------- NAMESPACE | 2 + R/html_dependencies.R | 15 +++++++- R/html_resources.R | 9 ++++- R/md_document.R | 4 +- R/output_format.R | 6 +-- R/pandoc.R | 12 ++++--- R/params.R | 11 +++++- R/powerpoint_presentation.R |only R/render.R | 64 +++++++++++++++++++++++++++----------- R/util.R | 6 ++- inst/NEWS | 23 +++++++++++++ man/ioslides_presentation.Rd | 4 +- man/output_metadata.Rd |only man/pandoc_available.Rd | 6 +-- man/pandoc_options.Rd | 2 - man/pandoc_self_contained_html.Rd | 2 - man/powerpoint_presentation.Rd |only man/render.Rd | 2 - tests/testthat/test-notebook.R | 8 ++-- tests/testthat/test-params.R | 51 ++++++++++++++++++++++++++++++ 22 files changed, 211 insertions(+), 68 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of use. Integer,
floating point and complex numbers are supported, as well as a subset of
trigonometric and statistics functions. Various matrix decompositions are
provided through optional integration with LAPACK and ATLAS libraries.
The 'RcppArmadillo' package includes the header files from the templated
'Armadillo' library. Thus users do not need to install 'Armadillo' itself in
order to use 'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is
licensed under Apache License 2; previous releases were under licensed as
MPL 2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'. Note that
Armadillo requires a fairly recent compiler; for the g++ family at least
version 4.6.* is required.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates and Binxiang Ni
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.8.300.1.0 dated 2017-12-06 and 0.8.400.0.0 dated 2018-03-01
ChangeLog | 36 DESCRIPTION | 8 MD5 | 144 +- configure | 20 configure.ac | 4 inst/NEWS.Rd | 23 inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/doc/RcppArmadillo-unitTests.pdf |binary inst/include/RcppArmadilloAs.h | 19 inst/include/RcppArmadilloConfig.h | 4 inst/include/RcppArmadilloConfigGenerated.h.in | 4 inst/include/RcppArmadilloSugar.h | 26 inst/include/armadillo | 15 inst/include/armadillo_bits/Cube_bones.hpp | 30 inst/include/armadillo_bits/Cube_meat.hpp | 12 inst/include/armadillo_bits/Mat_bones.hpp | 193 +- inst/include/armadillo_bits/Mat_meat.hpp | 478 ++++-- inst/include/armadillo_bits/Op_bones.hpp | 2 inst/include/armadillo_bits/SpMat_bones.hpp | 53 inst/include/armadillo_bits/SpMat_iterators_meat.hpp | 36 inst/include/armadillo_bits/SpMat_meat.hpp | 44 inst/include/armadillo_bits/SpSubview_bones.hpp | 3 inst/include/armadillo_bits/SpSubview_iterators_meat.hpp | 2 inst/include/armadillo_bits/arma_cmath.hpp | 14 inst/include/armadillo_bits/arma_config.hpp | 11 inst/include/armadillo_bits/arma_forward.hpp | 7 inst/include/armadillo_bits/arma_ostream_meat.hpp | 8 inst/include/armadillo_bits/arma_rng.hpp | 9 inst/include/armadillo_bits/arma_version.hpp | 6 inst/include/armadillo_bits/compiler_setup.hpp | 16 inst/include/armadillo_bits/config.hpp | 2 inst/include/armadillo_bits/debug.hpp | 1 inst/include/armadillo_bits/def_blas.hpp | 4 inst/include/armadillo_bits/def_lapack.hpp | 4 inst/include/armadillo_bits/diskio_bones.hpp | 11 inst/include/armadillo_bits/diskio_meat.hpp | 1041 ++++++--------- inst/include/armadillo_bits/eop_aux.hpp | 6 inst/include/armadillo_bits/fft_engine.hpp | 22 inst/include/armadillo_bits/field_bones.hpp | 16 inst/include/armadillo_bits/field_meat.hpp | 8 inst/include/armadillo_bits/fn_accu.hpp | 175 +- inst/include/armadillo_bits/fn_chi2rnd.hpp |only inst/include/armadillo_bits/fn_index_max.hpp | 17 inst/include/armadillo_bits/fn_index_min.hpp | 17 inst/include/armadillo_bits/fn_kron.hpp | 51 inst/include/armadillo_bits/fn_mvnrnd.hpp |only inst/include/armadillo_bits/fn_normcdf.hpp |only inst/include/armadillo_bits/fn_randg.hpp | 31 inst/include/armadillo_bits/fn_randi.hpp | 50 inst/include/armadillo_bits/fn_randn.hpp | 4 inst/include/armadillo_bits/fn_randu.hpp | 6 inst/include/armadillo_bits/fn_wishrnd.hpp |only inst/include/armadillo_bits/glue_intersect_meat.hpp | 2 inst/include/armadillo_bits/glue_mvnrnd_bones.hpp |only inst/include/armadillo_bits/glue_mvnrnd_meat.hpp |only inst/include/armadillo_bits/gmm_full_meat.hpp | 4 inst/include/armadillo_bits/memory.hpp | 21 inst/include/armadillo_bits/op_chi2rnd_bones.hpp |only inst/include/armadillo_bits/op_chi2rnd_meat.hpp |only inst/include/armadillo_bits/op_index_max_bones.hpp | 12 inst/include/armadillo_bits/op_index_max_meat.hpp | 246 +++ inst/include/armadillo_bits/op_index_min_bones.hpp | 12 inst/include/armadillo_bits/op_index_min_meat.hpp | 246 +++ inst/include/armadillo_bits/op_max_meat.hpp | 7 inst/include/armadillo_bits/op_min_meat.hpp | 7 inst/include/armadillo_bits/op_wishrnd_bones.hpp |only inst/include/armadillo_bits/op_wishrnd_meat.hpp |only inst/include/armadillo_bits/restrictors.hpp | 119 - inst/include/armadillo_bits/spglue_kron_bones.hpp |only inst/include/armadillo_bits/spglue_kron_meat.hpp |only inst/include/armadillo_bits/spop_misc_meat.hpp | 47 inst/include/armadillo_bits/subview_bones.hpp | 160 ++ inst/include/armadillo_bits/subview_cube_bones.hpp | 89 + inst/include/armadillo_bits/subview_cube_meat.hpp | 400 +++++ inst/include/armadillo_bits/subview_meat.hpp | 786 ++++++++++- inst/include/armadillo_bits/unwrap_cube.hpp | 10 inst/unitTests/cpp/sparse.cpp | 4 inst/unitTests/runit.sparseConversion.R | 6 79 files changed, 3516 insertions(+), 1355 deletions(-)
Title: Interface Between R and Qt
Description: Dynamic bindings to the Qt library for calling Qt
methods and extending Qt classes from R. Other packages build upon 'qtbase'
to provide special-purpose high-level interfaces to specific parts of Qt.
Author: Michael Lawrence, Deepayan Sarkar
Maintainer: Michael Lawrence <michafla@gene.com>
Diff between qtbase versions 1.0.12 dated 2017-04-15 and 1.0.13 dated 2018-03-01
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- build/vignette.rds |binary inst/doc/qtbase.pdf |binary src/Class.cpp | 1 + src/DataFrameModel.hpp | 6 +++--- src/DynamicBinding.hpp | 6 +++--- src/EventLoop.cpp | 4 ++-- src/MocStack.cpp | 2 +- src/NameOnlyClass.hpp | 2 +- src/RClass.cpp | 2 +- src/SmokeObject.cpp | 3 ++- src/dynamicqobject.cpp | 6 ++++++ src/dynamicqobject.h | 2 ++ src/smoke.cpp | 6 ++++-- src/symbols.rds |binary 16 files changed, 44 insertions(+), 32 deletions(-)
Title: Toolkit Implementation of gWidgets for RGtk2
Description: Port of the gWidgets API to the RGtk2 toolkit.
