Title: Nearest Neighbor Observation Imputation and Evaluation Tools
Description: Performs nearest neighbor-based imputation using one or more alternative
approaches to processing multivariate data. These include methods based on canonical
correlation analysis, canonical correspondence analysis, and a multivariate adaptation
of the random forest classification and regression techniques of Leo Breiman and Adele
Cutler. Additional methods are also offered. The package includes functions for
comparing the results from running alternative techniques, detecting imputation targets
that are notably distant from reference observations, detecting and correcting
for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston <ncrookston.fs@gmail.com>
Diff between yaImpute versions 1.0-23 dated 2014-12-01 and 1.0-24 dated 2015-05-16
DESCRIPTION | 16 ++++++------ MD5 | 40 +++++++++++++++---------------- NEWS | 24 +++++++++++++++++- R/asciigridimpute.R | 35 +++++++++++++++++++++------ R/ensembleImpute.R | 3 +- R/errorstats.R | 2 - R/impute.R | 45 +++++++++++++++++++++-------------- R/newtargets.R | 12 +++++---- R/print.yai.R | 5 ++- R/varSelection.R | 14 +++++----- R/yai.R | 46 +++++++++++++++++++++-------------- R/yaiRFsummary.R | 2 - R/yaiVarImp.R | 5 ++- data/MoscowMtStJoe.RData |binary data/TallyLake.RData |binary man/asciigridimpute.Rd | 30 ++++++++++++----------- man/errorStats.Rd | 4 +-- man/newtargets.Rd | 13 ++++++---- man/plot.notablydifferent.Rd | 7 +++-- man/yai.Rd | 55 +++++++++++++++++++++---------------------- man/yaiVarImp.Rd | 44 ++++++++++++++++++---------------- 21 files changed, 241 insertions(+), 161 deletions(-)
Title: Efficiently Read Sequence Data (VCF Format, BCF Format and METAL
Format) into R
Description: Integrate sequencing data (VCF/BCF) or meta-analysis results in R.
Author: Xiaowei Zhan <zhanxw@gmail.com> and Dajiang Liu
<dajiang.liu@gmail.com>, with contributions of Heng Li
<lh3@live.co.uk> (this author wrote tabix and with MIT license
we include tabix source codes).
Maintainer: Xiaowei Zhan <zhanxw@gmail.com>
Diff between seqminer versions 3.4 dated 2014-12-08 and 3.7 dated 2015-05-16
ChangeLog | 16 DESCRIPTION | 18 - MD5 | 38 +- R/seqminer.R | 75 ++-- README.md |only configure | 199 +++++------ configure.ac | 4 configure.win | 1 src/IO.cpp | 172 +++++---- src/IO.h | 456 ++++++++++++++------------ src/Makevars.in | 3 src/Makevars.win | 7 src/Profiler.cpp |only src/Profiler.h |only src/RangeList.cpp | 2 src/RangeList.h | 1 src/SimpleTimer.h |only src/TabixReader.h | 60 +-- src/VCFInputFile.cpp | 6 src/bgzf.c | 890 +++++++++++++++++++++++++-------------------------- src/knetfile.c |only src/knetfile.h |only src/rvMetaLoader.cpp | 762 ++++++++++++++++++++++--------------------- 23 files changed, 1428 insertions(+), 1282 deletions(-)
Title: Various Plotting Functions
Description: Lots of plots, various labeling, axis and color scaling functions.
