Title: Running 'MLwiN' from Within R
Description: An R command interface to the 'MLwiN' multilevel
modelling software package.
Author: Zhengzheng Zhang [aut, cre],
Chris Charlton [aut],
Richard Parker [aut],
George Leckie [aut],
William Browne [aut]
Maintainer: Zhengzheng Zhang <zhengzheng236@gmail.com>
Diff between R2MLwiN versions 0.8-3 dated 2016-09-07 and 0.8-4 dated 2017-06-24
DESCRIPTION | 10 +- MD5 | 114 ++++++++++++++++----------------- NAMESPACE | 1 NEWS | 8 ++ R/init.R | 12 ++- R/runMLwiN.R | 85 +++++++++++++++++++++--- R/write.IGLS.R | 9 ++ R/write.MCMC.R | 8 ++ man/BD.Rd | 9 +- man/Formula.translate.Rd | 9 +- man/Formula.translate.compat.Rd | 7 -- man/MCSE.Rd | 9 +- man/R2MLwiN.Rd | 2 man/Untoggle.Rd | 1 man/caterpillar.Rd | 7 -- man/caterpillarR.Rd | 7 -- man/coef-mlwinfitIGLS-method.Rd | 1 man/coef-mlwinfitMCMC-method.Rd | 1 man/deviance-mlwinfitIGLS-method.Rd | 1 man/df.residual-mlwinfitIGLS-method.Rd | 1 man/df2matrix.Rd | 7 -- man/double2singlePrecision.Rd | 1 man/extract-methods-igls.Rd | 1 man/extract-methods-mcmc.Rd | 1 man/extract-mlwinfitIGLS-method.Rd | 1 man/extract-mlwinfitMCMC-method.Rd | 1 man/fitted-mlwinfitIGLS-method.Rd | 1 man/fitted-mlwinfitMCMC-method.Rd | 1 man/formula-mlwinfitIGLS-method.Rd | 1 man/formula-mlwinfitMCMC-method.Rd | 1 man/getSummary-mlwinfitIGLS-method.Rd | 1 man/getSummary-mlwinfitMCMC-method.Rd | 1 man/logLik-mlwinfitIGLS-method.Rd | 1 man/matrix2df.Rd | 7 -- man/mlwin2bugs.Rd | 7 -- man/mlwinfitIGLS-class.Rd | 9 +- man/mlwinfitMCMC-class.Rd | 9 +- man/nobs-mlwinfitIGLS-method.Rd | 1 man/nobs-mlwinfitMCMC-method.Rd | 1 man/predCurves.Rd | 7 -- man/predLines.Rd | 7 -- man/predict-mlwinfitIGLS-method.Rd | 1 man/predict-mlwinfitMCMC-method.Rd | 1 man/prior2macro.Rd | 7 -- man/residuals-mlwinfitIGLS-method.Rd | 3 man/residuals-mlwinfitMCMC-method.Rd | 3 man/runMLwiN.Rd | 13 ++- man/sixway.Rd | 7 -- man/summary-methods-igls.Rd | 3 man/summary-methods-mcmc.Rd | 3 man/trajectories.Rd | 7 -- man/update-mlwinfitIGLS-method.Rd | 1 man/update-mlwinfitMCMC-method.Rd | 1 man/vcov-mlwinfitIGLS-method.Rd | 1 man/vcov-mlwinfitMCMC-method.Rd | 1 man/write.IGLS.Rd | 15 ++-- man/write.MCMC.Rd | 14 ++-- man/ws2foreign.Rd | 7 -- 58 files changed, 258 insertions(+), 199 deletions(-)
Title: Make 'ggplot2' Graphics Interactive
Description: Create interactive 'ggplot2' graphics using 'htmlwidgets'.