Author: Michael Lawrence, John Verzani
Maintainer: John Verzani <jverzani@gmail.com>
Diff between gWidgetsRGtk2 versions 0.0-85 dated 2018-01-04 and 0.0-86 dated 2018-03-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/gbutton.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Combination of Factorial Methods and Cluster Analysis
Description: Some functions of 'ade4' and 'stats' are combined in order to obtain a partition of the rows of a data table, with columns representing variables of scales: quantitative, qualitative or frequency.
First, a principal axes method is performed and then, a combination of Ward agglomerative hierarchical classification and K-means is performed, using some of the first coordinates obtained from the previous principal axes method.
The function 'kmeansW', a modification of 'kmeans', programmed in C++, is included, in order to permit to have different weights of the elements to be clustered. Some complementary functions and datasets are included.
See, for example:
Lebart, L. and Piron, M. and Morineau, A. (2006).
Statistique Exploratoire Multidimensionnelle, Dunod, Paris.
Author: Campo Elias Pardo <cepardot@unal.edu.co>,
Pedro Cesar del Campo <pcdelcampon@unal.edu.co> and
Camilo Jose Torres <cjtorresj@unal.edu.co>,
with the contributions from.
Ivan Diaz <ildiazm@unal.edu.co>,
Mauricio Sadinle <msadinleg@unal.edu.co>,
Jhonathan Medina <jmedinau@unal.edu.co>.
Maintainer: Campo Elias Pardo <cepardot@unal.edu.co>
Diff between FactoClass versions 1.1.6 dated 2017-09-01 and 1.2.4 dated 2018-03-01
FactoClass-1.1.6/FactoClass/data/BreedsDogs.rda |only FactoClass-1.1.6/FactoClass/man/BreedsDogs.Rd |only FactoClass-1.2.4/FactoClass/DESCRIPTION | 16 FactoClass-1.2.4/FactoClass/MD5 | 32 - FactoClass-1.2.4/FactoClass/NAMESPACE | 10 FactoClass-1.2.4/FactoClass/R/FactoClass.tex.R | 2 FactoClass-1.2.4/FactoClass/R/dudi.tex.R | 2 FactoClass-1.2.4/FactoClass/R/plot.dudi.R | 354 ++++++++++++++-------- FactoClass-1.2.4/FactoClass/R/plotFactoClass.R | 86 ++--- FactoClass-1.2.4/FactoClass/data/DogBreeds.rda |only FactoClass-1.2.4/FactoClass/man/DogBreeds.Rd |only FactoClass-1.2.4/FactoClass/man/Fac.Num.Rd | 64 +-- FactoClass-1.2.4/FactoClass/man/FactoClass.Rd | 230 +++++++------- FactoClass-1.2.4/FactoClass/man/FactoClass.tex.Rd | 168 +++++----- FactoClass-1.2.4/FactoClass/man/cluster.carac.Rd | 14 FactoClass-1.2.4/FactoClass/man/clusterchisq.Rd | 6 FactoClass-1.2.4/FactoClass/man/dudi.tex.Rd | 6 FactoClass-1.2.4/FactoClass/man/plot.dudi.Rd | 143 ++++---- FactoClass-1.2.4/FactoClass/man/plotFactoClass.Rd | 164 +++++----- 19 files changed, 709 insertions(+), 588 deletions(-)
Title: Small Helpers and Tricks for Epidemics Analysis
Description: A collection of small functions useful for epidemics analysis and infectious disease modelling. This includes computation of basic reproduction numbers from growth rates, generation of hashed labels to anonymise data, and fitting discretised Gamma distributions.