Author: Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle
Maintainer: Jim Lemon <drjimlemon@gmail.com>
Diff between plotrix versions 3.5-11 dated 2015-01-20 and 3.5-12 dated 2015-05-16
DESCRIPTION | 10 +++++----- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 1 + NEWS | 6 ++++++ R/color.scale.R | 3 ++- R/color2D.matplot.R | 1 + R/dispersion.R | 19 ++++++++++++------- R/gantt.R | 24 +++++++++++++++--------- R/gap.barplot.R | 8 ++++---- R/makeIntersectList.R | 1 + R/taylor.diagram.R | 2 +- data/soils.rda |binary man/box.heresy.Rd | 1 - man/dispersion.Rd | 8 +++++--- man/gantt.chart.Rd | 4 +++- man/gap.barplot.Rd | 4 +++- man/ladderplot.Rd | 4 +--- man/plotrix-package.Rd | 18 +++++++++--------- man/raw.means.plot.Rd | 3 --- man/soil.texture.Rd | 10 +++------- 20 files changed, 91 insertions(+), 74 deletions(-)
Title: Panel Data Regression: Threshold Model and Unit Root Tests
Description: Threshold model, panel version of Hylleberg et al. (1990) seasonal unit root tests, and panel unit root test of Chang (2002).
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@cc.shu.edu.tw>
Diff between pdR versions 1.2 dated 2014-12-03 and 1.3 dated 2015-05-16
DESCRIPTION | 12 ++++++------ MD5 | 29 ++++++++++++++++++++++------- R/hegy.R |only data/inf_M.rda |only data/inf_Q.rda |only man/HEGY.test.Rd |only man/IGF.Rd | 21 +++++++++++++-------- man/SeasComponent.Rd |only man/contts.Rd |only man/hegy.reg.Rd |only man/inf_M.Rd |only man/inf_Q.Rd |only man/interpolpval.Rd |only man/ipsHEGY.Rd |only man/lagSelect.Rd | 2 +- man/lookupCVtable.Rd |only man/pIGF.Rd | 14 ++++++++------ man/pdR-package.Rd | 30 +++++++++++++++--------------- man/ptm.Rd | 2 +- man/ret.Rd |only man/selPabic.Rd |only man/selPsignf.Rd |only man/tbar.Rd | 2 +- 23 files changed, 67 insertions(+), 45 deletions(-)
Title: Reliable Comparison of Floating Point Numbers
Description: Comparisons of floating point numbers are problematic due to errors
associated with the binary representation of decimal numbers.
Despite being aware of these problems, people still use numerical methods
that fail to account for these and other rounding errors (this pitfall is
the first to be highlighted in Circle 1 of Burns (2012)
[The R Inferno](http://www.burns-stat.com/pages/Tutor/R_inferno.pdf)).
This package provides new relational operators useful for performing
floating point number comparisons with a set tolerance.
Author: Alex M Chubaty [aut, cre],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@NRCan.gc.ca>
Diff between fpCompare versions 0.1.0 dated 2015-04-03 and 0.2.0 dated 2015-05-16
DESCRIPTION | 25 - MD5 | 30 - NAMESPACE | 14 NEWS | 29 + R/fpCompare.R | 128 ++++--- R/zzz.R | 14 README.md | 115 +++--- build/vignette.rds |binary inst/doc/fpCompare.Rmd | 141 ++++--- inst/doc/fpCompare.html | 501 ++++++++++++++++------------ inst/examples/examples.R | 32 - man/relational-operators.Rd | 143 ++++--- tests/test-all.R | 4 tests/testthat/test-numerical-comparisons.R | 61 +-- vignettes/bibliography.bib | 34 - vignettes/fpCompare.Rmd | 141 ++++--- 16 files changed, 805 insertions(+), 607 deletions(-)
Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease.
Epidemic model classes include deterministic compartmental models,
stochastic individual contact models, and stochastic network models.