Author: David Gohel [aut, cre],
Mike Bostock [cph] (d3.js),
Speros Kokenes [cph] (d3-lasso)
Maintainer: David Gohel <david.gohel@ardata.fr>
Diff between ggiraph versions 0.3.3 dated 2017-03-24 and 0.4.0 dated 2017-06-24
ggiraph-0.3.3/ggiraph/inst/doc/sizing.R |only ggiraph-0.3.3/ggiraph/inst/doc/sizing.Rmd |only ggiraph-0.3.3/ggiraph/inst/doc/sizing.html |only ggiraph-0.3.3/ggiraph/inst/htmlwidgets/lib/styles-0.0.1 |only ggiraph-0.3.3/ggiraph/vignettes/sizing.Rmd |only ggiraph-0.4.0/ggiraph/DESCRIPTION | 17 ggiraph-0.4.0/ggiraph/MD5 | 65 +- ggiraph-0.4.0/ggiraph/NAMESPACE | 1 ggiraph-0.4.0/ggiraph/NEWS | 12 ggiraph-0.4.0/ggiraph/R/ggiraph.R | 131 +++-- ggiraph-0.4.0/ggiraph/R/utils.R | 40 + ggiraph-0.4.0/ggiraph/README.md | 5 ggiraph-0.4.0/ggiraph/build/vignette.rds |binary ggiraph-0.4.0/ggiraph/inst/COPYRIGHTS | 34 + ggiraph-0.4.0/ggiraph/inst/doc/an_introduction.R | 18 ggiraph-0.4.0/ggiraph/inst/doc/an_introduction.Rmd | 20 ggiraph-0.4.0/ggiraph/inst/doc/an_introduction.html | 60 +- ggiraph-0.4.0/ggiraph/inst/doc/custom_animation_effects.R | 4 ggiraph-0.4.0/ggiraph/inst/doc/custom_animation_effects.Rmd | 6 ggiraph-0.4.0/ggiraph/inst/doc/custom_animation_effects.html | 57 +- ggiraph-0.4.0/ggiraph/inst/doc/shiny_usage.html | 20 ggiraph-0.4.0/ggiraph/inst/htmlwidgets/ggiraph.js | 255 ++++++++-- ggiraph-0.4.0/ggiraph/inst/htmlwidgets/ggiraph.yaml | 11 ggiraph-0.4.0/ggiraph/inst/htmlwidgets/lib/d3-lasso-0.0.5 |only ggiraph-0.4.0/ggiraph/inst/htmlwidgets/lib/ggiraph-0.2.0 |only ggiraph-0.4.0/ggiraph/inst/rmd/flexdashboard/flexdashboard.Rmd | 46 - ggiraph-0.4.0/ggiraph/inst/shiny/DT/server.R | 20 ggiraph-0.4.0/ggiraph/inst/shiny/DT/ui.R | 2 ggiraph-0.4.0/ggiraph/inst/shiny/crimes/server.R | 2 ggiraph-0.4.0/ggiraph/inst/shiny/crimes/ui.R | 6 ggiraph-0.4.0/ggiraph/inst/shiny/maps |only ggiraph-0.4.0/ggiraph/man/geom_boxplot_interactive.Rd | 4 ggiraph-0.4.0/ggiraph/man/geom_map_interactive.Rd | 2 ggiraph-0.4.0/ggiraph/man/ggiraph.Rd | 28 - ggiraph-0.4.0/ggiraph/vignettes/an_introduction.Rmd | 20 ggiraph-0.4.0/ggiraph/vignettes/custom_animation_effects.Rmd | 6 36 files changed, 611 insertions(+), 281 deletions(-)
Title: Add Marginal Histograms to 'ggplot2', and More 'ggplot2'
Enhancements
Description: Collection of functions and layers to enhance 'ggplot2'. The main
function is ggMarginal(), which can be used to add marginal
histograms/boxplots/density plots to 'ggplot2' scatterplots.
Author: Dean Attali [aut, cre],
Christopher Baker [ctb]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ggExtra versions 0.6 dated 2016-11-11 and 0.7 dated 2017-06-24
DESCRIPTION | 21 +- MD5 | 87 +++++++++--- NEWS.md | 17 ++ R/ggMarginal.R | 226 ++++++++++--------------------- R/ggMarginalHelpers.R | 339 +++++++++++++++++++++++++++++------------------ R/rotateTextX.R | 9 - README.md | 25 +-- build/vignette.rds |binary inst/doc/ggExtra.Rmd | 3 inst/doc/ggExtra.html | 46 +++--- inst/vignette_files |only man/ggExtra.Rd | 1 man/ggMarginal.Rd | 4 man/ggMarginalGadget.Rd | 1 man/plotCount.Rd | 1 man/print.ggExtraPlot.Rd | 6 man/removeGrid.Rd | 2 man/rotateTextX.Rd | 10 + man/runExample.Rd | 1 tests |only vignettes/ggExtra.Rmd | 3 21 files changed, 447 insertions(+), 355 deletions(-)
Title: Adaptive Sum of Powered Score Test
Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU')
tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests
and gene-based and some pathway based association tests (Pathway based Sum of
Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU'
test for multiple traits - single 'SNP' (single nucleotide polymorphism)
association in generalized estimation equations, 'MTaSPUs' test for multiple
traits - single 'SNP' association with Genome Wide Association Studies ('GWAS')
summary statistics, Gene-based Association Test that uses an extended 'Simes'
procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version
of 'GATES' test for pathway-based association testing ('GATES-Simes'). ).