Author: Thibaut Jombart [aut, cre],
Anne Cori [aut]
Maintainer: Thibaut Jombart <thibautjombart@gmail.com>
Diff between epitrix versions 0.1.1 dated 2018-01-24 and 0.1.2 dated 2018-03-01
DESCRIPTION | 6 +-- MD5 | 19 ++++++----- NEWS.md | 8 +++++ R/hash_names.R | 51 +++++++++++++++++++++----------- inst/doc/epitrix.html | 22 ++++++------- man/hash_names.Rd | 21 ++++++++++--- tests/testthat/rds/hashref_salt.rds |only tests/testthat/test_hash_names.R | 32 ++++++++++++++++++++ vignettes/figs-overview/fit_i-1.png |binary vignettes/figs-overview/sample_R0-1.png |binary vignettes/figs-overview/si-1.png |binary 11 files changed, 114 insertions(+), 45 deletions(-)
Title: Blind Source Separation Methods for Tensor-Valued Observations
Description: Contains several utility functions for manipulating tensor-valued data (centering, multiplication from a single mode etc.) and the implementations of the following blind source separation methods for tensor-valued data: 'tPCA', 'tFOBI', 'tJADE', k-tJADE', 'tgFOBI', 'tgJADE', 'tSOBI', 'tNSS.SD', 'tNSS.JD', 'tNSS.TD.JD' and 'tPP'.
Author: Joni Virta, Bing Li, Klaus Nordhausen, Hannu Oja
Maintainer: Joni Virta <joni.virta@outlook.com>
Diff between tensorBSS versions 0.3.3 dated 2017-10-06 and 0.3.4 dated 2018-03-01
tensorBSS-0.3.3/tensorBSS/src/tensorBSS_init.c |only tensorBSS-0.3.4/tensorBSS/DESCRIPTION | 14 - tensorBSS-0.3.4/tensorBSS/MD5 | 46 ++--- tensorBSS-0.3.4/tensorBSS/NAMESPACE | 3 tensorBSS-0.3.4/tensorBSS/R/RcppExports.R | 36 ++-- tensorBSS-0.3.4/tensorBSS/R/k_tJADE.R | 16 + tensorBSS-0.3.4/tensorBSS/R/tJADERotate.R | 27 +-- tensorBSS-0.3.4/tensorBSS/R/tPP.R |only tensorBSS-0.3.4/tensorBSS/R/tPPRotate.R |only tensorBSS-0.3.4/tensorBSS/build/partial.rdb |binary tensorBSS-0.3.4/tensorBSS/inst/ChangeLog | 8 tensorBSS-0.3.4/tensorBSS/man/k_tJADE.Rd | 8 tensorBSS-0.3.4/tensorBSS/man/mModeAutoCovariance.Rd | 2 tensorBSS-0.3.4/tensorBSS/man/tGFOBI.Rd | 8 tensorBSS-0.3.4/tensorBSS/man/tGJADE.Rd | 8 tensorBSS-0.3.4/tensorBSS/man/tJADE.Rd | 6 tensorBSS-0.3.4/tensorBSS/man/tNSS.JD.Rd | 6 tensorBSS-0.3.4/tensorBSS/man/tNSS.SD.Rd | 2 tensorBSS-0.3.4/tensorBSS/man/tNSS.TD.JD.Rd | 6 tensorBSS-0.3.4/tensorBSS/man/tPCA.Rd | 2 tensorBSS-0.3.4/tensorBSS/man/tPP.Rd |only tensorBSS-0.3.4/tensorBSS/man/tSIR.Rd | 4 tensorBSS-0.3.4/tensorBSS/man/tSOBI.Rd | 8 tensorBSS-0.3.4/tensorBSS/man/tensorBSS-package.Rd | 16 + tensorBSS-0.3.4/tensorBSS/src/RcppExports.cpp | 95 +++++++++- tensorBSS-0.3.4/tensorBSS/src/tensorBSS.cpp | 170 +++++++++++++++++++ 26 files changed, 390 insertions(+), 101 deletions(-)
Title: Full Factorials, Orthogonal Arrays and Base Utilities for DoE
Packages
Description: Creates full factorial experimental designs and designs based on orthogonal arrays for (industrial) experiments. Provides diverse quality criteria. Provides utility functions for the class design, which is also used by other packages for designed experiments.