Disease types include SI, SIR, and SIS epidemics with and without
demography, with tools available for expansion to model complex epidemic
processes.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Li Wang [ctb]
Maintainer: Samuel Jenness <sjenness@uw.edu>
Diff between EpiModel versions 1.1.4 dated 2015-04-12 and 1.1.6 dated 2015-05-16
EpiModel-1.1.4/EpiModel/tests/testthat/test-parallel.R |only EpiModel-1.1.6/EpiModel/DESCRIPTION | 15 EpiModel-1.1.6/EpiModel/MD5 | 260 ++++----- EpiModel-1.1.6/EpiModel/NAMESPACE | 3 EpiModel-1.1.6/EpiModel/NEWS | 37 + EpiModel-1.1.6/EpiModel/R/EpiModel-package.r | 8 EpiModel-1.1.6/EpiModel/R/as.data.frame.R | 16 EpiModel-1.1.6/EpiModel/R/dcm.R | 37 + EpiModel-1.1.6/EpiModel/R/dcm.mods.R | 350 +++++++------ EpiModel-1.1.6/EpiModel/R/get.R | 12 EpiModel-1.1.6/EpiModel/R/icm.mod.init.R | 17 EpiModel-1.1.6/EpiModel/R/icm.mod.status.R | 17 EpiModel-1.1.6/EpiModel/R/icm.mod.vital.R | 4 EpiModel-1.1.6/EpiModel/R/icm.utils.R | 4 EpiModel-1.1.6/EpiModel/R/merge.R | 21 EpiModel-1.1.6/EpiModel/R/net.mod.init.R | 18 EpiModel-1.1.6/EpiModel/R/net.mod.status.R | 2 EpiModel-1.1.6/EpiModel/R/net.mod.vital.R | 293 ++++------- EpiModel-1.1.6/EpiModel/R/net.utils.R | 150 ++++- EpiModel-1.1.6/EpiModel/R/netdx.R | 20 EpiModel-1.1.6/EpiModel/R/netest.R | 86 +++ EpiModel-1.1.6/EpiModel/R/netsim.R | 110 ---- EpiModel-1.1.6/EpiModel/R/plot.R | 78 +- EpiModel-1.1.6/EpiModel/R/saveout.R | 11 EpiModel-1.1.6/EpiModel/R/shiny.R | 4 EpiModel-1.1.6/EpiModel/R/summary.R | 114 ++-- EpiModel-1.1.6/EpiModel/R/test.R | 290 ++++++---- EpiModel-1.1.6/EpiModel/R/utils.R | 10 EpiModel-1.1.6/EpiModel/R/verbose.R | 23 EpiModel-1.1.6/EpiModel/build/vignette.rds |binary EpiModel-1.1.6/EpiModel/inst/doc/Intro.R | 6 EpiModel-1.1.6/EpiModel/inst/doc/Intro.html | 2 EpiModel-1.1.6/EpiModel/inst/shiny/epidcm/server.R | 7 EpiModel-1.1.6/EpiModel/inst/shiny/epidcm/ui.R | 385 ++++++-------- EpiModel-1.1.6/EpiModel/inst/shiny/epiicm/server.R | 4 EpiModel-1.1.6/EpiModel/inst/shiny/epiicm/ui.R | 450 +++++++---------- EpiModel-1.1.6/EpiModel/man/EpiModel-package.Rd | 6 EpiModel-1.1.6/EpiModel/man/as.data.frame.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/as.data.frame.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/bipvals.Rd | 2 EpiModel-1.1.6/EpiModel/man/births.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/births.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/brewer_ramp.Rd | 2 EpiModel-1.1.6/EpiModel/man/calc_eql.Rd |only EpiModel-1.1.6/EpiModel/man/check_bip_degdist.Rd | 2 EpiModel-1.1.6/EpiModel/man/color_tea.Rd | 2 EpiModel-1.1.6/EpiModel/man/comp_plot.Rd | 2 EpiModel-1.1.6/EpiModel/man/control.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/control.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/control.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/copy_toall_attr.Rd | 2 EpiModel-1.1.6/EpiModel/man/crosscheck.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/crosscheck.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/crosscheck.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/dcm.mods.Rd | 2 EpiModel-1.1.6/EpiModel/man/deaths.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/deaths.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/deleteAttr.Rd | 2 EpiModel-1.1.6/EpiModel/man/discord_edgelist.Rd | 2 EpiModel-1.1.6/EpiModel/man/dissolution_coefs.Rd | 2 EpiModel-1.1.6/EpiModel/man/edgelist_censor.Rd | 2 EpiModel-1.1.6/EpiModel/man/edgelist_meanage.Rd | 2 EpiModel-1.1.6/EpiModel/man/edges_correct.Rd | 2 EpiModel-1.1.6/EpiModel/man/epiweb.Rd | 6 EpiModel-1.1.6/EpiModel/man/get_attr_prop.