The tests can be used with genetic and other data sets with covariates. The
response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set
association with individual-level data ('aSPU', 'aSPUw', 'aSPUr'), (2) Single trait-'SNP'
set association with summary statistics ('aSPUs'), (3) Single trait-pathway
association with individual-level data ('aSPUpath'), (4) Single trait-pathway
association with summary statistics ('aSPUsPath'), (5) Multiple traits-single
'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-
single 'SNP' association with summary statistics ('MTaSPUs'), (7) Multiple traits-'SNP' set association with summary statistics('MTaSPUsSet'), (8) Multiple traits-pathway association with summary statistics('MTaSPUsSetPath').
Author: Il-Youp Kwak and others (See Author(s) in each function manual)
Maintainer: Il-Youp Kwak <ikwak@umn.edu>
Diff between aSPU versions 1.47 dated 2017-05-21 and 1.48 dated 2017-06-24
DESCRIPTION | 8 +++--- MD5 | 40 +++++++++++++++++----------------- R/MTaSPUsSet.R | 4 +-- R/MTaSPUsSetPath.R | 4 +-- R/MTaSPUsSetScore.R | 4 +-- R/aSPUd.R | 55 +++++++++++++++++++++++------------------------ R/aSPUr.R | 2 - R/aSPUsD.R | 7 +++-- R/aSPUsPath.r | 2 - R/plotPmat.r | 3 +- README.md | 20 ++++++++++++----- inst/doc/MTaSPUsSet.html | 32 +++++++++++++-------------- inst/doc/aSPUstat.html | 32 +++++++++++++-------------- man/MTaSPUsSet.Rd | 4 +-- man/MTaSPUsSetPath.Rd | 4 +-- man/MTaSPUsSetScore.Rd | 4 +-- man/aSPUd.Rd | 36 +++++++++++------------------- man/aSPUr.Rd | 2 - man/aSPUsD.Rd | 7 +++-- man/aSPUsPath.Rd | 2 - man/plotPmat.Rd | 3 +- 21 files changed, 141 insertions(+), 134 deletions(-)
Title: Portable System Utilities
Description: Powerful replacements for base system2 with consistent behavior
across platforms. Supports interruption, background tasks, and full control over
'STDOUT' / 'STDERR' binary or text streams. On Unix systems the package also has
functions for evaluating expressions inside a temporary fork. Such evaluations
have no side effects on the main R process, and support reliable interrupts and
timeouts. This provides the basis for a 'sandboxing' mechanism.
Author: Jeroen Ooms [aut, cre],
Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between sys versions 1.3 dated 2017-04-20 and 1.4 dated 2017-06-24
sys-1.3/sys/man/sys_config.Rd |only sys-1.4/sys/DESCRIPTION | 10 +++++----- sys-1.4/sys/MD5 | 20 ++++++++++---------- sys-1.4/sys/NAMESPACE | 6 ++++-- sys-1.4/sys/NEWS | 8 ++++++++ sys-1.4/sys/R/fork.R | 7 ++++--- sys-1.4/sys/R/util.R | 26 ++++++++++++++++++++++++++ sys-1.4/sys/man/config.Rd |only sys-1.4/sys/src/Makevars.win | 2 +- sys-1.4/sys/src/exec.c | 19 ++++++++++++++----- sys-1.4/sys/src/fork.c | 10 ++++++++-- sys-1.4/sys/src/util.c | 31 ++++++++++++++++++++++++++++++- 12 files changed, 110 insertions(+), 29 deletions(-)
Title: 'ODBC' Connection Class for Package stacomiR
Description: S4 class wrappers for the 'ODBC' connection, also provides some
utilities to paste small datasets to clipboard, rename columns. It is used by the package 'stacomiR' for
connections to the database. Development versions of 'stacomiR' are available in R-forge.
Author: Cedric Briand [aut, cre]
Maintainer: Cedric Briand <cedric.briand00@gmail.com>
Diff between stacomirtools versions 0.5.0 dated 2016-08-20 and 0.5.2 dated 2017-06-24
stacomirtools-0.5.0/stacomirtools/R/utilitaires.r |only stacomirtools-0.5.2/stacomirtools/DESCRIPTION | 20 - stacomirtools-0.5.2/stacomirtools/MD5 | 32 +- stacomirtools-0.5.2/stacomirtools/R/ConnectionODBC.r | 39 +- stacomirtools-0.5.2/stacomirtools/R/RequeteODBC.r | 138 +++++----- stacomirtools-0.5.2/stacomirtools/R/RequeteODBCwheredate.r | 8 stacomirtools-0.5.2/stacomirtools/R/utilities.r |only stacomirtools-0.5.2/stacomirtools/man/ConnectionODBC-class.Rd | 4 stacomirtools-0.5.2/stacomirtools/man/RequeteODBC-class.Rd | 4 stacomirtools-0.5.2/stacomirtools/man/chnames.Rd | 12 stacomirtools-0.5.2/stacomirtools/man/connect-methods.Rd | 17 - stacomirtools-0.5.2/stacomirtools/man/funout.Rd | 6 stacomirtools-0.5.2/stacomirtools/man/induk.Rd | 4 stacomirtools-0.5.2/stacomirtools/man/is.even.Rd | 4 stacomirtools-0.5.2/stacomirtools/man/is.odd.Rd | 5 stacomirtools-0.5.2/stacomirtools/man/killfactor.Rd | 12 stacomirtools-0.5.2/stacomirtools/man/stacomirtools-package.Rd | 6 stacomirtools-0.5.2/stacomirtools/man/tab2df.Rd | 6 18 files changed, 186 insertions(+), 131 deletions(-)
Title: Spatial Methods and Indices
Description: Functions for spatial methods based on generalized estimating equations (GEE) and
wavelet-revised methods (WRM), functions for scaling by wavelet multiresolution regression (WMRR),
conducting multi-model inference, and stepwise model selection. Further, contains functions
for spatially corrected model accuracy measures.