Author: Ulrike Groemping [aut, cre],
Boyko Amarov [ctb],
Hongquan Xu [ctb]
Maintainer: Ulrike Groemping <groemping@beuth-hochschule.de>
Diff between DoE.base versions 0.31 dated 2017-08-13 and 0.32 dated 2018-03-01
DESCRIPTION | 14 +- MD5 | 22 ++-- NAMESPACE | 4 R/SCFTs.R | 2 R/halfnormal.R | 2 R/lowerbound_AR.R |only R/oa.maxGR.R | 41 +++----- R/oa.min3.R | 193 ++++++++++++++++++++++++++++++++++++++--- inst/NEWS | 23 ++++ man/ICFTs.Rd | 4 man/generalized.word.length.Rd | 38 +++++--- man/lowerbound_AR.Rd |only man/planor2design.Rd | 2 13 files changed, 269 insertions(+), 76 deletions(-)
Title: Temporal Trend Analysis Graphical Interface
Description: This interface was created to develop a standard procedure
to analyse temporal trend in the framework of the OSPAR convention.
The analysis process run through 4 successive steps : 1) manipulate your data, 2)
select the parameters you want to analyse, 3) build your regulated
time series, 4) perform diagnosis and analysis and 5) read the results.
Statistical analysis call other package function such as Kendall tests
or cusum() function.
Author: David DEVREKER [aut, cre],
Alain LEFEBVRE [aut]
Maintainer: David DEVREKER <David.Devreker@ifremer.fr>
Diff between TTAinterfaceTrendAnalysis versions 1.5.3 dated 2016-09-07 and 1.5.4 dated 2018-03-01
DESCRIPTION | 14 - MD5 | 30 +- NAMESPACE | 8 NEWS | 8 R/FULLoption.r | 76 ++++- R/TTAinterface.R | 2 R/aide3.r | 2 R/aide4.r | 6 R/fixdata.R | 2 R/selectdirectory.R | 2 build/vignette.rds |binary inst/doc/TTAVignette.Rnw | 598 ++++++++++++++++++++++---------------------- inst/doc/TTAVignette.pdf |binary inst/doc/UserGuide.pdf |binary man/TTAinterface-package.Rd | 4 vignettes/TTAVignette.Rnw | 598 ++++++++++++++++++++++---------------------- 16 files changed, 698 insertions(+), 652 deletions(-)
More information about TTAinterfaceTrendAnalysis at CRAN
Permanent link
Title: Constrained Optimal Sample Allocation
Description: Implements generalized constrained optimal sample allocation framework for two-group multilevel regression discontinuity studies and multilevel randomized trials with continuous outcomes. Bulus, M. (2017). Design Considerations in Three-level Regression Discontinuity Studies (Doctoral dissertation). University of Missouri, Columbia, MO.