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_formula_terms.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_network.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_nwparam.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_nwstats.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_prev.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_prev.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_sims.Rd | 2 EpiModel-1.1.6/EpiModel/man/get_transmat.Rd | 2 EpiModel-1.1.6/EpiModel/man/icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/idmode.Rd | 2 EpiModel-1.1.6/EpiModel/man/infection.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/infection.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/init.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/init.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/init.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/init_pids.Rd | 2 EpiModel-1.1.6/EpiModel/man/init_status.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/init_status.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/initialize.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/initialize.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/mcat.Rd | 2 EpiModel-1.1.6/EpiModel/man/merge.icm.Rd | 12 EpiModel-1.1.6/EpiModel/man/merge.netsim.Rd | 2 EpiModel-1.1.6/EpiModel/man/modeids.Rd | 2 EpiModel-1.1.6/EpiModel/man/modules.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/modules.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/netdx.Rd | 2 EpiModel-1.1.6/EpiModel/man/netest.Rd | 9 EpiModel-1.1.6/EpiModel/man/netsim.Rd | 2 EpiModel-1.1.6/EpiModel/man/netsim_parallel.Rd | 64 -- EpiModel-1.1.6/EpiModel/man/node_active.Rd | 2 EpiModel-1.1.6/EpiModel/man/param.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/param.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/param.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/plot.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/plot.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/plot.netdx.Rd | 2 EpiModel-1.1.6/EpiModel/man/plot.netsim.Rd | 2 EpiModel-1.1.6/EpiModel/man/recovery.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/recovery.net.Rd | 2 EpiModel-1.1.6/EpiModel/man/resim_nets.Rd | 2 EpiModel-1.1.6/EpiModel/man/saveout.dcm.Rd | 4 EpiModel-1.1.6/EpiModel/man/saveout.icm.Rd | 4 EpiModel-1.1.6/EpiModel/man/saveout.net.Rd | 4 EpiModel-1.1.6/EpiModel/man/sim_nets.Rd | 2 EpiModel-1.1.6/EpiModel/man/split_bip.Rd | 2 EpiModel-1.1.6/EpiModel/man/ssample.Rd | 2 EpiModel-1.1.6/EpiModel/man/summary.dcm.Rd | 2 EpiModel-1.1.6/EpiModel/man/summary.icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/summary.netest.Rd | 2 EpiModel-1.1.6/EpiModel/man/summary.netsim.Rd | 2 EpiModel-1.1.6/EpiModel/man/test_icm.Rd | 2 EpiModel-1.1.6/EpiModel/man/test_net.Rd | 2 EpiModel-1.1.6/EpiModel/man/transco.Rd | 2 EpiModel-1.1.6/EpiModel/man/update_nwattr.Rd | 2 EpiModel-1.1.6/EpiModel/man/verbose.dcm.Rd | 4 EpiModel-1.1.6/EpiModel/man/verbose.icm.Rd | 4 EpiModel-1.1.6/EpiModel/man/verbose.net.Rd | 4 EpiModel-1.1.6/EpiModel/tests/testthat/test-dcm-dede.R | 2 EpiModel-1.1.6/EpiModel/tests/testthat/test-dcm-long.R | 224 ++++---- EpiModel-1.1.6/EpiModel/tests/testthat/test-dcm.R | 125 ++++ EpiModel-1.1.6/EpiModel/tests/testthat/test-net-long.R | 102 +++ EpiModel-1.1.6/EpiModel/tests/testthat/test-netest.R | 42 + EpiModel-1.1.6/EpiModel/tests/testthat/test-netsim.R | 4 EpiModel-1.1.6/EpiModel/tests/testthat/test-newdcm.R | 44 - EpiModel-1.1.6/EpiModel/tests/testthat/test-utils.R | 97 +++ 132 files changed, 2109 insertions(+), 1668 deletions(-)