Author: Gudrun Carl [cre, aut], Ingolf Kuehn [aut], Sam Levin [aut]
Maintainer: Sam Levin <levisc8@gmail.com>
Diff between spind versions 2.0.1 dated 2017-04-07 and 2.1.0 dated 2017-06-24
DESCRIPTION | 10 MD5 | 75 +++-- NAMESPACE | 1 R/AIC_Calc.R | 58 ++-- R/GEE.R | 324 +++++++++++++----------- R/Predict_WRM.R | 14 - R/WRM.R | 561 +++++++++++++++++++++++-------------------- R/acfft.R | 12 R/adjusted.actuals.R | 110 ++++---- R/mmiWMRR.R | 124 ++++----- R/plot_covar.R | 147 +++++++---- R/rvi_plot.R | 134 ++++++---- R/scale_WMRR.R | 24 - R/step_spind.R | 353 ++++++++++++--------------- R/th_dep.R | 147 ++++++----- R/th_indep.R | 199 ++++++++------- R/upscale.R | 116 +++++--- R/wavecovar.R | 82 +++--- R/wavevar.R | 59 ++-- build/vignette.rds |binary inst/doc/spind_vignette.R | 135 ++++------ inst/doc/spind_vignette.Rmd | 169 ++++++------ inst/doc/spind_vignette.html | 343 ++++++++++---------------- man/WRM.Rd | 5 man/acfft.Rd | 11 man/adjusted.actuals.Rd | 5 man/aic.calc.Rd | 6 man/mmiWMRR.Rd | 14 - man/rvi.plot.Rd | 4 man/scaleWMRR.Rd | 14 - man/th.dep.Rd | 12 man/th.indep.Rd | 14 - man/upscale.Rd | 17 - man/wavecovar.Rd | 17 - man/wavevar.Rd | 13 tests |only vignettes/spind_vignette.Rmd | 169 ++++++------ 37 files changed, 1823 insertions(+), 1675 deletions(-)
Title: PRIM Survival Regression Classification
Description: Performs a unified treatment of Bump Hunting by Patient Rule Induction Method (PRIM) in Survival, Regression and Classification settings (SRC). The current version is a development release that only implements the case of a survival response. New features will be added soon as they are available.
Author: Jean-Eudes Dazard [aut, cre], Michael Choe [ctb], Michael LeBlanc [ctb], Alberto Santana [ctb]
Maintainer: Jean-Eudes Dazard <jean-eudes.dazard@case.edu>
Diff between PRIMsrc versions 0.7.0 dated 2017-05-29 and 0.7.1 dated 2017-06-24
PRIMsrc-0.7.0/PRIMsrc/inst/doc/PRIMsrc_0.7.0.pdf |only PRIMsrc-0.7.1/PRIMsrc/DESCRIPTION | 8 PRIMsrc-0.7.1/PRIMsrc/MD5 | 50 - PRIMsrc-0.7.1/PRIMsrc/R/PRIMsrc.internal.r | 792 +++++++++++++---------- PRIMsrc-0.7.1/PRIMsrc/R/PRIMsrc.r | 59 + PRIMsrc-0.7.1/PRIMsrc/README.md | 29 PRIMsrc-0.7.1/PRIMsrc/inst/CITATION | 31 PRIMsrc-0.7.1/PRIMsrc/inst/NEWS | 20 PRIMsrc-0.7.1/PRIMsrc/inst/doc/PRIMsrc_0.7.1.pdf |only PRIMsrc-0.7.1/PRIMsrc/man/PRIMsrc-package.Rd | 36 - PRIMsrc-0.7.1/PRIMsrc/man/PRIMsrc.news.Rd | 5 PRIMsrc-0.7.1/PRIMsrc/man/Real.1-data.Rd | 17 PRIMsrc-0.7.1/PRIMsrc/man/Real.2-data.Rd | 17 PRIMsrc-0.7.1/PRIMsrc/man/Synthetic.1-data.Rd | 7 PRIMsrc-0.7.1/PRIMsrc/man/Synthetic.1b-data.Rd | 7 PRIMsrc-0.7.1/PRIMsrc/man/Synthetic.2-data.Rd | 7 PRIMsrc-0.7.1/PRIMsrc/man/Synthetic.3-data.Rd | 7 PRIMsrc-0.7.1/PRIMsrc/man/Synthetic.4-data.Rd | 7 PRIMsrc-0.7.1/PRIMsrc/man/plot.sbh.Rd | 5 PRIMsrc-0.7.1/PRIMsrc/man/plot_boxkm.Rd | 11 PRIMsrc-0.7.1/PRIMsrc/man/plot_boxtrace.Rd | 5 PRIMsrc-0.7.1/PRIMsrc/man/plot_boxtraj.Rd | 5 PRIMsrc-0.7.1/PRIMsrc/man/plot_profile.Rd | 5 PRIMsrc-0.7.1/PRIMsrc/man/predict.sbh.Rd | 5 PRIMsrc-0.7.1/PRIMsrc/man/print.sbh.Rd | 5 PRIMsrc-0.7.1/PRIMsrc/man/sbh.Rd | 54 - PRIMsrc-0.7.1/PRIMsrc/man/summary.sbh.Rd | 5 27 files changed, 769 insertions(+), 430 deletions(-)
Title: Measures, Tests and Removes Multivariate Skewness