Author: Metin Bulus [aut, cre, cph]
Maintainer: Metin Bulus <bulusmetin@gmail.com>
Diff between cosa versions 1.0.0 dated 2018-02-06 and 1.1.0 dated 2018-03-01
cosa-1.0.0/cosa/R/error.R |only cosa-1.0.0/cosa/inst/doc/multilevel_randomized_trials.R |only cosa-1.0.0/cosa/inst/doc/multilevel_randomized_trials.Rmd |only cosa-1.0.0/cosa/inst/doc/multilevel_randomized_trials.html |only cosa-1.0.0/cosa/inst/doc/multilevel_regression_discont.R |only cosa-1.0.0/cosa/inst/doc/multilevel_regression_discont.Rmd |only cosa-1.0.0/cosa/inst/doc/multilevel_regression_discont.html |only cosa-1.0.0/cosa/vignettes/multilevel_randomized_trials.Rmd |only cosa-1.0.0/cosa/vignettes/multilevel_regression_discont.Rmd |only cosa-1.1.0/cosa/DESCRIPTION | 10 cosa-1.1.0/cosa/MD5 | 79 +-- cosa-1.1.0/cosa/NAMESPACE | 41 + cosa-1.1.0/cosa/NEWS.md | 12 cosa-1.1.0/cosa/R/bcrd3f2.R |only cosa-1.1.0/cosa/R/bcrd3r2.R | 143 ++++- cosa-1.1.0/cosa/R/bcrd4f3.R |only cosa-1.1.0/cosa/R/bcrd4r2.R | 149 +++++ cosa-1.1.0/cosa/R/bcrd4r3.R | 145 ++++- cosa-1.1.0/cosa/R/bird2f1.R |only cosa-1.1.0/cosa/R/bird2r1.R | 134 ++++- cosa-1.1.0/cosa/R/bird3r1.R | 142 ++++- cosa-1.1.0/cosa/R/bird4r1.R | 144 ++++- cosa-1.1.0/cosa/R/cosa.R |only cosa-1.1.0/cosa/R/crd2r2.R | 140 ++++- cosa-1.1.0/cosa/R/crd3r3.R | 136 ++++- cosa-1.1.0/cosa/R/crd4r4.R | 139 ++++- cosa-1.1.0/cosa/R/ird1r1.R | 192 ++++++- cosa-1.1.0/cosa/R/mdes.R |only cosa-1.1.0/cosa/R/method.R |only cosa-1.1.0/cosa/R/plot.R |only cosa-1.1.0/cosa/R/power.R |only cosa-1.1.0/cosa/R/utils.R | 310 +++++++----- cosa-1.1.0/cosa/R/zzz.R |only cosa-1.1.0/cosa/README.md | 77 -- cosa-1.1.0/cosa/build/vignette.rds |binary cosa-1.1.0/cosa/inst/CITATION |only cosa-1.1.0/cosa/inst/doc/cosa_tutorial.R |only cosa-1.1.0/cosa/inst/doc/cosa_tutorial.Rmd |only cosa-1.1.0/cosa/inst/doc/cosa_tutorial.html |only cosa-1.1.0/cosa/man/bcrd3r2.Rd | 42 - cosa-1.1.0/cosa/man/bcrd4r2.Rd | 59 -- cosa-1.1.0/cosa/man/bcrd4r3.Rd | 46 - cosa-1.1.0/cosa/man/bird2r1.Rd | 41 - cosa-1.1.0/cosa/man/bird3r1.Rd | 45 - cosa-1.1.0/cosa/man/bird4r1.Rd | 48 - cosa-1.1.0/cosa/man/cosa-package.Rd | 119 +++- cosa-1.1.0/cosa/man/crd2r2.Rd | 68 +- cosa-1.1.0/cosa/man/crd3r3.Rd | 71 +- cosa-1.1.0/cosa/man/crd4r4.Rd | 44 - cosa-1.1.0/cosa/man/ird1r1.Rd | 73 ++ cosa-1.1.0/cosa/man/method.Rd |only cosa-1.1.0/cosa/man/plot.Rd |only cosa-1.1.0/cosa/vignettes/cosa_tutorial.Rmd |only 53 files changed, 2012 insertions(+), 637 deletions(-)
Title: Client for the YouTube API
Description: Get comments posted on YouTube videos, information on how many
times a video has been liked, search for videos with particular content, and
much more. You can also scrape captions from a few videos. To learn more about
the YouTube API, see <https://developers.google.com/youtube/v3/>.