Description: Computes the third multivariate cumulant of either the raw, centered or standardized data. Computes the main measures of multivariate skewness, together with their bootstrap distributions. Finally, computes the least skewed linear projections of the data.
Author: Cinzia Franceschini, Nicola Loperfido
Maintainer: Cinzia Franceschini <cinziafranceschini@msn.com>
Diff between MultiSkew versions 1.1 dated 2017-06-14 and 1.1.1 dated 2017-06-24
DESCRIPTION | 7 ++++--- MD5 | 16 ++++++++-------- NAMESPACE | 3 ++- R/FisherSkew.R | 4 ++-- R/SkewBoot.R | 22 ++++++++++++++-------- R/Third.R | 7 ++++--- man/MultiSkew-package.Rd | 25 +++++++++++++------------ man/PartialSkew.Rd | 6 +++--- man/SkewBoot.Rd | 11 +++++++---- 9 files changed, 57 insertions(+), 44 deletions(-)
Title: Multivariate Independent Comparison of Observations
Description: A procedure for comparing multivariate samples associated with
different groups. It uses principal component analysis to convert
multivariate observations into a set of linearly uncorrelated statistical
measures, which are then compared using a number of statistical methods. The
procedure is independent of the distributional properties of samples and
automatically selects features that best explain their differences, avoiding
manual selection of specific points or summary statistics. It is appropriate
for comparing samples of time series, images, spectrometric measures or
similar multivariate observations.
Author: Nuno Fachada [aut, cre]
Maintainer: Nuno Fachada <faken@fakenmc.com>
Diff between micompr versions 1.0.1 dated 2016-08-04 and 1.0.2 dated 2017-06-24
DESCRIPTION | 14 + MD5 | 104 +++++++------- R/latex_tables.R | 18 +- README.md | 17 +- build/vignette.rds |binary inst/CITATION | 16 +- inst/doc/paper.Rnw | 258 +++++++++++++++++++++++------------ inst/doc/paper.pdf |binary inst/doc/tolatex-examples.pdf |binary man/assumptions.Rd | 1 man/assumptions.cmpoutput.Rd | 1 man/assumptions.micomp.Rd | 1 man/assumptions_manova.Rd | 1 man/assumptions_paruv.Rd | 1 man/centerscale.Rd | 1 man/cmpoutput.Rd | 1 man/concat_outputs.Rd | 1 man/grpoutputs.Rd | 1 man/micomp.Rd | 1 man/micompr.Rd | 7 man/plot.assumptions_cmpoutput.Rd | 1 man/plot.assumptions_manova.Rd | 1 man/plot.assumptions_micomp.Rd | 1 man/plot.assumptions_paruv.Rd | 1 man/plot.cmpoutput.Rd | 1 man/plot.grpoutputs.Rd | 1 man/plot.micomp.Rd | 1 man/plotcols.Rd | 1 man/pphpc_diff.Rd | 1 man/pphpc_noshuff.Rd | 1 man/pphpc_ok.Rd | 1 man/pphpc_testvlo.Rd | 1 man/print.assumptions_cmpoutput.Rd | 1 man/print.assumptions_manova.Rd | 1 man/print.assumptions_micomp.Rd | 1 man/print.assumptions_paruv.Rd | 1 man/print.cmpoutput.Rd | 1 man/print.grpoutputs.Rd | 1 man/print.micomp.Rd | 1 man/pst.Rd | 1 man/pvalcol.Rd | 1 man/pvalf.Rd | 1 man/pvalf.default.Rd | 1 man/summary.assumptions_cmpoutput.Rd | 1 man/summary.assumptions_micomp.Rd | 1 man/summary.cmpoutput.Rd | 1 man/summary.grpoutputs.Rd | 1 man/summary.micomp.Rd | 1 man/tikzscat.Rd | 7 man/toLatex.cmpoutput.Rd | 1 man/toLatex.micomp.Rd | 5 man/tscat_apply.Rd | 5 vignettes/paper.Rnw | 258 +++++++++++++++++++++++------------ 53 files changed, 452 insertions(+), 296 deletions(-)
Title: Goodness of Fit Tests for Logistic Regression Models
Description: Functions to assess the goodness of fit of binary, multinomial and ordinal logistic models.
Included are the Hosmer-Lemeshow tests (binary, multinomial and ordinal) and the Lipsitz and
Pulkstenis-Robinson tests (ordinal).
Author: Matthew Jay [aut, cre]
Maintainer: Matthew Jay <matthew.jay.15@ucl.ac.uk>
Diff between generalhoslem versions 1.2.4 dated 2016-12-16 and 1.2.5 dated 2017-06-24
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/lipsitz.test.R | 2 +- R/logitgof.R | 2 ++ R/pulkrob.chisq.R | 2 +- build/partial.rdb |binary man/lipsitz.test.Rd | 6 +++--- man/logitgof.Rd | 4 +++- man/pulkrob.chisq.Rd | 4 ++-- 9 files changed, 24 insertions(+), 20 deletions(-)
Title: R Interface to the 'PostgreSQL' Database System
Description: Database interface and 'PostgreSQL' driver for 'R'.
This package provides a Database Interface 'DBI' compliant
driver for 'R' to access 'PostgreSQL' database systems.
In order to build and install this package from source, 'PostgreSQL'
itself must be present your system to provide 'PostgreSQL' functionality
via its libraries and header files. These files are provided as
'postgresql-devel' package under some Linux distributions.
On 'macOS' and 'Microsoft Windows' system the attached 'libpq' library source will be used.
Author: Joe Conway, Dirk Eddelbuettel, Tomoaki Nishiyama, Sameer Kumar Prayaga (during 2008), Neil Tiffin
Maintainer: Tomoaki Nishiyama <tomoakin@staff.kanazawa-u.ac.jp>
Diff between RPostgreSQL versions 0.4-1 dated 2016-05-08 and 0.6-2 dated 2017-06-24
RPostgreSQL-0.4-1/RPostgreSQL/config.guess |only RPostgreSQL-0.4-1/RPostgreSQL/config.sub |only RPostgreSQL-0.4-1/RPostgreSQL/inst/doc |only RPostgreSQL-0.4-1/RPostgreSQL/install-sh |only RPostgreSQL-0.4-1/RPostgreSQL/src/libpq/Makefile.port |only RPostgreSQL-0.4-1/RPostgreSQL/src/libpq/Makefile.shlib |only RPostgreSQL-0.6-2/RPostgreSQL/ChangeLog | 97 RPostgreSQL-0.6-2/RPostgreSQL/DESCRIPTION | 43 RPostgreSQL-0.6-2/RPostgreSQL/MD5 | 323 - RPostgreSQL-0.6-2/RPostgreSQL/NAMESPACE | 6 RPostgreSQL-0.6-2/RPostgreSQL/R/PostgreSQL.R | 34 RPostgreSQL-0.6-2/RPostgreSQL/R/PostgreSQLSupport.R | 95 RPostgreSQL-0.6-2/RPostgreSQL/R/S4R.R | 2 RPostgreSQL-0.6-2/RPostgreSQL/R/dbObjectId.R | 4 RPostgreSQL-0.6-2/RPostgreSQL/R/zzz.R | 2 RPostgreSQL-0.6-2/RPostgreSQL/configure | 1892 ++++------ RPostgreSQL-0.6-2/RPostgreSQL/configure.in | 29 RPostgreSQL-0.6-2/RPostgreSQL/inst/ANNOUNCEMENT | 12 RPostgreSQL-0.6-2/RPostgreSQL/inst/NEWS | 31 RPostgreSQL-0.6-2/RPostgreSQL/inst/TODO | 1 RPostgreSQL-0.6-2/RPostgreSQL/man/PostgreSQL.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/PostgreSQLConnection-class.Rd | 1 RPostgreSQL-0.6-2/RPostgreSQL/man/dbApply-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/dbCallProc-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/dbCommit-methods.Rd | 15 RPostgreSQL-0.6-2/RPostgreSQL/man/dbConnect-methods.Rd | 10 RPostgreSQL-0.6-2/RPostgreSQL/man/dbDataType-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/dbDriver-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/dbGetInfo-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/dbListTables-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/dbReadTable-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/dbSendQuery-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/dbSetDataMappings-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/fetch-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/make.db.names-methods.Rd | 2 RPostgreSQL-0.6-2/RPostgreSQL/man/postgresqlBuildTableDefinition.Rd | 5 RPostgreSQL-0.6-2/RPostgreSQL/man/postgresqlSupport.Rd | 19 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-DBI.c | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-DBI.h | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-PQescape.c | 83 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-PostgreSQL.c | 176 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-PostgreSQL.h | 19 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-pgsql-copy.c | 40 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-pgsql-getResult.c | 15 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-pgsql-pqexec.c | 16 RPostgreSQL-0.6-2/RPostgreSQL/src/RS-pgsql-pqexecparams.c | 16 RPostgreSQL-0.6-2/RPostgreSQL/src/S4R.h | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/config.guess |only RPostgreSQL-0.6-2/RPostgreSQL/src/config.sub |only RPostgreSQL-0.6-2/RPostgreSQL/src/install-sh |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/Makefile.darwin | 68 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/Makefile.global.darwin | 286 + RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/Makefile.global.win32 | 292 + RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/Makefile.global.win64 | 344 + RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/Makefile.shlib.darwin |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/Makefile.win | 46 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/Makefile.win32 |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/auth.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/bcc32.mak | 23 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/be-fsstubs.