Author: Gaurav Sood [aut, cre],
Kate Lyons [ctb]
Maintainer: Gaurav Sood <gsood07@gmail.com>
Diff between tuber versions 0.9.4 dated 2018-02-13 and 0.9.5 dated 2018-03-01
DESCRIPTION | 8 ++++---- MD5 | 22 ++++++++++++---------- NAMESPACE | 3 +++ NEWS.md | 5 +++++ R/get_all_channel_video_stats.R |only R/get_all_comments.R | 23 +++++++++++++---------- R/get_channel_stats.R | 23 +++++++++++++---------- R/list_caption_tracks.R | 2 +- R/tuber.R | 2 ++ inst/doc/tuber-ex.html | 4 ++-- man/get_all_channel_video_stats.Rd |only man/get_channel_stats.Rd | 4 +++- man/list_caption_tracks.Rd | 2 +- 13 files changed, 59 insertions(+), 39 deletions(-)
Title: Multiblock Sparse Multivariable Analysis
Description: Several functions can be used to analyze multiblock multivariable data. If the input is a single matrix, then principal components analysis (PCA) is implemented. If the input is a list of matrices, then multiblock PCA is implemented. If the input is two matrices, for exploratory and objective variables, then partial least squares (PLS) analysis is implemented. If the input is two lists of matrices, for exploratory and objective variables, then multiblock PLS analysis is implemented. Additionally, if an extra outcome variable is specified, then a supervised version of the methods above is implemented. For each method, sparse modeling is also incorporated. Functions for selecting the number of components and regularized parameters are also provided.
Author: Atsushi Kawaguchi
Maintainer: Atsushi Kawaguchi <kawa_a24@yahoo.co.jp>
Diff between msma versions 0.7 dated 2016-01-01 and 1.0 dated 2018-03-01
DESCRIPTION | 10 - MD5 | 26 +-- NAMESPACE | 1 R/src.r | 399 +++++++++++++++++++++++++++++++++------------------ inst |only man/cvmsma.Rd | 35 ++-- man/msma-internal.Rd | 13 - man/msma-package.Rd | 8 - man/msma.Rd | 73 ++++----- man/ncompsearch.Rd | 43 +++-- man/optparasearch.Rd |only man/predict.msma.Rd | 13 + man/regparasearch.Rd | 40 ++--- man/simdata.Rd | 17 +- man/summary.msma.Rd | 7 15 files changed, 410 insertions(+), 275 deletions(-)
Title: Programmatic Utilities for Manipulating Formulas, Expressions,
Calls, Assignments and Other R Objects
Description: These utilities facilitate the programmatic manipulations of
formulas, expressions, calls, assignments and other R language objects.
These objects all share the same structure: a left-hand side, operator and
right-hand side. This packages provides methods for accessing and
modifying this structures as well as extracting and replacing names and
symbols from these objects.
Author: Christopher Brown [aut, cre],
Decision Patterns [cph]
Maintainer: Christopher Brown <chris.brown@decisionpatterns.com>
Diff between formula.tools versions 1.6.8 dated 2017-09-21 and 1.7.1 dated 2018-03-01
formula.tools-1.6.8/formula.tools/R/catcont.R |only formula.tools-1.6.8/formula.tools/man/catcont.Rd |only formula.tools-1.6.8/formula.tools/tests/testthat/test-catcont.r |only formula.tools-1.6.8/formula.tools/tests/testthat/test-is.cat.r |only formula.tools-1.7.1/formula.tools/DESCRIPTION | 19 +- formula.tools-1.7.1/formula.tools/MD5 | 21 +- formula.tools-1.7.1/formula.tools/NAMESPACE | 14 + formula.tools-1.7.1/formula.tools/NEWS.md | 6 formula.tools-1.7.1/formula.tools/R/split.terms.R |only formula.tools-1.7.1/formula.tools/R/terms.R | 9 - formula.tools-1.7.1/formula.tools/R/toggle.sign.R |only formula.tools-1.7.1/formula.tools/README.md | 78 ++++++++-- formula.tools-1.7.1/formula.tools/man/split_terms.Rd |only formula.tools-1.7.1/formula.tools/man/terms.Rd | 6 formula.tools-1.7.1/formula.tools/man/toggle.sign.Rd |only formula.tools-1.7.1/formula.tools/tests/testthat/test-split_terms.R |only 16 files changed, 110 insertions(+), 43 deletions(-)
Title: HTTP Error Helpers
Description: HTTP error helpers. Methods included for general purpose HTTP
error handling, as well as individual methods for every HTTP status
code, both via status code numbers as well as their descriptive names.
Supports ability to adjust behavior to stop, message or warning.
Includes ability to use custom whisker template to have any configuration
of status code, short description, and verbose message. Currently
supports integration with 'crul', 'curl', and 'httr'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fauxpas versions 0.1.0 dated 2016-11-16 and 0.2.0 dated 2018-03-01
DESCRIPTION | 22 +- LICENSE | 2 MD5 | 39 ++- NAMESPACE | 1 NEWS.md | 20 ++ R/error_http_generated.R | 382 +++++++++++++++++++++++++++++++-------- R/errors-children.R | 67 +++++- R/errors.R | 98 ++++++++-- R/find_error_class.R |only R/s3-classes.R | 41 +++- README.md | 58 +++-- build |only inst |only man/Error-Classes.Rd | 153 ++++++++------- man/Error.Rd | 52 ++++- man/fauxpas-package.Rd | 3 man/find_error_class.Rd |only man/http.Rd | 28 ++ tests/testthat/cached_teapot.rda |only tests/testthat/test-Error.R | 50 ++++- tests/testthat/test-http.R | 12 + tests/testthat/test-http_star.R |only vignettes |only 23 files changed, 789 insertions(+), 239 deletions(-)
Title: Rubik's Cube Solving
Description: Functions for visualizing, animating, solving and
analyzing the Rubik's cube. Includes data structures for
solvable and unsolvable cubes, random moves and random
state scrambles and cubes, 3D displays and animations
using 'OpenGL', patterned cube generation, and lightweight
solvers. See Rokicki, T. (2008) <arXiv:0803.3435> for the
Kociemba solver.
Author: Alec Stephenson.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between cubing versions 1.0-1 dated 2017-12-06 and 1.0-2 dated 2018-03-01
cubing-1.0-1/cubing/man/plot3d.cube.Rd |only cubing-1.0-2/cubing/DESCRIPTION | 8 +- cubing-1.0-2/cubing/MD5 | 30 +++++----- cubing-1.0-2/cubing/NAMESPACE | 7 +- cubing-1.0-2/cubing/R/display.R | 5 + cubing-1.0-2/cubing/inst/doc/cubingintro.R | 78 +++++++++++++------------- cubing-1.0-2/cubing/inst/doc/cubingintro.Rnw | 17 +++-- cubing-1.0-2/cubing/inst/doc/cubingintro.pdf |binary cubing-1.0-2/cubing/man/animate.Rd | 4 - cubing-1.0-2/cubing/man/cubieCube.Rd | 4 - cubing-1.0-2/cubing/man/invCube.Rd | 4 - cubing-1.0-2/cubing/man/plot.cube.Rd | 2 cubing-1.0-2/cubing/man/plot3D.cube.Rd |only cubing-1.0-2/cubing/man/rotate.Rd | 2 cubing-1.0-2/cubing/man/solver.Rd | 2 cubing-1.0-2/cubing/man/stickerCube.Rd | 4 - cubing-1.0-2/cubing/vignettes/cubingintro.Rnw | 17 +++-- 17 files changed, 94 insertions(+), 90 deletions(-)
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Title: Functions for Planning and Managing Inventories in a Supply
Chain
Description: Implements different inventory models, the bullwhip effect and other supply chain performance variables. Marchena Marlene (2010) <arXiv:1009.3977>.
Author: Marlene Marchena
Maintainer: Marlene Marchena <marchenamarlene@gmail.com>
Diff between SCperf versions 1.1.0 dated 2018-02-23 and 1.1.1 dated 2018-03-01
DESCRIPTION | 6 +-- MD5 | 16 +++++----- NAMESPACE | 2 + R/SCperf.R | 2 - R/SSL.R | 2 - R/WW.R | 91 +++++++++++++++++++++++++++++------------------------------ R/bullwhip.R | 2 - README.md | 12 +++++-- man/WW.Rd | 26 +++++++++------- 9 files changed, 83 insertions(+), 76 deletions(-)
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