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/blibpqdll.def | 24 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/c.h | 402 +- RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/chklocale.c | 119 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/common |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/crypt.c | 28 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/crypt.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/encnames.c | 70 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/exports.txt | 11 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-auth.c | 369 - RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-auth.h | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-connect.c | 1804 +++++++-- RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-exec.c | 419 +- RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-lobj.c | 355 + RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-misc.c | 160 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-print.c | 34 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-protocol2.c | 298 + RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-protocol3.c | 655 ++- RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-secure-openssl.c |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/fe-secure.c | 1349 ------- RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/getaddrinfo.c | 27 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/getaddrinfo.h | 5 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/hba.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/ip.c | 102 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/ip.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq-be.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq-dist.rc | 10 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq-events.c | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq-events.h | 4 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq-fe.h | 73 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq-fs.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq-int.h | 105 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq.pc |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq.rc | 10 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq.rc.in | 10 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/auth.h | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/be-fsstubs.h | 5 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/crypt.h | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/hba.h | 25 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/ip.h | 11 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/libpq-be.h | 9 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/libpq-fs.h | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/libpq.h | 13 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/md5.h | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/pqcomm.h | 21 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/pqformat.h | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpq/pqsignal.h | 13 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpqddll.def | 15 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/libpqdll.def | 15 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/mb/pg_wchar.h | 251 - RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/md5.c | 12 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/md5.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/nls.mk | 9 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/noblock.c | 26 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/open.c | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pg_config.h.darwin | 299 - RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pg_config.h.win | 311 - RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pg_config_ext.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pg_config_ext.h.win32 |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pg_config_manual.h | 144 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pg_config_os.h.win | 95 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pg_config_paths.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pgsleep.c | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pgstrcasecmp.c | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/po |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/port.h | 188 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/postgres_ext.h | 15 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/postgres_fe.h | 4 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pqcomm.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pqexpbuffer.c | 173 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pqexpbuffer.h | 28 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pqformat.h |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pqsignal.c | 69 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pqsignal.h | 37 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/pthread-win32.c | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/snprintf.c | 196 - RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/strlcpy.c | 2 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/system.c |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/thread.c | 33 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/utils |only RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/wchar.c | 592 ++- RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/win32.c | 17 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/win32.h | 6 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/win32.mak | 38 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/win32error.c | 12 RPostgreSQL-0.6-2/RPostgreSQL/src/libpq/win32setlocale.c | 178 RPostgreSQL-0.6-2/RPostgreSQL/tests/connectWithNull.Rout.save | 13 RPostgreSQL-0.6-2/RPostgreSQL/tests/createTableMixedCaseTest.Rout.save | 18 RPostgreSQL-0.6-2/RPostgreSQL/tests/dataTypeTests.Rout.save | 20 RPostgreSQL-0.6-2/RPostgreSQL/tests/dateTZ.Rout.save | 85 RPostgreSQL-0.6-2/RPostgreSQL/tests/datetimeTests.R | 3 RPostgreSQL-0.6-2/RPostgreSQL/tests/datetimeTests.Rout.save | 37 RPostgreSQL-0.6-2/RPostgreSQL/tests/datetimestampwrite.Rout.save | 18 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbColumnInfo.R | 1 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbColumnInfo.Rout.save | 29 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbExistsIssue.Rout.save | 15 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbExistsq.Rout.save | 15 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbExistsqc.Rout.save | 24 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbGetQueryParams.Rout.save | 30 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbListFields.Rout.save | 17 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbTransactionTests.Rout.save | 25 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbWriteTableFailTest.Rout.save | 25 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbWriteTableSchema.Rout.save | 24 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbWriteTableTest.Rout.save | 23 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbWriteTabletypes.Rout.save | 41 RPostgreSQL-0.6-2/RPostgreSQL/tests/dbtemptable.Rout.save | 13 RPostgreSQL-0.6-2/RPostgreSQL/tests/escape.Rout.save | 13 RPostgreSQL-0.6-2/RPostgreSQL/tests/loadDriverAndConnect.Rout.save | 15 RPostgreSQL-0.6-2/RPostgreSQL/tests/openSendQuery.Rout.save | 17 RPostgreSQL-0.6-2/RPostgreSQL/tests/selectWhereZero.Rout.save | 22 RPostgreSQL-0.6-2/RPostgreSQL/tests/selectWithAlias.Rout.save | 24 RPostgreSQL-0.6-2/RPostgreSQL/tests/unknowntype.Rout.save | 20 172 files changed, 8527 insertions(+), 5462 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [cre, ctb],
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.10 dated 2016-10-11 and 0.10.1 dated 2017-06-24
DESCRIPTION | 10 +++++----- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 3 +++ NEWS | 6 ++++++ R/parse.r | 10 ++++++++++ man/create_traceback.Rd | 1 + man/evaluate.Rd | 1 + man/flush_console.Rd | 1 + man/inject_funs.Rd | 1 + man/is.message.Rd | 12 +++++++++--- man/line_prompt.Rd | 1 + man/new_output_handler.Rd | 1 + man/parse_all.Rd | 1 + man/replay.Rd | 1 + man/set_hooks.Rd | 1 + man/try_capture_stack.Rd | 1 + man/watchout.Rd | 1 + 17 files changed, 60 insertions(+), 24 deletions(-)
Title: Analysis and Visualization of Droplet Digital PCR in R and on
the Web
Description: An interface to explore, analyze, and visualize droplet digital PCR
(ddPCR) data in R. This is the first non-proprietary software for analyzing
two-channel ddPCR data. An interactive tool was also created and is available
online to facilitate this analysis for anyone who is not comfortable with
using R.
Author: Dean Attali [aut, cre]
Maintainer: Dean Attali <daattali@gmail.com>
Diff between ddpcr versions 1.6 dated 2016-11-11 and 1.8 dated 2017-06-24
DESCRIPTION | 6 MD5 | 84 +++++++----- NEWS.md | 10 + R/aaa.R | 3 R/empty.R | 87 ++++++------- R/plate-utils.R | 30 +++- R/pnpp_experiment-classify.R | 142 ++++++++++----------- R/pnpp_experiment-plot.R | 65 +++++---- R/read.R | 32 ++++ R/subset.R | 30 ++++ README.md | 195 +++++++++++++++-------------- build/vignette.rds |binary inst/doc/algorithm.html | 8 - inst/doc/extend.html | 105 ++++++++------- inst/doc/overview.Rmd | 3 inst/doc/overview.html | 227 ++++++++++++++++++---------------- inst/doc/technical_details.html | 8 - inst/sample_data/read_simple/test.csv | 8 - inst/sample_data/read_v174 |only inst/shiny/server.R | 1 inst/shiny/server/tab-dataset.R | 11 - inst/shiny/ui.R | 4 inst/shiny/ui/tab-about.R | 5 inst/shiny/ui/tab-analyze.R | 1 inst/shiny/ui/tab-dataset.R | 10 - inst/shiny/ui/tab-results.R | 1 inst/shiny/ui/tab-settings.R | 1 inst/shiny/www/style.css | 92 ++++++++++--- inst/vignette_files |only inst/vignettes-supp/algorithms-imgs.R | 20 +- inst/vignettes-supp/empty.png |binary inst/vignettes-supp/gating.png |binary man/classify_droplets.Rd | 2 man/remove_empty.Rd | 2 man/subset.ddpcr_plate.Rd | 6 tests/testthat/test-read.R | 8 + tests/testthat/test-subset.R | 14 +- tests/testthat/test-v174.R |only vignettes/overview.Rmd | 3 39 files changed, 718 insertions(+), 506 deletions(-)